Merge pull request #232 from Rosa-234/kortekaas-entries-10-2024

Added additional entries for IPF

data/image_resources.csv

@@ -218,4 +218,13 @@ CD11b_AF488/Mouse_tumor_CD11b_117312_CD11c_101217.jpg,"Mouse tumor: CD11c (cyan,
 CD206_AF488/Mouse_tumor_CD206_141710_CD3_557869.jpg,"Mouse tumor: CD206 (yellow, catalog number 141710) and CD3 (white, catalog number 557869)",e2add3bfcb443348402be37fafe59820,"['CD206_AF488/0009-0007-0646-7946.md', 'CD3_AF647/0009-0007-0646-7946.md']"
 Cytokeratin_AF488/Mouse_tumor_Cytokeratin_628608_SIRPalpha_144027.jpg,"Mouse tumor: Cytokeratin (yellow, catalog number 628608) and SIRPalpha (white, catalog number 144027)",33e8fcccbc2a85f5d24b3472b2f99fc2,"['Cytokeratin_AF488/0009-0007-0646-7946.md', 'SIRPalpha_AF647/0009-0007-0646-7946.md']"
 CD11b_AF594/Mouse_tumor_CD11b_101254_Vimentin_699305.jpg,"Mouse tumor: CD11b (yellow, catalog number 101254) and Vimentin (cyan, catalog number 699305)",1973e63c7b04db8d0bafe5789f2f71c7,"['CD11b_AF594/0009-0007-0646-7946.md', 'Vimentin_AF488/0009-0007-0646-7946.md']"
-CD8_AF647/Mouse_tumor_CD8_100724_CD44_104410C1.jpg,"Mouse tumor: CD8 (yellow, catalog number 100724) and CD44 (white, catalog number 104410C1)",594bc8cf83d3a195fc6639d8f772ccde,"['CD8_AF647/0009-0007-0646-7946.md', 'CD44_iF594/0009-0007-0646-7946.md']"
+CD8_AF647/Mouse_tumor_CD8_100724_CD44_104410C1.jpg,"Mouse tumor: CD8 (yellow, catalog number 100724) and CD44 (white, catalog number 104410C1)",594bc8cf83d3a195fc6639d8f772ccde,"['CD8_AF647/0009-0007-0646-7946.md', 'CD44_iF594/0009-0007-0646-7946.md']"
+SMAD3_Unconjugated/SMAD3_AF647_Human_Lung.jpg,"Human lung (Idiopathic Pulmonary Fibrosis) FFPE: SMAD3 (magenta) and DAPI (blue)",89bb51e62a1bd1d537ce29e62858229d,['SMAD3_Unconjugated/0000-0002-8728-1735.md']
+Phospho-TAK1_Unconjugated/pTAK1_AF647_Human_Lung.jpg,"Human lung (Idiopathic Pulmonary Fibrosis) FFPE: Phospho-TAK1 (magenta) and DAPI (blue)",e5cbab57d170e700a914623d0deed463,['Phospho-TAK1_Unconjugated/0000-0002-8728-1735.md']
+VWF_Unconjugated/VWF_AF647_Human_Lung.jpg,"Human lung (Idiopathic Pulmonary Fibrosis) FFPE: VWF (magenta) and DAPI (blue)",136e21ff420ff599b750f08615dc61bb,['VWF_Unconjugated/0000-0002-8728-1735.md']
+UCHL1_Unconjugated/UCHL1_AF647_Human_Lung.jpg,"Human lung (Idiopathic Pulmonary Fibrosis) FFPE: UCHL1 (magenta) and DAPI (blue)",3362f493ee47f52a64393722f451081b,['UCHL1_Unconjugated/0000-0002-8728-1735.md']
+SMAD2_Unconjugated/SMAD2_AF647_Human_Lung.jpg,"Human lung (Idiopathic Pulmonary Fibrosis) FFPE: SMAD2 (magenta) and DAPI (blue)",71b83e5a91ee19fac9799d821601215a,['SMAD2_Unconjugated/0000-0002-8728-1735.md']
+TAK1_Unconjugated/TAK1_AF488_Human_Lung.jpg,"Human lung (Idiopathic Pulmonary Fibrosis) FFPE: TAK1 (green) and DAPI (blue)",8b90fe4e4d22d782bdbf61937c10d372,['TAK1_Unconjugated/0000-0002-8728-1735.md']
+Podoplanin_Unconjugated/Podoplanin_AF647_Human_Lung.jpg,"Human lung (Idiopathic Pulmonary Fibrosis) FFPE: Podoplanin (magenta) and DAPI (blue)",0dfdae7b6b81fe9a76805bb68fb65a9b,['Podoplanin_Unconjugated/0000-0002-8728-1735.md']
+Phospho-SMAD1_5_Unconjugated/pSMAD1-5_AF647_Human_Lung.jpg,"Human lung (Idiopathic Pulmonary Fibrosis) FFPE: Phospho-SMAD1/5 (magenta) and DAPI (blue)",d7afba5084dba3992b4afbdf8b3fc901,['Phospho-SMAD1_5_Unconjugated/0000-0002-8728-1735.md']
+TGFBR2_Unconjugated/TGFBR2_AF647_Human_Lung.jpg,"Human lung (Idiopathic Pulmonary Fibrosis) FFPE: TGFBR2 (magenta) and DAPI (blue)",896ea55bacf80d87e7d96ea93fc3e311,['TGFBR2_Unconjugated/0000-0002-8728-1735.md']

data/reagent_resources.csv

@@ -1218,4 +1218,13 @@ P97797,Primary Antibody,SIRPalpha,Mouse,Rat,IgG1,P84,BioLegend,144027,AF647,AB_2
 P15379,Primary Antibody,CD44,Mouse,Rat,NA,IM7,AAT Bioquest,104410C1,iF594,NA,Stock,IBEX2D Manual,1:4 Cytofix/Cytoperm Fixed Frozen,Pancreatic Ductal Adenocarcinoma,Tumor,0.3% Triton-X-100,NA,1 mg/ml LiBH4 15 minutes,Yes,0009-0007-0646-7946,NA,0009-0007-0646-7946
 P22646,Primary Antibody,CD3,Mouse,Rat,IgG2b,17A2,BD Biosciences,557869,AF647,AB_396912,Stock,IBEX2D Manual,1:4 Cytofix/Cytoperm Fixed Frozen,Pancreatic Ductal Adenocarcinoma,Tumor,0.3% Triton-X-100,NA,1 mg/ml LiBH4 15 minutes,Yes,0009-0007-0646-7946,NA,0009-0007-0646-7946
 P22646,Primary Antibody,CD3,Mouse,Rat,IgG2b,17A2,Thermo Fisher Scientific,58-0032-80,AF532,AB_11220474,Stock,IBEX2D Manual,1:4 Cytofix/Cytoperm Fixed Frozen,Pancreatic Ductal Adenocarcinoma,Tumor,0.3% Triton-X-100,NA,1 mg/ml LiBH4 15 minutes,Yes,0009-0007-0646-7946,NA,0009-0007-0646-7946
-P01731,Primary Antibody,CD8,Mouse,Rat,IgG2a,53-6.7,BioLegend,100724,AF647,AB_389326,Stock,IBEX2D Manual,1:4 Cytofix/Cytoperm Fixed Frozen,Pancreatic Ductal Adenocarcinoma,Tumor,0.3% Triton-X-100,NA,1 mg/ml LiBH4 15 minutes,Yes,0009-0007-0646-7946,NA,0009-0007-0646-7946
+P01731,Primary Antibody,CD8,Mouse,Rat,IgG2a,53-6.7,BioLegend,100724,AF647,AB_389326,Stock,IBEX2D Manual,1:4 Cytofix/Cytoperm Fixed Frozen,Pancreatic Ductal Adenocarcinoma,Tumor,0.3% Triton-X-100,NA,1 mg/ml LiBH4 15 minutes,Yes,0009-0007-0646-7946,NA,0009-0007-0646-7946
+Q86YL7,Primary Antibody,Podoplanin,Human,Mouse,IgG1,D2-40,BioLegend,916601,Unconjugated,AB_2565182,Stock,IBEX2D Manual,FFPE,Lung,Idiopathic Pulmonary Fibrosis,0.3% Triton-X-100,10 mM citrate buffer (pH 6.0) for 30 minutes at 95C,NA,Yes,0000-0002-8728-1735,NA,0000-0002-8728-1735
+P09936,Primary Antibody,UCHL1,Human,Rabbit,IgG,Polyclonal,Proteintech,14730-1-AP,Unconjugated,AB_2210497,Stock,IBEX2D Manual,FFPE,Lung,Idiopathic Pulmonary Fibrosis,0.3% Triton-X-100,10 mM citrate buffer (pH 6.0) for 30 minutes at 95C,NA,Yes,0000-0002-8728-1735,NA,0000-0002-8728-1735
+P84022,Primary Antibody,SMAD3,Human,Rabbit,IgG,Polyclonal,Abcam,ab28379,Unconjugated,AB_2192903,Stock,IBEX2D Manual,FFPE,Lung,Idiopathic Pulmonary Fibrosis,0.3% Triton-X-100,10 mM citrate buffer (pH 6.0) for 30 minutes at 95C,NA,Yes,0000-0002-8728-1735,NA,0000-0002-8728-1735
+O43318,Primary Antibody,TAK1,Human,Rabbit,IgG,Polyclonal,Proteintech,12330-2-AP,Unconjugated,AB_2140101,Stock,IBEX2D Manual,FFPE,Lung,Idiopathic Pulmonary Fibrosis,0.3% Triton-X-100,10 mM citrate buffer (pH 6.0) for 30 minutes at 95C,NA,Yes,0000-0002-8728-1735,NA,0000-0002-8728-1735
+Q15796,Primary Antibody,SMAD2,Human,Mouse,IgG1,L16D3,Cell Signaling Technology,3103,Unconjugated,AB_490816,Stock,IBEX2D Manual,FFPE,Lung,Idiopathic Pulmonary Fibrosis,0.3% Triton-X-100,10 mM citrate buffer (pH 6.0) for 30 minutes at 95C,NA,Yes,0000-0002-8728-1735,NA,0000-0002-8728-1735
+P37173,Primary Antibody,TGFBR2,Human,Mouse,IgG1,MM0056-4F14,Abcam,ab78419,Unconjugated,AB_1603198,Stock,IBEX2D Manual,FFPE,Lung,Idiopathic Pulmonary Fibrosis,0.3% Triton-X-100,10 mM citrate buffer (pH 6.0) for 30 minutes at 95C,NA,Yes,0000-0002-8728-1735,NA,0000-0002-8728-1735
+NA,Primary Antibody,Phospho-SMAD1/5,Human,Rabbit,IgG,41D10,Cell Signaling Technology,9516,Unconjugated,AB_491015,Stock,IBEX2D Manual,FFPE,Lung,Idiopathic Pulmonary Fibrosis,0.3% Triton-X-100,10 mM citrate buffer (pH 6.0) for 30 minutes at 95C,NA,Yes,0000-0002-8728-1735,NA,0000-0002-8728-1735
+P04275,Primary Antibody,VWF,Human,Rabbit,IgG,D8L8G,Cell Signaling Technology,65707,Unconjugated,AB_2799692,Stock,IBEX2D Manual,FFPE,Lung,Idiopathic Pulmonary Fibrosis,0.3% Triton-X-100,10 mM citrate buffer (pH 6.0) for 30 minutes at 95C,NA,Yes,0000-0002-8728-1735,NA,0000-0002-8728-1735
+NA,Primary Antibody,Phospho-TAK1,Human,Rabbit,IgG,Polyclonal,Thermo Fisher Scientific,PA5-99340,Unconjugated,AB_2818273,Stock,IBEX2D Manual,FFPE,Lung,Idiopathic Pulmonary Fibrosis,0.3% Triton-X-100,10 mM citrate buffer (pH 6.0) for 30 minutes at 95C,NA,Yes,0000-0002-8728-1735,NA,0000-0002-8728-1735

docs/supporting_material/Phospho-SMAD1_5_Unconjugated/0000-0002-8728-1735.md

@@ -0,0 +1,23 @@
+---
+layout: default
+---
+
+# Configurations
+
+| UniProt Accession Number   | Reagent Type     | Target Name / Protein Biomarker   | Target Species   | Host Organism   | Isotype   |   Clonality | Vendor                    |   Catalog Number | Conjugate    | RRID       | Availability   | Method                 | Tissue Preservation   | Target Tissue   | Tissue State                  | Detergent         | Antigen Retrieval Conditions                                                               | Dye Inactivation Conditions   | Recommend   | Agree                                                        | Disagree   | Contributor                                                  | Notes       |
+|:---------------------------|:-----------------|:----------------------------------|:-----------------|:----------------|:----------|------------:|:--------------------------|-----------------:|:-------------|:-----------|:---------------|:-----------------------|:----------------------|:----------------|:------------------------------|:------------------|:-------------------------------------------------------------------------------------------|:------------------------------|:------------|:-------------------------------------------------------------|:-----------|:-------------------------------------------------------------|:------------|
+| NA                         | Primary Antibody | Phospho-SMAD1/5                   | Human            | Rabbit          | IgG       | 41D10       | Cell Signaling Technology           |             9516 | Unconjugated | AB_491015  | Stock          | IBEX2D Manual          | FFPE                  | Lung            | Idiopathic Pulmonary Fibrosis | 0.3% Triton-X-100 | 10 mM citrate buffer (pH 6.0) for 30 minutes at 95C                                        | NA                            | Yes         | [0000-0002-8728-1735](https://orcid.org/0000-0002-8728-1735) | NA         | [0000-0002-8728-1735](https://orcid.org/0000-0002-8728-1735) | [1](#notes) |
+
+
+# Publications
+
+
+
+# Additional Notes
+
+<a name="notes"></a>
+1. This antibody labels the anticipated subcellular compartment (nucleus). This antibody was detected using a secondary antibody (Abcam, ab150079). We used a secondary only control to test for non-specific binding of the secondary antibody and observed no signal as expected (not shown).
+
+| Human lung (Idiopathic Pulmonary Fibrosis) FFPE: Phospho-SMAD1/5 (magenta) and DAPI (blue) |
+|:-------:|
+| ![](pSMAD1-5_AF647_Human_Lung.jpg) |

docs/supporting_material/Phospho-TAK1_Unconjugated/0000-0002-8728-1735.md

@@ -0,0 +1,23 @@
+---
+layout: default
+---
+
+# Configurations
+
+| UniProt Accession Number   | Reagent Type     | Target Name / Protein Biomarker   | Target Species   | Host Organism   | Isotype   |   Clonality | Vendor                    |   Catalog Number | Conjugate    | RRID       | Availability   | Method                 | Tissue Preservation   | Target Tissue   | Tissue State                  | Detergent         | Antigen Retrieval Conditions                                                               | Dye Inactivation Conditions   | Recommend   | Agree                                                        | Disagree   | Contributor                                                  | Notes       |
+|:---------------------------|:-----------------|:----------------------------------|:-----------------|:----------------|:----------|------------:|:--------------------------|-----------------:|:-------------|:-----------|:---------------|:-----------------------|:----------------------|:----------------|:------------------------------|:------------------|:-------------------------------------------------------------------------------------------|:------------------------------|:------------|:-------------------------------------------------------------|:-----------|:-------------------------------------------------------------|:------------|
+| NA                         | Primary Antibody | Phospho-TAK1                      | Human            | Rabbit          | IgG       | Polyclonal  | Thermo Fisher Scientific             |        PA5-99340 | Unconjugated | AB_2818273 | Stock          | IBEX2D Manual          | FFPE                  | Lung            | Idiopathic Pulmonary Fibrosis | 0.3% Triton-X-100 | 10 mM citrate buffer (pH 6.0) for 30 minutes at 95C                                        | NA                            | Yes         | [0000-0002-8728-1735](https://orcid.org/0000-0002-8728-1735) | NA         | [0000-0002-8728-1735](https://orcid.org/0000-0002-8728-1735) | [1](#notes) |
+
+
+# Publications
+
+
+
+# Additional Notes
+
+<a name="notes"></a>
+1. This antibody labels the anticipated subcellular compartment (nucleus). This antibody was detected using a secondary antibody (Abcam, ab150079). We used a secondary only control to test for non-specific binding of the secondary antibody and observed no signal as expected (not shown).
+
+| Human lung (Idiopathic Pulmonary Fibrosis) FFPE: Phospho-TAK1 (magenta) and DAPI (blue) |
+|:-------:|
+| ![](pTAK1_AF647_Human_Lung.jpg) |

docs/supporting_material/Podoplanin_Unconjugated/0000-0002-8728-1735.md

@@ -0,0 +1,23 @@
+---
+layout: default
+---
+
+# Configurations
+
+| UniProt Accession Number   | Reagent Type     | Target Name / Protein Biomarker   | Target Species   | Host Organism   | Isotype   |   Clonality | Vendor                    |   Catalog Number | Conjugate    | RRID       | Availability   | Method                 | Tissue Preservation   | Target Tissue   | Tissue State                  | Detergent         | Antigen Retrieval Conditions                                                               | Dye Inactivation Conditions   | Recommend   | Agree                                                        | Disagree   | Contributor                                                  | Notes       |
+|:---------------------------|:-----------------|:----------------------------------|:-----------------|:----------------|:----------|------------:|:--------------------------|-----------------:|:-------------|:-----------|:---------------|:-----------------------|:----------------------|:----------------|:------------------------------|:------------------|:-------------------------------------------------------------------------------------------|:------------------------------|:------------|:-------------------------------------------------------------|:-----------|:-------------------------------------------------------------|:------------|
+| Q86YL7                     | Primary Antibody | Podoplanin                        | Human            | Mouse           | IgG1     | D2-40       | BioLegend                 |           916601 | Unconjugated | AB_2565182 | Stock          | IBEX2D Manual          | FFPE                  | Lung            | Idiopathic Pulmonary Fibrosis | 0.3% Triton-X-100 | 10 mM citrate buffer (pH 6.0) for 30 minutes at 95C                                        | NA                            | Yes         | [0000-0002-8728-1735](https://orcid.org/0000-0002-8728-1735) | NA         | [0000-0002-8728-1735](https://orcid.org/0000-0002-8728-1735) | [1](#notes) |
+
+
+# Publications
+
+
+
+# Additional Notes
+
+<a name="notes"></a>
+1. This antibody labels the anticipated cell type (lymphatic vessel). This antibody was detected using a secondary antibody (Abcam, ab150107). We used a secondary only control to test for non-specific binding of the secondary antibody and observed no signal as expected (not shown).
+
+| Human lung (Idiopathic Pulmonary Fibrosis) FFPE: Podoplanin (magenta) and DAPI (blue) |
+|:-------:|
+| ![](Podoplanin_AF647_Human_Lung.jpg) |

docs/supporting_material/SMAD2_Unconjugated/0000-0002-8728-1735.md

@@ -0,0 +1,23 @@
+---
+layout: default
+---
+
+# Configurations
+
+| UniProt Accession Number   | Reagent Type     | Target Name / Protein Biomarker   | Target Species   | Host Organism   | Isotype   |   Clonality | Vendor                    |   Catalog Number | Conjugate    | RRID       | Availability   | Method                 | Tissue Preservation   | Target Tissue   | Tissue State                  | Detergent         | Antigen Retrieval Conditions                                                               | Dye Inactivation Conditions   | Recommend   | Agree                                                        | Disagree   | Contributor                                                  | Notes       |
+|:---------------------------|:-----------------|:----------------------------------|:-----------------|:----------------|:----------|------------:|:--------------------------|-----------------:|:-------------|:-----------|:---------------|:-----------------------|:----------------------|:----------------|:------------------------------|:------------------|:-------------------------------------------------------------------------------------------|:------------------------------|:------------|:-------------------------------------------------------------|:-----------|:-------------------------------------------------------------|:------------|
+| Q15796                     | Primary Antibody | SMAD2                             | Human            | Mouse           | IgG1      | L16D3       | Cell Signaling Technology            |             3103 | Unconjugated | AB_490816  | Stock          | IBEX2D Manual          | FFPE                  | Lung            | Idiopathic Pulmonary Fibrosis | 0.3% Triton-X-100 | 10 mM citrate buffer (pH 6.0) for 30 minutes at 95C                                        | NA                            | Yes         | [0000-0002-8728-1735](https://orcid.org/0000-0002-8728-1735) | NA         | [0000-0002-8728-1735](https://orcid.org/0000-0002-8728-1735) | [1](#notes) |
+
+
+# Publications
+
+
+
+# Additional Notes
+
+<a name="notes"></a>
+1. This antibody labels the anticipated subcellular compartment (cytoplasm). This antibody was detected using a secondary antibody (Abcam, ab150107). We used a secondary only control to test for non-specific binding of the secondary antibody and observed no signal as expected (not shown).
+
+| Human lung (Idiopathic Pulmonary Fibrosis) FFPE: SMAD2 (magenta) and DAPI (blue) |
+|:-------:|
+| ![](SMAD2_AF647_Human_Lung.jpg) |

docs/supporting_material/SMAD3_Unconjugated/0000-0002-8728-1735.md

@@ -0,0 +1,23 @@
+---
+layout: default
+---
+
+# Configurations
+
+| UniProt Accession Number   | Reagent Type     | Target Name / Protein Biomarker   | Target Species   | Host Organism   | Isotype   |   Clonality | Vendor                    |   Catalog Number | Conjugate    | RRID       | Availability   | Method                 | Tissue Preservation   | Target Tissue   | Tissue State                  | Detergent         | Antigen Retrieval Conditions                                                               | Dye Inactivation Conditions   | Recommend   | Agree                                                        | Disagree   | Contributor                                                  | Notes       |
+|:---------------------------|:-----------------|:----------------------------------|:-----------------|:----------------|:----------|------------:|:--------------------------|-----------------:|:-------------|:-----------|:---------------|:-----------------------|:----------------------|:----------------|:------------------------------|:------------------|:-------------------------------------------------------------------------------------------|:------------------------------|:------------|:-------------------------------------------------------------|:-----------|:-------------------------------------------------------------|:------------|
+| P84022                     | Primary Antibody | SMAD3                             | Human            | Rabbit          | IgG       | Polyclonal  | Abcam                     |          ab28379 | Unconjugated | AB_2192903 | Stock          | IBEX2D Manual          | FFPE                  | Lung            | Idiopathic Pulmonary Fibrosis | 0.3% Triton-X-100 | 10 mM citrate buffer (pH 6.0) for 30 minutes at 95C                                        | NA                            | Yes         | [0000-0002-8728-1735](https://orcid.org/0000-0002-8728-1735) | NA         | [0000-0002-8728-1735](https://orcid.org/0000-0002-8728-1735) | [1](#notes) |
+
+
+# Publications
+
+
+
+# Additional Notes
+
+<a name="notes"></a>
+1. This antibody labels the anticipated subcellular compartment (nucleus, cytoplasm). This antibody was detected using a secondary antibody (Abcam, ab150079). We used a secondary only control to test for non-specific binding of the secondary antibody and observed no signal as expected (not shown).
+
+| Human lung (Idiopathic Pulmonary Fibrosis) FFPE: SMAD3 (magenta) and DAPI (blue) |
+|:-------:|
+| ![](SMAD3_AF647_Human_Lung.jpg) |