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Merge pull request #116 from zivy/addingReagents
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Adding reagent configurations.
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@zivy
zivy authored Feb 27, 2024
2 parents 4a16a18 + 76856b8 commit f96f8a8
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7 changes: 7 additions & 0 deletions data/reagent_resources.csv
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Expand Up @@ -1074,3 +1074,10 @@ P56485,Primary Antibody,CXCR7,Mouse,Rabbit,IgG,polyclonal,Novus Biologicals,NBP2
Q9QXH4,Primary Antibody,CD11c,Mouse,Armenian Hamster,IgG,N418,BioLegend,117314,AF647,AB_492850,Stock,Multiplexed 2D Imaging,4% PFA Fixed Frozen,Brain,Tumor,0.3% Triton-X-100,NA,NA,Yes,0000-0002-6944-6997,NA,0000-0002-6944-6997
P03995,Primary Antibody,GFAP,Mouse,Mouse,IgG1,GA5,Thermo Fisher Scientific,41-9892-82,eF570,AB_2573656,Stock,Multiplexed 2D Imaging,4% PFA Fixed Frozen,Brain,Tumor,0.3% Triton-X-100,NA,NA,Yes,0000-0002-6944-6997,NA,0000-0002-6944-6997
P56199,Primary Antibody,CD49a,Human,Mouse,IgG1,TS2/7,BioLegend,328303,PE,AB_1236441,Stock,IBEX2D Manual,1:4 Cytofix/Cytoperm Fixed Frozen,Lymph Node,NA,0.3% Triton-X-100,NA,1 mg/ml LiBH4 15 minutes,Yes,0000-0003-4379-8967,NA,0000-0003-4379-8967
P10415,Primary Antibody,BCL2,Human,Rabbit,IgG,SP66,Abcam,ab236221,Unconjugated,NA,Stock,Cell DIVE-IBEX,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
P10415,Primary Antibody,BCL2,Human,Rabbit,IgG,SP66,Abcam,ab236221,Unconjugated,NA,Stock,Cell DIVE-IBEX,FFPE,Lymph Node,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
P07766,Primary Antibody,CD3,Human,Rabbit,IgG,EP4426,Abcam,ab208514,AF555,AB_443425,Stock,Cell DIVE-IBEX,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,1 mg/ml LiBH4 15 minutes,Yes,0000-0003-4379-8967,NA,0000-0003-4379-8967
P07766,Primary Antibody,CD3,Human,Rabbit,IgG,EP4426,Abcam,ab208514,AF555,AB_443425,Stock,Cell DIVE-IBEX,FFPE,Lymph Node,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,1 mg/ml LiBH4 15 minutes,Yes,0000-0003-4379-8967,NA,0000-0003-4379-8967
P01730,Primary Antibody,CD4,Human,Rabbit,IgG,EPR6855,Abcam,ab196372,AF488,AB_2889191,Stock,Cell DIVE-IBEX,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,1 mg/ml LiBH4 15 minutes,Yes,0000-0003-4379-8967,NA,0000-0003-4379-8967
P01730,Primary Antibody,CD4,Human,Rabbit,IgG,EPR6855,Abcam,ab196372,AF488,AB_2889191,Stock,Cell DIVE-IBEX,FFPE,Lymph Node,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,1 mg/ml LiBH4 15 minutes,Yes,0000-0003-4379-8967,NA,0000-0003-4379-8967
P20023,Primary Antibody,CD21,Human,Rabbit,IgG,SP186,Abcam,ab306325,PE,NA,Stock,Cell DIVE-IBEX,FFPE,Lymph Node,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,1 mg/ml LiBH4 15 minutes,Yes,0000-0003-4379-8967,NA,0000-0003-4379-8967
12 changes: 12 additions & 0 deletions docs/supporting_material/BCL2_Unconjugated/0000-0003-4379-8967.md
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|:---------------------------|:-----------------|:----------------------------------|:-----------------|:----------------|:----------|:------------|:---------|:-----------------|:-------------|:-------|:---------------|:-----------------------|:----------------------|:----------------|:--------------------|:------------------|:-------------------------------------------------------------------------------------------|:------------------------------|:------------|:-----------------------------------------|:-----------|:--------------------|:------------|
| P10415 | Primary Antibody | BCL2 | Human | Rabbit | IgG | SP66 | Abcam | ab236221 | Unconjugated | NA | Stock | Multiplexed 2D Imaging | FFPE | Lymph Node | Follicular Lymphoma | 0.3% Triton-X-100 | pH 6 for 40 minutes at 95C (AR6 Akoya Biosciences AR600250ML) | NA | 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) | [1](#notes) |
| P10415 | Primary Antibody | BCL2 | Human | Rabbit | IgG | SP66 | Abcam | ab236221 | Unconjugated | NA | Stock | Cell DIVE-IBEX | 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) | |
| P10415 | Primary Antibody | BCL2 | Human | Rabbit | IgG | SP66 | Abcam | ab236221 | Unconjugated | NA | Stock | Cell DIVE-IBEX | 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) [[1](#publications)] | NA | [0000-0003-4379-8967](https://orcid.org/0000-0003-4379-8967) | |
| P10415 | Primary Antibody | BCL2 | Human | Rabbit | IgG | SP66 | Abcam | ab236221 | Unconjugated | NA | Stock | Cell DIVE-IBEX | FFPE | Lymph Node | 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) [[1](#publications)] | NA | [0000-0003-4379-8967](https://orcid.org/0000-0003-4379-8967) | |

# Publications

Expand All @@ -19,3 +21,13 @@ layout: default

<a name="notes"></a>
1. Validated in human follicular lymphoma FFPE samples; amplified with donkey anti-rabbit AF594 (Thermo Fisher Scientific A-21207).


| Human normal LN: BCL2 (cyan, catalog number ab236221 and A-31573), CD3 (magenta, catalog number ab208514), CD4 (blue, catalog number ab196372), CD21 (yellow, catalog number ab306325) |
|:-------:|
| ![](Human_normal_LN_BCL2_ab236221_CD3_ab208514_CD4_ab196372_CD21_ab306325.jpg) |


| Human FL LN: BCL2 (cyan, catalog number ab236221 and A-31573), CD3 (magenta, catalog number ab208514), CD4 (blue, catalog number ab196372), CD21 (yellow, catalog number ab306325) |
|:-------:|
| ![](Human_FL_LN_BCL2_ab236221_CD3_ab208514_CD4_ab196372_CD21_ab306325.jpg) |
Binary file added ...onjugated/Human_FL_LN_BCL2_ab236221_CD3_ab208514_CD4_ab196372_CD21_ab306325.jpg
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Binary file added ...gated/Human_normal_LN_BCL2_ab236221_CD3_ab208514_CD4_ab196372_CD21_ab306325.jpg
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7 changes: 7 additions & 0 deletions docs/supporting_material/CD21_PE/0000-0003-4379-8967.md
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Expand Up @@ -9,6 +9,7 @@ layout: default
| P20023 | Primary Antibody | CD21 | Human | Mouse | IgG1 | Bu32 | BioLegend | 354903 | PE | AB_2561406 | Stock | IBEX2D Manual | 1:4 Cytofix/Cytoperm Fixed Frozen | Lymph Node | 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) [[2](#publications), [1](#publications)] | NA | [0000-0003-4379-8967](https://orcid.org/0000-0003-4379-8967) | [1](#notes) |
| P20023 | Primary Antibody | CD21 | Human | Rabbit | IgG | SP186 | Abcam | ab306325 | PE | NA | Stock | Cell DIVE-IBEX | 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 | 1 mg/ml LiBH4 15 minutes | 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) |
| P20023 | Primary Antibody | CD21 | Human | Rabbit | IgG | SP186 | Abcam | ab306325 | PE | NA | Stock | Cell DIVE-IBEX | FFPE | Lymph Node | Follicular Lymphoma | 0.3% Triton-X-100 | pH 6 for 30 minutes ER1 (AR9961) using the Leica Bond | 1 mg/ml LiBH4 15 minutes | 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) |
| P20023 | Primary Antibody | CD21 | Human | Rabbit | IgG | SP186 | Abcam | ab306325 | PE | NA | Stock | Cell DIVE-IBEX | FFPE | Lymph Node | 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 | 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) | |

# Publications

Expand All @@ -20,6 +21,7 @@ layout: default

2. A. J. Radtke et al., "IBEX: A versatile multiplex optical imaging approach for deep phenotyping and spatial analysis of cells in complex tissues", *Proc Natl Acad Sci*, 117(52):33455–33465, 2020, [doi:10.1073/pnas.2018488117](https://doi.org/10.1073/pnas.2018488117)

3. A. J. Radtke et al., "A Multi-scale, Multiomic Atlas of Human Normal and Follicular Lymphoma Lymph Nodes", *bioRxiv*, 2022, [doi: 10.1101/2022.06.03.494716](https://doi.org/10.1101/2022.06.03.494716).

# Additional Notes

Expand All @@ -31,3 +33,8 @@ layout: default
|:-------:|:-------:|
| ![CD21 PE FL pH6and9](CD21_PE_FL_pH6and9.jpg) | ![CD21 PE FL pH6](CD21_PE_FL_pH6.jpg) |



| Human normal LN: BCL2 (cyan, catalog number ab236221 and A-31573), CD3 (magenta, catalog number ab208514), CD4 (blue, catalog number ab196372), CD21 (yellow, catalog number ab306325) |
|:-------:|
| ![](../BCL2_Unconjugated/Human_normal_LN_BCL2_ab236221_CD3_ab208514_CD4_ab196372_CD21_ab306325.jpg) |
13 changes: 13 additions & 0 deletions docs/supporting_material/CD3_AF555/0000-0003-4379-8967.md
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Expand Up @@ -12,6 +12,8 @@ layout: default
| P07766 | Primary Antibody | CD3 | Human | Rabbit | IgG | EP4426 | Abcam | ab208514 | AF555 | AB_443425 | 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) | [2](#notes) |
| P07766 | Primary Antibody | CD3 | Human | Rabbit | IgG | EP4426 | Abcam | ab208514 | AF555 | AB_443425 | Stock | Cell DIVE-IBEX | 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 | 1 mg/ml LiBH4 15 minutes | Yes | [0000-0003-4379-8967](https://orcid.org/0000-0003-4379-8967) | NA | [0000-0003-4379-8967](https://orcid.org/0000-0003-4379-8967) | [4](#notes) |
| P07766 | Primary Antibody | CD3 | Human | Rabbit | IgG | EP4426 | Abcam | ab208514 | AF555 | AB_443425 | Stock | Cell DIVE-IBEX | FFPE | Lung | Cancer | 0.3% Triton-X-100 | pH 6 for 30 minutes ER1 (AR9961) and pH 9 for 30 minutes ER2 (AR9640) using the Leica Bond | 1 mg/ml LiBH4 15 minutes | Yes | [0000-0003-4379-8967](https://orcid.org/0000-0003-4379-8967) | NA | [0000-0003-4379-8967](https://orcid.org/0000-0003-4379-8967) | [5](#notes) |
| P07766 | Primary Antibody | CD3 | Human | Rabbit | IgG | EP4426 | Abcam | ab208514 | AF555 | AB_443425 | Stock | Cell DIVE-IBEX | 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 | 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) | |
| P07766 | Primary Antibody | CD3 | Human | Rabbit | IgG | EP4426 | Abcam | ab208514 | AF555 | AB_443425 | Stock | Cell DIVE-IBEX | FFPE | Lymph Node | 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 | 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) | |

# Publications

Expand All @@ -23,6 +25,7 @@ layout: default

2. A. J. Radtke et al., "IBEX: A versatile multiplex optical imaging approach for deep phenotyping and spatial analysis of cells in complex tissues", *Proc Natl Acad Sci*, 117(52):33455–33465, 2020, [doi:10.1073/pnas.2018488117](https://doi.org/10.1073/pnas.2018488117)

3. A. J. Radtke et al., "A Multi-scale, Multiomic Atlas of Human Normal and Follicular Lymphoma Lymph Nodes", *bioRxiv*, 2022, [doi: 10.1101/2022.06.03.494716](https://doi.org/10.1101/2022.06.03.494716).

# Additional Notes

Expand All @@ -32,3 +35,13 @@ layout: default
3. Custom conjugate by BioLegend. Labels T cells in diverse tissues.
4. Antibody labels T cells. Preferred clone for FFPE samples. Works beautifully on Cell DIVE imager with IBEX dye inactivation protocol.
5. Labels T cells in lung. Great signal and works very well on Cell DIVE imager with IBEX dye inactivation protocol.


| Human normal LN: BCL2 (cyan, catalog number ab236221 and A-31573), CD3 (magenta, catalog number ab208514), CD4 (blue, catalog number ab196372), CD21 (yellow, catalog number ab306325) |
|:-------:|
| ![](../BCL2_Unconjugated/Human_normal_LN_BCL2_ab236221_CD3_ab208514_CD4_ab196372_CD21_ab306325.jpg) |


| Human FL LN: BCL2 (cyan, catalog number ab236221 and A-31573), CD3 (magenta, catalog number ab208514), CD4 (blue, catalog number ab196372), CD21 (yellow, catalog number ab306325) |
|:-------:|
| ![](../BCL2_Unconjugated/Human_FL_LN_BCL2_ab236221_CD3_ab208514_CD4_ab196372_CD21_ab306325.jpg) |
13 changes: 13 additions & 0 deletions docs/supporting_material/CD4_AF488/0000-0003-4379-8967.md
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Expand Up @@ -10,6 +10,8 @@ layout: default
| P06332 | Primary Antibody | CD4 | Mouse | Rat | IgG2a | RM4-5 | BD Biosciences | 557667 | AF488 | AB_396779 | Stock | IBEX2D Manual | 1:4 Cytofix/Cytoperm Fixed Frozen | Lymph Node | 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) [[2](#publications)] | NA | [0000-0003-4379-8967](https://orcid.org/0000-0003-4379-8967) | |
| P01730 | Primary Antibody | CD4 | Human | Rabbit | IgG | EPR6855 | Abcam | ab196372 | AF488 | AB_2889191 | 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) |
| P01730 | Primary Antibody | CD4 | Human | Rabbit | IgG | EPR6855 | Abcam | ab196372 | AF488 | AB_2889191 | Stock | Cell DIVE-IBEX | 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 | 1 mg/ml LiBH4 15 minutes | 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) |
| P01730 | Primary Antibody | CD4 | Human | Rabbit | IgG | EPR6855 | Abcam | ab196372 | AF488 | AB_2889191 | Stock | Cell DIVE-IBEX | 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 | 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) | |
| P01730 | Primary Antibody | CD4 | Human | Rabbit | IgG | EPR6855 | Abcam | ab196372 | AF488 | AB_2889191 | Stock | Cell DIVE-IBEX | FFPE | Lymph Node | 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 | 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) | |

# Publications

Expand All @@ -21,6 +23,7 @@ layout: default

2. A. J. Radtke et al., "IBEX: A versatile multiplex optical imaging approach for deep phenotyping and spatial analysis of cells in complex tissues", *Proc Natl Acad Sci*, 117(52):33455–33465, 2020, [doi:10.1073/pnas.2018488117](https://doi.org/10.1073/pnas.2018488117)

3. A. J. Radtke et al., "A Multi-scale, Multiomic Atlas of Human Normal and Follicular Lymphoma Lymph Nodes", *bioRxiv*, 2022, [doi: 10.1101/2022.06.03.494716](https://doi.org/10.1101/2022.06.03.494716).

# Additional Notes

Expand All @@ -31,3 +34,13 @@ layout: default
| Human lymph node: CD163 (red, catalog number 333620) and CD4 (blue, catalog number 300519) |
|:-------:|
| ![](../CD163_AF647/Human_LN_CD163_CD4.jpg) |


| Human normal LN: BCL2 (cyan, catalog number ab236221 and A-31573), CD3 (magenta, catalog number ab208514), CD4 (blue, catalog number ab196372), CD21 (yellow, catalog number ab306325) |
|:-------:|
| ![](../BCL2_Unconjugated/Human_normal_LN_BCL2_ab236221_CD3_ab208514_CD4_ab196372_CD21_ab306325.jpg) |


| Human FL LN: BCL2 (cyan, catalog number ab236221 and A-31573), CD3 (magenta, catalog number ab208514), CD4 (blue, catalog number ab196372), CD21 (yellow, catalog number ab306325) |
|:-------:|
| ![](../BCL2_Unconjugated/Human_FL_LN_BCL2_ab236221_CD3_ab208514_CD4_ab196372_CD21_ab306325.jpg) |

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