title: FGO_SN_M_K36me3_rep2

description: Library name: Sample 16

value: milrinone


title: E65ExE_KO_RNA_rep5

status: Public on Sep 27 2025

type: SRA

city: Shanghai

first: Yu

last: Zhang

address: 138 Yi Xue Yuan Road

country: China

institute: Fudan university

library_source: transcriptomic

data_processing:
Paired-end RNA-seq reads were trimmed and mapped to the mm9 genome by TopHat v2.1.1 (Trapnell et al., 2009). FPKM (Fragments per kilobase per million of sequenced reads) for gene expression was calculated using Cufflinks v2.2.1 (Trapnell et al., 2012) based on mm9 refFlat from the UCSC genome annotation database.
Assembly: mm9
Supplementary files format and content: bigWig

molecule: polyA RNA

organism: Mus musculus

source_name: Extra-embryonix ectoderm

growth_protocol: Serum/Lif (S/L) R1 mESCs were cultured in 0.1% gelatin-coated dishes in Dulbecco’s modified Eagle’s medium (Gibco, 11995065) containing 15% FBS (Gibco, 16000-044), 1000 IU/ml leukemia inhibitory factor (Lif) (Merck Millipore, ESG1107), 100 IU/ml penicillin and 100 μg/ml streptomycin (Merck Millipore, TMS-AB2-C), 2 mM GlutaMAX (Gibco, 35050061), 1% EmbryoMax nucleosides (Merck Millipore, ES-008-D), 0.1 mM nonessential amino acids (Gibco, 25-025-CIR), and 0.1 mM 2-mercaptoethanol (Gibco, 21985023). 2i mESCs were cultured on 0.2% gelatin-coated dishes in 2i/Lif medium (N2B27 medium supplemented with 1 μm PD0325901 (Tocris, 41921), 3 μm CHIR99021 (Tocris, 4423) and 1000 IU/ml Lif). Cells were routinely propagated every 2-3 days. The formative EpiLCs were induced as previously described (Hayashi et al., 2011). Briefly, 1.0×105 2i ESCs were plated in a well of a 12-well plate coated with Matrigel (BD, 356230/356231, diluted at a ratio of 1:100 in N2B27 medium). Cells were cultured in N2B27 medium containing activin A (20 ng/ml), bFGF (12 ng/ml), XAV939 (5 μM), and KSR (1%). EpiLCs were collected for analysis at the indicated time point.

extract_protocol:
Embryos or cells were lysed and used directly as input materials for subsequent RNA-seq library prepararion.
All RNA libraries were prepared using the Smart-seq2 method as previously reported (Picelli et al., 2014), and were sequenced by the Illumina Hiseq X Ten or Novaseq 6000 system according to the manufacturer’s instructions.

tag: tissue

value: Extra-embryonix ectoderm

tag: genotype

value: Nsd1 KO

tag: developmental stage/treatment


title: E65ExE_KO_RNA_rep4


title: FGO_SN_M_K36me3_rep1

description: Library name: Sample 15

library_source: genomic

data_processing:
Paired-end reads were first processed by TrimGalore (v.0.6.4) with default parameters to remove adaptor sequences and reads of low quality. The filtered reads were then mapped to the mm9 genome using Bowtie2 (v2.2.5) (Langmead and Salzberg, 2012) with the default parameters. Duplicates were removed with MarkDuplicates.jar. The unique mapped reads were then used to calculate the RPKM (Reads per kilobase per million of sequenced reads), which was further Z-score normalized to minimize the batch and cell type variation. The Pearson correlation was calculated for each sample with two biological replicates (10-kb bin). Replicates with good reproducibility were pooled together for downstream analyses. The UCSC genome browser was used for visualization.
Assembly: mm9
Supplementary files format and content: bigWig

molecule: genomic DNA

source_name: FGO

growth_protocol: Serum/Lif (S/L) R1 mESCs were cultured in 0.1% gelatin-coated dishes in Dulbecco’s modified Eagle’s medium (Gibco, 11995065) containing 15% FBS (Gibco, 16000-044), 1000 IU/ml leukemia inhibitory factor (Lif) (Merck Millipore, ESG1107), 100 IU/ml penicillin and 100 μg/ml streptomycin (Merck Millipore, TMS-AB2-C), 2 mM GlutaMAX (Gibco, 35050061), 1% EmbryoMax nucleosides (Merck Millipore, ES-008-D), 0.1 mM nonessential amino acids (Gibco, 25-025-CIR), and 0.1 mM 2-mercaptoethanol (Gibco, 21985023). 2i mESCs were cultured on 0.2% gelatin-coated dishes in 2i/Lif medium (N2B27 medium supplemented with 1 μm PD0325901 (Tocris, 41921), 3 μm CHIR99021 (Tocris, 4423) and 1000 IU/ml Lif). Cells were routinely propagated every 2-3 days. The formative EpiLCs were induced as previously described (Hayashi et al., 2011). Briefly, 1.0×105 2i ESCs were plated in a well of a 12-well plate coated with Matrigel (BD, 356230/356231, diluted at a ratio of 1:100 in N2B27 medium). Cells were cultured in N2B27 medium containing activin A (20 ng/ml), bFGF (12 ng/ml), XAV939 (5 μM), and KSR (1%). EpiLCs were collected for analysis at the indicated time point. Embryos were collected in vivo.

extract_protocol:
Embryos or cells were lysed in lysis buffer and subject to Mnase digestion, antibody immunoprecipitation, and subsequent library preparation.
STAR ChIP-seq was performed as previously described (Zhang et al., 2016) with modifications. Briefly, samples were suspended and lysed followed by chromatin fragmentation by micrococcal nuclease (MNase, Sigma-Aldrich, N3755-200UN) at 37°C for 5 min. After being terminated, the supernatant containing chromatin was incubated with 1 μg of primary antibody (H3K36me2, Active motif, 61019; H3K36me3, Active motif, 61021 or 61902) at 4°C overnight with rotation. The next day, 100 μg of Protein A/G dynabeads (mixed at 1:1, Thermo Fisher Scientific, 10001D for Protein A and 10004D for Protein G) was added to each sample and incubated at 4°C for 3 hours with rotation. The beads were next washed five times with 150 μl of RIPA buffer and once with 150 μl of LiCl buffer. For each sample, beads were resuspended with 28 μl of H2O, 1 μl of 10× Ex Taq buffer (Takara, RR006B), and 1 μl of proteinase K (NEB, P8107S) and incubated at 55°C for 90 min, followed by incubation at 72°C for 40 min to inactivate the proteinase K. Samples were then subjected to TruSeq library preparation using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645S). Libraries were sequenced using the Illumina Hiseq X Ten or Novaseq 6000 system according to the manufacturer’s protocol.

value: FGO

tag: chip antibody

value: H3K36me3 (active motif, 61021)

value: WT

tag: developmental stage

value: SN

tag: treatment


title: E85_Ctrl_ExE_RNA_rep1

value: control


title: E65ExE_KO_RNA_rep3


title: NSN_FGO_100_K36me2_rep1

description: Library name: Sample 17

value: H3K36me2 (active motif, 61019)

value: NSN


title: FGO_SN_M_K36me2_rep2

description: Library name: Sample 14


title: FGO_SN_M_K36me2_rep1

description: Library name: Sample 13


title: E65ExE_KO_RNA_rep2


title: E65ExE_Ctrl_RNA_rep5


title: FGO_SN_MD_K36me3_rep2

description: Library name: Sample 12

value: milrinone and Drb


title: E65ExE_KO_RNA_rep1


title: E85_KO_ExE_RNA_rep2


title: FGO_SN_MD_K36me3_rep1

description: Library name: Sample 11


title: E65ExE_Ctrl_RNA_rep4


title: FGO_SN_MD_K36me2_rep2

description: Library name: Sample 10


title: E65ExE_Ctrl_RNA_rep3


title: E65ExE_Ctrl_RNA_rep2


title: E65ExE_Ctrl_RNA_rep1


title: FGO_NSN_M_K36me3_rep2

description: Library name: Sample 8


title: FGO_NSN_M_K36me3_rep1

description: Library name: Sample 7


title: FGO_NSN_M_K36me2_rep2

description: Library name: Sample 6


title: E65Epi_KO_RNA_rep3

source_name: Epiblast

value: Epiblast


title: E65Epi_KO_RNA_rep5


title: E65Epi_KO_RNA_rep4


title: FGO_NSN_M_K36me2_rep1

description: Library name: Sample 5


title: FGO_NSN_MD_K36me3_rep2

description: Library name: Sample 4


title: E65Epi_KO_RNA_rep2


title: FGO_NSN_MD_K36me3_rep1

description: Library name: Sample 3


title: FGO_NSN_MD_K36me2_rep2

description: Library name: Sample 2


title: E65Epi_Ctrl_RNA_rep5


title: FGO_NSN_MD_K36me2_rep1

description: Library name: Sample 1


title: E65Epi_Ctrl_RNA_rep4


title: E65Epi_KO_RNA_rep1


title: E65Epi_Ctrl_RNA_rep1


title: E65Epi_Ctrl_RNA_rep2


title: E35_KO_single_Bl5_1st_RNA

source_name: Blastocyst

value: Blastocyst


title: ICM_Nsd1KO_WGBS_rep4

description: Library name: Sample 7

data_processing:
All paired-end reads were first processed using cutadapt (v1.18) (Martin, 2011) with the parameter -a GGGGGGGGGGGGX -a AGATCGGAAGAG -A AGATCGGAAGAG -A GGGGGGGGGGGGX -g CTCTTCCGATCT -G CTCTTCCGATCT -n 10 --max-n 0.05 -q 20,20 -u -10 -U 10 -m 30 -e 0.2, to remove adaptors and the low-quality reads before mapping. The filtered reads were then aligned to the mm9 genome using Bismark (v0.18.1) (Krueger and Andrews, 2011) with default parameters. After removing multiple-mapped reads and PCR duplicates, the unique-mapped reads were used for CpG methylation calling with bismark_methylation_extractor. CpG sites that were covered at least five times were used for downstream analyses. For 200-bp bin analyses, all reads covering CpG sites within the bin were pooled and used to estimate the methylation level for the bin. The methylation level was calculated as the ratio of methylated CpG to the total number of CpG sites within each bin. The λ-DNA was used for conversion rate calculation.
Assembly: mm9
Supplementary files format and content: bigWig

source_name: ICM

growth_protocol: Samples were collected in vivo

extract_protocol:
Cells were lysed in STEM-seq lysis buffer and subject to bisulfite conversion and subsequent library preparation.
ICMs were lysed with 10 μl of STEM-seq lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1 mM EDTA, pH 8.0, 0.5% NP-40) containing 1 μl of protease K (NEB, P8107S) for 3 h at 55 °C, followed by heat-inactivation for 1 h at 72 °C. Samples were then treated with 1 μl of dsDNA Fragmentase (NEB; M0348AA) for 30 min before being subjected to bisulfite conversion using EZ DNA Methylation-Lightning Kit (ZYMO, D5030). Libraries were prepared using the EpiArt DNA Methylation Library Kit (Vazyme, NE103) according to the manufacturer’s instructions. In brief, a 3’ adaptor was first added to the converted and denatured ssDNA. After DNA extension and purification, a 5’ adaptor was added. dsDNA with both 3’ and 5’ adaptors were then subjected to PCR amplification and libraries were sequenced using DNBSEQ-T7. For all samples, λ-DNA (Promega, D150A) was added with a mass ratio of 1:200 before bisulfite conversion for conversion rate analysis.

value: ICM


title: ICM_Nsd1KO_WGBS_rep3

description: Library name: Sample 6


title: ICM_Nsd1KO_WGBS_rep5

description: Library name: Sample 8


title: ICM_Nsd1KO_WGBS_rep2

description: Library name: Sample 5


title: E65Epi_Ctrl_RNA_rep3


title: FGO_SN_MD_K36me2_rep1

description: Library name: Sample 9


title: E35_KO_single_Bl4_3rd_RNA


title: ICM_Nsd1KO_WGBS_rep1

description: Library name: Sample 4


title: E35_KO_single_Bl2_3rd_RNA


title: E35_KO_single_Bl1_1st_RNA


title: ICM_Ctrl_WGBS_rep3

description: Library name: Sample 3

value: Control


title: ICM_Ctrl_WGBS_rep2

description: Library name: Sample 2


title: ICM_Ctrl_WGBS_rep1

description: Library name: Sample 1


title: E35_Ctrl_single_Bl3_3rd_RNA


title: L2C_Ctrl_RNA_rep1

description: Library name: Sample 7

source_name: late 2-cell

value: late 2-cell


title: L2C_Ctrl_RNA_rep2

description: Library name: Sample 8


title: L2C_amanitin_RNA_rep2

description: Library name: Sample 6

value: α-amanitin


title: E35_Ctrl_single_Bl1_1st_RNA


title: ICM_Nsd1KO_WGBS_rep6

description: Library name: Sample 9


title: DMSO_8C_rep2


title: L2C_amanitin_RNA_rep1

description: Library name: Sample 5


title: SN_FGO_RNA_rep2

description: Library name: Sample 4


title: APH_2C_rep2

value: APH


title: DMSO_8C_rep1


title: APH_2C_rep1


title: NSN_FGO_RNA_rep2

description: Library name: Sample 2


title: RNA_ctrl_8C_rep2


title: NSN_FGO_RNA_rep1

description: Library name: Sample 1


title: RNA_ctrl_8C_rep1


title: RNA_amanitin_2C_rep1

value: alpha-amanitin


title: SKONKO_mESC_DNMT3B1_WGBS

source_name: mESC

growth_protocol: Serum/Lif (S/L) R1 mESCs were cultured in 0.1% gelatin-coated dishes in Dulbecco’s modified Eagle’s medium (Gibco, 11995065) containing 15% FBS (Gibco, 16000-044), 1000 IU/ml leukemia inhibitory factor (Lif) (Merck Millipore, ESG1107), 100 IU/ml penicillin and 100 μg/ml streptomycin (Merck Millipore, TMS-AB2-C), 2 mM GlutaMAX (Gibco, 35050061), 1% EmbryoMax nucleosides (Merck Millipore, ES-008-D), 0.1 mM nonessential amino acids (Gibco, 25-025-CIR), and 0.1 mM 2-mercaptoethanol (Gibco, 21985023). 2i mESCs were cultured on 0.2% gelatin-coated dishes in 2i/Lif medium (N2B27 medium supplemented with 1 μm PD0325901 (Tocris, 41921), 3 μm CHIR99021 (Tocris, 4423) and 1000 IU/ml Lif). Cells were routinely propagated every 2-3 days. The formative EpiLCs were induced as previously described (Hayashi et al., 2011). Briefly, 1.0×105 2i ESCs were plated in a well of a 12-well plate coated with Matrigel (BD, 356230/356231, diluted at a ratio of 1:100 in N2B27 medium). Cells were cultured in N2B27 medium containing activin A (20 ng/ml), bFGF (12 ng/ml), XAV939 (5 μM), and KSR (1%). EpiLCs were collected for analysis at the indicated time point.Embryos were collected in vivo.

extract_protocol:
DNA was extracted from large amount of cells, or embryos or low input number of cells were lysed in STEM-seq lysis buffer and subject to bisulfite conversion and subsequent library preparation.
For cell samples, genomic DNA was first extracted using HiPure Universal DNA Kit (Magen, D3018-02), and was then subjected to bisulfite conversion using EpiArt DNA Methylation Bisulfite Kit (Vazyme, EM101) according to the manufacturer’s instructions. For embryo samples, Epi or ExE were lysed with 10 μl of STEM-seq lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1 mM EDTA, pH 8.0, 0.5% NP-40) containing 1 μl of protease K (NEB, P8107S) for 3 h at 55 °C, followed by heat-inactivation for 1 h at 72 °C. Samples were then treated with 1 μl of dsDNA Fragmentase (NEB; M0348AA) for 30 min before being subjected to bisulfite conversion using EZ DNA Methylation-Lightning Kit (ZYMO, D5030). Libraries were prepared using the EpiArt DNA Methylation Library Kit (Vazyme, NE103) according to the manufacturer’s instructions. In brief, a 3’ adaptor was first added to the converted and denatured ssDNA. After DNA extension and purification, a 5’ adaptor was added. dsDNA with both 3’ and 5’ adaptors were then subjected to PCR amplification and libraries were sequenced using Illumina Hiseq X Ten or Novaseq 6000 system. For all samples, λ-DNA (Promega, D150A) was added with a mass ratio of 1:200 before bisulfite conversion for conversion rate analysis.

value: mESC

value: SKO;Nsd1 KO

value: DNMT3B1 OE


title: RNA_amanitin_2C_rep2


title: SKO_mESC_GFP_WGBS_rep2

value: SKO

value: GFP OE


title: SKO_mESC_GFP_WGBS_rep1


title: E35_Ctrl_single_Bl5_3rd_RNA

value: control


title: E35_Ctrl_single_Bl3_1st_RNA


title: SKONKO_mESC_DNMT3A2noPWWP_WGBS

value: DNMT3A2{delta}PWWP OE


title: SKO_mESC_DNMT3B1_WGBS_rep2


title: E85Headfold_Ctrl_WGBS_rep2

source_name: Headfold

value: Headfold


title: E85Headfold_Ctrl_WGBS_rep1


title: SKO_mESC_DNMT3B1_WGBS_rep1


title: SKO_mESC_DNMT3B1noPWWP_WGBS_rep2


title: E85_ExE_KO_WGBS_rep2

source_name: Extra-embryonic ectoderm

value: Extra-embryonic ectoderm

value: Nsd1 KO


title: SKO_mESC_DNMT3B1noPWWP_WGBS_rep1


title: E85_ExE_KO_WGBS_rep1


title: SN_FGO_RNA_rep1

description: Library name: Sample 3

value: FGO

value: WT

value: SN


title: SKO_mESC_DNMT3A2_WGBS_rep2

value: DNMT3A2 OE


title: SKO_mESC_DNMT3A2noPWWP_WGBS_rep2


title: SKO_mESC_DNMT3A2_WGBS_rep1


title: E85_ExE_Ctrl_WGBS_rep2

value: Control


title: SKONKO_mESC_GFP_WGBS


title: E85Epi_KO_WGBS_rep2

value: Epiblast


title: SKONKO_mESC_DNMT3B1noPWWP_WGBS


title: E85Epi_KO_WGBS_rep1


title: WT_Day3_EpiLC_K36me3_rep2

source_name: EpiLC

value: EpiLC

value: H3K36me3 (active motif, 61902)

value: Day 3


title: SKONKO_mESC_DNMT3A2_WGBS

value: mESC

value: SKO;Nsd1 KO


title: WT_mESC_dTAG7d_WGBS_rep1

value: dTAG 7 day


title: WT_Day3_EpiLC_K36me3_rep1


title: WT_mESC_dTAG7d_WGBS_rep3


title: WT_mESC_dTAG7d_WGBS_rep2


title: WT_Day0_EpiLC_K36me3_rep2

source_name: 2i mESC

value: 2i mESC

value: Day 0


title: NSd1_KO_Day3_EpiLC_K36me3_rep2


title: NSd1_KO_Day3_EpiLC_K36me3_rep1


title: PRC1degNsd1KO_mESC_dTAG7d_WGBS_rep1

value: PRC1deg;Nsd1 KO


title: WT_Day0_EpiLC_K36me3_rep1


title: PRC1deg_mESC_dTAG7d_WGBS_rep3


title: NSd1_KO_Day0_EpiLC_K36me3_rep2


title: E85_ExE_Ctrl_WGBS_rep1

value: Extra-embryonic ectoderm


title: PRC1degNsd1KO_mESC_dTAG7d_WGBS_rep2


title: NSd1_KO_Day0_EpiLC_K36me3_rep1

value: Nsd1 KO


title: PRC1deg_mESC_dTAG7d_WGBS_rep1


title: lung, RHL3

city: Nanjing

first: Xinmei

last: Huang

address: No.321 Zhongshan Road

institute: Nanjing Drum Tower Hospital

description: Library name: Sample 11

data_processing:
Raw sequencing reads were first assessed for quality using FastQC.
Adapters and low-quality reads were trimmed using Trim Galore (v0.6.6).
Cleaned reads were aligned to the mouse reference genome using STAR aligner (v2.7.9a) with default settings.
Gene-level quantification was performed using featureCounts (Subread v2.0.1) with GENCODE mouse gene annotation.
Differential expression analysis was conducted using DESeq2 (v1.30.1) in R.
Assembly: GRCm38 (mm10)
Supplementary files format and content: Processed data files include normalized gene expression matrices of all samples.
Supplementary files format and content: Files are provided in Excel (.xlsx) format.

molecule: total RNA

source_name: lung

extract_protocol:
Total RNA was extracted from mouse lung tissues using TRIzol reagent (Invitrogen) according to the manufacturer's instructions, followed by purification using the RNeasy Mini Kit (Qiagen). RNA integrity was evaluated with an Agilent 2100 Bioanalyzer.
RNA-seq libraries were prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina (NEB), according to the manufacturer’s protocol. Polyadenylated mRNA was enriched using oligo(dT) magnetic beads, fragmented into ~200 bp fragments, and reverse-transcribed into first-strand cDNA. Second-strand cDNA synthesis, adaptor ligation, and PCR amplification were performed to complete the library. Libraries were sequenced on a DNBSEQ-G400 platform (MGI Tech Co., Ltd.).

treatment_protocol: Mice were first subjected to a combined bleomycin (BLM) and lipopolysaccharide (LPS) challenge to establish an acute exacerbation of pulmonary fibrosis (AE-PF) model. After model induction, mice received treatment with ND-RHL (liposomes co-loaded with nintedanib and dexamethasone, and surface-modified with both hyaluronic acid [HA] and RGD peptides). Lung tissues were collected at the model endpoint from three groups: saline control, AE-PF model (untreated), and ND-RHL-treated mice. Total RNA was extracted from lung tissues for transcriptome analysis via RNA sequencing.

value: lung


title: lung, RHL4

description: Library name: Sample 12


title: PRC1deg_mESC_dTAG7d_WGBS_rep2


title: Nsd1KO_mESC_dTAG7d_WGBS_rep3


title: lung, RHL1

description: Library name: Sample 9


title: lung, AE4

description: Library name: Sample 8


title: SKO_mESC_DNMT3A2noPWWP_WGBS_rep1

value: SKO

value: DNMT3A2{delta}PWWP OE


title: Nsd1KO_mESC_dTAG7d_WGBS_rep1


title: lung, RHL2

description: Library name: Sample 10


title: lung, AE3

description: Library name: Sample 7


title: Nsd1KO_mESC_DNMT3B1_WGBS

value: DNMT3B1 OE


title: Nsd1KO_mESC_DNMT3A2_WGBS

value: DNMT3A2 OE


title: Nsd1KO_mESC_GFP_WGBS

value: GFP OE


title: WT_EpiLC_Day3_WGBS_rep1

value: EpiLC

value: WT


title: PRC1degNsd1KO_mESC_dTAG7d_WGBS_rep3


title: lung, AE2

description: Library name: Sample 6


title: lung, con4

description: Library name: Sample 4


title: WT_EpiLC_Day3_WGBS_rep2

value: Day 3


title: WT_EpiLC_Day2_WGBS_rep1

value: Day 2


title: lung, con2

description: Library name: Sample 2


title: WT_EpiLC_Day2_WGBS_rep2


title: WT_EpiLC_Day1_WGBS_rep1

value: Day 1


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2L - cell 95

city: Guangzhou

first: Jinyi

last: Wu

state: Guangdong

address: No. 9 XingDaoHuanBei Road, Guangzhou International Bio Island

institute: Guangzhou Laboratory

library_source: transcriptomic single cell

data_processing:
For bulk RNA seq, we used Fastp (version 0.23.1) (Chen, S. , et al 2018) to perform basic statistics on the quality of the raw reads. The steps of data processing were as follows: (1) Discard a paired reads if either one read contains adapter contamination; (2) Discard a paired reads if more than 10% of bases are uncertain in either one read; (3) Discard a paired reads if the proportion of low quality (Phred quality <5) bases is over 50% in either one read.  Alignment, annotation, and gene expression quantification were performed with STAR software (v.2.7.9a). The second columns of the output ‘ReadsPerGene’ tables were aggregated into a gene count table. Single cell RNA-seq data were trimmed using Trim Galore coupled with FastQC (v.0.11.2) or fastp software with default parameters. Alignment, annotation, PCR duplicate removal and gene expression quantification were subsequently performed using the STARsolo pipeline.
Assembly: Ensembl GRCh38 release 104
Supplementary files format and content: Bulk RNAseq count table: gene by cell expression matrix generated with STAR; scRNAseq count tables: Filtered matrix of gene by cell expression, file with barcodes and file with expressed genes. Files are ready to be imported to Seurat package.

organism: Homo sapiens

extract_protocol:
For scRNA-seq, 120h SACs were dissociated and sorted by flow cytometer for Smart-seq2 library construction. 60h SACs were collected after replating on gelatinized plate for 30min for feeder removal; day6 stEM and e-stEM were manually picked with a cut-tip, washed once with DPBS and then dissociated with TrypLE Express (Gibco) at 37 °C in 20%O2 and 5% CO2 incubator for 45-60 min.
Library construction was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics). For NovaSeq 6000 library construction, the process begins with RNA extraction and quality control, followed by mRNA enrichment using polyA selection or rRNA depletion. First and second strand cDNA synthesis is performed, then the cDNA is fragmented and end-repaired. Sequencing adapters are ligated to the cDNA fragments, which are then purified and size-selected. The library is amplified by PCR, assessed for quality, and loaded onto the NovaSeq 6000 for sequencing. For MGISEQ-2000, the protocol similarly starts with RNA extraction and quality control, mRNA enrichment or rRNA depletion, cDNA synthesis, fragmentation, and end-repair. Sequencing adapters are ligated, followed by purification, size selection, and PCR amplification. Unique to MGISEQ-2000 is a circularization step converting the linear library into a circular DNA molecule before loading and sequencing on the MGISEQ-2000 platform.

tag: cell line

tag: cell type

value: pluripotent stem cell


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2L - cell 96


title: WT_EpiLC_Day0_WGBS_rep2

value: mESC

value: 2i mESC


title: Nsd1_KO_EpiLC_Day3_WGBS_rep2


title: WT_EpiLC_Day0_WGBS_rep1


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2L - cell 94


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2L - cell 93


title: Nsd1_KO_EpiLC_Day3_WGBS_rep1


title: Nsd1_KO_EpiLC_Day2_WGBS_rep1


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2L - cell 92


title: Nsd1_KO_EpiLC_Day2_WGBS_rep2


title: lung, AE1

description: Library name: Sample 5


title: Nsd1KO_mESC_dTAG7d_WGBS_rep2

value: dTAG 7 day


title: Nsd1_KO_EpiLC_Day1_WGBS_rep2


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2L - cell 91


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2L - cell 90


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2L - cell 89


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2L - cell 87


title: Nsd1_KO_EpiLC_Day0_WGBS_rep2


title: Nsd1_KO_EpiLC_Day0_WGBS_rep1


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2L - cell 88


title: Nsd1_KO_EpiLC_Day1_WGBS_rep1


title: lung, con3

description: Library name: Sample 3


title: WT_EpiLC_Day1_WGBS_rep2


title: lung, con1

description: Library name: Sample 1


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2L - cell 85


title: E75Exe_KO_WGBS_rep1

value: Extra-embryonic ectoderm


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2L - cell 84


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2L - cell 83


title: E75Exe_Ctrl_WGBS_rep2

value: Control


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2L - cell 82


title: E75Exe_Ctrl_WGBS_rep1


title: E75Ect_KO_WGBS_rep3

source_name: Ectoderm

value: Ectoderm

value: Nsd1 KO


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2L - cell 80


title: E75Ect_KO_WGBS_rep1


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2L - cell 81


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2L - cell 78


title: E75Ect_Ctrl_WGBS_rep3


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2L - cell 79


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2L - cell 86


title: E75Ect_Ctrl_WGBS_rep2


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2L - cell 77


title: E75Ect_Ctrl_WGBS_rep1


title: E75Ect_KO_WGBS_rep2


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2L - cell 75


title: E65ExE_KO_WGBS_rep3


title: E65ExE_KO_WGBS_rep2


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2L - cell 76


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2L - cell 73


title: E75Exe_KO_WGBS_rep2


title: E75Exe_KO_WGBS_rep3


title: Dam-Simba2, batch2, NSCs

city: Singapore

first: Hongyan

last: Wang

address: 8 College Rd

country: Singapore

institute: Duke-NUS Medical School

description: Library name: Simba2_Batch2

data_processing:
Basecalls performed using Illumina's bcl2fastq v2.19.0.316
Raw sequencing reads were quality-checked by FastQC and were aligned on Drosophila melanogaster (dm6) reference genome using Bowtie 2. The peak calling was done by MACS v3, and the nearest genes were annotated using ChIPseeker. Two biological replicates were performed for the profiling and analysis.
bedGraph were generated using MACS v3, score represent the normalized signal of DNA fragments at a given genome coordinates. peaks.xls were generated by MACS v3 with default setting.
Assembly: dm6
Supplementary files format and content: bedGraph, peaks.xls (except for Dam control)
Library strategy: DamID-Seq

organism: Drosophila melanogaster

source_name: Brain

growth_protocol: UASNDam-Simba1/2) or UAS-Dam control (pUAST attB-LT3-NDam) was expressed under the control of grh-Gal4, tub-Gal80ts driver. Embryos were collected in a 4 hours period and transferred into 18 °C (restrictive temperature) for 44 hours till hatching and then shifted into 29 °C for 24 h before dissection.

extract_protocol:
Genomic DNA was extracted and digested by DpnI (targets only methylated GATC sites). After that, methylated DNA was amplified by PCR The Illumina TruSeq DNA PCR-free library preparation kit were used according to the manufacturer’s protocol. Briefly, DNA was fragmented and end-repaired first. Then an adenine (A) nucleotide was added to the 3ʹ ends of the fragments to prevent self-ligation. After that, index adaptors were ligated and followed by quantifying. normalizing and pooling of libraries. The libraries were sequenced on the illumina MiSeq equipment.
Libraries were constructed from the amplified DNA samples using the illumina TruSeq DNA PCR-free library preparation kit according to the manufacturer’s protocol and sequenced on the illumina MiSeq equipment. Paired reads (2 × 250 bp) were sequenced from Dam-Simba1/2 or Dam-Control library.

value: Brain

value: Neural stem cells (NSCs)

tag: batch


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2L - cell 72


title: E65ExE_KO_WGBS_rep1


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2L - cell 71


title: Dam-Simba1, batch2, NSCs

description: Library name: Simba1_Batch2


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2L - cell 70


title: E65ExE_Ctrl_WGBS_rep2


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2L - cell 69


title: Dam-control, batch2, NSCs

description: Library name: Dam_Control_Batch2


title: E65ExE_Ctrl_WGBS_rep1


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2L - cell 67


title: Dam-Simba2, batch1, NSCs

description: Library name: Simba2_Batch1


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2L - cell 74


title: E65Epi_KO_WGBS_rep3

value: Epiblast


title: Dam-Simba1, batch1, NSCs

description: Library name: Simba1_Batch1


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2L - cell 64


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2L - cell 65


title: E65Epi_KO_WGBS_rep2


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2L - cell 63


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2L - cell 61


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2L - cell 62


title: Dam-control, batch1, NSCs

description: Library name: Dam_Control_Batch1


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2L - cell 60


title: E65Epi_KO_WGBS_rep1


title: E65Epi_Ctrl_WGBS_rep4


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2L - cell 58


title: E65Epi_Ctrl_WGBS_rep3


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2L - cell 59


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2L - cell 56


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2L - cell 57


title: E65Epi_Ctrl_WGBS_rep2


title: E65Epi_Ctrl_WGBS_rep1


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2L - cell 68


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2L - cell 54


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2L - cell 55


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2L - cell 53


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2L - cell 66


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2L - cell 52


title: MDA-MB-231 cells, dasatinib treatment, 48h_rep1

city: Taipa

first: feng

last: yu

address: Avenida de Universidade

country: Macau

institute: University of Macau

description: Library name: LG_231_48h_C

data_processing:
Raw reads from sequencing results were quality-checked using FastQC software and summary results were compiled using MultiQC
Adapter sequences were trimmed using Trim Galore to generate clean reads
Sequence alignment was performed using Spliced Transcripts Alignment to a Reference (STAR, v2.5.2b)
Gene-level read quantification was performed using FeatureCounts
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text file includes TPM values for each Sample

extract_protocol:
Total RNA was extracted from cultured cells using TRIzol reagent (Thermo Fisher Scientific, 15596026) and then purified using the RNeasy mini kit (QIAGEN, 74104).
Complementary DNA (cDNA) libraries for RNA-seq were prepared using the NEBNext® Ultra™ RNA Library Prep Kit for Illumina (New England Biolabs, E7770) and subjected to quality control. Sequencing was conducted on the NovaSeq 6000 platform (Illumina) using 150-base pair paired-end reads.

tag: biological replicates

value: biol rep 1

value: Human breast adenocarcinoma epithelial cell line

value: dasatinib treatment


title: WT_mESC_dTAG48h_K36me2_rep2

value: H3K36me2 (active motif, 61019)

value: WT

value: dTAG 48h


title: MDA-MB-231 cells, dasatinib treatment, 48h_rep2

description: Library name: LG_231_48h_D

value: biol rep 2


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2L - cell 51

value: pluripotent stem cell


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2L - cell 50


title: MDA-MB-231 cells, dasatinib treatment, 24h_rep2

description: Library name: LG_231_24h_D


title: WT_mESC_dTAG48h_K36me2_rep1

value: mESC


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2L - cell 49


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2L - cell 47


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2L - cell 48


title: MDA-MB-231 cells, dasatinib treatment, 24h_rep1

description: Library name: LG_231_24h_C


title: WT_mESC_dTAG48h_H3K36me3_rep2

value: H3K36me3 (active motif, 61021)


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2L - cell 43


title: MDA-MB-231 cells, dasatinib treatment, 12h_rep2

description: Library name: LG_231_12h_D


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2L - cell 44


title: PRC1degNsd1KO_mESC_dTAG48h_K36me3_rep1

value: PRC1deg;Nsd1 KO


title: MDA-MB-231 cells, dasatinib treatment, 6h_rep2

description: Library name: LG_231_6h_D


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2L - cell 42


title: PRC1degNsd1KO_mESC_dTAG48h_K36me2_rep2


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2L - cell 45


title: WT_mESC_dTAG48h_H3K36me3_rep1


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2L - cell 40


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2L - cell 46


title: PRC1degNsd1KO_mESC_dTAG48h_K36me3_rep2


title: MDA-MB-231 cells, dasatinib treatment, 6h_rep1

description: Library name: LG_231_6h_C


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2L - cell 39


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2L - cell 41


title: MDA-MB-231 cells, Sham_rep2

description: Library name: LG_231_0h_D


title: PRC1degNsd1KO_mESC_dTAG48h_K36me2_rep1


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2L - cell 38


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2L - cell 37


title: MDA-MB-231 cells, Sham_rep1

description: Library name: LG_231_0h_C


title: MDA-MB-231 cells, dasatinib treatment, 12h_rep1

description: Library name: LG_231_12h_C


title: PRC1deg_mESC_dTAG48h_K36me3_rep2


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2L - cell 36


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2L - cell 35


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2L - cell 34


title: PRC1deg_mESC_dTAG48h_K36me3_rep1


title: scRNA-seq (10X) of Day 4 e-stEM

description: Library name: e-stEM D4

source_name: pluripotent stem cell


title: PRMT5.Input1 rep1

first: Shan

last: Gao

address: No. 2 Sipailou, Xuanwu District

institute: Southeast University

library_source: other

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastp
All clean reads were mapped to human genome version hg38 by hisat2
peaks were called using exomePeak2
Assembly: Hg38
Supplementary files format and content: bigWig, peaks

molecule: other

source_name: jurkat

growth_protocol: Jurkat cells cultured in RPMI1640 medium (Gibco) with 10% fetal bovine serum and 1% penicillin/streptomycin (Invitrogen)

extract_protocol:
Cells were fixed with 264 nm UV for 400mJ, then lysed in protein lysis buffer
NEBNext Ultra Directional RNA Library Prep Kit

treatment_protocol: Jurkat cells stimulated with PHA 48 hours

value: jurkat

value: PHA


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2L - cell 32


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2L - cell 33


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2L - cell 30


title: PRC1deg_mESC_dTAG48h_K36me2_rep1


title: PRMT5.RIP2 rep2


title: Nsd1_KO_mESC_dTAG48h_K36me2_rep2

value: Nsd1 KO


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2L - cell 29


title: PRMT5.RIP1 rep1


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2L - cell 27


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2L - cell 26


title: Nsd1_KO_mESC_dTAG48h_K36me2_rep1


title: scRNA-seq (10X) of Day 6 e-stEM


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2L - cell 24


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2L - cell 23


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2L - cell 22


title: OGf.5iLA.p1

extract_protocol:
Samples were FAC sorted against SUSD2 antibody and the collected cells were spinned down and washed once wiht DPBS. Total RNAs were collected and isolated from cells using RNAiso Plus (Takara, 9109). mRNA was purified from total RNA using poly-T oligo-attached magnetic beads.
Sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA, Catalog #: E7530L) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEB Next First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEB Next Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beverly, USA). Then 3 µL USER Enzyme (NEB, USA) was used with size selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent 5400 system（Agilent，USA） and quantified by QPCR (1.5 nM). The qualified libraries were pooled and sequenced on Illumina platforms with PE150 strategy in Novogene Bioinformatics Technology Co., Ltd (Beijing, China), according to effective library concentration and data amount required.


title: PRMT5.Input2 rep2


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2L - cell 20


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2L - cell 21


title: Nsd1_KO_mESC_dTAG48h_H3K36me3_rep1


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2L - cell 31


title: OGf.Susd2H replicate 2


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2L - cell 19


title: SKONsd1KO_mESC_K36me3_rep2

value: H3K36me3 (active motif, 61902)


title: PRC1deg_mESC_dTAG48h_K36me2_rep2


title: OGf.Susd2H replicate 1


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2L - cell 18


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2L - cell 28


title: SKONsd1KO_mESC_K36me3_rep1


title: SKONsd1KO_mESC_K36me2_rep2


title: OG.Susd2H replicate 1


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2L - cell 16


title: OG.Susd2H replicate 2


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2L - cell 14


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2L - cell 13


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2L - cell 15


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2L - cell 25


title: SKONsd1KO_mESC_K36me2_rep1


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2L - cell 12


title: hiPSC-CM, D20, Sparse

city: Suwon-si

first: Soah

last: Lee

state: Geonggi-do

address: 2066 Seobu-ro, Jangan-gu, 530502

department: Pharmacy

country: South Korea

institute: Sungkyunkwan University

description:
Library name: Sparse
10X Genomics

data_processing:
The single cell library was sequenced with Illumina NovaSeq PE100/PE150 platform
10X Cell Ranger v3.1.0, a set of analysis pipelines that process Chromium single cell data, was used to pre-process scRNAseq data including sample demultiplexing, alignment, filtering, barcode processing, and gene counting. FASTQ files were generated by Illumina’s bcl2fastq. Then reads in FASTQ files were mapped to human reference genome (GRCh38-3.0.0). For the ‘Dense’ sample, 121 million reads from 909 cells were sequenced. 97.5% of these reads have valid barcodes. 96.3% of the reads mapped to genome. For the ‘Sparse’ sample, 138 million reads from 380 cells were sequenced. 97.4% of these reads have valid barcodes. 95.7% of the reads mapped to genome. Quality score of Q>30 reflected a low probability of base-calling errors in barcode, RNA read, sample index, and µMI (>90%) in both groups.
Assembly: GRCh38-3.0.0
Supplementary files format and content: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

source_name: hiPSC (SCVI-111)

growth_protocol: Human iPSCs (SCVI-111) were directed to differentiate into cardiomyocytes using well-established Wnt modulating protocol. hiPSC-CMs were cultured in cardiomyocyte maintenance media (RPMI supplemented with B27+Insulin and CHI99021).

extract_protocol:
On day 20, cells from both density conditions were dissociated into single-cell suspensions and loaded into the Chromium Controller (10x Genomics) for single-cell barcoded droplet generation, according to the manufacturer's protocol (CG000204-Rev D).
This step was done by following the 10x genomics single cell 3' end ibrary preparation protocol. Briefly, only the 3' end of mRNA fragements were used to make library. One end of the fragements were added P5, read1 illumina sequencing primer, 16 base pairs of 10x barcode, and UMI sequences; The other end ligated with P7, sample index sequences, and illumina read2 sequencing primer sequences.

treatment_protocol: Day 18 hiPSC-CMs were replated at either low (33,000 cells/cm2) or high cell density (181,000 cells/cm2), followed by a two-day culture period to allow for cellular adaptation and transcriptional stabilization.

value: hiPSC (SCVI-111)

value: cardiomyocyte


title: Nsd1_KO_mESC_dTAG48h_H3K36me3_rep2


title: SKO_mESC_10k_S2_20k_K36me3_rep3

value: SKO


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2L - cell 11


title: SKO_mESC_10k_S2_20k_K36me3_rep2


title: HaCaT cells, COL23A1 OE, 2hpi

city: Hannover

first: Shruti

last: Chopra

state: Lower Saxony

address: Carl-Neuberg-Str. 1

country: Germany

institute: Hannover Medical School

data_processing:
Raw data processing was conducted by use of nfcore/rnaseq (version 3.9).
Quality control of the sequenced raw FastQ-files was performed by nfcore/rnaseq (version 3.9) and mapped to the genome reference and annotation data, taken from GENCODE.org (Homo sapiens: GRCh38.p13; release 39).
Assembly: GRCh38.p13; release 39
Supplementary files format and content: Matrix table with raw counts for every gene and their corresponding Ensembl ID.

source_name: Skin

growth_protocol: HaCaT cells, a spontaneously immortalized keratinocyte cell line, were cultivated in RPMI 1640 medium (Gibco by Life Technologies, Thermo Fisher Scientific, MA, USA) supplemented with 2 mM L-glutamine (Bio & Sell GmbH, Feucht, Germany), 100 µg/ml penicillin-streptomycin (Bio & Sell), 1x non-essential amino acids (Bio & Sell), 0.05 mg/ml gentamycin (Bio & Sell) and 6% (vol/vol) fetal bovine serum (FBS; PAN Biotech, Aidenbach, Germany).

extract_protocol:
RNA was isolated using the Reliaprep™ RNA Miniprep Systems (Promega, Germany) according to the manufacturer’s instructions. 230ng of total RNA per sample were utilized as input for mRNA enrichment procedure with ‘NEBNext® Poly(A) mRNA Magnetic Isolation Module’ (E7490L; New England Biolabs) followed by stranded cDNA library generation using ‘NEBNext® Ultra II Directional RNA Library Prep Kit for Illumina’ (E7760L; New England Biolabs).
RNA libraries for RNA-seq were prepared using ‘NEBNext® Ultra II Directional RNA Library Prep Kit for Illumina’ (E7760L; New England Biolabs) following manufacturer's protocol.

treatment_protocol: To reach 80% confluency of cells on the day of infection, HaCaT cells were plated one day before infection. Next day, cells were washed with PBS (PAN Biotech, Aidenbach, Germany) and Keratinocyte Growth Medium 2 (PromoCell, Heidelberg, Germany) supplemented with Keratinocyte Supplement Pack (KGM2; PromoCell) containing HSV-1 inoculum (5pfu/cell) was added onto cells for 1 h and incubated at 37°C and 5% CO2. After 1 h incubation, the medium containing the virus was replaced with fresh  Keratinocyte Growth Medium 2 (PromoCell, Heidelberg, Germany) supplemented with Keratinocyte Supplement Pack (KGM2; PromoCell). A further incubation of either 2h (2hpi) or 6h (6hpi) was carried out at 37°C and 5% CO2.

value: Skin

value: HaCaT cells

value: Human epidermal keratinocytes

value: COL23A1 stable overexpression

value: Infected

tag: time


title: HaCaT cells, COL23A1 OE, 6hpi


title: SKO_mESC_10k_S2_20k_K36me3_rep1


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2L - cell 10


title: hiPSC-CM, D20, Dense

description:
Library name: Dense
10X Genomics


title: pUC19_DNA_5ng_Zymo-Gold_CBS-seq.biol_rep3

city: Chicago

first: Ruitu

last: Lyu

state: IL

address: 929 E 57th Street

department: Chemistry

country: USA

institute: The University of Chicago

description: Library name: Sample 108

data_processing:
Raw paired-end bisulfite sequencing reads of three methyl conversion methods (UMBS-seq, EM-seq, and CBS-seq) were first trimmed using Trim Galore (v 0.6.10), which removes Illumina adapter sequences and low-quality bases (Phred score <20).
The trimmed reads were then aligned to a bisulfite-converted reference genome using bismark (v0.24.0) with the Bowtie2 aligner. Prior to alignment, the reference genome (e.g., pUC19 DNA, lambda DNA and human genome) was prepared using bismark_genome_preparation, which generates bisulfite-specific indices.
Mapping was performed in paired-end mode with default parameters, and alignment outputs were stored in BAM format for downstream processing. Following alignment, PCR duplicates were removed using deduplicate_bismark in paired-end mode to minimize amplification bias.
To eliminate unconverted clusters in the EM-seq data, reads with more than 5 unconverted C sites or reads with more than one-third of the total C sites being unconverted were also discarded.
Methylation levels were extracted from the deduplicated BAM files using bismark_methylation_extractor with the --cytosine_report, --CX, and --bedGraph options enabled. This step generated methylation calls for cytosines in CpG, CHG, and CHH contexts, as well as genome-wide coverage files and per-base resolution methylation reports. The methylation extraction was performed using a buffer size of 10 G to ensure efficient processing of large files. All downstream data analysis, visualization, and quality control were conducted using custom Python and R scripts.
Assembly: hg19, lambda DNA, and pUC19 genome
Supplementary files format and content: txt, convertion ratios of each cytosine.
Supplementary files format and content: txt, C-to-U conversion report.

extract_protocol:
cfDNA was extracted and purified from pooled human plasma from Innovative Research Inc. using the Qiagen QIAamp Circulating Nucleic Acid kit. Two samples of ~250 ng of unmethylated Lambda genomic DNA (-dcm, -dam) from Thermo Fisher was fragmented with NEB UltraShear fragmentase for 25-30 minutes according to the NEB protocol.
End repair, A-tailing, and ligation of a sequencing adapter were completed with the KAPA EvoPrep Kit. The NEB single molecule Methylated Adapter was used during ligation, and 3 μL of USER enzyme was added to the ligation reaction mixture following ligation and heated at 37 °C for 15 minutes for opening of the NEB Methylated Adapter loop. A final Cytiva beads purification with a 0.8x beads ratio was used to purify the adaptor ligated libraries. A bioanalyzer trace confirmed an appropriate library size of ~340 bp.

treatment_protocol: Both fragmented lambda DNA and cfDNA were treated with UMBS-seq, EM-seq (NEB), and Zymo EZ-Gold Bisulfite methyl conversion methods.

tag: sample group


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2L - cell 17


title: HaCaT cells, COL23A1 OE, 0hpi

value: Uninfected


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2L - cell 9

value: pluripotent stem cell


title: SKO_mESC_10k_S2_20k_K36me2_rep2

value: mESC

value: H3K36me2 (active motif, 61019)


title: pUC19_DNA_5ng_Zymo-Gold_CBS-seq.biol_rep2

description: Library name: Sample 107


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2L - cell 8


title: pUC19_DNA_5ng_Zymo-Gold_CBS-seq.biol_rep1

description: Library name: Sample 106


title: HaCaT cells, control, 2hpi

value: WT


title: HaCaT cells, control, 6hpi


title: pUC19_DNA_5ng_UMBS-seq.biol_rep3

description: Library name: Sample 105


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2L - cell 7


title: XistPA_XEN_K36me3_rep2

source_name: XEN

value: XEN

value: Xist-PA

value: Xist depletion


title: HaCaT cells, control, 0hpi


title: XistPA_XEN_K36me3_rep1

value: H3K36me3 (active motif, 61902)


title: pUC19_DNA_5ng_UMBS-seq.biol_rep1

description: Library name: Sample 103


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2L - cell 6


title: pUC19_DNA_5ng_UMBS-seq.biol_rep2

description: Library name: Sample 104


title: XistPA_XEN_K36me2_rep2


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2L - cell 5


title: E15.5 Six2creWt1 paired kidneys_biol rep 2

city: Dallas

first: Keri

last: Drake

state: Texas

address: 5323 Harry Hines Boulevard

department: Pediatric Nephrology

institute: UTSW

description:
Library name: Sample 2
10x Genomics

data_processing:
The demultiplexing, barcode processing, gene counting, and aggregation were made using Cell Ranger software (Version 5.0.1).
Assembly: GRCm39
Supplementary files format and content: tab-separated values files and matrix files

molecule: nuclear RNA

source_name: embryonic kidney

extract_protocol:
Nuclei were isolated as previously reported from paired kidneys with Nuclei EZ Lysis buffer supplemented with protease inhibitor and RNase inhibitor. Samples were homogenized using a Dounce homogenizer in 2ml of ice-cold Nuclei EZ Lysis buffer first with a loose pestle, then passed through a 200 µm strainer into 50 ml conical tube and followed by homogenization with a tight pestle which was then filtered through a 40-µm cell strainer and incubated on ice for 5 minutes. The suspension was centrifuged at 500 g x for 5 min at 4 ºC with the pellet resuspended and washed with 4 ml of the buffer and incubated on ice for 5 min. After another centrifugation, the pellet was resuspended with Nuclei Suspension Buffer (1x PBS, 0.07% BSA, 0.1% RNase inhibitor) and filtered through a 5-µm cell strainer into a conical tube. The nuclei were counted with a disposable hemacytometer and diluted to a concentration of 700-1200 cells per µL.
Library was performed according to the manufacturer’s instructions (single cell 3’ GEX kit).

value: embryonic kidney


title: E15.5 Six2creWt1 paired kidneys_biol rep 3

description:
Library name: Sample 3
10x Genomics


title: XistPA_XEN_K36me2_rep1


title: pUC19_DNA_5ng_NEB_EM-seq.biol_rep3

description: Library name: Sample 102

data_processing:
Raw paired-end bisulfite sequencing reads of three methyl conversion methods (UMBS-seq, EM-seq, and CBS-seq) were first trimmed using Trim Galore (v 0.6.10), which removes Illumina adapter sequences and low-quality bases (Phred score <20).
The trimmed reads were then aligned to a bisulfite-converted reference genome using bismark (v0.24.0) with the Bowtie2 aligner. Prior to alignment, the reference genome (e.g., pUC19 DNA, lambda DNA and human genome) was prepared using bismark_genome_preparation, which generates bisulfite-specific indices.
Mapping was performed in paired-end mode with default parameters, and alignment outputs were stored in BAM format for downstream processing. Following alignment, PCR duplicates were removed using deduplicate_bismark in paired-end mode to minimize amplification bias.
To eliminate unconverted clusters in the EM-seq data, reads with more than 5 unconverted C sites or reads with more than one-third of the total C sites being unconverted were also discarded.
Methylation levels were extracted from the deduplicated BAM files using bismark_methylation_extractor with the --cytosine_report, --CX, and --bedGraph options enabled. This step generated methylation calls for cytosines in CpG, CHG, and CHH contexts, as well as genome-wide coverage files and per-base resolution methylation reports. The methylation extraction was performed using a buffer size of 10 G to ensure efficient processing of large files. All downstream data analysis, visualization, and quality control were conducted using custom Python and R scripts.
Assembly: hg19, lambda DNA, and pUC19 genome
Supplementary files format and content: txt, convertion ratios of each cytosine.
Supplementary files format and content: txt, C-to-U conversion report.
Library strategy: EM-seq


title: E15.5 Six2creWt1 paired kidneys_biol rep 1

description:
Library name: Sample 1
10x Genomics


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2L - cell 4


title: HA-FKBP-NIPBL NPCs, DMSO, input for RAD21 ChIP rep2

city: San Francisco

first: Elphege

middle: P

last: Nora

state: CA

address: 555 Mission Bay Blvd S

department: CVRI

institute: UCSF

description: Library name: RSC131

data_processing:
Fastq files were aligned to a catenated mm10 and hg38 reference genome using Bowtie2. Reads with a mapq score ≥ 30 were retained and duplicates were removed, using samtools. ChIP bigwigs were generated with the bamCoverage function from deepTools, with scaling factors calculated using the formula (human reads in input) / (mouse reads in input) / (human reads in ChIP) x 15000000. The multiplier of 15000000 was chosen arbitrarily to set the final scaling factors close to 1. Input bigwigs were normalized using RPKM.
To create bigwig files with multiple replicates combined, we took equal numbers of reads from each replicate (samtools view with subsample option), combined them, and created a bigwig normalized by RPKM.
To create lists of ChIP-seq peaks found in multiple replicates, we first used macs2 version 2.2.9.1 to call peaks on each replicate individually. For NIPBL and MAU2 peaks, we used the HA ChIP in untagged cells as the control. For CTCF and H3K27ac peaks, we used the input samples as the control. We used bedtools multiinter to identify the regions that were called as peaks in the majority of replicates. To define the peak widths, we used macs2 again to call peaks using all of the replicates together. We selected the peaks from this list that overlap with the regions called in the majority of replicates (using bedtools intersect -u). Finally, we removed peaks in ENCODE blacklisted regions using bedtools intersect -v.
Assembly: mm10
Supplementary files format and content: bigwig tracks

growth_protocol: mESCs were cultured in 2iSL medium [DMEM + GlutaMAX + sodium pyruvate (ThermoFisher 10569044) supplemented with 15% fetal bovine serum (Gibco SKU A5256701), 550 µM 2-mercaptoethanol (ThermoFisher 21985-023), 1X nonessential amino acids (ThermoFisher 11140-050), 10^4 U of Leukemia Inhibitory Factor (Millipore ESG1107), 1 µM PD0325901 (Apex Bio/Fischer A3013-25), and 3 µM CHIR99021 (Apex Bio/Fischer A3011-100)]. Cells were maintained at a density of 0.2-1.5 x 10^5 cells/cm2 by passaging using TrypLE (ThermoFisher 12605010) every 24-48 hours on 0.1% gelatin-coated dishes (Sigma-Aldrich G1890-100G in 1XPBS) at 37°C and 5% CO2. The medium was changed daily when cells were not passaged. Cells were checked for mycoplasma infection every 6 months and tested negative. To establish neural progenitors (NPCs), 0.2 million FKBP-NIPBL (EA18.1) ESCs were seeded in a T25 gelatinized flask in 2iSL medium. The following day, cells were rinsed twice in 1X PBS and switched to N2B27 medium [50% DMEM/F12 medium (Gibco 31330-038), 50% Neurobasal medium (Gibco 21103-049), 1X GlutaMAX (Gibco 35050061), 0.5X B27 (Gibco 17504-044), 0.5X N2 (Millipore SCM012), and 0.1 mM 2-mercaptoethanol]. After 7 days with daily media changes, cells were detached using TrypLE and seeded on nongelatinized bacterial dishes for suspension culture at 3 million cells per 75 cm2 and cultured in N2B27 containing 10 ng/mL EGF and FGF (Peprotech 315-09 and 100-18B). After 3 days, floating aggregates were seeded on gelatinized dishes. After 2-4 days, poorly attached aggregates were dislodged and discarded, and remaining adherent NPC cells were dissociated using Accutase (Innovative Cell Technologies AT104), passaged twice on gelatinized dishes in N2B27 + EGF/FGF and cryopreserved in 10% DMSO in N2B27 + EGF/FGF. Cells were thawed and cultured on gelatinized dishes in N2B27 + EGF/FGF and passaged by incubating in Accutase for 2-3 minutes at room temperature (RT).

extract_protocol:
For all NIPBL and MAU2 ChIP experiments, cells were double crosslinked in DSG followed by formaldehyde. First, cells were dissociated using TrypLE (ESCs) or Accutase (NPCs) and resuspended in culture medium, and 15 million cells were pelleted at 100g for 5 minutes at RT. Supernatant was discarded and cell pellets were washed once in PBS. Cells were resuspended in 10 mL PBS, and DSG (dissolved in DMSO) was added to a final concentration of 2 mM. Cells were fixed at room temperature for 45 minutes with rotation. Cells were then pelleted at 200g for 5 minutes and washed three times with PBS (each time pelleting at 200g for 5 minutes). Cells were then resuspended in 5 mL of 10% FBS prepared in PBS. To this, 5 mL of freshly prepared 2% formaldehyde solution was added to reach a final formaldehyde concentration of 1%. 2% formaldehyde was diluted from 16% methanol-free formaldehyde in 1X PBS with 10% FBS. Resuspended cells were fixed for 10 minutes at RT with rotation. To quench, 0.525 mL of 2.5 M glycine solution in PBS was added (final concentration 0.125 M glycine), and cells were incubated for 5 minutes at RT followed by 15 minutes on ice. Cells were pelleted by centrifuging at 200g for 5 minutes at 4° C. Cell pellets were resuspended in 1 mL of ice-cold 0.125M glycine in PBS, transferred to 1.5 ml tubes, and centrifuged at 300g for 5 minutes at 4° C. Supernatant was discarded and pellets were snap frozen on dry ice and stored at -70°C. For CTCF and RAD21 ChIP experiments, cells were dissociated, pelleted, and fixed in 1% formaldehyde for 10 minutes with the subsequent quenching and washes as above. Fixed cells were thawed on ice, resuspended in 1 mL of ice-cold lysis buffer [10 mM Tris HCl pH 7.5, 10 mM NaCl, 0.2% NP-40 (IGEPAL), 0.2% TritonX-100, 1 mM EDTA, 0.5 mM EGTA, supplemented with fresh protease inhibitor] and incubated on ice for 10 minutes. ~9.75 x 106 mouse nuclei were combined with ~0.25 x 106 double crosslinked HEK nuclei as spike-in. Nuclei were pelleted at 400g for 5 minutes at 4°C, supernatant discarded and nuclear pellets resuspended in 1 mL of shearing buffer (0.5% SDS, 10 mM Tris HCl pH 7.5, supplemented with fresh 1x protease inhibitor). Chromatin was sheared using a Covaris with settings PIP 105, Duty factor 5, Cycles per burst 200, total time 23 minutes for double-crosslinked cells or 15 minutes for formaldehyde-crosslinked cells. After shearing, samples were spun at 13,000 rpm for 5 minutes at 4° C. 2.5% of the sample was removed to use as input, and the remainder of the supernatant was used for ChIP. The ChIP reaction was assembled as follows: 900 ul chromatin, 442 μL 5X ChIP incubation buffer (5% TritonX-100, 0.75 M NaCl, 5 mM EDTA, 2.5 mM EGTA, 50 mM Tris-Cl pH7.5), 40 uL Dynabeads (pre-washed in ChIP incubation buffer), 10 ug HA antibody, 22.5 uL protease inhibitor, and 835.5 uL water. Tubes were incubated overnight at 4°C on a rocker. Following overnight incubation, beads were collected using a magnetic rack and washed sequentially with different wash buffers for 5 minutes each on a rocker at 4°C. Beads were washed twice with 500 μL of cold wash buffer 1 (0.1% SDS, 0.1% Sodium deoxycholate, 1% TritonX-100, 0.15 M NaCl, 1 mM EDTA, 0.5 mM EGTA, 10 mM Tris pH 8), once with 500 μL of cold wash buffer 2 (0.1% SDS, 0.1% Sodium deoxycholate, 1% TritonX-100, 0.5 M NaCl, 1 mM EDTA, 10 mM Tris pH 8), once with 500ul of cold wash buffer 3 [0.25 M LiCl, 0.5% Sodium deoxycholate, 0.5% NP-40 (IGEPAL), 1 mM EDTA, 0.5 mM EGTA, 10 mM Tris pH 8], and twice with 500 μL of cold wash buffer 4 (1 mM EDTA, 0.5 mM EGTA, 10 mM Tris pH 8). For elution, beads were resuspended in 200 μL of elution buffer (1% SDS, 0.1M NaHCO3) and incubated on a rocker for 20 minutes at RT. Beads were then separated using a magnetic rack and the eluate (supernatant) was transferred to a fresh tube. Input samples were thawed on ice and elution buffer was added to bring the volume to 200 μL. To each sample, 2 μL of 1 mg/ml RNaseA was added and incubated at 37°C for 30 minutes. To reverse crosslinks, 8 μL of 5 M NaCL and 5 μL of 10 mg/ml Proteinase K was added and samples were incubated overnight at 65°C. DNA was eluted using MinElute kit from Qiagen (28604).
Libraries were prepared using NEBNext Ultra II DNA library prep kit according to the manufacturer’s protocol (E7645S). The entire ChIP sample and 50 ng of the input samples were used for library prep. Libraries were amplified for 16 cycles, followed by 0.9X SPRI bead purification (Bulldog Bio CNGS005). The eluate was run on a 2% E-gel (Invitrogen G401002) and fragments between 200-600bp were excised and eluted using MinElute gel extraction kit (Qiagen 28604). Quality and quantity of libraries were assessed using Qubit and Bioanalyzer High Sensitivity DNA kit. Libraries were sequenced on NextSeq 2000 using 65 bp single-end reads. Some libraries were sequenced in a second lane for additional reads.

treatment_protocol: FKBP12F36V depletion was triggered using 500 nM of PROTAC dTAG-13 (dTAG) (Sigma-Aldrich SML2601) in the culture medium for 24 hours.

value: NPC

value: DMSO 24hr

value: input


title: XistPA_XEN_K27me3_rep2


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2L - cell 3


title: pUC19_DNA_5ng_NEB_EM-seq.biol_rep2

description: Library name: Sample 101


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2L - cell 2


title: pUC19_DNA_5ng_NEB_EM-seq.biol_rep1

description: Library name: Sample 100


title: SKO_mESC_10k_S2_20k_K36me2_rep1

value: SKO


title: pUC19_DNA_500pg_Zymo-Gold_CBS-seq.biol_rep3

description: Library name: Sample 99


title: XistPA_XEN_K27me3_rep1


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2H - cell 96


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2L - cell 1


title: HA-FKBP-NIPBL NPCs, DMSO, input for RAD21 ChIP rep1

description: Library name: RSC130


title: pUC19_DNA_500pg_Zymo-Gold_CBS-seq.biol_rep1

description: Library name: Sample 97


title: pUC19_DNA_500pg_Zymo-Gold_CBS-seq.biol_rep2

description: Library name: Sample 98


title: HA-FKBP-NIPBL NPCs, DMSO, RAD21 ChIP rep2

description: Library name: RSC129


title: XistPA_XEN_H2AK119ub1_rep1


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2H - cell 95


title: pUC19_DNA_500pg_UMBS-seq.biol_rep3

description: Library name: Sample 96


title: WT_XEN_K36me3_rep2


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2H - cell 94


title: HA-FKBP-NIPBL NPCs, DMSO, RAD21 ChIP rep1

description: Library name: RSC128


title: WT_XEN_K36me3_rep1


title: XistPA_XEN_H2AK119ub1_rep2


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2H - cell 93


title: pUC19_DNA_500pg_UMBS-seq.biol_rep1

description: Library name: Sample 94


title: WT_XEN_H3K36me2_rep2


title: HA-FKBP-NIPBL NPCs, DMSO, input for CTCF ChIP rep1

description: Library name: RSC120


title: pUC19_DNA_500pg_UMBS-seq.biol_rep2

description: Library name: Sample 95


title: HA-FKBP-NIPBL NPCs, DMSO, CTCF ChIP rep2

description: Library name: RSC117

value: CTCF_Active Motif_61311


title: WT_XEN_H3K36me2_rep1


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2H - cell 92


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2H - cell 91


title: Nsd1_KO_mESC_OENsd1_LTR_K36me2_rep2

value: Nsd1 KO

value: Nsd1_LTR OE


title: ActA_Dorsomorphin_IP_H3K9ac_exp1

city: Athens

first: Dimitris

last: Valakos

address: Soranou Ephessiou 4

department: Center of Basic Research

country: Greece

institute: Biomedical Reasearch Foundation Academy of Athens

description: Library name: ActA and Dorsomorphin, IP, H3K9ac, exp1

data_processing:
The quality of the generated fastq files was examined with the FASTQC software. Fastq files were aligned against mm10 mouse genome with Bowtie2 aligner. The output files were filtered for low quality reads, duplicates, blacklist regions and mitochondrial genome entries with custom made pipeline from Bedtools and Samtools. Peak calling was performed with MACS2 callpeak command with default parameters. For H3K9ac only, we defined the broadpeaks. Bedgraph files were generated with MACS2 bdgcomp using the subtract option to remove the respective Input signal from the IP signal, and then converted to bigwig format. Input file for experiment 1 is common for both H3K9ac and PCAF IP files for every condition.
Assembly: mm10
Supplementary files format and content: Bed files with peaks.
Supplementary files format and content: Bigwig files for every sample depicting IP signal after subtraction of Input signal.

source_name: Spleen

growth_protocol: anti-CD3 (1 ug/ml), anti-CD28 (1 ug/ml), IL-6 (20 ug/ml), IL-1b (20 ug/ml), IL-23 (20 ug/ml) in in RPMI 1640 Medium, GlutaMAX™ supplemented with 10% FBS, 100 U/ml penicillin/streptomycin and 50 uM β-Mercaptoethanol

extract_protocol:
On day 4, 4x10^6 cells from each cell culture were collected, washed and fixed for 10 min in FBS-free RPMI containing 1% formaldehyde at RT and quenched with 0.125M glycine. Fixed cells were washed with ice-cold PBS, nuclei were prepared by cell lysis and chromatin shearing was performed by Covaris sonication. After sonication, an aliquot of sheared chromatin was kept as input. The rest of the sheared chromatin samples were proceeded to immunoprecipitation using antibodies specific for H3K9ac and PCAF. The immunocomplexes were isolated using magnetic beads and washed 6 times with RIPA buffer. DNA was isolated from immunoprecipitated complexes through proteinase K treatment, followed by reverse crosslinking at 65°C. DNA fragments were purified using NGS magnetic beads.
ChIP-seq library construction and sequencing were carried out at the Greek Genome Center (GGC) of BRFAA. Libraries for H3K9ac and PCAF ChIPseq were generated with NEBNext Ultra II DNA Library Prep Kit for Illumina, as indicated by the manufacturer’s guidelines (NEB, E7645L) using 10ng of DNA (chromatin that was not incubated with the antibody was used as input DNA). The quality of the generated libraries was validated with the Agilent bioanalyzer DNA1000 chip. Subsequently, the libraries were quantitated with the qubit HS spectrophotometric method and pooled in equimolar amounts for Sequencing.

treatment_protocol: +/- Activin-A, +/- Dorsomorphin

value: Spleen

value: Wild type

value: Activin-A + Dorsomorphin


title: pUC19_DNA_500pg_NEB_EM-seq.biol_rep2

description: Library name: Sample 92


title: pUC19_DNA_500pg_NEB_EM-seq.biol_rep3

description: Library name: Sample 93


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2H - cell 90

value: pluripotent stem cell


title: HA-FKBP-NIPBL NPCs, DMSO, CTCF ChIP rep1

description: Library name: RSC115


title: Nsd1_KO_mESC_OENsd1_LTR_K36me2_rep1

value: mESC

value: H3K36me2 (active motif, 61019)


title: HA-FKBP-NIPBL NPCs, DMSO, input for CTCF ChIP rep2

description: Library name: RSC121


title: pUC19_DNA_500pg_NEB_EM-seq.biol_rep1

description: Library name: Sample 91


title: ActA_Dorsomorphin_Input_exp1

description: Library name: ActA and Dorsomorphin, Input, exp1


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2H - cell 89


title: Nsd1_KO_mESC_OENsd1_canonical_K36me2_rep2

value: Full-length Nsd1 OE


title: pUC19_DNA_50pg_Zymo-Gold_CBS-seq.biol_rep3

description: Library name: Sample 90


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2H - cell 88


title: Nsd1_KO_mESC_OENsd1_canonical_K36me2_rep1


title: pUC19_DNA_50pg_Zymo-Gold_CBS-seq.biol_rep2

description: Library name: Sample 89


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2H - cell 87


title: WT_mESC_mESC_10k_S2_20k_K36me3

value: H3K36me3 (active motif, 61021)

value: WT


title: PBS_IP_H3K9ac_exp1

description: Library name: PBS, IP, H3K9ac, exp1


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2H - cell 86


title: pUC19_DNA_50pg_Zymo-Gold_CBS-seq.biol_rep1

description: Library name: Sample 88


title: pUC19_DNA_50pg_UMBS-seq.biol_rep3

description: Library name: Sample 87


title: Nsd1KO_mESC_10k_S2_20k_K36me3


title: EA18.1_NPC_dTAG_input_rep2

data_processing:
Fastq files were aligned to a catenated mm10 and hg38 reference genome using Bowtie2. Reads with a mapq score ≥ 30 were retained and duplicates were removed, using samtools. ChIP bigwigs were generated with the bamCoverage function from deepTools, with scaling factors calculated using the formula (human reads in input) / (mouse reads in input) / (human reads in ChIP) x 15000000. The multiplier of 15000000 was chosen arbitrarily to set the final scaling factors close to 1. Input bigwigs were normalized using RPKM.
Assembly: mm10
Supplementary files format and content: bigwig tracks

extract_protocol:
Cells were double crosslinked in DSG followed by formaldehyde. First, cells were dissociated using TrypLE (ESCs) or Accutase (NPCs) and resuspended in culture medium, and 15 million cells were pelleted at 100g for 5 minutes at RT. Supernatant was discarded and cell pellets were washed once in PBS. Cells were resuspended in 10 mL PBS, and DSG (dissolved in DMSO) was added to a final concentration of 2 mM. Cells were fixed at room temperature for 45 minutes with rotation. Cells were then pelleted at 200g for 5 minutes and washed three times with PBS (each time pelleting at 200g for 5 minutes). Cells were then resuspended in 5 mL of 10% FBS prepared in PBS. To this, 5 mL of freshly prepared 2% formaldehyde solution was added to reach a final formaldehyde concentration of 1%. 2% formaldehyde was diluted from 16% methanol-free formaldehyde in 1X PBS with 10% FBS. Resuspended cells were fixed for 10 minutes at RT with rotation. To quench, 0.525 mL of 2.5 M glycine solution in PBS was added (final concentration 0.125 M glycine), and cells were incubated for 5 minutes at RT followed by 15 minutes on ice. Cells were pelleted by centrifuging at 200g for 5 minutes at 4° C. Cell pellets were resuspended in 1 mL of ice-cold 0.125M glycine in PBS, transferred to 1.5 ml tubes, and centrifuged at 300g for 5 minutes at 4° C. Supernatant was discarded and pellets were snap frozen on dry ice and stored at -70°C. Fixed cells were thawed on ice, resuspended in 1 mL of ice-cold lysis buffer [10 mM Tris HCl pH 7.5, 10 mM NaCl, 0.2% NP-40 (IGEPAL), 0.2% TritonX-100, 1 mM EDTA, 0.5 mM EGTA, supplemented with fresh protease inhibitor] and incubated on ice for 10 minutes. ~9.75 x 106 mouse nuclei were combined with ~0.25 x 106 double crosslinked HEK nuclei as spike-in. Nuclei were pelleted at 400g for 5 minutes at 4°C, supernatant discarded and nuclear pellets resuspended in 1 mL of shearing buffer (0.5% SDS, 10 mM Tris HCl pH 7.5, supplemented with fresh 1x protease inhibitor). Chromatin was sheared using a Covaris with settings PIP 105, Duty factor 5, Cycles per burst 200, total time 23 minutes. After shearing, samples were spun at 13,000 rpm for 5 minutes at 4° C. 2.5% of the sample was removed to use as input, and the remainder of the supernatant was used for ChIP. The ChIP reaction was assembled as follows: 900 ul chromatin, 442 μL 5X ChIP incubation buffer (5% TritonX-100, 0.75 M NaCl, 5 mM EDTA, 2.5 mM EGTA, 50 mM Tris-Cl pH7.5), 40 uL Dynabeads (pre-washed in ChIP incubation buffer), 10 ug HA antibody, 22.5 uL protease inhibitor, and 835.5 uL water. Tubes were incubated overnight at 4°C on a rocker. Following overnight incubation, beads were collected using a magnetic rack and washed sequentially with different wash buffers for 5 minutes each on a rocker at 4°C. Beads were washed twice with 500 μL of cold wash buffer 1 (0.1% SDS, 0.1% Sodium deoxycholate, 1% TritonX-100, 0.15 M NaCl, 1 mM EDTA, 0.5 mM EGTA, 10 mM Tris pH 8), once with 500 μL of cold wash buffer 2 (0.1% SDS, 0.1% Sodium deoxycholate, 1% TritonX-100, 0.5 M NaCl, 1 mM EDTA, 10 mM Tris pH 8), once with 500ul of cold wash buffer 3 [0.25 M LiCl, 0.5% Sodium deoxycholate, 0.5% NP-40 (IGEPAL), 1 mM EDTA, 0.5 mM EGTA, 10 mM Tris pH 8], and twice with 500 μL of cold wash buffer 4 (1 mM EDTA, 0.5 mM EGTA, 10 mM Tris pH 8). For elution, beads were resuspended in 200 μL of elution buffer (1% SDS, 0.1M NaHCO3) and incubated on a rocker for 20 minutes at RT. Beads were then separated using a magnetic rack and the eluate (supernatant) was transferred to a fresh tube. Input samples were thawed on ice and elution buffer was added to bring the volume to 200 μL. To each sample, 2 μL of 1 mg/ml RNaseA was added and incubated at 37°C for 30 minutes. To reverse crosslinks, 8 μL of 5 M NaCL and 5 μL of 10 mg/ml Proteinase K was added and samples were incubated overnight at 65°C. DNA was eluted using MinElute kit from Qiagen (28604).
Libraries were prepared using NEBNext Ultra II DNA library prep kit according to the manufacturer’s protocol (E7645S). The entire ChIP sample and 50 ng of the input samples were used for library prep. Libraries were amplified for 16 cycles, followed by 0.9X SPRI bead purification (Bulldog Bio CNGS005). The eluate was run on a 2% E-gel (Invitrogen G401002) and fragments between 200-600bp were excised and eluted using MinElute gel extraction kit (Qiagen 28604). Quality and quantity of libraries were assessed using Qubit and Bioanalyzer High Sensitivity DNA kit. Libraries were sequenced on NextSeq 2000 using 65 bp single-end reads. Some libraries were sequenced in a second lane for additional reads.

value: dTAG13 24hr


title: pUC19_DNA_50pg_UMBS-seq.biol_rep2

description: Library name: Sample 86


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2H - cell 84


title: EA18.1_NPC_DMSO_input_rep2

value: NPC


title: pUC19_DNA_50pg_UMBS-seq.biol_rep1

description: Library name: Sample 85


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2H - cell 83


title: EA18.1_NPC_dTAG_HA_rep2


title: WT_Day3_EpiLC_K36me2_rep2

value: EpiLC

value: Day 3


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2H - cell 82


title: ActA_Input_exp1

description: Library name: ActA, Input, exp1

value: Activin-A


title: Nsd1KO_mESC_10k_S2_20k_K36me2


title: pUC19_DNA_50pg_NEB_EM-seq.biol_rep3

description: Library name: Sample 84


title: ActA_IP_H3K9ac_exp1

description: Library name: ActA, IP, H3K9ac, exp1


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2H - cell 81


title: WT_Day3_EpiLC_K36me2_rep1


title: WT_Day0_EpiLC_K36me2_rep2

value: 2i mESC

value: Day 0


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2H - cell 80


title: pUC19_DNA_50pg_NEB_EM-seq.biol_rep1

description: Library name: Sample 82


title: EA18.1_NPC_dTAG_input_rep1

value: input


title: EA18.1_NPC_DMSO_input_rep1

value: DMSO 24hr


title: PBS_Input_exp1

description: Library name: PBS, Input, exp1

value: Spleen

value: Wild type


title: WT_mESC_mESC_10k_S2_20k_K36me2


title: WT_Day0_EpiLC_K36me2_rep1


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2H - cell 79

value: pluripotent stem cell


title: pUC19_DNA_10pg_Zymo-Gold_CBS-seq.biol_rep3

description: Library name: Sample 81


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2H - cell 85


title: EA18.1_NPC_dTAG_HA_rep1


title: pUC19_DNA_10pg_Zymo-Gold_CBS-seq.biol_rep2

description: Library name: Sample 80


title: NSd1_KO_Day3_EpiLC_K36me2_rep1

value: Nsd1 KO


title: pUC19_DNA_50pg_NEB_EM-seq.biol_rep2

description: Library name: Sample 83


title: pUC19_DNA_10pg_Zymo-Gold_CBS-seq.biol_rep1

description: Library name: Sample 79


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2H - cell 77


title: NSd1_KO_Day0_EpiLC_K36me2_rep2

value: H3K36me2 (active motif, 61019)


title: pUC19_DNA_10pg_UMBS-seq.biol_rep3

description: Library name: Sample 78


title: EA19.1_ESC_dTAG_input_rep3

value: ESC


title: pUC19_DNA_10pg_UMBS-seq.biol_rep2

description: Library name: Sample 77


title: EA18.1_NPC_DMSO_HA_rep2


title: EA19.1_ESC_DMSO_input_rep3


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2H - cell 75


title: Nsd1_E65ExE_KO_H3K36me2_rep2

source_name: extra-embryonic ectoderm

value: extra-embryonic ectoderm


title: EA18.1_ESC_dTAG_input_rep3


title: pUC19_DNA_10pg_UMBS-seq.biol_rep1

description: Library name: Sample 76


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2H - cell 74


title: Nsd1_E65ExE_KO_H3K36me2_rep1


title: EA18.1_ESC_DMSO_input_rep3


title: NSd1_KO_Day0_EpiLC_K36me2_rep1


title: pUC19_DNA_10pg_NEB_EM-seq.biol_rep3

description: Library name: Sample 75


title: NSd1_KO_Day3_EpiLC_K36me2_rep2


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2H - cell 76


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2H - cell 73


title: Nsd1_E65ExE_Ctrl_H3K36me2_rep2

value: Control


title: E14_ESC_input_rep3

value: wild type


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2H - cell 72


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2H - cell 78


title: pUC19_DNA_10pg_NEB_EM-seq.biol_rep2

description: Library name: Sample 74


title: Nsd1_E65ExE_Ctrl_H3K36me2_rep1


title: EA18.1_NPC_DMSO_HA_rep1

value: NPC


title: pUC19_DNA_10pg_NEB_EM-seq.biol_rep1

description: Library name: Sample 73


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2H - cell 71


title: EA19.1_ESC_DMSO_HA_rep3


title: Nsd1_E65Epi_KO_H3K36me2_rep2

source_name: epiblast

value: epiblast


title: Nsd1_E65Epi_KO_H3K36me2_rep1


title: EA18.1_ESC_dTAG_HA_rep3

value: dTAG13 24hr


title: Lambda_DNA_5ng_Zymo-Gold_CBS-seq.biol_rep2

description: Library name: Sample 71

source_name: Lambda DNA

value: Lambda DNA


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2H - cell 70


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2H - cell 69


title: EA18.1_ESC_DMSO_HA_rep3


title: Lambda_DNA_5ng_Zymo-Gold_CBS-seq.biol_rep1

description: Library name: Sample 70


title: Nsd1_E65Epi_Ctrl_H3K36me2_rep1


title: E14_ESC_HA_rep3


title: Lambda_DNA_5ng_UMBS-seq.biol_rep3

description: Library name: Sample 69


title: ctrl_8C_H3K36me2_rep2

value: WT

value: DMSO


title: EA19.1_ESC_input_rep2

value: input


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2H - cell 67


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2H - cell 66


title: Lambda_DNA_5ng_UMBS-seq.biol_rep2

description: Library name: Sample 68


title: EA18.1_ESC_input_rep2


title: Lambda_DNA_5ng_UMBS-seq.biol_rep1

description: Library name: Sample 67


title: ctrl_8C_H3K36me2_rep1


title: EA19.1_ESC_dTAG_HA_rep3


title: E14_ESC_input_rep2


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2H - cell 65


title: A485_8C_H3K36me2_rep2


title: Lambda_DNA_5ng_NEB_EM-seq.biol_rep3

description: Library name: Sample 66


title: A485_8C_H3K36me2_rep1


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2H - cell 64


title: Lambda_DNA_5ng_Zymo-Gold_CBS-seq.biol_rep3

description: Library name: Sample 72


title: Lambda_DNA_5ng_NEB_EM-seq.biol_rep2

description: Library name: Sample 65


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2H - cell 63


title: FGO_MD_24h_K36me3_rep1

source_name: FGO

value: FGO

value: H3K36me3 (active motif, 61021)

value: milrinone and Drb


title: Nsd1_E65Epi_Ctrl_H3K36me2_rep2


title: EA18.1_ESC_HA_rep2


title: Lambda_DNA_5ng_NEB_EM-seq.biol_rep1

description: Library name: Sample 64


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2H - cell 62

value: pluripotent stem cell


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2H - cell 68


title: FGO_MD_24h_K36me2_rep1


title: E14_ESC_HA_rep2


title: Lambda_DNA_500pg_Zymo-Gold_CBS-seq.biol_rep3

description: Library name: Sample 63


title: EA19.1_ESC_input_rep1


title: FGO_M_24h_K36me2_rep1

value: milrinone


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2H - cell 60


title: Lambda_DNA_500pg_Zymo-Gold_CBS-seq.biol_rep2

description: Library name: Sample 62


title: EA18.1_ESC_input_rep1


title: DMSO_8C_K36me3_rep2


title: E14_ESC_input_rep1


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2H - cell 59


title: EA19.1_ESC_HA_rep2


title: DMSO_8C_K36me3_rep1


title: Lambda_DNA_500pg_UMBS-seq.biol_rep3

description: Library name: Sample 60


title: EA19.1_ESC_HA_rep1


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2H - cell 57


title: DMSO_8C_K36me2_rep2

value: H3K36me2 (active motif, 61019)


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2H - cell 58


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2H - cell 56


title: Lambda_DNA_500pg_UMBS-seq.biol_rep2

description: Library name: Sample 59


title: DMSO_8C_K36me2_rep1


title: Lambda_DNA_500pg_UMBS-seq.biol_rep1

description: Library name: Sample 58


title: EA18.1_ESC_HA_rep1

value: ESC


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2H - cell 55


title: E14_ESC_HA_rep1


title: Lambda_DNA_500pg_NEB_EM-seq.biol_rep3

description: Library name: Sample 57


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2H - cell 61


title: Lambda_DNA_500pg_NEB_EM-seq.biol_rep2

description: Library name: Sample 56


title: FGO_M_24h_K36me3_rep1


title: APH_2C_K36me3_rep2

value: aphidicolin


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2H - cell 54


title: NSD1 frameshift mutation, rep3

city: Irvine

first: Minji

last: Byun

address: 829 Health Science Rd, 311

department: Microbiology and Molecular Genetics

institute: University of California Irvine

description: Library name: NSD1_4_CP3-G8

data_processing:
RNA-seq data were analyzed using Bioconductor packages Salmon, tximeta, and DESeq2.
Assembly: GRCh38
Supplementary files format and content: tab-delimitied text files includes normalized counts for each sample

growth_protocol: Human embryonic stem cells were maintained under feeder-free condition in StemFlex media (Thermo Fisher Scientific) on Cultrex (R&D Systems)-coated plates.

extract_protocol:
Total RNA was extracted using Quick-RNA prep kit (Zymo research).
RNA-seq libraries were prepared using Truseq Stranded Total RNA Gold kit (Illumina)  following manufacturer's protocols.

value: human embryonic stem cell

tag: mutation (cdna)

tag: mutation (protein)


title: Lambda_DNA_500pg_Zymo-Gold_CBS-seq.biol_rep1

description: Library name: Sample 61


title: APH_2C_K36me3_rep1

extract_protocol:
Embryos or cells were lysed in lysis buffer and subject to Mnase digestion, antibody immunoprecipitation, and subsequent library preparation.
STAR ChIP-seq was performed as previously described (Zhang et al., 2016) with modifications. Briefly, samples were suspended and lysed followed by chromatin fragmentation by micrococcal nuclease (MNase, Sigma-Aldrich, N3755-200UN) at 37°C for 5 min. After being terminated, the supernatant containing chromatin was incubated with 1 μg of primary antibody (H3K36me2, Active motif, 61019; H3K36me3, Active motif, 61021 or 61902) at 4°C overnight with rotation. The next day, 100 μg of Protein A/G dynabeads (mixed at 1:1, Thermo Fisher Scientific, 10001D for Protein A and 10004D for Protein G) was added to each sample and incubated at 4°C for 3 hours with rotation. The beads were next washed five times with 150 μl of RIPA buffer and once with 150 μl of LiCl buffer. For each sample, beads were resuspended with 28 μl of H2O, 1 μl of 10× Ex Taq buffer (Takara, RR006B), and 1 μl of proteinase K (NEB, P8107S) and incubated at 55°C for 90 min, followed by incubation at 72°C for 40 min to inactivate the proteinase K. Samples were then subjected to TruSeq library preparation using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645S). Libraries were sequenced using the Illumina Hiseq X Ten or Novaseq 6000 system according to the manufacturer’s protocol.


title: Lambda_DNA_500pg_NEB_EM-seq.biol_rep1

description: Library name: Sample 55


title: APH_2C_K36me2_rep2


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2H - cell 53


title: NSD1 frameshift mutation, rep1

description: Library name: NSD1_3_CP1-B8


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2H - cell 52


title: NSD1 frameshift mutation, rep2

description: Library name: NSD1_1_CP3-B7


title: Lambda_DNA_50pg_Zymo-Gold_CBS-seq.biol_rep3

description: Library name: Sample 54


title: APH_2C_K36me2_rep1


title: H2O_8C_H3K36me3_rep2


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2H - cell 51


title: DNMT3A gain of function mutation, rep4

description: Library name: GOF_3_1-61-2


title: DNMT3A gain of function mutation, rep2

description: Library name: GOF_2_R1-66-9


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2H - cell 50


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2H - cell 49


title: Lambda_DNA_50pg_Zymo-Gold_CBS-seq.biol_rep1

description: Library name: Sample 52


title: Lambda_DNA_50pg_UMBS-seq.biol_rep3

description: Library name: Sample 51


title: H2O_8C_H3K36me2_rep2


title: H2O_8C_H3K36me3_rep1


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2H - cell 48


title: Lambda_DNA_50pg_UMBS-seq.biol_rep2

description: Library name: Sample 50


title: H2O_8C_H3K36me2_rep1


title: DNMT3A R882H mutation, rep2

description: Library name: R882H_3_C28.4.1


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2H - cell 47


title: amanitin_2C_H3K36me3_rep2

value: α-amanitin


title: DNMT3A gain of function mutation, rep1

description: Library name: GOF_1_R1-81-9


title: DNMT3A R882H mutation, rep3

description: Library name: R882H_2_C24.7.2


title: NSD1 frameshift mutation, rep4

description: Library name: NSD1_2_SL1-G5


title: Lambda_DNA_50pg_UMBS-seq.biol_rep1

description: Library name: Sample 49


title: Lambda_DNA_50pg_NEB_EM-seq.biol_rep3

description: Library name: Sample 48


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2H - cell 46


title: DNMT3A R882H mutation, rep1

description: Library name: R882H_1_A50.1


title: amanitin_2C_H3K36me3_rep1


title: Lambda_DNA_50pg_NEB_EM-seq.biol_rep2

description: Library name: Sample 47


title: Lambda_DNA_50pg_Zymo-Gold_CBS-seq.biol_rep2

description: Library name: Sample 53


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2H - cell 45


title: wild type hESC, rep4

description: Library name: WT_3_CP3.B6.6


title: amanitin_2C_H3K36me2_rep2


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2H - cell 44


title: amanitin_2C_H3K36me2_rep1


title: Lambda_DNA_50pg_NEB_EM-seq.biol_rep1

description: Library name: Sample 46


title: wild type hESC, rep2

description: Library name: WT_2_g3-2


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2H - cell 43


title: Lambda_DNA_10pg_Zymo-Gold_CBS-seq.biol_rep3

description: Library name: Sample 45


title: E65VE_H3K36me2_rep2

source_name: viceral endoderm

value: viceral endoderm


title: wild type hESC, rep1

description: Library name: WT_1_H1


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2H - cell 42


title: E65VE_H3K36me2_rep1


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2H - cell 41


title: CCDC134, IP, rep2

first: Zhe

last: Ji

state: ILLINOIS

address: 303 E Superior St, Lurie 6-107

institute: Northwestern University

description: Library name: Sample 8

data_processing:
The sequencing reads were trimmed to remove the first 7 nucleotides (NNNNGGG) and A-tail adaptor sequence using Cutadapt v4.1. Trimmed reads were aligned to ribosomal RNA sequences (5S: NR_023363.1; 5.8S: NR_003285.3; 18S: NR_003286.4; 28S: NR_003287.4) using Bowtie v2.2.6 allowing up to 2 mismatches. The unmappable reads were then aligned to the human hg38 genome and RefSeq-defined transcriptome using TopHat v2.1.0. Uniquely mapped reads were used for downstream analyses.
RibORF was used to assess ribosome profiling data quality by examining the read distribution around start and stop codons, checking for 3-nt periodicity, and assigning reads to the ribosomal A-site. Two fragment size peaks (19 nt and 28 nt) were observed for all Rfoot-seq samples. Strong 3-nt periodicity was observed for reads with lengths between 18-20 and 26-29 nucleotides, and these reads were selected for further analysis. For each read, their genomic location was adjusted to the ribosomal A-site using the offset distance of 15 nt between the 5’-end of the fragment and the A-site.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Library strategy: Ribo-Seq

source_name: Embryonic kidney

growth_protocol: Flp-In T-REx 293 cells were maintained in DMEM supplemented with 10% FBS, 100 U/mL penicillin, and 0.1 mg/mL streptomycin mixture at 37 °C and 5% CO2.

extract_protocol:
All buffers were supplemented with 100 ng/mL cycloheximide. Microsomes were isolated from nine 15-cm dishes. After treatment with 10,000 U of micrococcal nuclease for 30 min at 37 °C, microsomes were pelleted and solubilized with digitonin. Ribosomal complexes in the soluble microsome fraction were isolated by ultracentrifugation through a sucrose cushion. The ribosomal pellet was resuspended and used as input. The elution following immunoprecipitation from M2 Flag resin was used as the IP fraction. To prepare RNase footprints, input and IP samples were digested with RNase 1 at 0.5 - 1 U/µL within a 90 µL reaction at room temperature for 1.5 h. RNase footprints were extracted by adding 400 µl of TRIzol, followed by 100 µl of chloroform. RNA in the aqueous layer was separated by centrifugation at 12000 g for 15 min at 4 ℃ and then precipitated overnight by adding 0.1 volume of 3 M sodium acetate, 10 mg of glycoblue, and 1.2 volumes of isopropanol.
Purified RNase footprints were used for library preparation. RNase footprints were resuspended in 5 µl PNK reaction mixture (1x PNK buffer, 10 U PNK (NEB), and 10 U SUPERase·In) and end-repaired at 37 ℃ for 1 h. The reaction was added with 5 µl of polyadenylation mix containing 10 U E. coli poly (A) polymerase (NEB), 2 µl of 5x first-strand buffer (250 mM Tris-HCl (pH 8.3), 375 mM KCl, 15 mM MgCl2), 0.25 mM ATP, and 10 U SUPERase·In and incubated at 37 ℃ for 2 h. The resulting polyadenylated RNA was then reverse transcribed by a SMART-RT reaction. The reaction mixture was first added with 2.5 µl of RT primer (10 µM, 5’-ACGTGTGCTCTTCCGATCTNNNNNNNNNNNNNNNTTTTTTTTTTTTTTTVN-3’, where “N” is any base and “V” is either “A”, “C” or “G”) and annealed by heating to 72 °C for 5 min and cooled on ice, and then supplemented with SMAT-RT mixture (2.5 µl dNTP (10 mM), 400 U Superscript II reverse transcriptase (Invitrogen), 10 U SUPERase·In, 4 µl Superscript II first-strand buffer (5x), 1.5 µl DTT (100 mM), 6 µl Betaine (5 mM), 0.12 µl MgCl2 (1 M), 0.5 µl template-switching oligos (100 µM 5’-CTCTTTCCCTACACGACGCTCTTCCGATCTNNNNrGrG+G-3’, where “N” is any base and “+G'' is a locked nucleic acid guanylate), and 0.5 µl nuclease-free water. Reverse transcription was carried out with incubation at 42 ℃ for 1 h, followed by 10 cycles of heating at 50 °C for 2 min and then incubating at 42 ℃ for 2 min. The reverse transcriptase was inactivated by heating at 70 ℃ for 10 min. RNA footprints hybridized to DNA were removed by incubating at 37 ℃ for 15 min with 5 U of RNase H. The resultant cDNA was amplified by a first round of PCR with 7 cycles, purified, and then amplified by a second round of PCR with 4 cycles. The DNA library was visualized and separated in a 4% agarose gel. DNA with a 15-35 bp insert was excised and recovered using a DNA gel recovery kit (Zymo). Equal amounts of barcoded libraries were pooled and sequenced with Illumina NovoSeq.

treatment_protocol: Cells were seeded in nine 15-cm dishes and harvested ~80% confluency with ice-cold PBS containing 100 ng/mL cycloheximide.

value: Embryonic kidney

value: Flp-In T-REx 293

value: CCDC134 knockout, doxycycline-inducible 3Flag-CCDC134 expressing

value: IP

value: replicate 2


title: E65EXE_H3K36me2_rep2

data_processing:
Paired-end reads were first processed by TrimGalore (v.0.6.4) with default parameters to remove adaptor sequences and reads of low quality. The filtered reads were then mapped to the mm9 genome using Bowtie2 (v2.2.5) (Langmead and Salzberg, 2012) with the default parameters. Duplicates were removed with MarkDuplicates.jar. The unique mapped reads were then used to calculate the RPKM (Reads per kilobase per million of sequenced reads), which was further Z-score normalized to minimize the batch and cell type variation. The Pearson correlation was calculated for each sample with two biological replicates (10-kb bin). Replicates with good reproducibility were pooled together for downstream analyses. The UCSC genome browser was used for visualization.
Assembly: mm9
Supplementary files format and content: bigWig

value: extra-embryonic ectoderm

value: WT


title: Lambda_DNA_10pg_Zymo-Gold_CBS-seq.biol_rep1

description: Library name: Sample 43

value: Lambda DNA


title: CCDC134, Input, rep2

description: Library name: Sample 7

value: Input


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2H - cell 40

value: pluripotent stem cell


title: Lambda_DNA_10pg_UMBS-seq.biol_rep3

description: Library name: Sample 42


title: Lambda_DNA_10pg_UMBS-seq.biol_rep2

description: Library name: Sample 41


title: E65EXE_H3K36me2_rep1


title: CCDC134, IP, rep1

description: Library name: Sample 6

value: replicate 1


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2H - cell 39


title: CCDC134, Input, rep1

description: Library name: Sample 5


title: E65Epi_H3K36me2_rep2

value: epiblast

value: H3K36me2 (active motif, 61019)


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2H - cell 38


title: Lambda_DNA_10pg_UMBS-seq.biol_rep1

description: Library name: Sample 40


title: E65Epi_H3K36me2_rep1


title: Lambda_DNA_10pg_NEB_EM-seq.biol_rep3

description: Library name: Sample 39


title: ICM_H3K36me2_rep2

source_name: ICM

value: ICM


title: Lambda_DNA_10pg_Zymo-Gold_CBS-seq.biol_rep2

description: Library name: Sample 44


title: FKBP11, Input, rep2

description: Library name: Sample 3

value: FKBP11 knockout, doxycycline-inducible 3Flag-FKBP11 expressing


title: FKBP11, IP, rep2

description: Library name: Sample 4


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2H - cell 36


title: ICM_H3K36me2_rep1


title: FKBP11, IP, rep1

description: Library name: Sample 2


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2H - cell 35


title: 8C_H3K36me2_rep2


title: FKBP11, Input, rep1

description: Library name: Sample 1


title: Lambda_DNA_10pg_NEB_EM-seq.biol_rep2

description: Library name: Sample 38


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2H - cell 34


title: 8C_H3K36me2_rep1


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2H - cell 33


title: ATAC-seq of hPSCs replicate 2

description: Library name: T2

data_processing:
ATAC-seq data were trimmed using Trim Galore with default parameters. Alignment, annotation, PCR duplicate removal and gene expression quantification were subsequently performed using the Bowtie2, Picard, SAMtools, and BEDTools.
Assembly: Ensembl GRCh38 release 104
Supplementary files format and content: BED files

extract_protocol:
Chromatin accessibility profiling was performed using the ATAC-seq protocol. Nuclei were isolated from cells and treated with Tn5 transposase to fragment open chromatin regions. The resulting DNA fragments were amplified with PCR to add sequencing adapters and generate the final library.
Library construction was performed according to the manufacter’s instructions.


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2H - cell 32


title: ATAC-seq of hPSCs replicate 1

description: Library name: T1


title: Human_5ng_cfDNA_Zymo-Gold_CBS-seq.biol_rep1

description: Library name: Sample 34

source_name: cell-free DNA (cfDNA)

value: cell-free DNA (cfDNA)


title: 4C_H3K36me2_rep1


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2H - cell 37


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2H - cell 31


title: Human_5ng_cfDNA_UMBS-seq.biol_rep3

description: Library name: Sample 33


title: 2C_H3K36me2_rep2


title: ATAC-seq of 120hr SACs replicate 3

description: Library name: SACD5_3


title: Human_5ng_cfDNA_UMBS-seq.biol_rep2

description: Library name: Sample 32


title: ATAC-seq of 120hr SACs replicate 2

description: Library name: SACD5_2


title: Lambda_DNA_10pg_NEB_EM-seq.biol_rep1

description: Library name: Sample 37


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2H - cell 29


title: Human_5ng_cfDNA_UMBS-seq.biol_rep1

description: Library name: Sample 31


title: 2C_H3K36me2_rep1


title: 1C_H3K36me2_rep2


title: ATAC-seq of 120hr SACs replicate 1

description: Library name: SACD5_1


title: Human_5ng_cfDNA_Zymo-Gold_CBS-seq.biol_rep3

description: Library name: Sample 36


title: Human_5ng_cfDNA_Zymo-Gold_CBS-seq.biol_rep2

description: Library name: Sample 35


title: 4C_H3K36me2_rep2


title: 1C_H3K36me2_rep1


title: WGBS of hPSCs

description: Library name: OG-BS

data_processing:
WGBS data were trimmed using Trim Galore with parameter “-j 4 --fastqc_args”. Alignment was performed using Bismark with parameter  “-N 1 –local” and duplication removal was performed using deduplicate_bismark with default parameters.
Assembly: hg19
Supplementary files format and content: WGBS: *.bw: bigwig

extract_protocol:
Whole-genome bisulfite sequencing was performed to profile DNA methylation. Genomic DNA was extracted, fragmented, and treated with bisulfite to convert unmethylated cytosines to uracil. The converted DNA was then amplified with PCR to add sequencing adapters and generate the final library.
Library construction was performed according to the manufacter’s instructions.


title: Human_5ng_cfDNA_NEB_EM-seq.biol_rep3

description: Library name: Sample 30


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2H - cell 28

data_processing:
For bulk RNA seq, we used Fastp (version 0.23.1) (Chen, S. , et al 2018) to perform basic statistics on the quality of the raw reads. The steps of data processing were as follows: (1) Discard a paired reads if either one read contains adapter contamination; (2) Discard a paired reads if more than 10% of bases are uncertain in either one read; (3) Discard a paired reads if the proportion of low quality (Phred quality <5) bases is over 50% in either one read.  Alignment, annotation, and gene expression quantification were performed with STAR software (v.2.7.9a). The second columns of the output ‘ReadsPerGene’ tables were aggregated into a gene count table. Single cell RNA-seq data were trimmed using Trim Galore coupled with FastQC (v.0.11.2) or fastp software with default parameters. Alignment, annotation, PCR duplicate removal and gene expression quantification were subsequently performed using the STARsolo pipeline.
Assembly: Ensembl GRCh38 release 104
Supplementary files format and content: Bulk RNAseq count table: gene by cell expression matrix generated with STAR; scRNAseq count tables: Filtered matrix of gene by cell expression, file with barcodes and file with expressed genes. Files are ready to be imported to Seurat package.

extract_protocol:
For scRNA-seq, 120h SACs were dissociated and sorted by flow cytometer for Smart-seq2 library construction. 60h SACs were collected after replating on gelatinized plate for 30min for feeder removal; day6 stEM and e-stEM were manually picked with a cut-tip, washed once with DPBS and then dissociated with TrypLE Express (Gibco) at 37 °C in 20%O2 and 5% CO2 incubator for 45-60 min.
Library construction was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics). For NovaSeq 6000 library construction, the process begins with RNA extraction and quality control, followed by mRNA enrichment using polyA selection or rRNA depletion. First and second strand cDNA synthesis is performed, then the cDNA is fragmented and end-repaired. Sequencing adapters are ligated to the cDNA fragments, which are then purified and size-selected. The library is amplified by PCR, assessed for quality, and loaded onto the NovaSeq 6000 for sequencing. For MGISEQ-2000, the protocol similarly starts with RNA extraction and quality control, mRNA enrichment or rRNA depletion, cDNA synthesis, fragmentation, and end-repair. Sequencing adapters are ligated, followed by purification, size selection, and PCR amplification. Unique to MGISEQ-2000 is a circularization step converting the linear library into a circular DNA molecule before loading and sequencing on the MGISEQ-2000 platform.


title: Human_5ng_cfDNA_NEB_EM-seq.biol_rep2

description: Library name: Sample 29


title: ATAC-seq of hPSCs replicate 3

description: Library name: T3


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2H - cell 27


title: MII_H3K36me2_rep2

source_name: MII

value: MII


title: WGBS of 120hr SACs

description: Library name: SACD5-BS


title: Human_5ng_cfDNA_NEB_EM-seq.biol_rep1

description: Library name: Sample 28


title: scRNA-seq (Smartseq2) of 120h SAC SUSD2H - cell 25