title: RAD21_dep BRD2 CUT&Tag

city: Berkeley

first: Robert

last: Tjian

address: LKS

institute: UC Berkeley/HHMI

library_source: genomic

data_processing:
library strategy: Micro-C
Illumina’s Bcl2tofastq2 v2.17 was used to convert BcL files to fastq files and to demultiplex the samples
ATAC-seq, CUT&Tag pair-end reads were first adapter removed by Cutadapt and mapped to mm10 genome build using Bowtie2 with the following parameters: --no-discordant --no-mixed --phred33 -X2000 –threads32. For Micro-C, Bowtie 2.3.0 with ‘very-sensitive-local’ mode was used.
Reads mapped to mitochondria/uncharacterized chromosomes (chrM/chrUn/random) and PCR duplicates were removed by samtools. For Micro-C, pairs with multiple hits, low MAPQ, singleton, dangling end, self-circle,PCR duplicates and contacts shorter than 200bp (unligated mono-nucleosomes)  were discarded
ATAC-seq peaks were called using the MACS2 callpeak function using the –f BAMPE parameter. CUT&Tag peaks were called by SEACR.
For Micro-C, contact matrices were then normalized by using iterative correction (IC) in COOL files (Imakaev et al., 2012) or Knight-Ruiz (KR) (Knight and Ruiz, 2013) in HIC files. Regions with low mappability and high noise were blocked before matrix normalization. We expect that matrix balancing normalization corrects systematic biases such as nucleosome occupancy, sequence uniqueness, GC content, or crosslinking effects as reported in Imakaev et al. 2012 and Rao et al. 2014.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig (bw), hic, mcool

molecule: genomic DNA

source_name: embryonic stem cells

growth_protocol: JM8.N4 mouse ESCs from the C57BL/6N strain and their genome edited derivatives were cultured on 0.1% gelatin coated plates without feeders at 37°C and 5% CO2. The ESC medium was composed of the knockout DMEM(1X) optimized for ESCs (Thermo Fisher Scientific 10829-018), 15% ESC qualified Fetal Bovine Serum (ATCC SCRR-30-2020), 1 mM GlutaMAX (Thermo Fisher Scientific 35050-061), 0.1 mM MEM nonessential amino acids (Thermo Fisher Scientific 11140-50), 0.1 mM 2-mercaptoethanol (Thermo Fisher Scientific 21985-023),1000 units of Leukemia inhibitory factor (LIF) (Millipore) and Antibiotic-Antimycotic (Thermo Fisher Scientific 15240-062).

extract_protocol:
CUT&Tag: BRD2 CUT&Tag was performed  by using the primary anti-BRD2 antibody from Bethyl Laboratory (A302-583A). pAG-Tn5 was ordered from EpiCypher (15-1017). Due to the high sensitivity and low background, we used SEACR package for peak calling with default parameters.
Micro-C: 5M ESC cells were resuspended by trypsin, fixed by freshly made 1% formaldehyde at room temperature for 10 min and quenched by adding Tris buffer (pH = 7.5) to the final 0.75 M at room temperature. Fixed cells were washed twice with 1X PBS and then were subjected to the second crosslinking reaction by 3 mM disuccinimidyl glutarate (DSG) (Thermo Fisher # 20593)  for 45 min at room temperature. The DSG solution was freshly made at a 300-mM concentration in DMSO and diluted to 3 mM in 1X PBS before use. The crosslinking reaction was quenched by 0.75 M Tris buffer and washed twice with 1X PBS. Crosslinked cells were snap-frozen in liquid nitrogen and stored at −80°C.  We performed chromatin fragmentation by the micrococcal nuclease (MNase) and optimize the MNase digestion level to have about 80 to 90% of mononucleosomes and 10 to 20% of di-nucleosomes. We typically use ∼20 units MNase for 1 million of JM8.N4 mESCs. Intact nuclei were extracted by treating cells with Micro-C Buffer #1 (50 mM NaCl, 10 mM Tris-HCl pH = 7.5, 5 mM MgCl2, 1M CaCl2, 0.2% NP-40, 1x Protease Inhibitor Cocktail) for 20 min on ice. Chromatin was digested with a pre-titrated MNase concentration (Worthington Biochem #LS004798) at 37°C for 10 min. MNase digestion was stopped by adding 4 mM EGTA and completely inactivated by incubating at 65°C for 10 min. Digested chromatin was washed twice with ice-cold Micro-C Buffer #2 (50 mM NaCl, 10 mM Tris-HCl pH = 7.5, 10 mM MgCl2).MNase digested chromatin was subjected to multiple steps of biochemical enzyme reactions to generate compatible ends for ligation of adapters for sequencing. Chromatin was incubated with T4 PNK (New England BioLabs # M0201)  in Micro-C end-repair buffer (50 mM NaCl, 10 mM Tris-HCl pH = 7.5, 10 mM MgCl2, 100 ug/mL BSA, 2 mM ATP, 5 mM DTT) at 37°C for 15 mi. We then incubate chromatin with Klenow Fragment in the Micro-C end-repair buffer with no dNTPs at 37°C for 15 min. The blunting and labeling reaction was triggered upon adding biotin-dATP (Jena Bioscience # NU-835-BIO14), biotin-dCTP (Jena Bioscience # NU-809-BIOX), dGTP, and dTTP to a final concentration of 66 mM each at room temperature for 45 min. The reaction was inactivated by adding 30 mM EDTA and incubating at 65°C for 20 min. Biotin-labeled chromatin was washed once by ice-cold Micro-C Buffer #3 (50 mM Tris-HCl pH = 7.5, 10 mM MgCl2). The crosslinked nucleosomes were then ligated by T4 DNA Ligase (New England BioLabs #M0202) in 500 μL solution at room temperature for at least 2 h, followed by exonuclease III (New England BioLabs #M0206) treatment to remove biotin-dNTPs on un-ligated ends by incubating ligated chromatin at 37°C for at least 15 min.To specifically extract the ligated di-nucleosomal DNA, the deproteinized chromatin was purified and separated on a low-melting agarose gel (Lonza #50081). A band at the size of 250 to 400 bp corresponding to the ligated dimers was gel-extracted for library preparation. The purified DNA with biotin-dNTPs was captured by Dynabeads® MyOne Streptavidin C1 (Thermo Fisher Scientific #65001). Standard Illumina library preparation protocol including end-repair, A-tailing, and adaptor ligation was performed on beads with the NEBnext Ultra II kit (New England BioLabs # E7645). An optimal PCR cycle for final library amplification was determined by quantification PCR (KAPA Biosystems #KK4602), typically between 5–10 cycles for the input cell number from 5M. The sequencing library was amplified by Kapa HiFi PCR enzyme (KAPA Biosystems #KK2601) with the lowest possible cycles to reduce PCR duplicates.
we performed ATAC-seq on 50,000 cells which were trypsinized, washed with PBS on ice, and resuspended in the reaction mix (25 μL of 2× TD buffer, 2.5 μL of transposase, 22.5 μL of nuclease-free H2O) for 30 min at 37°C. Following transposition, genomic DNA was purified and amplified by 10-14 cycles of PCR.Both ATAC-seq samples were sequenced in Illumina HiSeq 2500 or Nextseq with 150cycle paired-end sequencing

value: embryonic stem cell line

tag: strain background

tag: treatment/genotype

value: RAD21_dep, auxin 6 hour,  BRD2 CUT&Tag, pAG-Tn5


title: RS-03295761_PB_RS-03295743

status: Public on Feb 09 2022

type: SRA

city: Buffalo

first: Mark

middle: D

last: Long

state: NY

address: Elm & Carlton Streets

department: Bioinformatics & Biostatistics

country: USA

institute: Roswell Park Comprehensive Cancer Center

library_source: transcriptomic

data_processing:
Basecalling was done by Illumina analysis pipeline CASAVA (version 1.8.2).
SMART PCR primer sequences were trimmed with Trimmomatic
Transcript abundances were quantified from sequencing reads against the human reference genome (GRCh37.67) using salmon-0.14.1.
The differential gene expression was analyzed by R/Bioconductor package DESeq2 (version 1.24.0).
Genome_build: GRCh37.67
Supplementary_files_format_and_content: raw counts for all samples.

molecule: total RNA

organism: Homo sapiens

source_name: PBC

extract_protocol:
Total RNA was prepared from these sorted DCs using the miRNeasy mini kit (Qiagen).
SMART-Seq v4 was used for library preparation from low input.

treatment_protocol: sorted XCR1+CLEC9A+HLA-DR+CD11c+ cells differentiated from on-feeder (feeder+) and feeder-free (feeder-) cultures conditions

tag: condition

value: PBC

tag: cell type


title: RS-03295759_ff_RS-03295741

source_name: iPSC-derived DC

value: feeder-

value: iPSC-derived DC


title: B Cells-Naïve-rep2

city: San Diego

first: John

last: Sedy

state: CA

address: 10770 Wateridge Cir

institute: AnaptysBio

data_processing:
Illumina HiSeq 1500 was used to process  RNA samples and generate fastq files
Raw fastq files were indexed with Mus_mus GRC_m38 using Salmon (Patro, et al., 2017. Nature Methods) to generate quant.sf files
Indexed quant.sf files were further collated and analyzed using DESeq2
Genome_build: Mus_musculus.GRCm38.cdna.all.fa.gz
Supplementary_files_format_and_content: quant.sf files generated using Salmon

organism: Mus musculus

source_name: B cells

extract_protocol:
Cells were harvested for total RNA using Qiagen RNAeasy miniprep kit and frozen for later construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Purified lymphocytes were stimulated with primary activation antibodies (anti-CD3 or anti-IgM/G), soluble IFNb, or aldehyde sulfate beads coupled to primary stimulus and Ctrl Ig or anti-Btla for 18 hours.

tag: strain

tag: immunization

tag: activation

value: B cells


title: RAD21_dep IgG CUT&Tag

value: RAD21_dep, auxin 6hour,  IgG CUT&Tag, pAG-Tn5


title: Control BRD2 CUT&Tag

value: Control BRD2 CUT&Tag, pAG-Tn5


title: RS-03295760_on_RS-03295742

value: feeder+


title: RS-03295758_PB_RS-03279668


title: Control IgG CUT&Tag

value: Control IgG CUT&Tag, pAG-Tn5


title: HET2 adult kidney

city: Marseille

first: Laurent

last: Fasano

address: Parc Scientifique de Luminy

country: France

institute: CNRS-AMU

description: RNA-Seq of Tshz3 heterozygous adult kidney

data_processing:
Basecalls performed using RTA (Illumina)
Sequences (fastq format) were mapped to the mm10 version of the mouse genome to generate Sequence Alignment/Map (SAM/BAM) format.
After normalization, analysis of differentially expressed genes (DEGs) was performed using both the Bioconductor (http://www.bioconductor.org) package DESeq/DESeq2 and the package edgeR.
This analysis generated differential expression lists with False Discovery Rates (FDRs), which are derived from p-values corrected for multiple testing using the Benjamini-Hochberg method. 6 files in total were generated: FDR 1%, 10% for both UCSC (transcripts) and ENSEMBL (genes).
Genome_build: mm10
Supplementary_files_format_and_content: all_mm10_exon_counts_tpm.xlsx (exon counting)
Supplementary_files_format_and_content: DEG_HET_vs_WT_mm10_FDR10_logFC_ordered.xlsx (Differentially expressed genes)

molecule: polyA RNA

source_name: mouse adult kidney

extract_protocol:
Total individual kidney RNA was extracted using anRNeasy Maxi kit75162 Lot.260018727/ Lot.160012031 from Quiagen according to manufacturer's instructions. The integrity of RNA was assessed using a chip-based capillary electrophoresis machine and RNA concentration determined using a full spectrum (220-750nm) spectrophotometer. The quality control of the RNA was additionally checked with RNA 6000 Pico de Agilent Technologies, according to the manufacturer's instructions. To obtain two independent total RNA preparations from the two different conditions (wild type: WT1 & WT2; Tshz3+/LacZ: HET1 & HET2) we pooled RNA from 3 kidneys per group in the same proportion.
The starting material (1µg Total mRNA, dissolved in RNase-, DNase- and protease-free molecular grade water) was sent to GATC (Eurofins) for sequencing (Genome Sequencer Illumina HiSeq). DNA and mRNA libraries were prepared for sequencing using standard Illumina protocols

tag: developmental stage

value: adult

tag: tissue

value: kidney

tag: genotype

value: heterozygote for Tshz3


title: B Cells-Naïve+anti-IgM/G+anti-Btla-rep1

value: anti-IgM/G

value: anti-Btla


title: HET1 adult kidney


title: B Cells-Naïve+anti-IgM/G+CtrlIg+IFNb-rep1

value: IFNb


title: BRD2_dep_ATACseq

data_processing:
Illumina’s Bcl2tofastq2 v2.17 was used to convert BcL files to fastq files and to demultiplex the samples
ATAC-seq, CUT&Tag pair-end reads were first adapter removed by Cutadapt and mapped to mm10 genome build using Bowtie2 with the following parameters: --no-discordant --no-mixed --phred33 -X2000 –threads32. For Micro-C, Bowtie 2.3.0 with ‘very-sensitive-local’ mode was used.
Reads mapped to mitochondria/uncharacterized chromosomes (chrM/chrUn/random) and PCR duplicates were removed by samtools. For Micro-C, pairs with multiple hits, low MAPQ, singleton, dangling end, self-circle,PCR duplicates and contacts shorter than 200bp (unligated mono-nucleosomes)  were discarded
ATAC-seq peaks were called using the MACS2 callpeak function using the –f BAMPE parameter. CUT&Tag peaks were called by SEACR.
For Micro-C, contact matrices were then normalized by using iterative correction (IC) in COOL files (Imakaev et al., 2012) or Knight-Ruiz (KR) (Knight and Ruiz, 2013) in HIC files. Regions with low mappability and high noise were blocked before matrix normalization. We expect that matrix balancing normalization corrects systematic biases such as nucleosome occupancy, sequence uniqueness, GC content, or crosslinking effects as reported in Imakaev et al. 2012 and Rao et al. 2014.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig (bw), hic, mcool

value: 6hour dTAG13 treatment (100nM)


title: P02E02_585_mono_004

city: Edinburgh

first: Nizar

middle: N.

last: Batada

address: Crew Road

country: United Kingdom

institute: Institute for Genetics and Molecular Medicine, University of Edinburgh

data_processing:
base calling: Casava
alignment: BWA MEM
transcript count: HT-seq
Genome_build: mm10

source_name: monocytes

growth_protocol: Cells were isolated from B6Tg(MMTV-PyMT)634Mul/Lellj mice bearing late stage tumors (upto 24mm diameter) or from aged matched  C57BL/6JCrl controls

extract_protocol:
Cells were sorted into 96 well place containing 2 ul of lysis buffer in each well
as per Smart-seq2 protocol (Picelli et al 2013)

treatment_protocol: 40µL of blood containing x µl 0.5M EDTA was lysed 400µL RBC lysis buffer (Biolegend), cells washed in excess 10% FCS/PBS, and lysis repeated. Cells were then blocked with 20 µL block and stained with antibodies in 30µL FACS buffer and individual live, single CD11b+ CD45+ CD115+ CD3- CD19-NK1.1- cells were FACS sorted into 96 well plates containing 2 ul of the lysis buffer (0.2% Triton X100 containing 1:20 RNASE inhibitor) per well.

value: peripheral blood


title: B Cells-Naïve+anti-IgM/G+anti-Btla+IFNb-rep1


title: B Cells-Naïve+anti-IgM/G+CtrlIg-rep1


title: WT1 adult kidney

description: RNA-Seq of WT adult kidney

value: wild type


title: DMSO_ATACseq

value: embryonic stem cell line

value: DMSO treatment


title: RS-03295756_Off-2_RS-03279666

value: feeder-

value: iPSC-derived DC


title: B Cells-Naïve-rep1

value: B cells


title: BRD2 LCD repeat2 Micro-C

value: BRD2 LCD overexpression


title: AHR KO2_D4 ENR

city: London

first: Brigitta

last: Stockinger

address: 1 Midland Road

institute: Francis Crick Insititue

data_processing:
The nf-core/atacseq pipeline (version 1.2.1; Ewels et al., 2020; https://doi.org/10.5281/zenodo.2634133) written in the Nextflow domain specific language (version 19.10.0; Di Tommaso et al., 2017) was used to perform the primary analysis of the samples in conjunction with Singularity (version 2.6.0; Kurtzer et al., 2017).
The command used was "nextflow run nf-core/atacseq --design design.csv --genome GRCm38 -profile crick".
All data was processed relative to the mouse GRCm38 downloaded from AWS iGenomes (https://github.com/ewels/AWS-iGenomes).
For a condensed overview of the pipeline, the bioinformatics tools used in each step and an extensive list of citations please see the pipeline homepage (https://github.com/nf-core/atacseq).
Genome_build: GRCm38
Supplementary_files_format_and_content: Normalised genome-wide bigWig coverage files generated from the nf-core/atacseq pipeline command defined above. Normalisation factors were generated by scaling the number of mapped reads to 1 million.
Supplementary_files_format_and_content: MACS2 Peak files generated using from the nf-core/atacseq pipeline command defined above.

source_name: mouse colon organoids

extract_protocol:
50,000 live cells were sort purified and immediately resuspended in 50 µl of ATAC-Resuspension Buffer (0.1% NP40, 0.1% Tween-20, and 0.01% Digitonin) and incubated on ice for 3 minutes, and nuclei was spin pelleted and transposition was carried out for 30 minutes at 37C in a thermomixer
DNA was purified using the DNA Clean and Concentrator (D4014, Zymo Research) and transposed fragments were amplified for 10 cycles using NEBNext 2x MasterMix and adaptors to prepare libraries. Libraries were cleaned and quantified using Bioanalyzer followed by sequencing.Adapters used to prepare sample libraries were design as mentioned in Buenrostro et al., 2013 Nature Methods (DOI: https://doi.org/10.1038/nmeth.2688).

treatment_protocol: Organoids were grown for 4-5days post-spitting from single cell suspensions and grown in WENR media. After this period, organoids were either analyzed as WENR organoids, or switched to differentiating media (ENR) for 4 days.

value: AHR KO

value: Colon organoids

tag: treatment

value: 4 days post-Wnt3a withdrawal (ENR)


title: RS-03295754_PB_RS-03276035

value: PBC


title: RS-03295755_Off-1_RS-03279665


title: AHR KO3_WENR

value: WENR media


title: mist_tumor3

city: Nashville

first: Ken

last: Lau

state: TN

address: 2215 Garland Ave. MRBIV10475

department: Cell and Developmental Biology

institute: Vanderbilt University

description: dual index

data_processing:
After sequencing, reads were filtered, sorted by their barcode of origin and aligned to the reference transcriptome using DROPEST pipeline (https://github.com/hms-dbmi/dropEst). Mapped reads were quantified into UMI-filtered counts per gene, and barcodes that correspond to cells were retrieved based on previously established methods
Barcodes were filtered (Liu et al., 2018), resulting in the processed data table.
NextSeq: Technical read: read1 - 3' end - the oligo barcodes are TruDrop which is positioned exactly as in (Klein et al., 2015) Biological read: read2 -UMI/cell barcode
NovaSeq:Technical read: read1 - UMI/cell barcode - the oligo barcodes are TruDrop which is positioned exactly as in (Southard-Smith et al., 2020) Biological read: read2 - 3' end
Genome_build: Mouse: GRCm38.85
Supplementary_files_format_and_content: Delimited tables, with cells and genes, as columns and rows, filtered

source_name: colon

growth_protocol: primary cells

extract_protocol:
Human epithelial cell suspensions were obtained by EDTA chelation and cold protease dissociation. Cells were encapsulated using the inDrop platform (1CellBio), and RNA was extracted according to the protocol of Klein et al., 2015. MARIS libraries are generated according to Chen et al., 2021.
CEL-Seq linear amplification of using standard structure (single index) (Klein et al., 2015) or TruDrop library structure (dual index) (Southard-Smith et al., 2020)
RNA-Seq was performed on Novaseq6000 with a 2 x 150 paired-end kit standard run (for dual index)
RNA-Seq was performed on NextSeq500 with a 2 x 75 paired-end kit using custom read lengths (for single index)

tag: sample preparation

value: inDrop scRNA-seq

value: colon


title: lrig_tumor4

description: dual index

value: Lrig1creERT2; Apcfl/fl


title: BRD2 LCD repeat1 Micro-C


title: RS-03295757_On_RS-03279667

value: feeder+


title: RS-03295753_iDC_RS-03276034


title: BRD2 BD repeat1 Micro-C

value: BRD2 BD overexpression


title: BRD2 BD repeat2 Micro-C


title: DL1-Human-hiPSC-DC

data_processing:
generate feature-barcode matrices by cellranger v3.1.0
Genome_build: GRCh38
Supplementary_files_format_and_content: h5

extract_protocol:
Single cell suspensions of human iPSC-derived DCs were stained with a master mix of antibodies for surface staining including Live/Dead Fixable Aqua Dead, CD11c and HLA-DR after Fc block with human IgG. Sorting of live CD11c+HLA-II+cells were performed on a BD FACSAria II (BD Biosciences)
Chromium Single Cell 3’ Reagent Kit v3


title: WT2 adult kidney

description: RNA-Seq of WT adult kidney

value: adult

value: kidney

value: wild type


title: OP9-Human-hiPSC-DC


title: AHR KO2_WENR


title: DSS_recovered4

description: dual index

value: WT


title: BRD2 FL Micro-C(for BRD2 domain)

value: embryonic stem cell line

value: BRD2 FL overexpression (for BRD2 domain)


title: BMDMs, PYK2 KO3

city: Rehovot

first: Sima

last: Lev

address: 234 Herzl St.

department: Molecular Cell Biology

country: Israel

institute: Weizmann Institute of Science

data_processing:
Libraries were sequenced by the Illumina Novaseq 6000 using SP mode 100 cycles kit (Illumina)
Mapping of sequences to the genome was performed by the UTAP pipeline (UTAP: User-friendly Transcriptome Analysis Pipeline, Kohen et al. BMC Bioinformatics 2019, 20(1):154))
Reads were trimmed using cutadapt (DOI: 10.14806/ej.17.1.200) (parameters: -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -a “A{10}” –times 2 -u 3 -u -3 -q 20 -m 25).
Reads were mapped to genome (mm10) using STAR (DOI: 10.1093/bioinformatics/bts635) v2.4.2a (parameters: –alignEndsType EndToEnd, –outFilterMismatchNoverLmax 0.05, –twopassMode Basic, –alignSoftClipAtReferenceEnds No).
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with gene counts for every gene and every sample

source_name: Bone marrow derived macrophages (BMDMs)

growth_protocol: Bone marrow cells were obtained by flushing the femurs and tibias of mice with DMEM/F-12. After erythrocyte lysis with Red blood cell lysis buffer (1.55 M NH4Cl, 0.92 M NaHCO3, 1.0 mM EDTA) for 5min at RT, cells were washed twice with ice-cold PBS and bone marrow cell suspension was cultured at 4 x 10^6 cells/ml in BMMF medium (DMEM/F-12 medium with 10% heat-inactivated FBS (v/v), 100 U/ml penicillin, 100 μg/ml streptomycin, 2 mM L-glutamine, 5 mM Hepes pH 7.4, 2.5 μg/ml fungizone, 0.5 mg/ml gentamycin sulfate, and 20% L929-conditioned DMEM (v/v) as a source of M-CSF) for 7 days. After 3 days in culture, fresh BMMF medium was added.

extract_protocol:
RNA was extracted using TRI reagent (Sigma), following standard extraction protocol.
RNAseq libraries were constructed by applying a bulk adaptation of the MARS‐seq protocol (Jaitin et al. 2014 Science.343:776-9).

value: Bone marrow derived macrophages (BMDMs)

value: Pyk2 knock-out


title: Control  Micro-C(for BRD2 domain)

value: Control (for BRD2 domain)


title: BRD2_FL Rad21_dep Micro-C

value: BRD2 FL, auxin 6hour,depleting RAD21


title: AHR KO1_D4 ENR

value: AHR KO

value: Colon organoids

value: 4 days post-Wnt3a withdrawal (ENR)


title: BMDMs, PYK2 KO2


title: AHR KO1_WENR

value: WENR media


title: WT3_D4 ENR

value: Wild type


title: BMDMs, WT5


title: BMDMs, WT6


title: Rad21_dep Micro-C (for BRD2 FL)

value: auxin, 6hour, depleting RAD21, for BRD2 FL


title: Control  Micro-C(for BRD2 FL)

value: untreated for BRD2 FL


title: BMDMs, WT1


title: BMDMs, PYK2 KO4


title: 12099_MUT5_E6_LPS_IL-18_3

first: Eran

last: Hornstein

address: Hornstein lab, 1314 Mayer building, Dep. Molecular Genetics,

data_processing:
Illumina Novaseq 6000 sequencer, at an average sequencing depth of 10,000,000 reads per sample
Reads were trimmed using cutadapt (DOI: 10.14806/ej.17.1.200) (parameters: -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -a “A{10}” –times 2 -u 3 -u -3 -q 20 -m 25).
Reads were mapped to genome /shareDB/iGenomes/Homo_sapiens/UCSC/hg38/Sequence/hg38_star_index using STAR (DOI: 10.1093/bioinformatics/bts635) v2.4.2a (parameters: –alignEndsType EndToEnd, –outFilterMismatchNoverLmax 0.05, –twopassMode Basic, –alignSoftClipAtReferenceEnds No).
The pipeline quantifies the 3’ of Gencode annotated genes (The 3’ region contains 1,000 bases upstream of the 3’ end and 100 bases downstream):
 the 3’ end (1000bp) of the transcripts for counting the number of reads per gene. Counting (UMI counts) was done after marking duplicates (in-house script) using HTSeq-count (DOI: 10.1093/bioinformatics/btu638) in union mode.
Normalization of the counts and differential expression analysis was performed using DESeq2 (DOI: 10.1186/s13059-014-0550-8) with the parameters: betaPrior=True, cooksCutoff=FALSE, independentFiltering=FALSE. Raw P values were adjusted for multiple testing using the procedure of Benjamini and Hochberg (DOI: 10.1111/j.2517-6161.1995.tb02031.x). The djusted p-value were coreccted with FDR tools with normal null model used for statistic.v
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts, normalized gene counts, RLD, basemean, log2FC, pvalue, p-adjusterd for every gene and every sample.

source_name: Induced pluripotent stem cells

growth_protocol: Cell were grown in X-VIVO15 (Lonza, BE02-060Q) containing 100 ng/mL M-CSF (Peprotech, 300-25), 25 ng/ml IL-3 (Peprotech, 200-03), 1× Glutamax, 55 uM 2-mercaptoethanol (Gibco, 31350-10), 100 U/mL penicillin/streptomycin (Biological Industries, 03-031-1B).

extract_protocol:
Total RNA was extracted using miRNeasy micro Kit (QIAGEN, 217084) according to manufacturer instructions.
Afret cell lysis and RNA isolation,  the 3' ends of mRNAs were annealed to UMIs containing a T7 promoter. The mRNA was reverse-transcribed to cDNA and amplified by IVT. The RNA strands were fragmented and annealed to sequencing adapters, followed by RT to generate barcoded cDNA libraries that were ready for sequencing.
Bulk MARSseq

treatment_protocol: 200,000 ipMGs harboring variant or canonical IL18RAP 3'UTR (n=4) were treated with 100 ng/mL LPS + 100 ng/mL IL18 for 6 hrs in ipMG media (Advanced DMEM (Gibco, 12491-015) containing 1× N-2 supplement (Gibco, 17502-048), 2mM GlutaMAX (Gibco, 35050-038), 55 uM 2-mercaptoethanol (Gibco, 31350-10), 50 U/mL penicillin/streptomycin (Biological Industries, 03-031-1B) and 100 ng/mL IL-34 (Peprotech, 200-34).

value: iPSC derived progenitor microglia

value: Variant IL18RAP 3'UTR


title: 12099_MUT5_E6_LPS_IL-18_4

description: treated with 100 ng/mL LPS + 100 ng/mL IL18 for 6 hrs


title: Rad21 Halo AID 6h auxin 16HD ATACseq

data_processing:
Illumina’s Bcl2tofastq2 v2.17 was used to convert BcL files to fastq files and to demultiplex the samples
ATAC-seq, ChIP-seq pair-end reads were first adapter removed by Cutadapt and mapped to mm10 genome build using Bowtie2 with the following parameters: --no-discordant --no-mixed --phred33 -X2000 –threads32. For Micro-C, Bowtie 2.3.0 with ‘very-sensitive-local’ mode was used.
Reads mapped to mitochondria/uncharacterized chromosomes (chrM/chrUn/random) and PCR duplicates were removed by samtools. For Micro-C, pairs with multiple hits, low MAPQ, singleton, dangling end, self-circle,PCR duplicates and contacts shorter than 200bp (unligated mono-nucleosomes)  were discarded
ATAC-seq, ChIP-seq peaks were called using the MACS2 callpeak function using the –f BAMPE parameter.
For Micro-C, contact matrices were then normalized by using iterative correction (IC) in COOL files (Imakaev et al., 2012) or Knight-Ruiz (KR) (Knight and Ruiz, 2013) in HIC files. Regions with low mappability and high noise were blocked before matrix normalization. We expect that matrix balancing normalization corrects systematic biases such as nucleosome occupancy, sequence uniqueness, GC content, or crosslinking effects as reported in Imakaev et al. 2012 and Rao et al. 2014.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig (bw), hic, mcool

extract_protocol:
ChIP-seq: Cells were cross-linked for 10 min at room temperature with 1% methanol-free paraformaldehyde in PBS and quenched with 0.125 M glycine. Cells were scraped and resuspended in cold cell lysis buffer (5 mM PIPES at pH 8.0, 85 mM KCl, 0.5% NP-40) and incubated for 10 min on ice. After centrifuging, nuclear pellets were resuspended in at least 6 vol of sonication buffer (50 mM Tris-HCl at pH 8.1, 10 mM EDTA, 0.1% SDS), incubated for 10 min on ice, and sonicated using the Covaris S220 sonicator to obtain an average fragment length of ∼500 bp examined by electrophoresis. Sonicated chromatin was diluted in RIPA buffer, aliquoted, and incubated with Protein G Dynabeads that were prebound with individual antibodies for at least 1 h at room temperature. Immunoprecipitation was performed overnight at 4°C with 2–4 µg of antibodies. Ten percent of the chromatin was saved as input. Immunoprecipitated and input DNA was introduced with sequencing adaptors as described previously (Schmidl et al., 2015), washed extensively with RIPA buffer (low salt and high salt) and LiCl buffer, digested with proteinase K and RNase A, reverse-cross-linked at 60oC overnight followed by purification with the AmpureX beads. We also added the spike-in chromatin (active motif, 53083) and spike-in antibody (active motif, 61686) following the manufacturer’s instructions.
Micro-C: 5M ESC cells were resuspended by trypsin, fixed by freshly made 1% formaldehyde at room temperature for 10 min and quenched by adding Tris buffer (pH = 7.5) to the final 0.75 M at room temperature. Fixed cells were washed twice with 1X PBS and then were subjected to the second crosslinking reaction by 3 mM disuccinimidyl glutarate (DSG) (Thermo Fisher # 20593)  for 45 min at room temperature. The DSG solution was freshly made at a 300-mM concentration in DMSO and diluted to 3 mM in 1X PBS before use. The crosslinking reaction was quenched by 0.75 M Tris buffer and washed twice with 1X PBS. Crosslinked cells were snap-frozen in liquid nitrogen and stored at −80°C.  We performed chromatin fragmentation by the micrococcal nuclease (MNase) and optimize the MNase digestion level to have about 80 to 90% of mononucleosomes and 10 to 20% of di-nucleosomes. We typically use ∼20 units MNase for 1 million of JM8.N4 mESCs. Intact nuclei were extracted by treating cells with Micro-C Buffer #1 (50 mM NaCl, 10 mM Tris-HCl pH = 7.5, 5 mM MgCl2, 1M CaCl2, 0.2% NP-40, 1x Protease Inhibitor Cocktail) for 20 min on ice. Chromatin was digested with a pre-titrated MNase concentration (Worthington Biochem #LS004798) at 37°C for 10 min. MNase digestion was stopped by adding 4 mM EGTA and completely inactivated by incubating at 65°C for 10 min. Digested chromatin was washed twice with ice-cold Micro-C Buffer #2 (50 mM NaCl, 10 mM Tris-HCl pH = 7.5, 10 mM MgCl2).MNase digested chromatin was subjected to multiple steps of biochemical enzyme reactions to generate compatible ends for ligation of adapters for sequencing. Chromatin was incubated with T4 PNK (New England BioLabs # M0201)  in Micro-C end-repair buffer (50 mM NaCl, 10 mM Tris-HCl pH = 7.5, 10 mM MgCl2, 100 ug/mL BSA, 2 mM ATP, 5 mM DTT) at 37°C for 15 mi. We then incubate chromatin with Klenow Fragment in the Micro-C end-repair buffer with no dNTPs at 37°C for 15 min. The blunting and labeling reaction was triggered upon adding biotin-dATP (Jena Bioscience # NU-835-BIO14), biotin-dCTP (Jena Bioscience # NU-809-BIOX), dGTP, and dTTP to a final concentration of 66 mM each at room temperature for 45 min. The reaction was inactivated by adding 30 mM EDTA and incubating at 65°C for 20 min. Biotin-labeled chromatin was washed once by ice-cold Micro-C Buffer #3 (50 mM Tris-HCl pH = 7.5, 10 mM MgCl2). The crosslinked nucleosomes were then ligated by T4 DNA Ligase (New England BioLabs #M0202) in 500 μL solution at room temperature for at least 2 h, followed by exonuclease III (New England BioLabs #M0206) treatment to remove biotin-dNTPs on un-ligated ends by incubating ligated chromatin at 37°C for at least 15 min.To specifically extract the ligated di-nucleosomal DNA, the deproteinized chromatin was purified and separated on a low-melting agarose gel (Lonza #50081). A band at the size of 250 to 400 bp corresponding to the ligated dimers was gel-extracted for library preparation. The purified DNA with biotin-dNTPs was captured by Dynabeads® MyOne Streptavidin C1 (Thermo Fisher Scientific #65001). Standard Illumina library preparation protocol including end-repair, A-tailing, and adaptor ligation was performed on beads with the NEBnext Ultra II kit (New England BioLabs # E7645). An optimal PCR cycle for final library amplification was determined by quantification PCR (KAPA Biosystems #KK4602), typically between 5–10 cycles for the input cell number from 5M. The sequencing library was amplified by Kapa HiFi PCR enzyme (KAPA Biosystems #KK2601) with the lowest possible cycles to reduce PCR duplicates.
RNA-seq: Total RNA was isolated according to the manufacturer’s instruction, quantified by Nanodrop (Thermo Fisher Scientific) and diluted to 1 ng/µl in nuclease-free water.  A total of 1 ng of RNA was added to 2.5 µl of cell lysis buffer (nuclease-free water with 0.2 % v/v Triton X-100 and 0.1 U/µl RNase inhibitor), and subjected to cDNA synthesis and amplification as described before (Cembrowski et al., 2018). Libraries were prepared using a modified Nextera XT DNA protocol (Illumina, San Diego, CA) where 5 µM P5NEXTPT5 was substituted for the i5 primers in the kit. Libraries were quantified by qPCR (Roche), normalized to 2 nM, then pooled and sequenced on a NextSeq550 flowcell with 25 bases in read 1, 8 bases in the i7 index read, and 50 bases in read 2. The control library phiX (Illumina) was spiked in at a final concentration of 15% to improve color balance in read 1.
ATAC-seq: we performed ATAC-seq on 50,000 cells which were trypsinized, washed with PBS on ice, and resuspended in the reaction mix (25 μL of 2× TD buffer, 2.5 μL of transposase, 22.5 μL of nuclease-free H2O) for 30 min at 37°C. Following transposition, genomic DNA was purified and amplified by 10-14 cycles of PCR.Both ATAC-seq samples were sequenced in Illumina HiSeq 2500 or Nextseq with 150cycle paired-end sequencing

value: 6h auxin+1.5hour 1,6Hexanediol


title: Lin9KO rep3

city: Nanjing

first: wang

middle: cong

last: cong

state: Jiangsu

address: 12 Xuefu Road

country: China

institute: Nanjing University

description:
Embryonic stem cells are from the inner cell mass at blastocyst stage of C57BL/6 mice
Lin9FF_vs_Lin9KO

data_processing:
FastQc were used for data quality control.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using SeqPrep and Sickle
Paired-end clean reads were aligned to the reference genome using the HISAT2 2.1.0; RSEM was used to calculate FPKM.
Differential expression analysis was performed using the Deseq v1.26.0
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: xls files include RPKM values for each Sample ...

source_name: Embryonic stem cells

extract_protocol:
Cells were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruseqTM RNA sample prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Embryonic stem cells


title: WT2_D4 ENR


title: WT2_WENR


title: WT1_WENR


title: Lin9KO rep2


title: AHR KO-IP

data_processing:
Samples were sequenced on an Illumina HiSeq4000 generating 101bp single ended reads averaging 30 million reads per sample.  ChIP-seq reads were aligned to the mouse mm10 genome assembly using BWA version 0.7.15  with a maximum mismatch of 2 bases. Picard tools version 2.1.1 was used to sort, mark duplicates and index the resulting alignment BAM files. Normalised tdf files for visualisation purposes were created using the resulting BAM files using IGVtools version 2.3.75 software by extending reads by 50 bp and normalising to 10 million mapped reads per sample
Peaks were called by comparing IP samples to their respective input using MACS version 2.1.1, using the standard parameters. Replicate samples for IP and input were merged prior to peak calling. Peaks called by MACS were annotated using the ‘annotatePeaks’ function in the Homer (version 4.8) software package
Genome_build: mm10
Supplementary_files_format_and_content: bed file of peaks called using MACS

source_name: Colon organoids in stem cell condition

extract_protocol:
Wild type and AHR knockout colon organoids grown in WENR condition were stimulated with 5nM FICZ for 1 hour in a glass vial at 37oC. Samples were crosslinked with 1% formaldehyde (catalogue number: 28906; Thermofisher) for 8 minutes and quenched with 0.125M glycine at room temperature. Nuclei was extracted by Dounce homogenization and chromatin was sheared by sonication in a lysis buffer (0.25% SDS, 1mM EDTA, 1% Trition-X, 10mM Tris-HCl, pH 8). Debris was spin pelleted at 13,000 rpm for 30min at 4oC. Supernatant was diluted in RIPA buffer (0.2% deoxycholate, 280mM NaCl, 1.1% Triton-X in H2O) and cleaned with protein A/G Dynabeads (10003D & 10001D; Invitrogen) for 1 hour at 4oC. 10% of supernatant was used as input and the remaining sample was immunoprecipitated overnight at 4oC with anti-AhR antibody (BML-SA210; Enzo). Chromatin was then incubated with protein A/G Dynabeads for 3 hours at 4oC. Chromatin bound beads were washed twice in low-salt buffer (0.1% SDS, 1% Triton X-100, 1mM EDTA, , 140 mM NaCl, 0.1% deoxycholate, 20 mM Tris–HCl, pH 8), high-salt buffer (same as low salt except for 500 mM NaCl), LiCl wash buffer (250mM LiCl, 0.5% NP40, 0.5% deoxycholate, 1 mM EDTA, 10 mM Tris–HCl, pH 8) and with Tris-EDTA buffer (10 mM Tris–HCl 1mM EDTA). Protein-chromatin complexes were then eluted in elution buffer (1% SDS, 100 mM NaHCO3) and reverse cross-linked overnight with RNase and proteinase containing buffer (62.5 µg/ml RNaseA, 5 mg/ml proteinase K, 1.25M NaCl, 62.5mM EDTA pH 8, 250mM Tris-HCl pH 6.5). ChIP DNA was purified using the ChIP DNA Clean and Concentrator (D5205, Zymo Research) and quantified using Bioanalyzer followed by sequencing.
Libraries were prepare for sequencing using KAPA_Hyper_kit_ChIP

treatment_protocol: In vitro stimulation with 5nM FICZ for 1 hour

value: 5nM FICZ for 1 hour

value: Colon

tag: sample type

value: Organoids

tag: chip antibody

value: anti-AhR antibody (BML-SA210; Enzo)


title: Wild type-IP-M4


title: Wild type-IP-M3


title: WT1_D4 ENR


title: Rad21 Halo AID noauxin 16HD ATACseq

value: embryonic stem cell line

value: no auxin+1.5hour 1,6Hexanediol


title: Lin9KO rep1


title: Wild type-IP-M2


title: BRD2 FL Micro-C

value: BRD2 FL


title: 12099_WT_LPS_IL-18_4

value: Canonical IL18RAP 3'UTR


title: 12099_MUT5_E6_LPS_IL-18_2


title: Rad21 Halo AID 6h auxin ATACseq

value: 6hour auxin


title: Wild type-IP-M1


title: 12099_WT_LPS_IL-18_3


title: 12099_MUT5_E6_LPS_IL-18_1


title: Lin9F/F rep2


title: Lin9/FF rep3


title: 12099_WT_LPS_IL-18_2


title: Lin9F/F rep1


title: 12099_WT_LPS_IL-18_1


title: Wild type-input-M4


title: Lin37KO rep3

description:
Embryonic stem cells are from the inner cell mass at blastocyst stage of C57BL/6 mice
Lin37FF_vs_Lin37KO


title: Rad21 Halo AID noauxin ATACseq

value: no auxin


title: B3 dep Brd3 ChIP-seq

value: Brd3 depletion Brd3 ChIP


title: B3 dep Brd2 ChIP-seq

value: Brd3 depletion Brd2 ChIP


title: H1

city: Beijing

first: Yulin

last: Lyu

address: No.5 Yiheyuan Road Haidian District

department: School of Life Sciences

institute: Peking University

data_processing:
The clean single-cell RNA-seq reads were mapped to human reference genome hg19 using Cell Ranger v3.1.0.
Genome_build: hg19
Supplementary_files_format_and_content: .tar.gz files containing cellranger output

source_name: hES cells H1

growth_protocol: Human CiPS cells and hES cells (H1) were maintained in mTeSR™ Plus Medium on Matrigel coated plates under 21% O2, 5% CO2 at 37 ℃. Human embryonic fibroblasts (HEFs) were cultured in high glucose DMEM supplemented with 15% Fetal Bovine Serum (FBS), 1% GlutaMAX™, 1% MEM Non-Essential Amino Acids Solution (NEAA), 1% Penicillin-Streptomycin and 0.055 mM 2-mercaptoethanol under 21% O2, 5% CO2 at 37 ℃. Adult human adipose derived mesenchymal stromal cells (hADSCs) and human adult skin fibroblasts (hASFs) were cultured in Mesenchymal Stem Cell Growth Medium 2 under 21% O2, 5% CO2 at 37 ℃.

extract_protocol:
Using single cell 3’ Library and Gel Bead Kit V3.1 (10x Genomics, 1000075) and Chromium Single Cell B Chip Kit (10x Genomics, 1000074), the cell suspension (300-600 living cells per microliter determined by Count Star) was loaded onto the Chromium single cell controller (10x Genomics) to generate single-cell gel beads in the emulsion according to the manufacturer’s protocol. In short, cells at different time points throughout chemical reprogramming process were harvested and resuspended at 1 x 106 cells per milliliter in 1 x PBS with 0.04% BSA. About 1 x 104 cells were added to each channel, and the target cell will be recovered was estimated to be about 5 x 103 cells. Captured cells were lysed and the released RNA were barcoded through reverse transcription in individual GEMs. Reverse transcription was performed on a S1000TM Touch Thermal Cycler (Bio Rad) at 53 ℃ for 45 min, followed by 85 ℃ for 5 min, and hold at 4 ℃. The cDNA was generated and then amplified, and quality assessed using an Agilent 4200.
According to the manufacture’s introduction, Single-cell RNA-seq libraries were constructed using Single Cell 3’ Library and Gel Bead Kit V3.1 The libraries were finally sequenced using an IlluminaNovaseq6000 sequencer with a sequencing depth of at least 1 x 105 reads per cell with pair-end 150 bp (PE150) reading strategy (performed by CapitalBio Technology, Beijing).

treatment_protocol: Human somatic cells were treated with different small molecule combinations during human chemical reprogramming.

tag: cell line


title: Rad21 Halo AID 6h auxin washoff ATACseq

value: 6hour auxin+24h wash off


title: B3 dep Brd4 ChIP-seq

value: Brd3 depletion Brd4 ChIP


title: B3 dep CTCF ChIP-seq

value: Brd3 depletion CTCF ChIP


title: Wild type-input-M2

value: Wild type


title: hCiPSCs-1230

source_name: human chemically induced pluripotent stem cells from human adult skin fibroblasts


title: Lin37KO rep1

value: Embryonic stem cells


title: Wild type-input-M3

value: 5nM FICZ for 1 hour


title: B3 dep IgG ChIP-seq

value: Brd3 depletion  IgG ChIP


title: hCiPSCs-1117

source_name: human chemically induced pluripotent stem cells from human embryonic fibroblasts


title: Wild type-input-M1

value: Colon

value: Organoids


title: Lin37KO rep2


title: B3 ctr CTCF ChIP-seq

value: embryonic stem cell line

value: Brd3 degron line ctr CTCF ChIP


title: hCiPSCs-0809

source_name: human chemically induced pluripotent stem cells from adult human adipose derived mesenchymal stromal cells


title: MM2

city: shanghai

first: daofang

last: ding

address: 1200 Cai Lun Road,Zhangjiang Hi-TechPark,Pudong New Area

institute: Shanghai University of Traditional Chinese Medicine

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reads were mapped to mouse genome assembly GRCm38 (ftp://ftp.ensembl.org/pub/release-89/fasta/mus_musculus/dna/Mus_musculus.GRCm38.dna.toplevel.fa.gz) and rat genome assembly Rnor6 (ftp://ftp.ensembl.org/pub/release-89/fasta/rattus_norvegicus/dna/Rattus_norvegicus.Rnor_6.0.dna.toplevel.fa.gz) using HISAT2 with default parameters.
HTSeq v0.11.2 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. Mouse GTF file:ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M20/gencode.vM20.annotation.gtf.gz; Rat GTF file:ftp://ftp.ensembl.org/pub/release-89/gtf/rattus_norvegicus/Rattus_norvegicus.Rnor_6.0.89.gtf.gz
Genome_build: GRCm38 & Rnor6
Supplementary_files_format_and_content: tab-delimited text files include count and FPKM values for each Sample

source_name: mouse chondrocytes

growth_protocol: seed ed  at 5x 105 cells/ml; split saturated culture 1:2 to 1:3 every 2-3 days;

extract_protocol:
RNA was harvested using Trizol reagent.
A total amount of 1.5 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer's recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: The chondrocytes of rats and mice were divided into control group (RC=Rat Control group, MC=Mouse Control group) and model group (RM=Rat Model group, MM=Mouse Model group). The chondrocytes in model groups were all stimulated by 20 ng/ml IL-1β (R&D Company) for 24 hrs and extracted for sequencing.

value: mouse model

value: cartilage


title: AHR KO-input

value: AHR KO


title: Lin37/FF rep3


title: MM3


title: B3 ctr Brd4 ChIP-seq

source_name: embryonic stem cells

value: Brd3 degron line ctr Brd4 ChIP


title: Lin37F/F rep1


title: MM1


title: hCiPSCs-0618


title: StageIV_Day10-0618

source_name: human somatic cells during chemical reprogramming stage IV day 10


title: Lin52KO rep3

description:
Embryonic stem cells are from the inner cell mass at blastocyst stage of C57BL/6 mice
Lin52FF_vs_Lin52KO


title: Lin52KO rep2


title: StageIV_Day4-0618

source_name: human somatic cells during chemical reprogramming stage IV day 4


title: Lin37F/F rep2


title: MC1

value: mouse control


title: StageIV_Day2-0618

source_name: human somatic cells during chemical reprogramming stage IV day 2


title: Lin52KO rep1


title: B3 ctr Brd3 ChIP-seq

value: Brd3 degron line ctr Brd3 ChIP


title: B3 ctr Brd2 ChIP-seq

value: Brd3 degron line ctr Brd2 ChIP


title: MC2


title: StageIV_Day1-0618

source_name: human somatic cells during chemical reprogramming stage IV day 1


title: Lin52/FF rep3


title: Lin52F/F rep2


title: StageIII_Day8-0618

source_name: human somatic cells during chemical reprogramming stage III day 8


title: StageIII_Day4-0618

source_name: human somatic cells during chemical reprogramming stage III day 4


title: Lin52F/F rep1


title: B4 dep CTCF ChIP-seq

value: Brd4 depletion CTCF ChIP


title: gastric DLBCL, case HI7

type: RNA

city: Taipei

first: Chung-Wu

last: Lin

state: Taiwan

address: 7 South Chung-Shan Road

department: Pathology

country: Taiwan

institute: National Taiwan University

description: Genome-wide miRNA profiling was measured with the NanoString nCounter Human miRNA expression assay.

hyb_protocol: The miRtagged mature miRNAs were hybridized to fluorescent reporter probes and to capture probes.

scan_protocol: The samples were immobilized to a solid-phase cartridge, and a CCD digital analyzer was used for data acquisition.

data_processing:
CCD digital analyzer was used for data acquisition.
The data were normalized to the internal positive controls using nSolver Analysis Software at http://www.nanostring.com.

source_name: gastric DLBCL

label_protocol: Mature miRNAs were ligated to sequence-specific miRtags.

extract_protocol: Total RNA sample was extracted by TRIzol reagent (Invitrogen ). Approximately 0.1 ug of total RNAs were extracted from from formalin-fixed paraffin-embedded tissue blocks.

value: primary gastric  lymphoma

tag: phenotype

value: resistant to HPET

tag: histology

value: diffuse large B-cell lymphoma


title: Lin54KO rep3

description:
Embryonic stem cells are from the inner cell mass at blastocyst stage of C57BL/6 mice
Lin54FF_vs_Lin54KO

value: Embryonic stem cells


title: StageII_Day12-0618

source_name: human somatic cells during chemical reprogramming stage II day 12


title: B4 dep Brd4 ChIP-seq

value: Brd4 depletion Brd4 ChIP


title: gastric DLBCL, case HI6


title: MC3


title: B3 dep p300 ChIP-seq

value: Brd4 depletion p300 ChIP


title: B3 dep Input ChIP-seq

value: Brd4 depletion Input


title: B3 ctr IgG ChIP-seq

value: embryonic stem cell line

value: Brd3 degron line ctr IgG ChIP


title: B4 dep Brd3 ChIP-seq

value: Brd4 depletion Brd3 ChIP


title: gastric DLBCL, case HI5


title: Lin54KO rep2


title: Lin54/FF rep3


title: StageI_Day4-0618

source_name: human somatic cells during chemical reprogramming stage I day 4


title: StageII_Day4-0618

source_name: human somatic cells during chemical reprogramming stage II day 4


title: StageII_Day8-0618

source_name: human somatic cells during chemical reprogramming stage II day 8


title: gastric DLBCL, case HI8


title: gastric DLBCL, case HI4


title: StageII-0605

source_name: human somatic cells during chemical reprogramming stage II


title: Lin54F/F rep2

source_name: Embryonic stem cells


title: B4 dep Brd2 ChIP-seq

value: Brd4 depletion Brd2 ChIP


title: B4 ctr Input ChIP-seq

value: Brd4 degron line ctr Input


title: B4 dep IgG ChIP-seq

value: Brd4 depletion  IgG ChIP


title: gastric DLBCL, case HI3


title: B4 ctr p300 ChIP-seq

value: Brd4 degron line ctr p300 ChIP


title: Lin54F/F rep1


title: StageI-0605

source_name: human somatic cells during chemical reprogramming stage I


title: hADSCs-0809

source_name: adult human adipose derived mesenchymal stromal cells


title: B4 ctr CTCF ChIP-seq

value: Brd4 degron line ctr CTCF ChIP


title: B4 ctr Brd4 ChIP-seq

value: Brd4 degron line ctr Brd4 ChIP


title: hASFs-0605

source_name: human adult skin fibroblasts


title: gastric DLBCL, case HD9

value: sensitive to HPET


title: RNA-seq-control-3

first: Jinhua

last: Qin

address: Taiping Road

institute: Beijing Institute of Transfusion

data_processing:
The clustering of the index-coded samples was performed on a cBot cluster generation system using HiSeq PE Cluster Kit v4-cBot-HS (Illumina) according to the manufacturer’s instructions. After cluster generation, the libraries were sequenced on an Illumina platform and 150 bp paired-end reads were generated.
The cluster generation and sequencing were performed on Novaseq 6000 S4 platform ,using NovaSeq 6000 S4 Reagent kit V1.5.
The low-quality parts of the raw reads were filtered. Clean data were mapped to the reference genome using the HISAT2 v2.1.0. The read counts of each gene were summarized using HTSeq (http://www-huber.embl.de/users/anders/HTSeq/doc/overview.html). DEGseq2 v1.6.3 was used to detect differentially expressed genes (fold change above 1 with adjusted p-values below 0.01).
Genome_build: http://www.ensembl.org/index.html
Supplementary_files_format_and_content: tab-delimited text files include read counts of each gene for each sample

source_name: cord blood

growth_protocol: Stage I: HSPC Expansion Isolated HSPCs were expanded in StemSpan™ SFEM medium (STEMCELL Technologies) containing recombinant human stem cell factor (SCF, 50 ng/ml, Peprotech), recombinant human thrombopoietin (TPO, 50 ng/ml, Peprotech), interleukin (IL)-3 (20 ng/ml, Peprotech), and recombinant human Flt3-Ligand (FLT3-L, 50 ng/ml, Peprotech). Stage II: MK specification. After expansion for 7 days, cells were cultured in StemSpan™ SFEM medium containing SCF (50 ng/ml, Peprotech), TPO (50 ng/ml, Peprotech), IL-3 (20 ng/ml, Peprotech), IL-6 (50 ng/ml, Peprotech), IL-11 (20 ng/ml, Peprotech), with or without ricolinostat.

extract_protocol:
total RNA was isolated using an RNeasy extraction kit (Qiagen) and treated with Dnase
A total amount of 1-3μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina ® （NR604-01/02）following the manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Then we added fragmentation buffer to break the mRNA into short fragments. First strand cDNA was synthesized using random hexamer primer and RNase H. Second strand cDNA synthesis was subsequently performed using buffer, dNTPs, DNA polymerase I and RNase H. And then, the double stranded cDNA was purified byAMPure P beads or QiaQuick PCR kit. The purified double stranded cDNA was repaired at the end, added a tail and connected to the sequencing connector, then the fragment size was selected, and finally the final cDNA library was obtained by PCR enrichment.

treatment_protocol: CD34+CD41+ cells were sorted by flow cytometry on day 7. After 7 days of Ricolinostat treatment, the cells were collected and centrifuged at 2000 rpm.


title: dKO3

city: Milan

first: Stefano

middle: Carlo

last: Previtali

state: Milan

address: via Olgettina,60

department: INSPE

country: Italy

institute: IRCSS San Raffaele Scientific Institute

data_processing:
Sequencing was performed on a Illumina NovaSeq 6000 machine (Illumina, San Diego, CA) obtaining an average of 100 millions of paired-end reads per sample.
The raw reads produced from sequencing were trimmed using Trimmomatic, version 0.32, to remove adapters and to exclude low-quality reads from the analysis. The remaining reads were then aligned to the murine genome GRCm38 using STAR, version 2.5.3a.
Reads were eventually assigned to the corresponding genomic features using featureCounts, according to the Gencode basic annotations (Gencode version M22).
Quality of sequencing and alignment was assessed using the FastQC, RseQC and MultiQC tools. Expressed genes were defined as those genes showing at least 1 Count Per Million reads (CPM) on at least 4 samples, corresponding to the sample size of each group of samples (Chen et al., 2016). Low-expressed genes that did not match this criteria were excluded from the dataset.
Gene expression read counts were exported and analyzed in the R environment (v. 3.5.1) to identify differentially expressed genes (DEGs), using the DESeq2 Bioconductor library (v. 1.22.1, https://doi.org/10.1186/s13059-014-0550-8). P-values were adjusted using a threshold for false discovery rate (FDR) < 0.05 (Benjamini and Hochberg, 1995).
Functional enrichment analysis was conducted using the enrichR R package (v. 1.0, https://doi.org/10.1093/nar/gkw377), starting from the lists of differentially expressed genes as defined by FDR<0.05. The enrichment with a subset of selected gene-sets was further evaluated using the Pre-ranked Gene Set Enrichment Analysis (Pre-ranked GSEA), as reported (Subramanian et al., 2005)
The gene-sets included in the GSEA analyses were retrieved from the Gene Ontology Biological Process collection as reported in the MSigDB database, and from the senescence pathway as described (Zhao et al., 2016)
Genome_build: GRCm38
Supplementary_files_format_and_content: txt file with raw gene counts for every gene and every sample

source_name: O1+ Sorted Oligodendrocyte

extract_protocol:
Mice were anesthetized, perfused with saline and brain removed. Brains from 8 Wt, 8 Cnp-Cre:Jab1flfl mutant mice and 8 p21-/- Cnp-Cre:Jab1fl/fl double mutant mice at P40 were dissociated with 0.4 mg/ml of collagenase type IV (Sigma-Aldrich) and through a 18G syringe to obtain a homogeneous cell suspension. Cell suspensions were further enriched by an isotonic Percoll gradient, myelin was removed, cells washed in PBS and finally centrifuged and resuspended in MACS Buffer as described (Buttgereit et al., 2016).  Zombie Nir (BioLegend) was added to exclude non–viable cells. Samples were sorted on FACS Aria Fusion (BD Biosciences) and analyzed with Flow-jo (Three star). Mature oligodendrocytes were identified as single live cells CD45-O1+ and total RNA was isolated from sorted oligodendorcytes using ReliaPrepTM RNA Cell Miniprep System (Promega).
Libraries were prepared using the SMART-Seq® v4 Ultra® Low Input RNA Kit for Sequencing (Takara Bio USA). Sequencing was performed on a Illumina NovaSeq 6000 machine (Illumina, San Diego, CA) obtaining an average of 100 millions of paired-end reads per sample.

value: O1+ sorted oligodendrocyte derived from mouse brain

tag: age

value: post natal day 40

value: p21-/- Cnp-Cre:Jab1flfl


title: gastric DLBCL, case HI1

value: primary gastric  lymphoma

value: resistant to HPET

value: diffuse large B-cell lymphoma


title: dKO2


title: Lin54KO rep1

value: Embryonic stem cells


title: gastric DLBCL, case HD8


title: B4 ctr Brd3 ChIP-seq

source_name: embryonic stem cells

value: embryonic stem cell line

value: Brd4 degron line ctr Brd3 ChIP


title: gastric DLBCL, case HI2


title: dKO1


title: RNA-seq-control-1

value: CD34+CD41+ cells were sorted by flow cytometry on day 7


title: KO4


title: B4 ctr Brd2 ChIP-seq

value: Brd4 degron line ctr Brd2 ChIP


title: gastric DLBCL, case HD6


title: B4 ctr IgG ChIP-seq

value: Brd4 degron line ctr IgG ChIP


title: dKO5


title: RNA-seq-Ricolinostat-2


title: RNA-seq-Ricolinostat-3


title: B2 dep Input ChIP-seq

value: Brd2 depletion Input


title: gastric DLBCL, case HD5


title: B2 dep p300 ChIP-seq

value: Brd2 depletion p300 ChIP


title: gastric DLBCL, case HD3


title: RNA-seq-Ricolinostat-1


title: gastric DLBCL, case HD2


title: KO3


title: KO1


title: gastric DLBCL, case HD7


title: B2 dep CTCF ChIP-seq

value: Brd2 depletion CTCF ChIP


title: CT6

value: wild-type


title: gastric DLBCL, case HD1

value: sensitive to HPET


title: B2 dep Brd4 ChIP-seq

value: Brd2 depletion Brd4 ChIP


title: RAD21_dep BRD2 CUT&Tag (bethyl)

data_processing:
Library strategy: CUT&Tag
Illumina’s Bcl2tofastq2 v2.17 was used to convert BcL files to fastq files and to demultiplex the samples
CUT&Tag pair-end reads were first adapter removed by Cutadapt and mapped to mm10 genome build using Bowtie2 with the following parameters: --no-discordant --no-mixed --phred33 -X2000 –threads32. For Micro-C, Bowtie 2.3.0 with ‘very-sensitive-local’ mode was used.
Reads mapped to mitochondria/uncharacterized chromosomes (chrM/chrUn/random) and PCR duplicates were removed by samtools.
CUT&Tag peaks were called by SEACR.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig (bw)

extract_protocol: BRD2 CUT&Tag was performed  by using the primary anti-BRD2 antibody from Bethyl Laboratory (A302-583A). pAG-Tn5 was ordered from EpiCypher (15-1017). Due to the high sensitivity and low background, we used SEACR package for peak calling with default parameters.

value: embryonic stem cells

value: embryonic stem cell

value: auxin 6 hour,  BRD2 CUT&Tag, pAG-Tn5


title: scRNA-Seq StageII-JNKIN8-0330

source_name: human somatic cells during chemical reprogramming stage II without JNKIN8

growth_protocol: Human embryonic fibroblasts (HEFs) were cultured in high glucose DMEM supplemented with 15% Fetal Bovine Serum (FBS), 1% GlutaMAX™, 1% MEM Non-Essential Amino Acids Solution (NEAA), 1% Penicillin-Streptomycin and 0.055 mM 2-mercaptoethanol under 21% O2, 5% CO2 at 37 ℃. Adult human adipose derived mesenchymal stromal cells (hADSCs) were cultured in Mesenchymal Stem Cell Growth Medium 2 under 21% O2, 5% CO2 at 37 ℃.

extract_protocol:
Using single cell 3’ Library and Gel Bead Kit V3.1 (10x Genomics, 1000075) and Chromium Single Cell B Chip Kit (10x Genomics, 1000074), the cell suspension (300-600 living cells per microliter determined by Count Star) was loaded onto the Chromium single cell controller (10x Genomics) to generate single-cell gel beads in the emulsion according to the manufacturer’s protocol. In short, cells at different time points throughout chemical reprogramming process were harvested and resuspended at 1 x 106 cells per milliliter in 1 x PBS with 0.04% BSA. About 1 x 104 cells were added to each channel, and the target cell will be recovered was estimated to be about 5 x 103 cells. Captured cells were lysed and the released RNA were barcoded through reverse transcription in individual GEMs. Reverse transcription was performed on a S1000TM Touch Thermal Cycler (Bio Rad) at 53 ℃ for 45 min, followed by 85 ℃ for 5 min, and hold at 4 ℃. The cDNA was generated and then amplified, and quality assessed using an Agilent 4200.
According to the manufacture’s introduction, Single-cell RNA-seq libraries were constructed using Single Cell 3’ Library and Gel Bead Kit V3.1 The libraries were finally sequenced using an IlluminaNovaseq6000 sequencer with a sequencing depth of at least 1 x 105 reads per cell with pair-end 150 bp (PE150) reading strategy (performed by CapitalBio Technology, Beijing).
single cell RNA-seq


title: B2 dep Brd3 ChIP-seq

value: Brd2 depletion Brd3 ChIP


title: RNA-seq-control-2


title: CT5

value: O1+ sorted oligodendrocyte derived from mouse brain

value: post natal day 40


title: scRNA-Seq StageII-5azac-0330

source_name: human somatic cells during chemical reprogramming stage II without 5azac


title: Ctr BRD2 CUT&Tag (bethyl)

value: Control

value: BRD2 CUT&Tag, pAG-Tn5


title: CT3


title: gastric DLBCL, case HD4

value: primary gastric  lymphoma

value: diffuse large B-cell lymphoma


title: KO2


title: B2 dep IgG ChIP-seq

value: embryonic stem cell line

value: Brd2 depletion  IgG ChIP


title: KO_Aorta 780

city: Lund

first: Sebastian

last: Albinsson

address: BMC D12

country: Sweden

institute: Lund University

description: KO_Aorta 780

data_processing:
Demultiplexing: organized the FASTQ files based on the sample index information, and generated the statistics and reporting files. This task was performed using the bcl2fastq2 software with default settings
Raw Quality Control (QC): FastQC provided quality control analyses and checked on raw sequence data coming from the above Demultiplexing step of the pipeline.
Read Mapping: alignment of reads to the specified reference genome. This task was performed using the HISAT2 software package, and the reference genome sequence was from the Ensemble database, the Gallus Gallus 5.0, and the annotation (GTF) from the release 92.
Mapping QC: mapping quality control checked such as evaluating the distribution of reads mapped by the above mapping step.
Expression counts: assembled the alignments into full transcripts and quantified  the expression levels of each gene and transcript. This task was performed using the StringTie software package.
DE analysis: Differentially expressed genes (DEG) analysis was performed using DESeq2.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-separated text files generated by StringTie software package; contains expression counts

source_name: Aorta

growth_protocol: Animal were used after weaning at age of 5-7 weeks

extract_protocol:
RNA was extracted using Qiagen RNAeasy kit
Library was prepared according to TruSeq® Stranded mRNA Sample Preparation Guide (Part # 15031047 Rev. E) Modification of “Enrich DNA Fragment” step: from 15 to 13 PCR cycles.

treatment_protocol: Wwtr1/Yap1 floxed, Myh11CreERT2 positive (KO) or negative (WT) mice were injected with Tamoxifen (1mg/mouse/day) for 5 consecutive days. Tissues were extracted 7 days after the first tamoxifen treatment

tag: gender

value: Male

value: Thoracic aorta

tag: modification

value: SMC specific, inducible Yap1/Wwtr1 KO

value: 5-7 weeks


title: CT1

value: wild-type


title: scRNA-Seq stageII-0330


title: KO_Aorta 782

description: KO_Aorta 782


title: S2

city: Hefei

first: Keqiang

last: He

state: China

address: 17 Lujiang Road, P.R.China

institute: The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China

data_processing:
Illumina Casava1.7 software used for basecalling.
Bowtie2 v2.2.3 was used for building the genome index,  and Clean Data was then aligned to the reference genome using HISAT2 v2.1.0. HISAT2 is the  successor to TopHat2, which uses a modified BWT algorithm to convert reference genomes to  index for faster speed and fewer resources
In order to guarantee the data quality which was used to analysis, the useful Perl  script was used to filter the original data (Raw Data)
Reads Count for each gene in each sample was counted by HTSeq v0.6.0
Genome_build: mm10

source_name: Mus musculus

extract_protocol:
Total RNAs are extracted from hippocampal tissues using Trizol (Invitrogen) and subjected to DNase I digestion for genomic DNA removal. A total amount of 2 μg RNA per sample was used as input material for the RNA sample preparations.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Hippocampus

value: surgery


title: B2 ctr Input ChIP-seq

first: Robert

last: Tjian

address: LKS

tag: cell type

value: Brd2 degron line ctr Input


title: KO_Aorta 759

description: KO_Aorta 759


title: B2 ctr p300 ChIP-seq

tag: strain

value: Brd2 degron line ctr p300 ChIP


title: scRNA-Seq StageII-Tranyl-0330

source_name: human somatic cells during chemical reprogramming stage II without Tranyl


title: CTRL_Aorta 787

description: CTRL_Aorta 787

value: Cre negative Tamoxifen treated


title: StageIII_Day12-0618

source_name: human somatic cells during chemical reprogramming stage III


title: S1


title: StageI_Day8-0618


title: C2

value: sham


title: StageII_Day20-0618


title: CTRL_Aorta 785

description: CTRL_Aorta 785


title: B2 ctr CTCF ChIP-seq

value: Brd2 degron line ctr CTCF ChIP


title: B2 ctr Brd4 ChIP-seq

value: Brd2 degron line ctr Brd4 ChIP


title: scRNA-Seq hADSCs-0618


title: C1


title: CTRL_Aorta 788

description: CTRL_Aorta 788


title: B2 dep Brd2 ChIP-seq

value: Brd2 depletion Brd2 ChIP


title: scRNA-Seq HEFs-0330

source_name: human embryonic fibroblasts


title: B2 ctr Brd3 ChIP-seq

value: Brd2 degron line ctr Brd3 ChIP


title: MB-3

first: Weijian

last: YAO

state: Beijing

address: No. 8 Xishiku Street, Xicheng District

department: Renal division

institute: Peking university first hospital

data_processing:
The standard Chromium’s Cell Ranger pipeline (version 3.1.0) to align the raw sequence reads according to the reference genome (mm10-2.1.0) using STAR.
Genome_build: mm10
Supplementary_files_format_and_content: cell barcode files
Supplementary_files_format_and_content: gene files
Supplementary_files_format_and_content: gene-barcode counts

source_name: Blood

extract_protocol:
Single cells were suspended in calcium- and magnesium-free PBS containing 0.04% weight/volume BSA.Cells were resuspended to a final cell concentration of 700~1200 cells/μl with more than 85% viability. 8,000-12,000 cells were captured in droplets. After the reverse transcription step, emulsions were broken and barcoded-cDNA was purified with Dynabeads, followed by PCR amplification (at 98°C for 45 sec; at 98°C for 20 sec, 67°C for 30 sec, 72°C for 1 min with 13-18 cycles; at 72°C for 1 min). Amplified cDNA was then used for 3’ gene expression library construction.
RNA libraries were prepared with Chromium Single cell v2 or v3 Kits according to the manufacturer's protocol

value: unilateral ischemia-reperfusion renal injury (uIRI) 3day

value: Blood

tag: genptype

value: Wild type


title: B2 ctr Brd2 ChIP-seq

institute: UC Berkeley/HHMI

value: embryonic stem cell line

value: Brd2 degron line ctr Brd2 ChIP


title: WT_TREAT_3

city: Shanghai

first: Rui

last: Dong

address: Dongchuan Road

institute: Shanghai Jiao Tong University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence to get clean reads,the clean reads was compared to reference genomic sequences using HISAT, and the average ratio of each sample reached 97.51%.
Prediction of New transcript.The new transcription product was predicted by comparing the sequence alignment results with the reference gene sequences.We first selected potential regions with a length greater than 100 bp, an average coverage greater than 8 bp, and 60 bp away from upstream and downstream genes as candidate new transcripts. The genomic annotation information together with the new transcription products made up the integral reference genes that were used in the subsequent analyses.
The clean reads were mapped to the integral reference genes with Bowtie2 v2.2.5(Parameter: ：-q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -I 1 -X 1000 --no-mixed --no-discordant -p 1 -k 200) and the gene expression level was calculated by RSEM v1.2.12(Parameter：--forward-prob=0.0)
The fragments per kilobase of transcript per million mapped fragments (FPKM) incorporate normalization steps to ensure that expression levels for different genes and transcripts can be compared across runs. The DESeq2 method(parameter: abs log2(FoldChange) >= 1 && Adjusted Pvalue <= 0.05) was used to calculate the differentially expressed genes (DEG). Genes with fold change ≥ 2, Bonferroni-corrected P value (Padj) ≤0.05 and FPKM≥30 in at least one sample were determined to be DGEs.
Genome_build: Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S, complete genome  GenBank: CP001363.1
Supplementary_files_format_and_content: Excel files include GeneID, Normalized FPKM value of each sample, Padj Pvalue type , KEGG Orthology, GO Component, GO Function, GO Process, Blast nr

source_name: wild-type

growth_protocol: A single colony of WT or mutant was inoculated into fresh LB broth and grown at 37 °C with rotation at 200 rpm until an optical density at 600 nm (OD600) of 1.0 was achieved. Each culture was then inoculated at a dilution of 1:100 into 5 mL fresh LB and grown to mid-log phase.

extract_protocol:
RNA was extracted using TRIzol Reagent (Invitrogen, CAS 15596026) according to the manual.RNA quality and integrity was verified by electrophoretic analysis and UV spectroscopy using NanoDrop and Agilent 2100 instruments. The RNA integrity number for all samples were between 8.2 and 9.7.
The Strand-specific transcriptome library construction and RNA sequencing was done as follow. Briefly, 1 µg total RNA was digested with DNase I (Thermo Scientific) and treated with Ribo-Zero Magnetic Gold Kit (Epicenter) to deplete rRNA. The protocol of TruSeq RNA Sample Prep Kit v2 (Illumina) was used to construct the libraries. The RNA was fragmented into small pieces and first-strand cDNA was generated using Super Script II (Invitrogen). The products were purified and used in a Second Strand Master Mix containing dATP, dGTP, dCTP and dUTP. The purified fragmented cDNA was end-repaired and purified and A-tailed and adapters were attached. The purified product was digested with uracil-N-glycosylase to remove the dUTP containing second strand cDNA, followed by several rounds of PCR amplification to enrich the cDNA fragments. The PCR products were purified and the libraries were assessed using the Agilent 2100 Bioanalyzer and qPCR.

treatment_protocol: The culture of mid-log phase bacteria was treated with 3 mM H2O2 for 30 min.

tag: agent


title: WT_TREAT_2

organism: Salmonella enterica subsp. enterica serovar Typhimurium


title: B-1

value: unilateral ischemia-reperfusion renal injury (uIRI) 1day


title: ATAC-Seq hCiPSCs-1217-1#

data_processing:
Quality control was performed using FastQC.
The raw ATAC-seq reads were trimmed using Trimmomatic with parameter ‘ILLUMINACLIP:NexteraPE-PE.fa:2:30:7:1:true LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36’ to remove detected adapters.
The clean reads were mapped to human reference genome hg19 using Bowtie2 with parameter ‘--very-sensitive’.
The output SAM files were converted to BAM files and sorted by name using Samtools. Duplicated reads were removed using MarkDuplicates function of Picard tools. Low quality mapped reads and reads mapped to mitochondrial were filtered using Samtools.
After adjusting fragments 5bp forward to account for the Tn5 transposase occupancy, peak calling was performed to each sample using MACS2 with parameters ‘-g hs --nomodel --shift -100 --extsize 200 --keep-dup all’.
To keep only consensus peaks among replicates of the same sample, Irreproducible Discovery Rate (IDR) analysis was performed between each pair of replicates, only peaks with score > 540 in at least one test were preserved.The enrichment signals of multiple replicates were merged for visualization.
Overlapped peaks were merged  in different samples and defined sample specific peak sets using R package ChIPpeakAnno. Each peak was then annotated to a closest gene using R package ChIPseeker.
The ATAC signal strength around peak region or gene promoter region was quantified using Deeptools.
Genome_build: hg19
Supplementary_files_format_and_content: .bw file containing ATAC signal intensity of each sample

source_name: human chemically induced pluripotent stem cells

growth_protocol: Human CiPS cells and hES cells (H1 and H9) were maintained in mTeSR™ Plus Medium on Matrigel coated plates under 21% O2, 5% CO2 at 37 ℃. Human embryonic fibroblasts (HEFs) were cultured in high glucose DMEM supplemented with 15% Fetal Bovine Serum (FBS), 1% GlutaMAX™, 1% MEM Non-Essential Amino Acids Solution (NEAA), 1% Penicillin-Streptomycin and 0.055 mM 2-mercaptoethanol under 21% O2, 5% CO2 at 37 ℃. Adult human adipose derived mesenchymal stromal cells (hADSCs) were cultured in Mesenchymal Stem Cell Growth Medium 2 under 21% O2, 5% CO2 at 37 ℃.

extract_protocol:
Approximately 5 x 104 cells of each sample were collected and washed once with cold PBS and re-suspended in 50 µL Lysis buffer (10 mM Tris-HCl PH7.4, 10 mM NaCl, 3 mM MgCl2, 0.5% NP-40).
DNA library construction were prepared by TurePrep DNA Library Prep Kit V2 for Illumina (Vazyme, TD501-02) and amplified by PCR using TruePrep Index Kit V2 for Illumina (Vazyme, TD202 96rxn). All ATAC libraries were sequenced on an Illumina Novaseq 6000 platform and 150 bp paired-end reads were generated.


title: ATAC-Seq hCiPSCs-0809-3#


title: WT_TREAT_1

value: wild-type


title: MB-0

value: untreated


title: ATAC-Seq hCiPSCs-1117-2#


title: R21 dep rep CTCF ChIP-seq

value: R21-dep CTCF ChIP


title: R21 dep rep R21 ChIP-seq

value: R21-dep Rad21 ChIP


title: R21 dep rep Brd4 ChIP-seq

value: R21-dep Brd4 ChIP


title: WT_CK_1

value: LB


title: WT_CK_2


title: Platelet-E2: Platelet early tumor rep2

city: Xi'an

first: Yue

last: Yin

state: Shaanxi

address: No. 76, Yanta West Road

department: Histology and Embryology

institute: Guilin Medical University

description: Subcutaneous injection of 2 × 10^3 B16F10 cells per mouse and autopsy showing no visible tumor 14 days post-inoculation, pooled sample of 10

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts (Novogene, China).
Clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.16.1).
Genome_build: mm9
Supplementary_files_format_and_content: Matrix table with raw gene counts for platelet samples
Supplementary_files_format_and_content: Matrix table with raw gene counts for PBMC samples

source_name: Platelet

extract_protocol:
Blood samples were collected from retro-orbital sinuses of C57BL/6 mice. Blood is collected into a tube containing the anti-coagulant EDTA. Anti-coagulated blood was centrifuged at 180 g at room temperature for 10 min, resulting in platelet-rich plasma. Platelets were isolated from the platelet-rich plasma by centrifugation at room temperature for 10 min at 1,250 g, after which the platelet pellet was lysed in TRIzol Reagent (Invitrogen, ThermoFisher) and frozen at -80 °C for further use. The bottom layer of the first centrifuged blood sample was further used for peripheral blood mononuclear cell (PBMC) isolation via mouse PBMC isolation kit (TBD science, Tianjin) following the manufacturer’s instructions. The final PBMC pellet was resuspended and lysed in TRIzol and kept in -80 °C for further use. Total RNAs were extracted according to TRIzol manual instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: B16F10 cells suspended in 100 μl HBSS or HBSS control saline were injected under the right flank subcutaneously using a 30G needle.

tag: tumor stage

value: Early

value: PBMC


title: ATAC-Seq hADSCs-1217


title: Platelet-E3: Platelet early tumor rep3

tag: tissue


title: R21 dep rep Brd2 ChIP-seq

city: Berkeley

value: R21-dep Brd2 ChIP


title: R21 dep rep Brd3 ChIP-seq

value: R21-dep Brd3 ChIP


title: ATAC-Seq hADSCs-0809


title: ATAC-Seq hCiPSCs-1117-1#


title: MT_TREAT_3

source_name: DsrA-deletion mutant

tag: genotype

value: DsrA-deletion mutant


title: Platelet-E5: Platelet early tumor rep5


title: ATAC-Seq HEFs-1117


title: MT_TREAT_2


title: B2 ctr IgG ChIP-seq

tag: treatment

value: Brd2 degron line ctr IgG ChIP


title: Platelet-E1: Platelet early tumor rep1

value: Blood


title: Platelet-C5: Platelet ctrl rep5

description: Subcutaneous injection of 100 μl HBSS, pooled sample of 10

value: Control


title: ATAC-Seq H1

source_name: hES cells H1


title: R21 dep rep IgG ChIP-seq

value: embryonic stem cell line

value: R21-dep IgG ChIP


title: MT_TREAT_1


title: R21 ctr rep CTCF ChIP-seq

value: Control CTCF ChIP


title: WT_CK_3

value: wild-type


title: MT_CK_3


title: Platelet-E4: Platelet early tumor rep4


title: R21 ctr rep R21 ChIP-seq

value: Control Rad21 ChIP


title: MT_CK_2


title: Platelet-C3: Platelet ctrl rep3

description: Subcutaneous injection of 100 μl HBSS, pooled sample of 5


title: shLIMD2_3

city: Changchun

first: Lixin

last: Chen

address: 1266 Fujin Road

institute: Jilin University

data_processing:
Cutadapt software (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9) was used to remove the reads that contained adaptor contamination,(command line: ~cutadapt -a ADAPT1 -A ADAPT2 -o out1.fastq -p out2.fastq in1.fastq in2.fastq -O 5 -m 100).
we used HISAT2 software (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) to map reads to the genome (for example:Homo sapiens Ensembl v96),(command line: ~hisat2 -1 R1.fastq.gz -2 R1.fastq.gz -S sample_mapped.sam).
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d.Linux_x86_64) with default parameters (command line: ~stringtie -p 4 -G genome.gtf -o output.gtf -l sample input.bam).
all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8.Linux_x86_64).
after the final transcriptome was generated, StringTie and ballgown(http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression level for mRNAs by calculating FPKM (FPKM = [total_exon_fragments / mapped_reads(millions) × exon_length(kB)]),(command line: ~stringtie -e -B -p 4 -G merged.gtf -o samples.gtf samples.bam).
Genome_build: hg18
Supplementary_files_format_and_content: processed data files format is in xlsx, and content the fpkm of all the samples.

source_name: ovarian

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). The RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >7.0, and confirmed by electrophoresis with denaturing agarose gel. Poly (A) RNA is purified from 1μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) using two rounds of purification.
Then the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min. Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA）. An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

value: LIMD2 knockdown


title: Platelet-C2: Platelet ctrl rep2


title: Control

value: control


title: R21 ctr rep Brd3 ChIP-seq

extract_protocol:
ChIP-seq: Cells were cross-linked for 10 min at room temperature with 1% methanol-free paraformaldehyde in PBS and quenched with 0.125 M glycine. Cells were scraped and resuspended in cold cell lysis buffer (5 mM PIPES at pH 8.0, 85 mM KCl, 0.5% NP-40) and incubated for 10 min on ice. After centrifuging, nuclear pellets were resuspended in at least 6 vol of sonication buffer (50 mM Tris-HCl at pH 8.1, 10 mM EDTA, 0.1% SDS), incubated for 10 min on ice, and sonicated using the Covaris S220 sonicator to obtain an average fragment length of ∼500 bp examined by electrophoresis. Sonicated chromatin was diluted in RIPA buffer, aliquoted, and incubated with Protein G Dynabeads that were prebound with individual antibodies for at least 1 h at room temperature. Immunoprecipitation was performed overnight at 4°C with 2–4 µg of antibodies. Ten percent of the chromatin was saved as input. Immunoprecipitated and input DNA was introduced with sequencing adaptors as described previously (Schmidl et al., 2015), washed extensively with RIPA buffer (low salt and high salt) and LiCl buffer, digested with proteinase K and RNase A, reverse-cross-linked at 60oC overnight followed by purification with the AmpureX beads. We also added the spike-in chromatin (active motif, 53083) and spike-in antibody (active motif, 61686) following the manufacturer’s instructions.
Micro-C: 5M ESC cells were resuspended by trypsin, fixed by freshly made 1% formaldehyde at room temperature for 10 min and quenched by adding Tris buffer (pH = 7.5) to the final 0.75 M at room temperature. Fixed cells were washed twice with 1X PBS and then were subjected to the second crosslinking reaction by 3 mM disuccinimidyl glutarate (DSG) (Thermo Fisher # 20593)  for 45 min at room temperature. The DSG solution was freshly made at a 300-mM concentration in DMSO and diluted to 3 mM in 1X PBS before use. The crosslinking reaction was quenched by 0.75 M Tris buffer and washed twice with 1X PBS. Crosslinked cells were snap-frozen in liquid nitrogen and stored at −80°C.  We performed chromatin fragmentation by the micrococcal nuclease (MNase) and optimize the MNase digestion level to have about 80 to 90% of mononucleosomes and 10 to 20% of di-nucleosomes. We typically use ∼20 units MNase for 1 million of JM8.N4 mESCs. Intact nuclei were extracted by treating cells with Micro-C Buffer #1 (50 mM NaCl, 10 mM Tris-HCl pH = 7.5, 5 mM MgCl2, 1M CaCl2, 0.2% NP-40, 1x Protease Inhibitor Cocktail) for 20 min on ice. Chromatin was digested with a pre-titrated MNase concentration (Worthington Biochem #LS004798) at 37°C for 10 min. MNase digestion was stopped by adding 4 mM EGTA and completely inactivated by incubating at 65°C for 10 min. Digested chromatin was washed twice with ice-cold Micro-C Buffer #2 (50 mM NaCl, 10 mM Tris-HCl pH = 7.5, 10 mM MgCl2).MNase digested chromatin was subjected to multiple steps of biochemical enzyme reactions to generate compatible ends for ligation of adapters for sequencing. Chromatin was incubated with T4 PNK (New England BioLabs # M0201)  in Micro-C end-repair buffer (50 mM NaCl, 10 mM Tris-HCl pH = 7.5, 10 mM MgCl2, 100 ug/mL BSA, 2 mM ATP, 5 mM DTT) at 37°C for 15 mi. We then incubate chromatin with Klenow Fragment in the Micro-C end-repair buffer with no dNTPs at 37°C for 15 min. The blunting and labeling reaction was triggered upon adding biotin-dATP (Jena Bioscience # NU-835-BIO14), biotin-dCTP (Jena Bioscience # NU-809-BIOX), dGTP, and dTTP to a final concentration of 66 mM each at room temperature for 45 min. The reaction was inactivated by adding 30 mM EDTA and incubating at 65°C for 20 min. Biotin-labeled chromatin was washed once by ice-cold Micro-C Buffer #3 (50 mM Tris-HCl pH = 7.5, 10 mM MgCl2). The crosslinked nucleosomes were then ligated by T4 DNA Ligase (New England BioLabs #M0202) in 500 μL solution at room temperature for at least 2 h, followed by exonuclease III (New England BioLabs #M0206) treatment to remove biotin-dNTPs on un-ligated ends by incubating ligated chromatin at 37°C for at least 15 min.To specifically extract the ligated di-nucleosomal DNA, the deproteinized chromatin was purified and separated on a low-melting agarose gel (Lonza #50081). A band at the size of 250 to 400 bp corresponding to the ligated dimers was gel-extracted for library preparation. The purified DNA with biotin-dNTPs was captured by Dynabeads® MyOne Streptavidin C1 (Thermo Fisher Scientific #65001). Standard Illumina library preparation protocol including end-repair, A-tailing, and adaptor ligation was performed on beads with the NEBnext Ultra II kit (New England BioLabs # E7645). An optimal PCR cycle for final library amplification was determined by quantification PCR (KAPA Biosystems #KK4602), typically between 5–10 cycles for the input cell number from 5M. The sequencing library was amplified by Kapa HiFi PCR enzyme (KAPA Biosystems #KK2601) with the lowest possible cycles to reduce PCR duplicates.
RNA-seq: Total RNA was isolated according to the manufacturer’s instruction, quantified by Nanodrop (Thermo Fisher Scientific) and diluted to 1 ng/µl in nuclease-free water.  A total of 1 ng of RNA was added to 2.5 µl of cell lysis buffer (nuclease-free water with 0.2 % v/v Triton X-100 and 0.1 U/µl RNase inhibitor), and subjected to cDNA synthesis and amplification as described before (Cembrowski et al., 2018). Libraries were prepared using a modified Nextera XT DNA protocol (Illumina, San Diego, CA) where 5 µM P5NEXTPT5 was substituted for the i5 primers in the kit. Libraries were quantified by qPCR (Roche), normalized to 2 nM, then pooled and sequenced on a NextSeq550 flowcell with 25 bases in read 1, 8 bases in the i7 index read, and 50 bases in read 2. The control library phiX (Illumina) was spiked in at a final concentration of 15% to improve color balance in read 1.
ATAC-seq: we performed ATAC-seq on 50,000 cells which were trypsinized, washed with PBS on ice, and resuspended in the reaction mix (25 μL of 2× TD buffer, 2.5 μL of transposase, 22.5 μL of nuclease-free H2O) for 30 min at 37°C. Following transposition, genomic DNA was purified and amplified by 10-14 cycles of PCR.Both ATAC-seq samples were sequenced in Illumina HiSeq 2500 or Nextseq with 150cycle paired-end sequencing

value: Control Brd3 ChIP


title: MT_CK_1

value: LB


title: R21 ctr rep Brd4 ChIP-seq

value: Control Brd4 ChIP


title: Nerve injury group3

city: hangzhou

first: huang

last: jie

address: binwen Road

institute: Zhejiang University of Chinese Medicine

data_processing:
Firstly, Cutadapt was used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases.
Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). We used Bowtie2 and Hisat2 to map reads to the genome of species. Remaining reads (unmapped reads) were still mapped to genome using tophat-fusion. CIRCExplorer2  and CIRI was used to denovo assemble the mapped reads to circular RNAs at first; Then, back splicing reads were identified in unmapped reads by tophat-fusion.
Genome_build: rn6
Supplementary_files_format_and_content: tab-delimited text files include SRPBM values for each Sample …

organism: Rattus norvegicus

source_name: The cavernous tissue of the penis

extract_protocol:
The cavernous tissue of the penis were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Sprague Dawley

value: The cavernous tissue of the penis

value: Bilateral nerve injury


title: Platelet-C1: Platelet ctrl rep1

value: PBMC


title: R21 ctr rep Brd2 ChIP-seq

data_processing:
Illumina’s Bcl2tofastq2 v2.17 was used to convert BcL files to fastq files and to demultiplex the samples
ATAC-seq, ChIP-seq pair-end reads were first adapter removed by Cutadapt and mapped to mm10 genome build using Bowtie2 with the following parameters: --no-discordant --no-mixed --phred33 -X2000 –threads32. For Micro-C, Bowtie 2.3.0 with ‘very-sensitive-local’ mode was used.
Reads mapped to mitochondria/uncharacterized chromosomes (chrM/chrUn/random) and PCR duplicates were removed by samtools. For Micro-C, pairs with multiple hits, low MAPQ, singleton, dangling end, self-circle,PCR duplicates and contacts shorter than 200bp (unligated mono-nucleosomes)  were discarded
ATAC-seq, ChIP-seq peaks were called using the MACS2 callpeak function using the –f BAMPE parameter.
For Micro-C, contact matrices were then normalized by using iterative correction (IC) in COOL files (Imakaev et al., 2012) or Knight-Ruiz (KR) (Knight and Ruiz, 2013) in HIC files. Regions with low mappability and high noise were blocked before matrix normalization. We expect that matrix balancing normalization corrects systematic biases such as nucleosome occupancy, sequence uniqueness, GC content, or crosslinking effects as reported in Imakaev et al. 2012 and Rao et al. 2014.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig (bw), hic, mcool

value: Control Brd2 ChIP


title: Nerve injury group2


title: TGS

city: Guangzhou

first: Qing

last: Zhou

state: Guangdong

address: 106#，ZHONG SHAN ER ROAD

institute: Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China

data_processing:
Basecalls performed using CASAVA version 1.8
Umi-tools was utilized to calculate the raw counts and cell whitelist by default parameter
We applied the Seurat [https://satijalab.org/seurat/] package for cell normalization and cell filtering considering the MT percentage, minimum and maximum gene numbers under following criteria:  -MT% < 20%;   -Cell Gene Number < Median Gene Number * 2;  -Cell Gene Number > 200.  PCA and tSNE analysis was used for the single cell to cell relation description. Graphcluster and K-mean was utilized for cell clustering and based on the marker gene achieved some cluster was combined. Wilcox rank sum test was then used for marker gene analysis.
Genome_build: GRCh38
Supplementary_files_format_and_content: *.counts.tsv.gz contains gene counts of each sample;  *.cellname.list contains cell barcode of each sample

source_name: lung adenocarcinoma

extract_protocol:
Cells from each sample were used for single-cell isolation using BD Rhapsody Single-Cell Analysis System (BD Biosciences). Before single-cell isolation, all cells were labeled using a BD Single-Cell Multiplexing Kit.
Sequencing libraries were conducted using the BD Rhapsody Single-Cell Analysis System (BD Biosciences), following the manufacture's protocol.

value: lung adenocarcinoma

tag: location

value: Lung

tag: sampling time

value: Immediately after resection


title: ATAC-Seq H9

source_name: hES cells H9


title: Platelet-A5: Platelet large tumor rep5

description: Subcutaneous injection of 1 × 10^5 B16F10 cells per mouse, pooled sample of 5

value: Blood

value: Late


title: R21 ctr rep IgG ChIP-seq

source_name: embryonic stem cells

value: embryonic stem cell line

value: Control IgG ChIP


title: Nerve injury group1


title: normal group3

value: Normal controls


title: Platelet-C4: Platelet ctrl rep4

value: Control


title: Platelet-A4: Platelet large tumor rep4

description: Subcutaneous injection of 1 × 10^5 B16F10 cells per mouse, pooled sample of 3


title: XMS


title: shLIMD2_4

value: LIMD2 knockdown


title: Platelet-A3: Platelet large tumor rep3


title: R21 dep Brd4 ChIP-seq

value: R21-dep Brd4 ChIP


title: R21 dep Input ChIP-seq

value: R21-dep Input ChIP


title: Platelet-A2: Platelet large tumor rep2

description: Subcutaneous injection of 1 × 10^5 B16F10 cells per mouse, pooled sample of 4


title: normal group2

value: Sprague Dawley


title: R21 dep Brd3 ChIP-seq

value: R21-dep Brd3 ChIP


title: ZYQ


title: Platelet-A1: Platelet large tumor rep1


title: LYB.2


title: R21 dep Brd2 ChIP-seq

value: R21-dep Brd2 ChIP


title: normal group1

value: The cavernous tissue of the penis


title: R21 dep IgG ChIP-seq

value: R21-dep IgG ChIP


title: RM2

source_name: rat chondrocytes

value: rat model

value: SD

value: cartilage


title: RM3


title: LYB.1

value: lung adenocarcinoma

value: Lung

value: Immediately after resection


title: GBG


title: PBMC-E5: PBMC early tumor rep5

description: Subcutaneous injection of 2 × 10^3 B16F10 cells per mouse and autopsy showing no visible tumor 14 days post-inoculation, pooled sample of 5

source_name: PBMC

value: Blood

value: Early

value: PBMC


title: CYZ


title: PBMC-E4: PBMC early tumor rep4


title: LJQ


title: R21 ctr Input ChIP-seq

value: embryonic stem cell line

value: Control Input ChIP


title: PBMC-E2: PBMC early tumor rep2

description: Subcutaneous injection of 2 × 10^3 B16F10 cells per mouse and autopsy showing no visible tumor 14 days post-inoculation, pooled sample of 4


title: R21 ctr Brd4 ChIP-seq

value: Control Brd4 ChIP


title: PBMC-E3: PBMC early tumor rep3


title: RM1


title: RC3

value: rat control


title: RC2


title: PBMC-E1: PBMC early tumor rep1


title: inputHA

city: Tianjin

first: shengnan

last: yuan

address: 288 Nanjing Road

institute: State Key Laboratory of Experimental Hematology, National Clinical Research Center for Hematological Disorders

data_processing:
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using BWA (v 0.7.12) and clean reads were aligned to the reference genome using BWA mem (v 0.7.12).
After mapping reads to the reference genome, we used the MACS2(version 2.1.0) peak calling software to identify regions of IP enrichment over background. A q-value threshold of 0.05 was used for all data sets.
Genome_build: ftp://ftp.ensembl.org/pub/release-94/fasta/homo_sapiens/dna/
Supplementary_files_format_and_content: bw files and raw files
Supplementary_files_format_and_content: peaks excel files

source_name: Human cell line

growth_protocol: K562 cells (HA-PHF6-overexpression or HA-overexpression) were cultured in 1640 medium with 10% fetal bovine serum (FBS)

extract_protocol:
The ChIP assay was performed with a ChIP assay kit (Cell Signaling Technology, Boston, MA, USA) according to the manufacturer’s recommendations. Briefly, chromatin from cross-linked HA-PHF6 OE K562 cells or control cells was sheared using an ultrasonicator (Covaris, S220, ABI, New York, USA) to obtain DNA in the size range of 100–400 bp. Immunoprecipitation was conducted with ChIP-grade HA tag antibody (Abcam, ab9110, Cambridge, UK)
The purified DNA was used for ChIP-seq library preparation. The library was constructed by the Novogene Corporation (Beijing, China). Subsequently, paired-end sequencing of the sample was performed on an Illumina platform (Illumina, CA, USA). Library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: Untreated

value: K562 leukemia cell

value: Human cell line

tag: chip antibody

value: untreated


title: R21 ctr Brd2 ChIP-seq

value: Control Brd2 ChIP


title: CYD


title: PBMC-C5: PBMC ctrl rep5

value: Control


title: inputWT

tag: cell line


title: RC1

extract_protocol:
RNA was harvested using Trizol reagent.
A total amount of 1.5 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer's recommendations and index codes were added to attribute sequences to each sample.

value: SD


title: IPWT

value: HA antibody (Abcam, ab9110, Cambridge, UK)


title: PBMC-C4: PBMC ctrl rep4