Purification:Article Title: CDK4/6 inhibition reprograms the breast cancer immunopeptidome via Rb-dependent chromatin and transcriptomic remodeling.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-Human HLA-ABC (Clone W6/32, mouse IgG2a) Cedarlane Cat#CLHLA-01AP Purified Mouse IgG2a κ Isotype Control BD Pharmingen RRID:AB_479656 Phospho-Rb (Ser795) Rabbit Antibody Cell Signaling RRID:AB_479656 Phospho-Rb (Ser780) Rabbit Antibody Cell Signaling RRID:AB_330015 Rb (4H1) Mouse mAb Cell Signaling RRID:AB_823629 BRD4 Rabbit mAb Cell Signaling RRID:AB_268757 BRD2 Rabbit Antibody [BL-167-2A2] Abcam RRID:AB_3694209 BRD3 Rabbit mAb Cell Signaling Cat#94032 Anti-rabbit IgG, HRP-linked Antibody Cell Signaling RRID:AB_2099233 Anti-Mouse IgG, HRP-linked Antibody Cell Signaling RRID:AB_330924 Anti-Human HLA-ABC W6/32 antibody for IP BioXcell Cat#BE0079 HA-Tag (C29F4) Rabbit mAb Cell Signaling RRID:AB_1549585 Biological samples Healthy human peripheral blood BioIVT https://bioivt.com Chemicals, peptides, and recombinant proteins 4–12% Criterion TM XT Bis-Tris Protein Gel Bio-Rad Cat#3450124 and Cat#3450123 7-AAD BD Pharmingen Cat#559925 96 well plates U Sarstedt Cat#83.3925 Abemaciclib Toronto Research Chemicals Inc. Cat#A115153 Alpha Modification of Eagle’s Medium (AMEM) Wisent Cat#310-010-CL Amersham TM ECL Select TM Western Blotting Detection Reagent Cytiva Cat#RPN2235 Benzonase® Nuclease Sigma Cat#E1014-25KU Bio-Rad Protein Assay Dye Reagent Concentrate Bio-Rad Cat#5000006 BioTrace TM NT Nitrocellulose Transfer Membrane Cytiva Cat#66485 CNBR-activated Sepharose 4B beads Fisher Cat#45000066 dBET57 Cayman Chemical Cat#36626 Dulbecco’s Modified Eagle Medium (DMEM) Wisent Cat#319-005-CL Eagle’s Minimum Essential Medium (EMEM) ATCC Cat#30-2003 ELISpot Pro: Human IFN-γ (ALP) Mabtech Cat#3420-4APW-10 Fetal bovine serum (FBS) Wisent Cat#090150 Flt-3 Ligand Peprotech Cat#AF-300-19 Gentamicin (10 mg/mL) Thermofisher Scientific Cat#15710072 GlutaMAX TM Supplement Thermofisher Scientific Cat#35050061 GM-CSF Thermofisher Scientific Cat#300-03 HEPES (1M) Thermofisher Scientific Cat#15630080 Human CD45RO Microbeads Miltenyi Biotec Cat#130-046-001 Human CD57 Microbeads Miltenyi Biotec Cat#130-092-073 (Continued on next page) Cell Reports 44, 116676, December 23, 2025 19 .. REAGENT or RESOURCE SOURCE IDENTIFIER Fetal bovine serum (FBS) Wisent Cat#090150 Human recombinant insulin-zinc solution Gibco Cat#12585-014 Human serum Sigma Cat#H4522 Hybri-Care Medium ATCC Cat#46-X IL-15 Peprotech Cat#200-15 IL-1β Thermofisher Scientific Cat#F-200-01B IL-21 Thermofisher Scientific Cat#200-21 IL-21S Miltenyi Biotec Cat#130-097-745 IL-4 Peprotech Cat#200-04-250UG IL-7 Peprotech Cat#200-07 JQ1 Active Motif Cat#14141 LPS Sigma Cat#L4524-5MG LS columns Miltenyi Biotec Cat#130-042-401 McCoy’s 5A Medium ATCC Cat#30-2007 Minimum Essential Medium alpha Fisher Cat#12561056 PBS, 1X, w/o Calcium & Magnesium Wisent Cat#311-010 CL Phosphatase Inhibitor Cocktail 3 Sigma Cat#P0044 Pierce TM Anti-HA Magnetic Beads Thermofisher Scientific Cat# 88836 Pre-separation Filters 30μm Miltenyi Biotec Cat#130-041-407 Protease Inhibitor Cocktail Sigma Cat#P8340 R848 Invivogen Cat#tlrl-r848-10 RPMI 1640 Medium Thermofisher Scientific Cat#A1049101 RPMI 1640 Medium Thermofisher Scientific Cat#11875119 T cell TransAct Miltenyi Biotec Cat#130-111-160 TRIzol reagent Thermofisher Scientific Cat#15596018 TrypLE TM Express Enzyme (1X), no phenol red Gibco Cat#12604013 X-VIVO 15 media Lonza Cat#04-418Q Critical commercial assays Human CD8 + T cell Isolation Kit Miltenyi Biotec Cat#130-096-495 KAPA HyperPrep RNAseq stranded kit KAPA Cat#KK8421 Maxima First Strand cDNA Synthesis Kit for RT-qPCR Thermo Scientific Cat#K1671 Mycoplasma PCR Detection Kit Applied Biological Materials Cat#G238 Propidium Iodide Flow Cytometry Kit Abcam Cat#ab139418 QIFIKIT (Quantitative Analysis Kit) Agilent Dako Cat# K0078 RNeasy purification kit Qiagen Cat#74104 Deposited data ATAC-seq data from wildtype and shRB1 MCF7, wildtype MDAMB361, and wildtype MDAMB468 treated with DMSO or Abemaciclib Watt et al. 59 GEO:GSE157082 ChIP-seq and Cut&Run data from MDAMB231 left untreated or treated with JQ1 Wu et al. 93 GEO:GSE136151 FLAG-Rb, and E2F1 ChIP-seq from RPE1 cells Sanidas et al. 60 GEO:GSE176035 GeneHancer database (v5.22) Fishilevich et al. 94 https://www.genecards.org/ Guide/Datasets H3K27ac ChIP-seq data from wildtype MCF7 treated with DMSO, Abemaciclib, and/or Fulvestrant Watt et al. 59 GEO:GSE157222 (Continued on next page) 20 Cell Reports 44, 116676, December 23, 2025
Control:Article Title: CDK4/6 inhibition reprograms the breast cancer immunopeptidome via Rb-dependent chromatin and transcriptomic remodeling.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-Human HLA-ABC (Clone W6/32, mouse IgG2a) Cedarlane Cat#CLHLA-01AP Purified Mouse IgG2a κ Isotype Control BD Pharmingen RRID:AB_479656 Phospho-Rb (Ser795) Rabbit Antibody Cell Signaling RRID:AB_479656 Phospho-Rb (Ser780) Rabbit Antibody Cell Signaling RRID:AB_330015 Rb (4H1) Mouse mAb Cell Signaling RRID:AB_823629 BRD4 Rabbit mAb Cell Signaling RRID:AB_268757 BRD2 Rabbit Antibody [BL-167-2A2] Abcam RRID:AB_3694209 BRD3 Rabbit mAb Cell Signaling Cat#94032 Anti-rabbit IgG, HRP-linked Antibody Cell Signaling RRID:AB_2099233 Anti-Mouse IgG, HRP-linked Antibody Cell Signaling RRID:AB_330924 Anti-Human HLA-ABC W6/32 antibody for IP BioXcell Cat#BE0079 HA-Tag (C29F4) Rabbit mAb Cell Signaling RRID:AB_1549585 Biological samples Healthy human peripheral blood BioIVT https://bioivt.com Chemicals, peptides, and recombinant proteins 4–12% Criterion TM XT Bis-Tris Protein Gel Bio-Rad Cat#3450124 and Cat#3450123 7-AAD BD Pharmingen Cat#559925 96 well plates U Sarstedt Cat#83.3925 Abemaciclib Toronto Research Chemicals Inc. Cat#A115153 Alpha Modification of Eagle’s Medium (AMEM) Wisent Cat#310-010-CL Amersham TM ECL Select TM Western Blotting Detection Reagent Cytiva Cat#RPN2235 Benzonase® Nuclease Sigma Cat#E1014-25KU Bio-Rad Protein Assay Dye Reagent Concentrate Bio-Rad Cat#5000006 BioTrace TM NT Nitrocellulose Transfer Membrane Cytiva Cat#66485 CNBR-activated Sepharose 4B beads Fisher Cat#45000066 dBET57 Cayman Chemical Cat#36626 Dulbecco’s Modified Eagle Medium (DMEM) Wisent Cat#319-005-CL Eagle’s Minimum Essential Medium (EMEM) ATCC Cat#30-2003 ELISpot Pro: Human IFN-γ (ALP) Mabtech Cat#3420-4APW-10 Fetal bovine serum (FBS) Wisent Cat#090150 Flt-3 Ligand Peprotech Cat#AF-300-19 Gentamicin (10 mg/mL) Thermofisher Scientific Cat#15710072 GlutaMAX TM Supplement Thermofisher Scientific Cat#35050061 GM-CSF Thermofisher Scientific Cat#300-03 HEPES (1M) Thermofisher Scientific Cat#15630080 Human CD45RO Microbeads Miltenyi Biotec Cat#130-046-001 Human CD57 Microbeads Miltenyi Biotec Cat#130-092-073 (Continued on next page) Cell Reports 44, 116676, December 23, 2025 19 .. REAGENT or RESOURCE SOURCE IDENTIFIER Fetal bovine serum (FBS) Wisent Cat#090150 Human recombinant insulin-zinc solution Gibco Cat#12585-014 Human serum Sigma Cat#H4522 Hybri-Care Medium ATCC Cat#46-X IL-15 Peprotech Cat#200-15 IL-1β Thermofisher Scientific Cat#F-200-01B IL-21 Thermofisher Scientific Cat#200-21 IL-21S Miltenyi Biotec Cat#130-097-745 IL-4 Peprotech Cat#200-04-250UG IL-7 Peprotech Cat#200-07 JQ1 Active Motif Cat#14141 LPS Sigma Cat#L4524-5MG LS columns Miltenyi Biotec Cat#130-042-401 McCoy’s 5A Medium ATCC Cat#30-2007 Minimum Essential Medium alpha Fisher Cat#12561056 PBS, 1X, w/o Calcium & Magnesium Wisent Cat#311-010 CL Phosphatase Inhibitor Cocktail 3 Sigma Cat#P0044 Pierce TM Anti-HA Magnetic Beads Thermofisher Scientific Cat# 88836 Pre-separation Filters 30μm Miltenyi Biotec Cat#130-041-407 Protease Inhibitor Cocktail Sigma Cat#P8340 R848 Invivogen Cat#tlrl-r848-10 RPMI 1640 Medium Thermofisher Scientific Cat#A1049101 RPMI 1640 Medium Thermofisher Scientific Cat#11875119 T cell TransAct Miltenyi Biotec Cat#130-111-160 TRIzol reagent Thermofisher Scientific Cat#15596018 TrypLE TM Express Enzyme (1X), no phenol red Gibco Cat#12604013 X-VIVO 15 media Lonza Cat#04-418Q Critical commercial assays Human CD8 + T cell Isolation Kit Miltenyi Biotec Cat#130-096-495 KAPA HyperPrep RNAseq stranded kit KAPA Cat#KK8421 Maxima First Strand cDNA Synthesis Kit for RT-qPCR Thermo Scientific Cat#K1671 Mycoplasma PCR Detection Kit Applied Biological Materials Cat#G238 Propidium Iodide Flow Cytometry Kit Abcam Cat#ab139418 QIFIKIT (Quantitative Analysis Kit) Agilent Dako Cat# K0078 RNeasy purification kit Qiagen Cat#74104 Deposited data ATAC-seq data from wildtype and shRB1 MCF7, wildtype MDAMB361, and wildtype MDAMB468 treated with DMSO or Abemaciclib Watt et al. 59 GEO:GSE157082 ChIP-seq and Cut&Run data from MDAMB231 left untreated or treated with JQ1 Wu et al. 93 GEO:GSE136151 FLAG-Rb, and E2F1 ChIP-seq from RPE1 cells Sanidas et al. 60 GEO:GSE176035 GeneHancer database (v5.22) Fishilevich et al. 94 https://www.genecards.org/ Guide/Datasets H3K27ac ChIP-seq data from wildtype MCF7 treated with DMSO, Abemaciclib, and/or Fulvestrant Watt et al. 59 GEO:GSE157222 (Continued on next page) 20 Cell Reports 44, 116676, December 23, 2025
Recombinant:Article Title: CDK4/6 inhibition reprograms the breast cancer immunopeptidome via Rb-dependent chromatin and transcriptomic remodeling.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-Human HLA-ABC (Clone W6/32, mouse IgG2a) Cedarlane Cat#CLHLA-01AP Purified Mouse IgG2a κ Isotype Control BD Pharmingen RRID:AB_479656 Phospho-Rb (Ser795) Rabbit Antibody Cell Signaling RRID:AB_479656 Phospho-Rb (Ser780) Rabbit Antibody Cell Signaling RRID:AB_330015 Rb (4H1) Mouse mAb Cell Signaling RRID:AB_823629 BRD4 Rabbit mAb Cell Signaling RRID:AB_268757 BRD2 Rabbit Antibody [BL-167-2A2] Abcam RRID:AB_3694209 BRD3 Rabbit mAb Cell Signaling Cat#94032 Anti-rabbit IgG, HRP-linked Antibody Cell Signaling RRID:AB_2099233 Anti-Mouse IgG, HRP-linked Antibody Cell Signaling RRID:AB_330924 Anti-Human HLA-ABC W6/32 antibody for IP BioXcell Cat#BE0079 HA-Tag (C29F4) Rabbit mAb Cell Signaling RRID:AB_1549585 Biological samples Healthy human peripheral blood BioIVT https://bioivt.com Chemicals, peptides, and recombinant proteins 4–12% Criterion TM XT Bis-Tris Protein Gel Bio-Rad Cat#3450124 and Cat#3450123 7-AAD BD Pharmingen Cat#559925 96 well plates U Sarstedt Cat#83.3925 Abemaciclib Toronto Research Chemicals Inc. Cat#A115153 Alpha Modification of Eagle’s Medium (AMEM) Wisent Cat#310-010-CL Amersham TM ECL Select TM Western Blotting Detection Reagent Cytiva Cat#RPN2235 Benzonase® Nuclease Sigma Cat#E1014-25KU Bio-Rad Protein Assay Dye Reagent Concentrate Bio-Rad Cat#5000006 BioTrace TM NT Nitrocellulose Transfer Membrane Cytiva Cat#66485 CNBR-activated Sepharose 4B beads Fisher Cat#45000066 dBET57 Cayman Chemical Cat#36626 Dulbecco’s Modified Eagle Medium (DMEM) Wisent Cat#319-005-CL Eagle’s Minimum Essential Medium (EMEM) ATCC Cat#30-2003 ELISpot Pro: Human IFN-γ (ALP) Mabtech Cat#3420-4APW-10 Fetal bovine serum (FBS) Wisent Cat#090150 Flt-3 Ligand Peprotech Cat#AF-300-19 Gentamicin (10 mg/mL) Thermofisher Scientific Cat#15710072 GlutaMAX TM Supplement Thermofisher Scientific Cat#35050061 GM-CSF Thermofisher Scientific Cat#300-03 HEPES (1M) Thermofisher Scientific Cat#15630080 Human CD45RO Microbeads Miltenyi Biotec Cat#130-046-001 Human CD57 Microbeads Miltenyi Biotec Cat#130-092-073 (Continued on next page) Cell Reports 44, 116676, December 23, 2025 19 .. REAGENT or RESOURCE SOURCE IDENTIFIER Fetal bovine serum (FBS) Wisent Cat#090150 Human recombinant insulin-zinc solution Gibco Cat#12585-014 Human serum Sigma Cat#H4522 Hybri-Care Medium ATCC Cat#46-X IL-15 Peprotech Cat#200-15 IL-1β Thermofisher Scientific Cat#F-200-01B IL-21 Thermofisher Scientific Cat#200-21 IL-21S Miltenyi Biotec Cat#130-097-745 IL-4 Peprotech Cat#200-04-250UG IL-7 Peprotech Cat#200-07 JQ1 Active Motif Cat#14141 LPS Sigma Cat#L4524-5MG LS columns Miltenyi Biotec Cat#130-042-401 McCoy’s 5A Medium ATCC Cat#30-2007 Minimum Essential Medium alpha Fisher Cat#12561056 PBS, 1X, w/o Calcium & Magnesium Wisent Cat#311-010 CL Phosphatase Inhibitor Cocktail 3 Sigma Cat#P0044 Pierce TM Anti-HA Magnetic Beads Thermofisher Scientific Cat# 88836 Pre-separation Filters 30μm Miltenyi Biotec Cat#130-041-407 Protease Inhibitor Cocktail Sigma Cat#P8340 R848 Invivogen Cat#tlrl-r848-10 RPMI 1640 Medium Thermofisher Scientific Cat#A1049101 RPMI 1640 Medium Thermofisher Scientific Cat#11875119 T cell TransAct Miltenyi Biotec Cat#130-111-160 TRIzol reagent Thermofisher Scientific Cat#15596018 TrypLE TM Express Enzyme (1X), no phenol red Gibco Cat#12604013 X-VIVO 15 media Lonza Cat#04-418Q Critical commercial assays Human CD8 + T cell Isolation Kit Miltenyi Biotec Cat#130-096-495 KAPA HyperPrep RNAseq stranded kit KAPA Cat#KK8421 Maxima First Strand cDNA Synthesis Kit for RT-qPCR Thermo Scientific Cat#K1671 Mycoplasma PCR Detection Kit Applied Biological Materials Cat#G238 Propidium Iodide Flow Cytometry Kit Abcam Cat#ab139418 QIFIKIT (Quantitative Analysis Kit) Agilent Dako Cat# K0078 RNeasy purification kit Qiagen Cat#74104 Deposited data ATAC-seq data from wildtype and shRB1 MCF7, wildtype MDAMB361, and wildtype MDAMB468 treated with DMSO or Abemaciclib Watt et al. 59 GEO:GSE157082 ChIP-seq and Cut&Run data from MDAMB231 left untreated or treated with JQ1 Wu et al. 93 GEO:GSE136151 FLAG-Rb, and E2F1 ChIP-seq from RPE1 cells Sanidas et al. 60 GEO:GSE176035 GeneHancer database (v5.22) Fishilevich et al. 94 https://www.genecards.org/ Guide/Datasets H3K27ac ChIP-seq data from wildtype MCF7 treated with DMSO, Abemaciclib, and/or Fulvestrant Watt et al. 59 GEO:GSE157222 (Continued on next page) 20 Cell Reports 44, 116676, December 23, 2025
Article Title: Aryl hydrocarbon receptor activity downstream of IL-10 signaling is required to promote regulatory functions in human dendritic cells.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER String https://doi.org/10.1093/nar/gky1131 https://string-db.org Gene Set Enrichment Analysis (GSEA) https://doi.org/10.1073/PNAS.0506580102 https://www.gsea-msigdb.org/ gsea/index.jsp Other Recombinant human IL-4 Miltenyi Biotec Cat# 130-093-922 Recombinant human GM-CSF Miltenyi Biotec Cat# 130-093-867 Recombinant human IL-10 Cell Genix Cat# 1414-050 .. REAGENT or RESOURCE SOURCE IDENTIFIER Biotin Anti-Human and Viral IL-10 (clone JES3-12G8) BD Biosciences Cat# 554499; RRID:AB_395435 Biotin Anti-Human IFNg (clone 4S.B3) BD Biosciences Cat# 554550; RRID:AB_395472 Recombinant Human IL-10 protein Cell Genix Cat# 1414-050 Recombinant Human IFNg R&D Systems Cat# 285-IF100 Anti H3K27ac Abcam Cat# ab4729; RRID:AB_2118291 Anti H3K4me1 Abcam Cat# ab8895; RRID:AB_306847 Anti H3K9me3 Abcam Cat# ab8898 ;RRID:AB_306848 Chemicals, peptides, and recombinant proteins CH-223191 Invivogen Cat# INH-CH22 ITE Invivogen Cat# tlrl-ite MHY1485 Calbiochem Cat# 5005540001 Critical commercial assays Human CD14 MicroBeads Miltenyi Biotec Cat# 130-050-201 Human CD4 isolation kit Miltenyi Biotec Cat# 130-091-155 Human CD45RO MicroBeads Miltenyi Biotec Cat# 130-046-001 RNeasy Micro kit Qiagen Cat# 74034 miRNeasy Micro kit Qiagen Cat# 217084 Tagment DNA enzyme and buffer Small kit Illumina Cat# 20034197 Deposited data Ex vivo DC-10 and cDC RNA-seq https://doi.org/10.1038/s41423-019-0218-0 GEO: GSE117945 IL-10 stimulated monocyte Microarray https://doi.org/10.1186/s12865-017-0229-5 GEO: GSE82316 MS and HC monocyte RNA-seq https://doi.org/10.1093/brain/awaa421 GEO: GSE137143 ATAC-seq ex vivo DC-10/DC This paper GEO: GSE180753 ATAC-seq in vitro DC-10/DC/AHRinhDC-10 This paper GEO: GSE180754 RNA-seq in vitro DC-10/DC/AHRinhDC-10 This paper GEO: GSE180761 RNA-seq in vitro DC-10 MS/HC This paper GEO: GSE180760 RNA-seq ex vivo DC-10 MS/HC This paper GEO: GSE180755 Oligonucleotides CYP1A1 FAM-Probe Thermo-Fisher Cat# Hs00153120 IL-6 FAM-Probe Thermo-Fisher Cat# Hs00985639 IL-10 FAM-Probe Thermo-Fisher Cat# Hs00174086 ILT-4 (LIRB2) EvaGreen Bio-Rad Cat# dHSaEG5020183 SOCS3 EvaGreen Bio-Rad Cat# dHSaEG5001979 HPRT VIC-probe Bio-Rad Cat# 1409017 Software and algorithms FlowJo v10 BD https://www.flowjo.com/ Prism v9 and v10 GraphPad Software https://www.graphpad.com/ scientific-software/prism/ Morpheus Broad Institute https://software.broadinstitute.org/ morpheus/ DESeq2 https://doi.org/10.1186/s13059-014-0550-8 https://bioconductor.org/packages/ release/bioc/html/DESeq2.html EnrichR https://doi.org/10.1186/1471-2105-14-128 https://maayanlab.cloud/Enrichr/) Metascape https://doi.org/10.1186/1471-2105-14-128 metascape.org DiffBind http://bioconductor.org/packages/release/ bioc/vignettes/DiffBind/inst/doc/DiffBind.pdf https://bioconductor.org/packages/ release/bioc/html/DiffBind.html Regulatory Sequence Analysis Tools (RSAT) https://doi.org/10.1038/nprot.2012.088 http://rsat.sb-roscoff.fr/ TFmotifView https://doi.org/10.1093/nar/gkaa252 http://bardet.u-strasbg.fr/tfmotifview/ (Continued on next page) Cell Reports 42, 112193, March 28, 2023 19 .. REAGENT or RESOURCE SOURCE IDENTIFIER String https://doi.org/10.1093/nar/gky1131 https://string-db.org Gene Set Enrichment Analysis (GSEA) https://doi.org/10.1073/PNAS.0506580102 https://www.gsea-msigdb.org/ gsea/index.jsp Other Recombinant human IL-4 Miltenyi Biotec Cat# 130-093-922 Recombinant human GM-CSF Miltenyi Biotec Cat# 130-093-867 Recombinant human IL-10 Cell Genix Cat# 1414-050
Modification:Article Title: CDK4/6 inhibition reprograms the breast cancer immunopeptidome via Rb-dependent chromatin and transcriptomic remodeling.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-Human HLA-ABC (Clone W6/32, mouse IgG2a) Cedarlane Cat#CLHLA-01AP Purified Mouse IgG2a κ Isotype Control BD Pharmingen RRID:AB_479656 Phospho-Rb (Ser795) Rabbit Antibody Cell Signaling RRID:AB_479656 Phospho-Rb (Ser780) Rabbit Antibody Cell Signaling RRID:AB_330015 Rb (4H1) Mouse mAb Cell Signaling RRID:AB_823629 BRD4 Rabbit mAb Cell Signaling RRID:AB_268757 BRD2 Rabbit Antibody [BL-167-2A2] Abcam RRID:AB_3694209 BRD3 Rabbit mAb Cell Signaling Cat#94032 Anti-rabbit IgG, HRP-linked Antibody Cell Signaling RRID:AB_2099233 Anti-Mouse IgG, HRP-linked Antibody Cell Signaling RRID:AB_330924 Anti-Human HLA-ABC W6/32 antibody for IP BioXcell Cat#BE0079 HA-Tag (C29F4) Rabbit mAb Cell Signaling RRID:AB_1549585 Biological samples Healthy human peripheral blood BioIVT https://bioivt.com Chemicals, peptides, and recombinant proteins 4–12% Criterion TM XT Bis-Tris Protein Gel Bio-Rad Cat#3450124 and Cat#3450123 7-AAD BD Pharmingen Cat#559925 96 well plates U Sarstedt Cat#83.3925 Abemaciclib Toronto Research Chemicals Inc. Cat#A115153 Alpha Modification of Eagle’s Medium (AMEM) Wisent Cat#310-010-CL Amersham TM ECL Select TM Western Blotting Detection Reagent Cytiva Cat#RPN2235 Benzonase® Nuclease Sigma Cat#E1014-25KU Bio-Rad Protein Assay Dye Reagent Concentrate Bio-Rad Cat#5000006 BioTrace TM NT Nitrocellulose Transfer Membrane Cytiva Cat#66485 CNBR-activated Sepharose 4B beads Fisher Cat#45000066 dBET57 Cayman Chemical Cat#36626 Dulbecco’s Modified Eagle Medium (DMEM) Wisent Cat#319-005-CL Eagle’s Minimum Essential Medium (EMEM) ATCC Cat#30-2003 ELISpot Pro: Human IFN-γ (ALP) Mabtech Cat#3420-4APW-10 Fetal bovine serum (FBS) Wisent Cat#090150 Flt-3 Ligand Peprotech Cat#AF-300-19 Gentamicin (10 mg/mL) Thermofisher Scientific Cat#15710072 GlutaMAX TM Supplement Thermofisher Scientific Cat#35050061 GM-CSF Thermofisher Scientific Cat#300-03 HEPES (1M) Thermofisher Scientific Cat#15630080 Human CD45RO Microbeads Miltenyi Biotec Cat#130-046-001 Human CD57 Microbeads Miltenyi Biotec Cat#130-092-073 (Continued on next page) Cell Reports 44, 116676, December 23, 2025 19 .. REAGENT or RESOURCE SOURCE IDENTIFIER Fetal bovine serum (FBS) Wisent Cat#090150 Human recombinant insulin-zinc solution Gibco Cat#12585-014 Human serum Sigma Cat#H4522 Hybri-Care Medium ATCC Cat#46-X IL-15 Peprotech Cat#200-15 IL-1β Thermofisher Scientific Cat#F-200-01B IL-21 Thermofisher Scientific Cat#200-21 IL-21S Miltenyi Biotec Cat#130-097-745 IL-4 Peprotech Cat#200-04-250UG IL-7 Peprotech Cat#200-07 JQ1 Active Motif Cat#14141 LPS Sigma Cat#L4524-5MG LS columns Miltenyi Biotec Cat#130-042-401 McCoy’s 5A Medium ATCC Cat#30-2007 Minimum Essential Medium alpha Fisher Cat#12561056 PBS, 1X, w/o Calcium & Magnesium Wisent Cat#311-010 CL Phosphatase Inhibitor Cocktail 3 Sigma Cat#P0044 Pierce TM Anti-HA Magnetic Beads Thermofisher Scientific Cat# 88836 Pre-separation Filters 30μm Miltenyi Biotec Cat#130-041-407 Protease Inhibitor Cocktail Sigma Cat#P8340 R848 Invivogen Cat#tlrl-r848-10 RPMI 1640 Medium Thermofisher Scientific Cat#A1049101 RPMI 1640 Medium Thermofisher Scientific Cat#11875119 T cell TransAct Miltenyi Biotec Cat#130-111-160 TRIzol reagent Thermofisher Scientific Cat#15596018 TrypLE TM Express Enzyme (1X), no phenol red Gibco Cat#12604013 X-VIVO 15 media Lonza Cat#04-418Q Critical commercial assays Human CD8 + T cell Isolation Kit Miltenyi Biotec Cat#130-096-495 KAPA HyperPrep RNAseq stranded kit KAPA Cat#KK8421 Maxima First Strand cDNA Synthesis Kit for RT-qPCR Thermo Scientific Cat#K1671 Mycoplasma PCR Detection Kit Applied Biological Materials Cat#G238 Propidium Iodide Flow Cytometry Kit Abcam Cat#ab139418 QIFIKIT (Quantitative Analysis Kit) Agilent Dako Cat# K0078 RNeasy purification kit Qiagen Cat#74104 Deposited data ATAC-seq data from wildtype and shRB1 MCF7, wildtype MDAMB361, and wildtype MDAMB468 treated with DMSO or Abemaciclib Watt et al. 59 GEO:GSE157082 ChIP-seq and Cut&Run data from MDAMB231 left untreated or treated with JQ1 Wu et al. 93 GEO:GSE136151 FLAG-Rb, and E2F1 ChIP-seq from RPE1 cells Sanidas et al. 60 GEO:GSE176035 GeneHancer database (v5.22) Fishilevich et al. 94 https://www.genecards.org/ Guide/Datasets H3K27ac ChIP-seq data from wildtype MCF7 treated with DMSO, Abemaciclib, and/or Fulvestrant Watt et al. 59 GEO:GSE157222 (Continued on next page) 20 Cell Reports 44, 116676, December 23, 2025
Western Blot:Article Title: CDK4/6 inhibition reprograms the breast cancer immunopeptidome via Rb-dependent chromatin and transcriptomic remodeling.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-Human HLA-ABC (Clone W6/32, mouse IgG2a) Cedarlane Cat#CLHLA-01AP Purified Mouse IgG2a κ Isotype Control BD Pharmingen RRID:AB_479656 Phospho-Rb (Ser795) Rabbit Antibody Cell Signaling RRID:AB_479656 Phospho-Rb (Ser780) Rabbit Antibody Cell Signaling RRID:AB_330015 Rb (4H1) Mouse mAb Cell Signaling RRID:AB_823629 BRD4 Rabbit mAb Cell Signaling RRID:AB_268757 BRD2 Rabbit Antibody [BL-167-2A2] Abcam RRID:AB_3694209 BRD3 Rabbit mAb Cell Signaling Cat#94032 Anti-rabbit IgG, HRP-linked Antibody Cell Signaling RRID:AB_2099233 Anti-Mouse IgG, HRP-linked Antibody Cell Signaling RRID:AB_330924 Anti-Human HLA-ABC W6/32 antibody for IP BioXcell Cat#BE0079 HA-Tag (C29F4) Rabbit mAb Cell Signaling RRID:AB_1549585 Biological samples Healthy human peripheral blood BioIVT https://bioivt.com Chemicals, peptides, and recombinant proteins 4–12% Criterion TM XT Bis-Tris Protein Gel Bio-Rad Cat#3450124 and Cat#3450123 7-AAD BD Pharmingen Cat#559925 96 well plates U Sarstedt Cat#83.3925 Abemaciclib Toronto Research Chemicals Inc. Cat#A115153 Alpha Modification of Eagle’s Medium (AMEM) Wisent Cat#310-010-CL Amersham TM ECL Select TM Western Blotting Detection Reagent Cytiva Cat#RPN2235 Benzonase® Nuclease Sigma Cat#E1014-25KU Bio-Rad Protein Assay Dye Reagent Concentrate Bio-Rad Cat#5000006 BioTrace TM NT Nitrocellulose Transfer Membrane Cytiva Cat#66485 CNBR-activated Sepharose 4B beads Fisher Cat#45000066 dBET57 Cayman Chemical Cat#36626 Dulbecco’s Modified Eagle Medium (DMEM) Wisent Cat#319-005-CL Eagle’s Minimum Essential Medium (EMEM) ATCC Cat#30-2003 ELISpot Pro: Human IFN-γ (ALP) Mabtech Cat#3420-4APW-10 Fetal bovine serum (FBS) Wisent Cat#090150 Flt-3 Ligand Peprotech Cat#AF-300-19 Gentamicin (10 mg/mL) Thermofisher Scientific Cat#15710072 GlutaMAX TM Supplement Thermofisher Scientific Cat#35050061 GM-CSF Thermofisher Scientific Cat#300-03 HEPES (1M) Thermofisher Scientific Cat#15630080 Human CD45RO Microbeads Miltenyi Biotec Cat#130-046-001 Human CD57 Microbeads Miltenyi Biotec Cat#130-092-073 (Continued on next page) Cell Reports 44, 116676, December 23, 2025 19 .. REAGENT or RESOURCE SOURCE IDENTIFIER Fetal bovine serum (FBS) Wisent Cat#090150 Human recombinant insulin-zinc solution Gibco Cat#12585-014 Human serum Sigma Cat#H4522 Hybri-Care Medium ATCC Cat#46-X IL-15 Peprotech Cat#200-15 IL-1β Thermofisher Scientific Cat#F-200-01B IL-21 Thermofisher Scientific Cat#200-21 IL-21S Miltenyi Biotec Cat#130-097-745 IL-4 Peprotech Cat#200-04-250UG IL-7 Peprotech Cat#200-07 JQ1 Active Motif Cat#14141 LPS Sigma Cat#L4524-5MG LS columns Miltenyi Biotec Cat#130-042-401 McCoy’s 5A Medium ATCC Cat#30-2007 Minimum Essential Medium alpha Fisher Cat#12561056 PBS, 1X, w/o Calcium & Magnesium Wisent Cat#311-010 CL Phosphatase Inhibitor Cocktail 3 Sigma Cat#P0044 Pierce TM Anti-HA Magnetic Beads Thermofisher Scientific Cat# 88836 Pre-separation Filters 30μm Miltenyi Biotec Cat#130-041-407 Protease Inhibitor Cocktail Sigma Cat#P8340 R848 Invivogen Cat#tlrl-r848-10 RPMI 1640 Medium Thermofisher Scientific Cat#A1049101 RPMI 1640 Medium Thermofisher Scientific Cat#11875119 T cell TransAct Miltenyi Biotec Cat#130-111-160 TRIzol reagent Thermofisher Scientific Cat#15596018 TrypLE TM Express Enzyme (1X), no phenol red Gibco Cat#12604013 X-VIVO 15 media Lonza Cat#04-418Q Critical commercial assays Human CD8 + T cell Isolation Kit Miltenyi Biotec Cat#130-096-495 KAPA HyperPrep RNAseq stranded kit KAPA Cat#KK8421 Maxima First Strand cDNA Synthesis Kit for RT-qPCR Thermo Scientific Cat#K1671 Mycoplasma PCR Detection Kit Applied Biological Materials Cat#G238 Propidium Iodide Flow Cytometry Kit Abcam Cat#ab139418 QIFIKIT (Quantitative Analysis Kit) Agilent Dako Cat# K0078 RNeasy purification kit Qiagen Cat#74104 Deposited data ATAC-seq data from wildtype and shRB1 MCF7, wildtype MDAMB361, and wildtype MDAMB468 treated with DMSO or Abemaciclib Watt et al. 59 GEO:GSE157082 ChIP-seq and Cut&Run data from MDAMB231 left untreated or treated with JQ1 Wu et al. 93 GEO:GSE136151 FLAG-Rb, and E2F1 ChIP-seq from RPE1 cells Sanidas et al. 60 GEO:GSE176035 GeneHancer database (v5.22) Fishilevich et al. 94 https://www.genecards.org/ Guide/Datasets H3K27ac ChIP-seq data from wildtype MCF7 treated with DMSO, Abemaciclib, and/or Fulvestrant Watt et al. 59 GEO:GSE157222 (Continued on next page) 20 Cell Reports 44, 116676, December 23, 2025
Membrane:Article Title: CDK4/6 inhibition reprograms the breast cancer immunopeptidome via Rb-dependent chromatin and transcriptomic remodeling.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-Human HLA-ABC (Clone W6/32, mouse IgG2a) Cedarlane Cat#CLHLA-01AP Purified Mouse IgG2a κ Isotype Control BD Pharmingen RRID:AB_479656 Phospho-Rb (Ser795) Rabbit Antibody Cell Signaling RRID:AB_479656 Phospho-Rb (Ser780) Rabbit Antibody Cell Signaling RRID:AB_330015 Rb (4H1) Mouse mAb Cell Signaling RRID:AB_823629 BRD4 Rabbit mAb Cell Signaling RRID:AB_268757 BRD2 Rabbit Antibody [BL-167-2A2] Abcam RRID:AB_3694209 BRD3 Rabbit mAb Cell Signaling Cat#94032 Anti-rabbit IgG, HRP-linked Antibody Cell Signaling RRID:AB_2099233 Anti-Mouse IgG, HRP-linked Antibody Cell Signaling RRID:AB_330924 Anti-Human HLA-ABC W6/32 antibody for IP BioXcell Cat#BE0079 HA-Tag (C29F4) Rabbit mAb Cell Signaling RRID:AB_1549585 Biological samples Healthy human peripheral blood BioIVT https://bioivt.com Chemicals, peptides, and recombinant proteins 4–12% Criterion TM XT Bis-Tris Protein Gel Bio-Rad Cat#3450124 and Cat#3450123 7-AAD BD Pharmingen Cat#559925 96 well plates U Sarstedt Cat#83.3925 Abemaciclib Toronto Research Chemicals Inc. Cat#A115153 Alpha Modification of Eagle’s Medium (AMEM) Wisent Cat#310-010-CL Amersham TM ECL Select TM Western Blotting Detection Reagent Cytiva Cat#RPN2235 Benzonase® Nuclease Sigma Cat#E1014-25KU Bio-Rad Protein Assay Dye Reagent Concentrate Bio-Rad Cat#5000006 BioTrace TM NT Nitrocellulose Transfer Membrane Cytiva Cat#66485 CNBR-activated Sepharose 4B beads Fisher Cat#45000066 dBET57 Cayman Chemical Cat#36626 Dulbecco’s Modified Eagle Medium (DMEM) Wisent Cat#319-005-CL Eagle’s Minimum Essential Medium (EMEM) ATCC Cat#30-2003 ELISpot Pro: Human IFN-γ (ALP) Mabtech Cat#3420-4APW-10 Fetal bovine serum (FBS) Wisent Cat#090150 Flt-3 Ligand Peprotech Cat#AF-300-19 Gentamicin (10 mg/mL) Thermofisher Scientific Cat#15710072 GlutaMAX TM Supplement Thermofisher Scientific Cat#35050061 GM-CSF Thermofisher Scientific Cat#300-03 HEPES (1M) Thermofisher Scientific Cat#15630080 Human CD45RO Microbeads Miltenyi Biotec Cat#130-046-001 Human CD57 Microbeads Miltenyi Biotec Cat#130-092-073 (Continued on next page) Cell Reports 44, 116676, December 23, 2025 19 .. REAGENT or RESOURCE SOURCE IDENTIFIER Fetal bovine serum (FBS) Wisent Cat#090150 Human recombinant insulin-zinc solution Gibco Cat#12585-014 Human serum Sigma Cat#H4522 Hybri-Care Medium ATCC Cat#46-X IL-15 Peprotech Cat#200-15 IL-1β Thermofisher Scientific Cat#F-200-01B IL-21 Thermofisher Scientific Cat#200-21 IL-21S Miltenyi Biotec Cat#130-097-745 IL-4 Peprotech Cat#200-04-250UG IL-7 Peprotech Cat#200-07 JQ1 Active Motif Cat#14141 LPS Sigma Cat#L4524-5MG LS columns Miltenyi Biotec Cat#130-042-401 McCoy’s 5A Medium ATCC Cat#30-2007 Minimum Essential Medium alpha Fisher Cat#12561056 PBS, 1X, w/o Calcium & Magnesium Wisent Cat#311-010 CL Phosphatase Inhibitor Cocktail 3 Sigma Cat#P0044 Pierce TM Anti-HA Magnetic Beads Thermofisher Scientific Cat# 88836 Pre-separation Filters 30μm Miltenyi Biotec Cat#130-041-407 Protease Inhibitor Cocktail Sigma Cat#P8340 R848 Invivogen Cat#tlrl-r848-10 RPMI 1640 Medium Thermofisher Scientific Cat#A1049101 RPMI 1640 Medium Thermofisher Scientific Cat#11875119 T cell TransAct Miltenyi Biotec Cat#130-111-160 TRIzol reagent Thermofisher Scientific Cat#15596018 TrypLE TM Express Enzyme (1X), no phenol red Gibco Cat#12604013 X-VIVO 15 media Lonza Cat#04-418Q Critical commercial assays Human CD8 + T cell Isolation Kit Miltenyi Biotec Cat#130-096-495 KAPA HyperPrep RNAseq stranded kit KAPA Cat#KK8421 Maxima First Strand cDNA Synthesis Kit for RT-qPCR Thermo Scientific Cat#K1671 Mycoplasma PCR Detection Kit Applied Biological Materials Cat#G238 Propidium Iodide Flow Cytometry Kit Abcam Cat#ab139418 QIFIKIT (Quantitative Analysis Kit) Agilent Dako Cat# K0078 RNeasy purification kit Qiagen Cat#74104 Deposited data ATAC-seq data from wildtype and shRB1 MCF7, wildtype MDAMB361, and wildtype MDAMB468 treated with DMSO or Abemaciclib Watt et al. 59 GEO:GSE157082 ChIP-seq and Cut&Run data from MDAMB231 left untreated or treated with JQ1 Wu et al. 93 GEO:GSE136151 FLAG-Rb, and E2F1 ChIP-seq from RPE1 cells Sanidas et al. 60 GEO:GSE176035 GeneHancer database (v5.22) Fishilevich et al. 94 https://www.genecards.org/ Guide/Datasets H3K27ac ChIP-seq data from wildtype MCF7 treated with DMSO, Abemaciclib, and/or Fulvestrant Watt et al. 59 GEO:GSE157222 (Continued on next page) 20 Cell Reports 44, 116676, December 23, 2025
Enzyme-linked Immunospot:Article Title: CDK4/6 inhibition reprograms the breast cancer immunopeptidome via Rb-dependent chromatin and transcriptomic remodeling.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-Human HLA-ABC (Clone W6/32, mouse IgG2a) Cedarlane Cat#CLHLA-01AP Purified Mouse IgG2a κ Isotype Control BD Pharmingen RRID:AB_479656 Phospho-Rb (Ser795) Rabbit Antibody Cell Signaling RRID:AB_479656 Phospho-Rb (Ser780) Rabbit Antibody Cell Signaling RRID:AB_330015 Rb (4H1) Mouse mAb Cell Signaling RRID:AB_823629 BRD4 Rabbit mAb Cell Signaling RRID:AB_268757 BRD2 Rabbit Antibody [BL-167-2A2] Abcam RRID:AB_3694209 BRD3 Rabbit mAb Cell Signaling Cat#94032 Anti-rabbit IgG, HRP-linked Antibody Cell Signaling RRID:AB_2099233 Anti-Mouse IgG, HRP-linked Antibody Cell Signaling RRID:AB_330924 Anti-Human HLA-ABC W6/32 antibody for IP BioXcell Cat#BE0079 HA-Tag (C29F4) Rabbit mAb Cell Signaling RRID:AB_1549585 Biological samples Healthy human peripheral blood BioIVT https://bioivt.com Chemicals, peptides, and recombinant proteins 4–12% Criterion TM XT Bis-Tris Protein Gel Bio-Rad Cat#3450124 and Cat#3450123 7-AAD BD Pharmingen Cat#559925 96 well plates U Sarstedt Cat#83.3925 Abemaciclib Toronto Research Chemicals Inc. Cat#A115153 Alpha Modification of Eagle’s Medium (AMEM) Wisent Cat#310-010-CL Amersham TM ECL Select TM Western Blotting Detection Reagent Cytiva Cat#RPN2235 Benzonase® Nuclease Sigma Cat#E1014-25KU Bio-Rad Protein Assay Dye Reagent Concentrate Bio-Rad Cat#5000006 BioTrace TM NT Nitrocellulose Transfer Membrane Cytiva Cat#66485 CNBR-activated Sepharose 4B beads Fisher Cat#45000066 dBET57 Cayman Chemical Cat#36626 Dulbecco’s Modified Eagle Medium (DMEM) Wisent Cat#319-005-CL Eagle’s Minimum Essential Medium (EMEM) ATCC Cat#30-2003 ELISpot Pro: Human IFN-γ (ALP) Mabtech Cat#3420-4APW-10 Fetal bovine serum (FBS) Wisent Cat#090150 Flt-3 Ligand Peprotech Cat#AF-300-19 Gentamicin (10 mg/mL) Thermofisher Scientific Cat#15710072 GlutaMAX TM Supplement Thermofisher Scientific Cat#35050061 GM-CSF Thermofisher Scientific Cat#300-03 HEPES (1M) Thermofisher Scientific Cat#15630080 Human CD45RO Microbeads Miltenyi Biotec Cat#130-046-001 Human CD57 Microbeads Miltenyi Biotec Cat#130-092-073 (Continued on next page) Cell Reports 44, 116676, December 23, 2025 19 .. REAGENT or RESOURCE SOURCE IDENTIFIER Fetal bovine serum (FBS) Wisent Cat#090150 Human recombinant insulin-zinc solution Gibco Cat#12585-014 Human serum Sigma Cat#H4522 Hybri-Care Medium ATCC Cat#46-X IL-15 Peprotech Cat#200-15 IL-1β Thermofisher Scientific Cat#F-200-01B IL-21 Thermofisher Scientific Cat#200-21 IL-21S Miltenyi Biotec Cat#130-097-745 IL-4 Peprotech Cat#200-04-250UG IL-7 Peprotech Cat#200-07 JQ1 Active Motif Cat#14141 LPS Sigma Cat#L4524-5MG LS columns Miltenyi Biotec Cat#130-042-401 McCoy’s 5A Medium ATCC Cat#30-2007 Minimum Essential Medium alpha Fisher Cat#12561056 PBS, 1X, w/o Calcium & Magnesium Wisent Cat#311-010 CL Phosphatase Inhibitor Cocktail 3 Sigma Cat#P0044 Pierce TM Anti-HA Magnetic Beads Thermofisher Scientific Cat# 88836 Pre-separation Filters 30μm Miltenyi Biotec Cat#130-041-407 Protease Inhibitor Cocktail Sigma Cat#P8340 R848 Invivogen Cat#tlrl-r848-10 RPMI 1640 Medium Thermofisher Scientific Cat#A1049101 RPMI 1640 Medium Thermofisher Scientific Cat#11875119 T cell TransAct Miltenyi Biotec Cat#130-111-160 TRIzol reagent Thermofisher Scientific Cat#15596018 TrypLE TM Express Enzyme (1X), no phenol red Gibco Cat#12604013 X-VIVO 15 media Lonza Cat#04-418Q Critical commercial assays Human CD8 + T cell Isolation Kit Miltenyi Biotec Cat#130-096-495 KAPA HyperPrep RNAseq stranded kit KAPA Cat#KK8421 Maxima First Strand cDNA Synthesis Kit for RT-qPCR Thermo Scientific Cat#K1671 Mycoplasma PCR Detection Kit Applied Biological Materials Cat#G238 Propidium Iodide Flow Cytometry Kit Abcam Cat#ab139418 QIFIKIT (Quantitative Analysis Kit) Agilent Dako Cat# K0078 RNeasy purification kit Qiagen Cat#74104 Deposited data ATAC-seq data from wildtype and shRB1 MCF7, wildtype MDAMB361, and wildtype MDAMB468 treated with DMSO or Abemaciclib Watt et al. 59 GEO:GSE157082 ChIP-seq and Cut&Run data from MDAMB231 left untreated or treated with JQ1 Wu et al. 93 GEO:GSE136151 FLAG-Rb, and E2F1 ChIP-seq from RPE1 cells Sanidas et al. 60 GEO:GSE176035 GeneHancer database (v5.22) Fishilevich et al. 94 https://www.genecards.org/ Guide/Datasets H3K27ac ChIP-seq data from wildtype MCF7 treated with DMSO, Abemaciclib, and/or Fulvestrant Watt et al. 59 GEO:GSE157222 (Continued on next page) 20 Cell Reports 44, 116676, December 23, 2025
Isolation:Article Title: Aryl hydrocarbon receptor activity downstream of IL-10 signaling is required to promote regulatory functions in human dendritic cells.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER String https://doi.org/10.1093/nar/gky1131 https://string-db.org Gene Set Enrichment Analysis (GSEA) https://doi.org/10.1073/PNAS.0506580102 https://www.gsea-msigdb.org/ gsea/index.jsp Other Recombinant human IL-4 Miltenyi Biotec Cat# 130-093-922 Recombinant human GM-CSF Miltenyi Biotec Cat# 130-093-867 Recombinant human IL-10 Cell Genix Cat# 1414-050 .. REAGENT or RESOURCE SOURCE IDENTIFIER Biotin Anti-Human and Viral IL-10 (clone JES3-12G8) BD Biosciences Cat# 554499; RRID:AB_395435 Biotin Anti-Human IFNg (clone 4S.B3) BD Biosciences Cat# 554550; RRID:AB_395472 Recombinant Human IL-10 protein Cell Genix Cat# 1414-050 Recombinant Human IFNg R&D Systems Cat# 285-IF100 Anti H3K27ac Abcam Cat# ab4729; RRID:AB_2118291 Anti H3K4me1 Abcam Cat# ab8895; RRID:AB_306847 Anti H3K9me3 Abcam Cat# ab8898 ;RRID:AB_306848 Chemicals, peptides, and recombinant proteins CH-223191 Invivogen Cat# INH-CH22 ITE Invivogen Cat# tlrl-ite MHY1485 Calbiochem Cat# 5005540001 Critical commercial assays Human CD14 MicroBeads Miltenyi Biotec Cat# 130-050-201 Human CD4 isolation kit Miltenyi Biotec Cat# 130-091-155 Human CD45RO MicroBeads Miltenyi Biotec Cat# 130-046-001 RNeasy Micro kit Qiagen Cat# 74034 miRNeasy Micro kit Qiagen Cat# 217084 Tagment DNA enzyme and buffer Small kit Illumina Cat# 20034197 Deposited data Ex vivo DC-10 and cDC RNA-seq https://doi.org/10.1038/s41423-019-0218-0 GEO: GSE117945 IL-10 stimulated monocyte Microarray https://doi.org/10.1186/s12865-017-0229-5 GEO: GSE82316 MS and HC monocyte RNA-seq https://doi.org/10.1093/brain/awaa421 GEO: GSE137143 ATAC-seq ex vivo DC-10/DC This paper GEO: GSE180753 ATAC-seq in vitro DC-10/DC/AHRinhDC-10 This paper GEO: GSE180754 RNA-seq in vitro DC-10/DC/AHRinhDC-10 This paper GEO: GSE180761 RNA-seq in vitro DC-10 MS/HC This paper GEO: GSE180760 RNA-seq ex vivo DC-10 MS/HC This paper GEO: GSE180755 Oligonucleotides CYP1A1 FAM-Probe Thermo-Fisher Cat# Hs00153120 IL-6 FAM-Probe Thermo-Fisher Cat# Hs00985639 IL-10 FAM-Probe Thermo-Fisher Cat# Hs00174086 ILT-4 (LIRB2) EvaGreen Bio-Rad Cat# dHSaEG5020183 SOCS3 EvaGreen Bio-Rad Cat# dHSaEG5001979 HPRT VIC-probe Bio-Rad Cat# 1409017 Software and algorithms FlowJo v10 BD https://www.flowjo.com/ Prism v9 and v10 GraphPad Software https://www.graphpad.com/ scientific-software/prism/ Morpheus Broad Institute https://software.broadinstitute.org/ morpheus/ DESeq2 https://doi.org/10.1186/s13059-014-0550-8 https://bioconductor.org/packages/ release/bioc/html/DESeq2.html EnrichR https://doi.org/10.1186/1471-2105-14-128 https://maayanlab.cloud/Enrichr/) Metascape https://doi.org/10.1186/1471-2105-14-128 metascape.org DiffBind http://bioconductor.org/packages/release/ bioc/vignettes/DiffBind/inst/doc/DiffBind.pdf https://bioconductor.org/packages/ release/bioc/html/DiffBind.html Regulatory Sequence Analysis Tools (RSAT) https://doi.org/10.1038/nprot.2012.088 http://rsat.sb-roscoff.fr/ TFmotifView https://doi.org/10.1093/nar/gkaa252 http://bardet.u-strasbg.fr/tfmotifview/ (Continued on next page) Cell Reports 42, 112193, March 28, 2023 19 .. REAGENT or RESOURCE SOURCE IDENTIFIER String https://doi.org/10.1093/nar/gky1131 https://string-db.org Gene Set Enrichment Analysis (GSEA) https://doi.org/10.1073/PNAS.0506580102 https://www.gsea-msigdb.org/ gsea/index.jsp Other Recombinant human IL-4 Miltenyi Biotec Cat# 130-093-922 Recombinant human GM-CSF Miltenyi Biotec Cat# 130-093-867 Recombinant human IL-10 Cell Genix Cat# 1414-050
Ex Vivo:Article Title: Aryl hydrocarbon receptor activity downstream of IL-10 signaling is required to promote regulatory functions in human dendritic cells.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER String https://doi.org/10.1093/nar/gky1131 https://string-db.org Gene Set Enrichment Analysis (GSEA) https://doi.org/10.1073/PNAS.0506580102 https://www.gsea-msigdb.org/ gsea/index.jsp Other Recombinant human IL-4 Miltenyi Biotec Cat# 130-093-922 Recombinant human GM-CSF Miltenyi Biotec Cat# 130-093-867 Recombinant human IL-10 Cell Genix Cat# 1414-050 .. REAGENT or RESOURCE SOURCE IDENTIFIER Biotin Anti-Human and Viral IL-10 (clone JES3-12G8) BD Biosciences Cat# 554499; RRID:AB_395435 Biotin Anti-Human IFNg (clone 4S.B3) BD Biosciences Cat# 554550; RRID:AB_395472 Recombinant Human IL-10 protein Cell Genix Cat# 1414-050 Recombinant Human IFNg R&D Systems Cat# 285-IF100 Anti H3K27ac Abcam Cat# ab4729; RRID:AB_2118291 Anti H3K4me1 Abcam Cat# ab8895; RRID:AB_306847 Anti H3K9me3 Abcam Cat# ab8898 ;RRID:AB_306848 Chemicals, peptides, and recombinant proteins CH-223191 Invivogen Cat# INH-CH22 ITE Invivogen Cat# tlrl-ite MHY1485 Calbiochem Cat# 5005540001 Critical commercial assays Human CD14 MicroBeads Miltenyi Biotec Cat# 130-050-201 Human CD4 isolation kit Miltenyi Biotec Cat# 130-091-155 Human CD45RO MicroBeads Miltenyi Biotec Cat# 130-046-001 RNeasy Micro kit Qiagen Cat# 74034 miRNeasy Micro kit Qiagen Cat# 217084 Tagment DNA enzyme and buffer Small kit Illumina Cat# 20034197 Deposited data Ex vivo DC-10 and cDC RNA-seq https://doi.org/10.1038/s41423-019-0218-0 GEO: GSE117945 IL-10 stimulated monocyte Microarray https://doi.org/10.1186/s12865-017-0229-5 GEO: GSE82316 MS and HC monocyte RNA-seq https://doi.org/10.1093/brain/awaa421 GEO: GSE137143 ATAC-seq ex vivo DC-10/DC This paper GEO: GSE180753 ATAC-seq in vitro DC-10/DC/AHRinhDC-10 This paper GEO: GSE180754 RNA-seq in vitro DC-10/DC/AHRinhDC-10 This paper GEO: GSE180761 RNA-seq in vitro DC-10 MS/HC This paper GEO: GSE180760 RNA-seq ex vivo DC-10 MS/HC This paper GEO: GSE180755 Oligonucleotides CYP1A1 FAM-Probe Thermo-Fisher Cat# Hs00153120 IL-6 FAM-Probe Thermo-Fisher Cat# Hs00985639 IL-10 FAM-Probe Thermo-Fisher Cat# Hs00174086 ILT-4 (LIRB2) EvaGreen Bio-Rad Cat# dHSaEG5020183 SOCS3 EvaGreen Bio-Rad Cat# dHSaEG5001979 HPRT VIC-probe Bio-Rad Cat# 1409017 Software and algorithms FlowJo v10 BD https://www.flowjo.com/ Prism v9 and v10 GraphPad Software https://www.graphpad.com/ scientific-software/prism/ Morpheus Broad Institute https://software.broadinstitute.org/ morpheus/ DESeq2 https://doi.org/10.1186/s13059-014-0550-8 https://bioconductor.org/packages/ release/bioc/html/DESeq2.html EnrichR https://doi.org/10.1186/1471-2105-14-128 https://maayanlab.cloud/Enrichr/) Metascape https://doi.org/10.1186/1471-2105-14-128 metascape.org DiffBind http://bioconductor.org/packages/release/ bioc/vignettes/DiffBind/inst/doc/DiffBind.pdf https://bioconductor.org/packages/ release/bioc/html/DiffBind.html Regulatory Sequence Analysis Tools (RSAT) https://doi.org/10.1038/nprot.2012.088 http://rsat.sb-roscoff.fr/ TFmotifView https://doi.org/10.1093/nar/gkaa252 http://bardet.u-strasbg.fr/tfmotifview/ (Continued on next page) Cell Reports 42, 112193, March 28, 2023 19 .. REAGENT or RESOURCE SOURCE IDENTIFIER String https://doi.org/10.1093/nar/gky1131 https://string-db.org Gene Set Enrichment Analysis (GSEA) https://doi.org/10.1073/PNAS.0506580102 https://www.gsea-msigdb.org/ gsea/index.jsp Other Recombinant human IL-4 Miltenyi Biotec Cat# 130-093-922 Recombinant human GM-CSF Miltenyi Biotec Cat# 130-093-867 Recombinant human IL-10 Cell Genix Cat# 1414-050
RNA Sequencing:Article Title: Aryl hydrocarbon receptor activity downstream of IL-10 signaling is required to promote regulatory functions in human dendritic cells.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER String https://doi.org/10.1093/nar/gky1131 https://string-db.org Gene Set Enrichment Analysis (GSEA) https://doi.org/10.1073/PNAS.0506580102 https://www.gsea-msigdb.org/ gsea/index.jsp Other Recombinant human IL-4 Miltenyi Biotec Cat# 130-093-922 Recombinant human GM-CSF Miltenyi Biotec Cat# 130-093-867 Recombinant human IL-10 Cell Genix Cat# 1414-050 .. REAGENT or RESOURCE SOURCE IDENTIFIER Biotin Anti-Human and Viral IL-10 (clone JES3-12G8) BD Biosciences Cat# 554499; RRID:AB_395435 Biotin Anti-Human IFNg (clone 4S.B3) BD Biosciences Cat# 554550; RRID:AB_395472 Recombinant Human IL-10 protein Cell Genix Cat# 1414-050 Recombinant Human IFNg R&D Systems Cat# 285-IF100 Anti H3K27ac Abcam Cat# ab4729; RRID:AB_2118291 Anti H3K4me1 Abcam Cat# ab8895; RRID:AB_306847 Anti H3K9me3 Abcam Cat# ab8898 ;RRID:AB_306848 Chemicals, peptides, and recombinant proteins CH-223191 Invivogen Cat# INH-CH22 ITE Invivogen Cat# tlrl-ite MHY1485 Calbiochem Cat# 5005540001 Critical commercial assays Human CD14 MicroBeads Miltenyi Biotec Cat# 130-050-201 Human CD4 isolation kit Miltenyi Biotec Cat# 130-091-155 Human CD45RO MicroBeads Miltenyi Biotec Cat# 130-046-001 RNeasy Micro kit Qiagen Cat# 74034 miRNeasy Micro kit Qiagen Cat# 217084 Tagment DNA enzyme and buffer Small kit Illumina Cat# 20034197 Deposited data Ex vivo DC-10 and cDC RNA-seq https://doi.org/10.1038/s41423-019-0218-0 GEO: GSE117945 IL-10 stimulated monocyte Microarray https://doi.org/10.1186/s12865-017-0229-5 GEO: GSE82316 MS and HC monocyte RNA-seq https://doi.org/10.1093/brain/awaa421 GEO: GSE137143 ATAC-seq ex vivo DC-10/DC This paper GEO: GSE180753 ATAC-seq in vitro DC-10/DC/AHRinhDC-10 This paper GEO: GSE180754 RNA-seq in vitro DC-10/DC/AHRinhDC-10 This paper GEO: GSE180761 RNA-seq in vitro DC-10 MS/HC This paper GEO: GSE180760 RNA-seq ex vivo DC-10 MS/HC This paper GEO: GSE180755 Oligonucleotides CYP1A1 FAM-Probe Thermo-Fisher Cat# Hs00153120 IL-6 FAM-Probe Thermo-Fisher Cat# Hs00985639 IL-10 FAM-Probe Thermo-Fisher Cat# Hs00174086 ILT-4 (LIRB2) EvaGreen Bio-Rad Cat# dHSaEG5020183 SOCS3 EvaGreen Bio-Rad Cat# dHSaEG5001979 HPRT VIC-probe Bio-Rad Cat# 1409017 Software and algorithms FlowJo v10 BD https://www.flowjo.com/ Prism v9 and v10 GraphPad Software https://www.graphpad.com/ scientific-software/prism/ Morpheus Broad Institute https://software.broadinstitute.org/ morpheus/ DESeq2 https://doi.org/10.1186/s13059-014-0550-8 https://bioconductor.org/packages/ release/bioc/html/DESeq2.html EnrichR https://doi.org/10.1186/1471-2105-14-128 https://maayanlab.cloud/Enrichr/) Metascape https://doi.org/10.1186/1471-2105-14-128 metascape.org DiffBind http://bioconductor.org/packages/release/ bioc/vignettes/DiffBind/inst/doc/DiffBind.pdf https://bioconductor.org/packages/ release/bioc/html/DiffBind.html Regulatory Sequence Analysis Tools (RSAT) https://doi.org/10.1038/nprot.2012.088 http://rsat.sb-roscoff.fr/ TFmotifView https://doi.org/10.1093/nar/gkaa252 http://bardet.u-strasbg.fr/tfmotifview/ (Continued on next page) Cell Reports 42, 112193, March 28, 2023 19 .. REAGENT or RESOURCE SOURCE IDENTIFIER String https://doi.org/10.1093/nar/gky1131 https://string-db.org Gene Set Enrichment Analysis (GSEA) https://doi.org/10.1073/PNAS.0506580102 https://www.gsea-msigdb.org/ gsea/index.jsp Other Recombinant human IL-4 Miltenyi Biotec Cat# 130-093-922 Recombinant human GM-CSF Miltenyi Biotec Cat# 130-093-867 Recombinant human IL-10 Cell Genix Cat# 1414-050
Microarray:Article Title: Aryl hydrocarbon receptor activity downstream of IL-10 signaling is required to promote regulatory functions in human dendritic cells.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER String https://doi.org/10.1093/nar/gky1131 https://string-db.org Gene Set Enrichment Analysis (GSEA) https://doi.org/10.1073/PNAS.0506580102 https://www.gsea-msigdb.org/ gsea/index.jsp Other Recombinant human IL-4 Miltenyi Biotec Cat# 130-093-922 Recombinant human GM-CSF Miltenyi Biotec Cat# 130-093-867 Recombinant human IL-10 Cell Genix Cat# 1414-050 .. REAGENT or RESOURCE SOURCE IDENTIFIER Biotin Anti-Human and Viral IL-10 (clone JES3-12G8) BD Biosciences Cat# 554499; RRID:AB_395435 Biotin Anti-Human IFNg (clone 4S.B3) BD Biosciences Cat# 554550; RRID:AB_395472 Recombinant Human IL-10 protein Cell Genix Cat# 1414-050 Recombinant Human IFNg R&D Systems Cat# 285-IF100 Anti H3K27ac Abcam Cat# ab4729; RRID:AB_2118291 Anti H3K4me1 Abcam Cat# ab8895; RRID:AB_306847 Anti H3K9me3 Abcam Cat# ab8898 ;RRID:AB_306848 Chemicals, peptides, and recombinant proteins CH-223191 Invivogen Cat# INH-CH22 ITE Invivogen Cat# tlrl-ite MHY1485 Calbiochem Cat# 5005540001 Critical commercial assays Human CD14 MicroBeads Miltenyi Biotec Cat# 130-050-201 Human CD4 isolation kit Miltenyi Biotec Cat# 130-091-155 Human CD45RO MicroBeads Miltenyi Biotec Cat# 130-046-001 RNeasy Micro kit Qiagen Cat# 74034 miRNeasy Micro kit Qiagen Cat# 217084 Tagment DNA enzyme and buffer Small kit Illumina Cat# 20034197 Deposited data Ex vivo DC-10 and cDC RNA-seq https://doi.org/10.1038/s41423-019-0218-0 GEO: GSE117945 IL-10 stimulated monocyte Microarray https://doi.org/10.1186/s12865-017-0229-5 GEO: GSE82316 MS and HC monocyte RNA-seq https://doi.org/10.1093/brain/awaa421 GEO: GSE137143 ATAC-seq ex vivo DC-10/DC This paper GEO: GSE180753 ATAC-seq in vitro DC-10/DC/AHRinhDC-10 This paper GEO: GSE180754 RNA-seq in vitro DC-10/DC/AHRinhDC-10 This paper GEO: GSE180761 RNA-seq in vitro DC-10 MS/HC This paper GEO: GSE180760 RNA-seq ex vivo DC-10 MS/HC This paper GEO: GSE180755 Oligonucleotides CYP1A1 FAM-Probe Thermo-Fisher Cat# Hs00153120 IL-6 FAM-Probe Thermo-Fisher Cat# Hs00985639 IL-10 FAM-Probe Thermo-Fisher Cat# Hs00174086 ILT-4 (LIRB2) EvaGreen Bio-Rad Cat# dHSaEG5020183 SOCS3 EvaGreen Bio-Rad Cat# dHSaEG5001979 HPRT VIC-probe Bio-Rad Cat# 1409017 Software and algorithms FlowJo v10 BD https://www.flowjo.com/ Prism v9 and v10 GraphPad Software https://www.graphpad.com/ scientific-software/prism/ Morpheus Broad Institute https://software.broadinstitute.org/ morpheus/ DESeq2 https://doi.org/10.1186/s13059-014-0550-8 https://bioconductor.org/packages/ release/bioc/html/DESeq2.html EnrichR https://doi.org/10.1186/1471-2105-14-128 https://maayanlab.cloud/Enrichr/) Metascape https://doi.org/10.1186/1471-2105-14-128 metascape.org DiffBind http://bioconductor.org/packages/release/ bioc/vignettes/DiffBind/inst/doc/DiffBind.pdf https://bioconductor.org/packages/ release/bioc/html/DiffBind.html Regulatory Sequence Analysis Tools (RSAT) https://doi.org/10.1038/nprot.2012.088 http://rsat.sb-roscoff.fr/ TFmotifView https://doi.org/10.1093/nar/gkaa252 http://bardet.u-strasbg.fr/tfmotifview/ (Continued on next page) Cell Reports 42, 112193, March 28, 2023 19 .. REAGENT or RESOURCE SOURCE IDENTIFIER String https://doi.org/10.1093/nar/gky1131 https://string-db.org Gene Set Enrichment Analysis (GSEA) https://doi.org/10.1073/PNAS.0506580102 https://www.gsea-msigdb.org/ gsea/index.jsp Other Recombinant human IL-4 Miltenyi Biotec Cat# 130-093-922 Recombinant human GM-CSF Miltenyi Biotec Cat# 130-093-867 Recombinant human IL-10 Cell Genix Cat# 1414-050
In Vitro:Article Title: Aryl hydrocarbon receptor activity downstream of IL-10 signaling is required to promote regulatory functions in human dendritic cells.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER String https://doi.org/10.1093/nar/gky1131 https://string-db.org Gene Set Enrichment Analysis (GSEA) https://doi.org/10.1073/PNAS.0506580102 https://www.gsea-msigdb.org/ gsea/index.jsp Other Recombinant human IL-4 Miltenyi Biotec Cat# 130-093-922 Recombinant human GM-CSF Miltenyi Biotec Cat# 130-093-867 Recombinant human IL-10 Cell Genix Cat# 1414-050 .. REAGENT or RESOURCE SOURCE IDENTIFIER Biotin Anti-Human and Viral IL-10 (clone JES3-12G8) BD Biosciences Cat# 554499; RRID:AB_395435 Biotin Anti-Human IFNg (clone 4S.B3) BD Biosciences Cat# 554550; RRID:AB_395472 Recombinant Human IL-10 protein Cell Genix Cat# 1414-050 Recombinant Human IFNg R&D Systems Cat# 285-IF100 Anti H3K27ac Abcam Cat# ab4729; RRID:AB_2118291 Anti H3K4me1 Abcam Cat# ab8895; RRID:AB_306847 Anti H3K9me3 Abcam Cat# ab8898 ;RRID:AB_306848 Chemicals, peptides, and recombinant proteins CH-223191 Invivogen Cat# INH-CH22 ITE Invivogen Cat# tlrl-ite MHY1485 Calbiochem Cat# 5005540001 Critical commercial assays Human CD14 MicroBeads Miltenyi Biotec Cat# 130-050-201 Human CD4 isolation kit Miltenyi Biotec Cat# 130-091-155 Human CD45RO MicroBeads Miltenyi Biotec Cat# 130-046-001 RNeasy Micro kit Qiagen Cat# 74034 miRNeasy Micro kit Qiagen Cat# 217084 Tagment DNA enzyme and buffer Small kit Illumina Cat# 20034197 Deposited data Ex vivo DC-10 and cDC RNA-seq https://doi.org/10.1038/s41423-019-0218-0 GEO: GSE117945 IL-10 stimulated monocyte Microarray https://doi.org/10.1186/s12865-017-0229-5 GEO: GSE82316 MS and HC monocyte RNA-seq https://doi.org/10.1093/brain/awaa421 GEO: GSE137143 ATAC-seq ex vivo DC-10/DC This paper GEO: GSE180753 ATAC-seq in vitro DC-10/DC/AHRinhDC-10 This paper GEO: GSE180754 RNA-seq in vitro DC-10/DC/AHRinhDC-10 This paper GEO: GSE180761 RNA-seq in vitro DC-10 MS/HC This paper GEO: GSE180760 RNA-seq ex vivo DC-10 MS/HC This paper GEO: GSE180755 Oligonucleotides CYP1A1 FAM-Probe Thermo-Fisher Cat# Hs00153120 IL-6 FAM-Probe Thermo-Fisher Cat# Hs00985639 IL-10 FAM-Probe Thermo-Fisher Cat# Hs00174086 ILT-4 (LIRB2) EvaGreen Bio-Rad Cat# dHSaEG5020183 SOCS3 EvaGreen Bio-Rad Cat# dHSaEG5001979 HPRT VIC-probe Bio-Rad Cat# 1409017 Software and algorithms FlowJo v10 BD https://www.flowjo.com/ Prism v9 and v10 GraphPad Software https://www.graphpad.com/ scientific-software/prism/ Morpheus Broad Institute https://software.broadinstitute.org/ morpheus/ DESeq2 https://doi.org/10.1186/s13059-014-0550-8 https://bioconductor.org/packages/ release/bioc/html/DESeq2.html EnrichR https://doi.org/10.1186/1471-2105-14-128 https://maayanlab.cloud/Enrichr/) Metascape https://doi.org/10.1186/1471-2105-14-128 metascape.org DiffBind http://bioconductor.org/packages/release/ bioc/vignettes/DiffBind/inst/doc/DiffBind.pdf https://bioconductor.org/packages/ release/bioc/html/DiffBind.html Regulatory Sequence Analysis Tools (RSAT) https://doi.org/10.1038/nprot.2012.088 http://rsat.sb-roscoff.fr/ TFmotifView https://doi.org/10.1093/nar/gkaa252 http://bardet.u-strasbg.fr/tfmotifview/ (Continued on next page) Cell Reports 42, 112193, March 28, 2023 19 .. REAGENT or RESOURCE SOURCE IDENTIFIER String https://doi.org/10.1093/nar/gky1131 https://string-db.org Gene Set Enrichment Analysis (GSEA) https://doi.org/10.1073/PNAS.0506580102 https://www.gsea-msigdb.org/ gsea/index.jsp Other Recombinant human IL-4 Miltenyi Biotec Cat# 130-093-922 Recombinant human GM-CSF Miltenyi Biotec Cat# 130-093-867 Recombinant human IL-10 Cell Genix Cat# 1414-050
|
Miltenyi Biotec is a verified supplier 
Miltenyi Biotec manufactures this product 