diff --git a/tests/experiment_files/magetab/E-MTAB-2983/E-MTAB-2983.condensed-sdrf.tsv b/tests/experiment_files/magetab/E-MTAB-2983/E-MTAB-2983.condensed-sdrf.tsv new file mode 100644 index 0000000..049ac22 --- /dev/null +++ b/tests/experiment_files/magetab/E-MTAB-2983/E-MTAB-2983.condensed-sdrf.tsv @@ -0,0 +1,494 @@ +E-MTAB-2983 ERR647946 characteristic biopsy site ovarian cortex http://purl.obolibrary.org/obo/UBERON_0013191 +E-MTAB-2983 ERR647946 characteristic developmental stage adult http://www.ebi.ac.uk/efo/EFO_0001272 +E-MTAB-2983 ERR647946 characteristic disease normal http://purl.obolibrary.org/obo/PATO_0000461 +E-MTAB-2983 ERR647946 characteristic individual pooled cells from two individuals, 33 and 36 years old +E-MTAB-2983 ERR647946 characteristic organism Homo sapiens http://purl.obolibrary.org/obo/NCBITaxon_9606 +E-MTAB-2983 ERR647946 characteristic organism part ovary http://purl.obolibrary.org/obo/UBERON_0000992 +E-MTAB-2983 ERR647946 characteristic phenotype DDX4 antibody-positive +E-MTAB-2983 ERR647946 characteristic sex female http://purl.obolibrary.org/obo/PATO_0000383 +E-MTAB-2983 ERR647946 characteristic single cell quality OK +E-MTAB-2983 ERR647946 factor single cell identifier 24 +E-MTAB-2983 ERR647946 factor skin 24 +E-MTAB-2983 ERR647946 factor age 24 +E-MTAB-2983 ERR647946 factor bala 24 +E-MTAB-2983 ERR647947 characteristic biopsy site ovarian cortex http://purl.obolibrary.org/obo/UBERON_0013191 +E-MTAB-2983 ERR647947 characteristic developmental stage adult http://www.ebi.ac.uk/efo/EFO_0001272 +E-MTAB-2983 ERR647947 characteristic disease normal http://purl.obolibrary.org/obo/PATO_0000461 +E-MTAB-2983 ERR647947 characteristic individual pooled cells from two individuals, 33 and 36 years old +E-MTAB-2983 ERR647947 characteristic organism Homo sapiens http://purl.obolibrary.org/obo/NCBITaxon_9606 +E-MTAB-2983 ERR647947 characteristic organism part ovary http://purl.obolibrary.org/obo/UBERON_0000992 +E-MTAB-2983 ERR647947 characteristic phenotype DDX4 antibody-positive +E-MTAB-2983 ERR647947 characteristic sex female http://purl.obolibrary.org/obo/PATO_0000383 +E-MTAB-2983 ERR647947 characteristic single cell quality OK +E-MTAB-2983 ERR647947 factor single cell identifier 5 +E-MTAB-2983 ERR647947 factor skin 5 +E-MTAB-2983 ERR647947 factor age 5 +E-MTAB-2983 ERR647947 factor bala 5 +E-MTAB-2983 ERR647948 characteristic biopsy site ovarian cortex http://purl.obolibrary.org/obo/UBERON_0013191 +E-MTAB-2983 ERR647948 characteristic developmental stage adult http://www.ebi.ac.uk/efo/EFO_0001272 +E-MTAB-2983 ERR647948 characteristic disease normal http://purl.obolibrary.org/obo/PATO_0000461 +E-MTAB-2983 ERR647948 characteristic individual pooled cells from two individuals, 33 and 36 years old +E-MTAB-2983 ERR647948 characteristic organism Homo sapiens http://purl.obolibrary.org/obo/NCBITaxon_9606 +E-MTAB-2983 ERR647948 characteristic organism part ovary http://purl.obolibrary.org/obo/UBERON_0000992 +E-MTAB-2983 ERR647948 characteristic phenotype DDX4 antibody-positive +E-MTAB-2983 ERR647948 characteristic sex female http://purl.obolibrary.org/obo/PATO_0000383 +E-MTAB-2983 ERR647948 characteristic single cell quality OK +E-MTAB-2983 ERR647948 factor single cell identifier 27 +E-MTAB-2983 ERR647948 factor skin 27 +E-MTAB-2983 ERR647948 factor age 27 +E-MTAB-2983 ERR647948 factor bala 27 +E-MTAB-2983 ERR647949 characteristic biopsy site ovarian cortex http://purl.obolibrary.org/obo/UBERON_0013191 +E-MTAB-2983 ERR647949 characteristic developmental stage adult http://www.ebi.ac.uk/efo/EFO_0001272 +E-MTAB-2983 ERR647949 characteristic disease normal http://purl.obolibrary.org/obo/PATO_0000461 +E-MTAB-2983 ERR647949 characteristic individual pooled cells from two individuals, 33 and 36 years old +E-MTAB-2983 ERR647949 characteristic organism Homo sapiens http://purl.obolibrary.org/obo/NCBITaxon_9606 +E-MTAB-2983 ERR647949 characteristic organism part ovary http://purl.obolibrary.org/obo/UBERON_0000992 +E-MTAB-2983 ERR647949 characteristic phenotype DDX4 antibody-positive +E-MTAB-2983 ERR647949 characteristic sex female http://purl.obolibrary.org/obo/PATO_0000383 +E-MTAB-2983 ERR647949 characteristic single cell quality OK +E-MTAB-2983 ERR647949 factor single cell identifier 20 +E-MTAB-2983 ERR647949 factor skin 20 +E-MTAB-2983 ERR647949 factor age 20 +E-MTAB-2983 ERR647949 factor bala 20 +E-MTAB-2983 ERR647950 characteristic biopsy site ovarian cortex http://purl.obolibrary.org/obo/UBERON_0013191 +E-MTAB-2983 ERR647950 characteristic developmental stage adult http://www.ebi.ac.uk/efo/EFO_0001272 +E-MTAB-2983 ERR647950 characteristic disease normal http://purl.obolibrary.org/obo/PATO_0000461 +E-MTAB-2983 ERR647950 characteristic individual pooled cells from two individuals, 33 and 36 years old +E-MTAB-2983 ERR647950 characteristic organism Homo sapiens http://purl.obolibrary.org/obo/NCBITaxon_9606 +E-MTAB-2983 ERR647950 characteristic organism part ovary http://purl.obolibrary.org/obo/UBERON_0000992 +E-MTAB-2983 ERR647950 characteristic phenotype DDX4 antibody-positive +E-MTAB-2983 ERR647950 characteristic sex female http://purl.obolibrary.org/obo/PATO_0000383 +E-MTAB-2983 ERR647950 characteristic single cell quality OK +E-MTAB-2983 ERR647950 factor single cell identifier 17 +E-MTAB-2983 ERR647950 factor skin 17 +E-MTAB-2983 ERR647950 factor age 17 +E-MTAB-2983 ERR647950 factor bala 17 +E-MTAB-2983 ERR647951 characteristic biopsy site ovarian cortex http://purl.obolibrary.org/obo/UBERON_0013191 +E-MTAB-2983 ERR647951 characteristic developmental stage adult http://www.ebi.ac.uk/efo/EFO_0001272 +E-MTAB-2983 ERR647951 characteristic disease normal http://purl.obolibrary.org/obo/PATO_0000461 +E-MTAB-2983 ERR647951 characteristic individual pooled cells from two individuals, 33 and 36 years old +E-MTAB-2983 ERR647951 characteristic organism Homo sapiens http://purl.obolibrary.org/obo/NCBITaxon_9606 +E-MTAB-2983 ERR647951 characteristic organism part ovary http://purl.obolibrary.org/obo/UBERON_0000992 +E-MTAB-2983 ERR647951 characteristic phenotype DDX4 antibody-positive +E-MTAB-2983 ERR647951 characteristic sex female http://purl.obolibrary.org/obo/PATO_0000383 +E-MTAB-2983 ERR647951 characteristic single cell quality OK +E-MTAB-2983 ERR647951 factor single cell identifier 2 +E-MTAB-2983 ERR647951 factor skin 2 +E-MTAB-2983 ERR647951 factor age 2 +E-MTAB-2983 ERR647951 factor bala 2 +E-MTAB-2983 ERR647952 characteristic biopsy site ovarian cortex http://purl.obolibrary.org/obo/UBERON_0013191 +E-MTAB-2983 ERR647952 characteristic developmental stage adult http://www.ebi.ac.uk/efo/EFO_0001272 +E-MTAB-2983 ERR647952 characteristic disease normal http://purl.obolibrary.org/obo/PATO_0000461 +E-MTAB-2983 ERR647952 characteristic individual pooled cells from two individuals, 33 and 36 years old +E-MTAB-2983 ERR647952 characteristic organism Homo sapiens http://purl.obolibrary.org/obo/NCBITaxon_9606 +E-MTAB-2983 ERR647952 characteristic organism part ovary http://purl.obolibrary.org/obo/UBERON_0000992 +E-MTAB-2983 ERR647952 characteristic phenotype DDX4 antibody-positive +E-MTAB-2983 ERR647952 characteristic sex female http://purl.obolibrary.org/obo/PATO_0000383 +E-MTAB-2983 ERR647952 characteristic single cell quality OK +E-MTAB-2983 ERR647952 factor single cell identifier 13 +E-MTAB-2983 ERR647952 factor skin 13 +E-MTAB-2983 ERR647952 factor age 13 +E-MTAB-2983 ERR647952 factor bala 13 +E-MTAB-2983 ERR647953 characteristic biopsy site ovarian cortex http://purl.obolibrary.org/obo/UBERON_0013191 +E-MTAB-2983 ERR647953 characteristic developmental stage adult http://www.ebi.ac.uk/efo/EFO_0001272 +E-MTAB-2983 ERR647953 characteristic disease normal http://purl.obolibrary.org/obo/PATO_0000461 +E-MTAB-2983 ERR647953 characteristic individual pooled cells from two individuals, 33 and 36 years old +E-MTAB-2983 ERR647953 characteristic organism Homo sapiens http://purl.obolibrary.org/obo/NCBITaxon_9606 +E-MTAB-2983 ERR647953 characteristic organism part ovary http://purl.obolibrary.org/obo/UBERON_0000992 +E-MTAB-2983 ERR647953 characteristic phenotype DDX4 antibody-positive +E-MTAB-2983 ERR647953 characteristic sex female http://purl.obolibrary.org/obo/PATO_0000383 +E-MTAB-2983 ERR647953 characteristic single cell quality OK +E-MTAB-2983 ERR647953 factor single cell identifier 28 +E-MTAB-2983 ERR647953 factor skin 28 +E-MTAB-2983 ERR647953 factor age 28 +E-MTAB-2983 ERR647953 factor bala 28 +E-MTAB-2983 ERR647954 characteristic biopsy site ovarian cortex http://purl.obolibrary.org/obo/UBERON_0013191 +E-MTAB-2983 ERR647954 characteristic developmental stage adult http://www.ebi.ac.uk/efo/EFO_0001272 +E-MTAB-2983 ERR647954 characteristic disease normal http://purl.obolibrary.org/obo/PATO_0000461 +E-MTAB-2983 ERR647954 characteristic individual pooled cells from two individuals, 33 and 36 years old +E-MTAB-2983 ERR647954 characteristic organism Homo sapiens http://purl.obolibrary.org/obo/NCBITaxon_9606 +E-MTAB-2983 ERR647954 characteristic organism part ovary http://purl.obolibrary.org/obo/UBERON_0000992 +E-MTAB-2983 ERR647954 characteristic phenotype DDX4 antibody-positive +E-MTAB-2983 ERR647954 characteristic sex female http://purl.obolibrary.org/obo/PATO_0000383 +E-MTAB-2983 ERR647954 characteristic single cell quality OK +E-MTAB-2983 ERR647954 factor single cell identifier 23 +E-MTAB-2983 ERR647954 factor skin 23 +E-MTAB-2983 ERR647954 factor age 23 +E-MTAB-2983 ERR647954 factor bala 23 +E-MTAB-2983 ERR647955 characteristic biopsy site ovarian cortex http://purl.obolibrary.org/obo/UBERON_0013191 +E-MTAB-2983 ERR647955 characteristic developmental stage adult http://www.ebi.ac.uk/efo/EFO_0001272 +E-MTAB-2983 ERR647955 characteristic disease normal http://purl.obolibrary.org/obo/PATO_0000461 +E-MTAB-2983 ERR647955 characteristic individual pooled cells from two individuals, 33 and 36 years old +E-MTAB-2983 ERR647955 characteristic organism Homo sapiens http://purl.obolibrary.org/obo/NCBITaxon_9606 +E-MTAB-2983 ERR647955 characteristic organism part ovary http://purl.obolibrary.org/obo/UBERON_0000992 +E-MTAB-2983 ERR647955 characteristic phenotype DDX4 antibody-positive +E-MTAB-2983 ERR647955 characteristic sex female http://purl.obolibrary.org/obo/PATO_0000383 +E-MTAB-2983 ERR647955 characteristic single cell quality OK +E-MTAB-2983 ERR647955 factor single cell identifier 19 +E-MTAB-2983 ERR647955 factor skin 19 +E-MTAB-2983 ERR647955 factor age 19 +E-MTAB-2983 ERR647955 factor bala 19 +E-MTAB-2983 ERR647956 characteristic biopsy site ovarian cortex http://purl.obolibrary.org/obo/UBERON_0013191 +E-MTAB-2983 ERR647956 characteristic developmental stage adult http://www.ebi.ac.uk/efo/EFO_0001272 +E-MTAB-2983 ERR647956 characteristic disease normal http://purl.obolibrary.org/obo/PATO_0000461 +E-MTAB-2983 ERR647956 characteristic individual pooled cells from two individuals, 33 and 36 years old +E-MTAB-2983 ERR647956 characteristic organism Homo sapiens http://purl.obolibrary.org/obo/NCBITaxon_9606 +E-MTAB-2983 ERR647956 characteristic organism part ovary http://purl.obolibrary.org/obo/UBERON_0000992 +E-MTAB-2983 ERR647956 characteristic phenotype DDX4 antibody-positive +E-MTAB-2983 ERR647956 characteristic sex female http://purl.obolibrary.org/obo/PATO_0000383 +E-MTAB-2983 ERR647956 characteristic single cell quality OK +E-MTAB-2983 ERR647956 factor single cell identifier 38 +E-MTAB-2983 ERR647956 factor skin 38 +E-MTAB-2983 ERR647956 factor age 38 +E-MTAB-2983 ERR647956 factor bala 38 +E-MTAB-2983 ERR647957 characteristic biopsy site ovarian cortex http://purl.obolibrary.org/obo/UBERON_0013191 +E-MTAB-2983 ERR647957 characteristic developmental stage adult http://www.ebi.ac.uk/efo/EFO_0001272 +E-MTAB-2983 ERR647957 characteristic disease normal http://purl.obolibrary.org/obo/PATO_0000461 +E-MTAB-2983 ERR647957 characteristic individual pooled cells from two individuals, 33 and 36 years old +E-MTAB-2983 ERR647957 characteristic organism Homo sapiens http://purl.obolibrary.org/obo/NCBITaxon_9606 +E-MTAB-2983 ERR647957 characteristic organism part ovary http://purl.obolibrary.org/obo/UBERON_0000992 +E-MTAB-2983 ERR647957 characteristic phenotype DDX4 antibody-positive +E-MTAB-2983 ERR647957 characteristic sex female http://purl.obolibrary.org/obo/PATO_0000383 +E-MTAB-2983 ERR647957 characteristic single cell quality OK +E-MTAB-2983 ERR647957 factor single cell identifier 12 +E-MTAB-2983 ERR647957 factor skin 12 +E-MTAB-2983 ERR647957 factor age 12 +E-MTAB-2983 ERR647957 factor bala 12 +E-MTAB-2983 ERR647958 characteristic biopsy site ovarian cortex http://purl.obolibrary.org/obo/UBERON_0013191 +E-MTAB-2983 ERR647958 characteristic developmental stage adult http://www.ebi.ac.uk/efo/EFO_0001272 +E-MTAB-2983 ERR647958 characteristic disease normal http://purl.obolibrary.org/obo/PATO_0000461 +E-MTAB-2983 ERR647958 characteristic individual pooled cells from two individuals, 33 and 36 years old +E-MTAB-2983 ERR647958 characteristic organism Homo sapiens http://purl.obolibrary.org/obo/NCBITaxon_9606 +E-MTAB-2983 ERR647958 characteristic organism part ovary http://purl.obolibrary.org/obo/UBERON_0000992 +E-MTAB-2983 ERR647958 characteristic phenotype DDX4 antibody-positive +E-MTAB-2983 ERR647958 characteristic sex female http://purl.obolibrary.org/obo/PATO_0000383 +E-MTAB-2983 ERR647958 characteristic single cell quality OK +E-MTAB-2983 ERR647958 factor single cell identifier 26 +E-MTAB-2983 ERR647958 factor skin 26 +E-MTAB-2983 ERR647958 factor age 26 +E-MTAB-2983 ERR647958 factor bala 26 +E-MTAB-2983 ERR647959 characteristic biopsy site ovarian cortex http://purl.obolibrary.org/obo/UBERON_0013191 +E-MTAB-2983 ERR647959 characteristic developmental stage adult http://www.ebi.ac.uk/efo/EFO_0001272 +E-MTAB-2983 ERR647959 characteristic disease normal http://purl.obolibrary.org/obo/PATO_0000461 +E-MTAB-2983 ERR647959 characteristic individual pooled cells from two individuals, 33 and 36 years old +E-MTAB-2983 ERR647959 characteristic organism Homo sapiens http://purl.obolibrary.org/obo/NCBITaxon_9606 +E-MTAB-2983 ERR647959 characteristic organism part ovary http://purl.obolibrary.org/obo/UBERON_0000992 +E-MTAB-2983 ERR647959 characteristic phenotype DDX4 antibody-positive +E-MTAB-2983 ERR647959 characteristic sex female http://purl.obolibrary.org/obo/PATO_0000383 +E-MTAB-2983 ERR647959 characteristic single cell quality OK +E-MTAB-2983 ERR647959 factor single cell identifier 37 +E-MTAB-2983 ERR647959 factor skin 37 +E-MTAB-2983 ERR647959 factor age 37 +E-MTAB-2983 ERR647959 factor bala 37 +E-MTAB-2983 ERR647960 characteristic biopsy site ovarian cortex http://purl.obolibrary.org/obo/UBERON_0013191 +E-MTAB-2983 ERR647960 characteristic developmental stage adult http://www.ebi.ac.uk/efo/EFO_0001272 +E-MTAB-2983 ERR647960 characteristic disease normal http://purl.obolibrary.org/obo/PATO_0000461 +E-MTAB-2983 ERR647960 characteristic individual pooled cells from two individuals, 33 and 36 years old +E-MTAB-2983 ERR647960 characteristic organism Homo sapiens http://purl.obolibrary.org/obo/NCBITaxon_9606 +E-MTAB-2983 ERR647960 characteristic organism part ovary http://purl.obolibrary.org/obo/UBERON_0000992 +E-MTAB-2983 ERR647960 characteristic phenotype DDX4 antibody-positive +E-MTAB-2983 ERR647960 characteristic sex female http://purl.obolibrary.org/obo/PATO_0000383 +E-MTAB-2983 ERR647960 characteristic single cell quality OK +E-MTAB-2983 ERR647960 factor single cell identifier 18 +E-MTAB-2983 ERR647960 factor skin 18 +E-MTAB-2983 ERR647960 factor age 18 +E-MTAB-2983 ERR647960 factor bala 18 +E-MTAB-2983 ERR647961 characteristic biopsy site ovarian cortex http://purl.obolibrary.org/obo/UBERON_0013191 +E-MTAB-2983 ERR647961 characteristic developmental stage adult http://www.ebi.ac.uk/efo/EFO_0001272 +E-MTAB-2983 ERR647961 characteristic disease normal http://purl.obolibrary.org/obo/PATO_0000461 +E-MTAB-2983 ERR647961 characteristic individual pooled cells from two individuals, 33 and 36 years old +E-MTAB-2983 ERR647961 characteristic organism Homo sapiens http://purl.obolibrary.org/obo/NCBITaxon_9606 +E-MTAB-2983 ERR647961 characteristic organism part ovary http://purl.obolibrary.org/obo/UBERON_0000992 +E-MTAB-2983 ERR647961 characteristic phenotype DDX4 antibody-positive +E-MTAB-2983 ERR647961 characteristic sex female http://purl.obolibrary.org/obo/PATO_0000383 +E-MTAB-2983 ERR647961 characteristic single cell quality OK +E-MTAB-2983 ERR647961 factor single cell identifier 29 +E-MTAB-2983 ERR647961 factor skin 29 +E-MTAB-2983 ERR647961 factor age 29 +E-MTAB-2983 ERR647961 factor bala 29 +E-MTAB-2983 ERR647962 characteristic biopsy site ovarian cortex http://purl.obolibrary.org/obo/UBERON_0013191 +E-MTAB-2983 ERR647962 characteristic developmental stage adult http://www.ebi.ac.uk/efo/EFO_0001272 +E-MTAB-2983 ERR647962 characteristic disease normal http://purl.obolibrary.org/obo/PATO_0000461 +E-MTAB-2983 ERR647962 characteristic individual pooled cells from two individuals, 33 and 36 years old +E-MTAB-2983 ERR647962 characteristic organism Homo sapiens http://purl.obolibrary.org/obo/NCBITaxon_9606 +E-MTAB-2983 ERR647962 characteristic organism part ovary http://purl.obolibrary.org/obo/UBERON_0000992 +E-MTAB-2983 ERR647962 characteristic phenotype DDX4 antibody-positive +E-MTAB-2983 ERR647962 characteristic sex female http://purl.obolibrary.org/obo/PATO_0000383 +E-MTAB-2983 ERR647962 characteristic single cell quality OK +E-MTAB-2983 ERR647962 factor single cell identifier 36 +E-MTAB-2983 ERR647962 factor skin 36 +E-MTAB-2983 ERR647962 factor age 36 +E-MTAB-2983 ERR647962 factor bala 36 +E-MTAB-2983 ERR647963 characteristic biopsy site ovarian cortex http://purl.obolibrary.org/obo/UBERON_0013191 +E-MTAB-2983 ERR647963 characteristic developmental stage adult http://www.ebi.ac.uk/efo/EFO_0001272 +E-MTAB-2983 ERR647963 characteristic disease normal http://purl.obolibrary.org/obo/PATO_0000461 +E-MTAB-2983 ERR647963 characteristic individual pooled cells from two individuals, 33 and 36 years old +E-MTAB-2983 ERR647963 characteristic organism Homo sapiens http://purl.obolibrary.org/obo/NCBITaxon_9606 +E-MTAB-2983 ERR647963 characteristic organism part ovary http://purl.obolibrary.org/obo/UBERON_0000992 +E-MTAB-2983 ERR647963 characteristic phenotype DDX4 antibody-positive +E-MTAB-2983 ERR647963 characteristic sex female http://purl.obolibrary.org/obo/PATO_0000383 +E-MTAB-2983 ERR647963 characteristic single cell quality OK +E-MTAB-2983 ERR647963 factor single cell identifier 9 +E-MTAB-2983 ERR647963 factor skin 9 +E-MTAB-2983 ERR647963 factor age 9 +E-MTAB-2983 ERR647963 factor bala 9 +E-MTAB-2983 ERR647964 characteristic biopsy site ovarian cortex http://purl.obolibrary.org/obo/UBERON_0013191 +E-MTAB-2983 ERR647964 characteristic developmental stage adult http://www.ebi.ac.uk/efo/EFO_0001272 +E-MTAB-2983 ERR647964 characteristic disease normal http://purl.obolibrary.org/obo/PATO_0000461 +E-MTAB-2983 ERR647964 characteristic individual pooled cells from two individuals, 33 and 36 years old +E-MTAB-2983 ERR647964 characteristic organism Homo sapiens http://purl.obolibrary.org/obo/NCBITaxon_9606 +E-MTAB-2983 ERR647964 characteristic organism part ovary http://purl.obolibrary.org/obo/UBERON_0000992 +E-MTAB-2983 ERR647964 characteristic phenotype DDX4 antibody-positive +E-MTAB-2983 ERR647964 characteristic sex female http://purl.obolibrary.org/obo/PATO_0000383 +E-MTAB-2983 ERR647964 characteristic single cell quality OK +E-MTAB-2983 ERR647964 factor single cell identifier 8 +E-MTAB-2983 ERR647964 factor skin 8 +E-MTAB-2983 ERR647964 factor age 8 +E-MTAB-2983 ERR647964 factor bala 8 +E-MTAB-2983 ERR647965 characteristic biopsy site ovarian cortex http://purl.obolibrary.org/obo/UBERON_0013191 +E-MTAB-2983 ERR647965 characteristic developmental stage adult http://www.ebi.ac.uk/efo/EFO_0001272 +E-MTAB-2983 ERR647965 characteristic disease normal http://purl.obolibrary.org/obo/PATO_0000461 +E-MTAB-2983 ERR647965 characteristic individual pooled cells from two individuals, 33 and 36 years old +E-MTAB-2983 ERR647965 characteristic organism Homo sapiens http://purl.obolibrary.org/obo/NCBITaxon_9606 +E-MTAB-2983 ERR647965 characteristic organism part ovary http://purl.obolibrary.org/obo/UBERON_0000992 +E-MTAB-2983 ERR647965 characteristic phenotype DDX4 antibody-positive +E-MTAB-2983 ERR647965 characteristic sex female http://purl.obolibrary.org/obo/PATO_0000383 +E-MTAB-2983 ERR647965 characteristic single cell quality OK +E-MTAB-2983 ERR647965 factor single cell identifier 34 +E-MTAB-2983 ERR647965 factor skin 34 +E-MTAB-2983 ERR647965 factor age 34 +E-MTAB-2983 ERR647965 factor bala 34 +E-MTAB-2983 ERR647966 characteristic biopsy site ovarian cortex http://purl.obolibrary.org/obo/UBERON_0013191 +E-MTAB-2983 ERR647966 characteristic developmental stage adult http://www.ebi.ac.uk/efo/EFO_0001272 +E-MTAB-2983 ERR647966 characteristic disease normal http://purl.obolibrary.org/obo/PATO_0000461 +E-MTAB-2983 ERR647966 characteristic individual pooled cells from two individuals, 33 and 36 years old +E-MTAB-2983 ERR647966 characteristic organism Homo sapiens http://purl.obolibrary.org/obo/NCBITaxon_9606 +E-MTAB-2983 ERR647966 characteristic organism part ovary http://purl.obolibrary.org/obo/UBERON_0000992 +E-MTAB-2983 ERR647966 characteristic phenotype DDX4 antibody-positive +E-MTAB-2983 ERR647966 characteristic sex female http://purl.obolibrary.org/obo/PATO_0000383 +E-MTAB-2983 ERR647966 characteristic single cell quality OK +E-MTAB-2983 ERR647966 factor single cell identifier 7 +E-MTAB-2983 ERR647966 factor skin 7 +E-MTAB-2983 ERR647966 factor age 7 +E-MTAB-2983 ERR647966 factor bala 7 +E-MTAB-2983 ERR647967 characteristic biopsy site ovarian cortex http://purl.obolibrary.org/obo/UBERON_0013191 +E-MTAB-2983 ERR647967 characteristic developmental stage adult http://www.ebi.ac.uk/efo/EFO_0001272 +E-MTAB-2983 ERR647967 characteristic disease normal http://purl.obolibrary.org/obo/PATO_0000461 +E-MTAB-2983 ERR647967 characteristic individual pooled cells from two individuals, 33 and 36 years old +E-MTAB-2983 ERR647967 characteristic organism Homo sapiens http://purl.obolibrary.org/obo/NCBITaxon_9606 +E-MTAB-2983 ERR647967 characteristic organism part ovary http://purl.obolibrary.org/obo/UBERON_0000992 +E-MTAB-2983 ERR647967 characteristic phenotype DDX4 antibody-positive +E-MTAB-2983 ERR647967 characteristic sex female http://purl.obolibrary.org/obo/PATO_0000383 +E-MTAB-2983 ERR647967 characteristic single cell quality OK +E-MTAB-2983 ERR647967 factor single cell identifier 22 +E-MTAB-2983 ERR647967 factor skin 22 +E-MTAB-2983 ERR647967 factor age 22 +E-MTAB-2983 ERR647967 factor bala 22 +E-MTAB-2983 ERR647968 characteristic biopsy site ovarian cortex http://purl.obolibrary.org/obo/UBERON_0013191 +E-MTAB-2983 ERR647968 characteristic developmental stage adult http://www.ebi.ac.uk/efo/EFO_0001272 +E-MTAB-2983 ERR647968 characteristic disease normal http://purl.obolibrary.org/obo/PATO_0000461 +E-MTAB-2983 ERR647968 characteristic individual pooled cells from two individuals, 33 and 36 years old +E-MTAB-2983 ERR647968 characteristic organism Homo sapiens http://purl.obolibrary.org/obo/NCBITaxon_9606 +E-MTAB-2983 ERR647968 characteristic organism part ovary http://purl.obolibrary.org/obo/UBERON_0000992 +E-MTAB-2983 ERR647968 characteristic phenotype DDX4 antibody-positive +E-MTAB-2983 ERR647968 characteristic sex female http://purl.obolibrary.org/obo/PATO_0000383 +E-MTAB-2983 ERR647968 characteristic single cell quality OK +E-MTAB-2983 ERR647968 factor single cell identifier 14 +E-MTAB-2983 ERR647968 factor skin 14 +E-MTAB-2983 ERR647968 factor age 14 +E-MTAB-2983 ERR647968 factor bala 14 +E-MTAB-2983 ERR647969 characteristic biopsy site ovarian cortex http://purl.obolibrary.org/obo/UBERON_0013191 +E-MTAB-2983 ERR647969 characteristic developmental stage adult http://www.ebi.ac.uk/efo/EFO_0001272 +E-MTAB-2983 ERR647969 characteristic disease normal http://purl.obolibrary.org/obo/PATO_0000461 +E-MTAB-2983 ERR647969 characteristic individual pooled cells from two individuals, 33 and 36 years old +E-MTAB-2983 ERR647969 characteristic organism Homo sapiens http://purl.obolibrary.org/obo/NCBITaxon_9606 +E-MTAB-2983 ERR647969 characteristic organism part ovary http://purl.obolibrary.org/obo/UBERON_0000992 +E-MTAB-2983 ERR647969 characteristic phenotype DDX4 antibody-positive +E-MTAB-2983 ERR647969 characteristic sex female http://purl.obolibrary.org/obo/PATO_0000383 +E-MTAB-2983 ERR647969 characteristic single cell quality OK +E-MTAB-2983 ERR647969 factor single cell identifier 6 +E-MTAB-2983 ERR647969 factor skin 6 +E-MTAB-2983 ERR647969 factor age 6 +E-MTAB-2983 ERR647969 factor bala 6 +E-MTAB-2983 ERR647970 characteristic biopsy site ovarian cortex http://purl.obolibrary.org/obo/UBERON_0013191 +E-MTAB-2983 ERR647970 characteristic developmental stage adult http://www.ebi.ac.uk/efo/EFO_0001272 +E-MTAB-2983 ERR647970 characteristic disease normal http://purl.obolibrary.org/obo/PATO_0000461 +E-MTAB-2983 ERR647970 characteristic individual pooled cells from two individuals, 33 and 36 years old +E-MTAB-2983 ERR647970 characteristic organism Homo sapiens http://purl.obolibrary.org/obo/NCBITaxon_9606 +E-MTAB-2983 ERR647970 characteristic organism part ovary http://purl.obolibrary.org/obo/UBERON_0000992 +E-MTAB-2983 ERR647970 characteristic phenotype DDX4 antibody-positive +E-MTAB-2983 ERR647970 characteristic sex female http://purl.obolibrary.org/obo/PATO_0000383 +E-MTAB-2983 ERR647970 characteristic single cell quality OK +E-MTAB-2983 ERR647970 factor single cell identifier 21 +E-MTAB-2983 ERR647970 factor skin 21 +E-MTAB-2983 ERR647970 factor age 21 +E-MTAB-2983 ERR647970 factor bala 21 +E-MTAB-2983 ERR647971 characteristic biopsy site ovarian cortex http://purl.obolibrary.org/obo/UBERON_0013191 +E-MTAB-2983 ERR647971 characteristic developmental stage adult http://www.ebi.ac.uk/efo/EFO_0001272 +E-MTAB-2983 ERR647971 characteristic disease normal http://purl.obolibrary.org/obo/PATO_0000461 +E-MTAB-2983 ERR647971 characteristic individual pooled cells from two individuals, 33 and 36 years old +E-MTAB-2983 ERR647971 characteristic organism Homo sapiens http://purl.obolibrary.org/obo/NCBITaxon_9606 +E-MTAB-2983 ERR647971 characteristic organism part ovary http://purl.obolibrary.org/obo/UBERON_0000992 +E-MTAB-2983 ERR647971 characteristic phenotype DDX4 antibody-positive +E-MTAB-2983 ERR647971 characteristic sex female http://purl.obolibrary.org/obo/PATO_0000383 +E-MTAB-2983 ERR647971 characteristic single cell quality OK +E-MTAB-2983 ERR647971 factor single cell identifier 25 +E-MTAB-2983 ERR647971 factor skin 25 +E-MTAB-2983 ERR647971 factor age 25 +E-MTAB-2983 ERR647971 factor bala 25 +E-MTAB-2983 ERR647972 characteristic biopsy site ovarian cortex http://purl.obolibrary.org/obo/UBERON_0013191 +E-MTAB-2983 ERR647972 characteristic developmental stage adult http://www.ebi.ac.uk/efo/EFO_0001272 +E-MTAB-2983 ERR647972 characteristic disease normal http://purl.obolibrary.org/obo/PATO_0000461 +E-MTAB-2983 ERR647972 characteristic individual pooled cells from two individuals, 33 and 36 years old +E-MTAB-2983 ERR647972 characteristic organism Homo sapiens http://purl.obolibrary.org/obo/NCBITaxon_9606 +E-MTAB-2983 ERR647972 characteristic organism part ovary http://purl.obolibrary.org/obo/UBERON_0000992 +E-MTAB-2983 ERR647972 characteristic phenotype DDX4 antibody-positive +E-MTAB-2983 ERR647972 characteristic sex female http://purl.obolibrary.org/obo/PATO_0000383 +E-MTAB-2983 ERR647972 characteristic single cell quality OK +E-MTAB-2983 ERR647972 factor single cell identifier 32 +E-MTAB-2983 ERR647972 factor skin 32 +E-MTAB-2983 ERR647972 factor age 32 +E-MTAB-2983 ERR647972 factor bala 32 +E-MTAB-2983 ERR647973 characteristic biopsy site ovarian cortex http://purl.obolibrary.org/obo/UBERON_0013191 +E-MTAB-2983 ERR647973 characteristic developmental stage adult http://www.ebi.ac.uk/efo/EFO_0001272 +E-MTAB-2983 ERR647973 characteristic disease normal http://purl.obolibrary.org/obo/PATO_0000461 +E-MTAB-2983 ERR647973 characteristic individual pooled cells from two individuals, 33 and 36 years old +E-MTAB-2983 ERR647973 characteristic organism Homo sapiens http://purl.obolibrary.org/obo/NCBITaxon_9606 +E-MTAB-2983 ERR647973 characteristic organism part ovary http://purl.obolibrary.org/obo/UBERON_0000992 +E-MTAB-2983 ERR647973 characteristic phenotype DDX4 antibody-positive +E-MTAB-2983 ERR647973 characteristic sex female http://purl.obolibrary.org/obo/PATO_0000383 +E-MTAB-2983 ERR647973 characteristic single cell quality OK +E-MTAB-2983 ERR647973 factor single cell identifier 16 +E-MTAB-2983 ERR647973 factor skin 16 +E-MTAB-2983 ERR647973 factor age 16 +E-MTAB-2983 ERR647973 factor bala 16 +E-MTAB-2983 ERR647974 characteristic biopsy site ovarian cortex http://purl.obolibrary.org/obo/UBERON_0013191 +E-MTAB-2983 ERR647974 characteristic developmental stage adult http://www.ebi.ac.uk/efo/EFO_0001272 +E-MTAB-2983 ERR647974 characteristic disease normal http://purl.obolibrary.org/obo/PATO_0000461 +E-MTAB-2983 ERR647974 characteristic individual pooled cells from two individuals, 33 and 36 years old +E-MTAB-2983 ERR647974 characteristic organism Homo sapiens http://purl.obolibrary.org/obo/NCBITaxon_9606 +E-MTAB-2983 ERR647974 characteristic organism part ovary http://purl.obolibrary.org/obo/UBERON_0000992 +E-MTAB-2983 ERR647974 characteristic phenotype DDX4 antibody-positive +E-MTAB-2983 ERR647974 characteristic sex female http://purl.obolibrary.org/obo/PATO_0000383 +E-MTAB-2983 ERR647974 characteristic single cell quality OK +E-MTAB-2983 ERR647974 factor single cell identifier 10 +E-MTAB-2983 ERR647974 factor skin 10 +E-MTAB-2983 ERR647974 factor age 10 +E-MTAB-2983 ERR647974 factor bala 10 +E-MTAB-2983 ERR647975 characteristic biopsy site ovarian cortex http://purl.obolibrary.org/obo/UBERON_0013191 +E-MTAB-2983 ERR647975 characteristic developmental stage adult http://www.ebi.ac.uk/efo/EFO_0001272 +E-MTAB-2983 ERR647975 characteristic disease normal http://purl.obolibrary.org/obo/PATO_0000461 +E-MTAB-2983 ERR647975 characteristic individual pooled cells from two individuals, 33 and 36 years old +E-MTAB-2983 ERR647975 characteristic organism Homo sapiens http://purl.obolibrary.org/obo/NCBITaxon_9606 +E-MTAB-2983 ERR647975 characteristic organism part ovary http://purl.obolibrary.org/obo/UBERON_0000992 +E-MTAB-2983 ERR647975 characteristic phenotype DDX4 antibody-positive +E-MTAB-2983 ERR647975 characteristic sex female http://purl.obolibrary.org/obo/PATO_0000383 +E-MTAB-2983 ERR647975 characteristic single cell quality OK +E-MTAB-2983 ERR647975 factor single cell identifier 35 +E-MTAB-2983 ERR647975 factor skin 35 +E-MTAB-2983 ERR647975 factor age 35 +E-MTAB-2983 ERR647975 factor bala 35 +E-MTAB-2983 ERR647976 characteristic biopsy site ovarian cortex http://purl.obolibrary.org/obo/UBERON_0013191 +E-MTAB-2983 ERR647976 characteristic developmental stage adult http://www.ebi.ac.uk/efo/EFO_0001272 +E-MTAB-2983 ERR647976 characteristic disease normal http://purl.obolibrary.org/obo/PATO_0000461 +E-MTAB-2983 ERR647976 characteristic individual pooled cells from two individuals, 33 and 36 years old +E-MTAB-2983 ERR647976 characteristic organism Homo sapiens http://purl.obolibrary.org/obo/NCBITaxon_9606 +E-MTAB-2983 ERR647976 characteristic organism part ovary http://purl.obolibrary.org/obo/UBERON_0000992 +E-MTAB-2983 ERR647976 characteristic phenotype DDX4 antibody-positive +E-MTAB-2983 ERR647976 characteristic sex female http://purl.obolibrary.org/obo/PATO_0000383 +E-MTAB-2983 ERR647976 characteristic single cell quality OK +E-MTAB-2983 ERR647976 factor single cell identifier 33 +E-MTAB-2983 ERR647976 factor skin 33 +E-MTAB-2983 ERR647976 factor age 33 +E-MTAB-2983 ERR647976 factor bala 33 +E-MTAB-2983 ERR647977 characteristic biopsy site ovarian cortex http://purl.obolibrary.org/obo/UBERON_0013191 +E-MTAB-2983 ERR647977 characteristic developmental stage adult http://www.ebi.ac.uk/efo/EFO_0001272 +E-MTAB-2983 ERR647977 characteristic disease normal http://purl.obolibrary.org/obo/PATO_0000461 +E-MTAB-2983 ERR647977 characteristic individual pooled cells from two individuals, 33 and 36 years old +E-MTAB-2983 ERR647977 characteristic organism Homo sapiens http://purl.obolibrary.org/obo/NCBITaxon_9606 +E-MTAB-2983 ERR647977 characteristic organism part ovary http://purl.obolibrary.org/obo/UBERON_0000992 +E-MTAB-2983 ERR647977 characteristic phenotype DDX4 antibody-positive +E-MTAB-2983 ERR647977 characteristic sex female http://purl.obolibrary.org/obo/PATO_0000383 +E-MTAB-2983 ERR647977 characteristic single cell quality OK +E-MTAB-2983 ERR647977 factor single cell identifier 15 +E-MTAB-2983 ERR647977 factor skin 15 +E-MTAB-2983 ERR647977 factor age 15 +E-MTAB-2983 ERR647977 factor bala 15 +E-MTAB-2983 ERR647978 characteristic biopsy site ovarian cortex http://purl.obolibrary.org/obo/UBERON_0013191 +E-MTAB-2983 ERR647978 characteristic developmental stage adult http://www.ebi.ac.uk/efo/EFO_0001272 +E-MTAB-2983 ERR647978 characteristic disease normal http://purl.obolibrary.org/obo/PATO_0000461 +E-MTAB-2983 ERR647978 characteristic individual pooled cells from two individuals, 33 and 36 years old +E-MTAB-2983 ERR647978 characteristic organism Homo sapiens http://purl.obolibrary.org/obo/NCBITaxon_9606 +E-MTAB-2983 ERR647978 characteristic organism part ovary http://purl.obolibrary.org/obo/UBERON_0000992 +E-MTAB-2983 ERR647978 characteristic phenotype DDX4 antibody-positive +E-MTAB-2983 ERR647978 characteristic sex female http://purl.obolibrary.org/obo/PATO_0000383 +E-MTAB-2983 ERR647978 characteristic single cell quality OK +E-MTAB-2983 ERR647978 factor single cell identifier 1 +E-MTAB-2983 ERR647978 factor skin 1 +E-MTAB-2983 ERR647978 factor age 1 +E-MTAB-2983 ERR647978 factor bala 1 +E-MTAB-2983 ERR647979 characteristic biopsy site ovarian cortex http://purl.obolibrary.org/obo/UBERON_0013191 +E-MTAB-2983 ERR647979 characteristic developmental stage adult http://www.ebi.ac.uk/efo/EFO_0001272 +E-MTAB-2983 ERR647979 characteristic disease normal http://purl.obolibrary.org/obo/PATO_0000461 +E-MTAB-2983 ERR647979 characteristic individual pooled cells from two individuals, 33 and 36 years old +E-MTAB-2983 ERR647979 characteristic organism Homo sapiens http://purl.obolibrary.org/obo/NCBITaxon_9606 +E-MTAB-2983 ERR647979 characteristic organism part ovary http://purl.obolibrary.org/obo/UBERON_0000992 +E-MTAB-2983 ERR647979 characteristic phenotype DDX4 antibody-positive +E-MTAB-2983 ERR647979 characteristic sex female http://purl.obolibrary.org/obo/PATO_0000383 +E-MTAB-2983 ERR647979 characteristic single cell quality OK +E-MTAB-2983 ERR647979 factor single cell identifier 11 +E-MTAB-2983 ERR647979 factor skin 11 +E-MTAB-2983 ERR647979 factor age 11 +E-MTAB-2983 ERR647979 factor bala 11 +E-MTAB-2983 ERR647980 characteristic biopsy site ovarian cortex http://purl.obolibrary.org/obo/UBERON_0013191 +E-MTAB-2983 ERR647980 characteristic developmental stage adult http://www.ebi.ac.uk/efo/EFO_0001272 +E-MTAB-2983 ERR647980 characteristic disease normal http://purl.obolibrary.org/obo/PATO_0000461 +E-MTAB-2983 ERR647980 characteristic individual pooled cells from two individuals, 33 and 36 years old +E-MTAB-2983 ERR647980 characteristic organism Homo sapiens http://purl.obolibrary.org/obo/NCBITaxon_9606 +E-MTAB-2983 ERR647980 characteristic organism part ovary http://purl.obolibrary.org/obo/UBERON_0000992 +E-MTAB-2983 ERR647980 characteristic phenotype DDX4 antibody-positive +E-MTAB-2983 ERR647980 characteristic sex female http://purl.obolibrary.org/obo/PATO_0000383 +E-MTAB-2983 ERR647980 characteristic single cell quality OK +E-MTAB-2983 ERR647980 factor single cell identifier 4 +E-MTAB-2983 ERR647980 factor skin 4 +E-MTAB-2983 ERR647980 factor age 4 +E-MTAB-2983 ERR647980 factor bala 4 +E-MTAB-2983 ERR647981 characteristic biopsy site ovarian cortex http://purl.obolibrary.org/obo/UBERON_0013191 +E-MTAB-2983 ERR647981 characteristic developmental stage adult http://www.ebi.ac.uk/efo/EFO_0001272 +E-MTAB-2983 ERR647981 characteristic disease normal http://purl.obolibrary.org/obo/PATO_0000461 +E-MTAB-2983 ERR647981 characteristic individual pooled cells from two individuals, 33 and 36 years old +E-MTAB-2983 ERR647981 characteristic organism Homo sapiens http://purl.obolibrary.org/obo/NCBITaxon_9606 +E-MTAB-2983 ERR647981 characteristic organism part ovary http://purl.obolibrary.org/obo/UBERON_0000992 +E-MTAB-2983 ERR647981 characteristic phenotype DDX4 antibody-positive +E-MTAB-2983 ERR647981 characteristic sex female http://purl.obolibrary.org/obo/PATO_0000383 +E-MTAB-2983 ERR647981 characteristic single cell quality OK +E-MTAB-2983 ERR647981 factor single cell identifier 30 +E-MTAB-2983 ERR647981 factor skin 30 +E-MTAB-2983 ERR647981 factor age 30 +E-MTAB-2983 ERR647981 factor bala 30 +E-MTAB-2983 ERR647982 characteristic biopsy site ovarian cortex http://purl.obolibrary.org/obo/UBERON_0013191 +E-MTAB-2983 ERR647982 characteristic developmental stage adult http://www.ebi.ac.uk/efo/EFO_0001272 +E-MTAB-2983 ERR647982 characteristic disease normal http://purl.obolibrary.org/obo/PATO_0000461 +E-MTAB-2983 ERR647982 characteristic individual pooled cells from two individuals, 33 and 36 years old +E-MTAB-2983 ERR647982 characteristic organism Homo sapiens http://purl.obolibrary.org/obo/NCBITaxon_9606 +E-MTAB-2983 ERR647982 characteristic organism part ovary http://purl.obolibrary.org/obo/UBERON_0000992 +E-MTAB-2983 ERR647982 characteristic phenotype DDX4 antibody-positive +E-MTAB-2983 ERR647982 characteristic sex female http://purl.obolibrary.org/obo/PATO_0000383 +E-MTAB-2983 ERR647982 characteristic single cell quality OK +E-MTAB-2983 ERR647982 factor single cell identifier 31 +E-MTAB-2983 ERR647982 factor skin 31 +E-MTAB-2983 ERR647982 factor age 31 +E-MTAB-2983 ERR647982 factor bala 31 +E-MTAB-2983 ERR647983 characteristic biopsy site ovarian cortex http://purl.obolibrary.org/obo/UBERON_0013191 +E-MTAB-2983 ERR647983 characteristic developmental stage adult http://www.ebi.ac.uk/efo/EFO_0001272 +E-MTAB-2983 ERR647983 characteristic disease normal http://purl.obolibrary.org/obo/PATO_0000461 +E-MTAB-2983 ERR647983 characteristic individual pooled cells from two individuals, 33 and 36 years old +E-MTAB-2983 ERR647983 characteristic organism Homo sapiens http://purl.obolibrary.org/obo/NCBITaxon_9606 +E-MTAB-2983 ERR647983 characteristic organism part ovary http://purl.obolibrary.org/obo/UBERON_0000992 +E-MTAB-2983 ERR647983 characteristic phenotype DDX4 antibody-positive +E-MTAB-2983 ERR647983 characteristic sex female http://purl.obolibrary.org/obo/PATO_0000383 +E-MTAB-2983 ERR647983 characteristic single cell quality OK +E-MTAB-2983 ERR647983 factor single cell identifier 3 +E-MTAB-2983 ERR647983 factor skin 3 +E-MTAB-2983 ERR647983 factor age 3 +E-MTAB-2983 ERR647983 factor bala 3 diff --git a/tests/experiment_files/magetab/E-MTAB-2983/E-MTAB-2983.idf.txt b/tests/experiment_files/magetab/E-MTAB-2983/E-MTAB-2983.idf.txt new file mode 100644 index 0000000..7f7095b --- /dev/null +++ b/tests/experiment_files/magetab/E-MTAB-2983/E-MTAB-2983.idf.txt @@ -0,0 +1,63 @@ +MAGE-TAB Version 1.1 +Investigation Title Functional germ line stem cells do not exist in adult mammalian ovaries + +Experimental Design cell type comparison design +Experimental Design Term Source REF EFO +Experimental Design Term Accession Number + +Experimental Factor Name single cell identifier +Experimental Factor Type single cell identifier +Experimental Factor Term Source REF +Experimental Factor Term Accession Number + +Person Last Name Hovatta Edsgard Panula +Person First Name Outi Daniel Sarita +Person Mid Initials +Person Email Outi.Hovatta@ki.se daniel.edsgard@ki.se Sarita.Panula@ki.se +Person Phone +Person Fax +Person Affiliation Division of Obstetrics and Gynecology, Department of Clinical Sciences, Intervention and Technology, Karolinska Institute and Karolinska University Hospital Huddinge Department of Cell and Molecular Biology, Karolinska Institutet Division of Obstetrics and Gynecology, Department of Clinical Sciences, Intervention and Technology, Karolinska Institute and Karolinska University Hospital Huddinge +Person Address Stockholm, 141 86, Sweden 17177, Stockholm, Sweden 141 86, Stockholm, Sweden +Person Roles investigator data analyst;submitter experiment performer +Person Roles Term Source REF +Person Roles Term Accession Number + +Date of Experiment 2014-09-07 +Public Release Date 2015-10-01 + +PubMed ID 26444631 +Publication DOI 10.1038/nm.3775 +Publication Author List Hua Zhang, Sarita Panula, Sophie Petropoulos, Daniel Edsgärd, Kiran Busayavalasa, Lian Liu, Xin Li, Sanjiv Risal, Yan Shen, Jingchen Shao, Meng Liu, Susann Li, Dongdong Zhang, Xiaoxi Zhang, Romana Raphaela Gerner, Mona Sheikhi, Pauliina Damdimopoulou, Rickard Sandberg, Iyadh Douagi, Jan-Åke Gustafsson, Lin Liu, Fredrik Lanner, Outi Hovatta & Kui Liu +Publication Title Adult human and mouse ovaries lack DDX4-expressing functional oogonial stem cells +Publication Status published +Publication Status Term Source REF +Publication Status Term Accession Number + +Experiment Description Single-cell RNA-seq of DDX4 FACS sorted cells from ovarian cortical tissue. Regarding singe cell quality, genes were filtered based on a RPKM greater than or equal to 1 in at least one cell, where the RPKM cutoff was determined from histograms of number of expressed transcripts versus RPKM, and it was also sensible with respect to the number of molecules per RPKM estimated from the ERCC spike-in. Three clear outliers were observed in a principal component analysis and therefore removed from further analysis. + +Protocol Name P-MTAB-41450 P-MTAB-41449 P-MTAB-41471 +Protocol Type nucleic acid sequencing protocol nucleic acid library construction protocol sample collection protocol +Protocol Term Source REF EFO EFO EFO +Protocol Term Accession Number +Protocol Description Single-end sequencing was performed using the TrueSeq dual-index sequencing primers (Illumina) according to manufacturers recommendation on a HiSeq 2000. Picelli et al, Full-length RNA-seq from single cells using Smart-seq2, Nature Protocols, 2014 Single cells (n = 41) were randomly picked by mouth pipetting with a finely pulled glass capillary and placed directly into lysis buffer containing 1 uL of RNase inhibitor and 19 uL of 0.2% (vol/vol) Triton X-100 solution (Sigma-Aldrich, Germany). The 8-strip PCR tubes containing cells were immediately frozen on dry ice and kept at -80C for downstream applications. Regarding spike-ins: 0.1uL of a 4*10^-6 dilution of the ERCC RNA spike-in mix 1 (Ambion) was added to each sample. +Protocol Parameters +Protocol Hardware Illumina HiSeq 2000 +Protocol Software +Protocol Contact + +Term Source Name EFO ArrayExpress +Term Source File http://www.ebi.ac.uk/efo/ http://www.ebi.ac.uk/arrayexpress/ +Term Source Version 2.38 + +SDRF File E-MTAB-2983.sdrf.txt +Comment [Submitted Name] Functional germ line stem cells do not exist in adult mammalian ovaries +Comment [SecondaryAccession] ERP007170 +Comment [SequenceDataURI] http://www.ebi.ac.uk/ena/data/view/ERR647946-ERR647983 +Comment [AEExperimentType] RNA-seq of coding RNA from single cells +Comment[ArrayExpressAccession] E-MTAB-2983 +Comment [AdditionalFile:fa] ERCC92.fa + +Comment[EAExperimentType] baseline +Comment[EAAdditionalAttributes] +Comment[EAExpectedClusters] +Comment[EACurator] Anja Fullgrabe diff --git a/tests/experiment_files/magetab/E-MTAB-2983/E-MTAB-2983.sdrf.txt b/tests/experiment_files/magetab/E-MTAB-2983/E-MTAB-2983.sdrf.txt new file mode 100644 index 0000000..895c41f --- /dev/null +++ b/tests/experiment_files/magetab/E-MTAB-2983/E-MTAB-2983.sdrf.txt @@ -0,0 +1,38 @@ +Source Name Comment[ENA_SAMPLE] Characteristics [organism] Characteristics[sex] Characteristics [developmental stage] Characteristics[disease] Characteristics[individual] Characteristics[organism part] Characteristics[biopsy site] Characteristics[phenotype] Characteristics[single cell quality] Material Type Description Protocol REF Protocol REF Performer Extract Name Comment[single cell isolation] Comment[library construction] Comment[end bias] Comment[input molecule] Comment[primer] Comment[spike in] Comment[LIBRARY_STRAND] Comment[LIBRARY_LAYOUT] Comment[LIBRARY_SELECTION] Comment[LIBRARY_SOURCE] Comment[LIBRARY_STRATEGY] Comment[spike sequence file] Protocol REF Performer Assay Name Technology Type Comment[ENA_EXPERIMENT] Scan Name Comment[SUBMITTED_FILE_NAME] Comment[ENA_RUN] Comment[FASTQ_URI] FactorValue[single cell identifier] Factor Value[skin] Factor Value [age] FactorValue [bala] +P6 ERS559159 Homo sapiens female adult normal pooled cells from two individuals, 33 and 36 years old ovary ovarian cortex DDX4 antibody-positive OK cell DDX4 FACS sorted single cell. FACS was performed on pooled ovarian cortical tissue from two individuals, 33 and 36 years old. P-MTAB-41471 P-MTAB-41449 Sophie Petropoulos P6 mouth pipetting smart-seq2 none polyA RNA oligo-dT ERCC mix 1 not applicable SINGLE RANDOM TRANSCRIPTOMIC RNA-Seq ERCC92.fa P-MTAB-41450 Sophie Petropoulos P6 sequencing assay ERX604327 P6.fastq.gz P6.fastq.gz ERR647947 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR647/ERR647947/ERR647947.fastq.gz 5 5 5 5 +P28 ERS559166 Homo sapiens female adult normal pooled cells from two individuals, 33 and 36 years old ovary ovarian cortex DDX4 antibody-positive OK cell DDX4 FACS sorted single cell. FACS was performed on pooled ovarian cortical tissue from two individuals, 33 and 36 years old. P-MTAB-41471 P-MTAB-41449 Sophie Petropoulos P28 mouth pipetting smart-seq2 none polyA RNA oligo-dT ERCC mix 1 not applicable SINGLE RANDOM TRANSCRIPTOMIC RNA-Seq ERCC92.fa P-MTAB-41450 Sophie Petropoulos P28 sequencing assay ERX604334 P28.fastq.gz P28.fastq.gz ERR647948 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR647/ERR647948/ERR647948.fastq.gz 27 27 27 27 +P21 ERS559142 Homo sapiens female adult normal pooled cells from two individuals, 33 and 36 years old ovary ovarian cortex DDX4 antibody-positive OK cell DDX4 FACS sorted single cell. FACS was performed on pooled ovarian cortical tissue from two individuals, 33 and 36 years old. P-MTAB-41471 P-MTAB-41449 Sophie Petropoulos P21 mouth pipetting smart-seq2 none polyA RNA oligo-dT ERCC mix 1 not applicable SINGLE RANDOM TRANSCRIPTOMIC RNA-Seq ERCC92.fa P-MTAB-41450 Sophie Petropoulos P21 sequencing assay ERX604310 P21.fastq.gz P21.fastq.gz ERR647949 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR647/ERR647949/ERR647949.fastq.gz 20 20 20 20 +P18 ERS559163 Homo sapiens female adult normal pooled cells from two individuals, 33 and 36 years old ovary ovarian cortex DDX4 antibody-positive OK cell DDX4 FACS sorted single cell. FACS was performed on pooled ovarian cortical tissue from two individuals, 33 and 36 years old. P-MTAB-41471 P-MTAB-41449 Sophie Petropoulos P18 mouth pipetting smart-seq2 none polyA RNA oligo-dT ERCC mix 1 not applicable SINGLE RANDOM TRANSCRIPTOMIC RNA-Seq ERCC92.fa P-MTAB-41450 Sophie Petropoulos P18 sequencing assay ERX604331 P18.fastq.gz P18.fastq.gz ERR647950 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR647/ERR647950/ERR647950.fastq.gz 17 17 17 17 +P3 ERS559143 Homo sapiens female adult normal pooled cells from two individuals, 33 and 36 years old ovary ovarian cortex DDX4 antibody-positive OK cell DDX4 FACS sorted single cell. FACS was performed on pooled ovarian cortical tissue from two individuals, 33 and 36 years old. P-MTAB-41471 P-MTAB-41449 Sophie Petropoulos P3 mouth pipetting smart-seq2 none polyA RNA oligo-dT ERCC mix 1 not applicable SINGLE RANDOM TRANSCRIPTOMIC RNA-Seq ERCC92.fa P-MTAB-41450 Sophie Petropoulos P3 sequencing assay ERX604311 P3.fastq.gz P3.fastq.gz ERR647951 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR647/ERR647951/ERR647951.fastq.gz 2 2 2 2 +P14 ERS559150 Homo sapiens female adult normal pooled cells from two individuals, 33 and 36 years old ovary ovarian cortex DDX4 antibody-positive OK cell DDX4 FACS sorted single cell. FACS was performed on pooled ovarian cortical tissue from two individuals, 33 and 36 years old. P-MTAB-41471 P-MTAB-41449 Sophie Petropoulos P14 mouth pipetting smart-seq2 none polyA RNA oligo-dT ERCC mix 1 not applicable SINGLE RANDOM TRANSCRIPTOMIC RNA-Seq ERCC92.fa P-MTAB-41450 Sophie Petropoulos P14 sequencing assay ERX604318 P14.fastq.gz P14.fastq.gz ERR647952 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR647/ERR647952/ERR647952.fastq.gz 13 13 13 13 +P29 ERS559132 Homo sapiens female adult normal pooled cells from two individuals, 33 and 36 years old ovary ovarian cortex DDX4 antibody-positive OK cell DDX4 FACS sorted single cell. FACS was performed on pooled ovarian cortical tissue from two individuals, 33 and 36 years old. P-MTAB-41471 P-MTAB-41449 Sophie Petropoulos P29 mouth pipetting smart-seq2 none polyA RNA oligo-dT ERCC mix 1 not applicable SINGLE RANDOM TRANSCRIPTOMIC RNA-Seq ERCC92.fa P-MTAB-41450 Sophie Petropoulos P29 sequencing assay ERX604300 P29.fastq.gz P29.fastq.gz ERR647953 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR647/ERR647953/ERR647953.fastq.gz 28 28 28 28 +P24 ERS559167 Homo sapiens female adult normal pooled cells from two individuals, 33 and 36 years old ovary ovarian cortex DDX4 antibody-positive OK cell DDX4 FACS sorted single cell. FACS was performed on pooled ovarian cortical tissue from two individuals, 33 and 36 years old. P-MTAB-41471 P-MTAB-41449 Sophie Petropoulos P24 mouth pipetting smart-seq2 none polyA RNA oligo-dT ERCC mix 1 not applicable SINGLE RANDOM TRANSCRIPTOMIC RNA-Seq ERCC92.fa P-MTAB-41450 Sophie Petropoulos P24 sequencing assay ERX604335 P24.fastq.gz P24.fastq.gz ERR647954 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR647/ERR647954/ERR647954.fastq.gz 23 23 23 23 +P20 ERS559155 Homo sapiens female adult normal pooled cells from two individuals, 33 and 36 years old ovary ovarian cortex DDX4 antibody-positive OK cell DDX4 FACS sorted single cell. FACS was performed on pooled ovarian cortical tissue from two individuals, 33 and 36 years old. P-MTAB-41471 P-MTAB-41449 Sophie Petropoulos P20 mouth pipetting smart-seq2 none polyA RNA oligo-dT ERCC mix 1 not applicable SINGLE RANDOM TRANSCRIPTOMIC RNA-Seq ERCC92.fa P-MTAB-41450 Sophie Petropoulos P20 sequencing assay ERX604323 P20.fastq.gz P20.fastq.gz ERR647955 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR647/ERR647955/ERR647955.fastq.gz 19 19 19 19 +P41 ERS559158 Homo sapiens female adult normal pooled cells from two individuals, 33 and 36 years old ovary ovarian cortex DDX4 antibody-positive OK cell DDX4 FACS sorted single cell. FACS was performed on pooled ovarian cortical tissue from two individuals, 33 and 36 years old. P-MTAB-41471 P-MTAB-41449 Sophie Petropoulos P41 mouth pipetting smart-seq2 none polyA RNA oligo-dT ERCC mix 1 not applicable SINGLE RANDOM TRANSCRIPTOMIC RNA-Seq ERCC92.fa P-MTAB-41450 Sophie Petropoulos P41 sequencing assay ERX604326 P41.fastq.gz P41.fastq.gz ERR647956 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR647/ERR647956/ERR647956.fastq.gz 38 38 38 38 +P13 ERS559148 Homo sapiens female adult normal pooled cells from two individuals, 33 and 36 years old ovary ovarian cortex DDX4 antibody-positive OK cell DDX4 FACS sorted single cell. FACS was performed on pooled ovarian cortical tissue from two individuals, 33 and 36 years old. P-MTAB-41471 P-MTAB-41449 Sophie Petropoulos P13 mouth pipetting smart-seq2 none polyA RNA oligo-dT ERCC mix 1 not applicable SINGLE RANDOM TRANSCRIPTOMIC RNA-Seq ERCC92.fa P-MTAB-41450 Sophie Petropoulos P13 sequencing assay ERX604316 P13.fastq.gz P13.fastq.gz ERR647957 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR647/ERR647957/ERR647957.fastq.gz 12 12 12 12 +P27 ERS559160 Homo sapiens female adult normal pooled cells from two individuals, 33 and 36 years old ovary ovarian cortex DDX4 antibody-positive OK cell DDX4 FACS sorted single cell. FACS was performed on pooled ovarian cortical tissue from two individuals, 33 and 36 years old. P-MTAB-41471 P-MTAB-41449 Sophie Petropoulos P27 mouth pipetting smart-seq2 none polyA RNA oligo-dT ERCC mix 1 not applicable SINGLE RANDOM TRANSCRIPTOMIC RNA-Seq ERCC92.fa P-MTAB-41450 Sophie Petropoulos P27 sequencing assay ERX604328 P27.fastq.gz P27.fastq.gz ERR647958 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR647/ERR647958/ERR647958.fastq.gz 26 26 26 26 +P40 ERS559154 Homo sapiens female adult normal pooled cells from two individuals, 33 and 36 years old ovary ovarian cortex DDX4 antibody-positive OK cell DDX4 FACS sorted single cell. FACS was performed on pooled ovarian cortical tissue from two individuals, 33 and 36 years old. P-MTAB-41471 P-MTAB-41449 Sophie Petropoulos P40 mouth pipetting smart-seq2 none polyA RNA oligo-dT ERCC mix 1 not applicable SINGLE RANDOM TRANSCRIPTOMIC RNA-Seq ERCC92.fa P-MTAB-41450 Sophie Petropoulos P40 sequencing assay ERX604322 P40.fastq.gz P40.fastq.gz ERR647959 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR647/ERR647959/ERR647959.fastq.gz 37 37 37 37 +P19 ERS559164 Homo sapiens female adult normal pooled cells from two individuals, 33 and 36 years old ovary ovarian cortex DDX4 antibody-positive OK cell DDX4 FACS sorted single cell. FACS was performed on pooled ovarian cortical tissue from two individuals, 33 and 36 years old. P-MTAB-41471 P-MTAB-41449 Sophie Petropoulos P19 mouth pipetting smart-seq2 none polyA RNA oligo-dT ERCC mix 1 not applicable SINGLE RANDOM TRANSCRIPTOMIC RNA-Seq ERCC92.fa P-MTAB-41450 Sophie Petropoulos P19 sequencing assay ERX604332 P19.fastq.gz P19.fastq.gz ERR647960 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR647/ERR647960/ERR647960.fastq.gz 18 18 18 18 +P30 ERS559138 Homo sapiens female adult normal pooled cells from two individuals, 33 and 36 years old ovary ovarian cortex DDX4 antibody-positive OK cell DDX4 FACS sorted single cell. FACS was performed on pooled ovarian cortical tissue from two individuals, 33 and 36 years old. P-MTAB-41471 P-MTAB-41449 Sophie Petropoulos P30 mouth pipetting smart-seq2 none polyA RNA oligo-dT ERCC mix 1 not applicable SINGLE RANDOM TRANSCRIPTOMIC RNA-Seq ERCC92.fa P-MTAB-41450 Sophie Petropoulos P30 sequencing assay ERX604306 P30.fastq.gz P30.fastq.gz ERR647961 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR647/ERR647961/ERR647961.fastq.gz 29 29 29 29 +P39 ERS559139 Homo sapiens female adult normal pooled cells from two individuals, 33 and 36 years old ovary ovarian cortex DDX4 antibody-positive OK cell DDX4 FACS sorted single cell. FACS was performed on pooled ovarian cortical tissue from two individuals, 33 and 36 years old. P-MTAB-41471 P-MTAB-41449 Sophie Petropoulos P39 mouth pipetting smart-seq2 none polyA RNA oligo-dT ERCC mix 1 not applicable SINGLE RANDOM TRANSCRIPTOMIC RNA-Seq ERCC92.fa P-MTAB-41450 Sophie Petropoulos P39 sequencing assay ERX604307 P39.fastq.gz P39.fastq.gz ERR647962 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR647/ERR647962/ERR647962.fastq.gz 36 36 36 36 +P10 ERS559161 Homo sapiens female adult normal pooled cells from two individuals, 33 and 36 years old ovary ovarian cortex DDX4 antibody-positive OK cell DDX4 FACS sorted single cell. FACS was performed on pooled ovarian cortical tissue from two individuals, 33 and 36 years old. P-MTAB-41471 P-MTAB-41449 Sophie Petropoulos P10 mouth pipetting smart-seq2 none polyA RNA oligo-dT ERCC mix 1 not applicable SINGLE RANDOM TRANSCRIPTOMIC RNA-Seq ERCC92.fa P-MTAB-41450 Sophie Petropoulos P10 sequencing assay ERX604329 P10.fastq.gz P10.fastq.gz ERR647963 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR647/ERR647963/ERR647963.fastq.gz 9 9 9 9 +P9 ERS559141 Homo sapiens female adult normal pooled cells from two individuals, 33 and 36 years old ovary ovarian cortex DDX4 antibody-positive OK cell DDX4 FACS sorted single cell. FACS was performed on pooled ovarian cortical tissue from two individuals, 33 and 36 years old. P-MTAB-41471 P-MTAB-41449 Sophie Petropoulos P9 mouth pipetting smart-seq2 none polyA RNA oligo-dT ERCC mix 1 not applicable SINGLE RANDOM TRANSCRIPTOMIC RNA-Seq ERCC92.fa P-MTAB-41450 Sophie Petropoulos P9 sequencing assay ERX604309 P9.fastq.gz P9.fastq.gz ERR647964 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR647/ERR647964/ERR647964.fastq.gz 8 8 8 8 +P36 ERS559153 Homo sapiens female adult normal pooled cells from two individuals, 33 and 36 years old ovary ovarian cortex DDX4 antibody-positive OK cell DDX4 FACS sorted single cell. FACS was performed on pooled ovarian cortical tissue from two individuals, 33 and 36 years old. P-MTAB-41471 P-MTAB-41449 Sophie Petropoulos P36 mouth pipetting smart-seq2 none polyA RNA oligo-dT ERCC mix 1 not applicable SINGLE RANDOM TRANSCRIPTOMIC RNA-Seq ERCC92.fa P-MTAB-41450 Sophie Petropoulos P36 sequencing assay ERX604321 P36.fastq.gz P36.fastq.gz ERR647965 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR647/ERR647965/ERR647965.fastq.gz 34 34 34 34 +P8 ERS559168 Homo sapiens female adult normal pooled cells from two individuals, 33 and 36 years old ovary ovarian cortex DDX4 antibody-positive OK cell DDX4 FACS sorted single cell. FACS was performed on pooled ovarian cortical tissue from two individuals, 33 and 36 years old. P-MTAB-41471 P-MTAB-41449 Sophie Petropoulos P8 mouth pipetting smart-seq2 none polyA RNA oligo-dT ERCC mix 1 not applicable SINGLE RANDOM TRANSCRIPTOMIC RNA-Seq ERCC92.fa P-MTAB-41450 Sophie Petropoulos P8 sequencing assay ERX604336 P8.fastq.gz P8.fastq.gz ERR647966 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR647/ERR647966/ERR647966.fastq.gz 7 7 7 7 +P23 ERS559151 Homo sapiens female adult normal pooled cells from two individuals, 33 and 36 years old ovary ovarian cortex DDX4 antibody-positive OK cell DDX4 FACS sorted single cell. FACS was performed on pooled ovarian cortical tissue from two individuals, 33 and 36 years old. P-MTAB-41471 P-MTAB-41449 Sophie Petropoulos P23 mouth pipetting smart-seq2 none polyA RNA oligo-dT ERCC mix 1 not applicable SINGLE RANDOM TRANSCRIPTOMIC RNA-Seq ERCC92.fa P-MTAB-41450 Sophie Petropoulos P23 sequencing assay ERX604319 P23.fastq.gz P23.fastq.gz ERR647967 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR647/ERR647967/ERR647967.fastq.gz 22 22 22 22 +P15 ERS559162 Homo sapiens female adult normal pooled cells from two individuals, 33 and 36 years old ovary ovarian cortex DDX4 antibody-positive OK cell DDX4 FACS sorted single cell. FACS was performed on pooled ovarian cortical tissue from two individuals, 33 and 36 years old. P-MTAB-41471 P-MTAB-41449 Sophie Petropoulos P15 mouth pipetting smart-seq2 none polyA RNA oligo-dT ERCC mix 1 not applicable SINGLE RANDOM TRANSCRIPTOMIC RNA-Seq ERCC92.fa P-MTAB-41450 Sophie Petropoulos P15 sequencing assay ERX604330 P15.fastq.gz P15.fastq.gz ERR647968 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR647/ERR647968/ERR647968.fastq.gz 14 14 14 14 +P7 ERS559146 Homo sapiens female adult normal pooled cells from two individuals, 33 and 36 years old ovary ovarian cortex DDX4 antibody-positive OK cell DDX4 FACS sorted single cell. FACS was performed on pooled ovarian cortical tissue from two individuals, 33 and 36 years old. P-MTAB-41471 P-MTAB-41449 Sophie Petropoulos P7 mouth pipetting smart-seq2 none polyA RNA oligo-dT ERCC mix 1 not applicable SINGLE RANDOM TRANSCRIPTOMIC RNA-Seq ERCC92.fa P-MTAB-41450 Sophie Petropoulos P7 sequencing assay ERX604314 P7.fastq.gz P7.fastq.gz ERR647969 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR647/ERR647969/ERR647969.fastq.gz 6 6 6 6 +P22 ERS559144 Homo sapiens female adult normal pooled cells from two individuals, 33 and 36 years old ovary ovarian cortex DDX4 antibody-positive OK cell DDX4 FACS sorted single cell. FACS was performed on pooled ovarian cortical tissue from two individuals, 33 and 36 years old. P-MTAB-41471 P-MTAB-41449 Sophie Petropoulos P22 mouth pipetting smart-seq2 none polyA RNA oligo-dT ERCC mix 1 not applicable SINGLE RANDOM TRANSCRIPTOMIC RNA-Seq ERCC92.fa P-MTAB-41450 Sophie Petropoulos P22 sequencing assay ERX604312 P22.fastq.gz P22.fastq.gz ERR647970 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR647/ERR647970/ERR647970.fastq.gz 21 21 21 21 +P26 ERS559169 Homo sapiens female adult normal pooled cells from two individuals, 33 and 36 years old ovary ovarian cortex DDX4 antibody-positive OK cell DDX4 FACS sorted single cell. FACS was performed on pooled ovarian cortical tissue from two individuals, 33 and 36 years old. P-MTAB-41471 P-MTAB-41449 Sophie Petropoulos P26 mouth pipetting smart-seq2 none polyA RNA oligo-dT ERCC mix 1 not applicable SINGLE RANDOM TRANSCRIPTOMIC RNA-Seq ERCC92.fa P-MTAB-41450 Sophie Petropoulos P26 sequencing assay ERX604337 P26.fastq.gz P26.fastq.gz ERR647971 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR647/ERR647971/ERR647971.fastq.gz 25 25 25 25 +P34 ERS559157 Homo sapiens female adult normal pooled cells from two individuals, 33 and 36 years old ovary ovarian cortex DDX4 antibody-positive OK cell DDX4 FACS sorted single cell. FACS was performed on pooled ovarian cortical tissue from two individuals, 33 and 36 years old. P-MTAB-41471 P-MTAB-41449 Sophie Petropoulos P34 mouth pipetting smart-seq2 none polyA RNA oligo-dT ERCC mix 1 not applicable SINGLE RANDOM TRANSCRIPTOMIC RNA-Seq ERCC92.fa P-MTAB-41450 Sophie Petropoulos P34 sequencing assay ERX604325 P34.fastq.gz P34.fastq.gz ERR647972 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR647/ERR647972/ERR647972.fastq.gz 32 32 32 32 +P17 ERS559134 Homo sapiens female adult normal pooled cells from two individuals, 33 and 36 years old ovary ovarian cortex DDX4 antibody-positive OK cell DDX4 FACS sorted single cell. FACS was performed on pooled ovarian cortical tissue from two individuals, 33 and 36 years old. P-MTAB-41471 P-MTAB-41449 Sophie Petropoulos P17 mouth pipetting smart-seq2 none polyA RNA oligo-dT ERCC mix 1 not applicable SINGLE RANDOM TRANSCRIPTOMIC RNA-Seq ERCC92.fa P-MTAB-41450 Sophie Petropoulos P17 sequencing assay ERX604302 P17.fastq.gz P17.fastq.gz ERR647973 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR647/ERR647973/ERR647973.fastq.gz 16 16 16 16 +P11 ERS559145 Homo sapiens female adult normal pooled cells from two individuals, 33 and 36 years old ovary ovarian cortex DDX4 antibody-positive OK cell DDX4 FACS sorted single cell. FACS was performed on pooled ovarian cortical tissue from two individuals, 33 and 36 years old. P-MTAB-41471 P-MTAB-41449 Sophie Petropoulos P11 mouth pipetting smart-seq2 none polyA RNA oligo-dT ERCC mix 1 not applicable SINGLE RANDOM TRANSCRIPTOMIC RNA-Seq ERCC92.fa P-MTAB-41450 Sophie Petropoulos P11 sequencing assay ERX604313 P11.fastq.gz P11.fastq.gz ERR647974 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR647/ERR647974/ERR647974.fastq.gz 10 10 10 10 +P37 ERS559133 Homo sapiens female adult normal pooled cells from two individuals, 33 and 36 years old ovary ovarian cortex DDX4 antibody-positive OK cell DDX4 FACS sorted single cell. FACS was performed on pooled ovarian cortical tissue from two individuals, 33 and 36 years old. P-MTAB-41471 P-MTAB-41449 Sophie Petropoulos P37 mouth pipetting smart-seq2 none polyA RNA oligo-dT ERCC mix 1 not applicable SINGLE RANDOM TRANSCRIPTOMIC RNA-Seq ERCC92.fa P-MTAB-41450 Sophie Petropoulos P37 sequencing assay ERX604301 P37.fastq.gz P37.fastq.gz ERR647975 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR647/ERR647975/ERR647975.fastq.gz 35 35 35 35 +P35 ERS559149 Homo sapiens female adult normal pooled cells from two individuals, 33 and 36 years old ovary ovarian cortex DDX4 antibody-positive OK cell DDX4 FACS sorted single cell. FACS was performed on pooled ovarian cortical tissue from two individuals, 33 and 36 years old. P-MTAB-41471 P-MTAB-41449 Sophie Petropoulos P35 mouth pipetting smart-seq2 none polyA RNA oligo-dT ERCC mix 1 not applicable SINGLE RANDOM TRANSCRIPTOMIC RNA-Seq ERCC92.fa P-MTAB-41450 Sophie Petropoulos P35 sequencing assay ERX604317 P35.fastq.gz P35.fastq.gz ERR647976 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR647/ERR647976/ERR647976.fastq.gz 33 33 33 33 +P16 ERS559137 Homo sapiens female adult normal pooled cells from two individuals, 33 and 36 years old ovary ovarian cortex DDX4 antibody-positive OK cell DDX4 FACS sorted single cell. FACS was performed on pooled ovarian cortical tissue from two individuals, 33 and 36 years old. P-MTAB-41471 P-MTAB-41449 Sophie Petropoulos P16 mouth pipetting smart-seq2 none polyA RNA oligo-dT ERCC mix 1 not applicable SINGLE RANDOM TRANSCRIPTOMIC RNA-Seq ERCC92.fa P-MTAB-41450 Sophie Petropoulos P16 sequencing assay ERX604305 P16.fastq.gz P16.fastq.gz ERR647977 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR647/ERR647977/ERR647977.fastq.gz 15 15 15 15 +P1 ERS559156 Homo sapiens female adult normal pooled cells from two individuals, 33 and 36 years old ovary ovarian cortex DDX4 antibody-positive OK cell DDX4 FACS sorted single cell. FACS was performed on pooled ovarian cortical tissue from two individuals, 33 and 36 years old. P-MTAB-41471 P-MTAB-41449 Sophie Petropoulos P1 mouth pipetting smart-seq2 none polyA RNA oligo-dT ERCC mix 1 not applicable SINGLE RANDOM TRANSCRIPTOMIC RNA-Seq ERCC92.fa P-MTAB-41450 Sophie Petropoulos P1 sequencing assay ERX604324 P1.fastq.gz P1.fastq.gz ERR647978 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR647/ERR647978/ERR647978.fastq.gz 1 1 1 1 +P12 ERS559136 Homo sapiens female adult normal pooled cells from two individuals, 33 and 36 years old ovary ovarian cortex DDX4 antibody-positive OK cell DDX4 FACS sorted single cell. FACS was performed on pooled ovarian cortical tissue from two individuals, 33 and 36 years old. P-MTAB-41471 P-MTAB-41449 Sophie Petropoulos P12 mouth pipetting smart-seq2 none polyA RNA oligo-dT ERCC mix 1 not applicable SINGLE RANDOM TRANSCRIPTOMIC RNA-Seq ERCC92.fa P-MTAB-41450 Sophie Petropoulos P12 sequencing assay ERX604304 P12.fastq.gz P12.fastq.gz ERR647979 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR647/ERR647979/ERR647979.fastq.gz 11 11 11 11 +P5 ERS559147 Homo sapiens female adult normal pooled cells from two individuals, 33 and 36 years old ovary ovarian cortex DDX4 antibody-positive OK cell DDX4 FACS sorted single cell. FACS was performed on pooled ovarian cortical tissue from two individuals, 33 and 36 years old. P-MTAB-41471 P-MTAB-41449 Sophie Petropoulos P5 mouth pipetting smart-seq2 none polyA RNA oligo-dT ERCC mix 1 not applicable SINGLE RANDOM TRANSCRIPTOMIC RNA-Seq ERCC92.fa P-MTAB-41450 Sophie Petropoulos P5 sequencing assay ERX604315 P5.fastq.gz P5.fastq.gz ERR647980 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR647/ERR647980/ERR647980.fastq.gz 4 4 4 4 +P31 ERS559165 Homo sapiens female adult normal pooled cells from two individuals, 33 and 36 years old ovary ovarian cortex DDX4 antibody-positive OK cell DDX4 FACS sorted single cell. FACS was performed on pooled ovarian cortical tissue from two individuals, 33 and 36 years old. P-MTAB-41471 P-MTAB-41449 Sophie Petropoulos P31 mouth pipetting smart-seq2 none polyA RNA oligo-dT ERCC mix 1 not applicable SINGLE RANDOM TRANSCRIPTOMIC RNA-Seq ERCC92.fa P-MTAB-41450 Sophie Petropoulos P31 sequencing assay ERX604333 P31.fastq.gz P31.fastq.gz ERR647981 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR647/ERR647981/ERR647981.fastq.gz 30 30 30 30 +P33 ERS559140 Homo sapiens female adult normal pooled cells from two individuals, 33 and 36 years old ovary ovarian cortex DDX4 antibody-positive OK cell DDX4 FACS sorted single cell. FACS was performed on pooled ovarian cortical tissue from two individuals, 33 and 36 years old. P-MTAB-41471 P-MTAB-41449 Sophie Petropoulos P33 mouth pipetting smart-seq2 none polyA RNA oligo-dT ERCC mix 1 not applicable SINGLE RANDOM TRANSCRIPTOMIC RNA-Seq ERCC92.fa P-MTAB-41450 Sophie Petropoulos P33 sequencing assay ERX604308 P33.fastq.gz P33.fastq.gz ERR647982 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR647/ERR647982/ERR647982.fastq.gz 31 31 31 31 +P4 ERS559152 Homo sapiens female adult normal pooled cells from two individuals, 33 and 36 years old ovary ovarian cortex DDX4 antibody-positive OK cell DDX4 FACS sorted single cell. FACS was performed on pooled ovarian cortical tissue from two individuals, 33 and 36 years old. P-MTAB-41471 P-MTAB-41449 Sophie Petropoulos P4 mouth pipetting smart-seq2 none polyA RNA oligo-dT ERCC mix 1 not applicable SINGLE RANDOM TRANSCRIPTOMIC RNA-Seq ERCC92.fa P-MTAB-41450 Sophie Petropoulos P4 sequencing assay ERX604320 P4.fastq.gz P4.fastq.gz ERR647983 ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR647/ERR647983/ERR647983.fastq.gz 3 3 3 3 diff --git a/tests/random-data-set.bats b/tests/random-data-set.bats index 6b7d04b..7b29728 100644 --- a/tests/random-data-set.bats +++ b/tests/random-data-set.bats @@ -53,6 +53,36 @@ [ -f $expDesignFile ] } +@test "Loading: E-MTAB-2983 through CLI" { + export ACCESSIONS=E-MTAB-2983 + + run load_experiment_web_cli.sh + echo "output = ${output}" + [ "$status" -eq 0 ] +} + +@test "Loading: Check that E-MTAB-2983 was loaded" { + export EXP_ID=E-MTAB-2983 + export FIELDS=species + species=$(get_experiment_info.sh) + run [ "$species" == "Homos sapiens" ] + echo "output = ${output}" + [ "$status" -eq 0 ] +} + +@test "Loading: Update experiment design of E-MTAB-2983 after deleting file" { + export ACCESSIONS=E-MTAB-2983 + + expDesignFile=$EXPERIMENT_DESIGN_FILES/ExpDesign-${ACCESSIONS}.tsv + rm -rf $expDesignFile + + run update_experiment_web_cli.sh + + echo "output = ${output}" + [ "$status" -eq 0 ] + [ -f $expDesignFile ] +} + @test "Analytics: Delete experiment data-set-1" { export EXP_ID=TEST-EXP1 run delete_db_scxa_analytics.sh @@ -373,7 +403,7 @@ [ "$status" -eq 0 ] } -@test "Exp_Design: Load exp_design data" { +@test "Exp_Design: Load exp_design data E-CURD-4" { export CONDENSED_SDRF_FILE=${EXPERIMENT_FILES}/magetab/E-CURD-4/E-CURD-4.condensed-sdrf.tsv export SDRF_FILE=${EXPERIMENT_FILES}/magetab/E-CURD-4/E-CURD-4.sdrf.txt run load_exp_design.sh @@ -382,6 +412,15 @@ [ "$status" -eq 0 ] } +@test "Exp_Design: Load exp_design data E-MTAB-2983" { + export CONDENSED_SDRF_FILE=${EXPERIMENT_FILES}/magetab/E-MTAB-2983/E-MTAB-2983.condensed-sdrf.tsv + export SDRF_FILE=${EXPERIMENT_FILES}/magetab/E-MTAB-2983/E-MTAB-2983.sdrf.txt + run load_exp_design.sh + + echo "output = ${output}" + [ "$status" -eq 0 ] +} + @test "Collections: Create X" { export COLL_ID=MYCOLLX export COLL_NAME="My collection X"