Control:Article Title: Altered chromatin topologies caused by balanced chromosomal translocation lead to central iris hypoplasia.
Article Snippet: .. CUT&Tag library construction60,61 was performed as follows: Approximately 0.5 million iPSCs per sample from the patient and control were resuspended and attached to Concanavalin A beads (Bangs Laboratories, IN, USA). .. The iPSCs on ConA beads were incubated at RT with primary antibody against H3K27ac (#39133, 1:50 dilution, Activemotif) for one hour, and then with secondary antibody (#SAB3700894, 1:50 dilution, Sigma-Aldrich) for one hour.
Article Title: Altered chromatin topologies caused by balanced chromosomal translocation lead to central iris hypoplasia
Article Snippet: .. CUT&Tag library construction , was performed as follows: Approximately 0.5 million iPSCs per sample from the patient and control were resuspended and attached to Concanavalin A beads (Bangs Laboratories, IN, USA). .. The iPSCs on ConA beads were incubated at RT with primary antibody against H3K27ac (#39133, 1:50 dilution, Active motif) for one hour, and then with secondary antibody (#SAB3700894, 1:50 dilution, Sigma-Aldrich) for one hour.
Incubation:Article Title: KMT5C-H4K20me3 drives changes in epigenetic landscape independent of H3K9me3
Article Snippet: CUT&RUN was performed using the EpiCypher® CUTANATM CUT&RUN Protocol v2.0 as previously described [ ]. pAG-MNase was a gift from the laboratory of Patrick Murphy (University of Rochester). .. Briefly, 5*10 5 cells were incubated with Concanavalin-A beads (Bangs Laboratories, #BP531) followed with an overnight incubation with primary antibody at 4°C. ..
Virus:Article Title: Dissecting pre- to post-implantation transition of DNA methylome-transcriptome dynamics in early mammalian development.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Dnmt3a Cell Signaling Technology Cat# E9P2F; RRID:AB_2799365 Dnmt3b Cell Signaling Technology Cat# E4I4O; RRID:AB_2799339 ACTB Rabbit mAb AB clonal Cat# AC038; RRID:AB_2863784 pig anti-rabbit IgG secondary antibody Antibodies-Online Cat# ABIN101961; RRID:AB_10775589 Bacterial and virus strains TransT1 competent cells Vazyme Cat# C505 Chemicals, peptides, and recombinant proteins acidic Tyrode’s solution Sigma Cat# T1788 0.25% trypsin Gibco Cat# 25200056 Dynabeads MyOne Streptavidin C1 Beads Invitrogen Cat# 65001 DMEM/F12 Gibco Cat# 11330–032 Neurobasal Gibco Cat# 21103049 N2 Gibco Cat# 17502048 B27 Gibco Cat# 17504044 L-glutamax Thermo Cat# 35050061 Nonessential amino acids Gibco Cat# 11140–050 0.25 mg/mL Bovine Albumin Fraction V Gibco Cat# 15260037 Sodium Pyruvate Gibco Cat# 11360070 2-mercaptoethanol Gibco Cat# 21985023 Penicillin/Streptomycin Cyitva Cat# SV30010 PD0325901 LC laboratorial Cat# P-9688 CHIR9902 LC laboratorial Cat# C-6556 LIF Novoprotein Cat# C690 0.25% Trypsin solution Gibco Cat# 25200056 Concanavalin A beads Bangs Laboratories Cat# BP531 pA-Tn5 transposome Vazyme Cat# S603 0.5 M EDTA Sigma Cat# 03690 10% SDS Sigma Cat# L4509 Proteinase K Thermo Fisher Scientific Cat# EO0492 AMPure XP beads Beckman Counter Cat# A63881 Trizol protocol Invitogen Cat# 15596018 Critical commercial assays Kapa Hyper Prep Kits KAPA Cat# KK8504 EZ-96 DNA Methylation-Direct MagPrep Zymo Cat# D5044 Hyperactive ATAC-Seq Library Prep Kit for Illumina Vazyme Cat# TD711 HiScript III All-in-one RT SuperMix Vazyme Cat# R333-01 Genomic DNA extraction kit TIANGEN Cat# DP3G4 SuperScript II reverse transcriptase kit Invitrogen Cat# 18064071 DNA Methylation Bisulfite Kit Vazyme Cat# EM101 DNA Methylation Library Kit for Illumina V3 Vazyme Cat# NE103 NEBNext® Enzymatic 5hmC-seq Kit NEB Cat# E3350 TIANamp genomic DNA kit TIANGEN Cat# DP304 (Continued on next page) Cell Reports 44, 115790, June 24, 2025 17 .. REAGENT or RESOURCE SOURCE IDENTIFIER VAHTS® Universal V8 RNA-seq Library Prep Kit for Illumina Vazyme Cat# NR605 Deposited data scTrio-seq2_mouse This paper GSA: CRA013360 scRNAseq_Mouse Deng et al. 39 GEO: GSE45719 scRNAseq_Mouse Cheng et al. 64 GEO: GSE109071 scRNAseq_Mouse Mohammed et al. 37 GEO: GSE100597 STEM-seq_Mouse Zhang et al. 14 GEO: GSE76505 scCOOL-seq_Mouse Guo et al. 2 GEO: GSE78140 T-WGBS_ Monkey Gao et al. 19 GEO: GSE60166 scChaRM-seq_Monkey Zhai et al. 20 GEO: GSE74767 scPBAT_Human Zhu et al. 21 GEO: GSE81233 scTrio-seq2_Human Zhou et al. 4 GEO: GSE109555 Hi-C_mouse Zhang et al. 14 GEO: GSE76505 ATAC_mouse Wu et al. 50 GEO: GSE66390 CTCF_mouse Wang et al. 49 GSA: CRA011730 ChIP-seq_mouse Liu et al. 52 GEO: GSE217970 ChIP-seq_mouse Wang et al. 65 GEO: GSE97778 ChIP-seq_mouse and ATAC_mouse Xiang et al. 51 GEO: GSE125318 ChIP-seq_mouse Liu et al. 53 GEO: GSE73952 DNAme and RNA in DNMT and TET mutant mouse Li et al. 43 GEO: GSE162903 DNAme, RNA and H3K27me3 Yang et al. 38 GEO: GSE104243 Experimental models: Cell lines serum-based WT mESC Lab of Xiong Ji N/A Software and algorithms Trim Galore (v0.6.4) Babraham Bioinformatics https://github.com/FelixKrueger/TrimGalore Bismark (v0.7.6) Krueger et al. 66 https://github.com/FelixKrueger/Bismark Samtools (v0.1.18 and v1.10) Danecek et al. 67 https://github.com/samtools/samtools SNPsplit (v0.5.0) Krueger et al. 36 https://github.com/FelixKrueger/SNPsplit Bowtie (v1.0.0) Langmead et al. 68 https://bowtie-bio.sourceforge.net/manual.shtml Bowtie2 (v2.5.7) Langmead et al. 69 https://bowtie-bio.sourceforge.net/bowtie2/index.shtml Picard (v2.27.5) Broad Institute https://github.com/broadinstitute/picard MACS2 (v2.2.9.1) Zhang et al. 70 https://github.com/macs3-project/MACS DeepTools (v2.5.7) Ramı́rez et al. 71 https://github.com/deeptools/deepTools Fastp (v0.23.4) Chen et al. 72 https://github.com/OpenGene/fastp STAR (v2.7.8a) Dobin et al. 73 https://github.com/alexdobin/STAR featureCounts (v2.0.0) Liao et al. 74 https://subread.sourceforge.net/featureCounts.html R (v4.2.3) R Core Team https://www.r-project.org/ Seurat R package (v4.2.1) Butler et al. 75 https://github.com/satijalab/seurat SCTransform algorithm (v0.3.2) Hafemeister and Satija 76 https://github.com/satijalab/sctransform Trimmomatic (v0.39) Bolger et al. 77 https://github.com/usadellab/Trimmomatic biomaRt (v2.54.1) Durinck et al. 78 https://github.com/grimbough/biomaRt HOMER (v5.1) Heinz et al. 55 http://homer.ucsd.edu/homer/ Python (v3.11.4) N/A https://www.python.org/ ABC model (v1.1.2) Fulco et al. 79 https://github.com/broadinstitute/ABC-Enhancer- Gene-Prediction Juicer (v1.6) Durand et al. 80 https://github.com/aidenlab/juicer (Continued on next page) 18 Cell Reports 44, 115790, June 24, 2025
Recombinant:Article Title: Dissecting pre- to post-implantation transition of DNA methylome-transcriptome dynamics in early mammalian development.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Dnmt3a Cell Signaling Technology Cat# E9P2F; RRID:AB_2799365 Dnmt3b Cell Signaling Technology Cat# E4I4O; RRID:AB_2799339 ACTB Rabbit mAb AB clonal Cat# AC038; RRID:AB_2863784 pig anti-rabbit IgG secondary antibody Antibodies-Online Cat# ABIN101961; RRID:AB_10775589 Bacterial and virus strains TransT1 competent cells Vazyme Cat# C505 Chemicals, peptides, and recombinant proteins acidic Tyrode’s solution Sigma Cat# T1788 0.25% trypsin Gibco Cat# 25200056 Dynabeads MyOne Streptavidin C1 Beads Invitrogen Cat# 65001 DMEM/F12 Gibco Cat# 11330–032 Neurobasal Gibco Cat# 21103049 N2 Gibco Cat# 17502048 B27 Gibco Cat# 17504044 L-glutamax Thermo Cat# 35050061 Nonessential amino acids Gibco Cat# 11140–050 0.25 mg/mL Bovine Albumin Fraction V Gibco Cat# 15260037 Sodium Pyruvate Gibco Cat# 11360070 2-mercaptoethanol Gibco Cat# 21985023 Penicillin/Streptomycin Cyitva Cat# SV30010 PD0325901 LC laboratorial Cat# P-9688 CHIR9902 LC laboratorial Cat# C-6556 LIF Novoprotein Cat# C690 0.25% Trypsin solution Gibco Cat# 25200056 Concanavalin A beads Bangs Laboratories Cat# BP531 pA-Tn5 transposome Vazyme Cat# S603 0.5 M EDTA Sigma Cat# 03690 10% SDS Sigma Cat# L4509 Proteinase K Thermo Fisher Scientific Cat# EO0492 AMPure XP beads Beckman Counter Cat# A63881 Trizol protocol Invitogen Cat# 15596018 Critical commercial assays Kapa Hyper Prep Kits KAPA Cat# KK8504 EZ-96 DNA Methylation-Direct MagPrep Zymo Cat# D5044 Hyperactive ATAC-Seq Library Prep Kit for Illumina Vazyme Cat# TD711 HiScript III All-in-one RT SuperMix Vazyme Cat# R333-01 Genomic DNA extraction kit TIANGEN Cat# DP3G4 SuperScript II reverse transcriptase kit Invitrogen Cat# 18064071 DNA Methylation Bisulfite Kit Vazyme Cat# EM101 DNA Methylation Library Kit for Illumina V3 Vazyme Cat# NE103 NEBNext® Enzymatic 5hmC-seq Kit NEB Cat# E3350 TIANamp genomic DNA kit TIANGEN Cat# DP304 (Continued on next page) Cell Reports 44, 115790, June 24, 2025 17 .. REAGENT or RESOURCE SOURCE IDENTIFIER VAHTS® Universal V8 RNA-seq Library Prep Kit for Illumina Vazyme Cat# NR605 Deposited data scTrio-seq2_mouse This paper GSA: CRA013360 scRNAseq_Mouse Deng et al. 39 GEO: GSE45719 scRNAseq_Mouse Cheng et al. 64 GEO: GSE109071 scRNAseq_Mouse Mohammed et al. 37 GEO: GSE100597 STEM-seq_Mouse Zhang et al. 14 GEO: GSE76505 scCOOL-seq_Mouse Guo et al. 2 GEO: GSE78140 T-WGBS_ Monkey Gao et al. 19 GEO: GSE60166 scChaRM-seq_Monkey Zhai et al. 20 GEO: GSE74767 scPBAT_Human Zhu et al. 21 GEO: GSE81233 scTrio-seq2_Human Zhou et al. 4 GEO: GSE109555 Hi-C_mouse Zhang et al. 14 GEO: GSE76505 ATAC_mouse Wu et al. 50 GEO: GSE66390 CTCF_mouse Wang et al. 49 GSA: CRA011730 ChIP-seq_mouse Liu et al. 52 GEO: GSE217970 ChIP-seq_mouse Wang et al. 65 GEO: GSE97778 ChIP-seq_mouse and ATAC_mouse Xiang et al. 51 GEO: GSE125318 ChIP-seq_mouse Liu et al. 53 GEO: GSE73952 DNAme and RNA in DNMT and TET mutant mouse Li et al. 43 GEO: GSE162903 DNAme, RNA and H3K27me3 Yang et al. 38 GEO: GSE104243 Experimental models: Cell lines serum-based WT mESC Lab of Xiong Ji N/A Software and algorithms Trim Galore (v0.6.4) Babraham Bioinformatics https://github.com/FelixKrueger/TrimGalore Bismark (v0.7.6) Krueger et al. 66 https://github.com/FelixKrueger/Bismark Samtools (v0.1.18 and v1.10) Danecek et al. 67 https://github.com/samtools/samtools SNPsplit (v0.5.0) Krueger et al. 36 https://github.com/FelixKrueger/SNPsplit Bowtie (v1.0.0) Langmead et al. 68 https://bowtie-bio.sourceforge.net/manual.shtml Bowtie2 (v2.5.7) Langmead et al. 69 https://bowtie-bio.sourceforge.net/bowtie2/index.shtml Picard (v2.27.5) Broad Institute https://github.com/broadinstitute/picard MACS2 (v2.2.9.1) Zhang et al. 70 https://github.com/macs3-project/MACS DeepTools (v2.5.7) Ramı́rez et al. 71 https://github.com/deeptools/deepTools Fastp (v0.23.4) Chen et al. 72 https://github.com/OpenGene/fastp STAR (v2.7.8a) Dobin et al. 73 https://github.com/alexdobin/STAR featureCounts (v2.0.0) Liao et al. 74 https://subread.sourceforge.net/featureCounts.html R (v4.2.3) R Core Team https://www.r-project.org/ Seurat R package (v4.2.1) Butler et al. 75 https://github.com/satijalab/seurat SCTransform algorithm (v0.3.2) Hafemeister and Satija 76 https://github.com/satijalab/sctransform Trimmomatic (v0.39) Bolger et al. 77 https://github.com/usadellab/Trimmomatic biomaRt (v2.54.1) Durinck et al. 78 https://github.com/grimbough/biomaRt HOMER (v5.1) Heinz et al. 55 http://homer.ucsd.edu/homer/ Python (v3.11.4) N/A https://www.python.org/ ABC model (v1.1.2) Fulco et al. 79 https://github.com/broadinstitute/ABC-Enhancer- Gene-Prediction Juicer (v1.6) Durand et al. 80 https://github.com/aidenlab/juicer (Continued on next page) 18 Cell Reports 44, 115790, June 24, 2025
Methylation:Article Title: Dissecting pre- to post-implantation transition of DNA methylome-transcriptome dynamics in early mammalian development.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Dnmt3a Cell Signaling Technology Cat# E9P2F; RRID:AB_2799365 Dnmt3b Cell Signaling Technology Cat# E4I4O; RRID:AB_2799339 ACTB Rabbit mAb AB clonal Cat# AC038; RRID:AB_2863784 pig anti-rabbit IgG secondary antibody Antibodies-Online Cat# ABIN101961; RRID:AB_10775589 Bacterial and virus strains TransT1 competent cells Vazyme Cat# C505 Chemicals, peptides, and recombinant proteins acidic Tyrode’s solution Sigma Cat# T1788 0.25% trypsin Gibco Cat# 25200056 Dynabeads MyOne Streptavidin C1 Beads Invitrogen Cat# 65001 DMEM/F12 Gibco Cat# 11330–032 Neurobasal Gibco Cat# 21103049 N2 Gibco Cat# 17502048 B27 Gibco Cat# 17504044 L-glutamax Thermo Cat# 35050061 Nonessential amino acids Gibco Cat# 11140–050 0.25 mg/mL Bovine Albumin Fraction V Gibco Cat# 15260037 Sodium Pyruvate Gibco Cat# 11360070 2-mercaptoethanol Gibco Cat# 21985023 Penicillin/Streptomycin Cyitva Cat# SV30010 PD0325901 LC laboratorial Cat# P-9688 CHIR9902 LC laboratorial Cat# C-6556 LIF Novoprotein Cat# C690 0.25% Trypsin solution Gibco Cat# 25200056 Concanavalin A beads Bangs Laboratories Cat# BP531 pA-Tn5 transposome Vazyme Cat# S603 0.5 M EDTA Sigma Cat# 03690 10% SDS Sigma Cat# L4509 Proteinase K Thermo Fisher Scientific Cat# EO0492 AMPure XP beads Beckman Counter Cat# A63881 Trizol protocol Invitogen Cat# 15596018 Critical commercial assays Kapa Hyper Prep Kits KAPA Cat# KK8504 EZ-96 DNA Methylation-Direct MagPrep Zymo Cat# D5044 Hyperactive ATAC-Seq Library Prep Kit for Illumina Vazyme Cat# TD711 HiScript III All-in-one RT SuperMix Vazyme Cat# R333-01 Genomic DNA extraction kit TIANGEN Cat# DP3G4 SuperScript II reverse transcriptase kit Invitrogen Cat# 18064071 DNA Methylation Bisulfite Kit Vazyme Cat# EM101 DNA Methylation Library Kit for Illumina V3 Vazyme Cat# NE103 NEBNext® Enzymatic 5hmC-seq Kit NEB Cat# E3350 TIANamp genomic DNA kit TIANGEN Cat# DP304 (Continued on next page) Cell Reports 44, 115790, June 24, 2025 17 .. REAGENT or RESOURCE SOURCE IDENTIFIER VAHTS® Universal V8 RNA-seq Library Prep Kit for Illumina Vazyme Cat# NR605 Deposited data scTrio-seq2_mouse This paper GSA: CRA013360 scRNAseq_Mouse Deng et al. 39 GEO: GSE45719 scRNAseq_Mouse Cheng et al. 64 GEO: GSE109071 scRNAseq_Mouse Mohammed et al. 37 GEO: GSE100597 STEM-seq_Mouse Zhang et al. 14 GEO: GSE76505 scCOOL-seq_Mouse Guo et al. 2 GEO: GSE78140 T-WGBS_ Monkey Gao et al. 19 GEO: GSE60166 scChaRM-seq_Monkey Zhai et al. 20 GEO: GSE74767 scPBAT_Human Zhu et al. 21 GEO: GSE81233 scTrio-seq2_Human Zhou et al. 4 GEO: GSE109555 Hi-C_mouse Zhang et al. 14 GEO: GSE76505 ATAC_mouse Wu et al. 50 GEO: GSE66390 CTCF_mouse Wang et al. 49 GSA: CRA011730 ChIP-seq_mouse Liu et al. 52 GEO: GSE217970 ChIP-seq_mouse Wang et al. 65 GEO: GSE97778 ChIP-seq_mouse and ATAC_mouse Xiang et al. 51 GEO: GSE125318 ChIP-seq_mouse Liu et al. 53 GEO: GSE73952 DNAme and RNA in DNMT and TET mutant mouse Li et al. 43 GEO: GSE162903 DNAme, RNA and H3K27me3 Yang et al. 38 GEO: GSE104243 Experimental models: Cell lines serum-based WT mESC Lab of Xiong Ji N/A Software and algorithms Trim Galore (v0.6.4) Babraham Bioinformatics https://github.com/FelixKrueger/TrimGalore Bismark (v0.7.6) Krueger et al. 66 https://github.com/FelixKrueger/Bismark Samtools (v0.1.18 and v1.10) Danecek et al. 67 https://github.com/samtools/samtools SNPsplit (v0.5.0) Krueger et al. 36 https://github.com/FelixKrueger/SNPsplit Bowtie (v1.0.0) Langmead et al. 68 https://bowtie-bio.sourceforge.net/manual.shtml Bowtie2 (v2.5.7) Langmead et al. 69 https://bowtie-bio.sourceforge.net/bowtie2/index.shtml Picard (v2.27.5) Broad Institute https://github.com/broadinstitute/picard MACS2 (v2.2.9.1) Zhang et al. 70 https://github.com/macs3-project/MACS DeepTools (v2.5.7) Ramı́rez et al. 71 https://github.com/deeptools/deepTools Fastp (v0.23.4) Chen et al. 72 https://github.com/OpenGene/fastp STAR (v2.7.8a) Dobin et al. 73 https://github.com/alexdobin/STAR featureCounts (v2.0.0) Liao et al. 74 https://subread.sourceforge.net/featureCounts.html R (v4.2.3) R Core Team https://www.r-project.org/ Seurat R package (v4.2.1) Butler et al. 75 https://github.com/satijalab/seurat SCTransform algorithm (v0.3.2) Hafemeister and Satija 76 https://github.com/satijalab/sctransform Trimmomatic (v0.39) Bolger et al. 77 https://github.com/usadellab/Trimmomatic biomaRt (v2.54.1) Durinck et al. 78 https://github.com/grimbough/biomaRt HOMER (v5.1) Heinz et al. 55 http://homer.ucsd.edu/homer/ Python (v3.11.4) N/A https://www.python.org/ ABC model (v1.1.2) Fulco et al. 79 https://github.com/broadinstitute/ABC-Enhancer- Gene-Prediction Juicer (v1.6) Durand et al. 80 https://github.com/aidenlab/juicer (Continued on next page) 18 Cell Reports 44, 115790, June 24, 2025
DNA Extraction:Article Title: Dissecting pre- to post-implantation transition of DNA methylome-transcriptome dynamics in early mammalian development.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Dnmt3a Cell Signaling Technology Cat# E9P2F; RRID:AB_2799365 Dnmt3b Cell Signaling Technology Cat# E4I4O; RRID:AB_2799339 ACTB Rabbit mAb AB clonal Cat# AC038; RRID:AB_2863784 pig anti-rabbit IgG secondary antibody Antibodies-Online Cat# ABIN101961; RRID:AB_10775589 Bacterial and virus strains TransT1 competent cells Vazyme Cat# C505 Chemicals, peptides, and recombinant proteins acidic Tyrode’s solution Sigma Cat# T1788 0.25% trypsin Gibco Cat# 25200056 Dynabeads MyOne Streptavidin C1 Beads Invitrogen Cat# 65001 DMEM/F12 Gibco Cat# 11330–032 Neurobasal Gibco Cat# 21103049 N2 Gibco Cat# 17502048 B27 Gibco Cat# 17504044 L-glutamax Thermo Cat# 35050061 Nonessential amino acids Gibco Cat# 11140–050 0.25 mg/mL Bovine Albumin Fraction V Gibco Cat# 15260037 Sodium Pyruvate Gibco Cat# 11360070 2-mercaptoethanol Gibco Cat# 21985023 Penicillin/Streptomycin Cyitva Cat# SV30010 PD0325901 LC laboratorial Cat# P-9688 CHIR9902 LC laboratorial Cat# C-6556 LIF Novoprotein Cat# C690 0.25% Trypsin solution Gibco Cat# 25200056 Concanavalin A beads Bangs Laboratories Cat# BP531 pA-Tn5 transposome Vazyme Cat# S603 0.5 M EDTA Sigma Cat# 03690 10% SDS Sigma Cat# L4509 Proteinase K Thermo Fisher Scientific Cat# EO0492 AMPure XP beads Beckman Counter Cat# A63881 Trizol protocol Invitogen Cat# 15596018 Critical commercial assays Kapa Hyper Prep Kits KAPA Cat# KK8504 EZ-96 DNA Methylation-Direct MagPrep Zymo Cat# D5044 Hyperactive ATAC-Seq Library Prep Kit for Illumina Vazyme Cat# TD711 HiScript III All-in-one RT SuperMix Vazyme Cat# R333-01 Genomic DNA extraction kit TIANGEN Cat# DP3G4 SuperScript II reverse transcriptase kit Invitrogen Cat# 18064071 DNA Methylation Bisulfite Kit Vazyme Cat# EM101 DNA Methylation Library Kit for Illumina V3 Vazyme Cat# NE103 NEBNext® Enzymatic 5hmC-seq Kit NEB Cat# E3350 TIANamp genomic DNA kit TIANGEN Cat# DP304 (Continued on next page) Cell Reports 44, 115790, June 24, 2025 17 .. REAGENT or RESOURCE SOURCE IDENTIFIER VAHTS® Universal V8 RNA-seq Library Prep Kit for Illumina Vazyme Cat# NR605 Deposited data scTrio-seq2_mouse This paper GSA: CRA013360 scRNAseq_Mouse Deng et al. 39 GEO: GSE45719 scRNAseq_Mouse Cheng et al. 64 GEO: GSE109071 scRNAseq_Mouse Mohammed et al. 37 GEO: GSE100597 STEM-seq_Mouse Zhang et al. 14 GEO: GSE76505 scCOOL-seq_Mouse Guo et al. 2 GEO: GSE78140 T-WGBS_ Monkey Gao et al. 19 GEO: GSE60166 scChaRM-seq_Monkey Zhai et al. 20 GEO: GSE74767 scPBAT_Human Zhu et al. 21 GEO: GSE81233 scTrio-seq2_Human Zhou et al. 4 GEO: GSE109555 Hi-C_mouse Zhang et al. 14 GEO: GSE76505 ATAC_mouse Wu et al. 50 GEO: GSE66390 CTCF_mouse Wang et al. 49 GSA: CRA011730 ChIP-seq_mouse Liu et al. 52 GEO: GSE217970 ChIP-seq_mouse Wang et al. 65 GEO: GSE97778 ChIP-seq_mouse and ATAC_mouse Xiang et al. 51 GEO: GSE125318 ChIP-seq_mouse Liu et al. 53 GEO: GSE73952 DNAme and RNA in DNMT and TET mutant mouse Li et al. 43 GEO: GSE162903 DNAme, RNA and H3K27me3 Yang et al. 38 GEO: GSE104243 Experimental models: Cell lines serum-based WT mESC Lab of Xiong Ji N/A Software and algorithms Trim Galore (v0.6.4) Babraham Bioinformatics https://github.com/FelixKrueger/TrimGalore Bismark (v0.7.6) Krueger et al. 66 https://github.com/FelixKrueger/Bismark Samtools (v0.1.18 and v1.10) Danecek et al. 67 https://github.com/samtools/samtools SNPsplit (v0.5.0) Krueger et al. 36 https://github.com/FelixKrueger/SNPsplit Bowtie (v1.0.0) Langmead et al. 68 https://bowtie-bio.sourceforge.net/manual.shtml Bowtie2 (v2.5.7) Langmead et al. 69 https://bowtie-bio.sourceforge.net/bowtie2/index.shtml Picard (v2.27.5) Broad Institute https://github.com/broadinstitute/picard MACS2 (v2.2.9.1) Zhang et al. 70 https://github.com/macs3-project/MACS DeepTools (v2.5.7) Ramı́rez et al. 71 https://github.com/deeptools/deepTools Fastp (v0.23.4) Chen et al. 72 https://github.com/OpenGene/fastp STAR (v2.7.8a) Dobin et al. 73 https://github.com/alexdobin/STAR featureCounts (v2.0.0) Liao et al. 74 https://subread.sourceforge.net/featureCounts.html R (v4.2.3) R Core Team https://www.r-project.org/ Seurat R package (v4.2.1) Butler et al. 75 https://github.com/satijalab/seurat SCTransform algorithm (v0.3.2) Hafemeister and Satija 76 https://github.com/satijalab/sctransform Trimmomatic (v0.39) Bolger et al. 77 https://github.com/usadellab/Trimmomatic biomaRt (v2.54.1) Durinck et al. 78 https://github.com/grimbough/biomaRt HOMER (v5.1) Heinz et al. 55 http://homer.ucsd.edu/homer/ Python (v3.11.4) N/A https://www.python.org/ ABC model (v1.1.2) Fulco et al. 79 https://github.com/broadinstitute/ABC-Enhancer- Gene-Prediction Juicer (v1.6) Durand et al. 80 https://github.com/aidenlab/juicer (Continued on next page) 18 Cell Reports 44, 115790, June 24, 2025
Reverse Transcription:Article Title: Dissecting pre- to post-implantation transition of DNA methylome-transcriptome dynamics in early mammalian development.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Dnmt3a Cell Signaling Technology Cat# E9P2F; RRID:AB_2799365 Dnmt3b Cell Signaling Technology Cat# E4I4O; RRID:AB_2799339 ACTB Rabbit mAb AB clonal Cat# AC038; RRID:AB_2863784 pig anti-rabbit IgG secondary antibody Antibodies-Online Cat# ABIN101961; RRID:AB_10775589 Bacterial and virus strains TransT1 competent cells Vazyme Cat# C505 Chemicals, peptides, and recombinant proteins acidic Tyrode’s solution Sigma Cat# T1788 0.25% trypsin Gibco Cat# 25200056 Dynabeads MyOne Streptavidin C1 Beads Invitrogen Cat# 65001 DMEM/F12 Gibco Cat# 11330–032 Neurobasal Gibco Cat# 21103049 N2 Gibco Cat# 17502048 B27 Gibco Cat# 17504044 L-glutamax Thermo Cat# 35050061 Nonessential amino acids Gibco Cat# 11140–050 0.25 mg/mL Bovine Albumin Fraction V Gibco Cat# 15260037 Sodium Pyruvate Gibco Cat# 11360070 2-mercaptoethanol Gibco Cat# 21985023 Penicillin/Streptomycin Cyitva Cat# SV30010 PD0325901 LC laboratorial Cat# P-9688 CHIR9902 LC laboratorial Cat# C-6556 LIF Novoprotein Cat# C690 0.25% Trypsin solution Gibco Cat# 25200056 Concanavalin A beads Bangs Laboratories Cat# BP531 pA-Tn5 transposome Vazyme Cat# S603 0.5 M EDTA Sigma Cat# 03690 10% SDS Sigma Cat# L4509 Proteinase K Thermo Fisher Scientific Cat# EO0492 AMPure XP beads Beckman Counter Cat# A63881 Trizol protocol Invitogen Cat# 15596018 Critical commercial assays Kapa Hyper Prep Kits KAPA Cat# KK8504 EZ-96 DNA Methylation-Direct MagPrep Zymo Cat# D5044 Hyperactive ATAC-Seq Library Prep Kit for Illumina Vazyme Cat# TD711 HiScript III All-in-one RT SuperMix Vazyme Cat# R333-01 Genomic DNA extraction kit TIANGEN Cat# DP3G4 SuperScript II reverse transcriptase kit Invitrogen Cat# 18064071 DNA Methylation Bisulfite Kit Vazyme Cat# EM101 DNA Methylation Library Kit for Illumina V3 Vazyme Cat# NE103 NEBNext® Enzymatic 5hmC-seq Kit NEB Cat# E3350 TIANamp genomic DNA kit TIANGEN Cat# DP304 (Continued on next page) Cell Reports 44, 115790, June 24, 2025 17 .. REAGENT or RESOURCE SOURCE IDENTIFIER VAHTS® Universal V8 RNA-seq Library Prep Kit for Illumina Vazyme Cat# NR605 Deposited data scTrio-seq2_mouse This paper GSA: CRA013360 scRNAseq_Mouse Deng et al. 39 GEO: GSE45719 scRNAseq_Mouse Cheng et al. 64 GEO: GSE109071 scRNAseq_Mouse Mohammed et al. 37 GEO: GSE100597 STEM-seq_Mouse Zhang et al. 14 GEO: GSE76505 scCOOL-seq_Mouse Guo et al. 2 GEO: GSE78140 T-WGBS_ Monkey Gao et al. 19 GEO: GSE60166 scChaRM-seq_Monkey Zhai et al. 20 GEO: GSE74767 scPBAT_Human Zhu et al. 21 GEO: GSE81233 scTrio-seq2_Human Zhou et al. 4 GEO: GSE109555 Hi-C_mouse Zhang et al. 14 GEO: GSE76505 ATAC_mouse Wu et al. 50 GEO: GSE66390 CTCF_mouse Wang et al. 49 GSA: CRA011730 ChIP-seq_mouse Liu et al. 52 GEO: GSE217970 ChIP-seq_mouse Wang et al. 65 GEO: GSE97778 ChIP-seq_mouse and ATAC_mouse Xiang et al. 51 GEO: GSE125318 ChIP-seq_mouse Liu et al. 53 GEO: GSE73952 DNAme and RNA in DNMT and TET mutant mouse Li et al. 43 GEO: GSE162903 DNAme, RNA and H3K27me3 Yang et al. 38 GEO: GSE104243 Experimental models: Cell lines serum-based WT mESC Lab of Xiong Ji N/A Software and algorithms Trim Galore (v0.6.4) Babraham Bioinformatics https://github.com/FelixKrueger/TrimGalore Bismark (v0.7.6) Krueger et al. 66 https://github.com/FelixKrueger/Bismark Samtools (v0.1.18 and v1.10) Danecek et al. 67 https://github.com/samtools/samtools SNPsplit (v0.5.0) Krueger et al. 36 https://github.com/FelixKrueger/SNPsplit Bowtie (v1.0.0) Langmead et al. 68 https://bowtie-bio.sourceforge.net/manual.shtml Bowtie2 (v2.5.7) Langmead et al. 69 https://bowtie-bio.sourceforge.net/bowtie2/index.shtml Picard (v2.27.5) Broad Institute https://github.com/broadinstitute/picard MACS2 (v2.2.9.1) Zhang et al. 70 https://github.com/macs3-project/MACS DeepTools (v2.5.7) Ramı́rez et al. 71 https://github.com/deeptools/deepTools Fastp (v0.23.4) Chen et al. 72 https://github.com/OpenGene/fastp STAR (v2.7.8a) Dobin et al. 73 https://github.com/alexdobin/STAR featureCounts (v2.0.0) Liao et al. 74 https://subread.sourceforge.net/featureCounts.html R (v4.2.3) R Core Team https://www.r-project.org/ Seurat R package (v4.2.1) Butler et al. 75 https://github.com/satijalab/seurat SCTransform algorithm (v0.3.2) Hafemeister and Satija 76 https://github.com/satijalab/sctransform Trimmomatic (v0.39) Bolger et al. 77 https://github.com/usadellab/Trimmomatic biomaRt (v2.54.1) Durinck et al. 78 https://github.com/grimbough/biomaRt HOMER (v5.1) Heinz et al. 55 http://homer.ucsd.edu/homer/ Python (v3.11.4) N/A https://www.python.org/ ABC model (v1.1.2) Fulco et al. 79 https://github.com/broadinstitute/ABC-Enhancer- Gene-Prediction Juicer (v1.6) Durand et al. 80 https://github.com/aidenlab/juicer (Continued on next page) 18 Cell Reports 44, 115790, June 24, 2025
DNA Methylation Assay:Article Title: Dissecting pre- to post-implantation transition of DNA methylome-transcriptome dynamics in early mammalian development.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Dnmt3a Cell Signaling Technology Cat# E9P2F; RRID:AB_2799365 Dnmt3b Cell Signaling Technology Cat# E4I4O; RRID:AB_2799339 ACTB Rabbit mAb AB clonal Cat# AC038; RRID:AB_2863784 pig anti-rabbit IgG secondary antibody Antibodies-Online Cat# ABIN101961; RRID:AB_10775589 Bacterial and virus strains TransT1 competent cells Vazyme Cat# C505 Chemicals, peptides, and recombinant proteins acidic Tyrode’s solution Sigma Cat# T1788 0.25% trypsin Gibco Cat# 25200056 Dynabeads MyOne Streptavidin C1 Beads Invitrogen Cat# 65001 DMEM/F12 Gibco Cat# 11330–032 Neurobasal Gibco Cat# 21103049 N2 Gibco Cat# 17502048 B27 Gibco Cat# 17504044 L-glutamax Thermo Cat# 35050061 Nonessential amino acids Gibco Cat# 11140–050 0.25 mg/mL Bovine Albumin Fraction V Gibco Cat# 15260037 Sodium Pyruvate Gibco Cat# 11360070 2-mercaptoethanol Gibco Cat# 21985023 Penicillin/Streptomycin Cyitva Cat# SV30010 PD0325901 LC laboratorial Cat# P-9688 CHIR9902 LC laboratorial Cat# C-6556 LIF Novoprotein Cat# C690 0.25% Trypsin solution Gibco Cat# 25200056 Concanavalin A beads Bangs Laboratories Cat# BP531 pA-Tn5 transposome Vazyme Cat# S603 0.5 M EDTA Sigma Cat# 03690 10% SDS Sigma Cat# L4509 Proteinase K Thermo Fisher Scientific Cat# EO0492 AMPure XP beads Beckman Counter Cat# A63881 Trizol protocol Invitogen Cat# 15596018 Critical commercial assays Kapa Hyper Prep Kits KAPA Cat# KK8504 EZ-96 DNA Methylation-Direct MagPrep Zymo Cat# D5044 Hyperactive ATAC-Seq Library Prep Kit for Illumina Vazyme Cat# TD711 HiScript III All-in-one RT SuperMix Vazyme Cat# R333-01 Genomic DNA extraction kit TIANGEN Cat# DP3G4 SuperScript II reverse transcriptase kit Invitrogen Cat# 18064071 DNA Methylation Bisulfite Kit Vazyme Cat# EM101 DNA Methylation Library Kit for Illumina V3 Vazyme Cat# NE103 NEBNext® Enzymatic 5hmC-seq Kit NEB Cat# E3350 TIANamp genomic DNA kit TIANGEN Cat# DP304 (Continued on next page) Cell Reports 44, 115790, June 24, 2025 17 .. REAGENT or RESOURCE SOURCE IDENTIFIER VAHTS® Universal V8 RNA-seq Library Prep Kit for Illumina Vazyme Cat# NR605 Deposited data scTrio-seq2_mouse This paper GSA: CRA013360 scRNAseq_Mouse Deng et al. 39 GEO: GSE45719 scRNAseq_Mouse Cheng et al. 64 GEO: GSE109071 scRNAseq_Mouse Mohammed et al. 37 GEO: GSE100597 STEM-seq_Mouse Zhang et al. 14 GEO: GSE76505 scCOOL-seq_Mouse Guo et al. 2 GEO: GSE78140 T-WGBS_ Monkey Gao et al. 19 GEO: GSE60166 scChaRM-seq_Monkey Zhai et al. 20 GEO: GSE74767 scPBAT_Human Zhu et al. 21 GEO: GSE81233 scTrio-seq2_Human Zhou et al. 4 GEO: GSE109555 Hi-C_mouse Zhang et al. 14 GEO: GSE76505 ATAC_mouse Wu et al. 50 GEO: GSE66390 CTCF_mouse Wang et al. 49 GSA: CRA011730 ChIP-seq_mouse Liu et al. 52 GEO: GSE217970 ChIP-seq_mouse Wang et al. 65 GEO: GSE97778 ChIP-seq_mouse and ATAC_mouse Xiang et al. 51 GEO: GSE125318 ChIP-seq_mouse Liu et al. 53 GEO: GSE73952 DNAme and RNA in DNMT and TET mutant mouse Li et al. 43 GEO: GSE162903 DNAme, RNA and H3K27me3 Yang et al. 38 GEO: GSE104243 Experimental models: Cell lines serum-based WT mESC Lab of Xiong Ji N/A Software and algorithms Trim Galore (v0.6.4) Babraham Bioinformatics https://github.com/FelixKrueger/TrimGalore Bismark (v0.7.6) Krueger et al. 66 https://github.com/FelixKrueger/Bismark Samtools (v0.1.18 and v1.10) Danecek et al. 67 https://github.com/samtools/samtools SNPsplit (v0.5.0) Krueger et al. 36 https://github.com/FelixKrueger/SNPsplit Bowtie (v1.0.0) Langmead et al. 68 https://bowtie-bio.sourceforge.net/manual.shtml Bowtie2 (v2.5.7) Langmead et al. 69 https://bowtie-bio.sourceforge.net/bowtie2/index.shtml Picard (v2.27.5) Broad Institute https://github.com/broadinstitute/picard MACS2 (v2.2.9.1) Zhang et al. 70 https://github.com/macs3-project/MACS DeepTools (v2.5.7) Ramı́rez et al. 71 https://github.com/deeptools/deepTools Fastp (v0.23.4) Chen et al. 72 https://github.com/OpenGene/fastp STAR (v2.7.8a) Dobin et al. 73 https://github.com/alexdobin/STAR featureCounts (v2.0.0) Liao et al. 74 https://subread.sourceforge.net/featureCounts.html R (v4.2.3) R Core Team https://www.r-project.org/ Seurat R package (v4.2.1) Butler et al. 75 https://github.com/satijalab/seurat SCTransform algorithm (v0.3.2) Hafemeister and Satija 76 https://github.com/satijalab/sctransform Trimmomatic (v0.39) Bolger et al. 77 https://github.com/usadellab/Trimmomatic biomaRt (v2.54.1) Durinck et al. 78 https://github.com/grimbough/biomaRt HOMER (v5.1) Heinz et al. 55 http://homer.ucsd.edu/homer/ Python (v3.11.4) N/A https://www.python.org/ ABC model (v1.1.2) Fulco et al. 79 https://github.com/broadinstitute/ABC-Enhancer- Gene-Prediction Juicer (v1.6) Durand et al. 80 https://github.com/aidenlab/juicer (Continued on next page) 18 Cell Reports 44, 115790, June 24, 2025
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