Virus:Article Title: Single-cell multiome and enhancer connectome of human retinal pigment epithelium and choroid nominate causal variants in macular degeneration.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-histone H3 (acetyl K27) antibody Abcam Cat# ab4729; RRID: AB_2118291 Bacterial and virus strains MegaX DH10B T1R electrocompetent cells Thermo Fischer Scientific Cat# C640003 Biological samples Frozen adult postmortem human retinal pigment epithelium and choroid Lions VisionGift, Lions Gift of Sight N/A Chemicals, peptides, and recombinant proteins IGEPAL CA-630 Sigma-Aldrich Cat# I8896 RNase inhibitor New England BioLabs Cat# M0314 Protease inhibitor Roche Cat# 11697498001 Iodixanol Sigma-Aldrich Cat# D1556 Tween 20 Roche Cat# 11332465001 Bovine serum albumin Miltenyi Biotec Cat# 130-091-376 Digitonin Thermo Fischer Scientific Cat# BN2006 Glycerol Ricca Chemical Cat# 3290-16 Paraformaldehyde Electron Microscopy Sciences Cat# 50-980-487 Sodium dodecyl sulfate Invitrogen Cat# 15553027 Triton X-100 Sigma-Aldrich Cat# 93443 MboI New England BioLabs Cat# R0147 Biotin-14-dATP Jena Bioscience Cat# NU-835-BIO14 Klenow fragment New England BioLabs Cat# M0210 T4 DNA ligase New England BioLabs Cat# M0202 Dimethylformamide Sigma-Aldrich Cat# 227056 Sodium deoxycholate Bioworld Cat# 40430018 Normal human serum EMD Millipore Cat# S1-LITER Lipofectamine 3000 Invitrogen Cat# L3000001 Critical commercial assays Single Cell Multiome ATAC + Gene Expression kit 10× Genomics Cat# 1000285 KAPA HiFi HotStart ReadyMix Roche Cat# KK2601 M5 HiPer Universal RNA Mini Kit Mei5bio Cat# MF036-01 SuperScript III First-Strand Synthesis System Invitrogen Cat# 18080051 Dual-Luciferase Reporter 1000 Assay System Promega Cat# E1910 Deposited data scRNA-seq, scATAC-seq, and HiChIP data This paper GEO: GSE262151 STARR-seq data This paper GEO: GSE289703 ChromBPNet models This paper Zenodo: https://doi.org/10.5281/zenodo.14031498 Code for scRNA-seq and scATAC-seq This paper GitHub: https://github.com/seankwang/ RPEchoroid-multiome Experimental models: Cell lines ARPE-19 cells Procell Cat# CL-0026 Oligonucleotides STARR-seq primers (see Table S3) This paper N/A (Continued on next page) 16 Cell Reports 45, 116814, January 27, 2026 .. Postmortem adult human eyes (n = 14) were procured from consented donors (n = 9) by Lions VisionGift (Portland, OR, USA) or Lions Gift of Sight (St. Paul, MN, USA) under protocols approved by the Eye Bank Association of America.
Recombinant:Article Title: Single-cell multiome and enhancer connectome of human retinal pigment epithelium and choroid nominate causal variants in macular degeneration.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-histone H3 (acetyl K27) antibody Abcam Cat# ab4729; RRID: AB_2118291 Bacterial and virus strains MegaX DH10B T1R electrocompetent cells Thermo Fischer Scientific Cat# C640003 Biological samples Frozen adult postmortem human retinal pigment epithelium and choroid Lions VisionGift, Lions Gift of Sight N/A Chemicals, peptides, and recombinant proteins IGEPAL CA-630 Sigma-Aldrich Cat# I8896 RNase inhibitor New England BioLabs Cat# M0314 Protease inhibitor Roche Cat# 11697498001 Iodixanol Sigma-Aldrich Cat# D1556 Tween 20 Roche Cat# 11332465001 Bovine serum albumin Miltenyi Biotec Cat# 130-091-376 Digitonin Thermo Fischer Scientific Cat# BN2006 Glycerol Ricca Chemical Cat# 3290-16 Paraformaldehyde Electron Microscopy Sciences Cat# 50-980-487 Sodium dodecyl sulfate Invitrogen Cat# 15553027 Triton X-100 Sigma-Aldrich Cat# 93443 MboI New England BioLabs Cat# R0147 Biotin-14-dATP Jena Bioscience Cat# NU-835-BIO14 Klenow fragment New England BioLabs Cat# M0210 T4 DNA ligase New England BioLabs Cat# M0202 Dimethylformamide Sigma-Aldrich Cat# 227056 Sodium deoxycholate Bioworld Cat# 40430018 Normal human serum EMD Millipore Cat# S1-LITER Lipofectamine 3000 Invitrogen Cat# L3000001 Critical commercial assays Single Cell Multiome ATAC + Gene Expression kit 10× Genomics Cat# 1000285 KAPA HiFi HotStart ReadyMix Roche Cat# KK2601 M5 HiPer Universal RNA Mini Kit Mei5bio Cat# MF036-01 SuperScript III First-Strand Synthesis System Invitrogen Cat# 18080051 Dual-Luciferase Reporter 1000 Assay System Promega Cat# E1910 Deposited data scRNA-seq, scATAC-seq, and HiChIP data This paper GEO: GSE262151 STARR-seq data This paper GEO: GSE289703 ChromBPNet models This paper Zenodo: https://doi.org/10.5281/zenodo.14031498 Code for scRNA-seq and scATAC-seq This paper GitHub: https://github.com/seankwang/ RPEchoroid-multiome Experimental models: Cell lines ARPE-19 cells Procell Cat# CL-0026 Oligonucleotides STARR-seq primers (see Table S3) This paper N/A (Continued on next page) 16 Cell Reports 45, 116814, January 27, 2026 .. Postmortem adult human eyes (n = 14) were procured from consented donors (n = 9) by Lions VisionGift (Portland, OR, USA) or Lions Gift of Sight (St. Paul, MN, USA) under protocols approved by the Eye Bank Association of America.
Article Title: Single-cell multiome of the human retina and deep learning nominate causal variants in complex eye diseases
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-histone H3 (acetyl K27) antibody Abcam Cat# ab4729; RRID: AB_2118291 Biological samples Frozen adult postmortem human retinas Lions VisionGift, Lions Gift of Sight N/A Chemicals, peptides, and recombinant proteins IGEPAL CA-630 Sigma-Aldrich Cat# I8896 RNase inhibitor New England BioLabs Cat# M0314 Protease inhibitor Roche Cat# 11697498001 Iodixanol Sigma-Aldrich Cat# D1556 Tween-20 Roche Cat# 11332465001 Bovine serum albumin Miltenyi Biotec Cat# 130-091-376 Digitonin Thermo Fischer Scientific Cat# BN2006 Glycerol Ricca Chemical Cat# 3290-16 Paraformaldehyde Electron Microscopy Sciences Cat# 50-980-487 Sodium dodecyl sulfate Invitrogen Cat# 15553027 Triton X-100 Sigma-Aldrich Cat# 93443 MboI New England BioLabs Cat# R0147 Biotin-14-dATP Jena Bioscience Cat# NU-835-BIO14 Klenow fragment New England BioLabs Cat# M0210 T4 DNA ligase New England BioLabs Cat# M0202 Dimethylformamide Sigma-Aldrich Cat# 227056 Sodium deoxycholate Bioworld Cat# 40430018 Critical commercial assays Single Cell Multiome ATAC + Gene Expression kit 10x Genomics Cat# 1000285 Deposited data scRNA-seq, scATAC-seq, and HiChIP data This paper Gene Expression Omnibus: GSE196235 BPNet models This paper Zenodo: https://doi.org/10.5281/zenodo.6330053 Software and algorithms Cell Ranger-ARC 10x Genomics v2.0.0 ArchR Granja et al., 2021 v1.01 Seurat Stuart et al., 2019 v3.1.5 Harmony Korsunsky et al., 2019 v1.0 MACS2 Feng et al., 2012 v2.1.1 BEDTools Quinlan et al., 2010 v2.30.0 LDlinkR Myers et al., 2020 v1.2.0 HiC-Pro Servant et al., 2015 v2.11.0 Juicer Rao et al., 2014 v1.6 Juicebox Durand et al., 2016 v1.11.08 Logomaker Tareen et al., 2020 v0.8 Other Dounce homogenizers Sigma-Aldrich Cat# D8938 SPRIselect beads Beckman Coulter Cat# B23317 Protein A Dynabeads Invitrogen Cat# 10001D Streptavidin Dynabeads Invitrogen Cat# 65001 Cell Genomics 2, 100164, August 10, 2022 e1 Resource ll OPEN ACCESS ..
Protease Inhibitor:Article Title: Single-cell multiome and enhancer connectome of human retinal pigment epithelium and choroid nominate causal variants in macular degeneration.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-histone H3 (acetyl K27) antibody Abcam Cat# ab4729; RRID: AB_2118291 Bacterial and virus strains MegaX DH10B T1R electrocompetent cells Thermo Fischer Scientific Cat# C640003 Biological samples Frozen adult postmortem human retinal pigment epithelium and choroid Lions VisionGift, Lions Gift of Sight N/A Chemicals, peptides, and recombinant proteins IGEPAL CA-630 Sigma-Aldrich Cat# I8896 RNase inhibitor New England BioLabs Cat# M0314 Protease inhibitor Roche Cat# 11697498001 Iodixanol Sigma-Aldrich Cat# D1556 Tween 20 Roche Cat# 11332465001 Bovine serum albumin Miltenyi Biotec Cat# 130-091-376 Digitonin Thermo Fischer Scientific Cat# BN2006 Glycerol Ricca Chemical Cat# 3290-16 Paraformaldehyde Electron Microscopy Sciences Cat# 50-980-487 Sodium dodecyl sulfate Invitrogen Cat# 15553027 Triton X-100 Sigma-Aldrich Cat# 93443 MboI New England BioLabs Cat# R0147 Biotin-14-dATP Jena Bioscience Cat# NU-835-BIO14 Klenow fragment New England BioLabs Cat# M0210 T4 DNA ligase New England BioLabs Cat# M0202 Dimethylformamide Sigma-Aldrich Cat# 227056 Sodium deoxycholate Bioworld Cat# 40430018 Normal human serum EMD Millipore Cat# S1-LITER Lipofectamine 3000 Invitrogen Cat# L3000001 Critical commercial assays Single Cell Multiome ATAC + Gene Expression kit 10× Genomics Cat# 1000285 KAPA HiFi HotStart ReadyMix Roche Cat# KK2601 M5 HiPer Universal RNA Mini Kit Mei5bio Cat# MF036-01 SuperScript III First-Strand Synthesis System Invitrogen Cat# 18080051 Dual-Luciferase Reporter 1000 Assay System Promega Cat# E1910 Deposited data scRNA-seq, scATAC-seq, and HiChIP data This paper GEO: GSE262151 STARR-seq data This paper GEO: GSE289703 ChromBPNet models This paper Zenodo: https://doi.org/10.5281/zenodo.14031498 Code for scRNA-seq and scATAC-seq This paper GitHub: https://github.com/seankwang/ RPEchoroid-multiome Experimental models: Cell lines ARPE-19 cells Procell Cat# CL-0026 Oligonucleotides STARR-seq primers (see Table S3) This paper N/A (Continued on next page) 16 Cell Reports 45, 116814, January 27, 2026 .. Postmortem adult human eyes (n = 14) were procured from consented donors (n = 9) by Lions VisionGift (Portland, OR, USA) or Lions Gift of Sight (St. Paul, MN, USA) under protocols approved by the Eye Bank Association of America.
Article Title: Single-cell multiome of the human retina and deep learning nominate causal variants in complex eye diseases
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-histone H3 (acetyl K27) antibody Abcam Cat# ab4729; RRID: AB_2118291 Biological samples Frozen adult postmortem human retinas Lions VisionGift, Lions Gift of Sight N/A Chemicals, peptides, and recombinant proteins IGEPAL CA-630 Sigma-Aldrich Cat# I8896 RNase inhibitor New England BioLabs Cat# M0314 Protease inhibitor Roche Cat# 11697498001 Iodixanol Sigma-Aldrich Cat# D1556 Tween-20 Roche Cat# 11332465001 Bovine serum albumin Miltenyi Biotec Cat# 130-091-376 Digitonin Thermo Fischer Scientific Cat# BN2006 Glycerol Ricca Chemical Cat# 3290-16 Paraformaldehyde Electron Microscopy Sciences Cat# 50-980-487 Sodium dodecyl sulfate Invitrogen Cat# 15553027 Triton X-100 Sigma-Aldrich Cat# 93443 MboI New England BioLabs Cat# R0147 Biotin-14-dATP Jena Bioscience Cat# NU-835-BIO14 Klenow fragment New England BioLabs Cat# M0210 T4 DNA ligase New England BioLabs Cat# M0202 Dimethylformamide Sigma-Aldrich Cat# 227056 Sodium deoxycholate Bioworld Cat# 40430018 Critical commercial assays Single Cell Multiome ATAC + Gene Expression kit 10x Genomics Cat# 1000285 Deposited data scRNA-seq, scATAC-seq, and HiChIP data This paper Gene Expression Omnibus: GSE196235 BPNet models This paper Zenodo: https://doi.org/10.5281/zenodo.6330053 Software and algorithms Cell Ranger-ARC 10x Genomics v2.0.0 ArchR Granja et al., 2021 v1.01 Seurat Stuart et al., 2019 v3.1.5 Harmony Korsunsky et al., 2019 v1.0 MACS2 Feng et al., 2012 v2.1.1 BEDTools Quinlan et al., 2010 v2.30.0 LDlinkR Myers et al., 2020 v1.2.0 HiC-Pro Servant et al., 2015 v2.11.0 Juicer Rao et al., 2014 v1.6 Juicebox Durand et al., 2016 v1.11.08 Logomaker Tareen et al., 2020 v0.8 Other Dounce homogenizers Sigma-Aldrich Cat# D8938 SPRIselect beads Beckman Coulter Cat# B23317 Protein A Dynabeads Invitrogen Cat# 10001D Streptavidin Dynabeads Invitrogen Cat# 65001 Cell Genomics 2, 100164, August 10, 2022 e1 Resource ll OPEN ACCESS ..
Electron Microscopy:Article Title: Single-cell multiome and enhancer connectome of human retinal pigment epithelium and choroid nominate causal variants in macular degeneration.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-histone H3 (acetyl K27) antibody Abcam Cat# ab4729; RRID: AB_2118291 Bacterial and virus strains MegaX DH10B T1R electrocompetent cells Thermo Fischer Scientific Cat# C640003 Biological samples Frozen adult postmortem human retinal pigment epithelium and choroid Lions VisionGift, Lions Gift of Sight N/A Chemicals, peptides, and recombinant proteins IGEPAL CA-630 Sigma-Aldrich Cat# I8896 RNase inhibitor New England BioLabs Cat# M0314 Protease inhibitor Roche Cat# 11697498001 Iodixanol Sigma-Aldrich Cat# D1556 Tween 20 Roche Cat# 11332465001 Bovine serum albumin Miltenyi Biotec Cat# 130-091-376 Digitonin Thermo Fischer Scientific Cat# BN2006 Glycerol Ricca Chemical Cat# 3290-16 Paraformaldehyde Electron Microscopy Sciences Cat# 50-980-487 Sodium dodecyl sulfate Invitrogen Cat# 15553027 Triton X-100 Sigma-Aldrich Cat# 93443 MboI New England BioLabs Cat# R0147 Biotin-14-dATP Jena Bioscience Cat# NU-835-BIO14 Klenow fragment New England BioLabs Cat# M0210 T4 DNA ligase New England BioLabs Cat# M0202 Dimethylformamide Sigma-Aldrich Cat# 227056 Sodium deoxycholate Bioworld Cat# 40430018 Normal human serum EMD Millipore Cat# S1-LITER Lipofectamine 3000 Invitrogen Cat# L3000001 Critical commercial assays Single Cell Multiome ATAC + Gene Expression kit 10× Genomics Cat# 1000285 KAPA HiFi HotStart ReadyMix Roche Cat# KK2601 M5 HiPer Universal RNA Mini Kit Mei5bio Cat# MF036-01 SuperScript III First-Strand Synthesis System Invitrogen Cat# 18080051 Dual-Luciferase Reporter 1000 Assay System Promega Cat# E1910 Deposited data scRNA-seq, scATAC-seq, and HiChIP data This paper GEO: GSE262151 STARR-seq data This paper GEO: GSE289703 ChromBPNet models This paper Zenodo: https://doi.org/10.5281/zenodo.14031498 Code for scRNA-seq and scATAC-seq This paper GitHub: https://github.com/seankwang/ RPEchoroid-multiome Experimental models: Cell lines ARPE-19 cells Procell Cat# CL-0026 Oligonucleotides STARR-seq primers (see Table S3) This paper N/A (Continued on next page) 16 Cell Reports 45, 116814, January 27, 2026 .. Postmortem adult human eyes (n = 14) were procured from consented donors (n = 9) by Lions VisionGift (Portland, OR, USA) or Lions Gift of Sight (St. Paul, MN, USA) under protocols approved by the Eye Bank Association of America.
Article Title: Single-cell multiome of the human retina and deep learning nominate causal variants in complex eye diseases
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-histone H3 (acetyl K27) antibody Abcam Cat# ab4729; RRID: AB_2118291 Biological samples Frozen adult postmortem human retinas Lions VisionGift, Lions Gift of Sight N/A Chemicals, peptides, and recombinant proteins IGEPAL CA-630 Sigma-Aldrich Cat# I8896 RNase inhibitor New England BioLabs Cat# M0314 Protease inhibitor Roche Cat# 11697498001 Iodixanol Sigma-Aldrich Cat# D1556 Tween-20 Roche Cat# 11332465001 Bovine serum albumin Miltenyi Biotec Cat# 130-091-376 Digitonin Thermo Fischer Scientific Cat# BN2006 Glycerol Ricca Chemical Cat# 3290-16 Paraformaldehyde Electron Microscopy Sciences Cat# 50-980-487 Sodium dodecyl sulfate Invitrogen Cat# 15553027 Triton X-100 Sigma-Aldrich Cat# 93443 MboI New England BioLabs Cat# R0147 Biotin-14-dATP Jena Bioscience Cat# NU-835-BIO14 Klenow fragment New England BioLabs Cat# M0210 T4 DNA ligase New England BioLabs Cat# M0202 Dimethylformamide Sigma-Aldrich Cat# 227056 Sodium deoxycholate Bioworld Cat# 40430018 Critical commercial assays Single Cell Multiome ATAC + Gene Expression kit 10x Genomics Cat# 1000285 Deposited data scRNA-seq, scATAC-seq, and HiChIP data This paper Gene Expression Omnibus: GSE196235 BPNet models This paper Zenodo: https://doi.org/10.5281/zenodo.6330053 Software and algorithms Cell Ranger-ARC 10x Genomics v2.0.0 ArchR Granja et al., 2021 v1.01 Seurat Stuart et al., 2019 v3.1.5 Harmony Korsunsky et al., 2019 v1.0 MACS2 Feng et al., 2012 v2.1.1 BEDTools Quinlan et al., 2010 v2.30.0 LDlinkR Myers et al., 2020 v1.2.0 HiC-Pro Servant et al., 2015 v2.11.0 Juicer Rao et al., 2014 v1.6 Juicebox Durand et al., 2016 v1.11.08 Logomaker Tareen et al., 2020 v0.8 Other Dounce homogenizers Sigma-Aldrich Cat# D8938 SPRIselect beads Beckman Coulter Cat# B23317 Protein A Dynabeads Invitrogen Cat# 10001D Streptavidin Dynabeads Invitrogen Cat# 65001 Cell Genomics 2, 100164, August 10, 2022 e1 Resource ll OPEN ACCESS ..
Single Cell:Article Title: Single-cell multiome and enhancer connectome of human retinal pigment epithelium and choroid nominate causal variants in macular degeneration.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-histone H3 (acetyl K27) antibody Abcam Cat# ab4729; RRID: AB_2118291 Bacterial and virus strains MegaX DH10B T1R electrocompetent cells Thermo Fischer Scientific Cat# C640003 Biological samples Frozen adult postmortem human retinal pigment epithelium and choroid Lions VisionGift, Lions Gift of Sight N/A Chemicals, peptides, and recombinant proteins IGEPAL CA-630 Sigma-Aldrich Cat# I8896 RNase inhibitor New England BioLabs Cat# M0314 Protease inhibitor Roche Cat# 11697498001 Iodixanol Sigma-Aldrich Cat# D1556 Tween 20 Roche Cat# 11332465001 Bovine serum albumin Miltenyi Biotec Cat# 130-091-376 Digitonin Thermo Fischer Scientific Cat# BN2006 Glycerol Ricca Chemical Cat# 3290-16 Paraformaldehyde Electron Microscopy Sciences Cat# 50-980-487 Sodium dodecyl sulfate Invitrogen Cat# 15553027 Triton X-100 Sigma-Aldrich Cat# 93443 MboI New England BioLabs Cat# R0147 Biotin-14-dATP Jena Bioscience Cat# NU-835-BIO14 Klenow fragment New England BioLabs Cat# M0210 T4 DNA ligase New England BioLabs Cat# M0202 Dimethylformamide Sigma-Aldrich Cat# 227056 Sodium deoxycholate Bioworld Cat# 40430018 Normal human serum EMD Millipore Cat# S1-LITER Lipofectamine 3000 Invitrogen Cat# L3000001 Critical commercial assays Single Cell Multiome ATAC + Gene Expression kit 10× Genomics Cat# 1000285 KAPA HiFi HotStart ReadyMix Roche Cat# KK2601 M5 HiPer Universal RNA Mini Kit Mei5bio Cat# MF036-01 SuperScript III First-Strand Synthesis System Invitrogen Cat# 18080051 Dual-Luciferase Reporter 1000 Assay System Promega Cat# E1910 Deposited data scRNA-seq, scATAC-seq, and HiChIP data This paper GEO: GSE262151 STARR-seq data This paper GEO: GSE289703 ChromBPNet models This paper Zenodo: https://doi.org/10.5281/zenodo.14031498 Code for scRNA-seq and scATAC-seq This paper GitHub: https://github.com/seankwang/ RPEchoroid-multiome Experimental models: Cell lines ARPE-19 cells Procell Cat# CL-0026 Oligonucleotides STARR-seq primers (see Table S3) This paper N/A (Continued on next page) 16 Cell Reports 45, 116814, January 27, 2026 .. Postmortem adult human eyes (n = 14) were procured from consented donors (n = 9) by Lions VisionGift (Portland, OR, USA) or Lions Gift of Sight (St. Paul, MN, USA) under protocols approved by the Eye Bank Association of America.
Article Title: Single-cell multiome of the human retina and deep learning nominate causal variants in complex eye diseases
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-histone H3 (acetyl K27) antibody Abcam Cat# ab4729; RRID: AB_2118291 Biological samples Frozen adult postmortem human retinas Lions VisionGift, Lions Gift of Sight N/A Chemicals, peptides, and recombinant proteins IGEPAL CA-630 Sigma-Aldrich Cat# I8896 RNase inhibitor New England BioLabs Cat# M0314 Protease inhibitor Roche Cat# 11697498001 Iodixanol Sigma-Aldrich Cat# D1556 Tween-20 Roche Cat# 11332465001 Bovine serum albumin Miltenyi Biotec Cat# 130-091-376 Digitonin Thermo Fischer Scientific Cat# BN2006 Glycerol Ricca Chemical Cat# 3290-16 Paraformaldehyde Electron Microscopy Sciences Cat# 50-980-487 Sodium dodecyl sulfate Invitrogen Cat# 15553027 Triton X-100 Sigma-Aldrich Cat# 93443 MboI New England BioLabs Cat# R0147 Biotin-14-dATP Jena Bioscience Cat# NU-835-BIO14 Klenow fragment New England BioLabs Cat# M0210 T4 DNA ligase New England BioLabs Cat# M0202 Dimethylformamide Sigma-Aldrich Cat# 227056 Sodium deoxycholate Bioworld Cat# 40430018 Critical commercial assays Single Cell Multiome ATAC + Gene Expression kit 10x Genomics Cat# 1000285 Deposited data scRNA-seq, scATAC-seq, and HiChIP data This paper Gene Expression Omnibus: GSE196235 BPNet models This paper Zenodo: https://doi.org/10.5281/zenodo.6330053 Software and algorithms Cell Ranger-ARC 10x Genomics v2.0.0 ArchR Granja et al., 2021 v1.01 Seurat Stuart et al., 2019 v3.1.5 Harmony Korsunsky et al., 2019 v1.0 MACS2 Feng et al., 2012 v2.1.1 BEDTools Quinlan et al., 2010 v2.30.0 LDlinkR Myers et al., 2020 v1.2.0 HiC-Pro Servant et al., 2015 v2.11.0 Juicer Rao et al., 2014 v1.6 Juicebox Durand et al., 2016 v1.11.08 Logomaker Tareen et al., 2020 v0.8 Other Dounce homogenizers Sigma-Aldrich Cat# D8938 SPRIselect beads Beckman Coulter Cat# B23317 Protein A Dynabeads Invitrogen Cat# 10001D Streptavidin Dynabeads Invitrogen Cat# 65001 Cell Genomics 2, 100164, August 10, 2022 e1 Resource ll OPEN ACCESS ..
Gene Expression:Article Title: Single-cell multiome and enhancer connectome of human retinal pigment epithelium and choroid nominate causal variants in macular degeneration.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-histone H3 (acetyl K27) antibody Abcam Cat# ab4729; RRID: AB_2118291 Bacterial and virus strains MegaX DH10B T1R electrocompetent cells Thermo Fischer Scientific Cat# C640003 Biological samples Frozen adult postmortem human retinal pigment epithelium and choroid Lions VisionGift, Lions Gift of Sight N/A Chemicals, peptides, and recombinant proteins IGEPAL CA-630 Sigma-Aldrich Cat# I8896 RNase inhibitor New England BioLabs Cat# M0314 Protease inhibitor Roche Cat# 11697498001 Iodixanol Sigma-Aldrich Cat# D1556 Tween 20 Roche Cat# 11332465001 Bovine serum albumin Miltenyi Biotec Cat# 130-091-376 Digitonin Thermo Fischer Scientific Cat# BN2006 Glycerol Ricca Chemical Cat# 3290-16 Paraformaldehyde Electron Microscopy Sciences Cat# 50-980-487 Sodium dodecyl sulfate Invitrogen Cat# 15553027 Triton X-100 Sigma-Aldrich Cat# 93443 MboI New England BioLabs Cat# R0147 Biotin-14-dATP Jena Bioscience Cat# NU-835-BIO14 Klenow fragment New England BioLabs Cat# M0210 T4 DNA ligase New England BioLabs Cat# M0202 Dimethylformamide Sigma-Aldrich Cat# 227056 Sodium deoxycholate Bioworld Cat# 40430018 Normal human serum EMD Millipore Cat# S1-LITER Lipofectamine 3000 Invitrogen Cat# L3000001 Critical commercial assays Single Cell Multiome ATAC + Gene Expression kit 10× Genomics Cat# 1000285 KAPA HiFi HotStart ReadyMix Roche Cat# KK2601 M5 HiPer Universal RNA Mini Kit Mei5bio Cat# MF036-01 SuperScript III First-Strand Synthesis System Invitrogen Cat# 18080051 Dual-Luciferase Reporter 1000 Assay System Promega Cat# E1910 Deposited data scRNA-seq, scATAC-seq, and HiChIP data This paper GEO: GSE262151 STARR-seq data This paper GEO: GSE289703 ChromBPNet models This paper Zenodo: https://doi.org/10.5281/zenodo.14031498 Code for scRNA-seq and scATAC-seq This paper GitHub: https://github.com/seankwang/ RPEchoroid-multiome Experimental models: Cell lines ARPE-19 cells Procell Cat# CL-0026 Oligonucleotides STARR-seq primers (see Table S3) This paper N/A (Continued on next page) 16 Cell Reports 45, 116814, January 27, 2026 .. Postmortem adult human eyes (n = 14) were procured from consented donors (n = 9) by Lions VisionGift (Portland, OR, USA) or Lions Gift of Sight (St. Paul, MN, USA) under protocols approved by the Eye Bank Association of America.
Article Title: Single-cell multiome of the human retina and deep learning nominate causal variants in complex eye diseases
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-histone H3 (acetyl K27) antibody Abcam Cat# ab4729; RRID: AB_2118291 Biological samples Frozen adult postmortem human retinas Lions VisionGift, Lions Gift of Sight N/A Chemicals, peptides, and recombinant proteins IGEPAL CA-630 Sigma-Aldrich Cat# I8896 RNase inhibitor New England BioLabs Cat# M0314 Protease inhibitor Roche Cat# 11697498001 Iodixanol Sigma-Aldrich Cat# D1556 Tween-20 Roche Cat# 11332465001 Bovine serum albumin Miltenyi Biotec Cat# 130-091-376 Digitonin Thermo Fischer Scientific Cat# BN2006 Glycerol Ricca Chemical Cat# 3290-16 Paraformaldehyde Electron Microscopy Sciences Cat# 50-980-487 Sodium dodecyl sulfate Invitrogen Cat# 15553027 Triton X-100 Sigma-Aldrich Cat# 93443 MboI New England BioLabs Cat# R0147 Biotin-14-dATP Jena Bioscience Cat# NU-835-BIO14 Klenow fragment New England BioLabs Cat# M0210 T4 DNA ligase New England BioLabs Cat# M0202 Dimethylformamide Sigma-Aldrich Cat# 227056 Sodium deoxycholate Bioworld Cat# 40430018 Critical commercial assays Single Cell Multiome ATAC + Gene Expression kit 10x Genomics Cat# 1000285 Deposited data scRNA-seq, scATAC-seq, and HiChIP data This paper Gene Expression Omnibus: GSE196235 BPNet models This paper Zenodo: https://doi.org/10.5281/zenodo.6330053 Software and algorithms Cell Ranger-ARC 10x Genomics v2.0.0 ArchR Granja et al., 2021 v1.01 Seurat Stuart et al., 2019 v3.1.5 Harmony Korsunsky et al., 2019 v1.0 MACS2 Feng et al., 2012 v2.1.1 BEDTools Quinlan et al., 2010 v2.30.0 LDlinkR Myers et al., 2020 v1.2.0 HiC-Pro Servant et al., 2015 v2.11.0 Juicer Rao et al., 2014 v1.6 Juicebox Durand et al., 2016 v1.11.08 Logomaker Tareen et al., 2020 v0.8 Other Dounce homogenizers Sigma-Aldrich Cat# D8938 SPRIselect beads Beckman Coulter Cat# B23317 Protein A Dynabeads Invitrogen Cat# 10001D Streptavidin Dynabeads Invitrogen Cat# 65001 Cell Genomics 2, 100164, August 10, 2022 e1 Resource ll OPEN ACCESS ..
HiChIP:Article Title: Single-cell multiome and enhancer connectome of human retinal pigment epithelium and choroid nominate causal variants in macular degeneration.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-histone H3 (acetyl K27) antibody Abcam Cat# ab4729; RRID: AB_2118291 Bacterial and virus strains MegaX DH10B T1R electrocompetent cells Thermo Fischer Scientific Cat# C640003 Biological samples Frozen adult postmortem human retinal pigment epithelium and choroid Lions VisionGift, Lions Gift of Sight N/A Chemicals, peptides, and recombinant proteins IGEPAL CA-630 Sigma-Aldrich Cat# I8896 RNase inhibitor New England BioLabs Cat# M0314 Protease inhibitor Roche Cat# 11697498001 Iodixanol Sigma-Aldrich Cat# D1556 Tween 20 Roche Cat# 11332465001 Bovine serum albumin Miltenyi Biotec Cat# 130-091-376 Digitonin Thermo Fischer Scientific Cat# BN2006 Glycerol Ricca Chemical Cat# 3290-16 Paraformaldehyde Electron Microscopy Sciences Cat# 50-980-487 Sodium dodecyl sulfate Invitrogen Cat# 15553027 Triton X-100 Sigma-Aldrich Cat# 93443 MboI New England BioLabs Cat# R0147 Biotin-14-dATP Jena Bioscience Cat# NU-835-BIO14 Klenow fragment New England BioLabs Cat# M0210 T4 DNA ligase New England BioLabs Cat# M0202 Dimethylformamide Sigma-Aldrich Cat# 227056 Sodium deoxycholate Bioworld Cat# 40430018 Normal human serum EMD Millipore Cat# S1-LITER Lipofectamine 3000 Invitrogen Cat# L3000001 Critical commercial assays Single Cell Multiome ATAC + Gene Expression kit 10× Genomics Cat# 1000285 KAPA HiFi HotStart ReadyMix Roche Cat# KK2601 M5 HiPer Universal RNA Mini Kit Mei5bio Cat# MF036-01 SuperScript III First-Strand Synthesis System Invitrogen Cat# 18080051 Dual-Luciferase Reporter 1000 Assay System Promega Cat# E1910 Deposited data scRNA-seq, scATAC-seq, and HiChIP data This paper GEO: GSE262151 STARR-seq data This paper GEO: GSE289703 ChromBPNet models This paper Zenodo: https://doi.org/10.5281/zenodo.14031498 Code for scRNA-seq and scATAC-seq This paper GitHub: https://github.com/seankwang/ RPEchoroid-multiome Experimental models: Cell lines ARPE-19 cells Procell Cat# CL-0026 Oligonucleotides STARR-seq primers (see Table S3) This paper N/A (Continued on next page) 16 Cell Reports 45, 116814, January 27, 2026 .. Postmortem adult human eyes (n = 14) were procured from consented donors (n = 9) by Lions VisionGift (Portland, OR, USA) or Lions Gift of Sight (St. Paul, MN, USA) under protocols approved by the Eye Bank Association of America.
Article Title: Single-cell multiome of the human retina and deep learning nominate causal variants in complex eye diseases
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-histone H3 (acetyl K27) antibody Abcam Cat# ab4729; RRID: AB_2118291 Biological samples Frozen adult postmortem human retinas Lions VisionGift, Lions Gift of Sight N/A Chemicals, peptides, and recombinant proteins IGEPAL CA-630 Sigma-Aldrich Cat# I8896 RNase inhibitor New England BioLabs Cat# M0314 Protease inhibitor Roche Cat# 11697498001 Iodixanol Sigma-Aldrich Cat# D1556 Tween-20 Roche Cat# 11332465001 Bovine serum albumin Miltenyi Biotec Cat# 130-091-376 Digitonin Thermo Fischer Scientific Cat# BN2006 Glycerol Ricca Chemical Cat# 3290-16 Paraformaldehyde Electron Microscopy Sciences Cat# 50-980-487 Sodium dodecyl sulfate Invitrogen Cat# 15553027 Triton X-100 Sigma-Aldrich Cat# 93443 MboI New England BioLabs Cat# R0147 Biotin-14-dATP Jena Bioscience Cat# NU-835-BIO14 Klenow fragment New England BioLabs Cat# M0210 T4 DNA ligase New England BioLabs Cat# M0202 Dimethylformamide Sigma-Aldrich Cat# 227056 Sodium deoxycholate Bioworld Cat# 40430018 Critical commercial assays Single Cell Multiome ATAC + Gene Expression kit 10x Genomics Cat# 1000285 Deposited data scRNA-seq, scATAC-seq, and HiChIP data This paper Gene Expression Omnibus: GSE196235 BPNet models This paper Zenodo: https://doi.org/10.5281/zenodo.6330053 Software and algorithms Cell Ranger-ARC 10x Genomics v2.0.0 ArchR Granja et al., 2021 v1.01 Seurat Stuart et al., 2019 v3.1.5 Harmony Korsunsky et al., 2019 v1.0 MACS2 Feng et al., 2012 v2.1.1 BEDTools Quinlan et al., 2010 v2.30.0 LDlinkR Myers et al., 2020 v1.2.0 HiC-Pro Servant et al., 2015 v2.11.0 Juicer Rao et al., 2014 v1.6 Juicebox Durand et al., 2016 v1.11.08 Logomaker Tareen et al., 2020 v0.8 Other Dounce homogenizers Sigma-Aldrich Cat# D8938 SPRIselect beads Beckman Coulter Cat# B23317 Protein A Dynabeads Invitrogen Cat# 10001D Streptavidin Dynabeads Invitrogen Cat# 65001 Cell Genomics 2, 100164, August 10, 2022 e1 Resource ll OPEN ACCESS ..
Software:Article Title: Single-cell multiome of the human retina and deep learning nominate causal variants in complex eye diseases
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-histone H3 (acetyl K27) antibody Abcam Cat# ab4729; RRID: AB_2118291 Biological samples Frozen adult postmortem human retinas Lions VisionGift, Lions Gift of Sight N/A Chemicals, peptides, and recombinant proteins IGEPAL CA-630 Sigma-Aldrich Cat# I8896 RNase inhibitor New England BioLabs Cat# M0314 Protease inhibitor Roche Cat# 11697498001 Iodixanol Sigma-Aldrich Cat# D1556 Tween-20 Roche Cat# 11332465001 Bovine serum albumin Miltenyi Biotec Cat# 130-091-376 Digitonin Thermo Fischer Scientific Cat# BN2006 Glycerol Ricca Chemical Cat# 3290-16 Paraformaldehyde Electron Microscopy Sciences Cat# 50-980-487 Sodium dodecyl sulfate Invitrogen Cat# 15553027 Triton X-100 Sigma-Aldrich Cat# 93443 MboI New England BioLabs Cat# R0147 Biotin-14-dATP Jena Bioscience Cat# NU-835-BIO14 Klenow fragment New England BioLabs Cat# M0210 T4 DNA ligase New England BioLabs Cat# M0202 Dimethylformamide Sigma-Aldrich Cat# 227056 Sodium deoxycholate Bioworld Cat# 40430018 Critical commercial assays Single Cell Multiome ATAC + Gene Expression kit 10x Genomics Cat# 1000285 Deposited data scRNA-seq, scATAC-seq, and HiChIP data This paper Gene Expression Omnibus: GSE196235 BPNet models This paper Zenodo: https://doi.org/10.5281/zenodo.6330053 Software and algorithms Cell Ranger-ARC 10x Genomics v2.0.0 ArchR Granja et al., 2021 v1.01 Seurat Stuart et al., 2019 v3.1.5 Harmony Korsunsky et al., 2019 v1.0 MACS2 Feng et al., 2012 v2.1.1 BEDTools Quinlan et al., 2010 v2.30.0 LDlinkR Myers et al., 2020 v1.2.0 HiC-Pro Servant et al., 2015 v2.11.0 Juicer Rao et al., 2014 v1.6 Juicebox Durand et al., 2016 v1.11.08 Logomaker Tareen et al., 2020 v0.8 Other Dounce homogenizers Sigma-Aldrich Cat# D8938 SPRIselect beads Beckman Coulter Cat# B23317 Protein A Dynabeads Invitrogen Cat# 10001D Streptavidin Dynabeads Invitrogen Cat# 65001 Cell Genomics 2, 100164, August 10, 2022 e1 Resource ll OPEN ACCESS ..
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