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Adding contributions from Yuri Lin ORCID 0009-0006-9784-2694.
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Adding reagent information contributed by Yuri Lin.
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@zivy
zivy committed Jun 10, 2024
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Showing 19 changed files with 181 additions and 7 deletions.
5 changes: 5 additions & 0 deletions .zenodo.json
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"name": "Lamborn, Ian",
"orcid": "0009-0006-1490-3667"
},
{
"affiliation": "National Institutes of Health",
"name": "Lin, Yuri",
"orcid": "0009-0006-9784-2694"
},
{
"affiliation": "National Institutes of Health",
"name": "Makranz, Chen",
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7 changes: 7 additions & 0 deletions data/image_resources.csv
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Expand Up @@ -157,3 +157,10 @@ B220_AF488/Mouse_LN_B220_cyan_BD_557669_CD3_red_BioLegend_100240.jpg,"Mouse lymp
CD35_BV510/Mouse_LN_CD35_yellow_BD_740132_ColIV_blue_ab19808_A-11009.jpg,"Mouse lymph node: CD35 (yellow, catalog number 740132) and Collagen IV (blue, catalog number ab19808 and A-11009)",ceb4fd8cd2cc42201659aa8226b9f07a,"['CD35_BV510/0000-0003-1118-7432.md','Collagen_IV_Unconjugated/0000-0003-1118-7432.md','Rabbit_IgG__H+L__AF532/0000-0003-1118-7432.md']"
CD169_PE/Mouse_LN_CD169_green_BioLegend_142404_Ki67_magenta_BD_561277.jpg,"Mouse lymph node: CD169 (green, catalog number 142404) and Ki-67 (magenta, catalog number 561277)",8a6567cde9020c3f7cf4baa8a32666f2,"['Ki-67_AF700/0000-0003-1118-7432.md','CD169_PE/0000-0003-1118-7432.md']"
PD-1_BV421/Mouse_LN_PD1_cyan_135218_CD11c_magenta_117312.jpg,"Mouse lymph node: PD-1 (cyan, catalog number 135218) and CD11c (magenta, catalog number 117312)",28a7b8aa0b9b5764fe0061fb69312229,"['CD11c_AF647/0000-0003-1118-7432.md','PD-1_BV421/0000-0003-1118-7432.md']"
CD34_PE/Human_Tonsil_FFPE_Hoechst_blue_CD34_green.jpg,"Human tonsil: Hoechst (blue, Biotium cat. no. 40046) and CD34 (green, Thermo Fisher Scientific cat. no. MA1-10205)",c76364415c790451b7a0d30a401b5132,"['CD34_PE/0009-0006-9784-2694.md']"
CD3_AF555/Human_Tonsil_FFPE_Hoechst_blue_CD3_green.jpg,"Human tonsil: Hoechst (blue, Biotium cat. no. 40046) and CD3 (green, Abcam cat. no. ab208514)",bdacb094d7c4f19d787ad3231b261d1e,"['CD3_AF555/0009-0006-9784-2694.md']"
CD45_AF488/Human_Tonsil_FFPE_Hoechst_blue_CD45_AF488_green.jpg,"Human tonsil: Hoechst (blue, Biotium cat. no. 40046) and CD45 (green, Novus Biologicals cat. no. NBP2-34528AF488)",5e5dfd4b6720c2abba3f740ca32a35e7,"['CD45_AF488/0009-0006-9784-2694.md']"
CD45_PE/Human_Tonsil_FFPE_Hoechst_blue_CD45_PE_green.jpg,"Human tonsil: Hoechst (blue, Biotium cat. no. 40046) and CD45 (green, Novus Biologicals cat. no. NBP2-34528PE)",41b039e9d46868bc4769f264d795effb,"['CD45_PE/0009-0006-9784-2694.md']"
CD8_AF647/Human_Tonsil_FFPE_Hoechst_blue_CD8_red.jpg,"Human tonsil: Hoechst (blue, Biotium cat. no. 40046) and CD8 (red, BioLegend cat. no. 372906)",e2a8ea56916b2337125ea81c18050771,"['CD8_AF647/0009-0006-9784-2694.md']"
CTLA4_AF647/Human_Tonsil_FFPE_Hoechst_blue_CTLA4_red.jpg,"Human tonsil: Hoechst (blue, Biotium cat. no. 40046) and CTLA4 (red, Abcam cat. no. ab270127)",0319ef9d4863816c1d28cfa5e3ec8258,"['CTLA4_AF647/0009-0006-9784-2694.md']"
PD-1_AF555/Human_Tonsil_FFPE_Hoechst_blue_PD1_green.jpg,"Human tonsil: Hoechst (blue, Biotium cat. no. 40046) and PD-1 (green, Abcam cat. no. ab275126)",32a9ea3243d06baf17be375554c5a9d7,"['PD-1_AF555/0009-0006-9784-2694.md']"
15 changes: 10 additions & 5 deletions data/reagent_resources.csv
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Original file line number Diff line number Diff line change
Expand Up @@ -732,7 +732,7 @@ Q13509,Primary Antibody,Tubulin beta-3 chain,Mouse,Mouse,IgG2a,TUJ1,BioLegend,80
P22646,Primary Antibody,CD3,Mouse,Rat,IgG2b,17A2,BioLegend,100210,AF488,AB_389301,Stock,IBEX2D Manual,"AntigenFix (2h, 4 degrees) Fixed Frozen",Kidney,NA,0.3% Triton-X-100,NA,1 mg/ml LiBH4 15 minutes,Yes,0000-0002-7422-3237,NA,0000-0002-7422-3237
P24788,Primary Antibody,CD11b,Mouse,Rat,IgG2b,M1/70,BioLegend,101208,PE,AB_312791,Stock,IBEX2D Manual,"AntigenFix (2h, 4 degrees) Fixed Frozen",Kidney,NA,0.3% Triton-X-100,NA,1 mg/ml LiBH4 15 minutes,Yes,0000-0002-7422-3237,NA,0000-0002-7422-3237
Q9QXH4,Primary Antibody,CD11c,Mouse,Armenian Hamster,IgG,N418,BioLegend,117308,PE,AB_313777,Stock,IBEX2D Manual,"AntigenFix (2h, 4 degrees) Fixed Frozen",Kidney,NA,0.3% Triton-X-100,NA,1 mg/ml LiBH4 15 minutes,Yes,0000-0002-7422-3237,NA,0000-0002-7422-3237
A0A0B4J1G0,Primary Antibody,CD16.2,Mouse,Armenian Hamster,IgG,9.00E+09,BioLegend,149503,PE,AB_2565810,Stock,IBEX2D Manual,"AntigenFix (2h, 4 degrees) Fixed Frozen",Kidney,NA,0.3% Triton-X-100,NA,1 mg/ml LiBH4 15 minutes,Yes,0000-0002-7422-3237,NA,0000-0002-7422-3237
A0A0B4J1G0,Primary Antibody,CD16.2,Mouse,Armenian Hamster,IgG,9E9,BioLegend,149503,PE,AB_2565810,Stock,IBEX2D Manual,"AntigenFix (2h, 4 degrees) Fixed Frozen",Kidney,NA,0.3% Triton-X-100,NA,1 mg/ml LiBH4 15 minutes,Yes,0000-0002-7422-3237,NA,0000-0002-7422-3237
P08101,Primary Antibody,CD16/32,Mouse,Goat,IgG,Polyclonal,R&D Systems,AF1460-SP,Unconjugated,NA,Stock,IBEX2D Manual,"AntigenFix (2h, 4 degrees) Fixed Frozen",Kidney,NA,0.3% Triton-X-100,NA,NA,Yes,0000-0002-7422-3237,NA,0000-0002-7422-3237
P26151,Primary Antibody,CD64,Mouse,Mouse,IgG1,X54-5/7.1,BioLegend,139304,PE,AB_10612740,Stock,IBEX2D Manual,"AntigenFix (2h, 4 degrees) Fixed Frozen",Kidney,NA,0.3% Triton-X-100,NA,1 mg/ml LiBH4 15 minutes,Yes,0000-0002-7422-3237,NA,0000-0002-7422-3237
Q08481,Primary Antibody,CD31,Mouse,Rat,IgG2a,MEC13.3,BD Biosciences,553373,PE,AB_394819,Stock,IBEX2D Manual,"AntigenFix (2h, 4 degrees) Fixed Frozen",Kidney,NA,0.3% Triton-X-100,NA,1 mg/ml LiBH4 15 minutes,Yes,0000-0002-7422-3237,NA,0000-0002-7422-3237
Expand Down Expand Up @@ -963,9 +963,9 @@ P20023,Primary Antibody,CD21,Human,Rabbit,IgG,SP186,Abcam,ab306325,PE,NA,Stock,C
P56199,Primary Antibody,CD49a,Human,Mouse,IgG1,CL7207,Abcam,ab243032,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,Yes,0000-0003-4379-8967,NA,0000-0003-4379-8967
P56199,Primary Antibody,CD49a,Human,Mouse,IgG1,CL7207,Abcam,ab243032,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,NA,0000-0003-4379-8967
NA,Secondary Antibody,Fluorescein/Oregon Green,Human,Rabbit,IgG,Polyclonal,Thermo Fisher Scientific,A-11090,AF488,AB_221562,Stock,Multiplexed 2D Imaging,1:4 Cytofix/Cytoperm Fixed Frozen,Lymph Node,NA,0.3% Triton-X-100,NA,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,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
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;0009-0006-9784-2694,NA,0000-0003-4379-8967
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,NA,0000-0003-4379-8967
P01732,Primary Antibody,CD8,Human,Mouse,IgG1,C8/144B,BioLegend,372906,AF647,AB_2650712,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
P01732,Primary Antibody,CD8,Human,Mouse,IgG1,C8/144B,BioLegend,372906,AF647,AB_2650712,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;0009-0006-9784-2694,NA,0000-0003-4379-8967
P01732,Primary Antibody,CD8,Human,Mouse,IgG1,C8/144B,BioLegend,372906,AF647,AB_2650712,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,NA,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,NA,0000-0003-4379-8967
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,NA,0000-0003-4379-8967
Expand All @@ -984,7 +984,7 @@ Q8TDQ0,Primary Antibody,Tim-3,Human,Rat,IgG2a,344823,R&D Systems,MAB2365,Unconju
P11836,Primary Antibody,CD20,Human,Mouse,IgG2a,L26,Thermo Fisher Scientific,42-0202-82,eF615,AB_10853517,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
P13591,Primary Antibody,CD56,Human,Mouse,IgG1,123C3.D5,Novus Biologicals,NBP2-33132AF647,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,No,0000-0003-4379-8967,NA,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,NA,0000-0003-4379-8967
P01106,Primary Antibody,c-Myc,Human,Mouse,IgG1,9.00E+10,Novus Biologicals,NB600-302IR,DL755,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
P01106,Primary Antibody,c-Myc,Human,Mouse,IgG1,9E10,Novus Biologicals,NB600-302IR,DL755,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
P01903,Primary Antibody,HLA-DR,Human,Mouse,IgG2b,LN-3,Novus Biologicals,NBP2-47670AF488,AF488,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
P01903,Primary Antibody,HLA-DR,Human,Mouse,IgG2b,LN-3,Novus Biologicals,NBP2-47670AF750,AF750,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
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
Expand Down Expand Up @@ -1086,4 +1086,9 @@ P62736,Primary Antibody,Alpha smooth muscle actin,Human,Mouse,IgG2a,1A4,Thermo F
P60709,Cell Structure Reagent,Phalloidin,Human,NA,NA,NA,AAT Bioquest,23122,iF594,NA,Stock,IBEX2D Manual,1:4 Cytofix/Cytoperm Fixed Frozen,Retina,NA,0.1% Saponin,NA,1 mg/ml LiBH4 15 minutes,Yes,0000-0003-2088-8310,NA,0000-0003-2088-8310
NA,Lectin,PNA,Human,NA,NA,NA,Thermo Fisher Scientific,L21409,AF488,NA,Stock,IBEX2D Manual,1:4 Cytofix/Cytoperm Fixed Frozen,Retina,NA,0.1% Saponin,NA,1 mg/ml LiBH4 15 minutes,Yes,0000-0003-2088-8310,NA,0000-0003-2088-8310
NA,Lectin,Isolectin GS-IB4,Human,NA,NA,NA,Thermo Fisher Scientific,I21412,AF568,NA,Stock,IBEX2D Manual,1:4 Cytofix/Cytoperm Fixed Frozen,Retina,NA,0.1% Saponin,NA,NA,Yes,0000-0003-2088-8310,NA,0000-0003-2088-8310
NA,Secondary Antibody,Rabbit IgG (H+L),Mouse,Goat,IgG,Polyclonal,Thermo Fisher Scientific,A-11009,AF532,AB_2534076,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,0000-0003-1118-7432,NA,0000-0003-1118-7432
NA,Secondary Antibody,Rabbit IgG (H+L),Mouse,Goat,IgG,Polyclonal,Thermo Fisher Scientific,A-11009,AF532,AB_2534076,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,0000-0003-1118-7432,NA,0000-0003-1118-7432
P28906,Primary Antibody,CD34,Human,Mouse,IgG1,QBEND/10,Thermo Fisher Scientific,MA1-10205,PE,AB_11152571,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,0009-0006-9784-2694,NA,0009-0006-9784-2694
P08575,Primary Antibody,CD45,Human,Mouse,IgG1,2B11+PD7/26,Novus Biologicals,NBP2-34528PE,PE,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,0009-0006-9784-2694,NA,0009-0006-9784-2694
P08575,Primary Antibody,CD45,Human,Mouse,IgG1,2B11+PD7/26,Novus Biologicals,NBP2-34528AF488,AF488,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,0009-0006-9784-2694,NA,0009-0006-9784-2694
P16410,Primary Antibody,CTLA4,Human,Rabbit,IgG,CAL49,Abcam,ab270127,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,0009-0006-9784-2694,NA,0009-0006-9784-2694
Q15116,Primary Antibody,PD-1,Human,Rabbit,IgG,EPR4877(2),Abcam,ab275126,AF555,AB_2728811,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,0009-0006-9784-2694,NA,0009-0006-9784-2694
22 changes: 22 additions & 0 deletions docs/supporting_material/CD34_PE/0009-0006-9784-2694.md
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---
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 |
|:---------------------------|:-----------------|:----------------------------------|:-----------------|:----------------|:----------|:------------|:-------------------------|:-----------------|:------------|:------------|:---------------|:-----------------------|:----------------------|:----------------|:---------------|:------------------|:-------------------------------------------------------------------------------------------|:------------------------------|:------------|:-------------------------------------------------------------|:-----------|:-------------------------------------------------------------|:------------|
| P28906 | Primary Antibody | CD34 | Human | Mouse | IgG1 | QBEND/10 | Thermo Fisher Scientific | MA1-10205 | PE | AB_11152571 | 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 | [0009-0006-9784-2694](https://orcid.org/0009-0006-9784-2694) | NA | [0009-0006-9784-2694](https://orcid.org/0009-0006-9784-2694) | [1](#notes) |

# Publications



# Additional Notes

<a name="notes"></a>
1. used AF546 preset setting to capture PE signal. RBCs are visible in the snapshot and difficult to differentiate.

| Human tonsil: Hoechst (blue, Biotium cat. no. 40046) and CD34 (green, Thermo Fisher Scientific cat. no. MA1-10205) |
|:-------:|
| ![](Human_Tonsil_FFPE_Hoechst_blue_CD34_green.jpg) |
Binary file added docs/supporting_material/CD34_PE/Human_Tonsil_FFPE_Hoechst_blue_CD34_green.jpg
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