title: cWX2200_96H_Azure_10percent_Sau3AI_rep2

description: Library name: cWX2200_96H_Azure_10percent_Sau3AI_rep2

value: wild type


title: cWX2200_exp_Azure_10percent_Sau3AI_rep2

status: Public on Jan 06 2026

type: SRA

city: Bloomington

first: Xindan

last: Wang

state: IN

address: 1001 E 3rd St

department: Biology

country: USA

institute: Indiana University at Bloomington

description: Library name: cWX2200_exp_Azure_10percent_Sau3AI_rep2

library_source: genomic

data_processing:
Reads from each end of a DNA fragment were represented in each of the two FASTQ files generated by Illumina paired-end sequencing.
For Escherichia coli Hi-C, we mapped reads in each FASTQ file back to the genome of Escherichia coli W3110 (NCBI Reference Sequence: NC_007779.1) independently by Bowtie version 2.1.0 to preserve the order of reads. All the processing steps afterwards were performed using an in-house Perl scripts.  For ChIP-seq and WGS, we mapped reads in each FASTQ file back to the genome of Escherichia coli W3110 (NCBI Reference Sequence: NC_007779.1) using CLC genomics workbench 8.0, and exported .csv file.
For Hi-C, the two resulting SAM files were then merged together. Unaligned reads were discarded.
For Hi-C, the Escherichia coli W3110 genome was divided into Sau3AI restriction fragments. Each aligned read was sorted into its corresponding restriction fragment. We inferred that a DNA fragment resulted from non-ligation or self-ligation if reads from both ends were from the same restriction fragment; these reads were discarded. Only DNA fragments for which the reads came from different restriction fragments were retained and used for construction of a Hi-C contact map.
For Hi-C, the genome of Escherichia coli (W3110) was then divided into 10 kb bins and the remaining reads were allocated to their corresponding bin. We then counted the number of fragments having reads within different bins. A raw Hi-C contact map is the matrix of read counts in which each entry, mij, indicates the number of fragments with ends mapping to bins i and j. The raw Hi-C contact map/matrix is biased due to the uneven distribution of restriction enzyme sites and, to a lesser extent, differences in GC content and the mappability of individual reads. We normalized raw contact maps using an iterative normalization procedure (Imakaev et al., 2012 PMID: 22941365). Essentially, we converted the number of interactions, or read counts, into Hi-C scores by applying the following equation and iteratively repeating it for the resulting contact map after each cycle:  mij =mij * (total reads) / (total reads in bin i * total reads in bin j). The iterative procedure was repeated until the maximum relative error of the total number of Hi-C scores in a bin was less than 10-5. Resulting matrices were normalized so that Hi-C scores for each row and column sum to 1. Subsequent analysis and visualization was done using R scripts.
Assembly: Escherichia coli W3110 (NCBI Reference Sequence: NC_007779.1)
Supplementary files format and content: Files ending with .matrix.txt: tab-delimited text files of the iteratively-corrected Hi-C contact maps/matrices. Files ending with .csv files are comma-separated values files of ChIP-seq/WGS results.

molecule: genomic DNA

organism: Escherichia coli str. K-12 substr. W3110

source_name: bacterial culture

extract_protocol:
Wild type and mutant cells of Escherichia coli W3110 growing in Hi-Def Azure media suplemented with 0.2% glucose were crosslinked using either 10% formaldehyde for Hi-C or 3% formaldehyde for ChIP-seq and then lysed by treatment with 4 mg/ml lysozyme and 1% SDS as previouly described (Wang et al., 2022 PMID: 35101983). The solubilized chromatin was digested with Sau3AI for 2 hours at 37°C.
Standard library construction protocol was used for Illumina Nextseq500/Nextseq2000 sequencing platforms. Illumina Truseq indexes were used.

tag: cell type

value: bacterial culture

tag: genotype

tag: treatment

value: Cells grown in Hi-Def Azure medium supplemented with 0.2% glucose at 37°C


title: WGS_cWX2200_exp_rep2_ChIPinput

description: Library name: WGS_cWX2200_exp_rep2_ChIPinput


title: 13_Pol2-ChIP-seq_DLD-1_18hDox_GFP-BRD2_3hJQ1

city: Chicago

first: Ali

last: Shilatifard

state: IL

address: 320 E Superior St

department: Department of Biochemistry and Molecular Genetics

institute: Northwestern University Feinberg School of Medicine

description: Library name: S13

data_processing:
Basecalls were performed using bcl2fastq v2.19 for Illumina output.
ChIP-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChIP-seq reads were aligned to the hg38 and dm6 (spike-in) genomes using Bowtie2. Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments,  normalized using spike-in reads and reformatted in the bigWig file format. GFP ChIP was not spike-in normalized since different construct has different expression level except for JQ1 treatment. Spikein normalization was not used for some BRD2 and histone acetylation samples, as indicated in Methods.
Assembly: hg38, dm6 for spike-in reads
Supplementary files format and content: bigWig

organism: Homo sapiens

source_name: colon

growth_protocol: All cell lines were cultured in DMEM (Corning, #10013CV), supplemented with 10% FBS (Sigma-Aldrich, #F2442), 1% Glutmax (Gibco, #35050061), and 1% PS (Gibco, #15140122), in 37°C incubator with 5% CO2.

extract_protocol:
DNA was purified with either QIAquick PCR purification kit (Qiagen, #28106) or ChIP DNA Clean & Concentrator kit (Zymo Research, #D5205).
Libraries were prepared by using the KAPA HTP library preparation kit (Roche, #07961901001) and sequenced on the Illumina NovaSeq 6000 or NextSeq 2000.

treatment_protocol: Auxin (#ab146403) was purchased from abcam. Doxycycline (#72742) was obtained from Stem Cell Technologies. dEBT6 (#S8762) was purchased from Selleckchem. JQ1 (#4499) was purchased from Tocris.BET and mutant expression were achieved by adding 50nM Dox into the medium and incubating for 36 or 48h.

tag: tissue

value: colon

tag: cell line

value: epithelial

tag: antibody

value: RPB1 NTD

tag: construct

tag: treatment 1

tag: treatment 2


title: cWX2979_96H_Azure_10percent_Sau3AI_rep1

description: Library name: cWX2979_96H_Azure_10percent_Sau3AI_rep1

value: W3110 delta_dps FRT-KanR-FRT


title: WGS_cWX2200_96H_rep1_ChIPinput

description: Library name: WGS_cWX2200_96H_rep1_ChIPinput


title: ChIP_anti-Dps_cWX2200_exp_rep1

description: Library name: ChIP_anti-Dps_cWX2200_exp_rep1


title: 24_TBP-ChIP-seq_DLD-1_3hJQ1

description: Library name: S24

value: TBP


title: cWX2200_24H_Azure_10percent_Sau3AI_rep1

description: Library name: cWX2200_24H_Azure_10percent_Sau3AI_rep1


title: ChIP_anti-mCherry_cWX2200_96H_rep1

description: Library name: ChIP_anti-mCherry_cWX2200_96H_rep1


title: ChIP_anti-Dps_cWX2200_24H_rep1

description: Library name: ChIP_anti-Dps_cWX2200_24H_rep1


title: ChIP_anti-Dps_cWX2200_96H_rep1

description: Library name: ChIP_anti-Dps_cWX2200_96H_rep1


title: WGS_cWX2200_24H_rep1_ChIPinput

description: Library name: WGS_cWX2200_24H_rep1_ChIPinput


title: 95P_1455

city: Seattle

first: Shivani

last: Srivastava

state: WA

address: 1100 Fairview Ave N

institute: Fred Hutchinson Cancer Center

description:
Library name: lib101932
lib101932

library_source: transcriptomic

data_processing:
Transcripts were aligned using STAR with GRCm38 reference sequence
Count matrix was generated using summarizeOverlaps in R
Assembly: GRCm38
Supplementary files format and content: .RDS

molecule: polyA RNA

organism: Mus musculus

source_name: Lung

extract_protocol:
Cryopreserved lung tumor cell suspensions were thawed, washed with PBS, and stained with Live/Dead Fixable Aqua Dye (Invitrogen) and surface markers in FACS Buffer. One thousand live CD45PECy7-CD8+GFP+ CAR-T cells were sorted directly into reaction buffer from the SMART-Seq mRNA Kit (Takara), and reverse transcription was performed followed by PCR amplification to generate full-length amplified cDNA.
Sequencing libraries were constructed using the NexteraXT DNA sample preparation kit with unique dual indexes (Illumina) to generate Illumina-compatible barcoded libraries.  Libraries were pooled and quantified using a Qubit® Fluorometer (Life Technologies).  Sequencing of pooled libraries was carried out on a NextSeq 2000 sequencer using an XLEAP-SBS flowcell (Illumina) with paired-end 59-base reads (Illumina) with a target depth of 5 million reads per sample.

treatment_protocol: KP-ROR1 tumor-bearing mice were injected intraperitoneally with 150 mg/kg cyclophosphamide and 24 hrs later were infused with  ROR1 or cJun.ROR1 CAR-T cells (1:1 ratio of CD8:CD4 T cells). Vehicle (PBS) or anti-PD-L1 antibody were administered on days 1 and 4 following CAR-T infusion. Five days post-CAR-T infusion, mice were injected intravenously with 400 ng PECy7-conjugated anti-CD45 antibody (clone 30-F11, BioLegend)  5 min prior to euthanasia to distinguish vascular and non-vascular cells in the lung. Lungs were digested to single cell suspension and cryopreserved in complete RPMI supplemented with 10% FBS and 10% DMSO.

value: Lung

value: CD8+ CAR-T cell

value: cJun.ROR1 CAR-T + aPD-L1


title: 95P_1485

description:
Library name: lib101931
lib101931


title: 95_1419

description:
Library name: lib101927
lib101927

value: cJun.ROR1 CAR-T + vehicle (PBS)


title: 95P_1473

description:
Library name: lib101928
lib101928


title: 95_1499

description:
Library name: lib101926
lib101926


title: 95P_1474

description:
Library name: lib101930
lib101930


title: 78P_1496

description:
Library name: lib101922
lib101922

value: ROR1 CAR-T + aPD-L1


title: 95_1462

description:
Library name: lib101924
lib101924


title: 78P_1486

description:
Library name: lib101923
lib101923


title: 95_1392

description:
Library name: lib101925
lib101925


title: 78_1490

description:
Library name: lib101920
lib101920

value: ROR1 CAR-T + vehicle (PBS)


title: 78P_1396

description:
Library name: lib101921
lib101921


title: 78_1487

description:
Library name: lib101919
lib101919


title: WGS_cWX2200_96H_rep2_ChIPinput

description: Library name: WGS_cWX2200_96H_rep2_ChIPinput


title: 78_1393

description:
Library name: lib101917
lib101917


title: 18_D8_SN10_17

description:
Library name: lib112934
18_D8_SN10_17

data_processing:
Base calls were processed to FASTQs on BaseSpace (Illumina). A base call quality-trimming step was applied to remove low-confidence base calls from the ends of reads using fastp (0.23.1). Cutadapt was applied to remove adapter sequences. STAR with 2-pass mapping was used to align reads to mm10 reference genome and GENCODE gene annotation vM23 along with quantification of gene-level expression. FastQC, RNA-SeQC, RSeQC were used to examine QC metrics including insert fragment size, read quality, read duplication rates, rRNA rates, gene body coverage and read distribution in different genomic regions. Bioconductor package edgeR was used to detect differential expression between sample groups. Genes with low expression were excluded using edgeR function filterByExpr with min.count = 10 and min.total.count = 15. The filtered expression matrix was normalized by TMM method. Statistical test was using quasi-likelihood pipeline implemented in edgeR. A gene was deemed differentially expressed if meeting the cutoffs of fold change > 1.5 in either direction and Benjamini-Hochberg adjusted p-values < 0.05. Motif enrichment among differentially expressed genes was implemented using HOMER findMotifs.pl by searching gene promoters (1 Kb upstream to 100 bp downstream of TSS).
Assembly: mm10
Supplementary files format and content: tab-delimited file containing gene-level raw counts across all samples

molecule: total RNA

source_name: T cells from tumors

extract_protocol:
Cryopreserved CAR-T cell infusion products and lung tumor cell suspensions were thawed, washed with PBS, and stained with Live/Dead Fixable Aqua Dye (Invitrogen) and surface markers in FACS Buffer. One thousand live CD45PECy7-CD8+GFP+ CAR-T cells were sorted directly into reaction buffer from the SMART-Seq mRNA Kit (Takara), and reverse transcription was performed followed by PCR amplification to generate full-length amplified cDNA.
Sequencing libraries were constructed using the NexteraXT DNA sample preparation kit with unique dual indexes (Illumina) to generate Illumina-compatible barcoded libraries.  Libraries were pooled and quantified using a Qubit® Fluorometer (Life Technologies).  Sequencing of pooled libraries was carried out on a NextSeq 2000 sequencer using an XLEAP-SBS flowcell (Illumina) with paired-end 59-base reads (Illumina) with a target depth of 5 million reads per sample.

treatment_protocol: KP-ROR1 tumor-bearing mice were injected intraperitoneally with 150 mg/kg cyclophosphamide and 24 hrs later were infused with  ROR1 CAR-T, cJun.ROR1 CAR-T, or BATF.ROR1 CAR-T cells. Eight  days post-CAR-T infusion, mice were injected intravenously with 400 ng PECy7-conjugated anti-CD45 antibody (clone 30-F11, BioLegend)  5 min prior to euthanasia to distinguish vascular and non-vascular cells in the lung. Lungs were digested to single cell suspension and cryopreserved in complete RPMI supplemented with 10% FBS and 10% DMSO.

value: T cells from tumors

value: BATF.ROR1 CAR-T infusion sorted from tumors 8 days post-infusion


title: 16_D8_SN10_14

description:
Library name: lib112932
16_D8_SN10_14


title: 15_D8_95_11

description:
Library name: lib112931
15_D8_95_11

value: cJun.ROR1 CAR-T infusion sorted from tumors 8 days post-infusion


title: 14_D8_95_10

description:
Library name: lib112930
14_D8_95_10


title: 13_D8_95_6

description:
Library name: lib112929
13_D8_95_6


title: 11_D8_78_4

description:
Library name: lib112927
11_D8_78_4

value: ROR1 CAR-T infusion sorted from tumors 8 days post-infusion


title: 7_IP_SN10_rep1

description:
Library name: lib112923
7_IP_SN10_rep1

source_name: T cells

value: T cells

value: BATF.ROR1 CAR-T infusion product


title: 9_IP_SN10_rep3

description:
Library name: lib112925
9_IP_SN10_rep3


title: 12_D8_78_5

description:
Library name: lib112928
12_D8_78_5


title: 10_D8_78_2

description:
Library name: lib112926
10_D8_78_2


title: 5_IP_95_rep2

description:
Library name: lib112921
5_IP_95_rep2

value: cJun.ROR1 CAR-T infusion product


title: 95P_1362

description:
Library name: lib101929
lib101929


title: 2_IP_78_rep2

description:
Library name: lib112918
2_IP_78_rep2

value: ROR1 CAR-T infusion product


title: 4_IP_95_rep1

description:
Library name: lib112920
4_IP_95_rep1


title: 3_IP_78_rep3

description:
Library name: lib112919
3_IP_78_rep3


title: 1_IP_78_rep1

description:
Library name: lib112917
1_IP_78_rep1


title: 78_1339

description:
Library name: lib101918
lib101918


title: SS95 CAR-T, IP D9 D30, VDJ

description:
Library name: SS95-VDJ
10X Genomics

data_processing:
Barcoded processing, gene counting, and VDJ transcript sequence assembly were done using cellranger (v.8.0.1)
Assembly: Mouse mm10 + CAR, Cd19-GFP, and cJun sequences
Supplementary files format and content: Tab separated values files (barcodes, features), Comma- separated values files (metadata, filtered contig annotations) and matrix files.
Library strategy: TCR-Seq

source_name: Lungs

extract_protocol:
Lungs were isolated and placed in GentleMACS C Tubes with 6 ml of complete RPMI supplemented with 2 mg/ml collagenase IV (Worthington) and 80 U/ml DNAse I (Worthington). Lungs were minced using the “m_impTumor_01_01” program on a GentleMACS Octo Dissociator and incubated in a 37°C shaker at 120 rpm for 30 min. Cells were filtered through a 100 μm filter, lysed with ACK lysing buffer (Gibco), and resuspended as single cell suspensions. Lung single cell suspensions were cryopreserved in complete RPMI supplemented with 10% FBS and 10% DMSO. Cryopreserved lung tumor cell suspensions and CAR-T infusion products were thawed, washed, and labeled with TotalSeq-C anti-mouse Hashtags (Biolegend) according to the manufacturer’s protocol. Following hashing, equal numbers of live cells were pooled from 3 mice in each treatment group to form 4 pools: D9 ROR1 CAR, D9 cJun.ROR1 CAR, D30 ROR1 CAR, D30 cJun.ROR1 CAR. For analysis of T cells, CD8+ T cells were isolated from each pool using the Mouse CD8a Positive Selection Kit II (Stem Cell). For analysis of the TME, each pool was stained Live/Dead Fixable Aqua Dead Cell stain kit (Invitrogen) and live CD45-PECy7- cells were sorted. For analysis of CAR-T infusion products, CAR-T cells were used directly after hashing.
Libraries from CAR-T infusion product, T cell, and TME samples were prepared using the 10X Genomics Chromium GEM-X Single Cell 5’ Kit as per the manufacturer’s instructions and were sequenced on an Illumina NextSeq 2000 according to the standard 10X Genomics protocol.

value: Lungs

value: Kras-LSLG12D/+; P53f/f

value: cJun.ROR1 CAR-T cells


title: 6_IP_95_rep3

description:
Library name: lib112922
6_IP_95_rep3


title: 8_IP_SN10_rep2

description:
Library name: lib112924
8_IP_SN10_rep2


title: SS78-treated TME, UT D9 D30, VDJ

description:
Library name: TME_1-VDJ
10X Genomics

value: TME

value: ROR1 CAR-T cells


title: SS78 CAR-T, IP D9 D30, VDJ

description:
Library name: SS78-VDJ
10X Genomics


title: SS95-treated TME, UT D9 D30, GEX

description:
Library name: TME_2-GEX
10X Genomics
CAR_TME_RNA_metadata.csv
CAR_TME_RNA_barcodes.tsv.gz
CAR_TME_RNA_matrix.mtx.gz
Tcells_RNA_features.tsv.gz
TME_RNA_metadata.csv
TME_RNA_barcodes.tsv.gz
TME_RNA_matrix.mtx.gz
Tcells_RNA_features.tsv.gz

library_source: transcriptomic single cell

data_processing:
Barcoded processing, gene counting, and VDJ transcript sequence assembly were done using cellranger (v.8.0.1)
Assembly: Mouse mm10 + CAR, Cd19-GFP, and cJun sequences
Supplementary files format and content: Tab separated values files (barcodes, features), Comma- separated values files (metadata, filtered contig annotations) and matrix files.


title: SS95-treated TME, UT D9 D30, VDJ

description:
Library name: TME_2-VDJ
10X Genomics


title: SS95 CAR-T, IP D9 D30, GEX

description:
Library name: SS95-GEX
10X Genomics
CAR_Tcells_RNA_metadata.csv
CAR_Tcells_RNA_barcodes.tsv.gz
CAR_Tcells_RNA_matrix.mtx.gz
Tcells_RNA_features.tsv.gz
Tcells_RNA_metadata.csv
Tcells_RNA_barcodes.tsv.gz
Tcells_RNA_matrix.mtx.gz
Tcells_RNA_features.tsv.gz


title: 17_D8_SN10_16

description:
Library name: lib112933
17_D8_SN10_16

value: CD8+ CAR-T cell


title: SS78 CAR-T, IP D9 D30, GEX

description:
Library name: SS78-GEX
10X Genomics
CAR_Tcells_RNA_metadata.csv
CAR_Tcells_RNA_barcodes.tsv.gz
CAR_Tcells_RNA_matrix.mtx.gz
Tcells_RNA_features.tsv.gz
Tcells_RNA_metadata.csv
Tcells_RNA_barcodes.tsv.gz
Tcells_RNA_matrix.mtx.gz
Tcells_RNA_features.tsv.gz


title: SS95-treated TME, UT D9 D30, hash

description:
Library name: TME_2-CSP
10X Genomics
CAR_TME_RNA_metadata.csv
CAR_TME_RNA_barcodes.tsv.gz
CAR_TME_HTO_matrix.mtx.gz
Tcells_HTO_features.tsv.gz
TME_RNA_metadata.csv
TME_RNA_barcodes.tsv.gz
TME_HTO_matrix.mtx.gz
Tcells_HTO_features.tsv.gz

data_processing:
Barcoded processing, gene counting, and VDJ transcript sequence assembly were done using cellranger (v.8.0.1)
Assembly: Mouse mm10 + CAR, Cd19-GFP, and cJun sequences
Supplementary files format and content: Tab separated values files (barcodes, features), Comma- separated values files (metadata, filtered contig annotations) and matrix files.
Library strategy: CITE-seq


title: SS95 CAR-Ts, IP D9 D30, hash

description:
Library name: SS95-CSP
10X Genomics
CAR_Tcells_RNA_metadata.csv
CAR_Tcells_RNA_barcodes.tsv.gz
CAR_Tcells_HTO_matrix.mtx.gz
Tcells_HTO_features.tsv.gz
Tcells_RNA_metadata.csv
Tcells_RNA_barcodes.tsv.gz
Tcells_HTO_matrix.mtx.gz
Tcells_HTO_features.tsv.gz


title: SS78-treated TME, UT D9 D30, hash

description:
Library name: TME_1-CSP
10X Genomics
CAR_TME_RNA_metadata.csv
CAR_TME_RNA_barcodes.tsv.gz
CAR_TME_HTO_matrix.mtx.gz
Tcells_HTO_features.tsv.gz
TME_RNA_metadata.csv
TME_RNA_barcodes.tsv.gz
TME_HTO_matrix.mtx.gz
Tcells_HTO_features.tsv.gz


title: SS78 CAR-Ts, IP D9 D30, hash

description:
Library name: SS78-CSP
10X Genomics
CAR_Tcells_RNA_metadata.csv
CAR_Tcells_RNA_barcodes.tsv.gz
CAR_Tcells_HTO_matrix.mtx.gz
Tcells_HTO_features.tsv.gz
Tcells_RNA_metadata.csv
Tcells_RNA_barcodes.tsv.gz
Tcells_HTO_matrix.mtx.gz
Tcells_HTO_features.tsv.gz


title: TripleNegative_PBS_HTO [NGS4272]

city: South San Francisco

first: Jason

middle: Anthony

last: Vander Heiden

state: CA

address: 1 DNA Way

department: Biological Research AI Development

institute: Genentech

description:
SAM24411450_HTO
hashtag library

data_processing:
FASTQ files were generated using the Cell Ranger v6.0.1 (10X Genomics) bcl2fastq (Illumina) wrapper.
Sequencing reads were assembled and aligned against the GENCODE basic mouse reference using Cell Ranger v6.0.1 (10X Genomics) to generate count matrices.
Assembly: GRCm38
Supplementary files format and content: HDF5 feature count matrices.

source_name: lung

extract_protocol:
Total RNA was extracted using the Qiagen RNeasy kit.
Single-cell RNA-seq library preparation was performed using the 10x Genomics Chromium platform with the Single Cell 3’ Library and Gel bead kit following the manufacturer’s user guide.

treatment_protocol: Cells were pelleted right after sorting. Supernatant was discarded and pellet was resuspended in RLT buffer.

value: lung

value: CD45- CD31- EpCAM-

value: PBS

tag: time point

value: day 14


title: CD45_PBS_HTO [NGS4272]

description:
SAM24411448_HTO
hashtag library


title: CD31_EPCAM_PBS_HTO [NGS4272]

description:
SAM24411449_HTO
hashtag library

value: CD45- CD31+ EpCAM+


title: CD31_EPCAM_BLM_aOSM_aIL6R_HTO [NGS4272]

description:
SAM24411446_HTO
hashtag library

value: bleomycin + anti-IL6R + anti-OSM


title: CD45_BLM_aIL6R_HTO [NGS4272]

description:
SAM24411442_HTO
hashtag library

value: bleomycin + anti-IL6R


title: TripleNegative_BLM_aOSM_aIL6R_HTO [NGS4272]

description:
SAM24411447_HTO
hashtag library


title: CD45_BLM_aOSM_aIL6R_HTO [NGS4272]

description:
SAM24411445_HTO
hashtag library


title: CD31_EPCAM_BLM_Control_HTO [NGS4272]

description:
SAM24411437_HTO
hashtag library

value: bleomycin + isotype control


title: CD31_EPCAM_BLM_aOSM_HTO [NGS4272]

description:
SAM24411440_HTO
hashtag library

value: bleomycin + anti-OSM


title: SS78-treated TME, UT D9 D30, GEX

description:
Library name: TME_1-GEX
10X Genomics
CAR_TME_RNA_metadata.csv
CAR_TME_RNA_barcodes.tsv.gz
CAR_TME_RNA_matrix.mtx.gz
Tcells_RNA_features.tsv.gz
TME_RNA_metadata.csv
TME_RNA_barcodes.tsv.gz
TME_RNA_matrix.mtx.gz
Tcells_RNA_features.tsv.gz


title: CD31_EPCAM_BLM_aIL6R_HTO [NGS4272]

description:
SAM24411443_HTO
hashtag library


title: TripleNegative_BLM_Control_HTO [NGS4272]

description:
SAM24411438_HTO
hashtag library


title: TripleNegative_BLM_aOSM_HTO [NGS4272]

description:
SAM24411441_HTO
hashtag library


title: TripleNegative_BLM_aIL6R_HTO [NGS4272]

description:
SAM24411444_HTO
hashtag library


title: CD45_BLM_Control_HTO [NGS4272]

description:
SAM24411436_HTO
hashtag library


title: ISCs, ChIRP, Scramble probe

city: Beijing

first: Jiacheng

last: He

state: Beijing

address: No.15 DaTun Road

country: China

institute: IBP

description: Library name: Scramble, ChIRP

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseg output.
Assembly: mm39
Supplementary files format and content: bigWig (except for Input sample)
Library strategy: ChIRP-seq

source_name: Small intestine

extract_protocol:
Crypts isolated from WT mice aged 8 weeks were digested into single cells. ISCs were isolated by FACS and cross-linked with 1% formaldehyde at 37°C for 10 min and quenched by 0.1 M glycine for 5min. Then cells were washed twice with PBS, lysed with Lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris, supplemented with PMSF, proteinase inhibitor cocktails and M5 RNase inhibitor) and sonicated to produce 200~500 bp DNA fragments. Lysates were incubated with biotinylated antisense probes against Snora61 for 4 hours at 37°C. Streptavidin magnetic beads were then added to isolate probe-binding complex. After washing steps, DNA were extracted from beads and analyzed by qPCR using primer pairs listed in Supplementary Table 3. The ChIRP-seq assay was performed by Novogene Co., Ltd. (Beijing).
ChIP-seq libraries were prepared using the KAPA HTP Library Preparation Kitcomplemented with NEXTflex DNA Barcodes from Bio Scientific. 10 ng of DNA wasused as starting material for input and ip samples. Libraries were amplified using13cycles on the thermocycler. Post amplification libraries were size selected at250-450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Librarieswere validated using the Agilent High Sensitivity DNA Kit.

value: Small intestine

value: Small intestinal stem cells


title: ISCs, ChIRP, Snora61 probe

description: Library name: Snora61, ChIRP


title: mESCs, cKO (tamoxifen) and SCR ASO, R3

city: Irvine

first: Ivan

last: Marazzi

address: 839 Health Sciences Road

department: Department of Biological Chemistry

institute: University of California

description: Library name: mESCs, cKO (tamoxifen) and SCR ASO, rep3

data_processing:
Illumina Short Reads were mapped onto the WT and Exosc3 cKO mESCs and EpiLCs novel transcriptome using STAR using the following parameters: --outFilterMultimapNmax 100 --winAnchorMultimapNmax 100. Gene- and TE-level quantification was performed with TEcount using the RepeatMasker gtf file generated from the mm10 genome. Isoform-level quantification was performed with RSEM. Differential expression was calculated using DESeq2 with default parameters.
Assembly: Novel transcriptome generated with the WT and Exosc3 cKO mESCs and EpiLCs long and short-read RNA-seq (GEO:GSE205211) based on mm10.
Supplementary files format and content: tab-deliminated TEcount gene and TE expression counts. Column titles are numbered by the sample id, i.e. 1 is 'mESCs, EtOH and U1 AMO, rep1', 2 is 'mESCs, EtOH and U6atac AMO, rep1', etc.

source_name: mESCs

growth_protocol: mESCs were cultured in 2i/Lif media.

extract_protocol:
On the day of collection, cells were collected in TRIzol and RNA was isolated following the manufacturer’s recommendations.
RNA libraries were prepared using either the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB) or TruSeq kit (Illumina) following the manufacturer’s recommendations.

treatment_protocol: Exosc3 cKO was induced by the addition of 100 nM tamoxifen (4-OHT). Control wells were treated with ethanol (EtOH) alone. ASOs was transfected with Lipofectamine RNAiMAX (Thermofisher scientific) at a final concentration of 100nM. AMOs were added to the cell suspensions at a final concentration of 15μM and electroporated into cells using the Biorad Gene Pulser XCell electroporation system.

value: mESCs


title: mESCs, cKO (tamoxifen) and MERVL ASO, R3

description: Library name: mESCs, cKO (tamoxifen) and MERVL ASO, rep3


title: mESCs, cKO (tamoxifen) and SCR ASO, R2

description: Library name: mESCs, cKO (tamoxifen) and SCR ASO, rep2


title: mESCs, EtOH and SCR ASO, R3

description: Library name: mESCs, EtOH and SCR ASO, rep3


title: mESCs, cKO (tamoxifen) and MERVL ASO, R2

description: Library name: mESCs, cKO (tamoxifen) and MERVL ASO, rep2


title: mESCs, EtOH and MERVL ASO, R1

description: Library name: mESCs, EtOH and MERVL ASO, rep1


title: mESCs, cKO (tamoxifen) and SCR ASO, R1

description: Library name: mESCs, cKO (tamoxifen) and SCR ASO, rep1


title: mESCs, cKO (tamoxifen) and MERVL ASO, R1

description: Library name: mESCs, cKO (tamoxifen) and MERVL ASO, rep1


title: mESCs, EtOH and MERVL ASO, R2

description: Library name: mESCs, EtOH and MERVL ASO, rep2


title: CD45_BLM_aOSM_HTO [NGS4272]

description:
SAM24411439_HTO
hashtag library


title: mESCs, EtOH and SCR ASO, R2

description: Library name: mESCs, EtOH and SCR ASO, rep2


title: mESCs, EtOH and SCR ASO, R1

description: Library name: mESCs, EtOH and SCR ASO, rep1


title: mESCs, EtOH and MERVL ASO, R3

description: Library name: mESCs, EtOH and MERVL ASO, rep3


title: ISCs, ChIRP, Input

description: Library name: Input


title: MN high IAA 3

city: Lausanne

first: David

middle: Michael

last: Suter

address: EPFL SV-IN Station 19

department: Institute of Bioengineering

country: Switzerland

institute: École polytechnique fédérale de Lausanne

data_processing:
Reads were aligned to the mouse reference genome mm10  using STAR with settings ‘--alignMatesGapMax 2000 --alignIntronMax 1 --alignEndsType EndtoEnd -- outFilterMultimapNmax 1’. Duplicate reads were removed with Picard (Broad Institute) and reads not mapping to chromosomes 1–19, X, or Y were removed. Normalization factors were calculated based on the total number of readsfor each sample and applied to downsample the total number of reads mapped to mouse genome. For each sample, peaks were called with MACS2 with settings ‘-f BAMPE -g mm’.
Assembly: mm10
Supplementary files format and content: bigWig files computed by DANPOS3 software

source_name: SYAT

growth_protocol: SYAT mESC  were routinely cultured at 37 °C and 5% CO2 on cell culture-treated dishes coated with 0.1% gelatin using the following culture medium: GMEM supplemented with 10% ES-cell qualified fetal bovine serum, 1% nonessential amino acids, 2mM L-glutamine,  2mM sodium pyruvate, 100μM 2-mercaptoethanol, 1% penicillin and streptomycin, in-house produced leukemia inhibitory factor (LIF), CHIR99021 at 3 μM and PD184352 at 0.8 μM. Cells were passaged by trypsinization every two to three days. Three days before all experiments, mESC medium was changed to Serum LIF medium: GMEM supplemented with 10% ES-cell qualified fetal bovine serum, nonessential amino acids, 2 mM L-glutamine, sodium pyruvate, 100 μM 2-mercaptoethanol, penicillin and streptomycin, in-house produced leukemia inhibitory factor (LIF). SYAT cells were cultured routinely with 200nM Auxinole (Control condition) to avoid basal degradation of SRCAP. For SRCAP degradation, SYAT cells were treated for 4 h with 500µM Indole-3-Acetic Acid (IAA).

extract_protocol:
Micrococcal Nuclease S7 was resuspended to 15U/µL in 20mM Tris-HCl pH 7.5, 50mM NaCl, 50% Glycerol. For high digestion conditions, MNase was diluted at 100 U/mL in MNase Digestion buffer (50mM Tris-HCl pH 8, 150mM sucrose, 50mM NaCl, 5mM CaCl2). For low digestion conditions, MNase was diluted at 6.25U/mL in MNase Digestion Buffer. SYAT cells were treated for 4 h with 500µM IAA or 200nM Auxinole before collection. 5x106 cells were used for each MNase digestion condition. After cell collection, cell pellets were resuspended in 50µL Resuspension Buffer (35mM HEPES pH 7.4, 150mM sucrose, 80mM KCl, 5mM KH2PO4, 5mM MgCl2, 0.2%NP-40). Then, 500 µL of MNase solution were added to the cells and incubated for exactly 10 min at 37°C before inactivation of MNase by addition of 11 µL of 0.5M EDTA to the reaction. Next, 550 µL of Lysis Buffer (50mM Tris-HCl pH 8, 1% SDS, 10mM EDTA) was added and samples were incubated on ice for 10 min. After addition of 1.1mL DNAse-free water, samples were digested for 2 h at 37°C with RNase (50µg per reaction). Finally, 3200 U of Proteinase K were added, and digestion was performed at 56°C for 2 h. Digested DNA was purified using DNA Purification kit. Then, 500 ng of DNA for the High digestion condition and 1500 ng of DNA for the Low digestion condition were loaded on a 1.5% agarose gel and the band below 200bp was cut out and gel-purified.
Libraries were prepared with NEBNext Ultra II DNA Library Prep Master Mix Set (NEB, #E7103) using insert size selection of 250 bp. Sequencing was performed using 75 nt paired end reads on an Illumina NextSeq 500.

treatment_protocol: SRCAP degradation was induced by 4-hour treatment with 500µM IAA.

value: SYAT

value: mESC

value: IAA 500uM 4h


title: MN high IAA 2


title: MN high NT 3

value: Control


title: MN low IAA 3


title: MN high NT 2


title: MN low NT 3


title: MN high IAA 1


title: MN low IAA 2


title: MN high NT 1


title: SYAT NT GFP 2

data_processing:
Reads were aligned to the mouse reference genome mm10 and the Drosophila reference genome dm6 using STAR with settings ‘--alignMatesGapMax 2000 --alignIntronMax 1 --alignEndsType EndtoEnd -- outFilterMultimapNmax 1’. Duplicate reads were removed with Picard (Broad Institute) and reads not mapping to chromosomes 1–19, X, or Y were removed. Normalization factors were calculated on the number of non-duplicated reads uniquely mapped to Drosophila genome for each sample and applied to downsample the total number of reads mapped to mouse genome. For each sample, peaks were called with MACS2 with settings ‘-f BAMPE -g mm’.
Assembly: mm10
Supplementary files format and content: bigWig files include RPKM normalized reads
Supplementary files format and content: bed files with peaks obtained using MACS2

growth_protocol: SYAT mESC were routinely cultured at 37 °C and 5% CO2 on cell culture-treated dishes coated with 0.1% gelatin using the following culture medium: GMEM supplemented with 10% ES-cell qualified fetal bovine serum, 1% nonessential amino acids, 2mM L-glutamine,  2mM sodium pyruvate, 100μM 2-mercaptoethanol, 1% penicillin and streptomycin, in-house produced leukemia inhibitory factor (LIF), CHIR99021 at 3 μM and PD184352 at 0.8 μM. Cells were passaged by trypsinization every two to three days. Three days before all experiments, mESC medium was changed to Serum LIF medium: GMEM supplemented with 10% ES-cell qualified fetal bovine serum, nonessential amino acids, 2 mM L-glutamine, sodium pyruvate, 100 μM 2-mercaptoethanol, penicillin and streptomycin, in-house produced leukemia inhibitory factor (LIF). SYAT cells were cultured routinely with 200nM Auxinole (Control condition) to avoid basal degradation of SRCAP.

extract_protocol:
CUT&Tag experiments were performed in duplicates using the CUT&Tag-IT Assay Kit (Active Motif #53160) and following manufacturer instructions. Briefly, 200,000 SYAT  cells were mixed with 10,000 cryo-preserved Drosophila nuclei (Active Motif #53168) for spike-in. Cells were then bound on Concanavalin A beads prior to incubation overnight with a mix of 1:50 anti-GFP rabbit antibody (abcam ab290) and 1:100 Spike-In anti-H2Av antibody (Active Motif #53168). Next, cells were incubated with a secondary antibody, pA-Tn5-transposomes, and washed according to manufacturer instructions. Transposition was subsequently performed for 1 h at 37°C, and transposed DNA was purified prior to Library Preparation and size exclusion with SPRI beads using a 0.5X ratio while keeping the unbound fraction and 1X ratio on the left side, taking the bound fraction.
Libraries were prepared with NEBNext Ultra II DNA Library Prep Master Mix Set (NEB, #E7103) using insert size selection of 250 bp. Sequencing was performed using 37 nt paired end reads on an Illumina NextSeq 500.

tag: chip antibody

value: abcam ab290


title: MN low IAA 1


title: SYAT NT GFP 1


title: SYAT_control_Input

growth_protocol: CGR8 mouse ES cells, SYAT mESC and ZHBTc4 mESC were routinely cultured at 37 °C and 5% CO2 on cell culture-treated dishes coated with 0.1% gelatin using the following culture medium: GMEM supplemented with 10% ES-cell qualified fetal bovine serum, 1% nonessential amino acids, 2mM L-glutamine,  2mM sodium pyruvate, 100μM 2-mercaptoethanol, 1% penicillin and streptomycin, in-house produced leukemia inhibitory factor (LIF), CHIR99021 at 3 μM and PD184352 at 0.8 μM. Cells were passaged by trypsinization every two to three days. Three days before all experiments, mESC medium was changed to Serum LIF medium: GMEM supplemented with 10% ES-cell qualified fetal bovine serum, nonessential amino acids, 2 mM L-glutamine, sodium pyruvate, 100 μM 2-mercaptoethanol, penicillin and streptomycin, in-house produced leukemia inhibitory factor (LIF). SYAT cells were cultured routinely with 200nM Auxinole (Control condition) to avoid basal degradation of SRCAP. For SRCAP degradation, SYAT cells were treated for 1, 2, 4, 6 or 8 h with 500µM Indole-3-Acetic Acid (IAA). For induction of Oct4 knock-down in ZHBTc4 cells, 1µg/mL Doxycycline was added for 9 or 12 h prior cell collection.

extract_protocol:
1-5 million cells were fixed in 1% formaldehyde or formaldehyde+2mM DSG for TF for 10 min at room temperature, quenched with 250 mM Tris-HCl pH 8.0, washed with PBS, spun down, and stored at −80 °C. The cell pellet was resuspended in 1.5 ml LB1 (50 mM HEPES-KOH pH 7.4, 140 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 10% Glycerol, 0.5% NP40, 0.25% TritonX-100), incubated 10 min at 4 °C, spun down, and resuspended in 1.5 ml LB2 (10 mM Tris-HCl pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA), and incubated 10 min at 4 °C. The pellet was spun down and rinsed twice with SDS shearing buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA, 0.15% SDS), and finally resuspended in 0.9 ml SDS shearing buffer. All buffers contain 1:100 diluted Protease Inhibitor Cocktail in DMSO (Sigma). The suspension was transferred to a milliTUBE 1 ml AFA fiber and sonicatedon a E220 focused ultrasonicator (Covaris) using the following settings: 20 min, 200 cycles, 5% duty, 140W, and input sample aliquots were taken.1.5-5μg of sonicated chromatin was incubated with suitable antibody and for normalization 10ng Drosophila chromatin (Active Motif) and 0.5μg anti-H2Av drosophila-specific antibody (Active Motif)/µg of mouse chromatin. ChIP was performed using ChIP-IT High Sensitivity kit (Active Motif) following manufacturer protocol.
Libraries were prepared with NEBNext Ultra II DNA Library Prep Master Mix Set (NEB, #E7103) using insert size selection of 250 bp. Sequencing was performed using 37 nt paired end reads on an Illumina NextSeq 500.

treatment_protocol: SRCAP degradation was induced by 2,4,6 or 8-hour treatment with 500µM IAA. Oct4 knockdown was induced for 9 or 12 hours with 500ng/µL Doxycycline. wtSRCAP or cdSRCAP overexpression was induced by treatment with 1µg/mL Doxycycline for 24h.


title: MN low NT 2


title: CGR8_M_Input


title: CGR8_AS_Input


title: SYAT IAA8h H2Aub 1

value: Cell Signaling Technology #8240

value: IAA 500uM 8h


title: SYAT IAA8h H3K27me3

value: Abcam #ab195477


title: SRCAPwt high NT H2AZ

value: Abcam #ab4174

value: Dox 1ug/mL 24h


title: SYAT IAA4h H2Aub 1


title: MN low NT 1


title: SRCAPcd high NT H2AZ


title: SYAT IAA6h H3K27me3

value: IAA 500uM 6h


title: SRCAPwt high IAA H2AZ

value: Dox 1ug/mL 24h + IAA 500uM 4h


title: SRCAPcd high IAA H2AZ


title: SYAT IAA4h H3K27me3


title: SYAT IAA6h H2Aub 1


title: SYAT NT H3K27me3


title: SYAT IAA4h H3K4me3 1

value: Abcam #ab8580


title: SYAT IAA8h H3K4me3 1


title: SYAT IAA6h NFYa 1

value: Santa-Cruz sc-17753


title: SYAT IAA8h NFYa 1


title: SYAT IAA6h H3K4me3 1


title: SYAT unt NFYa 1


title: SYAT IAA4h Sox2 2

value: Cell Signaling Technology #23064


title: SYAT IAA6h Nanog 1

value: Cell Signaling Technology #8822


title: SYAT IAA4h NFYa 1


title: SYAT IAA4h Nanog 1


title: SYAT IAA8h Sox2 2


title: SYAT IAA8h Nanog 1


title: SYAT Unt Nanog 1


title: SYAT IAA6h Sox2 2


title: SYAT IAA4h Sox2 1


title: SYAT IAA6h Oct4 2

value: Cell Signaling Technology #5677


title: SYAT unt Oct4 2

value: SYAT


title: SYAT IAA6h Sox2 1

value: mESC


title: SYAT IAA8h Sox2 1


title: SYAT unt Sox2 1


title: SYAT IAA8h Oct4 1


title: SYAT IAA4h Oct4 2

value: IAA 500uM 4h


title: SYAT IAA8h YY1 1

value: Cell Signaling Technology #46395


title: SYAT NT H3K4me3 1

value: Control


title: SYAT unt Oct4 1


title: SYAT unt YY1 1


title: SYAT IAA6h Oct4 1


title: SYAT IAA4h YY1 1


title: ZHBTc4 Dox9h 2 H2AZ

value: Doxycycline 1ug/mL 9h


title: SYAT unt H2Aub 1

value: Cell Signaling Technology #8240


title: SYAT unt Sox2 2


title: ZHBTc4 Dox12h 2 H2AZ

value: Doxycycline 1ug/mL 12h


title: ZHBTc4 Dox12h 1 H2AZ

value: Abcam #ab4174


title: SYAT IAA8h Oct4 2

value: IAA 500uM 8h


title: ZHBTc4 unt 2 H2AZ


title: ZHBTc4 Dox9h 1 H2AZ


title: M IAA H2AZ

value: IAA 500uM 1h


title: M unt H2AZ


title: ZHBTc4 unt 1 H2AZ


title: acH2AZ M 1

value: ThermoFisher Scientific PA540095


title: AS unt H2AZ


title: acH2AZ M 2


title: AS IAA H2AZ


title: acH2AZ AS 2


title: G2 H2AZ 2


title: SYAT IAA4h Oct4 1


title: S H2AZ 2


title: LG1 H2AZ 2


title: AS H2AZ 2


title: SYAT IAA6h YY1 1

value: IAA 500uM 6h


title: M H2AZ 2


title: EG1 H2AZ 1


title: EG1 H2AZ 2


title: SYAT IAA6h H2A 2

value: Abcam #ab18255


title: SYAT IAA8h H2A 1


title: G2 H2AZ 1


title: AS H2AZ 1


title: SYAT IAA8h H2A 2


title: S H2AZ 1


title: SYAT unt H2A 2


title: SYAT IAA2h H2A 2

value: IAA 500uM 2h


title: M H2AZ 1


title: SYAT IAA4h H2A 2


title: SYAT unt H2A 1


title: SYAT IAA6h H2A 1


title: SYAT IAA8 1 H2AZ


title: SYAT IAA8 2 H2AZ


title: SYAT IAA2h H2A 1


title: SYAT IAA6 2 H2AZ


title: acH2AZ AS 1


title: SYAT IAA6 1 H2AZ


title: SYAT IAA4 1 H2AZ


title: SYAT IAA4 2 H2AZ


title: SYAT IAA2 2 H2AZ


title: SYAT IAA2 1 H2AZ


title: SRCAPcd IAA 2 ATAC

data_processing:
Reads were aligned to the mouse reference genome mm10  using STAR with settings ‘--alignMatesGapMax 2000 --alignIntronMax 1 --alignEndsType EndtoEnd -- outFilterMultimapNmax 1’. Duplicate reads were removed with Picard (Broad Institute) and reads not mapping to chromosomes 1–19, X, or Y were removed. Normalization factors were calculated based on the total number of readsfor each sample and applied to downsample the total number of reads mapped to mouse genome. For each sample, peaks were called with MACS2 with settings ‘-f BAMPE -g mm’.
Assembly: mm10
Supplementary files format and content: bigWig files include RPKM normalized reads
Supplementary files format and content: bed files with peaks obtained using MACS2

growth_protocol: CGR8 mouse ES cells and SYAT mESC  were routinely cultured at 37 °C and 5% CO2 on cell culture-treated dishes coated with 0.1% gelatin using the following culture medium: GMEM supplemented with 10% ES-cell qualified fetal bovine serum, 1% nonessential amino acids, 2mM L-glutamine,  2mM sodium pyruvate, 100μM 2-mercaptoethanol, 1% penicillin and streptomycin, in-house produced leukemia inhibitory factor (LIF), CHIR99021 at 3 μM and PD184352 at 0.8 μM. Cells were passaged by trypsinization every two to three days. Three days before all experiments, mESC medium was changed to Serum LIF medium: GMEM supplemented with 10% ES-cell qualified fetal bovine serum, nonessential amino acids, 2 mM L-glutamine, sodium pyruvate, 100 μM 2-mercaptoethanol, penicillin and streptomycin, in-house produced leukemia inhibitory factor (LIF). SYAT cells were cultured routinely with 200nM Auxinole (Control condition) to avoid basal degradation of SRCAP. For SRCAP degradation, SYAT cells were treated for 1, 2, 4, 6 or 8 h with 500µM Indole-3-Acetic Acid (IAA). For induction of wtSRCAP or cdSRCAP overexpression, 1µg/mL Doxycycline was added for 24 h prior cell collection.

extract_protocol:
50,000 cells were collected either directly after trypsinization or after sorting as described above, and subjected to ATAC-seq. All centrifugation steps were done at 800 g at 4°C. Cells  were centrifuged for 5 min and washed with cold PBS, then centrifuged for 5 min and resuspended in cold lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40), and centrifuged for 10 min. Subsequently, nuclei were resuspended in a solution of 0.5 mM Tn5 in TAPS-DMF buffer (10 mM TAPS-NaOH, 5 mM Mgcl2, 10% DMF) and incubated for 30 min at 37°C. DNA was immediately purified using column purification  and eluted in 10 ml nuclease-free H2O. Transposed DNA was amplified in a solution containing 1X NEBNextHigh Fidelity PCR Master Mix, 0.5 μM of Ad1_1 universal primer, 0.5 μM of Ad2.x indexing primer and 0.6x SYBR Green I using 72°C for 5 min, 98°C for 30 s, and 5 cycles of 98°C for 1 s, 63°C for 30 s, and 72°C for 60 s. 10 μl of amplified DNA was analyzed by qPCR to determine the total number of cycles to avoid amplification saturation and accordingly amplified with additional 3–7 cycles at 98°C for 10 s, 63°C for 30 s, and 72°C for 60 s. DNA was purified using column purification and size-selected by taking the unbound fraction of 0.55X AMPure XP beads followed by the bound fraction of 1.2X AMPure XP beads.
Libraries were prepared with NEBNext Ultra II DNA Library Prep Master Mix Set (NEB, #E7103) using insert size selection of 250 bp. Sequencing was performed using 75 nt paired end reads on an Illumina NextSeq 500.

treatment_protocol: SRCAP degradation was induced by 2,4,6 or 8-hour treatment with 500µM IAA. wtSRCAP or cdSRCAP overexpression was induced by a 24-hour Doxycyline treatment (1µg/mL)

value: Dox 1ug/mL 24h +IAA 500uM 4h


title: LG1 H2AZ 1


title: SRCAPwt NT 2 ATAC

value: Dox 1ug/mL 24h


title: SYAT unt H2AZ

value: SYAT


title: SRCAPcd NT 2 ATAC

value: mESC


title: SRCAPwt IAA 2 ATAC


title: SRCAPwt IAA 1 ATAC


title: SRCAPcd NT 1 ATAC


title: SYAT DNMTi NT 1 ATAC

value: DNMTi 6j


title: SRCAPwt NT 1 ATAC


title: SYAT DNMTi NT 2 ATAC


title: CGR8 IAA ATAC 2

value: IAA 500uM 4h


title: SYAT DNMTi IAA 2 ATAC

value: DNMTi 6j + IAA 500uM 4h


title: SYAT DNMTi IAA 1 ATAC


title: SYAT IAA4h H2A 1


title: IAA telo 2


title: unt EG1 2

value: Control


title: unt telo 2


title: CGR8 NT ATAC 2


title: IAA EG1 2


title: unt telo 1


title: IAA EG1 1


title: SRCAPcd IAA 1 ATAC


title: IAA telo 1


title: SYAT IAA2h ATAC 2


title: SYAT IAA4h ATAC 1


title: SYAT unt ATAC 2


title: SYAT IAA6h ATAC 1


title: SYAT IAA6h ATAC 2


title: SYAT IAA8h ATAC 2


title: SYAT IAA4h ATAC 2


title: CGR8 NT ATAC 1


title: CGR8 IAA ATAC 1


title: Ovary, KO_6

city: Ube

first: Yoichi

last: Mizukami

state: Yamaguchi

department: Science Research Center

country: Japan

institute: Yamaguchi university

data_processing:
Reads with >2 ambiguous nucleotides and reads with quality scores of <20 as calculated by the Phred program were removed using CLC Genomics Work Bench (version 8.01, Qiagen)
In addition, long reads with >1000 nucleotides and short reads with <20 nucleotides were discarded.
Trimmed reads were mapped to the mouse reference genome GRCm38/mm10 in default settings.
Read count normalization were performed using CLC Genomics Work Bench.
Assembly: GRCm38/mm10
Supplementary files format and content: tab-delimited text files include RPKM and TPM values for each sample.

source_name: Ovary

extract_protocol:
Total RNA was extracted from the ovaries using the RNeasy Mini Kit (Qiagen), and mRNA was purified with Oligo dT beads (NEBNext Poly (A) mRNA magnet Isolation Module, New England Biolabs).
NEBNext Ultra II RNA library Prep kit (NEB) and NEBNext Multiplex Oligos (Illumina) were used to generate cDNA libraries.

treatment_protocol: Mice were intraperitoneal administered pregnant mare serum gonadotropin (PMSG, 5 IU) and human Chorionic Gonadotropin (hCG, 5 IU) at 48-hour intervals. Ovaries clollected at indicated time point were stored in RNAlater.

value: Ovary

tag: time

value: 24h after hCG i.p.

tag: age

tag: strain

value: ICR (Crl:CD1)


title: Ovary, KO_2


title: SYAT IAA2h ATAC 1


title: Ovary, KO_1


title: Ovary, KO_5


title: Ovary, KO_7


title: Ovary, KO_3


title: SYAT IAA8h ATAC 1

value: IAA 500uM 8h


title: Ovary, WT_10

value: WT


title: Ovary, WT_8


title: Ovary, WT_7


title: Ovary, WT_1


title: Ovary, WT_9


title: 6-DM8

city: Shuozhou

first: Dan

last: Li

state: Shanxi

address: No. 11, Changning Street

institute: Shanxi College of Technology

description:
Library name: 6-DM8
6-DM8_FPKM

data_processing:
The normalized expression levels of different samples were converted to FPKM (Fragments Per Kilobase of transcript per Million mapped fragments). The edgeR package of R was used to analyze the difference between intergroup gene expression, the P-values were calculated, and the multiple hypothesis test was performed. The P-value threshold was determined by controlling the FDR (False Discovery Rate) with the Benjamini algorithm. The corrected P-value is called the q-value. Differentially expressed genes (DEGs) were defined as transcripts with a fold change in expression level (according to the FPKM value) greater than 2.0 and a q-value less than 0.05. GO enrichment analysis was performed with the clusterProfiler package of R and the enrichment criteria including a q-value < 0.05. Heatmaps of specific genes were generated using the pheatmap package of R. PCA analysis was visualized using the scatterplot3d package of R.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: csv files include FPKM values for each Sample

extract_protocol:
The total RNA was extracted using TransZol Up Plus RNA Kit (Cat#ER501–01, Trans) according to the manufacturer’s instruction, and RNA integrity was checked using an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US). Total RNA was qualified and purified using RNA Clean XP Kit (Cat A63987, Beckman  Coulter, Inc., CA, USA) and RNase-Free DNase Set (Cat#79254, QIA_x0002_GEN, GmBH, Germany).
The sample library was constructed from the purified total RNA through a series of steps, including mRNA separation, fragmentation, first-strand cDNA synthesis, second-strand cDNA synthesis, end repair, 3′ end addition, ligation, and enrichment. The concentration and size of the sample library were determined using Qubit® 2.0 Fluorometer and Agilent 2100, respectively. The sequencing process was run and monitored using Illumina HiSeq 2500 System, and real-time data analysis was performed using HiSep Control software.

value: lung

value: tissue

value: DINP


title: Ovary, WT_2


title: unt EG1 1


title: 6-CM7

description:
Library name: 6-CM7
6-CM7_FPKM


title: 6-DM6

description:
Library name: 6-DM6
6-DM6_FPKM


title: 3-DM7

description:
Library name: 3-DM7
3-DM7_FPKM


title: 6-CM6

description:
Library name: 6-CM6
6-CM6_FPKM


title: 6-CM5

description:
Library name: 6-CM5
6-CM5_FPKM


title: 3-DM6

description:
Library name: 3-DM6
3-DM6_FPKM


title: SYAT unt ATAC 1


title: 6-DM7

description:
Library name: 6-DM7
6-DM7_FPKM


title: 3-CM7

description:
Library name: 3-CM7
3-CM7_FPKM


title: 3-DM5

description:
Library name: 3-DM5
3-DM5_FPKM


title: 3-CM2

description:
Library name: 3-CM2
3-CM2_FPKM


title: Human epithelal PDI replicate 3

city: Leeds

first: LeedsOmics

last: UoLeeds

state: West Yorkshire

address: Clarendon Way

department: Cross-faculty

country: United Kingdom

institute: University of Leeds

description:
Library name: Hs Ishi PDI rep 3
R_Ishi_P4HB_3

data_processing:
To analyze differences in expression, adapter trimming was done by Cutadapt24 and the reads were filtered using fastq_quality_filter as part of FASTX-toolkit with parameters including “-q 20” and “-p 90”. The bovine (Bos taurus) and human (Homo sapiens) reference genome and gene annotation files were retrieved from the Ensembl genome database (release 96)25 and GENCODE (release 31),26 respectively. With the help of the Rsubread package,27 read mapping was performed by means of Subread aligners with only uniquely mapped reads reported in the final alignment and read summarization and quantification was carried out using the featureCounts function. Statistical analysis for differential gene expression was conducted via DESeq228 with the cutoffs of log2FoldChange > 1 (or <−1) and padj < .05.
Assembly: The bovine (Bos taurus) and human (Homo sapiens) reference genome and gene annotation files were retrieved from the Ensembl genome database (release 96) and GENCODE (release 31), respectively
Supplementary files format and content: gene_counts_PoolE.txt = readCounts matrix of the bEECs on a tab-delimited plain text format; gene_counts_PoolS.txt = readCounts matrix of the bESCs on a tab-delimited plain text format; gene_counts_human_CAPG.txt = readCounts matrix of the hEECs on a tab-delimited plain text format;

source_name: Endometrium

growth_protocol: Primary bovine endometrial cell culture Primary bovine endometrial epithelial cells (bEECs) and primary bovine endometrial stromal cells (bESCs) were isolated by enzymatic digestion from late-luteal phase uterine tracts (n=3). bEECs and bESCs were maintained in complete bovine medium (RPMI 1640 [Gibco, Massachusetts, US], 10% charcoal-stripped FBS [PAA Cell Culture Company, UK], 1% antibiotic antimycotic solution [ABAM, Sigma-Aldrich, Missouri, USA]). bESCs at a concentration of 150,000 cells per well (n=5) and bEECs at a concentration of 300,000 cells per well (n=5) were plated into separate 6-well plates in 2 mL complete bovine medium. All cultures were maintained at 37C/5% CO2 in a humidified incubator. At 70% confluence bEECs and bESCs were treated with one of the following for 24 hr: (1) Media control, (2) Vehicle control (PBS only), (3) 1000 ng/ml rbPDI, 4) 1000ng/mL rbPSAT1, 5) 1000ng/mL rbCAPG, or (6) 1000 ng/ml rbPDI/CAPG/PSAT1 combined with 100 ng/ml roIFNT. Human endometrial cell culture Ishikawa (ECACC 99040201, passage 10) immortalised human endometrial epithelial cells (hEECs) were plated in biological technical triplicate at 300,000 cells per well in a 6 well plate, in 2 mL complete human medium (DMEM/F12 [Gibco, Massachusetts, US], 10% FBS [PAA Cell Culture Company, UK], 1% Glutamine SStreptomycin PPenicillin [Gibco, Massachusetts, US]). The three replicates were from three different flasks of passage 10 cells, which had been split from a single flask of passage 9 Ishikawa cells. All cultures were maintained at 37 C/5% CO2 in a humidified incubator. At 70% confluence hEECs were treated with one of the following for 24 hours: (1) Media control, (2) Vehicle control (PBS only), (3) 1000ng/mL rbCAPG (4) 1000 ng/ml rbPDI, or (5) 1000 ng/ml rbPSAT1.

extract_protocol:
RNA extraction and sequencing Following treatment cells were washed with PBS, lysed in 400µL mirVana lysis solution from mirVana RNA extraction kit (Invitrogen, St. Louis, US) and snap frozen. RNA was extracted from the cell pellets using the MirVana RNA extraction kit (Invitrogen, St. Louis, US) as per manufacturer’s protocol. Genomic DNA removal was carried out using the DNA free kit (Thermo Fisher Scientific, Massachusetts, US) as per the manufacturer’s protocol.
RNA libraries were sequenced at the NGS Facility at the University of Leeds where they were prepared and sequenced as per their standard protocols using the Illumina TruSeq Stranded Total kit according to manufacturer’s guidelines. The RNA libraries were sequenced using the Illumina NextSeq 500 machine (Illumina, California, USA) with a single end 75 bp length read.

value: Endometrium

value: Ishikawa cell line

value: Epithelial

value: PDI


title: Human epithelal PDI replicate 1

description:
Library name: Hs Ishi PDI rep 1
R_Ishi_P4HB_1


title: Human epithelal PDI replicate 2

description:
Library name: Hs Ishi PDI rep 2
R_Ishi_P4HB_2


title: Ovary, WT_3


title: 3-CM6

description:
Library name: 3-CM6
3-CM6_FPKM


title: Human epithelal CAPG replicate 1

description:
Library name: Hs Ishi CAPG rep 1
R_Ishi_CAPG_1

value: CAPG


title: Human epithelal vehicle control replicate 2

description:
Library name: Hs Ishi vehicle control rep 2
R_Ishi_VC_2

value: vehicle control


title: Human epithelal vehicle control replicate 1

description:
Library name: Hs Ishi vehicle control rep 1
R_Ishi_VC_1


title: Human epithelal vehicle control replicate 3

description:
Library name: Hs Ishi vehicle control rep 3
R_Ishi_VC_3


title: Human epithelal control replicate 3

description:
Library name: Hs Ishi Control rep 3
R_Ishi_Ctrl_3


title: Human epithelal control replicate 1

description:
Library name: Hs Ishi Control rep 1
R_Ishi_Ctrl_1


title: Human epithelal control replicate 2

description:
Library name: Hs Ishi Control rep 2
R_Ishi_Ctrl_2


title: DMSO_0-1_donor3_R19_P7

city: Ottawa

first: Matthew

last: Meier

state: Ontario

address: 251 Sir Frederick Banting Driveway

department: Health Canada

country: Canada

institute: Government of Canada

description: Library name: s669

data_processing:
Reads were demultiplexed from the BCL files and processed into FASTQ files using  DRAGEN analysis v1.3.0 on the Illumina Basespace Sequence Hub (Illumina, Inc., San Diego, CA, USA). Processing and quality control of the FASTQ files, differential expression analysis, and exploratory statistical analyses were performed using the R-ODAF_Health_Canada pipeline (https://github.com/R-ODAF/R-ODAF_Health_Canada; accessed December 2024), which manages workflows using snakemake v8.0 (Mölder et al., 2021) and relies on scripts in R (v.4.3.2). The preprocessing steps use fastp v0.23.2 for trimming (Chen et al., 2018), STAR v2.7.8a (Dobin et al., 2013) to perform alignment of raw reads to the reference sequence, and the qCount function of the QuasR R package (v1.30.0; Gaidatzis et al., 2015) to extract the feature counts from the aligned reads (BAM files) using features specified in a GTF file. A samples-by-probes count matrix was produced.
Assembly: Probe sequence set provided by biospyder based on Human Whole Transcriptome kit v2.1
Supplementary files format and content: Tab-delimited table containing read counts per TempO-Seq probe

source_name: Mammary

growth_protocol: HMECs from three biological donors were kept at low passage and not allowed to exceed 80% confluency to preserve epithelial subpopulations and maintained in complete media. Cells were cultured in T75 flasks supplemented Mammary Epithelial Cell Growth Medium containing phenol red at 37°C in a humidified atmosphere (5% CO2).

extract_protocol:
Cells were washed with phosphate-buffered saline and lysed in situ using 2x TempO-Seq lysis buffer diluted with an equal amount of PBS for TempO-Seq library building.
Gene expression was measured using the TempO-Seq Human Whole Transcriptome v2.0 and 2.1 kits (BioSpyder Technologies Inc, Carlsbad, California) as per the manufacturer’s instructions

treatment_protocol: For the experiment, cells (passage 7) were seeded at 20,000 cells per well in 96-well plates in supplemented MEGM without phenol red (Lonza Bioscience). After 48 h, the media were removed and replaced with supplement-free MEGM without phenol red containing chemicals of interest at eight concentrations (0.001, 0.01, 0.1, 0.5, 1, 5, 10, 50 µM) and E2 (0.1 and 1 nM). The experiment included at least six plate-matched solvent controls (0.1% DMSO) and four technical replicates from each donor were exposed for 48 h.

value: Mammary

value: Primary

tag: chemical

value: dimethyl sulfoxide

tag: dose

tag: donor

tag: batch


title: DMSO_0-1_donor3_R16_P7

description: Library name: s666

tag: cell type

tag: genotype


title: DMSO_0-1_donor2_R18_P7

description: Library name: s662

tag: tissue

tag: treatment


title: DMSO_0-1_donor3_R18_P7

description: Library name: s668

tag: cell line


title: DMSO_0-1_donor3_R17_P7

description: Library name: s667


title: DMSO_0-1_donor3_R20_P7

description: Library name: s670


title: DMSO_0-1_donor2_R19_P7

description: Library name: s663


title: DMSO_0-1_donor2_R20_P7

description: Library name: s664


title: DMSO_0-1_donor2_R14_P7

description: Library name: s658


title: DMSO_0-1_donor2_R16_P7

description: Library name: s660


title: DMSO_0-1_donor2_R17_P7

description: Library name: s661


title: DMSO_0-1_donor1_R19_P7

description: Library name: s653


title: Human epithelal CAPG replicate 3

description:
Library name: Hs Ishi CAPG rep 3
R_Ishi_CAPG_3


title: DMSO_0-1_donor1_R20_P7

description: Library name: s654


title: DMSO_0-1_donor2_R13_P7

description: Library name: s657


title: Human epithelal CAPG replicate 2

description:
Library name: Hs Ishi CAPG rep 2
R_Ishi_CAPG_2


title: DMSO_0-1_donor3_R15_P7

description: Library name: s665


title: DMSO_0-1_donor1_R17_P7

description: Library name: s651


title: DMSO_0-1_donor1_R16_P7

description: Library name: s650


title: E2_10_donor3_R4_P7

description: Library name: s648

value: chemical exposure


title: DMSO_0-1_donor1_R15_P7

description: Library name: s649


title: DMSO_0-1_donor2_R15_P7

description: Library name: s659


title: DMSO_0-1_donor1_R18_P7

description: Library name: s652


title: E2_1_donor3_R3_P7

description: Library name: s645


title: E2_10_donor1_R3_P7

description: Library name: s642


title: E2_10_donor3_R3_P7

description: Library name: s646


title: E2_1_donor3_R4_P7

description: Library name: s647


title: E2_1_donor2_R3_P7

description: Library name: s643


title: E2_10_donor2_R3_P7

description: Library name: s644


title: E2_1_donor1_R3_P7

description: Library name: s641


title: BPS_5_donor3_R4_P7

description: Library name: s638

value: 4,4'-bisphenol S


title: BPS_50_donor3_R4_P7

description: Library name: s640


title: BPS_0-1_donor3_R4_P7

description: Library name: s635


title: BPS_10_donor3_R4_P7

description: Library name: s639


title: BPS_1_donor3_R4_P7

description: Library name: s637


title: BPC_1_donor3_R4_P7

description: Library name: s629

value: bisphenol C


title: BPS_0-01_donor3_R4_P7

description: Library name: s634


title: BPC_10_donor3_R4_P7

description: Library name: s631


title: BPS_0-5_donor3_R4_P7

description: Library name: s636


title: BPS_0-001_donor3_R4_P7

description: Library name: s633


title: BPC_5_donor3_R4_P7

description: Library name: s630


title: BPS_50_donor3_R3_P7

description: Library name: s624


title: BPC_50_donor3_R4_P7

description: Library name: s632


title: BPS_5_donor3_R3_P7

description: Library name: s622


title: BPC_0-1_donor3_R4_P7

description: Library name: s627


title: BPC_0-5_donor3_R4_P7

description: Library name: s628


title: BPC_0-01_donor3_R4_P7

description: Library name: s626


title: BPS_10_donor3_R3_P7

description: Library name: s623


title: BPS_1_donor3_R3_P7

description: Library name: s621


title: BPC_50_donor3_R3_P7

description: Library name: s616


title: BPC_0-001_donor3_R4_P7

description: Library name: s625


title: BPS_0-001_donor3_R3_P7

description: Library name: s617


title: BPS_0-5_donor3_R3_P7

description: Library name: s620


title: BPC_10_donor3_R3_P7

description: Library name: s615


title: BPS_0-01_donor3_R3_P7

description: Library name: s618


title: BPS_0-1_donor3_R3_P7

description: Library name: s619


title: BPC_0-5_donor3_R3_P7

description: Library name: s612


title: BPC_1_donor3_R3_P7

description: Library name: s613


title: BPC_0-01_donor3_R3_P7

description: Library name: s610


title: BPC_0-1_donor3_R3_P7

description: Library name: s611


title: BPS_1_donor2_R3_P7

description: Library name: s605


title: BPS_50_donor2_R3_P7

description: Library name: s608


title: BPS_0-1_donor2_R3_P7

description: Library name: s603


title: BPC_0-001_donor3_R3_P7

description: Library name: s609


title: BPS_5_donor2_R3_P7

description: Library name: s606


title: BPC_10_donor2_R3_P7

description: Library name: s599


title: BPS_10_donor2_R3_P7

description: Library name: s607


title: BPS_0-01_donor2_R3_P7

description: Library name: s602


title: BPC_5_donor2_R3_P7

description: Library name: s598


title: BPS_0-5_donor2_R3_P7

description: Library name: s604


title: BPS_0-001_donor2_R3_P7

description: Library name: s601


title: BPC_0-5_donor2_R3_P7

description: Library name: s596


title: BPC_1_donor2_R3_P7

description: Library name: s597


title: BPC_50_donor2_R3_P7

description: Library name: s600


title: BPC_0-01_donor2_R3_P7

description: Library name: s594


title: tcx56

city: Shanghai

first: wenjie

last: liang

address: Guoquan North Road

institute: Fudan university

description:
Library name: Sample4
Arabidopsis thaliana seedlings WGBS Raw sequence reads

data_processing:
methylpy version 1.3
Assembly: TAIR10
Supplementary files format and content: bigWig file

organism: Arabidopsis thaliana

source_name: seedlings

extract_protocol:
The total DNA of the genome was extracted by DNeasy plant mini kit (QIAGEN) after the plant material was grown on the petri dish for 14 days
BGI used Bisulfite processing to construct the library

value: seedlings

value: TCX5 and TCX6 knockout


title: sog1-10

description:
Library name: Sample3
Arabidopsis thaliana seedlings WGBS Raw sequence reads

value: SOG1 knockout


title: BPC_5_donor3_R3_P7

description: Library name: s614

value: WT


title: zdp-1ape2-2 ros1-4

description:
Library name: Sample1
Arabidopsis thaliana seedlings WGBS Raw sequence reads

value: ZDP and APE2 and ROS1 knockout


title: zdp-1ape2-2 ros1-4MMS

description:
Library name: Sample2
Arabidopsis thaliana seedlings WGBS Raw sequence reads

value: ZDP and APE2 and ROS knockout


title: BPC_0-001_donor2_R3_P7

description: Library name: s593


title: RNA-seq of CNE-2 CSPG4-Hu repeat-2

city: shanghai

first: wang

last: zhitong

state: shanghai

address: No. 138, Fenyang Road, Xuhui District

department: Otorhinolaryngology

institute: Eye & ENT Hospital

description: Library name: QSZ031-2 R

data_processing:
Raw FASTQ reads were evaluated using FastQC for base quality, GC distribution and adapter contamination.
Assembly: Human reference genome: GRCh38 (hg38)
Supplementary files format and content: Normalized expression matrices are provided in tab-delimited .txt format.

source_name: Nasopharynx

extract_protocol:
Total RNA was extracted using TRIzol reagent following manufacturer instructions. RNA integrity and concentration were measured using Bioanalyzer or TapeStation. Samples with RIN ≥ 7 were used for library preparation.
RNA-seq libraries were generated from poly(A)-selected or rRNA-depleted total RNA using a stranded library construction kit according to manufacturer guidelines. Libraries were barcoded, quantified, pooled, and sequenced on an Illumina HiSeq 2500 platform (paired-end, 150 bp).

value: Nasopharynx

value: Nasopharyngeal carcinoma epithelial cells


title: RNA-seq of CNE-2 CSPG4-Hu repeat-3

description: Library name: QSZ031-3 R


title: BPS_50_donor1_R3_P7

description: Library name: s592

value: Epithelial


title: RNA-seq of CNE-2 CSPG4-Hu repeat-1

description: Library name: QSZ031-1 R


title: RNA-seq of CNE-2  CSPG4-WT repeat-3

description: Library name: CJ017-3 R


title: BPS_10_donor1_R3_P7

description: Library name: s591


title: RNA-seq of CNE-2 CSPG4-WT repeat-2

description: Library name: CJ017-2 R


title: RNA-seq of CNE-2 CSPG4-WT repeat-1

description: Library name: CJ017-1 R


title: BPS_1_donor1_R3_P7

description: Library name: s589


title: BPC_0-1_donor2_R3_P7

description: Library name: s595


title: tcx56MMS

description:
Library name: Sample5
Arabidopsis thaliana seedlings WGBS Raw sequence reads


title: BPS_0-1_donor1_R3_P7

description: Library name: s587


title: MGHU3 erdafitinib

city: Gif-sur-Yvette

first: Lilia

last: Estrada Virrueta

address: 1, Avenue de la Terrasse

country: France

description:
Library name: MGHU3_ERDA
10x Genomics

data_processing:
The sequencing output was processed using Cell Ranger from 10x Genomics
Assembly: hg38
Supplementary files format and content: filtered feature and barcodes matrix exported from CellRanger

source_name: bladder cancer

growth_protocol: Cells were cultured in DMEM supplemented with 10% fetal bovine serum at 37°C under a 5% CO2 atmosphere.

extract_protocol:
3' Reagent Kit protocol (10X Genomics)
10,000 cells were loaded per sample using the single-cell 3' Reagent Kit protocol (10X Genomics), and the cells were sequenced at a mean depth of 50,000 using a NovaSeq 6000

treatment_protocol: MGH-U3 and RT112 cells treated with DMSO or 100 nM erdafitinib for 38 h.  The PDX was treated with BGJ398, a pan‐FGFR inhibitor, for 4 days

value: bladder cancer

value: tumor derived bladder cancer cells

value: erdafitnib


title: BPS_0-01_donor1_R3_P7

description: Library name: s586

value: Mammary

value: Primary


title: BPC_50_donor1_R3_P7

description: Library name: s584

value: chemical exposure


title: CITE_PostBlip_3

city: London

first: Laura

middle: E

last: McCoy

address: Pears Building, Rowland Hill Street

institute: University College London

description:
Library name: LM088_9_CITE
LM088_9_filtered_feature_bc_matrix.h5

library_source: other

data_processing:
Droplet libraries were processed using Cell Ranger v7.0.1; reads were aligned to the GRCh38 human genome (version refdata-gex-GRCh38-2020-A, 10X Genomics). CITE-seq UMIs were counted for GEX and ADT libraries simultaneously to generate feature-X droplet UMI count matrices.
Single-cell V(D)J data from the 5′ Chromium 10x kit were initially processed with Cell Ranger multi pipeline (v7.0.1).
Assembly: GRCh38-2020-A
Supplementary files format and content: CellRanger output files (GEX & ADT): filtered_feature_bc_matrix.h5, feature_reference.csv
Supplementary files format and content: CellRanger output files (VDJ): all_contig.fasta, all_contig_annotations.csv
Library strategy: CITE-seq

molecule: protein

source_name: PBMCs / B cells

extract_protocol:
Frozen PBMCs from an elite HIV controller were thawed and MACS-selected for B cells. After isolation, B cells were mixed with unselected PBMC at a 3:1 ratio. This mixure was then stained with CITE-Seq antibodies before undegoing 10X Genomics encapsulation (three lanes of 20k cells loaded on 10X chip).
cDNA generation and library prep done using 10x 5′ single cell capture (Chromium Next GEM Single Cell V(D)J Reagent Kit v2 with Feature Barcoding technology for cell Surface Protein-Rev F protocol).

value: PBMCs / B cells

value: Post-viral blip


title: CITE_PostBlip_2

description:
Library name: LM088_8_CITE
LM088_8_filtered_feature_bc_matrix.h5


title: CITE_Blip_3

description:
Library name: LM088_6_CITE
LM088_6_filtered_feature_bc_matrix.h5

value: Viral blip


title: BPC_10_donor1_R3_P7

description: Library name: s583

value: bisphenol C


title: BPS_0-5_donor1_R3_P7

description: Library name: s588

value: 4,4'-bisphenol S


title: CITE_PostBlip_1

description:
Library name: LM088_7_CITE
LM088_7_filtered_feature_bc_matrix.h5


title: BPC_1_donor1_R3_P7

description: Library name: s581

value: WT


title: BPS_0-001_donor1_R3_P7

description: Library name: s585


title: MGHU3 ctrl

description:
Library name: MGHU3_DMSO
10x Genomics

value: DMSO


title: BPC_0-5_donor1_R3_P7

description: Library name: s580


title: BPC_5_donor1_R3_P7

description: Library name: s582


title: CITE_Blip_2

description:
Library name: LM088_5_CITE
LM088_5_filtered_feature_bc_matrix.h5


title: CITE_Blip_1

description:
Library name: LM088_4_CITE
LM088_4_filtered_feature_bc_matrix.h5


title: BPC_0-1_donor1_R3_P7

description: Library name: s579


title: BPS_5_donor1_R3_P7

description: Library name: s590


title: BPC_0-01_donor1_R3_P7

description: Library name: s578


title: CITE_PreBlip_1

description:
Library name: LM088_1_CITE
LM088_1_filtered_feature_bc_matrix.h5

value: Pre-viral blip


title: VDJ_PostBlip_2

description: Library name: LM088_8_VDJ

data_processing:
Droplet libraries were processed using Cell Ranger v7.0.1; reads were aligned to the GRCh38 human genome (version refdata-gex-GRCh38-2020-A, 10X Genomics). CITE-seq UMIs were counted for GEX and ADT libraries simultaneously to generate feature-X droplet UMI count matrices.
Single-cell V(D)J data from the 5′ Chromium 10x kit were initially processed with Cell Ranger multi pipeline (v7.0.1).
Assembly: GRCh38-2020-A
Supplementary files format and content: CellRanger output files (GEX & ADT): filtered_feature_bc_matrix.h5, feature_reference.csv
Supplementary files format and content: CellRanger output files (VDJ): all_contig.fasta, all_contig_annotations.csv
Library strategy: BCR-Seq


title: CITE_PreBlip_2

description:
Library name: LM088_2_CITE
LM088_2_filtered_feature_bc_matrix.h5


title: DMSO_0-1_donor3_R14_P6

description: Library name: s576

value: vehicle control

value: dimethyl sulfoxide


title: VDJ_Blip_3

description: Library name: LM088_6_VDJ


title: VDJ_PostBlip_1

description: Library name: LM088_7_VDJ


title: DMSO_0-1_donor3_R12_P6

description: Library name: s574

value: Epithelial


title: DMSO_0-1_donor3_R11_P6

description: Library name: s573


title: VDJ_Blip_1

description: Library name: LM088_4_VDJ


title: VDJ_Blip_2

description: Library name: LM088_5_VDJ


title: CITE_PreBlip_3

description:
Library name: LM088_3_CITE
LM088_3_filtered_feature_bc_matrix.h5


title: DMSO_0-1_donor3_R9_P6

description: Library name: s571


title: VDJ_PreBlip_3

description: Library name: LM088_3_VDJ


title: DMSO_0-1_donor3_R8_P6

description: Library name: s570


title: DMSO_0-1_donor3_R7_P6

description: Library name: s569


title: VDJ_PreBlip_2

description: Library name: LM088_2_VDJ


title: BPC_0-001_donor1_R3_P7

description: Library name: s577


title: DMSO_0-1_donor2_R10_P6

description: Library name: s564


title: DMSO_0-1_donor2_R12_P6

description: Library name: s566


title: VDJ_PostBlip_3

description: Library name: LM088_9_VDJ


title: GEX_PostBlip_1

description: Library name: LM088_7_GEX

data_processing:
Droplet libraries were processed using Cell Ranger v7.0.1; reads were aligned to the GRCh38 human genome (version refdata-gex-GRCh38-2020-A, 10X Genomics). CITE-seq UMIs were counted for GEX and ADT libraries simultaneously to generate feature-X droplet UMI count matrices.
Single-cell V(D)J data from the 5′ Chromium 10x kit were initially processed with Cell Ranger multi pipeline (v7.0.1).
Assembly: GRCh38-2020-A
Supplementary files format and content: CellRanger output files (GEX & ADT): filtered_feature_bc_matrix.h5, feature_reference.csv
Supplementary files format and content: CellRanger output files (VDJ): all_contig.fasta, all_contig_annotations.csv


title: GEX_Blip_3

description: Library name: LM088_6_GEX


title: DMSO_0-1_donor3_R13_P6

description: Library name: s575


title: DMSO_0-1_donor2_R11_P6

description: Library name: s565


title: GEX_PostBlip_3

description: Library name: LM088_9_GEX


title: GEX_PostBlip_2

description: Library name: LM088_8_GEX


title: VDJ_PreBlip_1

description: Library name: LM088_1_VDJ


title: DMSO_0-1_donor2_R9_P6

description: Library name: s563


title: DMSO_0-1_donor2_R7_P6

description: Library name: s561


title: GEX_Blip_2

description: Library name: LM088_5_GEX


title: DMSO_0-1_donor1_R14_P6

description: Library name: s558


title: DMSO_0-1_donor2_R8_P6

description: Library name: s562


title: GEX_PreBlip_3

description: Library name: LM088_3_GEX


title: DMSO_0-1_donor3_R10_P6

description: Library name: s572


title: GEX_PreBlip_2

description: Library name: LM088_2_GEX


title: DMSO_0-1_donor1_R13_P6

description: Library name: s557


title: GEX_PreBlip_1

description: Library name: LM088_1_GEX


title: DMSO_0-1_donor1_R12_P6

description: Library name: s556


title: GEX_Blip_1

description: Library name: LM088_4_GEX


title: HA_12

first: Jiren

last: Yan

state: Shanghai

address: 600 Yishan Road, Xuhui District, Shanghai

institute: Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

description: Library name: HUVEC_L4

data_processing:
Raw reads were filtered using fastp for quality control and adapter removal. Clean reads were aligned to the human reference genome (GRCh38) using STAR.
Differential gene expression analysis was performed with DESeq2, applying a threshold of fold change >2 and adjusted p < 0.05.
Heatmaps were generated to visualize global transcriptomic shifts.
Gene set enrichment analysis (GSEA) was conducted using the MSigDB database to identify significantly enriched pathways.
Assembly: GRCh38
Supplementary files format and content: csv files include FPKM values for each Sample

source_name: HUVEC

extract_protocol:
HUVECs were cultured with HA/Mg scaffolds or TABS for 3 days under standard conditions, with four replicates per group. Total RNA was extracted using TRIzol, and RNA integrity was assessed with an Agilent 2100 Bioanalyzer (RIN > 7).
Libraries were prepared using the NEBNext Ultra RNA Library Prep Kit and sequenced on an Illumina NovaSeq platform to generate 150-bp paired-end reads.

value: HUVEC


title: HA_11

description: Library name: HUVEC_L3


title: DMSO_0-1_donor1_R10_P6

description: Library name: s554


title: HA_10

description: Library name: HUVEC_L2


title: DMSO_0-1_donor1_R9_P6

description: Library name: s553


title: E2_10_donor2_R4_P6

description: Library name: s552


title: HA_9

description: Library name: HUVEC_L1


title: E2_1_donor3_R2_P6

description: Library name: s549


title: E2_10_donor3_R2_P6

description: Library name: s550


title: TABS_12

description: Library name: HUVEC_H4


title: TABS_11

description: Library name: HUVEC_H3


title: TABS_10

description: Library name: HUVEC_H2


title: E2_1_donor2_R2_P6

description: Library name: s547


title: DMSO_0-1_donor1_R11_P6

description: Library name: s555


title: SC06_sFGR_Smaller

first: Yan

last: Bi

address: 910 Hengshan Road, Xuhui District

institute: International Peace Maternity and Child Health Hospital, Shanghai Jiao Tong University

description:
Library name: SC06-F2
10x Genomics

data_processing:
scRNA-seq data analysis was performed by NovelBio Co.,Ltd. with NovelBrain Cloud Analysis Platform.
We applied fastp (v0.21.0) with default parameter filtering the adaptor sequence and removed the low-quality reads to achieve the clean data.
Cellranger (v7.1.0) was utilized to calculate the feature-barcode matrices. Cells contained over 500 expressed genes and mitochondria UMI rate below 30%  passed the cell quality filtering and mitochondria genes were removed in the expression table. Seurat package (version:4.1.0, https://satijalab.org/seurat/) was used for cell normalization and regression based on the expression table according to the UMI counts of each sample and percent of mitochondria rate to obtain the scaled data. The Seurat integration (CCA)function from R package scran (v1.6.2) was used to apply mutual nearest neighbor method to correct for batch effect among samples. PCA was constructed based on the scaled data with top 2000 high variable genes and top 10 principals were used for tSNE construction and UMAP construction. Utilizing graph-based cluster method, we acquired the unsupervised cell cluster result based the PCA top 10 principal and we calculated the marker genes by FindAllMarkers function with wilcox rank sum test algorithm under following criteria:1. Log2FC > 0.25; 2. p value<0.05; 3. min.pct>0.1
Assembly: GRCh38(Ensembl104)
Supplementary files format and content: MTX file and TSV file contain counts for each barcodes and genes

source_name: Placenta

growth_protocol: Not applicable (primary tissue sample).

extract_protocol:
Dissociated cells were collected at 20 min intervals to maximize yield and viability. Single-cell suspensions were sequentially filtered through a 40 μm nylon strainer, treated with 1× Red Blood Cell Lysis Solution (Thermo Fisher Scientific, Cat. no. 00-4333-57), and washed with DPBS containing 2% FBS. Single-cell suspensions were processed using the Chromium Single Cell 3′ v3 platform (10x Genomics) following the manufacturer's protocols (CG000204 Rev B). Briefly, individual cells were partitioned into Gel Bead-In-Emulsions (GEMs) containing barcoded oligonucleotides with unique molecular identifiers (UMIs). After cell lysis and reverse transcription, cDNA molecules were tagged with cell-specific barcodes and UMIs. Libraries were generated through second-strand synthesis, adaptor ligation, and amplification, enriching for 3′ transcript ends. Quality and concentration of libraries were assessed using the High Sensitivity DNA Kit (Agilent Bioanalyzer 2100) and Qubit High Sensitivity DNA Assay Kit (Thermo Fisher Scientific). Libraries were sequenced on an Illumina NovaSeq 6000 platform using paired-end 150 bp reads.
Single-cell libraries were prepared using the Chromium Single Cell 3′ v3 platform (10x Genomics) according to the manufacturer's protocol

treatment_protocol: No treatment was applied.

value: Placenta

value: Human Fresh Placental Villie


title: TABS_9

description: Library name: HUVEC_H1


title: SC06_sFGR_Larger

description:
Library name: SC06-F1
10x Genomics


title: E2_10_donor1_R2_P6

description: Library name: s546

value: Mammary


title: E2_1_donor1_R2_P6

description: Library name: s545

value: Primary


title: E2_10_donor2_R2_P6

description: Library name: s548

value: chemical exposure


title: SC03_sFGR_Larger

description:
Library name: SC03-F1
10x Genomics


title: BPS_5_donor2_R4_P6

description: Library name: s542


title: BPS_50_donor2_R4_P6

description: Library name: s544


title: SC01_sFGR_Smaller

description:
Library name: SC01-F2
10x Genomics


title: SC03_sFGR_Smaller

description:
Library name: SC03-F2
10x Genomics


title: BPS_1_donor2_R4_P6

description: Library name: s541


title: Human3_TAID_rep3

city: Hefei

first: Caoling

last: Xu

state: Anhui

address: 96 Jinzhai Road

department: Department of Life Sciences and Medicine

institute: University of Science and Technology of China

description: Library name: Human3_TAID_rep3

data_processing:
Trim_galore removes adapters and low-quality reads
Mapping to the mouse genome(mm10) or human genome(hg38)
Standardized to obtain the bw file
Peak calling by MACS
Assembly: mm10 or hg38
Supplementary files format and content: bw files of tag density

source_name: Testis

extract_protocol:
For each sample, 10 µL of Concanavalin A (ConA) beads were washed with 100 µL Wash Buffer, resuspended in 10 µL Binding Buffer, and incubated with 200,000–300,000 cells for 10 min at room temperature (RT). After magnetic separation, the primary antibody diluted in Antibody Buffer was added and incubated overnight at 4 °C. The beads were then washed, incubated with secondary antibody for 1 hours at RT, and washed three times with Dig-Wash Buffer. Subsequently, pA–Tn5 Buffer was added, and samples were incubated for 1 hour at RT, followed by three washes with Dig-400 Buffer. Tagmentation was performed with 40 µL of Tagmentation Buffer at 37 °C for 1 hour. The reaction was stopped with EDTA, SDS, and Proteinase K, followed by incubation at 55 °C for 1 hour and 75 °C for 15 min. DNA was purified using Speed Beads, washed twice with 80% ethanol, and eluted in pre-heated dd-water containing 0.1% Tween-20.
A 10 µL aliquot of eluted DNA was extended with 15 µL 2× Equinox PCR mix, 0.375 µL Bst 3.0 DNA polymerase (8 U/µL), and 5 µL nuclease-free water, incubated at 68 °C for 30 min to fill adapter gaps, followed by 95 °C for 5 min to inactivate the enzyme. Index 5 and Index 7 primers were then added, and PCR amplification was performed as described (Supplementary Table 11.3). The final library was purified using DNA Clean beads (1.2× sample volume) for downstream applications.

value: Testis

value: Germ cells

value: Spermatocyte

value: Normal


title: BPS_10_donor2_R4_P6

description: Library name: s543

value: 4,4'-bisphenol S


title: Human3_TAID_rep2

description: Library name: Human3_TAID_rep2


title: E2_1_donor2_R4_P6

description: Library name: s551

value: WT


title: BPS_0-5_donor2_R4_P6

description: Library name: s540


title: BPS_0-1_donor2_R4_P6

description: Library name: s539


title: Human3_TAID_rep1

description: Library name: Human3_TAID_rep1


title: SC01_sFGR_Larger

description:
Library name: SC01-F1
10x Genomics


title: Human2_TAID_rep3

description: Library name: Human2_TAID_rep3


title: BPS_0-01_donor2_R4_P6

description: Library name: s538


title: Human2_TAID_rep2

description: Library name: Human2_TAID_rep2


title: BPC_50_donor2_R4_P6

description: Library name: s536

value: bisphenol C


title: BPS_0-001_donor2_R4_P6

description: Library name: s537


title: Human1_TAID_rep1

description: Library name: Human1_TAID_rep1


title: BPC_0-5_donor2_R4_P6

description: Library name: s532


title: Human1_TAID_rep2

description: Library name: Human1_TAID_rep2


title: Human2_TAID_rep1

description: Library name: Human2_TAID_rep1


title: BPC_10_donor2_R4_P6

description: Library name: s535


title: Human3_H3K4me3

description: Library name: Human3_H3K4me3_CUTTag

data_processing:
Trim_galore removes adapters and low-quality reads
Mapping to the mouse genome(mm10) or human genome(hg38)
Standardized to obtain the bw file
Peak calling by MACS2
Assembly: mm10 or hg38
Supplementary files format and content: bw files of tag density
Library strategy: CUT&Tag

extract_protocol:
For each sample, 10 µL of Concanavalin A (ConA) beads were washed with 100 µL Wash Buffer, resuspended in 10 µL Binding Buffer, and incubated with 200,000–300,000 cells for 10 min at room temperature (RT). After magnetic separation, the primary antibody diluted in Antibody Buffer was added and incubated overnight at 4 °C. The beads were then washed, incubated with secondary antibody for 1 hours at RT, and washed three times with Dig-Wash Buffer. Subsequently, pA–Tn5 Buffer was added, and samples were incubated for 1 hour at RT, followed by three washes with Dig-400 Buffer. Tagmentation was performed with 40 µL of Tagmentation Buffer at 37 °C for 1 hour. The reaction was stopped with EDTA, SDS, and Proteinase K, followed by incubation at 55 °C for 1 hour and 75 °C for 15 min. DNA was purified using Speed Beads, washed twice with 80% ethanol, and eluted in pre-heated dd-water containing 0.1% Tween-20.
Index 5 and Index 7 primers were then added, and PCR amplification was performed as described (Supplementary Table 11.3). The final library was purified using DNA Clean beads (1.2× sample volume) for downstream applications.

value: Extracting the cell nuclei from the frozen testicular tissue


title: BPC_0-01_donor2_R4_P6

description: Library name: s530


title: BPC_1_donor2_R4_P6

description: Library name: s533


title: BPC_5_donor2_R4_P6

description: Library name: s534


title: BPS_50_donor3_R2_P6

description: Library name: s528


title: Human1_noAb

description: Library name: Human1_noAb


title: BPS_10_donor3_R2_P6

description: Library name: s527


title: BPC_0-001_donor2_R4_P6

description: Library name: s529


title: Human2_H3K27ac

description: Library name: Human2_H3K27ac_CUTTag


title: Human2_H3K9me3

description: Library name: Human2_H3K9me3_CUTTag


title: BPS_5_donor3_R2_P6

description: Library name: s526


title: Human1_H3K9me3

description: Library name: Human1_H3K9me3_CUTTag


title: BPS_1_donor3_R2_P6

description: Library name: s525


title: Human3_H3K9me3

description: Library name: Human3_H3K9me3_CUTTag


title: Human2_H3K4me3

description: Library name: Human2_H3K4me3_CUTTag


title: HCT116-GFP-RPB1, NVP2, Rep3 (EnChAMP-seq)

city: Ithaca

first: Abdullah

last: Ozer

state: NY

address: 526 Campus Road

department: Molecular Biology and Genetics

institute: Cornell University

description: Library name: HCT116-GFP-RPB1_NVP2_Rep3

data_processing:
Adapter sequences were removed using cutadapt (ver3.7) and mapped to the human hg38 genome using bowtie2 –local (ver2.5.1). The sam file was converted to an indexed bam file with samtools view, sort, and index (ver1.7). Finally, the indexed bam file was converted to a RPKM normalized bigwig file using DeepTools bamCoverage (ver3.5.2).
Assembly: GRCh38/hg38
Supplementary files format and content: RPKM normalized bigwig files with 5bp bins.

growth_protocol: Parental and engineered HCT116 cells were cultured in McCoy’s 5A media (Thermo Fisher Scientific, Cat# 16600-108) supplemented with 10% Fetal Bovine Serum (VWR, Cat# MP1300500H) and 100 U/ml Pen-Strep (Thermo Fisher Scientific, Cat# 15140122) in a humidified cell culture incubator at 37 °C with 5% CO2 atmosphere.

extract_protocol:
Cells were harvested at ~90% confluency (~20 million cells/15cm plate). Cells were washed with DPBS, scraped, and collected by centrifugation at 800g for 5 minutes at 4°C. Supernatants were discarded. Nuclei Isolation: Cell pellets were resuspended in 1 mL of ice-cold Hi-C Buffer A (10 mM HEPES [pH 7.5], 10 mM KCl, 1.5 mM MgCl2, 1 mM CaCl2, 0.1% Digitonin (Millipore Sigma, Cat# 300410), with 1X Phosphatase (Sigma Aldrich, Cat# P2850) and 1X Protease inhibitor cocktails (Thermo Fisher Scientific, Cat# A32965), and 1 mM PMSF (Cell Signalling, Cat# 8553S)) and incubated on ice for 30 minutes to allow cell swelling. After incubation, aliquots were taken for western blot analysis. The remaining lysates were centrifuged at 1000g for 15 minutes at 4°C. Nuclei pellets were washed with 1 mL of cold Hi-C Wash Buffer B (Hi-C Buffer A supplemented with 250 mM sucrose), centrifuged as above, and supernatants containing cytoplasmic fraction was discarded. Chromatin Isolation: Nuclei pellets were resuspended in 500 μL of 1.5% Digitonin Chromatin Isolation Buffer A (10 mM HEPES [pH 7.5], 20 mM KCl, 150 mM NaCl, 1.5 mM MgCl2, 1 mM CaCl2, 15% Glycerol, 1.5% Digitonin, with phosphatase and protease inhibitors, and PMSF) and incubated on ice for 30 minutes. Samples were centrifuged at 1000g for 30 minutes at 4°C, and supernatants containing nucleoplasmic fraction were discarded. The pellets were resuspended in 500 μL of fresh Buffer A, and 3 μL of 250 U/μL Benzonase® Nuclease (Millipore Sigma, Cat# E1014) was added for chromatin shearing. The samples were rotated at 4°C for 1 hour, followed by centrifugation at 1000g for 30 minutes at 4°C. Soluble chromatin proteins were collected as supernatants, while the insoluble chromatin fractions were discarded. Affinity purification with anti-GFP nanobody: During Benzonase digestion of chromatin, per sample 10 μL of GFP-Trap® M-270 magnetic particles (ChromoTek, Cat#gtd) were washed three times with Chromatin Isolation Buffer B (10 mM HEPES [pH 7.5], 20 mM KCl, 150 mM NaCl, 1.5 mM MgCl2, 1 mM CaCl2, 15% Glycerol) and resuspend in 50 μL of Buffer B. Soluble chromatin proteins (~500 μL) were incubated with 50 μL of pre-washed magnetic particles per sample overnight at 4°C. Beads were washed sequentially with Chromatin Isolation Buffer B: a 5-minute rotation wash, followed by two stationary washes, and a final transfer to a clean tube. Beads were eluted with 200 μL of 100 mM HEPES (pH 7.5) containing 1% SDS at 65°C for 15 minutes. The supernatants (eluted chromatin) were collected for downstream analysis.
Eluates  of ~5M cell equivalent from EnChAMP experiments were brought to 300ul with 1X TE buffer (10 mM Tris-Cl pH 8.0, 0.1 mM EDTA), extracted once with equal volume Phenol:Chloroform mix pH 8.0 (Thermo Fisher Scientific, Cat# 17909), extracted with equal volume Chloroform, EtOH precipitated (1/10th volume 3M NaAcetate pH 5.2, 2 μl GlycoBlue  co-precipitant (Thermo Fisher Scientific, Cat# AM9516), and 3 volumes 100% EtOH, washed with 70% EtOH, and air dried pellet was resuspended in MilliQ-H2O. DNA amount was quantitated by Qubit dsDNA HS Assay (Thermo Fisher Scientific, Cat# Q32851). 2-40 ng DNA was end-repaired in the presence of a 250 μM dNTP mix (each), 1x T4 DNA Ligase Buffer (NEB), 6 units T4 DNA Polymerase (NEB, Cat# M0203L), 20 units T4 PNK (NEB, Cat# M0201L), and 2.5 units Klenow Polymerase (NEB, Cat# M0210L) at RT for 30 min on a Thermomixer at 600 rpm. End-repaired DNA was purified using MinElute Reaction Clean-up Kit (Qiagen, Cat# 28204) and A-tailed in the presence of 1x Buffer #2 (NEB), 200 uM dATP, and 10 units Klenow exo- polymerase (NEB, Cat# M0212L) at 37C for 30 min on a Thermomixer at 600 rpm. A-tailed DNA was purified using MinElute Reaction Clean-up Kit (Qiagen, Cat# 28204) and ligated to Illumina TRUseq adapters in the presence of 12-120 nM TRUseq Index adapter, 1x T4 DNA Ligase buffer (NEB), 1,200 units T4 DNA Ligase (NEB, Cat# M0202L) at 18 ºC O/N. TRUseq adapter ligated DNA was purified using MinElute Reaction Clean-up Kit (Qiagen) and subjected to a pilot PCR using P5 and P7 oligos to determine appropriate number of PCR cycles to generate a library. Final PCR reactions were carried 11-15 cycles and purified using MinElute PCR Clean-up Kit (Qiagen, Cat# 28004). After quality check with BioAnalyzer analysis, if deemed necessary the libraries were gel purified (150-350 bp region) using 8% native PAGE to get rid of the adapter dimer (~130 bp). Equal amounts of 8-12 samples were pooled and sequenced either by 2x150nt on an Illumina NovaSeq 6000 instrument (NovaGene) or by 2x80nt on an Element Biosciences AVITI instrument (EGC Core Facility).

treatment_protocol: 500 nM of NVP-2 (MedchemExpress, Cat# HY-12214A) for 1 hours, 1 µM of Triptolide (Millipore Sigma, Cat# T3652) for 20 minutes, or left untreated.

value: 500nM NVP-2 for 1h


title: Human1_H3K4me3

description: Library name: Human1_H3K4me3_CUTTag


title: HCT116-NELFA-GFP, NVP2, Rep1 (EnChAMP-seq)

description: Library name: HCT116-NELFA-GFP_NVP2_Rep1

value: NELFA-GFP


title: BPS_0-5_donor3_R2_P6

description: Library name: s524

value: Epithelial


title: BPS_0-1_donor3_R2_P6

description: Library name: s523


title: BPS_0-01_donor3_R2_P6

description: Library name: s522


title: BPC_0-1_donor2_R4_P6

description: Library name: s531


title: BPC_50_donor3_R2_P6

description: Library name: s520


title: HCT116-GFP-RPB1, NoNVP2, Rep3 (EnChAMP-seq)

description: Library name: HCT116-GFP-RPB1_NoNVP2_Rep3


title: BPS_0-001_donor3_R2_P6

description: Library name: s521


title: HCT116-NELFA-GFP, NoNVP2, Rep1 (EnChAMP-seq)

description: Library name: HCT116-NELFA-GFP_NoNVP2_Rep1


title: HCT116-GFP-RPB1, NVP2, Rep2 (EnChAMP-seq)

description: Library name: HCT116-GFP-RPB1_NVP2_Rep2


title: HCT116-GFP, NoNVP2, Rep3 (EnChAMP-seq)

description: Library name: HCT116-GFP_NoNVP2_Rep3

source_name: HCT116-GFP, NoNVP2, Rep3 (EnChAMP-seq)

value: HCT116-GFP, NoNVP2, Rep3 (EnChAMP-seq)

value: GFP (control)

value: GFP


title: BPC_0-5_donor3_R2_P6

description: Library name: s516

value: Mammary


title: BPC_10_donor3_R2_P6

description: Library name: s519

value: Primary


title: HCT116-GFP-RPB1, NoNVP2, Rep2 (EnChAMP-seq)

description: Library name: HCT116-GFP-RPB1_NoNVP2_Rep2


title: BPC_5_donor3_R2_P6

description: Library name: s518

value: chemical exposure


title: BPC_0-1_donor3_R2_P6

description: Library name: s515


title: HCT116-GFP, NVP2, Rep1 (EnChAMP-seq)

description: Library name: HCT116-GFP_NVP2_Rep1

source_name: HCT116-GFP, NVP2, Rep1 (EnChAMP-seq)

value: HCT116-GFP, NVP2, Rep1 (EnChAMP-seq)


title: BPC_0-001_donor3_R2_P6

description: Library name: s513


title: BPC_0-01_donor3_R2_P6

description: Library name: s514


title: HCT116-GFP-RPB1, NVP2, Rep1 (EnChAMP-seq)

description: Library name: HCT116-GFP-RPB1_NVP2_Rep1


title: HCT116-GFP-RPB1, NoNVP2, Rep1 (EnChAMP-seq)

description: Library name: HCT116-GFP-RPB1_NoNVP2_Rep1


title: HCT116-GFP, NVP2, Rep3 (EnChAMP-seq)

description: Library name: HCT116-GFP_NVP2_Rep3

source_name: HCT116-GFP, NVP2, Rep3 (EnChAMP-seq)

value: HCT116-GFP, NVP2, Rep3 (EnChAMP-seq)


title: BPS_50_donor2_R2_P6

description: Library name: s512


title: IDH1R132H immortalized human astrocytes,shRNA KMT2A, replicate 3

city: Heidelberg

first: Sevin

last: Turcan

address: Im Neuenheimer Feld 420

country: Germany

institute: University Hospital Heidelberg

description: Library name: KMT2A KD 3

data_processing:
BAM files were produced with the following configurations: RNA paired bulk,  Reference genome: 1KGRef_PhiX, Alignment program: STAR Version 2.5.3a, Merging/duplication marking program: Sambamba Version 0.6.5
Assembly: 1KGRef_PhiX
Supplementary files format and content: KMT2Akd_normCPM_tables2.txt

source_name: astrocytes

extract_protocol:
For RNA-Seq, samples were seeded in triplicates and harvested 72 hours. RNA was isolated with the Rneasy Mini Kit (Qiagen).
TruSeq Stranded, DT-ILMN TruSeq DNA/RNA UDI

value: astrocytes

value: immortalized IDH1R132H astrocytes

value: astrocyte


title: HCT116-GFP, NoNVP2, Rep1 (EnChAMP-seq)

description: Library name: HCT116-GFP_NoNVP2_Rep1

source_name: HCT116-GFP, NoNVP2, Rep1 (EnChAMP-seq)

value: HCT116-GFP, NoNVP2, Rep1 (EnChAMP-seq)


title: BPS_5_donor2_R2_P6

description: Library name: s510

value: WT

value: 4,4'-bisphenol S


title: IDH1R132H immortalized human astrocytes, shRNA KMT2A, replicate 1

description: Library name: KMT2A KD 1


title: BPS_0-5_donor2_R2_P6

description: Library name: s508


title: BPS_10_donor2_R2_P6

description: Library name: s511


title: HCT116-GFP, NoNVP2, Rep2 (EnChAMP-seq)

description: Library name: HCT116-GFP_NoNVP2_Rep2

source_name: HCT116-GFP, NoNVP2, Rep2 (EnChAMP-seq)

value: HCT116-GFP, NoNVP2, Rep2 (EnChAMP-seq)


title: IDH1R132H immortalized human astrocytes, scrambled control, replicate 2

description: Library name: SCR control 2


title: BPS_0-1_donor2_R2_P6

description: Library name: s507


title: BPS_1_donor2_R2_P6

description: Library name: s509


title: IDH1R132H immortalized human astrocytes, shRNA KMT2A, replicate 2

description: Library name: KMT2A KD 2


title: BPS_0-01_donor2_R2_P6

description: Library name: s506


title: HCT116-GFP, NVP2, Rep2 (EnChAMP-seq)

description: Library name: HCT116-GFP_NVP2_Rep2

source_name: HCT116-GFP, NVP2, Rep2 (EnChAMP-seq)

value: HCT116-GFP, NVP2, Rep2 (EnChAMP-seq)

value: 500nM NVP-2 for 1h


title: IDH1R132H immortalized human astrocytes, scrambled control, replicate 1

description: Library name: SCR control 1


title: IDH1R132H immortalized human astrocytes, treatment, H3K4me3, replicate 3

description:
Library name: CT002-24
DEGup_promoters_K4me3_RPKM.txt

data_processing:
After alignment with bowtie2, peaks analysis was performed using SEACR, deeptools and bedtools.
Assembly: hg38
Supplementary files format and content: RPKM.txt files
Library strategy: CUT&Tag

extract_protocol:
CUT&Tag was performed with 60,000 cells per sample in triplicates. After bead-binding, cells were permeabilized and incubated with primary antibodies directed at H3K4me1 (Active Motif), H3K4me3 (Active Motif), H3K27me3 (Cell signaling) and H3K27ac (Active Motif), followed by secondary antibody incubation (guinea pig anti-rabbit, Antibodies online). For chromatin cleavage and adapter ligation, pAG-Tn-5 (Epicypher) was used.
Library preparation was conducted by PCR with barcoded primers. Samples underwent quality control utilizing D1000 Screen Tape on a Tapestation 4200 (Agilent).


title: IDH1R132H immortalized human astrocytes, scrambled control, replicate 3

description: Library name: SCR control 3


title: BPS_0-001_donor2_R2_P6

description: Library name: s505

value: Epithelial


title: IDH1R132H immortalized human astrocytes, treatment, H3K4me3, replicate 1

description:
Library name: CT002-22
DEGup_promoters_K4me3_RPKM.txt


title: BPC_10_donor2_R2_P6

description: Library name: s503

value: bisphenol C


title: BPC_5_donor2_R2_P6

description: Library name: s502


title: IDH1R132H immortalized human astrocytes, control, H3K4me3, replicate 3

description:
Library name: CT002-12
DEGdn_promoters_K4me3_RPKM.txt


title: IDH1R132H immortalized human astrocytes, control, H3K4me3, replicate 2

description:
Library name: CT002-11
DEGup_promoters_K4me3_RPKM.txt


title: BPC_0-5_donor2_R2_P6

description: Library name: s500


title: IDH1R132H immortalized human astrocytes, control, H3K4me3, replicate 1

description:
Library name: CT002-10
DEGdn_promoters_K4me3_RPKM.txt


title: BPC_50_donor2_R2_P6

description: Library name: s504


title: BPC_1_donor3_R2_P6

description: Library name: s517


title: BPC_0-1_donor2_R2_P6

description: Library name: s499