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Additional reagents #98

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Dec 15, 2023
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Additional reagents #98

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ba45fa1
Adding guidance with respect to editing the reagent_resources.csv
zivy Dec 13, 2023
26206e7
Adding validated reagents and supporting material.
zivy Dec 13, 2023
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13 changes: 13 additions & 0 deletions data/reagent_resources.csv
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Expand Up @@ -1049,3 +1049,16 @@ P01903,Primary Antibody,HLA-DR,Human,Mouse,IgG2b,LN-3,Novus Biologicals,NBP2-476
Q15116,Primary Antibody,PD-1,Human,Rabbit,IgG,EPR4877(2),Abcam,ab275126,AF555,AB_2728811,Stock,Multiplexed 2D Imaging,FFPE,Lymph node,Follicular Lymphoma,0.3% Triton-X-100,pH 6 for 30 minutes ER1 (AR9961) and pH 9 for 30 minutes ER2 (AR9640) using the Leica Bond,NA,Yes,0000-0003-4379-8967,NA,0000-0003-4379-8967
P16410,Primary Antibody,CTLA4,Human,Rabbit,IgG,CAL49,Abcam,ab270127,AF647,NA,Stock,Multiplexed 2D Imaging,FFPE,Lymph node,Follicular Lymphoma,0.3% Triton-X-100,pH 6 for 30 minutes ER1 (AR9961) and pH 9 for 30 minutes ER2 (AR9640) using the Leica Bond,NA,Yes,0000-0003-4379-8967,NA,0000-0003-4379-8967
P22646,Primary Antibody,CD3,Mouse,Rat,IgG2b,17A2,BioLegend,100281,Spark Red 718,AB_2924440,Stock,Multiplexed 2D Imaging,1:4 Cytofix/Cytoperm Fixed Frozen,Spleen,NA,0.3% Triton-X-100,NA,NA,Yes,0000-0003-1130-1899,NA,0000-0003-1130-1899
Q9BZS1,Primary Antibody,FOXP3,Human,Mouse,IgG1,236A/E7,Thermo Fisher Scientific,41-4777-82,eF570,AB_2573609,Stock,Multiplexed 2D Imaging,FFPE,Tonsil,NA,0.3% Triton-X-100,pH 6 for 30 minutes ER1 (AR9961) and pH 9 for 30 minutes ER2 (AR9640) using the Leica Bond,NA,No,0000-0003-4379-8967,NA,0000-0003-4379-8967
P01903,Primary Antibody,HLA-DR,Human,Mouse,IgG2a,LN-3,Novus Biologicals,NBP2-47670AF647,AF647,NA,Stock,Multiplexed 2D Imaging,FFPE,Tonsil,NA,0.3% Triton-X-100,pH 6 for 30 minutes ER1 (AR9961) and pH 9 for 30 minutes ER2 (AR9640) using the Leica Bond,NA,Yes,0000-0003-4379-8967,NA,0000-0003-4379-8967
O00329,Primary Antibody,PI3 Kinase p110 delta,Human,Rabbit,IgG,E2T2N,Cell Signaling Technology,19591S,Unconjugated,NA,Stock,Multiplexed 2D Imaging,FFPE,Tonsil,NA,0.3% Triton-X-100,pH 6 for 30 minutes ER1 (AR9961) and pH 9 for 30 minutes ER2 (AR9640) using the Leica Bond,NA,No,0000-0003-4379-8967,NA,0000-0003-4379-8967
P01106,Primary Antibody,c-Myc,Human,Mouse,IgG1,9E10,R&D Systems,MAB3696-SP,Unconjugated,NA,Stock,Multiplexed 2D Imaging,FFPE,Lymph Node,Follicular Lymphoma,0.3% Triton-X-100,pH 6 for 30 minutes ER1 (AR9961) and pH 9 for 30 minutes ER2 (AR9640) using the Leica Bond,NA,No,0000-0003-4379-8967,NA,0000-0003-4379-8967
P31751,Primary Antibody,Phospho-Akt,Human,Rabbit,IgG,D9E,Cell Signaling Technology,4060T,Unconjugated,AB_2315049,Stock,Multiplexed 2D Imaging,FFPE,Lymph Node,Follicular Lymphoma,0.3% Triton-X-100,pH 6 for 30 minutes ER1 (AR9961) and pH 9 for 30 minutes ER2 (AR9640) using the Leica Bond,NA,No,0000-0003-4379-8967,NA,0000-0003-4379-8967
P19838,Primary Antibody,Phospho NF-Kappa B p105,Human,Rabbit,IgG,178F3,Cell Signaling Technology,PA5-79525,Unconjugated,NA,Stock,Multiplexed 2D Imaging,FFPE,Lymph Node,Follicular Lymphoma,0.3% Triton-X-100,pH 6 for 30 minutes ER1 (AR9961) and pH 9 for 30 minutes ER2 (AR9640) using the Leica Bond,NA,No,0000-0003-4379-8967,NA,0000-0003-4379-8967
P15104,Primary Antibody,Glutamine Synthetase,Human,Mouse,IgG2a,OTI1F4,Novus Biologicals,NBP2-70834AF647,AF647,NA,Stock,Multiplexed 2D Imaging,FFPE,Lymph Node,Follicular Lymphoma,0.3% Triton-X-100,pH 6 for 30 minutes ER1 (AR9961) and pH 9 for 30 minutes ER2 (AR9640) using the Leica Bond,NA,No,0000-0003-4379-8967,NA,0000-0003-4379-8967
P15104,Primary Antibody,Glutamine Synthetase,Human,Rabbit,IgG,EPR13022(B),Abcam,Ab302584,AF488,NA,Stock,Multiplexed 2D Imaging,FFPE,Lymph Node,Follicular Lymphoma,0.3% Triton-X-100,pH 6 for 30 minutes ER1 (AR9961) and pH 9 for 30 minutes ER2 (AR9640) using the Leica Bond,NA,No,0000-0003-4379-8967,NA,0000-0003-4379-8967
Q16832,Primary Antibody,DDR2,Human,Goat,IgG,Polyclonal,R&D Systems,AF2538,Unconjugated,AB_416613,Stock,Multiplexed 2D Imaging,FFPE,Lymph Node,Follicular Lymphoma,0.3% Triton-X-100,pH 6 for 30 minutes ER1 (AR9961) and pH 9 for 30 minutes ER2 (AR9640) using the Leica Bond,NA,No,0000-0003-4379-8967,NA,0000-0003-4379-8967
P49840,Primary Antibody,Phospho-GSK-3alpha,Human,Rabbit,IgG,36E9,Cell Signaling Technology,9316,Unconjugated,AB_659836,Stock,Multiplexed 2D Imaging,FFPE,Lymph Node,Follicular Lymphoma,0.3% Triton-X-100,pH 6 for 30 minutes ER1 (AR9961) and pH 9 for 30 minutes ER2 (AR9640) using the Leica Bond,NA,No,0000-0003-4379-8967,NA,0000-0003-4379-8967
Q9Y5Y7,Primary Antibody,LYVE-1,Human,Goat,IgG,Polyclonal,R&D Systems,AF2089,Unconjugated,AB_355144,Stock,Multiplexed 2D Imaging,FFPE,Lymph Node,Follicular Lymphoma,0.3% Triton-X-100,pH 6 for 30 minutes ER1 (AR9961) and pH 9 for 30 minutes ER2 (AR9640) using the Leica Bond,NA,Yes,0000-0003-4379-8967,NA,0000-0003-4379-8967
P08575,Primary Antibody,CD45,Human,Mouse,IgG1,2B11 + PD7/26,Novus Biologicals,NBP2-34528AF700,AF700,NA,Stock,Multiplexed 2D Imaging,FFPE,Lymph Node,Follicular Lymphoma,0.3% Triton-X-100,pH 6 for 30 minutes ER1 (AR9961) and pH 9 for 30 minutes ER2 (AR9640) using the Leica Bond,NA,Yes,0000-0003-4379-8967,NA,0000-0003-4379-8967
Q6FHL8,Primary Antibody,CTGF,Human,Rabbit,IgG,OT11F4,FabGennix,CTGF-FITC,FITC,NA,Stock,Multiplexed 2D Imaging,FFPE,Lymph Node,Follicular Lymphoma,0.3% Triton-X-100,pH 6 for 30 minutes ER1 (AR9961) and pH 9 for 30 minutes ER2 (AR9640) using the Leica Bond,NA,No,0000-0003-4379-8967,NA,0000-0003-4379-8967
6 changes: 6 additions & 0 deletions docs/supporting_material/CD45_AF700/0000-0003-4379-8967.md
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|:---------------------------|:-----------------|:----------------------------------|:-----------------|:----------------|:----------|:------------|:------------------|:-----------------|:------------|:----------|:---------------|:-----------------------|:----------------------------------|:----------------|:---------------|:------------------|:-------------------------------------------------------------------------------------------|:------------------------------|:------------|:-----------------------------------------|:-----------|:--------------------|:------------|
| P06800 | Primary Antibody | CD45 | Mouse | Rat | IgG2b | 30-F11 | BioLegend | 103128 | AF700 | AB_493715 | Stock | IBEX2D Manual | 1:4 Cytofix/Cytoperm Fixed Frozen | Thymus | NA | 0.3% Triton-X-100 | NA | 1 mg/ml LiBH4 15 minutes | Yes | [0000-0003-4379-8967](https://orcid.org/0000-0003-4379-8967) [[1](#publications)] | NA | [0000-0003-4379-8967](https://orcid.org/0000-0003-4379-8967) | |
| P08575 | Primary Antibody | CD45 | Human | Mouse | IgG1 | 2B11+PD7/26 | Novus Biologicals | NBP2-34528AF700 | AF700 | NA | Stock | Multiplexed 2D Imaging | FFPE | Tonsil | NA | 0.3% Triton-X-100 | pH 6 for 30 minutes ER1 (AR9961) and pH 9 for 30 minutes ER2 (AR9640) using the Leica Bond | NA | Yes | [0000-0003-4379-8967](https://orcid.org/0000-0003-4379-8967) | NA | [0000-0003-4379-8967](https://orcid.org/0000-0003-4379-8967) | [1](#notes) |
| P08575 | Primary Antibody | CD45 | Human | Mouse | IgG1 | 2B11 + PD7/26 | Novus Biologicals | NBP2-34528AF700 | AF700 | NA | Stock | Multiplexed 2D Imaging | FFPE | Lymph Node | Follicular Lymphoma | 0.3% Triton-X-100 | pH 6 for 30 minutes ER1 (AR9961) and pH 9 for 30 minutes ER2 (AR9640) using the Leica Bond | NA | Yes | [0000-0003-4379-8967](https://orcid.org/0000-0003-4379-8967) | NA | [0000-0003-4379-8967](https://orcid.org/0000-0003-4379-8967) | [2](#notes) |

# Publications

Expand All @@ -19,3 +20,8 @@ layout: default

<a name="notes"></a>
1. Labels immune cells. Beautiful signal in a difficult conjugate. Use at a 1:25 dilution.
2. Antibody labels membranes of immune cells in FFPE tissues. Strong signal in a difficult conjugate (AF700). Multi-clonal (2B11 + PD7/26) works in many FFPE tissues and conjugates.

| Human follicular lymphoma FFPE : CD45 (magenta, catalog number NBP2-34528AF700) |
|:-------:|
| ![](FL_FFPE_CD45_NBP2-34528AF700.jpg) |
Binary file added docs/supporting_material/CD45_AF700/FL_FFPE_CD45_NBP2-34528AF700.jpg
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22 changes: 22 additions & 0 deletions docs/supporting_material/CTGF_FITC/0000-0003-4379-8967.md
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layout: default
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# 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 |
|:---------------------------|:-----------------|:----------------------------------|:-----------------|:----------------|:----------|:------------|:----------|:-----------------|:------------|:-------|:---------------|:-----------------------|:----------------------|:----------------|:--------------------|:------------------|:-------------------------------------------------------------------------------------------|:------------------------------|:------------|:-------------------------------------------------------------|:-----------|:-------------------------------------------------------------|:------------|
| Q6FHL8 | Primary Antibody | CTGF | Human | Rabbit | IgG | OT11F4 | FabGennix | CTGF-FITC | FITC | NA | Stock | Multiplexed 2D Imaging | FFPE | Lymph Node | Follicular Lymphoma | 0.3% Triton-X-100 | pH 6 for 30 minutes ER1 (AR9961) and pH 9 for 30 minutes ER2 (AR9640) using the Leica Bond | NA | No | [0000-0003-4379-8967](https://orcid.org/0000-0003-4379-8967) | NA | [0000-0003-4379-8967](https://orcid.org/0000-0003-4379-8967) | [1](#notes) |

# Publications



# Additional Notes

<a name="notes"></a>
1. Antibody labeling is inconclusive and appears to label most cells in a follicular lymphoma FFPE tissue section. Used at a dilution of 1:50.

| Human follicular lymphoma FFPE : CTGF (green, catalog number FITC-CTGF) |
|:-------:|
| ![](FL_FFPE_CTGF_FITC-CTGF.jpg) |
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22 changes: 22 additions & 0 deletions docs/supporting_material/DDR2_Unconjugated/0000-0003-4379-8967.md
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# 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 |
|:---------------------------|:-----------------|:----------------------------------|:-----------------|:----------------|:----------|:------------|:------------|:-----------------|:-------------|:----------|:---------------|:-----------------------|:----------------------|:----------------|:--------------------|:------------------|:-------------------------------------------------------------------------------------------|:------------------------------|:------------|:-------------------------------------------------------------|:-----------|:-------------------------------------------------------------|:------------|
| Q16832 | Primary Antibody | DDR2 | Human | Goat | IgG | Polyclonal | R&D Systems | AF2538 | Unconjugated | AB_416613 | Stock | Multiplexed 2D Imaging | FFPE | Lymph Node | Follicular Lymphoma | 0.3% Triton-X-100 | pH 6 for 30 minutes ER1 (AR9961) and pH 9 for 30 minutes ER2 (AR9640) using the Leica Bond | NA | No | [0000-0003-4379-8967](https://orcid.org/0000-0003-4379-8967) | NA | [0000-0003-4379-8967](https://orcid.org/0000-0003-4379-8967) | [1](#notes) |

# Publications



# Additional Notes

<a name="notes"></a>
1. Antibody labels most cells in a follicular lymphoma FFPE tissue section. Used at a dilution of 1:50 with an anti-goat AF555 secondary antibody (Thermo Fisher Scientific catalog number A-21432).

| Human follicular lymphoma FFPE : DDR2 (green, catalog number AF2538) |
|:-------:|
| ![](FL_FFPE_DDR2_AF555_AF2538.jpg) |
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6 changes: 6 additions & 0 deletions docs/supporting_material/FOXP3_eF570/0000-0003-4379-8967.md
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Expand Up @@ -10,6 +10,7 @@ layout: default
| Q99JB6 | Primary Antibody | FOXP3 | Mouse | Rat | IgG2a | FJK-16s | Thermo Fisher Scientific | 41-5773-82 | eF570 | AB_11219073 | Stock | IBEX2D Manual | 1:4 Cytofix/Cytoperm Fixed Frozen | Small Intestine | NA | 0.3% Triton-X-100 | NA | 1 mg/ml LiBH4 15 minutes | Yes | [0000-0003-4379-8967](https://orcid.org/0000-0003-4379-8967) [[3](#publications)] | NA | [0000-0003-4379-8967](https://orcid.org/0000-0003-4379-8967) | [1](#notes) |
| Q9BZS1 | Primary Antibody | FOXP3 | Human | Mouse | IgG1 | 236A/E7 | Thermo Fisher Scientific | 41-4777-82 | eF570 | AB_2573609 | Stock | IBEX2D Manual | 1:4 Cytofix/Cytoperm Fixed Frozen | Lymph Node | Follicular Lymphoma | 0.3% Triton-X-100 | NA | 1 mg/ml LiBH4 15 minutes | Yes | [0000-0003-4379-8967](https://orcid.org/0000-0003-4379-8967) [[2](#publications)] | NA | [0000-0003-4379-8967](https://orcid.org/0000-0003-4379-8967) | |
| Q9BZS1 | Primary Antibody | FOXP3 | Human | Mouse | IgG1 | 236A/E7 | Thermo Fisher Scientific | 41-4777-82 | eF570 | AB_2573609 | Stock | Multiplexed 2D Imaging | FFPE | Tonsil | NA | 0.3% Triton-X-100 | pH 6 for 30 minutes ER1 (AR9961) and pH 9 for 30 minutes ER2 (AR9640) using the Leica Bond | NA | No | [0000-0003-4379-8967](https://orcid.org/0000-0003-4379-8967) | NA | [0000-0003-4379-8967](https://orcid.org/0000-0003-4379-8967) | [2](#notes) |
| Q9BZS1 | Primary Antibody | FOXP3 | Human | Mouse | IgG1 | 236A/E7 | Thermo Fisher Scientific | 41-4777-82 | eF570 | AB_2573609 | Stock | Multiplexed 2D Imaging | FFPE | Tonsil | NA | 0.3% Triton-X-100 | pH 6 for 30 minutes ER1 (AR9961) and pH 9 for 30 minutes ER2 (AR9640) using the Leica Bond | NA | No | [0000-0003-4379-8967](https://orcid.org/0000-0003-4379-8967) | NA | [0000-0003-4379-8967](https://orcid.org/0000-0003-4379-8967) | [3](#notes) |

# Publications

Expand All @@ -29,3 +30,8 @@ layout: default
<a name="notes"></a>
1. Validated by Evelyn Kandov (No ORCID)
2. This antibody works well in fixed frozen tissues but is very dim in human FFPE samples. This conjugate is particularly challenging due to autofluorescence from red blood cells. Red blood cells are small and round like the anticipated nuclear pattern of FOXP3. FOXP3 needs to be amplified with a secondary antibody in human FFPE samples. Clone also appears to be sensitive to antigen retrieval conditions (pH 9 is best).
3. Antibody labels nuclei of T cells in FFPE tissues after dual antigen retrieval (pH 6 and pH 9). Signal is dim and the eF570 conjugate can give a false positive with autofluorescence from red blood cells. Recommendations: Amplify signal with a secondary antibody, perform dual antigen retrieval, and use at a concentration of 1:25 for best signal.

| Human tonsil FFPE : FOXP3 (yellow, catalog number 41-4777-82) and Hoechst (blue, catalog number 40046) |
|:-------:|
| ![](Tonsil_FOXP3_eF570_Thermo_41-4777-82_Picture1.jpg) |
Binary file added ...pporting_material/FOXP3_eF570/Tonsil_FOXP3_eF570_Thermo_41-4777-82_Picture1.jpg
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22 changes: 22 additions & 0 deletions docs/supporting_material/Glutamine_Synthetase_AF647/0000-0003-4379-8967.md
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# 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 |
|:---------------------------|:-----------------|:----------------------------------|:-----------------|:----------------|:----------|:------------|:------------------|:-----------------|:------------|:-------|:---------------|:-----------------------|:----------------------|:----------------|:--------------------|:------------------|:-------------------------------------------------------------------------------------------|:------------------------------|:------------|:-------------------------------------------------------------|:-----------|:-------------------------------------------------------------|:------------|
| P15104 | Primary Antibody | Glutamine Synthetase | Human | Mouse | IgG2a | OTI1F4 | Novus Biologicals | NBP2-70834AF647 | AF647 | NA | Stock | Multiplexed 2D Imaging | FFPE | Lymph Node | Follicular Lymphoma | 0.3% Triton-X-100 | pH 6 for 30 minutes ER1 (AR9961) and pH 9 for 30 minutes ER2 (AR9640) using the Leica Bond | NA | No | [0000-0003-4379-8967](https://orcid.org/0000-0003-4379-8967) | NA | [0000-0003-4379-8967](https://orcid.org/0000-0003-4379-8967) | [1](#notes) |

# Publications



# Additional Notes

<a name="notes"></a>
1. Antibody labeling is inconclusive and appears to label stromal cells (based on morphology and location) in a follicular lymphoma FFPE tissue section. Used at a dilution of 1:50. Requires a good positive control and further testing. Does colocalize with other glutamine synthetase antibody (Ab302584).

| Human follicular lymphoma FFPE : Glutamine synthetase (magenta, catalog number NBP2-70834AF647) |
|:-------:|
| ![](FL_FFPE_GS_AF647_NBP2-70834AF647.jpg) |
Binary file added ...orting_material/Glutamine_Synthetase_AF647/FL_FFPE_GS_AF647_NBP2-70834AF647.jpg
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