From bcc08011d4fa462bd8c29c482f69ba40d21678ec Mon Sep 17 00:00:00 2001 From: Ziv Yaniv Date: Mon, 29 Apr 2024 09:45:17 -0400 Subject: [PATCH] Harmonizing the naming of LYVE1 vs. LYVE-1. The naming was harmonized to LYVE-1. resolves #119 --- data/reagent_resources.csv | 26 ++++++++-------- .../0000-0003-4379-8967.md | 4 +-- ..._LYVE1_RD_AF2089_Desmin_Abcam_Ab185033.jpg | Bin .../0000-0001-9561-4256.md | 2 +- .../0000-0003-0666-4804.md | 2 +- .../0000-0003-4379-8967.md | 20 ++++++++++--- .../LYVE-1_eF570/0000-0003-4379-8967.md | 22 ++++++++++++++ .../0000-0001-9561-4256.md | 4 +-- .../LYVE1_Unconjugated/0000-0003-4379-8967.md | 28 ------------------ .../LYVE1_eF570/0000-0003-4379-8967.md | 22 -------------- 10 files changed, 57 insertions(+), 73 deletions(-) rename docs/supporting_material/{LYVE1_AF532 => LYVE-1_AF532}/0000-0003-4379-8967.md (66%) rename docs/supporting_material/{LYVE1_AF532 => LYVE-1_AF532}/Hoechst_LYVE1_RD_AF2089_Desmin_Abcam_Ab185033.jpg (100%) rename docs/supporting_material/{LYVE1_Unconjugated => LYVE-1_Unconjugated}/0000-0001-9561-4256.md (73%) rename docs/supporting_material/{LYVE1_Unconjugated => LYVE-1_Unconjugated}/0000-0003-0666-4804.md (65%) create mode 100644 docs/supporting_material/LYVE-1_eF570/0000-0003-4379-8967.md rename docs/supporting_material/{LYVE1_iF594 => LYVE-1_iF594}/0000-0001-9561-4256.md (54%) delete mode 100644 docs/supporting_material/LYVE1_Unconjugated/0000-0003-4379-8967.md delete mode 100644 docs/supporting_material/LYVE1_eF570/0000-0003-4379-8967.md diff --git a/data/reagent_resources.csv b/data/reagent_resources.csv index 59f5bdf..20d641e 100644 --- a/data/reagent_resources.csv +++ b/data/reagent_resources.csv @@ -11,9 +11,9 @@ P05362,Primary Antibody,CD54,Human,Mouse,IgG1,HA58,BioLegend,353114,AF647,AB_271 P05362,Primary Antibody,CD54,Human,Mouse,IgG1,HA58,BioLegend,353114,AF647,AB_2715942,Stock,IBEX2D Automated,1:4 Cytofix/Cytoperm Fixed Frozen,Lymph Node,NA,0.3% Triton-X-100,NA,0.5 mg/ml LiBH4 10 minutes continuous exchange with automated protocol,Yes,0000-0003-4379-8967,NA,0000-0003-4379-8967 P05362,Primary Antibody,CD54,Human,Mouse,IgG1,HA58,BioLegend,353114,AF647,AB_2715942,Stock,IBEX2D Automated,1:4 Cytofix/Cytoperm Fixed Frozen,Skin,NA,0.3% Triton-X-100,NA,0.5 mg/ml LiBH4 10 minutes continuous exchange with automated protocol,Yes,0000-0003-4379-8967,NA,0000-0003-4379-8967 P05362,Primary Antibody,CD54,Human,Mouse,IgG1,HA58,BioLegend,353114,AF647,AB_2715942,Stock,IBEX2D Manual,1:4 Cytofix/Cytoperm Fixed Frozen,Spleen,NA,0.3% Triton-X-100,NA,1 mg/ml LiBH4 15 minutes,Yes,0000-0003-4379-8967,NA,0000-0003-4379-8967 -Q9Y5Y7,Primary Antibody,LYVE1,Human,Goat,IgG,Polyclonal,R&D Systems,AF2089,Unconjugated,AB_355144,Stock,IBEX2D Automated,1:4 Cytofix/Cytoperm Fixed Frozen,Jejunum,NA,0.3% Triton-X-100,NA,NA,Yes,0000-0003-4379-8967,NA,0000-0003-4379-8967 -Q9Y5Y7,Primary Antibody,LYVE1,Human,Goat,IgG,Polyclonal,R&D Systems,AF2089,Unconjugated,AB_355144,Stock,IBEX2D Manual,1:4 Cytofix/Cytoperm Fixed Frozen,Liver,NA,0.3% Triton-X-100,NA,NA,Yes,0000-0003-4379-8967,NA,0000-0003-4379-8967 -Q9Y5Y7,Primary Antibody,LYVE1,Human,Goat,IgG,Polyclonal,R&D Systems,AF2089,Unconjugated,AB_355144,Stock,IBEX2D Automated,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 +Q9Y5Y7,Primary Antibody,LYVE-1,Human,Goat,IgG,Polyclonal,R&D Systems,AF2089,Unconjugated,AB_355144,Stock,IBEX2D Automated,1:4 Cytofix/Cytoperm Fixed Frozen,Jejunum,NA,0.3% Triton-X-100,NA,NA,Yes,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,IBEX2D Manual,1:4 Cytofix/Cytoperm Fixed Frozen,Liver,NA,0.3% Triton-X-100,NA,NA,Yes,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,IBEX2D Automated,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 NA,Secondary Antibody,Goat IgG (H+L),Human,Donkey,IgG,Polyclonal,Thermo Fisher Scientific,A-21432,AF555,AB_2535853,Stock,IBEX2D Automated,1:4 Cytofix/Cytoperm Fixed Frozen,Jejunum,NA,0.3% Triton-X-100,NA,0.5 mg/ml LiBH4 10 minutes continuous exchange with automated protocol,Yes,0000-0003-4379-8967,NA,0000-0003-4379-8967 NA,Secondary Antibody,Goat IgG (H+L),Human,Donkey,IgG,Polyclonal,Thermo Fisher Scientific,A-21432,AF555,AB_2535853,Stock,IBEX2D Automated,1:4 Cytofix/Cytoperm Fixed Frozen,Lymph Node,NA,0.3% Triton-X-100,NA,0.5 mg/ml LiBH4 10 minutes continuous exchange with automated protocol,Yes,0000-0003-4379-8967,NA,0000-0003-4379-8967 P56199,Primary Antibody,CD49a,Human,Mouse,IgG1,TS2/7,BioLegend,328310,AF647,AB_2129242,Stock,IBEX2D Automated,1:4 Cytofix/Cytoperm Fixed Frozen,Jejunum,NA,0.3% Triton-X-100,NA,0.5 mg/ml LiBH4 10 minutes continuous exchange with automated protocol,Yes,0000-0003-4379-8967,NA,0000-0003-4379-8967 @@ -162,7 +162,7 @@ Q15306,Primary Antibody,IRF4,Human,Rat,IgG1,IRF4.3E4,BioLegend,646404,PE,AB_2563 Q9Y6W8,Primary Antibody,ICOS,Human,Armenian Hamster,IgG,CS98.4A,BioLegend,313514,AF488,AB_2122584,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 Q53X90,Primary Antibody,CXCL13,Human,Goat,IgG,Polyclonal,R&D Systems,AF801 (Unconjugated),AF532,AB_2892755,Custom,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 NA,Primary Antibody,TCR Valpha7.2,Human,Mouse,IgG1,3C10,BioLegend,351726,AF647,AB_2566335,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 -Q9Y5Y7,Primary Antibody,LYVE1,Human,Goat,IgG,Polyclonal,R&D Systems,AF2089 (Unconjugated),AF532,AB_2892756,Custom,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 +Q9Y5Y7,Primary Antibody,LYVE-1,Human,Goat,IgG,Polyclonal,R&D Systems,AF2089 (Unconjugated),AF532,AB_2892756,Custom,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 Q9NNX6,Primary Antibody,DC-SIGN,Human,Mouse,IgG2a,9E9A8,BioLegend,330112,AF647,AB_1186092,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 Q6UXN8,Primary Antibody,CLEC9a,Human,Mouse,IgG2a,8F9,BioLegend,353802 (Unconjugated),AF488,NA,Custom,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 P51884,Primary Antibody,Lumican,Human,Goat,IgG,Polyclonal,R&D Systems,AF2846,Unconjugated,AB_2139484,Stock,IBEX2D Automated,1:4 Cytofix/Cytoperm Fixed Frozen,Skin,NA,0.3% Triton-X-100,NA,NA,Yes,0000-0002-5187-810X,NA,0000-0002-5187-810X @@ -292,9 +292,9 @@ P06800,Primary Antibody,CD45,Mouse,Rat,IgG2b,30-F11,BioLegend,103128,AF700,AB_49 NA,Primary Antibody,Cytokeratin,Mouse,Mouse,IgG1,C-11,BioLegend,628604,AF647,AB_2563652,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,NA,0000-0003-4379-8967 P06332,Primary Antibody,CD4,Mouse,Rat,IgG2a,RM4-5,Thermo Fisher Scientific,58-0042-80,AF532,AB_11219484,Stock,IBEX2D Manual,1:4 Cytofix/Cytoperm Fixed Frozen,Lung,NA,0.3% Triton-X-100,NA,1 mg/ml LiBH4 15 minutes,Yes,0000-0003-4379-8967,NA,0000-0003-4379-8967 P06332,Primary Antibody,CD4,Mouse,Rat,IgG2a,RM4-5,Thermo Fisher Scientific,58-0042-80,AF532,AB_11219484,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,NA,0000-0003-4379-8967 -Q8BHC0,Primary Antibody,LYVE1,Mouse,Rat,IgG1,ALY7,Thermo Fisher Scientific,41-0443-82,eF570,AB_2573596,Stock,IBEX2D Manual,1:4 Cytofix/Cytoperm Fixed Frozen,Lung,NA,0.3% Triton-X-100,NA,1 mg/ml LiBH4 15 minutes,Yes,0000-0003-4379-8967,NA,0000-0003-4379-8967 -Q8BHC0,Primary Antibody,LYVE1,Mouse,Rat,IgG1,ALY7,Thermo Fisher Scientific,41-0443-82,eF570,AB_2573596,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,NA,0000-0003-4379-8967 -Q8BHC0,Primary Antibody,LYVE1,Mouse,Rat,IgG1,ALY7,Thermo Fisher Scientific,41-0443-82,eF570,AB_2573596,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 +Q8BHC0,Primary Antibody,LYVE-1,Mouse,Rat,IgG1,ALY7,Thermo Fisher Scientific,41-0443-82,eF570,AB_2573596,Stock,IBEX2D Manual,1:4 Cytofix/Cytoperm Fixed Frozen,Lung,NA,0.3% Triton-X-100,NA,1 mg/ml LiBH4 15 minutes,Yes,0000-0003-4379-8967,NA,0000-0003-4379-8967 +Q8BHC0,Primary Antibody,LYVE-1,Mouse,Rat,IgG1,ALY7,Thermo Fisher Scientific,41-0443-82,eF570,AB_2573596,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,NA,0000-0003-4379-8967 +Q8BHC0,Primary Antibody,LYVE-1,Mouse,Rat,IgG1,ALY7,Thermo Fisher Scientific,41-0443-82,eF570,AB_2573596,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 Q08481,Primary Antibody,CD31,Mouse,Rat,IgG2a,MEC13.3,BioLegend,102520,AF594,AB_2563319,Stock,IBEX2D Manual,1:4 Cytofix/Cytoperm Fixed Frozen,Lung,NA,0.3% Triton-X-100,NA,1 mg/ml LiBH4 for more than 120 minutes,Yes,0000-0003-4379-8967,NA,0000-0003-4379-8967 Q8R2S8,Primary Antibody,Ly-6G,Mouse,Rat,IgG2a,1A8,BioLegend,127626,AF488,AB_2561340,Stock,IBEX2D Manual,1:4 Cytofix/Cytoperm Fixed Frozen,Lung,NA,0.3% Triton-X-100,NA,1 mg/ml LiBH4 15 minutes,Yes,0000-0003-4379-8967,NA,0000-0003-4379-8967 O88713,Primary Antibody,KLRG1,Mouse,Syrian Hamster,IgG2,2F1,BD Biosciences,561619,AF488,AB_10898017,Stock,IBEX2D Manual,1:4 Cytofix/Cytoperm Fixed Frozen,Lung,NA,0.3% Triton-X-100,NA,1 mg/ml LiBH4 15 minutes,Yes,0000-0003-4379-8967,NA,0000-0003-4379-8967 @@ -764,7 +764,7 @@ P13688,Primary Antibody,CD66abce,Rhesus Macaque,Mouse,IgG2b,Tet2,Miltenyi Biotec P05784,Primary Antibody,Cytokeratin 18,Mouse,Rabbit,IgG,Polyclonal,Thermo Fisher Scientific,PA5-14263,Unconjugated,AB_2133178,Stock,Opal-plex,10% Formalin for 7 Days,Liver,Infected,Akoya Antibody Diluent,Akoya AR6,NA,Yes,0000-0003-0666-4804,NA,0000-0003-0666-4804 P70194,Primary Antibody,CLEC4F,Mouse,Goat,IgG,Polyclonal,R&D Systems,AF2784,Unconjugated,NA,Stock,Opal-plex,10% Formalin for 7 Days,Liver,Infected,Akoya Antibody Diluent,Akoya AR6,NA,Yes,0000-0003-0666-4804,NA,0000-0003-0666-4804 NA,Primary Antibody,SARS-NP,Rhesus Macaque,Rabbit,IgG,Polyclonal,Novus Biologicals,NB100-56576,Unconjugated,NA,Stock,Opal-plex,10% Formalin for 7 Days,Lung,Infected,Akoya Antibody Diluent,Akoya AR6,NA,Yes,0000-0003-0666-4804,NA,0000-0003-0666-4804 -Q8BHC0,Primary Antibody,LYVE1,Mouse,Rabbit,IgG,E3L3V,Cell Signaling Technology,67538,Unconjugated,NA,Stock,Opal-plex,10% Formalin for 7 Days,Lymph Node,Infected,Akoya Antibody Diluent,Akoya AR6,NA,Yes,0000-0003-0666-4804,NA,0000-0003-0666-4804 +Q8BHC0,Primary Antibody,LYVE-1,Mouse,Rabbit,IgG,E3L3V,Cell Signaling Technology,67538,Unconjugated,NA,Stock,Opal-plex,10% Formalin for 7 Days,Lymph Node,Infected,Akoya Antibody Diluent,Akoya AR6,NA,Yes,0000-0003-0666-4804,NA,0000-0003-0666-4804 P06800,Primary Antibody,CD45,Mouse,Rat,IgG2b,30-F11,BioLegend,103128,AF700,AB_493715,Stock,IBEX2D Manual,1:4 Cytofix/Cytoperm Fixed Frozen,Uterus,NA,0.3% Triton-X-100,NA,1 mg/ml LiBH4 15 minutes,Yes,0000-0003-2634-6838,NA,0000-0003-2634-6838 P14719,Primary Antibody,ST2 (IL-33R),Mouse,Rat,IgG2a,U29-93,BD Biosciences,566311,PE,AB_2744490,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,0000-0002-1461-0999,NA,0000-0002-1461-0999 P06336,Primary Antibody,IgE,Mouse,Rat,IgG1,RME-1,BioLegend,406908,PE,AB_493290,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,0000-0002-1461-0999,NA,0000-0002-1461-0999 @@ -802,7 +802,7 @@ P01730,Primary Antibody,CD4,Human,Goat,IgG,Polyclonal,R&D Systems,FAB8165G,AF488 Q15116,Primary Antibody,PD-1,Human,Goat,IgG,Polyclonal,R&D Systems,AF1086,Unconjugated,AB_354588,Stock,IBEX2D Manual,FFPE,Liver,Metastatic Ovarian Cancer,0.3% Triton-X-100,pH 9.5 for 15 minutes in a pressure cooker (Borg Decloaker BD1000),NA,Yes,0000-0001-9561-4256,NA,0000-0001-9561-4256 P01732,Primary Antibody,CD8,Human,Mouse,IgG1,C8/144B,BioLegend,372906,AF647,AB_2650712,Stock,IBEX2D Manual,FFPE,Liver,Metastatic Ovarian Cancer,0.3% Triton-X-100,pH 9.5 for 15 minutes in a pressure cooker (Borg Decloaker BD1000),1 mg/ml LiBH4 15 minutes (3 exchanges for a total of 45 minutes),Yes,0000-0001-9561-4256,NA,0000-0001-9561-4256 P28906,Primary Antibody,CD34,Human,Mouse,IgG1,QBEND/10,Thermo Fisher Scientific,MA1-10205,PE,AB_11152571,Stock,IBEX2D Manual,FFPE,Liver,Metastatic Ovarian Cancer,0.3% Triton-X-100,pH 9.5 for 15 minutes in a pressure cooker (Borg Decloaker BD1000),1 mg/ml LiBH4 15 minutes (3 exchanges for a total of 45 minutes),Yes,0000-0001-9561-4256,NA,0000-0001-9561-4256 -Q9Y5Y7,Primary Antibody,LYVE1,Human,Goat,IgG,Polyclonal,R&D Systems,AF2089 (Unconjugated),iF594,NA,Custom,IBEX2D Manual,FFPE,Liver,Metastatic Ovarian Cancer,0.3% Triton-X-100,pH 9.5 for 15 minutes in a pressure cooker (Borg Decloaker BD1000),1 mg/ml LiBH4 15 minutes (3 exchanges for a total of 45 minutes),Yes,0000-0001-9561-4256,NA,0000-0001-9561-4256 +Q9Y5Y7,Primary Antibody,LYVE-1,Human,Goat,IgG,Polyclonal,R&D Systems,AF2089 (Unconjugated),iF594,NA,Custom,IBEX2D Manual,FFPE,Liver,Metastatic Ovarian Cancer,0.3% Triton-X-100,pH 9.5 for 15 minutes in a pressure cooker (Borg Decloaker BD1000),1 mg/ml LiBH4 15 minutes (3 exchanges for a total of 45 minutes),Yes,0000-0001-9561-4256,NA,0000-0001-9561-4256 P62737,Primary Antibody,Alpha smooth muscle actin,Mouse,Mouse,IgG2a,1A4,Thermo Fisher Scientific,53-9760-82,AF488,AB_2574461,Stock,IBEX2D Manual,FFPE,Liver,Metastatic Ovarian Cancer,0.3% Triton-X-100,pH 9.5 for 15 minutes in a pressure cooker (Borg Decloaker BD1000),1 mg/ml LiBH4 15 minutes (3 exchanges for a total of 45 minutes),Yes,0000-0001-9561-4256,NA,0000-0001-9561-4256 Q9BZS1,Primary Antibody,FOXP3,Human,Mouse,IgG1,236A/E7,Thermo Fisher Scientific,41-4777-82,eF570,AB_2573609,Stock,IBEX2D Manual,FFPE,Liver,Metastatic Ovarian Cancer,0.3% Triton-X-100,pH 9.5 for 15 minutes in a pressure cooker (Borg Decloaker BD1000),1 mg/ml LiBH4 15 minutes (3 exchanges for a total of 45 minutes),Yes,0000-0001-9561-4256,NA,0000-0001-9561-4256 P07766,Primary Antibody,CD3,Human,Rabbit,IgG,SP7,Abcam,ab16669,Unconjugated,AB_443425,Stock,IBEX2D Manual,FFPE,Liver,Metastatic Ovarian Cancer,0.3% Triton-X-100,pH 9.5 for 15 minutes in a pressure cooker (Borg Decloaker BD1000),NA,Yes,0000-0001-9561-4256,NA,0000-0001-9561-4256 @@ -822,7 +822,7 @@ P01730,Primary Antibody,CD4,Human,Goat,IgG,Polyclonal,R&D Systems,FAB8165G,AF488 Q15116,Primary Antibody,PD-1,Human,Goat,IgG,Polyclonal,R&D Systems,AF1086,Unconjugated,AB_354588,Stock,IBEX2D Manual,FFPE,Tonsil,Metastatic Ovarian Cancer,0.3% Triton-X-100,pH 9.5 for 15 minutes in a pressure cooker (Borg Decloaker BD1000),NA,Yes,0000-0001-9561-4256,NA,0000-0001-9561-4256 P01732,Primary Antibody,CD8,Human,Mouse,IgG1,C8/144B,BioLegend,372906,AF647,AB_2650712,Stock,IBEX2D Manual,FFPE,Tonsil,Metastatic Ovarian Cancer,0.3% Triton-X-100,pH 9.5 for 15 minutes in a pressure cooker (Borg Decloaker BD1000),1 mg/ml LiBH4 15 minutes (3 exchanges for a total of 45 minutes),Yes,0000-0001-9561-4256,NA,0000-0001-9561-4256 P28906,Primary Antibody,CD34,Human,Mouse,IgG1,QBEND/10,Thermo Fisher Scientific,MA1-10205,PE,AB_11152571,Stock,IBEX2D Manual,FFPE,Tonsil,Metastatic Ovarian Cancer,0.3% Triton-X-100,pH 9.5 for 15 minutes in a pressure cooker (Borg Decloaker BD1000),1 mg/ml LiBH4 15 minutes (3 exchanges for a total of 45 minutes),Yes,0000-0001-9561-4256,NA,0000-0001-9561-4256 -Q9Y5Y7,Primary Antibody,LYVE1,Human,Goat,IgG,Polyclonal,R&D Systems,AF2089 (Unconjugated),iF594,NA,Custom,IBEX2D Manual,FFPE,Tonsil,Metastatic Ovarian Cancer,0.3% Triton-X-100,pH 9.5 for 15 minutes in a pressure cooker (Borg Decloaker BD1000),1 mg/ml LiBH4 15 minutes (3 exchanges for a total of 45 minutes),Yes,0000-0001-9561-4256,NA,0000-0001-9561-4256 +Q9Y5Y7,Primary Antibody,LYVE-1,Human,Goat,IgG,Polyclonal,R&D Systems,AF2089 (Unconjugated),iF594,NA,Custom,IBEX2D Manual,FFPE,Tonsil,Metastatic Ovarian Cancer,0.3% Triton-X-100,pH 9.5 for 15 minutes in a pressure cooker (Borg Decloaker BD1000),1 mg/ml LiBH4 15 minutes (3 exchanges for a total of 45 minutes),Yes,0000-0001-9561-4256,NA,0000-0001-9561-4256 P62737,Primary Antibody,Alpha smooth muscle actin,Mouse,Mouse,IgG2a,1A4,Thermo Fisher Scientific,53-9760-82,AF488,AB_2574461,Stock,IBEX2D Manual,FFPE,Tonsil,NA,0.3% Triton-X-100,pH 9.5 for 15 minutes in a pressure cooker (Borg Decloaker BD1000),1 mg/ml LiBH4 15 minutes (3 exchanges for a total of 45 minutes),Yes,0000-0001-9561-4256,NA,0000-0001-9561-4256 Q9BZS1,Primary Antibody,FOXP3,Human,Mouse,IgG1,236A/E7,Thermo Fisher Scientific,41-4777-82,eF570,AB_2573609,Stock,IBEX2D Manual,FFPE,Tonsil,Metastatic Ovarian Cancer,0.3% Triton-X-100,pH 9.5 for 15 minutes in a pressure cooker (Borg Decloaker BD1000),1 mg/ml LiBH4 15 minutes (3 exchanges for a total of 45 minutes),Yes,0000-0001-9561-4256,NA,0000-0001-9561-4256 P07766,Primary Antibody,CD3,Human,Rabbit,IgG,SP7,Abcam,ab16669,Unconjugated,AB_443425,Stock,IBEX2D Manual,FFPE,Tonsil,Metastatic Ovarian Cancer,0.3% Triton-X-100,pH 9.5 for 15 minutes in a pressure cooker (Borg Decloaker BD1000),NA,Yes,0000-0001-9561-4256,NA,0000-0001-9561-4256 @@ -879,7 +879,7 @@ Q53X90,Primary Antibody,CXCL13,Human,Goat,IgG,Polyclonal,R&D Systems,AF801 (Unco Q15116,Primary Antibody,PD-1,Human,Mouse,IgG1,EH12.2H7,BioLegend,329906,PE,AB_940483,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,NA,0000-0003-4379-8967 Q07108,Primary Antibody,CD69,Human,Mouse,IgG1,FN50,BioLegend,310918,AF647,AB_528871,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,NA,0000-0003-4379-8967 P55772,Primary Antibody,CD39,Human,Mouse,IgG1,A1,BioLegend,328205,FITC,AB_940423,Stock,IBEX2D Manual,1:4 Cytofix/Cytoperm Fixed Frozen,Lymph Node,Follicular Lymphoma,0.3% Triton-X-100,NA,1 mg/ml LiBH4 30 minutes,Yes,0000-0003-4379-8967,NA,0000-0003-4379-8967 -Q9Y5Y7,Primary Antibody,LYVE1,Human,Goat,IgG,Polyclonal,R&D Systems,AF2089 (Unconjugated),AF532,AB_2892756,Custom,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,NA,0000-0003-4379-8967 +Q9Y5Y7,Primary Antibody,LYVE-1,Human,Goat,IgG,Polyclonal,R&D Systems,AF2089 (Unconjugated),AF532,AB_2892756,Custom,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,NA,0000-0003-4379-8967 P17927,Primary Antibody,CD35,Human,Mouse,IgG1,E11,BioLegend,333406,PE,AB_2292231,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,NA,0000-0003-4379-8967 P34810,Primary Antibody,CD68,Human,Mouse,IgG1,KP1,Santa Cruz Biotechnology,sc-20060 AF647,AF647,AB_3073741,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,NA,0000-0003-4379-8967 P62736,Primary Antibody,Alpha smooth muscle actin,Human,Mouse,IgG2a,1A4,Thermo Fisher Scientific,53-9760-82,AF488,AB_2574461,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,NA,0000-0003-4379-8967 @@ -998,7 +998,7 @@ P15104,Primary Antibody,Glutamine synthetase,Human,Rabbit,IgG,EPR13022(B),Abcam, P15104,Primary Antibody,Glutamine synthetase,Human,Mouse,IgG2a,OTI1F4,Novus Biologicals,NBP2-70834AF488,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 P15104,Primary Antibody,Glutamine synthetase,Human,Mouse,IgG2bc,GLUL/6600,Novus Biologicals,NBP3-14023AF488,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 Q12884,Primary Antibody,Fibroblast activation protein alpha,Human,Rabbit,IgG,Polyclonal,MilliporeSigma,ABT11,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 -Q9Y5Y7,Primary Antibody,LYVE1,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 +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,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 P16284,Primary Antibody,CD31,Human,Mouse,IgG1,C31.3+C31.7+C31.10,Novus Biologicals,NBP2-47785AF700,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,NA,0000-0003-4379-8967 Q9NNX6,Primary Antibody,DC-SIGN,Human,Rat,IgG2a,h209,LSBio,LS-B3782,Unconjugated,AB_10689801,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 @@ -1040,7 +1040,7 @@ F7DAU3,Primary Antibody,CD163,Rhesus Macaque,Mouse,IgG2b,EDHu-1,Novus Biological NA,Primary Antibody,PD-1,Rhesus Macaque,Goat,IgG,Polyclonal,R&D Systems,BAF1086,Biotin,AB_355833,Stock,Multiplexed 2D Imaging,FFPE,Lymph Node,Infected,0.3% Triton-X-100,pH 9.5 for 15 minutes in a pressure cooker (Borg Decloaker BD1000),NA,Yes,0000-0001-9561-4256,NA,0000-0001-9561-4256 NA,Primary Antibody,PD-1,Rhesus Macaque,Goat,IgG,Polyclonal,R&D Systems,FAB7115G,AF488,AB_10973668,Stock,Multiplexed 2D Imaging,FFPE,Lymph Node,Infected,0.3% Triton-X-100,pH 9.5 for 15 minutes in a pressure cooker (Borg Decloaker BD1000),NA,Yes,0000-0001-9561-4256,NA,0000-0001-9561-4256 A0A5F7Z8X0,Primary Antibody,CD31,Rhesus Macaque,Rabbit,IgG,Polyclonal,Abcam,ab28364,Unconjugated,AB_726362,Stock,Multiplexed 2D Imaging,FFPE,Lymph Node,Infected,0.3% Triton-X-100,pH 9.5 for 15 minutes in a pressure cooker (Borg Decloaker BD1000),NA,Yes,0000-0001-9561-4256,NA,0000-0001-9561-4256 -F7AVS7,Primary Antibody,LYVE1,Rhesus Macaque,Goat,IgG,Polyclonal,R&D Systems,AF2089,Unconjugated,AB_355144,Stock,Multiplexed 2D Imaging,FFPE,Lymph Node,Infected,0.3% Triton-X-100,pH 9.5 for 15 minutes in a pressure cooker (Borg Decloaker BD1000),NA,Yes,0000-0001-9561-4256,NA,0000-0001-9561-4256 +F7AVS7,Primary Antibody,LYVE-1,Rhesus Macaque,Goat,IgG,Polyclonal,R&D Systems,AF2089,Unconjugated,AB_355144,Stock,Multiplexed 2D Imaging,FFPE,Lymph Node,Infected,0.3% Triton-X-100,pH 9.5 for 15 minutes in a pressure cooker (Borg Decloaker BD1000),NA,Yes,0000-0001-9561-4256,NA,0000-0001-9561-4256 NA,Primary Antibody,TCR gamma delta,Mouse,Armenian Hamster,IgG,GL3,BioLegend,118108,PE,AB_313832,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,NA,0000-0003-4379-8967 Q99JW5,Primary Antibody,EpCAM,Mouse,Rat,IgG2a,G8.8,BioLegend,118212,AF647,AB_1134101,Stock,IBEX2D Manual,1:4 Cytofix/Cytoperm Fixed Frozen,Lung,NA,0.3% Triton-X-100,NA,1 mg/ml LiBH4 15 minutes,Yes,0000-0003-4379-8967,NA,0000-0003-4379-8967 Q9ERD7,Primary Antibody,Tubulin beta-3 chain,Mouse,Mouse,IgG2a,AA10,BioLegend,657402 (Unconjugated),AF532,NA,Custom,IBEX2D Manual,1:4 Cytofix/Cytoperm Fixed Frozen,Lung,NA,0.3% Triton-X-100,NA,1 mg/ml LiBH4 15 minutes,Yes,0000-0003-4379-8967,NA,0000-0003-4379-8967 diff --git a/docs/supporting_material/LYVE1_AF532/0000-0003-4379-8967.md b/docs/supporting_material/LYVE-1_AF532/0000-0003-4379-8967.md similarity index 66% rename from docs/supporting_material/LYVE1_AF532/0000-0003-4379-8967.md rename to docs/supporting_material/LYVE-1_AF532/0000-0003-4379-8967.md index 96ae4d2..1e0bda1 100644 --- a/docs/supporting_material/LYVE1_AF532/0000-0003-4379-8967.md +++ b/docs/supporting_material/LYVE-1_AF532/0000-0003-4379-8967.md @@ -6,8 +6,8 @@ layout: default | 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 | |:---------------------------|:-----------------|:----------------------------------|:-----------------|:----------------|:----------|:------------|:------------|:----------------------|:------------|:-----------|:---------------|:--------------|:----------------------------------|:----------------|:--------------------|:------------------|:-------------------------------|:------------------------------|:------------|:-------------------------------------------------------------|:-----------|:--------------------|:------------| -| Q9Y5Y7 | Primary Antibody | LYVE1 | Human | Goat | IgG | Polyclonal | R&D Systems | AF2089 (Unconjugated) | AF532 | AB_2892756 | Custom | 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) [[3](#publications), [1](#publications)] | NA | [0000-0003-4379-8967](https://orcid.org/0000-0003-4379-8967) | [1](#notes) | -| Q9Y5Y7 | Primary Antibody | LYVE1 | Human | Goat | IgG | Polyclonal | R&D Systems | AF2089 (Unconjugated) | AF532 | AB_2892756 | Custom | 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) | [1](#notes) | +| Q9Y5Y7 | Primary Antibody | LYVE-1 | Human | Goat | IgG | Polyclonal | R&D Systems | AF2089 (Unconjugated) | AF532 | AB_2892756 | Custom | 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) [[3](#publications), [1](#publications)] | NA | [0000-0003-4379-8967](https://orcid.org/0000-0003-4379-8967) | [1](#notes) | +| Q9Y5Y7 | Primary Antibody | LYVE-1 | Human | Goat | IgG | Polyclonal | R&D Systems | AF2089 (Unconjugated) | AF532 | AB_2892756 | Custom | 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) | [1](#notes) | # Publications diff --git a/docs/supporting_material/LYVE1_AF532/Hoechst_LYVE1_RD_AF2089_Desmin_Abcam_Ab185033.jpg b/docs/supporting_material/LYVE-1_AF532/Hoechst_LYVE1_RD_AF2089_Desmin_Abcam_Ab185033.jpg similarity index 100% rename from docs/supporting_material/LYVE1_AF532/Hoechst_LYVE1_RD_AF2089_Desmin_Abcam_Ab185033.jpg rename to docs/supporting_material/LYVE-1_AF532/Hoechst_LYVE1_RD_AF2089_Desmin_Abcam_Ab185033.jpg diff --git a/docs/supporting_material/LYVE1_Unconjugated/0000-0001-9561-4256.md b/docs/supporting_material/LYVE-1_Unconjugated/0000-0001-9561-4256.md similarity index 73% rename from docs/supporting_material/LYVE1_Unconjugated/0000-0001-9561-4256.md rename to docs/supporting_material/LYVE-1_Unconjugated/0000-0001-9561-4256.md index 9753edc..ea0f2ae 100644 --- a/docs/supporting_material/LYVE1_Unconjugated/0000-0001-9561-4256.md +++ b/docs/supporting_material/LYVE-1_Unconjugated/0000-0001-9561-4256.md @@ -6,7 +6,7 @@ layout: default | 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 | |:---------------------------|:-----------------|:----------------------------------|:-----------------|:----------------|:----------|:------------|:------------|:-----------------|:-------------|:----------|:---------------|:-----------------------|:----------------------|:----------------|:---------------|:------------------|:-------------------------------------------------------------------|:------------------------------|:------------|:----------------------------------------------------------------------------------|:-----------|:-------------------------------------------------------------|:------------| -| F7AVS7 | Primary Antibody | LYVE1 | Rhesus Macaque | Goat | IgG | Polyclonal | R&D Systems | AF2089 | Unconjugated | AB_355144 | Stock | Multiplexed 2D Imaging | FFPE | Lymph Node | Infected | 0.3% Triton-X-100 | pH 9.5 for 15 minutes in a pressure cooker (Borg Decloaker BD1000) | NA | Yes | [0000-0001-9561-4256](https://orcid.org/0000-0001-9561-4256) [[1](#publications)] | NA | [0000-0001-9561-4256](https://orcid.org/0000-0001-9561-4256) | [1](#notes) | +| F7AVS7 | Primary Antibody | LYVE-1 | Rhesus Macaque | Goat | IgG | Polyclonal | R&D Systems | AF2089 | Unconjugated | AB_355144 | Stock | Multiplexed 2D Imaging | FFPE | Lymph Node | Infected | 0.3% Triton-X-100 | pH 9.5 for 15 minutes in a pressure cooker (Borg Decloaker BD1000) | NA | Yes | [0000-0001-9561-4256](https://orcid.org/0000-0001-9561-4256) [[1](#publications)] | NA | [0000-0001-9561-4256](https://orcid.org/0000-0001-9561-4256) | [1](#notes) | # Publications diff --git a/docs/supporting_material/LYVE1_Unconjugated/0000-0003-0666-4804.md b/docs/supporting_material/LYVE-1_Unconjugated/0000-0003-0666-4804.md similarity index 65% rename from docs/supporting_material/LYVE1_Unconjugated/0000-0003-0666-4804.md rename to docs/supporting_material/LYVE-1_Unconjugated/0000-0003-0666-4804.md index d9d712f..c24a9ec 100644 --- a/docs/supporting_material/LYVE1_Unconjugated/0000-0003-0666-4804.md +++ b/docs/supporting_material/LYVE-1_Unconjugated/0000-0003-0666-4804.md @@ -6,7 +6,7 @@ layout: default | 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 | |:---------------------------|:-----------------|:----------------------------------|:-----------------|:----------------|:----------|:------------|:--------------------------|-----------------:|:-------------|:-------|:---------------|:----------|:------------------------|:----------------|:---------------|:-----------------------|:-------------------------------|:------------------------------|:------------|:--------------------|:-----------|:--------------------|:--------| -| Q8BHC0 | Primary Antibody | LYVE1 | Mouse | Rabbit | IgG | E3L3V | Cell Signaling Technology | 67538 | Unconjugated | NA | Stock | Opal-plex | 10% Formalin for 7 Days | Lymph Node | Infected | Akoya Antibody Diluent | Akoya AR6 | NA | Yes | [0000-0003-0666-4804](https://orcid.org/0000-0003-0666-4804) | NA | [0000-0003-0666-4804](https://orcid.org/0000-0003-0666-4804) | | +| Q8BHC0 | Primary Antibody | LYVE-1 | Mouse | Rabbit | IgG | E3L3V | Cell Signaling Technology | 67538 | Unconjugated | NA | Stock | Opal-plex | 10% Formalin for 7 Days | Lymph Node | Infected | Akoya Antibody Diluent | Akoya AR6 | NA | Yes | [0000-0003-0666-4804](https://orcid.org/0000-0003-0666-4804) | NA | [0000-0003-0666-4804](https://orcid.org/0000-0003-0666-4804) | | # Publications diff --git a/docs/supporting_material/LYVE-1_Unconjugated/0000-0003-4379-8967.md b/docs/supporting_material/LYVE-1_Unconjugated/0000-0003-4379-8967.md index 42efa7b..0d2df41 100644 --- a/docs/supporting_material/LYVE-1_Unconjugated/0000-0003-4379-8967.md +++ b/docs/supporting_material/LYVE-1_Unconjugated/0000-0003-4379-8967.md @@ -4,18 +4,30 @@ 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 | -|:---------------------------|:-----------------|:----------------------------------|:-----------------|:----------------|:----------|:------------|:------------|:-----------------|:-------------|:----------|:---------------|:-----------------------|:----------------------|:----------------|:--------------------|:------------------|:-------------------------------------------------------------------------------------------|:------------------------------|:------------|:-------------------------------------------------------------|:-----------|:-------------------------------------------------------------|:------------| -| 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](https://orcid.org/0000-0003-4379-8967) | NA | [0000-0003-4379-8967](https://orcid.org/0000-0003-4379-8967) | [1](#notes) | +| 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 | +|:---------------------------|:-----------------|:----------------------------------|:-----------------|:----------------|:----------|:------------|:------------|:-----------------|:-------------|:----------|:---------------|:-----------------------|:----------------------------------|:----------------|:--------------------|:------------------|:-------------------------------------------------------------------------------------------|:------------------------------|:------------|:-------------------------------------------------------------|:-----------|:--------------------|:------------| +| Q9Y5Y7 | Primary Antibody | LYVE-1 | Human | Goat | IgG | Polyclonal | R&D Systems | AF2089 | Unconjugated | AB_355144 | Stock | IBEX2D Automated | 1:4 Cytofix/Cytoperm Fixed Frozen | Jejunum | NA | 0.3% Triton-X-100 | NA | 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) | | +| Q9Y5Y7 | Primary Antibody | LYVE-1 | Human | Goat | IgG | Polyclonal | R&D Systems | AF2089 | Unconjugated | AB_355144 | Stock | IBEX2D Manual | 1:4 Cytofix/Cytoperm Fixed Frozen | Liver | NA | 0.3% Triton-X-100 | NA | NA | 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) | | +| Q9Y5Y7 | Primary Antibody | LYVE-1 | Human | Goat | IgG | Polyclonal | R&D Systems | AF2089 | Unconjugated | AB_355144 | Stock | IBEX2D Automated | 1:4 Cytofix/Cytoperm Fixed Frozen | Lymph Node | NA | 0.3% Triton-X-100 | NA | 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) | | +| 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](https://orcid.org/0000-0003-4379-8967) | NA | [0000-0003-4379-8967](https://orcid.org/0000-0003-4379-8967) | [1](#notes) | +| 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](https://orcid.org/0000-0003-4379-8967) | NA | [0000-0003-4379-8967](https://orcid.org/0000-0003-4379-8967) | [2](#notes) | # Publications + +1. A. J. Radtke et al., "IBEX: an iterative immunolabeling and chemical bleaching + method for high-content imaging of diverse tissues", *Nat. Protoc.*, 17(2):378-401, 2022, [doi: 10.1038/s41596-021-00644-9](https://doi.org/10.1038/s41596-021-00644-9). + + A. J. Radtke et al., "Accompanying dataset for: IBEX: An iterative immunolabeling and chemical bleaching method for high-content imaging of diverse tissues", [doi: 10.5281/zenodo.5244550](https://doi.org/10.5281/zenodo.5244551). + +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) # Additional Notes -1. Antibody labels lymphatic endothelial cells and vessels in FFPE tissues. Excellent antibody used throughout many studies. Used at a dilution of 1:100 with an anti-goat AF555 secondary antibody (Thermo Fisher Scientific catalog number A-21432). +1. Antibody labels lymphatic endothelial cells and macrophages as expected. +2. Antibody labels lymphatic endothelial cells and vessels in FFPE tissues. Excellent antibody used throughout many studies. Used at a dilution of 1:100 with an anti-goat AF555 secondary antibody (Thermo Fisher Scientific catalog number A-21432). | Human follicular lymphoma FFPE: LYVE-1 (yellow, catalog number AF2089) and Hoechst (blue, catalog number 40046) | |:-------:| diff --git a/docs/supporting_material/LYVE-1_eF570/0000-0003-4379-8967.md b/docs/supporting_material/LYVE-1_eF570/0000-0003-4379-8967.md new file mode 100644 index 0000000..53504ed --- /dev/null +++ b/docs/supporting_material/LYVE-1_eF570/0000-0003-4379-8967.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 | +|:---------------------------|:-----------------|:----------------------------------|:-----------------|:----------------|:----------|:------------|:-------------------------|:-----------------|:------------|:-----------|:---------------|:--------------|:----------------------------------|:----------------|:---------------|:------------------|:-------------------------------|:------------------------------|:------------|:-----------------------------------------|:-----------|:--------------------|:------------| +| Q8BHC0 | Primary Antibody | LYVE-1 | Mouse | Rat | IgG1 | ALY7 | Thermo Fisher Scientific | 41-0443-82 | eF570 | AB_2573596 | Stock | IBEX2D Manual | 1:4 Cytofix/Cytoperm Fixed Frozen | Lung | NA | 0.3% Triton-X-100 | NA | 1 mg/ml LiBH4 15 minutes | Yes | [0000-0003-4379-8967](https://orcid.org/0000-0003-4379-8967) [[1](#publications)] | NA | [0000-0003-4379-8967](https://orcid.org/0000-0003-4379-8967) | [1](#notes) | +| Q8BHC0 | Primary Antibody | LYVE-1 | Mouse | Rat | IgG1 | ALY7 | Thermo Fisher Scientific | 41-0443-82 | eF570 | AB_2573596 | 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) [[1](#publications)] | NA | [0000-0003-4379-8967](https://orcid.org/0000-0003-4379-8967) | [1](#notes) | +| Q8BHC0 | Primary Antibody | LYVE-1 | Mouse | Rat | IgG1 | ALY7 | Thermo Fisher Scientific | 41-0443-82 | eF570 | AB_2573596 | 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) [[1](#publications)] | NA | [0000-0003-4379-8967](https://orcid.org/0000-0003-4379-8967) | | + +# Publications + + +1. 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) + + +# Additional Notes + + +1. Validated by Evelyn Kandov (No ORCID) diff --git a/docs/supporting_material/LYVE1_iF594/0000-0001-9561-4256.md b/docs/supporting_material/LYVE-1_iF594/0000-0001-9561-4256.md similarity index 54% rename from docs/supporting_material/LYVE1_iF594/0000-0001-9561-4256.md rename to docs/supporting_material/LYVE-1_iF594/0000-0001-9561-4256.md index db0734b..ebc1701 100644 --- a/docs/supporting_material/LYVE1_iF594/0000-0001-9561-4256.md +++ b/docs/supporting_material/LYVE-1_iF594/0000-0001-9561-4256.md @@ -6,8 +6,8 @@ layout: default | 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 | |:---------------------------|:-----------------|:----------------------------------|:-----------------|:----------------|:----------|:------------|:------------|:----------------------|:------------|:-------|:---------------|:--------------|:----------------------|:----------------|:--------------------------|:------------------|:-------------------------------------------------------------------|:-----------------------------------------------------------------|:------------|:--------------------|:-----------|:--------------------|:------------| -| Q9Y5Y7 | Primary Antibody | LYVE1 | Human | Goat | IgG | Polyclonal | R&D Systems | AF2089 (Unconjugated) | iF594 | NA | Custom | IBEX2D Manual | FFPE | Liver | Metastatic Ovarian Cancer | 0.3% Triton-X-100 | pH 9.5 for 15 minutes in a pressure cooker (Borg Decloaker BD1000) | 1 mg/ml LiBH4 15 minutes (3 exchanges for a total of 45 minutes) | Yes | [0000-0001-9561-4256](https://orcid.org/0000-0001-9561-4256) | NA | [0000-0001-9561-4256](https://orcid.org/0000-0001-9561-4256) | [1](#notes) | -| Q9Y5Y7 | Primary Antibody | LYVE1 | Human | Goat | IgG | Polyclonal | R&D Systems | AF2089 (Unconjugated) | iF594 | NA | Custom | IBEX2D Manual | FFPE | Tonsil | Metastatic Ovarian Cancer | 0.3% Triton-X-100 | pH 9.5 for 15 minutes in a pressure cooker (Borg Decloaker BD1000) | 1 mg/ml LiBH4 15 minutes (3 exchanges for a total of 45 minutes) | Yes | [0000-0001-9561-4256](https://orcid.org/0000-0001-9561-4256) | NA | [0000-0001-9561-4256](https://orcid.org/0000-0001-9561-4256) | [1](#notes) | +| Q9Y5Y7 | Primary Antibody | LYVE-1 | Human | Goat | IgG | Polyclonal | R&D Systems | AF2089 (Unconjugated) | iF594 | NA | Custom | IBEX2D Manual | FFPE | Liver | Metastatic Ovarian Cancer | 0.3% Triton-X-100 | pH 9.5 for 15 minutes in a pressure cooker (Borg Decloaker BD1000) | 1 mg/ml LiBH4 15 minutes (3 exchanges for a total of 45 minutes) | Yes | [0000-0001-9561-4256](https://orcid.org/0000-0001-9561-4256) | NA | [0000-0001-9561-4256](https://orcid.org/0000-0001-9561-4256) | [1](#notes) | +| Q9Y5Y7 | Primary Antibody | LYVE-1 | Human | Goat | IgG | Polyclonal | R&D Systems | AF2089 (Unconjugated) | iF594 | NA | Custom | IBEX2D Manual | FFPE | Tonsil | Metastatic Ovarian Cancer | 0.3% Triton-X-100 | pH 9.5 for 15 minutes in a pressure cooker (Borg Decloaker BD1000) | 1 mg/ml LiBH4 15 minutes (3 exchanges for a total of 45 minutes) | Yes | [0000-0001-9561-4256](https://orcid.org/0000-0001-9561-4256) | NA | [0000-0001-9561-4256](https://orcid.org/0000-0001-9561-4256) | [1](#notes) | # Publications diff --git a/docs/supporting_material/LYVE1_Unconjugated/0000-0003-4379-8967.md b/docs/supporting_material/LYVE1_Unconjugated/0000-0003-4379-8967.md deleted file mode 100644 index 84e20a6..0000000 --- a/docs/supporting_material/LYVE1_Unconjugated/0000-0003-4379-8967.md +++ /dev/null @@ -1,28 +0,0 @@ ---- -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 | -|:---------------------------|:-----------------|:----------------------------------|:-----------------|:----------------|:----------|:------------|:------------|:-----------------|:-------------|:----------|:---------------|:-----------------------|:----------------------------------|:----------------|:--------------------|:------------------|:-------------------------------------------------------------------------------------------|:------------------------------|:------------|:-------------------------------------------------------------|:-----------|:--------------------|:------------| -| Q9Y5Y7 | Primary Antibody | LYVE1 | Human | Goat | IgG | Polyclonal | R&D Systems | AF2089 | Unconjugated | AB_355144 | Stock | IBEX2D Automated | 1:4 Cytofix/Cytoperm Fixed Frozen | Jejunum | NA | 0.3% Triton-X-100 | NA | 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) | | -| Q9Y5Y7 | Primary Antibody | LYVE1 | Human | Goat | IgG | Polyclonal | R&D Systems | AF2089 | Unconjugated | AB_355144 | Stock | IBEX2D Manual | 1:4 Cytofix/Cytoperm Fixed Frozen | Liver | NA | 0.3% Triton-X-100 | NA | NA | 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) | | -| Q9Y5Y7 | Primary Antibody | LYVE1 | Human | Goat | IgG | Polyclonal | R&D Systems | AF2089 | Unconjugated | AB_355144 | Stock | IBEX2D Automated | 1:4 Cytofix/Cytoperm Fixed Frozen | Lymph Node | NA | 0.3% Triton-X-100 | NA | 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) | | -| Q9Y5Y7 | Primary Antibody | LYVE1 | 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](https://orcid.org/0000-0003-4379-8967) | NA | [0000-0003-4379-8967](https://orcid.org/0000-0003-4379-8967) | [1](#notes) | - -# Publications - - -1. A. J. Radtke et al., "IBEX: an iterative immunolabeling and chemical bleaching - method for high-content imaging of diverse tissues", *Nat. Protoc.*, 17(2):378-401, 2022, [doi: 10.1038/s41596-021-00644-9](https://doi.org/10.1038/s41596-021-00644-9). - - A. J. Radtke et al., "Accompanying dataset for: IBEX: An iterative immunolabeling and chemical bleaching method for high-content imaging of diverse tissues", [doi: 10.5281/zenodo.5244550](https://doi.org/10.5281/zenodo.5244551). - -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) - - -# Additional Notes - - -1. Antibody labels lymphatic endothelial cells and macrophages as expected. diff --git a/docs/supporting_material/LYVE1_eF570/0000-0003-4379-8967.md b/docs/supporting_material/LYVE1_eF570/0000-0003-4379-8967.md deleted file mode 100644 index 2a8951c..0000000 --- a/docs/supporting_material/LYVE1_eF570/0000-0003-4379-8967.md +++ /dev/null @@ -1,22 +0,0 @@ ---- -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 | -|:---------------------------|:-----------------|:----------------------------------|:-----------------|:----------------|:----------|:------------|:-------------------------|:-----------------|:------------|:-----------|:---------------|:--------------|:----------------------------------|:----------------|:---------------|:------------------|:-------------------------------|:------------------------------|:------------|:-----------------------------------------|:-----------|:--------------------|:------------| -| Q8BHC0 | Primary Antibody | LYVE1 | Mouse | Rat | IgG1 | ALY7 | Thermo Fisher Scientific | 41-0443-82 | eF570 | AB_2573596 | Stock | IBEX2D Manual | 1:4 Cytofix/Cytoperm Fixed Frozen | Lung | NA | 0.3% Triton-X-100 | NA | 1 mg/ml LiBH4 15 minutes | Yes | [0000-0003-4379-8967](https://orcid.org/0000-0003-4379-8967) [[1](#publications)] | NA | [0000-0003-4379-8967](https://orcid.org/0000-0003-4379-8967) | [1](#notes) | -| Q8BHC0 | Primary Antibody | LYVE1 | Mouse | Rat | IgG1 | ALY7 | Thermo Fisher Scientific | 41-0443-82 | eF570 | AB_2573596 | 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) [[1](#publications)] | NA | [0000-0003-4379-8967](https://orcid.org/0000-0003-4379-8967) | [1](#notes) | -| Q8BHC0 | Primary Antibody | LYVE1 | Mouse | Rat | IgG1 | ALY7 | Thermo Fisher Scientific | 41-0443-82 | eF570 | AB_2573596 | 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) [[1](#publications)] | NA | [0000-0003-4379-8967](https://orcid.org/0000-0003-4379-8967) | | - -# Publications - - -1. 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) - - -# Additional Notes - - -1. Validated by Evelyn Kandov (No ORCID)