Merge pull request #217 from Rosa-234/kortekaas-phospho-smad3

Added pSMAD3 for Human Lung
IBEXImagingCommunity · Sep 12, 2024 · 1206ba3 · 1206ba3
2 parents fbd6ed6 + 075d5c1
commit 1206ba3
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Showing 6 changed files with 35 additions and 4 deletions.
diff --git a/.github/data_validation_configs/reagent_resources.json b/.github/data_validation_configs/reagent_resources.json
@@ -220,7 +220,8 @@
           "NA",
           "Tumor",
           "GFP transgenic line",
-          "Melanoma"
+          "Melanoma",
+          "Idiopathic Pulmonary Fibrosis"
        ],
        "Detergent":[
           "0.1% Saponin",
@@ -239,7 +240,8 @@
           "pH 9.5 for 15 minutes in a pressure cooker (Borg Decloaker BD1000)",
           "pH 6 (10 mM Sodium Citrate) for 20 minutes in a pressure cooker",
           "pH 6 (Sodium Citrate buffer) for 45 minutes",
-          "pH 6 for 20 minutes ER1 (AR9961) using the Leica Bond"
+          "pH 6 for 20 minutes ER1 (AR9961) using the Leica Bond",
+          "10 mM citrate buffer (pH 6.0) for 30 minutes at 95C"
        ],
        "Dye Inactivation Conditions":[
           "0.5 mg/ml LiBH4 10 minutes continuous exchange with automated protocol",

diff --git a/.zenodo.json b/.zenodo.json
@@ -132,6 +132,11 @@
             "name": "Koenig, Joshua F. E.",
             "orcid": "0000-0002-8909-5039"
         },
+        {
+            "affiliation": "McMaster University",
+            "name": "Kortekaas, Rosa K.",
+            "orcid": "0000-0002-8728-1735"
+        },
         {
             "affiliation": "University College London",
             "name": "Kothurkar, Aanandita",

diff --git a/data/image_resources.csv b/data/image_resources.csv
@@ -211,4 +211,5 @@ CD4_AF488/Human_tonsil_FFPE_CD4_AF488_FAB8165G.jpg,"Human tonsil FFPE: CD4 (gree
 CXCR3_AF700/Human_Tonsil_FFPE_CXCR3_FAB160N.jpg,"Human tonsil FFPE: CXCR3 (cyan, catalog number FAB160N)",282723d37e8b3bfc2fe3a57fa805f7bc,['CXCR3_AF700/0000-0002-6604-2065.md']
 CD20_eF615/Human_Tonsil_FFPE_CD20_eF615_42-0202-82.jpg,"Human tonsil FFPE: CD20 (red, catalog number 42-0202-82)",77e6ac7e3a9009daa030e9f17c118f0c,['CD20_eF615/0000-0002-6604-2065.md']
 E-cadherin_AF647/Ecadherin_Yellow_DAPI_Cyan_EpCAM_Blue.jpg,"Human Nasal Polyp: E-Cadherin (yellow, catalog number 147307), EpCAM (blue, catalog number 324228) and DAPI (cyan)",9b79c06f612c26ba7af3cb03c4e21298,['E-cadherin_AF647/0009-0004-8162-409X.md']
-E-cadherin_AF647/Ecadherin_Yellow_DAPI_Cyan.jpg,"Human Nasal Polyp: E-Cadherin (yellow, catalog number 147307), and DAPI (cyan)",4dc47ddf0a00a3ad872b91ba448f914a,['E-cadherin_AF647/0009-0004-8162-409X.md']
+E-cadherin_AF647/Ecadherin_Yellow_DAPI_Cyan.jpg,"Human Nasal Polyp: E-Cadherin (yellow, catalog number 147307), and DAPI (cyan)",4dc47ddf0a00a3ad872b91ba448f914a,['E-cadherin_AF647/0009-0004-8162-409X.md']
+Phospho-SMAD3_Unconjugated/pSMAD3_AF647_Human_Lung.jpg,"Human lung (Idiopathic Pulmonary Fibrosis) FFPE: Phospho-SMAD3 (magenta) and DAPI (blue)",944bcbc69d59d8973393e9c7c04239d2,['Phospho-SMAD3_Unconjugated/0000-0002-8728-1735.md']
diff --git a/data/reagent_resources.csv b/data/reagent_resources.csv
@@ -1205,4 +1205,5 @@ P06800,Primary Antibody,CD45,Mouse,Rat,IgG2b,30-F11,BioLegend,103144,AF594,AB_25
 Q920G3,Primary Antibody,SiglecF,Mouse,Rat,IgG2a,E50-2440,BD Biosciences,552126,PE,AB_394341,Stock,IBEX2D Manual,1:4 Cytofix/Cytoperm Fixed Frozen,Lung,NA,0.3% Triton-X-100,NA,1 mg/ml LiBH4 15 minutes,Yes,0000-0001-5813-2581,NA,0000-0001-5813-2581
 P62737,Primary Antibody,Alpha smooth muscle actin,Mouse,Mouse,IgG2a,1A4,Thermo Fisher Scientific,50-9760-82,eF660,AB_2574362,Stock,IBEX2D Manual,1:4 Cytofix/Cytoperm Fixed Frozen,Lung,NA,0.3% Triton-X-100,NA,1 mg/ml LiBH4 15 minutes,Yes,0000-0001-5813-2581,NA,0000-0001-5813-2581
 P05089,Primary Antibody,Arginase-1,Mouse,Rabbit,IgG,D4E3M,Cell Signaling Technology,93668,Unconjugated,AB_2800207,Stock,IBEX2D Manual,1:4 Cytofix/Cytoperm Fixed Frozen,Lung,NA,0.3% Triton-X-100,NA,1 mg/ml LiBH4 15 minutes,Yes,0000-0001-5813-2581,NA,0000-0001-5813-2581
-Q61830,Primary Antibody,CD206,Mouse,Rat,IgG2a,C068C2,BioLegend,141709,AF488,AB_10933252,Stock,IBEX2D Manual,1:4 Cytofix/Cytoperm Fixed Frozen,Lung,NA,0.3% Triton-X-100,NA,1 mg/ml LiBH4 15 minutes,Yes,0000-0001-5813-2581,NA,0000-0001-5813-2581
+Q61830,Primary Antibody,CD206,Mouse,Rat,IgG2a,C068C2,BioLegend,141709,AF488,AB_10933252,Stock,IBEX2D Manual,1:4 Cytofix/Cytoperm Fixed Frozen,Lung,NA,0.3% Triton-X-100,NA,1 mg/ml LiBH4 15 minutes,Yes,0000-0001-5813-2581,NA,0000-0001-5813-2581
+NA,Primary Antibody,Phospho-SMAD3,Human,Rabbit,IgG,EP823Y,Abcam,ab52903,Unconjugated,AB_882596,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
diff --git a/docs/supporting_material/Phospho-SMAD3_Unconjugated/0000-0002-8728-1735.md b/docs/supporting_material/Phospho-SMAD3_Unconjugated/0000-0002-8728-1735.md
@@ -0,0 +1,22 @@
+---
+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-SMAD3                     | Human            | Rabbit          | IgG       | EP823Y      | Abcam                     |          ab52903 | Unconjugated | AB_882596 | 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). The following antibody was tested for Phospho-SMAD3 and is not recommended: Cell Signaling Technology, 9520.
+
+| Human lung (Idiopathic Pulmonary Fibrosis) FFPE: Phospho-SMAD3 (magenta) and DAPI (blue) |
+|:-------:|
+| ![](pSMAD3_AF647_Human_Lung.jpg) |
diff --git a/docs/supporting_material/Phospho-SMAD3_Unconjugated/pSMAD3_AF647_Human_Lung.jpg b/docs/supporting_material/Phospho-SMAD3_Unconjugated/pSMAD3_AF647_Human_Lung.jpg