Adding contributions from Wanjing Shang ORCID 0009-0007-0646-7946

Reagent validations for Pancreatic Ductal Adenocarcinoma in mouse.
IBEXImagingCommunity · Sep 13, 2024 · b9f92c9 · b9f92c9
1 parent 76ca300
commit b9f92c9
Show file tree

Hide file tree

Showing 21 changed files with 283 additions and 2 deletions.
diff --git a/.zenodo.json b/.zenodo.json
@@ -177,6 +177,11 @@
             "name": "Richoz, Nathan",
             "orcid": "0000-0002-7422-3237"
         },
+        {
+            "affiliation": "National Institutes of Health",
+            "name": "Shang, Wanjing",
+            "orcid": "0009-0007-0646-7946"
+        },
         {
             "affiliation": "National Institutes of Health",
             "name": "Shi, Lihong",

diff --git a/data/image_resources.csv b/data/image_resources.csv
@@ -212,4 +212,10 @@ CXCR3_AF700/Human_Tonsil_FFPE_CXCR3_FAB160N.jpg,"Human tonsil FFPE: CXCR3 (cyan,
 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']
-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']
+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']
+CD3_AF532/Mouse_tumor_CD3_58-0032-80_CD45-103128.jpg,"Mouse tumor: CD3 (cyan, catalog number 58-0032-80) and CD45 (yellow, catalog number 103128)",fffc63b0307e56a20f9d7564ee5b84a5,"['CD3_AF532/0009-0007-0646-7946.md', 'CD45_AF700/0009-0007-0646-7946.md']"
+CD11b_AF488/Mouse_tumor_CD11b_117312_CD11c_101217.jpg,"Mouse tumor: CD11c (cyan, catalog number 117312) and CD11b (yellow, catalog number 101217)",1df7b3063e259b3b6dc0a9a658720178,"['CD11b_AF488/0009-0007-0646-7946.md', 'CD11c_AF647/0009-0007-0646-7946.md']"
+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']"
diff --git a/data/reagent_resources.csv b/data/reagent_resources.csv
@@ -1206,4 +1206,16 @@ Q920G3,Primary Antibody,SiglecF,Mouse,Rat,IgG2a,E50-2440,BD Biosciences,552126,P
 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
-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
+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
+Q61830,Primary Antibody,CD206,Mouse,Rat,IgG2a,C068C2,BioLegend,141710,AF488,AB_2562232,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
+Q9QXH4,Primary Antibody,CD11c,Mouse,Armenian Hamster,IgG,N418,BioLegend,117312,AF647,AB_492850,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
+P24788,Primary Antibody,CD11b,Mouse,Rat,IgG2b,M1/70,BioLegend,101254,AF594,AB_2563231,Stock,IBEX2D Manual,1:4 Cytofix/Cytoperm Fixed Frozen,Pancreatic Ductal Adenocarcinoma,Tumor,0.3% Triton-X-100,NA,NA,Yes,0009-0007-0646-7946,NA,0009-0007-0646-7946
+P24788,Primary Antibody,CD11b,Mouse,Rat,IgG2b,M1/70,BioLegend,101217,AF488,AB_389305,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
+P06800,Primary Antibody,CD45,Mouse,Rat,IgG2b,30-F11,BioLegend,103128,AF700,AB_493715,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
+NA,Primary Antibody,Cytokeratin,Mouse,Mouse,IgG1,C-11,BioLegend,628608,AF488,AB_2563652,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
+P20152,Primary Antibody,Vimentin,Mouse,Rat,IgG2a,W16220A,BioLegend,699305,AF488,AB_2888889,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
+P97797,Primary Antibody,SIRPalpha,Mouse,Rat,IgG1,P84,BioLegend,144027,AF647,AB_2721300,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
+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
diff --git a/docs/supporting_material/CD11b_AF488/0009-0007-0646-7946.md b/docs/supporting_material/CD11b_AF488/0009-0007-0646-7946.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   |
+|:---------------------------|:-----------------|:----------------------------------|:-----------------|:----------------|:----------|:------------|:----------|-----------------:|:------------|:----------|:---------------|:--------------|:----------------------------------|:---------------------------------|:---------------|:------------------|:-------------------------------|:------------------------------|:------------|:-------------------------------------------------------------|:-----------|:-------------------------------------------------------------|:--------|
+| P24788                     | Primary Antibody | CD11b                             | Mouse            | Rat             | IgG2b     | M1/70       | BioLegend |           101217 | AF488       | AB_389305 | 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](https://orcid.org/0009-0007-0646-7946) | NA         | [0009-0007-0646-7946](https://orcid.org/0009-0007-0646-7946) |         |
+
+# Publications
+
+
+
+# Additional Notes
+
+<a name="notes"></a>
+
+
+| Mouse tumor: CD11c (cyan, catalog number 117312) and CD11b (yellow, catalog number 101217) |
+|:-------:|
+| ![](Mouse_tumor_CD11b_117312_CD11c_101217.jpg) |
diff --git a/docs/supporting_material/CD11b_AF488/Mouse_tumor_CD11b_117312_CD11c_101217.jpg b/docs/supporting_material/CD11b_AF488/Mouse_tumor_CD11b_117312_CD11c_101217.jpg
diff --git a/docs/supporting_material/CD11b_AF594/0009-0007-0646-7946.md b/docs/supporting_material/CD11b_AF594/0009-0007-0646-7946.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       |
+|:---------------------------|:-----------------|:----------------------------------|:-----------------|:----------------|:----------|:------------|:----------|-----------------:|:------------|:-----------|:---------------|:--------------|:----------------------------------|:---------------------------------|:---------------|:------------------|:-------------------------------|:------------------------------|:------------|:-------------------------------------------------------------|:-----------|:-------------------------------------------------------------|:------------|
+| P24788                     | Primary Antibody | CD11b                             | Mouse            | Rat             | IgG2b     | M1/70       | BioLegend |           101254 | AF594       | AB_2563231 | Stock          | IBEX2D Manual | 1:4 Cytofix/Cytoperm Fixed Frozen | Pancreatic Ductal Adenocarcinoma | Tumor          | 0.3% Triton-X-100 | NA                             | NA                            | Yes         | [0009-0007-0646-7946](https://orcid.org/0009-0007-0646-7946) | NA         | [0009-0007-0646-7946](https://orcid.org/0009-0007-0646-7946) | [1](#notes) |
+
+# Publications
+
+
+
+# Additional Notes
+
+<a name="notes"></a>
+1. Difficult dye inactivation using 1 mg/ml LiBH4 for 15 minutes. Put this in the 1st panel is suggested.
+
+| Mouse tumor: CD11b (yellow, catalog number 101254) and Vimentin (cyan, catalog number 699305) |
+|:-------:|
+| ![](Mouse_tumor_CD11b_101254_Vimentin_699305.jpg) |
diff --git a/docs/supporting_material/CD11b_AF594/Mouse_tumor_CD11b_101254_Vimentin_699305.jpg b/docs/supporting_material/CD11b_AF594/Mouse_tumor_CD11b_101254_Vimentin_699305.jpg
diff --git a/docs/supporting_material/CD11c_AF647/0009-0007-0646-7946.md b/docs/supporting_material/CD11c_AF647/0009-0007-0646-7946.md
@@ -0,0 +1,21 @@
+---
+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   |
+|:---------------------------|:-----------------|:----------------------------------|:-----------------|:-----------------|:----------|:------------|:----------|-----------------:|:------------|:----------|:---------------|:--------------|:----------------------------------|:---------------------------------|:---------------|:------------------|:-------------------------------|:------------------------------|:------------|:-------------------------------------------------------------|:-----------|:-------------------------------------------------------------|:--------|
+| Q9QXH4                     | Primary Antibody | CD11c                             | Mouse            | Armenian Hamster | IgG       | N418        | BioLegend |           117312 | AF647       | AB_492850 | 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](https://orcid.org/0009-0007-0646-7946) | NA         | [0009-0007-0646-7946](https://orcid.org/0009-0007-0646-7946) |         |
+
+# Publications
+
+
+
+# Additional Notes
+
+<a name="notes"></a>
+
+| Mouse tumor: CD11c (cyan, catalog number 117312) and CD11b (yellow, catalog number 101217) |
+|:-------:|
+| ![](../CD11b_AF488/Mouse_tumor_CD11b_117312_CD11c_101217.jpg) |
diff --git a/docs/supporting_material/CD206_AF488/0009-0007-0646-7946.md b/docs/supporting_material/CD206_AF488/0009-0007-0646-7946.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   |
+|:---------------------------|:-----------------|:----------------------------------|:-----------------|:----------------|:----------|:------------|:----------|-----------------:|:------------|:-----------|:---------------|:--------------|:----------------------------------|:---------------------------------|:---------------|:------------------|:-------------------------------|:------------------------------|:------------|:-------------------------------------------------------------|:-----------|:-------------------------------------------------------------|:--------|
+| Q61830                     | Primary Antibody | CD206                             | Mouse            | Rat             | IgG2a     | C068C2      | BioLegend |           141710 | AF488       | AB_2562232 | 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](https://orcid.org/0009-0007-0646-7946) | NA         | [0009-0007-0646-7946](https://orcid.org/0009-0007-0646-7946) |         |
+
+# Publications
+
+
+
+# Additional Notes
+
+<a name="notes"></a>
+
+
+| Mouse tumor: CD206 (yellow, catalog number 141710) and CD3 (white, catalog number 557869) |
+|:-------:|
+| ![](Mouse_tumor_CD206_141710_CD3_557869.jpg) |
diff --git a/docs/supporting_material/CD206_AF488/Mouse_tumor_CD206_141710_CD3_557869.jpg b/docs/supporting_material/CD206_AF488/Mouse_tumor_CD206_141710_CD3_557869.jpg
diff --git a/docs/supporting_material/CD3_AF532/0009-0007-0646-7946.md b/docs/supporting_material/CD3_AF532/0009-0007-0646-7946.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       |
+|:---------------------------|:-----------------|:----------------------------------|:-----------------|:----------------|:----------|:------------|:-------------------------|:-----------------|:------------|:------------|:---------------|:--------------|:----------------------------------|:---------------------------------|:---------------|:------------------|:-------------------------------|:------------------------------|:------------|:-------------------------------------------------------------|:-----------|:-------------------------------------------------------------|:------------|
+| 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](https://orcid.org/0009-0007-0646-7946) | NA         | [0009-0007-0646-7946](https://orcid.org/0009-0007-0646-7946) | [1](#notes) |
+
+# Publications
+
+
+
+# Additional Notes
+
+<a name="notes"></a>
+1. Works well both in AF532 nd AF647.
+
+| Mouse tumor: CD3 (cyan, catalog number 58-0032-80) and CD45 (yellow, catalog number 103128) |
+|:-------:|
+| ![](Mouse_tumor_CD3_58-0032-80_CD45-103128.jpg) |
diff --git a/docs/supporting_material/CD3_AF532/Mouse_tumor_CD3_58-0032-80_CD45-103128.jpg b/docs/supporting_material/CD3_AF532/Mouse_tumor_CD3_58-0032-80_CD45-103128.jpg