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fc 131 1096 slide seq arrays fei chen lab n a dead cell removal kit milteny biotec  (Miltenyi Biotec)


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    Miltenyi Biotec fc 131 1096 slide seq arrays fei chen lab n a dead cell removal kit milteny biotec
    Fc 131 1096 Slide Seq Arrays Fei Chen Lab N A Dead Cell Removal Kit Milteny Biotec, supplied by Miltenyi Biotec, used in various techniques. Bioz Stars score: 99/100, based on 2564 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/array-seq+slide/Dead+Cell+Removal+Kit/pm37393620-462-300-311
    Average 99 stars, based on 2564 article reviews
    fc 131 1096 slide seq arrays fei chen lab n a dead cell removal kit milteny biotec - by Bioz Stars, 2026-11
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    Single Cell:

    Article Title: Tumor DNA methylation subtypes and expression levels of CFISH predict response and overall survival to immunochemotherapy.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Durvalumab AstraZeneca UK, Ltd N/A Tremelimumab AstraZeneca UK, Ltd N/A Biological samples Biopsies of tumor and normal upper gastrointestinal tract tissues from esophageal cancer patients LUD2015-005 clinical trial NCT02735239, EudraCT 2015-005298-19 Chemicals, peptides, and recombinant proteins Heat-inactivated human serum Sigma-Aldrich Cat#H3667 Fetal Bovine Serum Sigma-Aldrich F9665 DMEM/F-12 Gibco Cat#11330032 PBS Gibco Cat#11590476 Bovine Serum Albumin Fraction V Apollo Scientific Cat#BIA3981 Acid-Phenol:Chloroform, pH 4.5 (with IAA, 125:24:1) Invitrogen Cat#AM9720 TURBO DNA-free Kit ThermoFisher Cat#AM1907 Red Blood Cell Lysis Solution (10×) Miltenyi Cat#130-094-183 Animal Free Collagenase/Dispase Blend II Sigma-Aldrich Cat#SCR140 DNAse I Sigma-Aldrich Cat#D5025 Collagenase D Sigma-Aldrich Cat#11088866001 Liberase DL Sigma-Aldrich Cat#5466202001 Oxaliplatin Eloxatin N/A Capecitabine Xeloda N/A Nuclease-free water Ambion AM9937 qPCR primers ThermoFisher N/A mTet1CD Produced in-house per Liu et al.49 N/A Borane-pyridine complex, 95% Alfa Aesar L13178.09 HEPES (pH 8.0) ThermoFisher J63578-AP Ammonium iron (II) sulfate hexahydrate Merck 09719 Alpha–ketoglutarate Merck K3752 Ascorbic acid Merck 95210 Dithiothreitol (DTT) Merck D9779 NaCl ThermoFisher AM9759 ATP Fisher Scientific 10326943 KAPA Hyper Prep Kit PCR-free Roche KK8505 KAPA HiFi HotStart Uracil+ Kit Roche KK2802 KAPA Unique Dual-Indexed Adapters Roche KK8726 Proteinase K ThermoFisher EO0491 Sodium acetate ThermoFisher J63669.AE Tris-HCl ThermoFisher 15567027 Complete Protease Inhibitor Cocktail Roche 4693116001 Triton X-100 ThermoFisher A16046.AE ANTI-FLAG M2 Affinity Gel Millipore A2220 Pierce 3X DYKDDDDK Peptide ThermoFisher A36805 ExpiFectamine 293 Transfection Kit Gibco A14525 Expi293 Expression Medium Gibco A1435101 (Continued on next page) Med 7, 101327, November 13, 2026 e1 Article ll OPEN ACCESS .. REAGENT or RESOURCE SOURCE IDENTIFIER Opti-MEM Reduced Serum Medium Gibco 31985070 Critical commercial assays Chromium Single Cell Immune Profiling Assay (v2) 10x Genomics https://www.10xgenomics.com/products/single- cell-immune-profiling mirVana miRNA Isolation Kit ThermoFisher Cat#AM1560 Dead Cell Removal Kit Miltenyi Cat130-090-101 TruSeq Stranded Total RNA Library Prep Human/ Mouse/Rat Kit Illumina Cat#20020596 GeneJET Genomic DNA Purification Kit ThermoFisher Cat#K0722 Qubit RNA BR Assay ThermoFisher Cat#Q10211 Qubit dsDNA HS Assay ThermoFisher Cat#Q32851 Tapestation High Sensitivity DNA Kit Agilent 5067-4626 Tapestation High Sensitivity RNA Kit Agilent 5067-5579 HiScript IV RT SuperMix for qPCR (+gDNA wiper) Vazyme R423 SYBR qPCR Master Mix Vazyme Q713 Deposited data LUD2015-inop demographics and clinical outcomes (cut-off date 16 October 2020) This paper Tables S1, S2, and S3 LUD2015-inop bulk RNA sequencing Carroll et al.19 EGA :EGAS00001006468 LUD2015-inop single-cell RNA sequencing Carroll et al.19 EGA :EGAS00001006469 LUD2015-inop whole genome sequencing Carroll et al.19 EGA :EGAS00001006470 International Cancer Genome Consortium: ESADUK cohort RNA sequencing counts, mutational burden Frankell et al.32 EGA :EGAD00001004423; https://dcc.icgc.org Bulk RNA sequencing data for ICI-treated gastric cancer (Samsung cohort) Kim et al.29 ENA: PRJEB25780 Bulk RNA sequencing data for ICI-treated gastric cancer (Yonsei and St. Mary’s cohorts) Cheong et al.28 EGA: EGAD00001008091 Control dataset of patients wtih upper gastrointestinal cancers treated in the local NHS Trust during the treatment period of the LUD2015005 study Oxford University NHS Foundation Trust NA Processed RNAseq counts from ICI-treated melanoma Gide et al.30 ENA: PRJEB23709 Processed RNAseq counts from ICI-treated NSCLC Cho et al.,31 GEO: GSE135222 LUD2015-op demographics and clinical outcomes (cut-off date 22 November 2022) This paper Tables S1 and S3, this paper. .. LUD2015-op bulk RNA sequencing This paper EGA: EGAS00001008543 LUD2015-op single-cell RNA sequencing This paper EGA: EGAS00001008543 LUD2015-op whole genome sequencing This paper EGA: EGAS00001008543 Whole genome methylation data for LUD2015-inop (23 patients), and LUD2015-op (29 patients), Barretts2016 (9 samples from 2 patients) This paper EGA: EGAS00001008543 Software and algorithms DESeq2 v1.38.3 Love et al.,79 https://bioconductor.org/packages/release/bioc/ html/DESeq2.html Cell Ranger v7.1.0 10x Genomics https://support.10xgenomics.com/single-cell- gene-expression/software/downloads/3.1/ BayesPrism v2.0 Chu et al.,27 https://github.com/Danko-Lab/TED/ Seurat v4.3.0 Stuart et al.,80 https://satijalab.org/seurat/index.html (Continued on next page) e2 Med 7, 101327, November 13, 2026 Article ll OPEN ACCESS

    Profiling:

    Article Title: Tumor DNA methylation subtypes and expression levels of CFISH predict response and overall survival to immunochemotherapy.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Durvalumab AstraZeneca UK, Ltd N/A Tremelimumab AstraZeneca UK, Ltd N/A Biological samples Biopsies of tumor and normal upper gastrointestinal tract tissues from esophageal cancer patients LUD2015-005 clinical trial NCT02735239, EudraCT 2015-005298-19 Chemicals, peptides, and recombinant proteins Heat-inactivated human serum Sigma-Aldrich Cat#H3667 Fetal Bovine Serum Sigma-Aldrich F9665 DMEM/F-12 Gibco Cat#11330032 PBS Gibco Cat#11590476 Bovine Serum Albumin Fraction V Apollo Scientific Cat#BIA3981 Acid-Phenol:Chloroform, pH 4.5 (with IAA, 125:24:1) Invitrogen Cat#AM9720 TURBO DNA-free Kit ThermoFisher Cat#AM1907 Red Blood Cell Lysis Solution (10×) Miltenyi Cat#130-094-183 Animal Free Collagenase/Dispase Blend II Sigma-Aldrich Cat#SCR140 DNAse I Sigma-Aldrich Cat#D5025 Collagenase D Sigma-Aldrich Cat#11088866001 Liberase DL Sigma-Aldrich Cat#5466202001 Oxaliplatin Eloxatin N/A Capecitabine Xeloda N/A Nuclease-free water Ambion AM9937 qPCR primers ThermoFisher N/A mTet1CD Produced in-house per Liu et al.49 N/A Borane-pyridine complex, 95% Alfa Aesar L13178.09 HEPES (pH 8.0) ThermoFisher J63578-AP Ammonium iron (II) sulfate hexahydrate Merck 09719 Alpha–ketoglutarate Merck K3752 Ascorbic acid Merck 95210 Dithiothreitol (DTT) Merck D9779 NaCl ThermoFisher AM9759 ATP Fisher Scientific 10326943 KAPA Hyper Prep Kit PCR-free Roche KK8505 KAPA HiFi HotStart Uracil+ Kit Roche KK2802 KAPA Unique Dual-Indexed Adapters Roche KK8726 Proteinase K ThermoFisher EO0491 Sodium acetate ThermoFisher J63669.AE Tris-HCl ThermoFisher 15567027 Complete Protease Inhibitor Cocktail Roche 4693116001 Triton X-100 ThermoFisher A16046.AE ANTI-FLAG M2 Affinity Gel Millipore A2220 Pierce 3X DYKDDDDK Peptide ThermoFisher A36805 ExpiFectamine 293 Transfection Kit Gibco A14525 Expi293 Expression Medium Gibco A1435101 (Continued on next page) Med 7, 101327, November 13, 2026 e1 Article ll OPEN ACCESS .. REAGENT or RESOURCE SOURCE IDENTIFIER Opti-MEM Reduced Serum Medium Gibco 31985070 Critical commercial assays Chromium Single Cell Immune Profiling Assay (v2) 10x Genomics https://www.10xgenomics.com/products/single- cell-immune-profiling mirVana miRNA Isolation Kit ThermoFisher Cat#AM1560 Dead Cell Removal Kit Miltenyi Cat130-090-101 TruSeq Stranded Total RNA Library Prep Human/ Mouse/Rat Kit Illumina Cat#20020596 GeneJET Genomic DNA Purification Kit ThermoFisher Cat#K0722 Qubit RNA BR Assay ThermoFisher Cat#Q10211 Qubit dsDNA HS Assay ThermoFisher Cat#Q32851 Tapestation High Sensitivity DNA Kit Agilent 5067-4626 Tapestation High Sensitivity RNA Kit Agilent 5067-5579 HiScript IV RT SuperMix for qPCR (+gDNA wiper) Vazyme R423 SYBR qPCR Master Mix Vazyme Q713 Deposited data LUD2015-inop demographics and clinical outcomes (cut-off date 16 October 2020) This paper Tables S1, S2, and S3 LUD2015-inop bulk RNA sequencing Carroll et al.19 EGA :EGAS00001006468 LUD2015-inop single-cell RNA sequencing Carroll et al.19 EGA :EGAS00001006469 LUD2015-inop whole genome sequencing Carroll et al.19 EGA :EGAS00001006470 International Cancer Genome Consortium: ESADUK cohort RNA sequencing counts, mutational burden Frankell et al.32 EGA :EGAD00001004423; https://dcc.icgc.org Bulk RNA sequencing data for ICI-treated gastric cancer (Samsung cohort) Kim et al.29 ENA: PRJEB25780 Bulk RNA sequencing data for ICI-treated gastric cancer (Yonsei and St. Mary’s cohorts) Cheong et al.28 EGA: EGAD00001008091 Control dataset of patients wtih upper gastrointestinal cancers treated in the local NHS Trust during the treatment period of the LUD2015005 study Oxford University NHS Foundation Trust NA Processed RNAseq counts from ICI-treated melanoma Gide et al.30 ENA: PRJEB23709 Processed RNAseq counts from ICI-treated NSCLC Cho et al.,31 GEO: GSE135222 LUD2015-op demographics and clinical outcomes (cut-off date 22 November 2022) This paper Tables S1 and S3, this paper. .. LUD2015-op bulk RNA sequencing This paper EGA: EGAS00001008543 LUD2015-op single-cell RNA sequencing This paper EGA: EGAS00001008543 LUD2015-op whole genome sequencing This paper EGA: EGAS00001008543 Whole genome methylation data for LUD2015-inop (23 patients), and LUD2015-op (29 patients), Barretts2016 (9 samples from 2 patients) This paper EGA: EGAS00001008543 Software and algorithms DESeq2 v1.38.3 Love et al.,79 https://bioconductor.org/packages/release/bioc/ html/DESeq2.html Cell Ranger v7.1.0 10x Genomics https://support.10xgenomics.com/single-cell- gene-expression/software/downloads/3.1/ BayesPrism v2.0 Chu et al.,27 https://github.com/Danko-Lab/TED/ Seurat v4.3.0 Stuart et al.,80 https://satijalab.org/seurat/index.html (Continued on next page) e2 Med 7, 101327, November 13, 2026 Article ll OPEN ACCESS

    Isolation:

    Article Title: Tumor DNA methylation subtypes and expression levels of CFISH predict response and overall survival to immunochemotherapy.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Durvalumab AstraZeneca UK, Ltd N/A Tremelimumab AstraZeneca UK, Ltd N/A Biological samples Biopsies of tumor and normal upper gastrointestinal tract tissues from esophageal cancer patients LUD2015-005 clinical trial NCT02735239, EudraCT 2015-005298-19 Chemicals, peptides, and recombinant proteins Heat-inactivated human serum Sigma-Aldrich Cat#H3667 Fetal Bovine Serum Sigma-Aldrich F9665 DMEM/F-12 Gibco Cat#11330032 PBS Gibco Cat#11590476 Bovine Serum Albumin Fraction V Apollo Scientific Cat#BIA3981 Acid-Phenol:Chloroform, pH 4.5 (with IAA, 125:24:1) Invitrogen Cat#AM9720 TURBO DNA-free Kit ThermoFisher Cat#AM1907 Red Blood Cell Lysis Solution (10×) Miltenyi Cat#130-094-183 Animal Free Collagenase/Dispase Blend II Sigma-Aldrich Cat#SCR140 DNAse I Sigma-Aldrich Cat#D5025 Collagenase D Sigma-Aldrich Cat#11088866001 Liberase DL Sigma-Aldrich Cat#5466202001 Oxaliplatin Eloxatin N/A Capecitabine Xeloda N/A Nuclease-free water Ambion AM9937 qPCR primers ThermoFisher N/A mTet1CD Produced in-house per Liu et al.49 N/A Borane-pyridine complex, 95% Alfa Aesar L13178.09 HEPES (pH 8.0) ThermoFisher J63578-AP Ammonium iron (II) sulfate hexahydrate Merck 09719 Alpha–ketoglutarate Merck K3752 Ascorbic acid Merck 95210 Dithiothreitol (DTT) Merck D9779 NaCl ThermoFisher AM9759 ATP Fisher Scientific 10326943 KAPA Hyper Prep Kit PCR-free Roche KK8505 KAPA HiFi HotStart Uracil+ Kit Roche KK2802 KAPA Unique Dual-Indexed Adapters Roche KK8726 Proteinase K ThermoFisher EO0491 Sodium acetate ThermoFisher J63669.AE Tris-HCl ThermoFisher 15567027 Complete Protease Inhibitor Cocktail Roche 4693116001 Triton X-100 ThermoFisher A16046.AE ANTI-FLAG M2 Affinity Gel Millipore A2220 Pierce 3X DYKDDDDK Peptide ThermoFisher A36805 ExpiFectamine 293 Transfection Kit Gibco A14525 Expi293 Expression Medium Gibco A1435101 (Continued on next page) Med 7, 101327, November 13, 2026 e1 Article ll OPEN ACCESS .. REAGENT or RESOURCE SOURCE IDENTIFIER Opti-MEM Reduced Serum Medium Gibco 31985070 Critical commercial assays Chromium Single Cell Immune Profiling Assay (v2) 10x Genomics https://www.10xgenomics.com/products/single- cell-immune-profiling mirVana miRNA Isolation Kit ThermoFisher Cat#AM1560 Dead Cell Removal Kit Miltenyi Cat130-090-101 TruSeq Stranded Total RNA Library Prep Human/ Mouse/Rat Kit Illumina Cat#20020596 GeneJET Genomic DNA Purification Kit ThermoFisher Cat#K0722 Qubit RNA BR Assay ThermoFisher Cat#Q10211 Qubit dsDNA HS Assay ThermoFisher Cat#Q32851 Tapestation High Sensitivity DNA Kit Agilent 5067-4626 Tapestation High Sensitivity RNA Kit Agilent 5067-5579 HiScript IV RT SuperMix for qPCR (+gDNA wiper) Vazyme R423 SYBR qPCR Master Mix Vazyme Q713 Deposited data LUD2015-inop demographics and clinical outcomes (cut-off date 16 October 2020) This paper Tables S1, S2, and S3 LUD2015-inop bulk RNA sequencing Carroll et al.19 EGA :EGAS00001006468 LUD2015-inop single-cell RNA sequencing Carroll et al.19 EGA :EGAS00001006469 LUD2015-inop whole genome sequencing Carroll et al.19 EGA :EGAS00001006470 International Cancer Genome Consortium: ESADUK cohort RNA sequencing counts, mutational burden Frankell et al.32 EGA :EGAD00001004423; https://dcc.icgc.org Bulk RNA sequencing data for ICI-treated gastric cancer (Samsung cohort) Kim et al.29 ENA: PRJEB25780 Bulk RNA sequencing data for ICI-treated gastric cancer (Yonsei and St. Mary’s cohorts) Cheong et al.28 EGA: EGAD00001008091 Control dataset of patients wtih upper gastrointestinal cancers treated in the local NHS Trust during the treatment period of the LUD2015005 study Oxford University NHS Foundation Trust NA Processed RNAseq counts from ICI-treated melanoma Gide et al.30 ENA: PRJEB23709 Processed RNAseq counts from ICI-treated NSCLC Cho et al.,31 GEO: GSE135222 LUD2015-op demographics and clinical outcomes (cut-off date 22 November 2022) This paper Tables S1 and S3, this paper. .. LUD2015-op bulk RNA sequencing This paper EGA: EGAS00001008543 LUD2015-op single-cell RNA sequencing This paper EGA: EGAS00001008543 LUD2015-op whole genome sequencing This paper EGA: EGAS00001008543 Whole genome methylation data for LUD2015-inop (23 patients), and LUD2015-op (29 patients), Barretts2016 (9 samples from 2 patients) This paper EGA: EGAS00001008543 Software and algorithms DESeq2 v1.38.3 Love et al.,79 https://bioconductor.org/packages/release/bioc/ html/DESeq2.html Cell Ranger v7.1.0 10x Genomics https://support.10xgenomics.com/single-cell- gene-expression/software/downloads/3.1/ BayesPrism v2.0 Chu et al.,27 https://github.com/Danko-Lab/TED/ Seurat v4.3.0 Stuart et al.,80 https://satijalab.org/seurat/index.html (Continued on next page) e2 Med 7, 101327, November 13, 2026 Article ll OPEN ACCESS

    Article Title: Cabergoline Suppresses Postpartum Breast Cancer by Enhancing Mammary Gland Involution in Brca1-Mutant Mice and Is Associated with Reduced Risk in Younger Women
    Article Snippet: .. Viable cells 1185 were isolated using the Dead Cell Removal Kit (Miltenyi Biotec, 130-090-101) and MS 1186 columns (Miltenyi Biotec, 130-122-727). ..

    DNA Purification:

    Article Title: Tumor DNA methylation subtypes and expression levels of CFISH predict response and overall survival to immunochemotherapy.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Durvalumab AstraZeneca UK, Ltd N/A Tremelimumab AstraZeneca UK, Ltd N/A Biological samples Biopsies of tumor and normal upper gastrointestinal tract tissues from esophageal cancer patients LUD2015-005 clinical trial NCT02735239, EudraCT 2015-005298-19 Chemicals, peptides, and recombinant proteins Heat-inactivated human serum Sigma-Aldrich Cat#H3667 Fetal Bovine Serum Sigma-Aldrich F9665 DMEM/F-12 Gibco Cat#11330032 PBS Gibco Cat#11590476 Bovine Serum Albumin Fraction V Apollo Scientific Cat#BIA3981 Acid-Phenol:Chloroform, pH 4.5 (with IAA, 125:24:1) Invitrogen Cat#AM9720 TURBO DNA-free Kit ThermoFisher Cat#AM1907 Red Blood Cell Lysis Solution (10×) Miltenyi Cat#130-094-183 Animal Free Collagenase/Dispase Blend II Sigma-Aldrich Cat#SCR140 DNAse I Sigma-Aldrich Cat#D5025 Collagenase D Sigma-Aldrich Cat#11088866001 Liberase DL Sigma-Aldrich Cat#5466202001 Oxaliplatin Eloxatin N/A Capecitabine Xeloda N/A Nuclease-free water Ambion AM9937 qPCR primers ThermoFisher N/A mTet1CD Produced in-house per Liu et al.49 N/A Borane-pyridine complex, 95% Alfa Aesar L13178.09 HEPES (pH 8.0) ThermoFisher J63578-AP Ammonium iron (II) sulfate hexahydrate Merck 09719 Alpha–ketoglutarate Merck K3752 Ascorbic acid Merck 95210 Dithiothreitol (DTT) Merck D9779 NaCl ThermoFisher AM9759 ATP Fisher Scientific 10326943 KAPA Hyper Prep Kit PCR-free Roche KK8505 KAPA HiFi HotStart Uracil+ Kit Roche KK2802 KAPA Unique Dual-Indexed Adapters Roche KK8726 Proteinase K ThermoFisher EO0491 Sodium acetate ThermoFisher J63669.AE Tris-HCl ThermoFisher 15567027 Complete Protease Inhibitor Cocktail Roche 4693116001 Triton X-100 ThermoFisher A16046.AE ANTI-FLAG M2 Affinity Gel Millipore A2220 Pierce 3X DYKDDDDK Peptide ThermoFisher A36805 ExpiFectamine 293 Transfection Kit Gibco A14525 Expi293 Expression Medium Gibco A1435101 (Continued on next page) Med 7, 101327, November 13, 2026 e1 Article ll OPEN ACCESS .. REAGENT or RESOURCE SOURCE IDENTIFIER Opti-MEM Reduced Serum Medium Gibco 31985070 Critical commercial assays Chromium Single Cell Immune Profiling Assay (v2) 10x Genomics https://www.10xgenomics.com/products/single- cell-immune-profiling mirVana miRNA Isolation Kit ThermoFisher Cat#AM1560 Dead Cell Removal Kit Miltenyi Cat130-090-101 TruSeq Stranded Total RNA Library Prep Human/ Mouse/Rat Kit Illumina Cat#20020596 GeneJET Genomic DNA Purification Kit ThermoFisher Cat#K0722 Qubit RNA BR Assay ThermoFisher Cat#Q10211 Qubit dsDNA HS Assay ThermoFisher Cat#Q32851 Tapestation High Sensitivity DNA Kit Agilent 5067-4626 Tapestation High Sensitivity RNA Kit Agilent 5067-5579 HiScript IV RT SuperMix for qPCR (+gDNA wiper) Vazyme R423 SYBR qPCR Master Mix Vazyme Q713 Deposited data LUD2015-inop demographics and clinical outcomes (cut-off date 16 October 2020) This paper Tables S1, S2, and S3 LUD2015-inop bulk RNA sequencing Carroll et al.19 EGA :EGAS00001006468 LUD2015-inop single-cell RNA sequencing Carroll et al.19 EGA :EGAS00001006469 LUD2015-inop whole genome sequencing Carroll et al.19 EGA :EGAS00001006470 International Cancer Genome Consortium: ESADUK cohort RNA sequencing counts, mutational burden Frankell et al.32 EGA :EGAD00001004423; https://dcc.icgc.org Bulk RNA sequencing data for ICI-treated gastric cancer (Samsung cohort) Kim et al.29 ENA: PRJEB25780 Bulk RNA sequencing data for ICI-treated gastric cancer (Yonsei and St. Mary’s cohorts) Cheong et al.28 EGA: EGAD00001008091 Control dataset of patients wtih upper gastrointestinal cancers treated in the local NHS Trust during the treatment period of the LUD2015005 study Oxford University NHS Foundation Trust NA Processed RNAseq counts from ICI-treated melanoma Gide et al.30 ENA: PRJEB23709 Processed RNAseq counts from ICI-treated NSCLC Cho et al.,31 GEO: GSE135222 LUD2015-op demographics and clinical outcomes (cut-off date 22 November 2022) This paper Tables S1 and S3, this paper. .. LUD2015-op bulk RNA sequencing This paper EGA: EGAS00001008543 LUD2015-op single-cell RNA sequencing This paper EGA: EGAS00001008543 LUD2015-op whole genome sequencing This paper EGA: EGAS00001008543 Whole genome methylation data for LUD2015-inop (23 patients), and LUD2015-op (29 patients), Barretts2016 (9 samples from 2 patients) This paper EGA: EGAS00001008543 Software and algorithms DESeq2 v1.38.3 Love et al.,79 https://bioconductor.org/packages/release/bioc/ html/DESeq2.html Cell Ranger v7.1.0 10x Genomics https://support.10xgenomics.com/single-cell- gene-expression/software/downloads/3.1/ BayesPrism v2.0 Chu et al.,27 https://github.com/Danko-Lab/TED/ Seurat v4.3.0 Stuart et al.,80 https://satijalab.org/seurat/index.html (Continued on next page) e2 Med 7, 101327, November 13, 2026 Article ll OPEN ACCESS

    Qubit:

    Article Title: Tumor DNA methylation subtypes and expression levels of CFISH predict response and overall survival to immunochemotherapy.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Durvalumab AstraZeneca UK, Ltd N/A Tremelimumab AstraZeneca UK, Ltd N/A Biological samples Biopsies of tumor and normal upper gastrointestinal tract tissues from esophageal cancer patients LUD2015-005 clinical trial NCT02735239, EudraCT 2015-005298-19 Chemicals, peptides, and recombinant proteins Heat-inactivated human serum Sigma-Aldrich Cat#H3667 Fetal Bovine Serum Sigma-Aldrich F9665 DMEM/F-12 Gibco Cat#11330032 PBS Gibco Cat#11590476 Bovine Serum Albumin Fraction V Apollo Scientific Cat#BIA3981 Acid-Phenol:Chloroform, pH 4.5 (with IAA, 125:24:1) Invitrogen Cat#AM9720 TURBO DNA-free Kit ThermoFisher Cat#AM1907 Red Blood Cell Lysis Solution (10×) Miltenyi Cat#130-094-183 Animal Free Collagenase/Dispase Blend II Sigma-Aldrich Cat#SCR140 DNAse I Sigma-Aldrich Cat#D5025 Collagenase D Sigma-Aldrich Cat#11088866001 Liberase DL Sigma-Aldrich Cat#5466202001 Oxaliplatin Eloxatin N/A Capecitabine Xeloda N/A Nuclease-free water Ambion AM9937 qPCR primers ThermoFisher N/A mTet1CD Produced in-house per Liu et al.49 N/A Borane-pyridine complex, 95% Alfa Aesar L13178.09 HEPES (pH 8.0) ThermoFisher J63578-AP Ammonium iron (II) sulfate hexahydrate Merck 09719 Alpha–ketoglutarate Merck K3752 Ascorbic acid Merck 95210 Dithiothreitol (DTT) Merck D9779 NaCl ThermoFisher AM9759 ATP Fisher Scientific 10326943 KAPA Hyper Prep Kit PCR-free Roche KK8505 KAPA HiFi HotStart Uracil+ Kit Roche KK2802 KAPA Unique Dual-Indexed Adapters Roche KK8726 Proteinase K ThermoFisher EO0491 Sodium acetate ThermoFisher J63669.AE Tris-HCl ThermoFisher 15567027 Complete Protease Inhibitor Cocktail Roche 4693116001 Triton X-100 ThermoFisher A16046.AE ANTI-FLAG M2 Affinity Gel Millipore A2220 Pierce 3X DYKDDDDK Peptide ThermoFisher A36805 ExpiFectamine 293 Transfection Kit Gibco A14525 Expi293 Expression Medium Gibco A1435101 (Continued on next page) Med 7, 101327, November 13, 2026 e1 Article ll OPEN ACCESS .. REAGENT or RESOURCE SOURCE IDENTIFIER Opti-MEM Reduced Serum Medium Gibco 31985070 Critical commercial assays Chromium Single Cell Immune Profiling Assay (v2) 10x Genomics https://www.10xgenomics.com/products/single- cell-immune-profiling mirVana miRNA Isolation Kit ThermoFisher Cat#AM1560 Dead Cell Removal Kit Miltenyi Cat130-090-101 TruSeq Stranded Total RNA Library Prep Human/ Mouse/Rat Kit Illumina Cat#20020596 GeneJET Genomic DNA Purification Kit ThermoFisher Cat#K0722 Qubit RNA BR Assay ThermoFisher Cat#Q10211 Qubit dsDNA HS Assay ThermoFisher Cat#Q32851 Tapestation High Sensitivity DNA Kit Agilent 5067-4626 Tapestation High Sensitivity RNA Kit Agilent 5067-5579 HiScript IV RT SuperMix for qPCR (+gDNA wiper) Vazyme R423 SYBR qPCR Master Mix Vazyme Q713 Deposited data LUD2015-inop demographics and clinical outcomes (cut-off date 16 October 2020) This paper Tables S1, S2, and S3 LUD2015-inop bulk RNA sequencing Carroll et al.19 EGA :EGAS00001006468 LUD2015-inop single-cell RNA sequencing Carroll et al.19 EGA :EGAS00001006469 LUD2015-inop whole genome sequencing Carroll et al.19 EGA :EGAS00001006470 International Cancer Genome Consortium: ESADUK cohort RNA sequencing counts, mutational burden Frankell et al.32 EGA :EGAD00001004423; https://dcc.icgc.org Bulk RNA sequencing data for ICI-treated gastric cancer (Samsung cohort) Kim et al.29 ENA: PRJEB25780 Bulk RNA sequencing data for ICI-treated gastric cancer (Yonsei and St. Mary’s cohorts) Cheong et al.28 EGA: EGAD00001008091 Control dataset of patients wtih upper gastrointestinal cancers treated in the local NHS Trust during the treatment period of the LUD2015005 study Oxford University NHS Foundation Trust NA Processed RNAseq counts from ICI-treated melanoma Gide et al.30 ENA: PRJEB23709 Processed RNAseq counts from ICI-treated NSCLC Cho et al.,31 GEO: GSE135222 LUD2015-op demographics and clinical outcomes (cut-off date 22 November 2022) This paper Tables S1 and S3, this paper. .. LUD2015-op bulk RNA sequencing This paper EGA: EGAS00001008543 LUD2015-op single-cell RNA sequencing This paper EGA: EGAS00001008543 LUD2015-op whole genome sequencing This paper EGA: EGAS00001008543 Whole genome methylation data for LUD2015-inop (23 patients), and LUD2015-op (29 patients), Barretts2016 (9 samples from 2 patients) This paper EGA: EGAS00001008543 Software and algorithms DESeq2 v1.38.3 Love et al.,79 https://bioconductor.org/packages/release/bioc/ html/DESeq2.html Cell Ranger v7.1.0 10x Genomics https://support.10xgenomics.com/single-cell- gene-expression/software/downloads/3.1/ BayesPrism v2.0 Chu et al.,27 https://github.com/Danko-Lab/TED/ Seurat v4.3.0 Stuart et al.,80 https://satijalab.org/seurat/index.html (Continued on next page) e2 Med 7, 101327, November 13, 2026 Article ll OPEN ACCESS

    Sensitivity:

    Article Title: Tumor DNA methylation subtypes and expression levels of CFISH predict response and overall survival to immunochemotherapy.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Durvalumab AstraZeneca UK, Ltd N/A Tremelimumab AstraZeneca UK, Ltd N/A Biological samples Biopsies of tumor and normal upper gastrointestinal tract tissues from esophageal cancer patients LUD2015-005 clinical trial NCT02735239, EudraCT 2015-005298-19 Chemicals, peptides, and recombinant proteins Heat-inactivated human serum Sigma-Aldrich Cat#H3667 Fetal Bovine Serum Sigma-Aldrich F9665 DMEM/F-12 Gibco Cat#11330032 PBS Gibco Cat#11590476 Bovine Serum Albumin Fraction V Apollo Scientific Cat#BIA3981 Acid-Phenol:Chloroform, pH 4.5 (with IAA, 125:24:1) Invitrogen Cat#AM9720 TURBO DNA-free Kit ThermoFisher Cat#AM1907 Red Blood Cell Lysis Solution (10×) Miltenyi Cat#130-094-183 Animal Free Collagenase/Dispase Blend II Sigma-Aldrich Cat#SCR140 DNAse I Sigma-Aldrich Cat#D5025 Collagenase D Sigma-Aldrich Cat#11088866001 Liberase DL Sigma-Aldrich Cat#5466202001 Oxaliplatin Eloxatin N/A Capecitabine Xeloda N/A Nuclease-free water Ambion AM9937 qPCR primers ThermoFisher N/A mTet1CD Produced in-house per Liu et al.49 N/A Borane-pyridine complex, 95% Alfa Aesar L13178.09 HEPES (pH 8.0) ThermoFisher J63578-AP Ammonium iron (II) sulfate hexahydrate Merck 09719 Alpha–ketoglutarate Merck K3752 Ascorbic acid Merck 95210 Dithiothreitol (DTT) Merck D9779 NaCl ThermoFisher AM9759 ATP Fisher Scientific 10326943 KAPA Hyper Prep Kit PCR-free Roche KK8505 KAPA HiFi HotStart Uracil+ Kit Roche KK2802 KAPA Unique Dual-Indexed Adapters Roche KK8726 Proteinase K ThermoFisher EO0491 Sodium acetate ThermoFisher J63669.AE Tris-HCl ThermoFisher 15567027 Complete Protease Inhibitor Cocktail Roche 4693116001 Triton X-100 ThermoFisher A16046.AE ANTI-FLAG M2 Affinity Gel Millipore A2220 Pierce 3X DYKDDDDK Peptide ThermoFisher A36805 ExpiFectamine 293 Transfection Kit Gibco A14525 Expi293 Expression Medium Gibco A1435101 (Continued on next page) Med 7, 101327, November 13, 2026 e1 Article ll OPEN ACCESS .. REAGENT or RESOURCE SOURCE IDENTIFIER Opti-MEM Reduced Serum Medium Gibco 31985070 Critical commercial assays Chromium Single Cell Immune Profiling Assay (v2) 10x Genomics https://www.10xgenomics.com/products/single- cell-immune-profiling mirVana miRNA Isolation Kit ThermoFisher Cat#AM1560 Dead Cell Removal Kit Miltenyi Cat130-090-101 TruSeq Stranded Total RNA Library Prep Human/ Mouse/Rat Kit Illumina Cat#20020596 GeneJET Genomic DNA Purification Kit ThermoFisher Cat#K0722 Qubit RNA BR Assay ThermoFisher Cat#Q10211 Qubit dsDNA HS Assay ThermoFisher Cat#Q32851 Tapestation High Sensitivity DNA Kit Agilent 5067-4626 Tapestation High Sensitivity RNA Kit Agilent 5067-5579 HiScript IV RT SuperMix for qPCR (+gDNA wiper) Vazyme R423 SYBR qPCR Master Mix Vazyme Q713 Deposited data LUD2015-inop demographics and clinical outcomes (cut-off date 16 October 2020) This paper Tables S1, S2, and S3 LUD2015-inop bulk RNA sequencing Carroll et al.19 EGA :EGAS00001006468 LUD2015-inop single-cell RNA sequencing Carroll et al.19 EGA :EGAS00001006469 LUD2015-inop whole genome sequencing Carroll et al.19 EGA :EGAS00001006470 International Cancer Genome Consortium: ESADUK cohort RNA sequencing counts, mutational burden Frankell et al.32 EGA :EGAD00001004423; https://dcc.icgc.org Bulk RNA sequencing data for ICI-treated gastric cancer (Samsung cohort) Kim et al.29 ENA: PRJEB25780 Bulk RNA sequencing data for ICI-treated gastric cancer (Yonsei and St. Mary’s cohorts) Cheong et al.28 EGA: EGAD00001008091 Control dataset of patients wtih upper gastrointestinal cancers treated in the local NHS Trust during the treatment period of the LUD2015005 study Oxford University NHS Foundation Trust NA Processed RNAseq counts from ICI-treated melanoma Gide et al.30 ENA: PRJEB23709 Processed RNAseq counts from ICI-treated NSCLC Cho et al.,31 GEO: GSE135222 LUD2015-op demographics and clinical outcomes (cut-off date 22 November 2022) This paper Tables S1 and S3, this paper. .. LUD2015-op bulk RNA sequencing This paper EGA: EGAS00001008543 LUD2015-op single-cell RNA sequencing This paper EGA: EGAS00001008543 LUD2015-op whole genome sequencing This paper EGA: EGAS00001008543 Whole genome methylation data for LUD2015-inop (23 patients), and LUD2015-op (29 patients), Barretts2016 (9 samples from 2 patients) This paper EGA: EGAS00001008543 Software and algorithms DESeq2 v1.38.3 Love et al.,79 https://bioconductor.org/packages/release/bioc/ html/DESeq2.html Cell Ranger v7.1.0 10x Genomics https://support.10xgenomics.com/single-cell- gene-expression/software/downloads/3.1/ BayesPrism v2.0 Chu et al.,27 https://github.com/Danko-Lab/TED/ Seurat v4.3.0 Stuart et al.,80 https://satijalab.org/seurat/index.html (Continued on next page) e2 Med 7, 101327, November 13, 2026 Article ll OPEN ACCESS

    Real-time Polymerase Chain Reaction:

    Article Title: Tumor DNA methylation subtypes and expression levels of CFISH predict response and overall survival to immunochemotherapy.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Durvalumab AstraZeneca UK, Ltd N/A Tremelimumab AstraZeneca UK, Ltd N/A Biological samples Biopsies of tumor and normal upper gastrointestinal tract tissues from esophageal cancer patients LUD2015-005 clinical trial NCT02735239, EudraCT 2015-005298-19 Chemicals, peptides, and recombinant proteins Heat-inactivated human serum Sigma-Aldrich Cat#H3667 Fetal Bovine Serum Sigma-Aldrich F9665 DMEM/F-12 Gibco Cat#11330032 PBS Gibco Cat#11590476 Bovine Serum Albumin Fraction V Apollo Scientific Cat#BIA3981 Acid-Phenol:Chloroform, pH 4.5 (with IAA, 125:24:1) Invitrogen Cat#AM9720 TURBO DNA-free Kit ThermoFisher Cat#AM1907 Red Blood Cell Lysis Solution (10×) Miltenyi Cat#130-094-183 Animal Free Collagenase/Dispase Blend II Sigma-Aldrich Cat#SCR140 DNAse I Sigma-Aldrich Cat#D5025 Collagenase D Sigma-Aldrich Cat#11088866001 Liberase DL Sigma-Aldrich Cat#5466202001 Oxaliplatin Eloxatin N/A Capecitabine Xeloda N/A Nuclease-free water Ambion AM9937 qPCR primers ThermoFisher N/A mTet1CD Produced in-house per Liu et al.49 N/A Borane-pyridine complex, 95% Alfa Aesar L13178.09 HEPES (pH 8.0) ThermoFisher J63578-AP Ammonium iron (II) sulfate hexahydrate Merck 09719 Alpha–ketoglutarate Merck K3752 Ascorbic acid Merck 95210 Dithiothreitol (DTT) Merck D9779 NaCl ThermoFisher AM9759 ATP Fisher Scientific 10326943 KAPA Hyper Prep Kit PCR-free Roche KK8505 KAPA HiFi HotStart Uracil+ Kit Roche KK2802 KAPA Unique Dual-Indexed Adapters Roche KK8726 Proteinase K ThermoFisher EO0491 Sodium acetate ThermoFisher J63669.AE Tris-HCl ThermoFisher 15567027 Complete Protease Inhibitor Cocktail Roche 4693116001 Triton X-100 ThermoFisher A16046.AE ANTI-FLAG M2 Affinity Gel Millipore A2220 Pierce 3X DYKDDDDK Peptide ThermoFisher A36805 ExpiFectamine 293 Transfection Kit Gibco A14525 Expi293 Expression Medium Gibco A1435101 (Continued on next page) Med 7, 101327, November 13, 2026 e1 Article ll OPEN ACCESS .. REAGENT or RESOURCE SOURCE IDENTIFIER Opti-MEM Reduced Serum Medium Gibco 31985070 Critical commercial assays Chromium Single Cell Immune Profiling Assay (v2) 10x Genomics https://www.10xgenomics.com/products/single- cell-immune-profiling mirVana miRNA Isolation Kit ThermoFisher Cat#AM1560 Dead Cell Removal Kit Miltenyi Cat130-090-101 TruSeq Stranded Total RNA Library Prep Human/ Mouse/Rat Kit Illumina Cat#20020596 GeneJET Genomic DNA Purification Kit ThermoFisher Cat#K0722 Qubit RNA BR Assay ThermoFisher Cat#Q10211 Qubit dsDNA HS Assay ThermoFisher Cat#Q32851 Tapestation High Sensitivity DNA Kit Agilent 5067-4626 Tapestation High Sensitivity RNA Kit Agilent 5067-5579 HiScript IV RT SuperMix for qPCR (+gDNA wiper) Vazyme R423 SYBR qPCR Master Mix Vazyme Q713 Deposited data LUD2015-inop demographics and clinical outcomes (cut-off date 16 October 2020) This paper Tables S1, S2, and S3 LUD2015-inop bulk RNA sequencing Carroll et al.19 EGA :EGAS00001006468 LUD2015-inop single-cell RNA sequencing Carroll et al.19 EGA :EGAS00001006469 LUD2015-inop whole genome sequencing Carroll et al.19 EGA :EGAS00001006470 International Cancer Genome Consortium: ESADUK cohort RNA sequencing counts, mutational burden Frankell et al.32 EGA :EGAD00001004423; https://dcc.icgc.org Bulk RNA sequencing data for ICI-treated gastric cancer (Samsung cohort) Kim et al.29 ENA: PRJEB25780 Bulk RNA sequencing data for ICI-treated gastric cancer (Yonsei and St. Mary’s cohorts) Cheong et al.28 EGA: EGAD00001008091 Control dataset of patients wtih upper gastrointestinal cancers treated in the local NHS Trust during the treatment period of the LUD2015005 study Oxford University NHS Foundation Trust NA Processed RNAseq counts from ICI-treated melanoma Gide et al.30 ENA: PRJEB23709 Processed RNAseq counts from ICI-treated NSCLC Cho et al.,31 GEO: GSE135222 LUD2015-op demographics and clinical outcomes (cut-off date 22 November 2022) This paper Tables S1 and S3, this paper. .. LUD2015-op bulk RNA sequencing This paper EGA: EGAS00001008543 LUD2015-op single-cell RNA sequencing This paper EGA: EGAS00001008543 LUD2015-op whole genome sequencing This paper EGA: EGAS00001008543 Whole genome methylation data for LUD2015-inop (23 patients), and LUD2015-op (29 patients), Barretts2016 (9 samples from 2 patients) This paper EGA: EGAS00001008543 Software and algorithms DESeq2 v1.38.3 Love et al.,79 https://bioconductor.org/packages/release/bioc/ html/DESeq2.html Cell Ranger v7.1.0 10x Genomics https://support.10xgenomics.com/single-cell- gene-expression/software/downloads/3.1/ BayesPrism v2.0 Chu et al.,27 https://github.com/Danko-Lab/TED/ Seurat v4.3.0 Stuart et al.,80 https://satijalab.org/seurat/index.html (Continued on next page) e2 Med 7, 101327, November 13, 2026 Article ll OPEN ACCESS

    Bulk RNA Sequencing:

    Article Title: Tumor DNA methylation subtypes and expression levels of CFISH predict response and overall survival to immunochemotherapy.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Durvalumab AstraZeneca UK, Ltd N/A Tremelimumab AstraZeneca UK, Ltd N/A Biological samples Biopsies of tumor and normal upper gastrointestinal tract tissues from esophageal cancer patients LUD2015-005 clinical trial NCT02735239, EudraCT 2015-005298-19 Chemicals, peptides, and recombinant proteins Heat-inactivated human serum Sigma-Aldrich Cat#H3667 Fetal Bovine Serum Sigma-Aldrich F9665 DMEM/F-12 Gibco Cat#11330032 PBS Gibco Cat#11590476 Bovine Serum Albumin Fraction V Apollo Scientific Cat#BIA3981 Acid-Phenol:Chloroform, pH 4.5 (with IAA, 125:24:1) Invitrogen Cat#AM9720 TURBO DNA-free Kit ThermoFisher Cat#AM1907 Red Blood Cell Lysis Solution (10×) Miltenyi Cat#130-094-183 Animal Free Collagenase/Dispase Blend II Sigma-Aldrich Cat#SCR140 DNAse I Sigma-Aldrich Cat#D5025 Collagenase D Sigma-Aldrich Cat#11088866001 Liberase DL Sigma-Aldrich Cat#5466202001 Oxaliplatin Eloxatin N/A Capecitabine Xeloda N/A Nuclease-free water Ambion AM9937 qPCR primers ThermoFisher N/A mTet1CD Produced in-house per Liu et al.49 N/A Borane-pyridine complex, 95% Alfa Aesar L13178.09 HEPES (pH 8.0) ThermoFisher J63578-AP Ammonium iron (II) sulfate hexahydrate Merck 09719 Alpha–ketoglutarate Merck K3752 Ascorbic acid Merck 95210 Dithiothreitol (DTT) Merck D9779 NaCl ThermoFisher AM9759 ATP Fisher Scientific 10326943 KAPA Hyper Prep Kit PCR-free Roche KK8505 KAPA HiFi HotStart Uracil+ Kit Roche KK2802 KAPA Unique Dual-Indexed Adapters Roche KK8726 Proteinase K ThermoFisher EO0491 Sodium acetate ThermoFisher J63669.AE Tris-HCl ThermoFisher 15567027 Complete Protease Inhibitor Cocktail Roche 4693116001 Triton X-100 ThermoFisher A16046.AE ANTI-FLAG M2 Affinity Gel Millipore A2220 Pierce 3X DYKDDDDK Peptide ThermoFisher A36805 ExpiFectamine 293 Transfection Kit Gibco A14525 Expi293 Expression Medium Gibco A1435101 (Continued on next page) Med 7, 101327, November 13, 2026 e1 Article ll OPEN ACCESS .. REAGENT or RESOURCE SOURCE IDENTIFIER Opti-MEM Reduced Serum Medium Gibco 31985070 Critical commercial assays Chromium Single Cell Immune Profiling Assay (v2) 10x Genomics https://www.10xgenomics.com/products/single- cell-immune-profiling mirVana miRNA Isolation Kit ThermoFisher Cat#AM1560 Dead Cell Removal Kit Miltenyi Cat130-090-101 TruSeq Stranded Total RNA Library Prep Human/ Mouse/Rat Kit Illumina Cat#20020596 GeneJET Genomic DNA Purification Kit ThermoFisher Cat#K0722 Qubit RNA BR Assay ThermoFisher Cat#Q10211 Qubit dsDNA HS Assay ThermoFisher Cat#Q32851 Tapestation High Sensitivity DNA Kit Agilent 5067-4626 Tapestation High Sensitivity RNA Kit Agilent 5067-5579 HiScript IV RT SuperMix for qPCR (+gDNA wiper) Vazyme R423 SYBR qPCR Master Mix Vazyme Q713 Deposited data LUD2015-inop demographics and clinical outcomes (cut-off date 16 October 2020) This paper Tables S1, S2, and S3 LUD2015-inop bulk RNA sequencing Carroll et al.19 EGA :EGAS00001006468 LUD2015-inop single-cell RNA sequencing Carroll et al.19 EGA :EGAS00001006469 LUD2015-inop whole genome sequencing Carroll et al.19 EGA :EGAS00001006470 International Cancer Genome Consortium: ESADUK cohort RNA sequencing counts, mutational burden Frankell et al.32 EGA :EGAD00001004423; https://dcc.icgc.org Bulk RNA sequencing data for ICI-treated gastric cancer (Samsung cohort) Kim et al.29 ENA: PRJEB25780 Bulk RNA sequencing data for ICI-treated gastric cancer (Yonsei and St. Mary’s cohorts) Cheong et al.28 EGA: EGAD00001008091 Control dataset of patients wtih upper gastrointestinal cancers treated in the local NHS Trust during the treatment period of the LUD2015005 study Oxford University NHS Foundation Trust NA Processed RNAseq counts from ICI-treated melanoma Gide et al.30 ENA: PRJEB23709 Processed RNAseq counts from ICI-treated NSCLC Cho et al.,31 GEO: GSE135222 LUD2015-op demographics and clinical outcomes (cut-off date 22 November 2022) This paper Tables S1 and S3, this paper. .. LUD2015-op bulk RNA sequencing This paper EGA: EGAS00001008543 LUD2015-op single-cell RNA sequencing This paper EGA: EGAS00001008543 LUD2015-op whole genome sequencing This paper EGA: EGAS00001008543 Whole genome methylation data for LUD2015-inop (23 patients), and LUD2015-op (29 patients), Barretts2016 (9 samples from 2 patients) This paper EGA: EGAS00001008543 Software and algorithms DESeq2 v1.38.3 Love et al.,79 https://bioconductor.org/packages/release/bioc/ html/DESeq2.html Cell Ranger v7.1.0 10x Genomics https://support.10xgenomics.com/single-cell- gene-expression/software/downloads/3.1/ BayesPrism v2.0 Chu et al.,27 https://github.com/Danko-Lab/TED/ Seurat v4.3.0 Stuart et al.,80 https://satijalab.org/seurat/index.html (Continued on next page) e2 Med 7, 101327, November 13, 2026 Article ll OPEN ACCESS

    RNA Sequencing:

    Article Title: Tumor DNA methylation subtypes and expression levels of CFISH predict response and overall survival to immunochemotherapy.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Durvalumab AstraZeneca UK, Ltd N/A Tremelimumab AstraZeneca UK, Ltd N/A Biological samples Biopsies of tumor and normal upper gastrointestinal tract tissues from esophageal cancer patients LUD2015-005 clinical trial NCT02735239, EudraCT 2015-005298-19 Chemicals, peptides, and recombinant proteins Heat-inactivated human serum Sigma-Aldrich Cat#H3667 Fetal Bovine Serum Sigma-Aldrich F9665 DMEM/F-12 Gibco Cat#11330032 PBS Gibco Cat#11590476 Bovine Serum Albumin Fraction V Apollo Scientific Cat#BIA3981 Acid-Phenol:Chloroform, pH 4.5 (with IAA, 125:24:1) Invitrogen Cat#AM9720 TURBO DNA-free Kit ThermoFisher Cat#AM1907 Red Blood Cell Lysis Solution (10×) Miltenyi Cat#130-094-183 Animal Free Collagenase/Dispase Blend II Sigma-Aldrich Cat#SCR140 DNAse I Sigma-Aldrich Cat#D5025 Collagenase D Sigma-Aldrich Cat#11088866001 Liberase DL Sigma-Aldrich Cat#5466202001 Oxaliplatin Eloxatin N/A Capecitabine Xeloda N/A Nuclease-free water Ambion AM9937 qPCR primers ThermoFisher N/A mTet1CD Produced in-house per Liu et al.49 N/A Borane-pyridine complex, 95% Alfa Aesar L13178.09 HEPES (pH 8.0) ThermoFisher J63578-AP Ammonium iron (II) sulfate hexahydrate Merck 09719 Alpha–ketoglutarate Merck K3752 Ascorbic acid Merck 95210 Dithiothreitol (DTT) Merck D9779 NaCl ThermoFisher AM9759 ATP Fisher Scientific 10326943 KAPA Hyper Prep Kit PCR-free Roche KK8505 KAPA HiFi HotStart Uracil+ Kit Roche KK2802 KAPA Unique Dual-Indexed Adapters Roche KK8726 Proteinase K ThermoFisher EO0491 Sodium acetate ThermoFisher J63669.AE Tris-HCl ThermoFisher 15567027 Complete Protease Inhibitor Cocktail Roche 4693116001 Triton X-100 ThermoFisher A16046.AE ANTI-FLAG M2 Affinity Gel Millipore A2220 Pierce 3X DYKDDDDK Peptide ThermoFisher A36805 ExpiFectamine 293 Transfection Kit Gibco A14525 Expi293 Expression Medium Gibco A1435101 (Continued on next page) Med 7, 101327, November 13, 2026 e1 Article ll OPEN ACCESS .. REAGENT or RESOURCE SOURCE IDENTIFIER Opti-MEM Reduced Serum Medium Gibco 31985070 Critical commercial assays Chromium Single Cell Immune Profiling Assay (v2) 10x Genomics https://www.10xgenomics.com/products/single- cell-immune-profiling mirVana miRNA Isolation Kit ThermoFisher Cat#AM1560 Dead Cell Removal Kit Miltenyi Cat130-090-101 TruSeq Stranded Total RNA Library Prep Human/ Mouse/Rat Kit Illumina Cat#20020596 GeneJET Genomic DNA Purification Kit ThermoFisher Cat#K0722 Qubit RNA BR Assay ThermoFisher Cat#Q10211 Qubit dsDNA HS Assay ThermoFisher Cat#Q32851 Tapestation High Sensitivity DNA Kit Agilent 5067-4626 Tapestation High Sensitivity RNA Kit Agilent 5067-5579 HiScript IV RT SuperMix for qPCR (+gDNA wiper) Vazyme R423 SYBR qPCR Master Mix Vazyme Q713 Deposited data LUD2015-inop demographics and clinical outcomes (cut-off date 16 October 2020) This paper Tables S1, S2, and S3 LUD2015-inop bulk RNA sequencing Carroll et al.19 EGA :EGAS00001006468 LUD2015-inop single-cell RNA sequencing Carroll et al.19 EGA :EGAS00001006469 LUD2015-inop whole genome sequencing Carroll et al.19 EGA :EGAS00001006470 International Cancer Genome Consortium: ESADUK cohort RNA sequencing counts, mutational burden Frankell et al.32 EGA :EGAD00001004423; https://dcc.icgc.org Bulk RNA sequencing data for ICI-treated gastric cancer (Samsung cohort) Kim et al.29 ENA: PRJEB25780 Bulk RNA sequencing data for ICI-treated gastric cancer (Yonsei and St. Mary’s cohorts) Cheong et al.28 EGA: EGAD00001008091 Control dataset of patients wtih upper gastrointestinal cancers treated in the local NHS Trust during the treatment period of the LUD2015005 study Oxford University NHS Foundation Trust NA Processed RNAseq counts from ICI-treated melanoma Gide et al.30 ENA: PRJEB23709 Processed RNAseq counts from ICI-treated NSCLC Cho et al.,31 GEO: GSE135222 LUD2015-op demographics and clinical outcomes (cut-off date 22 November 2022) This paper Tables S1 and S3, this paper. .. LUD2015-op bulk RNA sequencing This paper EGA: EGAS00001008543 LUD2015-op single-cell RNA sequencing This paper EGA: EGAS00001008543 LUD2015-op whole genome sequencing This paper EGA: EGAS00001008543 Whole genome methylation data for LUD2015-inop (23 patients), and LUD2015-op (29 patients), Barretts2016 (9 samples from 2 patients) This paper EGA: EGAS00001008543 Software and algorithms DESeq2 v1.38.3 Love et al.,79 https://bioconductor.org/packages/release/bioc/ html/DESeq2.html Cell Ranger v7.1.0 10x Genomics https://support.10xgenomics.com/single-cell- gene-expression/software/downloads/3.1/ BayesPrism v2.0 Chu et al.,27 https://github.com/Danko-Lab/TED/ Seurat v4.3.0 Stuart et al.,80 https://satijalab.org/seurat/index.html (Continued on next page) e2 Med 7, 101327, November 13, 2026 Article ll OPEN ACCESS

    Whole-Genome Sequencing:

    Article Title: Tumor DNA methylation subtypes and expression levels of CFISH predict response and overall survival to immunochemotherapy.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Durvalumab AstraZeneca UK, Ltd N/A Tremelimumab AstraZeneca UK, Ltd N/A Biological samples Biopsies of tumor and normal upper gastrointestinal tract tissues from esophageal cancer patients LUD2015-005 clinical trial NCT02735239, EudraCT 2015-005298-19 Chemicals, peptides, and recombinant proteins Heat-inactivated human serum Sigma-Aldrich Cat#H3667 Fetal Bovine Serum Sigma-Aldrich F9665 DMEM/F-12 Gibco Cat#11330032 PBS Gibco Cat#11590476 Bovine Serum Albumin Fraction V Apollo Scientific Cat#BIA3981 Acid-Phenol:Chloroform, pH 4.5 (with IAA, 125:24:1) Invitrogen Cat#AM9720 TURBO DNA-free Kit ThermoFisher Cat#AM1907 Red Blood Cell Lysis Solution (10×) Miltenyi Cat#130-094-183 Animal Free Collagenase/Dispase Blend II Sigma-Aldrich Cat#SCR140 DNAse I Sigma-Aldrich Cat#D5025 Collagenase D Sigma-Aldrich Cat#11088866001 Liberase DL Sigma-Aldrich Cat#5466202001 Oxaliplatin Eloxatin N/A Capecitabine Xeloda N/A Nuclease-free water Ambion AM9937 qPCR primers ThermoFisher N/A mTet1CD Produced in-house per Liu et al.49 N/A Borane-pyridine complex, 95% Alfa Aesar L13178.09 HEPES (pH 8.0) ThermoFisher J63578-AP Ammonium iron (II) sulfate hexahydrate Merck 09719 Alpha–ketoglutarate Merck K3752 Ascorbic acid Merck 95210 Dithiothreitol (DTT) Merck D9779 NaCl ThermoFisher AM9759 ATP Fisher Scientific 10326943 KAPA Hyper Prep Kit PCR-free Roche KK8505 KAPA HiFi HotStart Uracil+ Kit Roche KK2802 KAPA Unique Dual-Indexed Adapters Roche KK8726 Proteinase K ThermoFisher EO0491 Sodium acetate ThermoFisher J63669.AE Tris-HCl ThermoFisher 15567027 Complete Protease Inhibitor Cocktail Roche 4693116001 Triton X-100 ThermoFisher A16046.AE ANTI-FLAG M2 Affinity Gel Millipore A2220 Pierce 3X DYKDDDDK Peptide ThermoFisher A36805 ExpiFectamine 293 Transfection Kit Gibco A14525 Expi293 Expression Medium Gibco A1435101 (Continued on next page) Med 7, 101327, November 13, 2026 e1 Article ll OPEN ACCESS .. REAGENT or RESOURCE SOURCE IDENTIFIER Opti-MEM Reduced Serum Medium Gibco 31985070 Critical commercial assays Chromium Single Cell Immune Profiling Assay (v2) 10x Genomics https://www.10xgenomics.com/products/single- cell-immune-profiling mirVana miRNA Isolation Kit ThermoFisher Cat#AM1560 Dead Cell Removal Kit Miltenyi Cat130-090-101 TruSeq Stranded Total RNA Library Prep Human/ Mouse/Rat Kit Illumina Cat#20020596 GeneJET Genomic DNA Purification Kit ThermoFisher Cat#K0722 Qubit RNA BR Assay ThermoFisher Cat#Q10211 Qubit dsDNA HS Assay ThermoFisher Cat#Q32851 Tapestation High Sensitivity DNA Kit Agilent 5067-4626 Tapestation High Sensitivity RNA Kit Agilent 5067-5579 HiScript IV RT SuperMix for qPCR (+gDNA wiper) Vazyme R423 SYBR qPCR Master Mix Vazyme Q713 Deposited data LUD2015-inop demographics and clinical outcomes (cut-off date 16 October 2020) This paper Tables S1, S2, and S3 LUD2015-inop bulk RNA sequencing Carroll et al.19 EGA :EGAS00001006468 LUD2015-inop single-cell RNA sequencing Carroll et al.19 EGA :EGAS00001006469 LUD2015-inop whole genome sequencing Carroll et al.19 EGA :EGAS00001006470 International Cancer Genome Consortium: ESADUK cohort RNA sequencing counts, mutational burden Frankell et al.32 EGA :EGAD00001004423; https://dcc.icgc.org Bulk RNA sequencing data for ICI-treated gastric cancer (Samsung cohort) Kim et al.29 ENA: PRJEB25780 Bulk RNA sequencing data for ICI-treated gastric cancer (Yonsei and St. Mary’s cohorts) Cheong et al.28 EGA: EGAD00001008091 Control dataset of patients wtih upper gastrointestinal cancers treated in the local NHS Trust during the treatment period of the LUD2015005 study Oxford University NHS Foundation Trust NA Processed RNAseq counts from ICI-treated melanoma Gide et al.30 ENA: PRJEB23709 Processed RNAseq counts from ICI-treated NSCLC Cho et al.,31 GEO: GSE135222 LUD2015-op demographics and clinical outcomes (cut-off date 22 November 2022) This paper Tables S1 and S3, this paper. .. LUD2015-op bulk RNA sequencing This paper EGA: EGAS00001008543 LUD2015-op single-cell RNA sequencing This paper EGA: EGAS00001008543 LUD2015-op whole genome sequencing This paper EGA: EGAS00001008543 Whole genome methylation data for LUD2015-inop (23 patients), and LUD2015-op (29 patients), Barretts2016 (9 samples from 2 patients) This paper EGA: EGAS00001008543 Software and algorithms DESeq2 v1.38.3 Love et al.,79 https://bioconductor.org/packages/release/bioc/ html/DESeq2.html Cell Ranger v7.1.0 10x Genomics https://support.10xgenomics.com/single-cell- gene-expression/software/downloads/3.1/ BayesPrism v2.0 Chu et al.,27 https://github.com/Danko-Lab/TED/ Seurat v4.3.0 Stuart et al.,80 https://satijalab.org/seurat/index.html (Continued on next page) e2 Med 7, 101327, November 13, 2026 Article ll OPEN ACCESS

    Control:

    Article Title: Tumor DNA methylation subtypes and expression levels of CFISH predict response and overall survival to immunochemotherapy.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Durvalumab AstraZeneca UK, Ltd N/A Tremelimumab AstraZeneca UK, Ltd N/A Biological samples Biopsies of tumor and normal upper gastrointestinal tract tissues from esophageal cancer patients LUD2015-005 clinical trial NCT02735239, EudraCT 2015-005298-19 Chemicals, peptides, and recombinant proteins Heat-inactivated human serum Sigma-Aldrich Cat#H3667 Fetal Bovine Serum Sigma-Aldrich F9665 DMEM/F-12 Gibco Cat#11330032 PBS Gibco Cat#11590476 Bovine Serum Albumin Fraction V Apollo Scientific Cat#BIA3981 Acid-Phenol:Chloroform, pH 4.5 (with IAA, 125:24:1) Invitrogen Cat#AM9720 TURBO DNA-free Kit ThermoFisher Cat#AM1907 Red Blood Cell Lysis Solution (10×) Miltenyi Cat#130-094-183 Animal Free Collagenase/Dispase Blend II Sigma-Aldrich Cat#SCR140 DNAse I Sigma-Aldrich Cat#D5025 Collagenase D Sigma-Aldrich Cat#11088866001 Liberase DL Sigma-Aldrich Cat#5466202001 Oxaliplatin Eloxatin N/A Capecitabine Xeloda N/A Nuclease-free water Ambion AM9937 qPCR primers ThermoFisher N/A mTet1CD Produced in-house per Liu et al.49 N/A Borane-pyridine complex, 95% Alfa Aesar L13178.09 HEPES (pH 8.0) ThermoFisher J63578-AP Ammonium iron (II) sulfate hexahydrate Merck 09719 Alpha–ketoglutarate Merck K3752 Ascorbic acid Merck 95210 Dithiothreitol (DTT) Merck D9779 NaCl ThermoFisher AM9759 ATP Fisher Scientific 10326943 KAPA Hyper Prep Kit PCR-free Roche KK8505 KAPA HiFi HotStart Uracil+ Kit Roche KK2802 KAPA Unique Dual-Indexed Adapters Roche KK8726 Proteinase K ThermoFisher EO0491 Sodium acetate ThermoFisher J63669.AE Tris-HCl ThermoFisher 15567027 Complete Protease Inhibitor Cocktail Roche 4693116001 Triton X-100 ThermoFisher A16046.AE ANTI-FLAG M2 Affinity Gel Millipore A2220 Pierce 3X DYKDDDDK Peptide ThermoFisher A36805 ExpiFectamine 293 Transfection Kit Gibco A14525 Expi293 Expression Medium Gibco A1435101 (Continued on next page) Med 7, 101327, November 13, 2026 e1 Article ll OPEN ACCESS .. REAGENT or RESOURCE SOURCE IDENTIFIER Opti-MEM Reduced Serum Medium Gibco 31985070 Critical commercial assays Chromium Single Cell Immune Profiling Assay (v2) 10x Genomics https://www.10xgenomics.com/products/single- cell-immune-profiling mirVana miRNA Isolation Kit ThermoFisher Cat#AM1560 Dead Cell Removal Kit Miltenyi Cat130-090-101 TruSeq Stranded Total RNA Library Prep Human/ Mouse/Rat Kit Illumina Cat#20020596 GeneJET Genomic DNA Purification Kit ThermoFisher Cat#K0722 Qubit RNA BR Assay ThermoFisher Cat#Q10211 Qubit dsDNA HS Assay ThermoFisher Cat#Q32851 Tapestation High Sensitivity DNA Kit Agilent 5067-4626 Tapestation High Sensitivity RNA Kit Agilent 5067-5579 HiScript IV RT SuperMix for qPCR (+gDNA wiper) Vazyme R423 SYBR qPCR Master Mix Vazyme Q713 Deposited data LUD2015-inop demographics and clinical outcomes (cut-off date 16 October 2020) This paper Tables S1, S2, and S3 LUD2015-inop bulk RNA sequencing Carroll et al.19 EGA :EGAS00001006468 LUD2015-inop single-cell RNA sequencing Carroll et al.19 EGA :EGAS00001006469 LUD2015-inop whole genome sequencing Carroll et al.19 EGA :EGAS00001006470 International Cancer Genome Consortium: ESADUK cohort RNA sequencing counts, mutational burden Frankell et al.32 EGA :EGAD00001004423; https://dcc.icgc.org Bulk RNA sequencing data for ICI-treated gastric cancer (Samsung cohort) Kim et al.29 ENA: PRJEB25780 Bulk RNA sequencing data for ICI-treated gastric cancer (Yonsei and St. Mary’s cohorts) Cheong et al.28 EGA: EGAD00001008091 Control dataset of patients wtih upper gastrointestinal cancers treated in the local NHS Trust during the treatment period of the LUD2015005 study Oxford University NHS Foundation Trust NA Processed RNAseq counts from ICI-treated melanoma Gide et al.30 ENA: PRJEB23709 Processed RNAseq counts from ICI-treated NSCLC Cho et al.,31 GEO: GSE135222 LUD2015-op demographics and clinical outcomes (cut-off date 22 November 2022) This paper Tables S1 and S3, this paper. .. LUD2015-op bulk RNA sequencing This paper EGA: EGAS00001008543 LUD2015-op single-cell RNA sequencing This paper EGA: EGAS00001008543 LUD2015-op whole genome sequencing This paper EGA: EGAS00001008543 Whole genome methylation data for LUD2015-inop (23 patients), and LUD2015-op (29 patients), Barretts2016 (9 samples from 2 patients) This paper EGA: EGAS00001008543 Software and algorithms DESeq2 v1.38.3 Love et al.,79 https://bioconductor.org/packages/release/bioc/ html/DESeq2.html Cell Ranger v7.1.0 10x Genomics https://support.10xgenomics.com/single-cell- gene-expression/software/downloads/3.1/ BayesPrism v2.0 Chu et al.,27 https://github.com/Danko-Lab/TED/ Seurat v4.3.0 Stuart et al.,80 https://satijalab.org/seurat/index.html (Continued on next page) e2 Med 7, 101327, November 13, 2026 Article ll OPEN ACCESS

    Single Cell RNA-Seq:

    Article Title: Thymic stromal defects and immune dysregulation in hypomorphic Rag deficiency: implications for hematopoietic cell transplantation.
    Article Snippet: .. 180 181 Single cell RNA-seq 182 Thymocytes were enriched for live cells using the Dead Cell Removal Kit (Miltenyi Biotec), 183 according to the manufacturer instructions. .. EpCAM+ thymic epithelial cells were isolated by Aria 184 II cell sorter (BD Bioscience) from each sample.

    Mass Spectrometry:

    Article Title: Cabergoline Suppresses Postpartum Breast Cancer by Enhancing Mammary Gland Involution in Brca1-Mutant Mice and Is Associated with Reduced Risk in Younger Women
    Article Snippet: .. Viable cells 1185 were isolated using the Dead Cell Removal Kit (Miltenyi Biotec, 130-090-101) and MS 1186 columns (Miltenyi Biotec, 130-122-727). ..



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    KEY RESOURCES TABLE

    Journal: Cell reports

    Article Title: Dissecting the spermatogonial stem cell niche using spatial transcriptomics

    doi: 10.1016/j.celrep.2023.112737

    Figure Lengend Snippet: KEY RESOURCES TABLE

    Article Snippet: Slide-seq Arrays , Fei Chen Lab , N/A.

    Techniques: Recombinant, DNA Library Preparation, Software