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For_Chunan
Possibly Longitudinal
Gene-Environment Interactions at the Skin Surface looks to be part of HMP mentions Atopic dermatitis (AD). 4664 biosamples 3389 SRA. Links to Non-tumor DNA sample from volar forearm of a human male participant in the dbGaP study "Skin Microbiome in Disease States: Atopic Dermatitis and Immunodeficiency" so related to other dbGaP samples. seems to have tumor or not and mentions a longiudinal cohort. Big dataset would be cool example if we can sort it out. Might find simpler examples though. Might be related to 1) from the MGNIFY results.
34) 16S rRNA gene profiling of atopic dermatitis and psoriasis patients compared to healthy volunteers
Says only 1 sample but ther are actually 531 samples. Has an associated paper maybe worth looking at the paper and seeing if there anything to it that you can use.
Skin swabs were collected from the lesional skin of a large cohort of atopic dermatitis and psoriasis patients and subjected to 16S rRNA sequencing on the Roche 454 platform.
https://www.ncbi.nlm.nih.gov/bioproject/779324 Skin microbiota in atopic dermatitis maybe? Lots of samples but less metadata.
https://www.ncbi.nlm.nih.gov/bioproject/715292 human skin microbe
To explore the differences of microbial species and microflora structure on human antecubital fossa between healthy volunteers and patients with atopic dermatitis diseases
Metadata on NCBI might actually be reconcilable between healthy and atopic dermatitis patients.
16S rRNA gene fragments from skin and guts of early infants suffering from atopic dermatitis (AD) and/or food allergy (FA) - a pilot study
2 associated publications a ton of supplemental metadata could be interesting.
human skin metagenome in Atopic Dermatitis 29 SRA EXPs which have basic metadata on disease vs control/
Antimicrobial function of skin microbiome in atopic dermatitis only 40 samples but has skin with/without staph infection lesion site and tissue sample site. Maybe.
20 more samples about atopic dermatitis (AD). Maybe if you do that topic.
Skin microbiome associated with atopic dermatitis 324 samples legion and non legion. Adult vs child (or similar factor). I think has associated metatranscriptom https://www.ncbi.nlm.nih.gov/bioproject/268353 but not public.
https://www.ebi.ac.uk/metagenomics/browse?lineage=root:Host-associated:Human:Skin#studies 35 studies, sort by samples
Seems good, lots of samples 2758, part of HMP, MGNIFY has some metadata per sample about the body site and sex. Perhaps worth looking at. Has papers associated can get more metadata from them
FACTOR exp?
Gene-Environment Interactions at the Skin Surface - Demonstration project for Human Microbiome Project (HMP) 4695 biosamples 3434 SRA. In theory has disease states but I don't see any obviously identifiable in the biosamples. Maybe can get the metadata from elsewhere?
Many samples 1968, has skin oral and fecal, (could subset down to only skin). Amplicon, has some metadata. https://www.ncbi.nlm.nih.gov/bioproject/378368
3) Topical treatment interventions elicit personalized and site-specific shifts in human skin bacterial communities
Lots of samples 1484, theoretical has different treatment groups but lacks metadata on MGNIFY, amplicon https://www.ncbi.nlm.nih.gov/bioproject/395539 has it on NCBI this could be interesting.
760 samples all forehead skin, amplicon. Might be timepoints based on the lables but hard to tell. Unpublished and not well doccumented. https://www.ncbi.nlm.nih.gov/bioproject/265952 better on NCBI.
related to: 19) Flores_palm_EBI
109 samples, seem like it's related to 4. May or maynot be able to make sense of these labels to make a coherent dataset. No publication. Amplicon. Better on NCBI https://www.ncbi.nlm.nih.gov/bioproject/265951 932 samples PCR amplicon. Lots of metadata in biosamples uberon terms diseases like chicken pox etc could be cool.
5) Body site is a more determinant factor than human population diversity in healthy skin microbiome
Works as a SURVERY
644 samplels amplicon. Has publication which might have more metadata if not skip.
645 more skin site examples. Also has ethic group but probably not a useful metadata field.
585 samples, amplicon. Sample lables have free text body sites. Could ontologize and search for these. https://www.ncbi.nlm.nih.gov/bioproject/251922 900 samples in NCBI. Could be used to populate a catolog of UBERON body sites. Lots of metadata but not much more that can be done than that.
7) Patterns in the skin microbiota differ in children and teenagers between rural and urban environments
584 samples, metadata not great.
527 samples. Study seemed good explored the differences in the bacterial community structure associated with seven skin sites in 71 healthy Chinese over six days and its correlations with age, gender, physical skin parameters .... but unfotunately the info didn't make it into MGNIFY and there's not publication. Looking on NCBI https://www.ncbi.nlm.nih.gov/bioproject/PRJNA269787 there might be enough info in the sample names to piece this together. E.g. lable DNA-Seq of subject 1111's back of hands: elderly Male suburb P1 can work with this. INVESTIGATE
https://www.ncbi.nlm.nih.gov/bioproject/269787 1364 samples on NCBI
In this study, we explored the differences in the bacterial community structure associated with seven skin sites in 71 healthy Chinese over six days and its correlations with age, gender, physical skin parameters, and whether participants lived in an urban versus suburban location of the same city
In theory this is a cool timeseries but the Biosample data isn't great, SRAs are better maybe able to piece together the timeseries. Be cool if we can make this work. TBD. Idea from Ramona's playbook we can compare data of ages against qualtiative terms like adolescence with a bit of reasoning or a script as to normalize that data using semantics. to compare across datasets.
9) EMG produced TPA metagenomics assembly of the PRJNA266117 data set (Human skin bacterial metagenome and Virome Metagenome).
504 samples, From an EBI paper which might have more metadata to pull. Maybe assemblies not amplicon.
503 Samples but not in MGNIFY links to the above study so it's just a dulicate of the above 9).
15) EMG produced TPA metagenomics assembly of the PRJEB26427 data set (Understanding the microbial basis of body odor in teenagers and kids).
175 samples, I think this is the same as or related to 14) but the assemblies done for a separate EBI paper. Group together with 14.
179 samples. Metagenomics samples of multiple skin sites (underarm, neck & head scalp) from teenagers and kids. Has a publication associated with it. Might be able to infer from lables e.g. Underarm_kid_1h, Assemblies not amplicon. Paper associated with it.
16) EMG produced TPA metagenomics assembly of PRJNA415710 data set (Elucidating the dandruff and non-dandruff scalp microbiome in Indian women and assessing the effect of coconut oil on it).
143 samples. Links to EBI paper maybe. https://www.ncbi.nlm.nih.gov/bioproject/415710
17) Elucidating the dandruff and non-dandruff scalp microbiome in Indian women and assessing the effect of coconut oil on it
142 samples I think related to or same as above) 16 no samples on EBI so probably the same as above or not usable.
106 samples lack of metadata be hard to use alone I think. although it links to 22 EMG produced TPA metagenomics assembly of the Human Skin Microbiome Metagenome (human skin metagenome) data set. Maybe can be used if there's more metadata there.
23) EMG produced TPA metagenomics assembly of the Human Skin Microbiome Metagenome (human skin metagenome) data set.
94 Samples. Links to 19 and an EBI paper EBI Metagenomics in 2017: enriching the analysis of microbial communities, from sequence reads to assemblies. maybe can get something from there? Maybe of these dataset link to that paper or similar EBI papers. Unfortunately here the metadata is very minimal. Amplicon and assembly probably not useful. https://www.ncbi.nlm.nih.gov/bioproject/496628
47 samples Links to EBI 2017 paper. Assemblies and I think these are about skin contact with trains. Assemblies
46 samples, linked to above 25) project but no samples here so only above has value. This and above are probably not useful unless there is something about them in the paper.
27) EMG produced TPA metagenomics assembly of the Skin metagenomes (human skin metagenome) data set.
33 samples, links to 22) above 26) Skin shotgun metagenomes from psoriasis patients These are the assemblies probably of the metagenomes from that other dataset. Unclear if this and the above are decipherable alone. https://www.ncbi.nlm.nih.gov/bioproject/513679
28) EMG produced TPA metagenomics assembly of the Isolation and Identification of the Follicular Microbiome: Implications for Acne Research (PRJNA435265) data set.
16 samples. Links to 21) above Probably the assemblies to the metagenomes in the above project, which lacks metadata.
30) EMG produced TPA metagenomics assembly of the Identification of fungi and ameba from human wound genomic sequencing (human wound) data set
13 samples but not actually anthying there. Also links to the EBI 2017 paper. Check that paper but this is not useful.
18) EMG produced TPA metagenomics fasta_path of the Longitudinal_Nasopharyngeal_Microbiome_Dynamics_in_Infants_from_the_Maela_ARI_Birth_Cohort (PRJEB25223) data set.
120 samples. Links to EBI paper. Assemblies sparse metadata.
258 samples. Is this one that you've seen before? from http://dx.doi.org/10.7717/peerj.3543
Ten type II diabetic subjects with chronic foot ulcers were followed over a time course of 10 weeks
Some metadata, I'm guessing you've seen this or this is one of the studies you already have/want to use? Can mine info from the samples names: Sample Patient 5 skin adjacent to wound time 4
12) Impact of the Mk VI SkinSuit on skin microbiota of terrestrial volunteers and an International Space Station-bound astronaut
204 samples. Maybe not relevant? Has an associated publication. Basically no metadata on MGNIFY.
191 samples Infected people with a skin bacteria have time points could be relevant. Have a treatment and longitudinal study. No publication but might be able to figure out treatments from the sample labels Sample 398-3-D1, Sample 396-2-Pre perhaps replicate 2? pre-inoculation, description is H. ducreyi 35000HP inoculated Maybe could be useful. https://www.ncbi.nlm.nih.gov/bioproject/278873 Skin microbiome in human volunteers inoculated with H. ducreyi Raw sequence reads Skin with/without H. ducreyi infection Some interesting metadata 191 samples on NCBI.
101 samples, lack of metadata be hard to use.
96 samples.
[From] skin bacterial and fungal microbiotas from healthy and dandruff subjects, comparing scalp and forehead (lesional and non-lesional skin sites).
Could be good if you can make sense of the samples, e.g., LH06-T1-16S_S86_L001_R1_001 no publication. Some metadata. Amplicon.
73 samples. Skin shotgun metagenomes from psoriasis patients. Links to a publication can maybe get more metadata from it. Some metadata maybe useful?
14 Samples topic is related to what you want. Has an associated paper, Metadata on MGNIFY isn't great but the paper might have stuff that's useful. Worth checking out. Amplicon.
31) These samples are selections from a larger cohort that were selected for the participation in the EBI metagenomics training in Sept. 2015
10 samples Illumina WGS metagenomes Metadata is not great maybe can make sense of lables AD posterior_thigh PT NON_LES Probably not worth it.
8 samples Links to a paper which might be relvant but in MGNIFY there is no data here.
2 samples WGS from palms not super helpful.
https://www.ncbi.nlm.nih.gov/bioproject/782120 human skin metagenome
Skin microbiome of Japanese elderly in relation to the onset of pressure ulcers (Staphylococcus species-targeted sequencing) One of the most prevalence and challenging problems for elderly in Japan is the onset of pressure ulcers (PU) during being cared in hospitals and/or their home. Could be relevant. 58 samples 16S.
https://www.ncbi.nlm.nih.gov/bioproject/750391 The human skin and oral microbiome in healthy individuals with psoriasis risk factor LCE3B/C-del Maybe metadata is a bit subpar.
https://www.ncbi.nlm.nih.gov/bioproject/743060 if you can find (Nejman et al. Science 2020) as a paper to get context. Biosamples are soil. Forget this.
https://www.ncbi.nlm.nih.gov/bioproject/736423 Aging Associated Changes in the Adult Human Skin Microbiome and the Host Factors That Affect Skin Microbiome Composition lots of samples but doesnt' look like we can infer the ages.
https://www.ncbi.nlm.nih.gov/bioproject/735376 Human Skin Microbiome Data treatments of skin before and after swimming in the ocean. Maybe could work.
Deciphering the role of skin surface microbiome on skin health: an integrative multi-omics approach reveals three distinct microbial / metabolic clusters Has age gender and skin site. Only 16 samples but decent metadata. Amplicon.
Puberty associated changes in skin (longitudinal study) 327 samples has associated paper could mine this.
70 samples has data on patient age and gender but just "skin" nothing more specific. Amplicon.
Allergy, living environment, lifestyle as well as skin and gut microbiota in dogs and their owners sounds like Alise's Lab with a large questionaire, unfortunately useless without the metadata bout the dogs/environments. Alise?
idea is good but metadata is missing.
Changes in the skin microbiome associated with squamous cell carcinoma in transplant recipients Mabye.
Perioral skin in healthy subjects vs. perioral dermatitis
has data on dermitological disorder sex face or hand dominant hand. Could be cool 88 samples.
Human Facial Skin Mycobiomes in Korea Women with Sensitive and Non-sensitive Skin
Maybe if you want fungus. Has seemingly assocatied project Human Facial Skin Microbiomes in Korea Women with Sensitive and Non-sensitive Skin https://www.ncbi.nlm.nih.gov/bioproject/627788 which is microbiomes. Might also be associated with https://www.ncbi.nlm.nih.gov/bioproject/614620 and https://www.ncbi.nlm.nih.gov/bioproject/613934.
Skin microbiome of Japanese elderly in relation to the onset of pressure ulcers Could be cool if you can figure out the treaments, not clear from the metadata but age and sex it.
would be very cool with antibiotic treatments but I don't see any data.
Could be cool across elevations but data isn't clear.
Taxonomic profiling of skin microbiome and correlation with clinical skin parameters in healthy Koreans. Can get young vs old and male vs female 102 samples.
Fecal and skin sample collection from hidradenitis suppurativa and healthy subjects lesion non-lesions but only a few skin samples.
Evidence for cutaneous dysbiosis in dystrophic epidermolysis bullosa
Eight DEB patients were sampled at three different sites: untreated wound, perilesional skin and normal (uninvolved) skin.
Maybe
Knight infant time series - 1 massive 1000 sample dataset with lots of metadata maybe look at?
MG_baby timeseries similar to above Knight infant time series - 1 also about babies and metadata about parents.
Microbial predictors of healing and short-term effect of debridement on the microbiome of chronic wounds
Wounds mabye relevant but metadata is unclear to me
Microbial composition of diabetic skin
Impact of topical emollient therapy with sunflower seed oil on the skin and gut microbiomes of children with severe acute malnutrition in Bangladesh 1190 samples with treatment famine status and skin or fecal samples. Maybe not.
Skin microbiome from hidradenitis suppurativa patients
Maybe has some metadata like dermatology disorder.
"New insights into the factors driving the skin microbiome" 2548 samples different skin locations 16S, said they did a questionaire, but it's not linked if you could find it i'd be great, but otherwise it's just decent. Maybe.
Longitudinal assessment of the influence of lifestyle homogenization on the microbiome in a cohort of United States Air Force Cadets Might be cool but it's mostly dust not skin samples it seems.
The Fecal, Oral, and Skin Microbiota of Children with Chagas Disease treated with Benznidazole Work looking into 255 samples (I guess a 3rd of which skin) Lots of metadata including UBERON terms and treatment type. Maybe a time sereies with at least pre and post treatment. Investigate
Human Skin Microbiomes in Young and Old Women Raw sequence reads more from Chung-Ang University (Korea). Has young and old skin samples. Many datasets like this.
human skin metagenome Targeted loci environmental 170 samples Maybe has dermis and epidermis samples and body site.
Acne microbiome modulation 241 biosamples. Description has enough metadata that you might be able to piece this together.
Human skin metagenome associated with acne (human) 82 samples. Has decent metadata and a way to get more though the dbGaP authorized access system. https://www.ncbi.nlm.nih.gov/bioproject/507061 also seems to be the same.
Metagenomics samples from neuropathic diabetic foot ulcer (DFU) Metagenome 199 biosamples lots of metadata relevant to topic. Check it's the same as the MGNFIY study. YES
Saudi Diabetic foot ulcer microbiome "Investigation of the neuropathic and neuroischemic Diabetic Foot Ulcer Microbiome" 76SRA 38 biosamples. ION Torrent WGS but one useful metadata field isolation source about the condition. SRA name also could be useful e.g. Neuroischaimic ulcer Could fit into analysis.
Bacteria communities of human skin skin several sites on children between 1 and 10 years of age, along with the participants’ mothers. Maybe can piece it together from metadata? Maybe not.
Bacterial and fungal communities of psoriatic patients 522 samples has metadata on disease state and skin location. Could be ok.
Chinese human skin metagenome 860 samples metdata about sample location but nothing interesting like treatments
16S amplicon sequence analysis of skin microbiomes from Japanese individual 148 samples from various skin sites. This could work with other projects if we want to do general comparisons like scalp vs Forehead etc.
Human skin metagenome and 16S Swabs and scrapes from different skin types 188 SRA Experiments various body sites in metadata maybe scrap vs swab but not clear.
PMS Skin microbiome data 52 healthy skins with age no.
Ulcers but only 3 samples no.
The impact of skin care products on skin chemistry and microbiome timeseries with products but may not be able to piece together from metadata.
The Effect of Dog Ownership on the Microbiome of Elderly Humans 544 samples lots of metadata! pretty cool study if topical. Time points after getting a dog. Could be cool as an example of timepoints with a treatment.
Isotretinoin and lymecycline treatments modify the skin microbiota in acne 133 samples good metadata Treatments with diff drugs different sites. Could be a decent example.
Microbiome of healthy and leprous skin over multi-drug therapy disease vs healthy but no obvious data on treatments so no.
human skin temporal metagenome Raw sequence reads 484 samples with some metadata of where on body.
Topical antimicrobial treatments elicit shifts to resident skin bacterial communities and reduce colonization by Staphylococcus aureus competitors 608 samples but I think it's mouse and maybe also human. Effects of antibiotics on recolonization by staph. MAYBE.
The skin microbiome of very low birth weight neonates Helsinki Finland again sounds like alise's lab. Decent metadata but is more about neonatal babies. https://www.ncbi.nlm.nih.gov/bioproject/377454 is similar also finland but no metdata about age
Skin microbiome in small and large plaque parapsoriasis 52 samples Helsinki Finland again Better metadata stuff like earlier parapsoriasis diagnoses ==07/2013 parapsoriasis Maybe can do something with this.
Genomics, Biomarkers and Mechanisms of Healing in Chronic Wounds 82 samples chronic wounds maybe interesting.
Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample - 3 prime Some skin samples but only has useful metadata about uberon site.
340 SRA. Relationship between the skin microbial communities from a variety of body regions of intimate cohabiting couples. Lots of metadata surveys, where the skin is from. Worth checking out.
Puerto Rico and Plantanal 767 Samples. Lots of metadata longitudinal baby study. Oral Skin and other sites. Perhaps interesting, Questions like the microbiome of any babies that had a C-section.
Bacterial colonization and succession in a newly opened hospital 2756 samples UBERON site data could be to just populate the get me any data bout x body site. Interesting though Not a timeseries.
Temporal stability in chronic wound microbiota is associated with poor healing 382 samples. About diabetic foot ulcers. Lots of metdata (also lots of NA's) but could be interesting about wound healing, diabetes types etc. Timeseries though maybe a bit unclear how to work it out. Amplicon. Has this seemingly parallel project https://www.ncbi.nlm.nih.gov/bioproject/324668 about fungi same grants and researchers.
More helsinki stuff. 64 samples about skin melanomas decent metadata.
An 8-week single centre, double-blind, randomised controlled, home-use study to evaluate effects on skin bacteria and protection of skin with resilience under tracked city environmental aggressors 582 samples. Can extract timeseries from biosamples along with UBERON terms for sites. Consider checking out. I think pairs with https://www.ncbi.nlm.nih.gov/bioproject/757525 for fungus.
Developmental Ecology of the Human Microbiome - Restoration Study of babies. 1016 samples About vaginal vs C section births but has lots of metdata may or maynot be able to reconstruct the time series or which mother is with which baby.
American Gut Project 32100 biosamples from a vareity of body sites with a ton of metdata maybe not as much skin and the questions are more about diet but could be cool to take the skin from this if making a larger DB of UBERON annotated SKIN sites. MAYBE.
150 samples metadata not great prob no.
Cutaneous Burn Injury Promotes Defects in the Bacterial Microbiome in Autologous Donor Skin: Implications for Skin Grafting Outcomes Only 25 samples but seems to be burn and not burnt and I think skin grafts. MAYBE.
Many like this from City University of Hong Kong but barley any metadata so probably not worth it even if 200 samples.
and https://www.ncbi.nlm.nih.gov/bioproject/281352 maybe more of these, uncontacted indegious people in South America contains skin samples could be interesting to compare to non indeginous modern folk. 66 samples each.
300 samples The cutaneous microbiome in out-patients presenting acutely with skin abscesses with/without absescesses metadata not great but can prob get those control and condition.
The microbiological signature of human cutaneous leishmaniasis lesions chronic skin ulcers only 10 samples but maybe enough metadata to be interesting disease stage treatment age sex sample location.
Viruses if desired? Some more similar things not noted above.
Longitudinal 1625 samples Longitudinal analysis of microbial interaction between humans and the indoor environment env skin interplay may or maynot be relevant but could be a good dataset if we choose to do something like that.
FACTOR experiment.
89 samples. Comparison of skin microbial communities at the site of mosquito bites. Probaby can get the 2 conditions bit unbit although 16 maybe unavailable? Maybe.
FACTOR experiment. Environmental biodiversity, human microbiota and allergy Helsinki again Decent metadata stuff about allergy tests etc. Cool if this is something of interest. Have other Factor exps to use if not.
Factor experiment.
Metagenomic study of the human skin microbiome associated with acne - Demonstration project for Human Microbiome Project (HMP) 300 biosamples 209 SRA. I see dbGaP study so maybe related to https://www.ncbi.nlm.nih.gov/bioproject/507062? Might be able to scrape subject affected by acne, sex and skin, study disease Acne Vulgaris. Could work.
Finished lookin at all of the https://www.ncbi.nlm.nih.gov/bioproject with human skin metagenome 251 results
Organize these down to find relevant datasets