title: MDA-MB-231 cells, NatD-KO, KO2

city: Nanjing

first: Mengying

last: Xing

address: 163 Xianlin Avenue

department: The State Key Laboratory of Pharmaceutical Biotechnology

institute: Nanjing University

data_processing:
The raw reads were filtered by removing reads containing adapter, ploy-N and low quality reads for subsequent analysis. The steps of sequencing data filtering:
1) removing reads containing adapter;
2) removing reads containing poly-N (i.e., unrecognized bases), reads with a ratio greater than 5%
3) removing low-quality reads (the number of base which is Q≤10 is more than 50% of the entire read);
All the downstream analyses were based on clean data with high quality
Supplementary files format and content: hg38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: breast cancer

growth_protocol: MDA-MB-231 breast cancer cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Trizol (Takara). A total amount of 1μg qualified RNA per sample was used as input material for the library preparation.
The sequencing libraries were generated using the VAHTS mRNA-seq v2 Library Prep Kit for Illumina® (Vazyme, NR601) following manufacturer’s recommendations.Firstly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was performed using divalent cations under elevated temperature in Vazyme Frag/Prime Buffer. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. Second strand cDNA synthesis was subsequently performed using buffer, dNTPs, DNA polymerase I and RNase H. Then, the cDNA fragments were end repaired with the addition of a single ‘A’ base at the 3'-end of each strand, ligated with the special sequencing adapters (Vazyme, N803) subsequently. The products were purified and size selected with VAHTS TM DNA Clean Beads (Vazyme, N411) in order to get appropriate size for sequencing. PCR was performed and aimed products were purified.

treatment_protocol: NatD-KO Lentivirus production in HEK293T cells and infection of MDA-MB-231 and MCF7 cells were performed in accordance with standard protocols.

value: breast cancer

value: breast cancer cells

value: NatD knockout

value: CRISPR


title: Pachon25k

status: Public on Jun 13 2023

type: SRA

city: Kansas City

first: Huzaifa

last: Hassan

state: MO

country: USA

institute: Stowers Institute for Medical Research

description: Libraries were pooled, requantified, and sequenced as 75bp single reads on a high-output flow cell using the Illumina NextSeq 500 instrument

library_source: transcriptomic

data_processing:
Raw reads were demultiplexed into Fastq format allowing up to one mismatch using Illumina bcl-convert (v 3.10.5). Reads were aligned to UCSC genome Astyanax mexicanus 2.0 with STAR aligner (V 2.7.3a ), using Ensembl 102 gene models. TPM values were generated using RSEM (v 1.3.0 )
Assembly: Astyanax mexicanus 2.0
Supplementary files format and content: TPM gene expression in text file

molecule: total RNA

organism: Astyanax mexicanus

source_name: CFL

growth_protocol: Cells were seeded at different densities (10k; 25k; 50k & 100k cells/well) in ultra-low-attachment 96-well round-bottomed plates for 3D spheroid culture with 100µL complete media per well and maintained at 27C

extract_protocol:
Total RNA was extracted using the mirVana RNA isolation kit (Catalog number: AM1560) according to the manufacturer's instructions
Libraries were made according to the manufacturer’s directions for the TruSeq Stranded mRNA Library Prep kit (Illumina, Cat. No. 20020594)

treatment_protocol: Cell were freely grown in 3D Spheroid culture

tag: time

tag: cell line

value: CFL

tag: cell type

value: Cave Liver-derived cells

tag: genotype

value: WT

tag: treatment

value: 3D Spheroid culture


title: MDA-MB-231 cells, WT, WT2

country: China

organism: Homo sapiens

tag: tissue


title: WT cells, 48h activated in vitro; IL-12 + ACBI1, ChIP

city: San Diego

first: Bryan

last: McDonald

state: CA

address: 10010 N Torrey Pines Rd

institute: Salk Institute for Biological Studies

library_source: genomic

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
Single-end 75-bp reads were aligned to the M. musculus mm10 genome using STAR (Dobin et al., 2013) with default parameters.
ChIP-seq peaks were called using findPeaks within HOMER using -style factor and an -i input control. Differential ChIP peaks were called using getDiffExpression.pl with fold change ≥ 1.5 or ≤ 1.5, Poisson P value < 0.0001. ChIP-seq peaks were annotated by mapping to the nearest transcription start site (TSS) using the annotatePeaks.pl program.
Metaplots were generated using annotatePeaks.pl with parameters -size 2000 and -hist 10. Heatmaps showing overlap of binding sites were generated using mergePeaks in HOMER with flag -matrix, which outputs hypergeometric P values of overlap and the observed/expected ratio of overlap. Peaks sets were annotated with HOMER, and visualizations were created using deepTools.
bigWig files were generated using makeUCSCfile program in HOMER using -style chipseq and an -i input control
Assembly: mm10
Supplementary files format and content: bigWig (except for Input sample)

molecule: genomic DNA

organism: Mus musculus

source_name: WT

extract_protocol:
Cells were cross linked in 3 mM disuccinimidyl glutarate for 30 min then in 1% formaldehyde for 10 min at room temperature. After quenching with 125 mM glycine, the cells were washed in 1× PBS, pelleted, flash frozen in liquid nitrogen, and stored at 80 °C. Cell pellets were thawed on ice and incubated in lysis solution (50 mM Hepes KOH pH 8, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, and 0.25% Triton X-100) for 10 min. The isolated nuclei were washed (10 mM TrisHCl pH 8, 1 mM EDTA, 0.5 mM EGTA, and 200 mM NaCl) and sheared in (0.1% SDS, 1 mM EDTA, and 10 mM TrisHCl pH 8) with the Covaris E229 sonicator for 10 min. After centrifugation, chromatin was immunoprecipitated overnight at 4 °C with 1:50 T-bet/TBX21 (Cell Signaling Technology, mAb #97135S). The next day, the antibody-bound DNA was incubated with Protein A+G Dynabeads (Invitrogen) in ChIP buffer (50 mM Hepes KOH pH 7.5, 300 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, and 0.1% SDS), washed, and treated with Proteinase K and RNase A and reverse cross linked.
Purified ChIP DNA was used for library generation (NEBNext Ultra II DNA Library Prep Kit for Illumina) according to manufacturer’s instructions

value: CD8+ T cell

value: IL-12 + ACBI1

tag: chip antibody

value: T-bet


title: Pachon10k


title: Pachon100k


title: Pachon50k


title: Surface10k

source_name: SFL

value: SFL

value: Surface Liver-derived cells


title: Surface100k


title: Surface50k


title: MDA-MB-231 cells, WT, WT1


title: WT cells, 48h activated in vitro; IL-12, ChIP


title: iPS-AATSI-1

city: Beijing

first: Jie

state: Beijing

address: Tsinghua University

department: Basic Medical Sciences, School of Medicine

institute: Tsinghua University

description:
human iPSCs from CD34 cord blood
cultured cells

data_processing:
Illumina Casava software was used for basecalling.
Sequenced reads were trimmed for adaptor sequences, and masked for low-complexity or low-quality sequences, then mapped to hg38 genome using Bowtie2.
Peaks were called using MACS2.
TF motif binding were analyzed using Homer
Bigwig files were generated using Deeptools
Genome_build: hg38
Supplementary_files_format_and_content: bigwig file for each sample

source_name: human iPSCs from CD34 cord blood

growth_protocol: Undifferentiated hPSCs were cultured in E8 medium without feeders.

extract_protocol:
/
ATAC-seq library was prepared followed the omini-ATAC-seq protocol (Corces et al., 2017)

treatment_protocol: Human pluripotent stem cells were induced in AATS or AATSI medium supplemented with BMP4 and CHIR99021 for 3 days, and then FLK1+ cells were sorted and subjected to ATAC-seq.

value: induced pluripotent stem cells(iPSCs)

tag: passage number


title: iPS-AATSI-2


title: iPS-AATS-2


title: H1-AATSI-1

description: cultured cells

source_name: human embryonic stem cell line H1

value: Embryonic stem cells

value: human embryonic stem cell line H1


title: iPS-AATS-1


title: H1-AATSI-2

description: cultured cells


title: H1-AATS-1

description: cultured cells


title: GT/M1

type: RNA

city: Shinjuku-ku

first: Hidenori

last: Kojima

state: Tokyo

address: 5 Shinanomachi

department: Cardiology

country: Japan

institute: Keio University School of Medicine

hyb_protocol: Fragmented and labeled ss-cDNA were hybridized for 16 hr at 45°C on GeneChip Clariom S Array. GeneChips were washed and stained in the GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G.

data_processing: Raw data were processed with Affymetrix Expression Console software version 1.4 for normalization.

label: biotin

source_name: GT/M1 transduced MEFs

label_protocol: Biotinylated ss-cDNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (GeneChip WT PLUS Reagent Kit User Manual,  Affymetrix). Biotinylated ss-cDNA yield were checked with the NanoDrop ND-2000c Spectrophotometer.

growth_protocol: MEFs were transduced with the retrovirus (Gata4 and Tbx5 and either of Mef2c isoform1, 2, 6, or isoform2 fused with MyoD transactivation domain) and siRNA for control or Ep300 as indicated. The medium was replaced with DMEM/M199/10%FBS medium, which contained DMEM (high glucose) with L-glutamate and phenol red (Wako, Tokyo, Japan, 044-29765); Medium199 with Earle’s Salts, L-glutamate and 22 g/L sodium bicarbonate (Gibco, 11150-059); and 10% Hyclone Characterized FBS (Thermo Scientific, SV30014.03) after 24 hr of infection. Cells were collected after 1 week. The medium was changed two times a week.

extract_protocol: RNA was extracted using the ReliaPrep RNA Cell Miniprep System (Promega, Z6012). The RNA quality was determined by the RNA Integrity Number (RIN) value with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA)). Only specimens with RIN>7.0 were used in this study.

value: mouse embryonic fibroblast (MEF)

value: GT/M1 transduced


title: GT/M2

source_name: GT/M2 transduced MEFs

value: GT/M2 transduced


title: GT/M2+siEp300

source_name: GT/M2TAD/siEp300 transduced MEFs

value: GT/M2TAD/siEp300 transduced


title: MEFs

source_name: non treated MEFs

value: non treated


title: GT/M6

source_name: GT/M6 transduced MEFs

value: GT/M6 transduced


title: GT/M2+siCtrl

source_name: GT/M2TAD/siCtrl transduced MEFs

value: GT/M2TAD/siCtrl transduced


title: GT/M2TAD

source_name: GT/M2TAD transduced MEFs

value: GT/M2TAD transduced


title: Surface25k

value: WT

value: 3D Spheroid culture


title: H9-AATSI-2

description: cultured cells

source_name: human embryonic stem cell line H9

value: human embryonic stem cell line H9


title: MDA-MB-231 cells, NatD-KO, KO1

value: breast cancer

value: breast cancer cells

value: NatD knockout

value: CRISPR


title: H9-AATS-2

description: cultured cells

value: Embryonic stem cells


title: H1-AATS-2

description: cultured cells

value: human embryonic stem cell line H1


title: H9-AATS-1

description: cultured cells


title: H9-AATSI-1

description: cultured cells


title: priB_PROseq_WT_rep1

city: Vienna

first: Tobias

last: Neumann

address: Campus-Vienna-Biocenter 1

country: Austria

institute: IMP

description:
PRO-seq
none

data_processing:
library strategy: PRO-seq
3' adaptors were removed using cutadapt v1.4.2 with -O 5 -a NNNNTGGAATTCTCGGTGCC) and 9 nucleotides from their 5′ were removed and subsequently reverse complemented using fastx_reverse_complement (http://hannonlab.cshl.edu/fastx_toolkit; version 0.0.13)
Trimmed reads longer than 18bp were aligned to a hybrid mouse drosophila genome (mouse genome build NCBI m37, GCA_000001635.18, drosophila FlyBase release 5) using bowtie v1.0.0 with -v 2 --best --strata --tryhard -m 1 --chunkmbs 256
Unique mappers from the resulting BAM file were used to create unstranded, stranded and reverse stranded coverage tracks for visualisation using bedtools v2.27.1 bedtools genomecov -split -bg, bedtools genomecov  -split -bg -strand '+', bedtools genomecov -split -bg -strand '-') and bedGraphToBigWig from the kent-tools bedGraphToBigWig v4, bedGraphToBigWig -blockSize=256 -itemsPerSlot=1024
Normalised coverage tracks were created by dividing the coverage at each position with the total number of aligned reads per million. Spike-in normalised coverage tracks were generated with deeptools bamCoverage v2.1.0 by applying 1,000,000/count_of_Spike as scaling factor
Assembly: mm9

source_name: priB

growth_protocol: CH12 cells cultured in complete RPMI medium wit IL4/CD40/TGF beta stimulation,primary B cells were isolated from C57BL/6 (WT/WT) mice spleens using anti-CD43 MicroBeads (Miltenyi Biotec) and expanded in complete RPMI containing 5 µg/ml LPS (Sigma-Aldrich) and 5 ng/ml mouse recombinant IL-4 (Sigma-Aldrich) to allow B cell activation and class switch recombination to IgG1. B cells were harvested 72h after activation and 4 x 10^7 cells

extract_protocol:
trizol extraction
PRO-seq was performed as described previously with minor modifications. To isolate nuclei, CH12 cells and Drosphila S2 cells were resuspended in cold Buffer IA (160mM sucrose, 10mM Tris-Cl pH 8, 3mM CaCl2, 2mM MgAc2, 0.5% NP-40, 1mM DTT added fresh), incubated on ice for 3 min and centrifuged at 700g for 5 min. The pellet was resuspended in nuclei resuspension buffer NRB (50mM Tris-Cl pH 8, 40% glycerol, 5mM MgCl2, 0.1mM EDTA). For each run-on, 10 million CH12 nuclei were spiked with 10% Drosophila S2 nuclei in a total of 100µL NRB and incubated at 30°C for 3 min with 100 µL 2x NRO buffer including 5µl of each 1mM NTP (biotinylated ATP and GTP, and unlabelled UTP and CTP). The following steps were performed as described62 with the following changes: (1) we used different adapters, namely, 3' RNA adapter 5Phos/NNNNNNNGAUCGUCGGACUGUAGAACUCUGAAC/3InvdT-3’ and 5’RNA adapter: 5’-CCUUGGCACCCGAGAAUUCCANNNN-3’. (2) 3’ and 5’ ligations which were done at 16°C overnight, and (3) CapClip pyrophosphatase (Cellscript) used for 5’ decapping. RNA was reverse transcribed by SuperScript III RT (Invitrogen) with RP1 Illumina primer to generate cDNA libraries. Libraries were amplified using barcoding Illumina RPI-x primers and the universal RP1 and KAPA HiFi Real-Time PCR Library Amplification Kit. Amplified libraries were subjected to electrophoresis on 2.5% low melting agarose gel and amplicons from 150-350 bp were extracted from the gel, multiplexed and sequenced on Illumina platform NextSeq 550 SR75 high. Bioinformatics analyses were performed as described62 but additionally the random 8-mer was used to exclude PCR duplicates and only deduplicated reads were aligned.

value: primary B cells

tag: strain

value: C57BL/6 (WT/WT)


title: HiChIP H3K4me3 80% epiboly stage, atRA, replicate 2

city: Seville

first: José

middle: M.

last: Santos-Pereira

address: Avda. Manuel Siurot s/n

country: Spain

institute: IBiS, Universidad de Sevilla-CSIC

data_processing:
Reads from biological replicates were pooled and aligned using GEM
Ligation events were detected using TADbit and filtered for non-ligated and self-ligated events
Binary multiresolution hic files were generated using Juicer Tools Pre
Assembly: Zebrafish September 2014 (GRCz10/danRer10)
Supplementary files format and content: multiresolution hic files
Library strategy: Hi-ChIP

organism: Danio rerio

source_name: whole embryo

growth_protocol: Embryos were grown at 28°C in E3 medium until desired developmental stage

extract_protocol:
Embryos were fixed in 1% paraformaldehyde and quenched with 0.125M Glycine. Cell were lyses and extracted nuclei were processed for HiChIP preparation as previously described (Mumbach et al. 2016). Briefly, chromatin was digested with DpnII, fragment-ends were blunted and marked with dATP-biotin, followed by proximity ligation. Chromatin was sonicated in a Covaris M220 sonicator for fragments around 300 bp and immunoprecipitated with anti-H3K4me3 (abcam). DNA was extracted after cross-link reversal and biotinylated products were recovered with streptavidin-coated beads, TAGmented with Tn5 transposase and purified for library preparation.
Preparation of HiChIP libraries was performed as described for ATAC-seq assays in Buenrostro et al., 2015

treatment_protocol: Embryos were treated or not with 0.1 µM atRA at 30% epiboly and collected at 80% epiboly

value: whole embryo

tag: developmental stage

value: 80% epiboly

value: wild-type

value: H3K4me3 (Abcam, #ab8580)

value: atRA


title: CH12_PROseq_shLacZ_rep1

description:
PRO-seq
CH12_PROseq_shLacZ_20kb.bw

value: shLacZ


title: CH12_PROseq_shLacZ_rep2

description:
PRO-seq
CH12_PROseq_shLacZ_20kb.bw


title: ChIP-seq Sox3 80% epiboly stage, control, replicate 1

data_processing:
Reads were aligned using Bowtie
Filtering duplicates: duplicated pairs were removed using Samtools software
Peaks were called using MACS2 software with  q<0.05
Visualization: bigWig files were visualized using UCSC Browser
Assembly: Zebrafish September 2014 (GRCz10/danRer10)
Supplementary files format and content: Called peaks in narrowPeak format
Supplementary files format and content: Binary Big Wig files with reads extended 300 bp

extract_protocol:
Embryos were fixed in 1% paraformaldehide and quenched with 0.125M Glycine. Nuclei were extracted and lysed, and chromatin sonicated in a Covaris M220 sonicator to an average of 300bp fragments. Sonicated chromatin was divided in 6 aliquots and incubated overnight at 4ºC with 2µg of antibody per aliquiot. Immunoprecipitated chromatin was then incubated with magnetic beads, washed, TAGmented with Tn5 transposase (Schmidl et al., 2015) and eluted from beads. Then, chromatin was decrosslinked and DNA was purified using Minelute kit (Qiagen)
Preparation of ChIPmentation libraries was performed as described for ATAC-seq assays in Buenrostro et al., 2015

value: Sox3 (GeneTex, #GTX132494)

value: control


title: E. coli, zinc pre-exposed, Day 5, biol rep 2

city: Boston

first: Mark

last: Suprenant

state: MA

address: 44 Cummington Mall

department: BME

institute: Boston University

description:
Zn_R2_Exposed_5D_Zn
Processed Data Normalized Counts Zn R2 vs WT.xlsx

data_processing:
Quality control and adapter trimming was performed with bcl-convert (v 4.1.5 default parameters) . Read mapping was performed with HISAT2 (v 2.2.0 default parameters + '--very-sensitive'
Read quanitification was performed using Subread's featureCounts (v 2.0.1 default parameters + '-Q 20') functionality. Read counts loaded into R (v 4.0.2 default parameters) were normalized using edgeR's (v 1.14.5 default parameters) Trimmed Mean of M values algorithm.
Susequent values were then ocnverted to counts per million. Differential expression analysis was performed using edgeR's exact test for differences between two groups of ngetive-bionomial counts with an estimated dispersion value of .1.
Assembly: U00096
Supplementary files format and content: microsoft excel file includes all gene locustags, gene names, descriptions, feature type, log of fold change of expresson level, p value, false discovery rate and normalized counts per million.

organism: Escherichia coli str. K-12 substr. MG1655

source_name: E. coli MG1655

growth_protocol: E. coli MG 1655 cells were grown for five days in Lysogeny Broth at 37C with shaking at 180rpm

extract_protocol:
Samples were shipped as pellets on dry ice to SeqCenter (Pittsburgh, PA, USA) for extraction and sequencing. RNA extraction was performed using Qiagen RNeasy kits with Dnase treatment
Per SeqCenter (Pittsburgh, PA, USA) instructions, samples were DNAse treated with Invitrogen DNAse (RNAse free) and library prep was completed with Illumina’s Standard Total RNA Prep ligation with Ribo-Zero Plus kit and 10bp unique dual indices.

treatment_protocol: Zinc pre-exposure was accomplished by supplementing Lysogeny Broth with 0.5 mM of zinc in the form of zinc sulfate. Zinc pre-exposure was maintained for five days with RNA extraction performed at the end of the pre-exposure time period.

value: E. coli MG1655

value: bacteria

value: WT

value: 0.5mM Zinc

value: Day 5


title: ChIP-seq Meis2b 80% epiboly stage, atRA, replicate 1

value: Meis2b (GeneTex, #GTX127229)


title: ChIP-seq Sox3 80% epiboly stage, atRA, replicate 1


title: HiChIP H3K4me3 80% epiboly stage, control, replicate 1

description: HiChIP_H3K4me3_80epi_control_combined.hic


title: E. coli, WT control, Day 5

description:
WT_R2_Exposed_5D_LB
Processed Data Normalized Counts Zn R1 vs WT.xlsx
Processed Data Normalized Counts Zn R2 vs WT.xlsx

value: 0mM Zinc


title: ChIP-seq Sox3 80% epiboly stage, control, replicate 2


title: ChIP-seq Sox3 80% epiboly stage, atRA, replicate 2


title: HiChIP H3K4me3 80% epiboly stage, control, replicate 2


title: HiChIP H3K4me3 80% epiboly stage, atRA, replicate 1


title: ChIP-seq Meis2b 80% epiboly stage, control, replicate 1


title: 14d_HAV_rep_3

city: CHAPEL HILL

first: Jason

last: Whitmire

state: NC

address: 5062 Genetic Medicine Bldg

institute: UNIVERSITY OF NORTH CAROLINA AT CHAPEL HILL

data_processing:
Sequencing reads were aligned to the human genome hg38 with STAR 2.6 and transcripts quantified using Salmon 0.7 and Gencode v40
Differential expression analysis was carried out using default settings in the DESeq2 package in R4.0
Assembly: hg38
Supplementary files format and content: excel spreadsheet of normalized counts for each sample

extract_protocol:
mirVana kit
Illumina TruSeq RNA Library Prep Kit

value: HAV


title: 14d_HAV_rep_1


title: 14d_HAV_rep_2


title: 14d_Mock_rep_3

value: Mock


title: ChIP-seq Meis2b 80% epiboly stage, atRA, replicate 2

value: whole embryo


title: ChIP-seq Hoxb1b 80% epiboly stage, atRA, replicate 2

value: 80% epiboly

value: Hoxb1b (GeneTex, #GTX128322)


title: ChIP-seq Hoxb1b 80% epiboly stage, atRA, replicate 1

value: wild-type


title: ChIP-seq Hoxb1b 80% epiboly stage, control, replicate 2


title: priB_PROseq_WT_rep2

description:
PRO-seq
none

value: primary B cells

value: C57BL/6 (WT/WT)


title: 14d_Mock_rep_2


title: 14d_Mock_rep_1


title: ChIP-seq Meis2b 80% epiboly stage, control, replicate 2


title: E. coli, zinc pre-exposed, Day 5, biol rep 1

description:
Zn_R1_Exposed_5D_Zn
Processed Data Normalized Counts Zn R1 vs WT.xlsx


title: ChIP-seq RARaa 24 hpf stage, control, replicate 1

value: 24 hpf

value: RARaa (GeneTex, #GTX124492)


title: 7d_HAV_rep_3


title: ChIP-seq RARaa 24 hpf stage, control, replicate 2

value: control


title: 7d_HAV_rep_1


title: 7d_Mock_rep_1


title: 7d_Mock_rep_2


title: 7d_Mock_rep_3


title: ChIP-seq Hoxb1b 80% epiboly stage, control, replicate 1


title: ChIP-seq RARaa 80% epiboly stage, atRA, replicate 1

value: atRA


title: ChIP-seq RARaa 80% epiboly stage, control, replicate 1


title: 7d_HAV_rep_2


title: ChIP-seq RARaa 5 somites stage, control, replicate 1

value: 5 somites


title: Adult, replicate 1, scRNAseq

city: Windsor

first: Phillip

last: Karpowicz

state: ON

address: 401 Sunset Avenue

department: Biomedical Sciences

country: Canada

institute: University of Windsor

library_source: transcriptomic single cell

data_processing:
Cell Ranger version 3.0.2
Assembly: Drosophila reference genome 6.25
Supplementary files format and content: Tab seperated values and matrix files

organism: Drosophila melanogaster

source_name: Intestine

extract_protocol:
Briefly, samples were dissected within 1h from ZT0-1, then were dissociated and filtered, counted and diluted to 800cells/ul. This protocol was completed (including dissections) within 3h.
Libraries were prepared according to 10xGenomics, 3' library (v3.1).

value: Intestine

tag: age

value: Day 7-8 Adult

tag: Sex

value: Female

value: CantonS(per01 background)


title: Input, SMS-CTR, for H3K27ac, rep1

city: Columbus

first: Benjamin

last: Stanton

state: Ohio

address: 700 Children's Drive

department: Center for Childhood Cancer

institute: Nationwide Children's Hospital

data_processing:
All ChIP data were processed with ENCODE ChIP-seq pipeline (v2.1.2) with chip.xcor_exclusion_range_max set at 25
ENCODE ChIP-seq alignment: normalized paired-end  fastqs were aligned with bowtie2 aligner to human genome UCSC hg38, with parameters bowtie2 -X2000 --mm
ENCODE ChIP-seq read filtering: black listed region, unmapped, mate unmapped, not primary alignment, multi-mapped, low mapping quality (MAPQ<30), duplicate reads and PCR duplicate were removed
ENCODE ChIP-seq peak calling: Peaks were called with MACS2, with parameters -p 1e-2 --nomodel --shift 0 --extsize ${FRAGLEN} --keep-dup all -B –SPMR. IDR analyses were performed on peaks from replicate samples, with threshold 0.05
Assembly: hg38
Supplementary files format and content: peak text files, BED format
Supplementary files format and content: bigwig files, signals represent fold change over Input

source_name: RD

growth_protocol: RH4, RH30, RD, SMS-CTR, and C2C12 were grown in DMEM supplemented with 10% FBS.

extract_protocol:
For spike-in normalized ChIP-seq, human RMS cells and mouse C2C12 cells were fixed in 1% formaldehyde for 10 minutes before quenching with 125 mM glycine. Cells were combined in a ratio of 3 human:1 mouse cell equivalents for each experiment prior to sonication. Sonicated chromatin was immunoprecipitated with antibodies against H3K27ac (Active Motif #39133), H3K9me3 (Active Motif #39062), MYOD1 (CST #13812), or CTCF (Millipore #07-729). Input and ChIP-enriched DNA was decrosslinked and purified using Qiagen MinElute PCR Purification columns prior to library preparation.
H3K27ac, MYOD1, and CTCF ChIP and Input DNA libraries were prepared by blunt end repair using the Lucigen End-It DNA End-Repair Kit, 3’ A-tailing by Klenow fragment (3’-5’ exo-) (NEB), adaptor ligation by T4 DNA ligase(NEB), and size selection on an E-Gel 2% EX agarose gel. Libraries were amplified with barcoded primers and isolated from unreacted primers by gel purification. Decrosslinked H3K9me3 ChIP and Input DNA was sonicated to enrich fragments 200-500-bp. Library prep was then performed without further size selection. Excess adapter and unused primers were removed with AmpureXP beads.  Libraries were sequenced on the HiSeq4000 or NovaSeq6000 platform running in PEx150bp mode.

value: RD

tag: antibody

value: Input

tag: antibody vendor/catalog


title: Immature Adult, replicate 1, scRNAseq

value: Day 1 Adult


title: ChIP-seq RARaa 80% epiboly stage, control, replicate 2

value: whole embryo

value: 80% epiboly


title: Pupa, replicate 1, scRNAseq

value: Red-eye pupa


title: Input, RD, for H3K27ac, rep1


title: H3K27ac, RH30, rep1

source_name: SMS-CTR

value: SMS-CTR

value: Active Motif, 39133


title: H3K27ac, RD, rep1


title: Veh_TC

city: Winston-Salem

first: Qianqian

last: Song

address: 1 Medical Center Boulevard

department: Cancer Genomics and Precision Oncology

institute: Wake Forest Baptist Comprehensive Cancer Center

data_processing:
Run cellranger mkfastq on the Illumina BCL output folder to generate FASTQ files.
Run cellranger count on each library that was demultiplexed by cellranger mkfastq.
Run cellranger aggr to aggregate multiple libraries from a single experiment that were analyzed by cellranger count.
Assembly: mm10 (CLF_CR, CLF_TC, Veh_CR, Veh_TC) and GRCh38 (HuTh17_CLF and HuTh17_Veh)
Supplementary files format and content: tab-delimited text files include UMI counts for each Sample …

molecule: polyA RNA

source_name: large intestinal lamina propria

extract_protocol:
Cells were isolated from colonic tissues via enzymatic digestion and density gradient protocol. Isolated cells were purified for Th17 cells by sorting RORgt-EGFP+ cells via FACS prior to extraction. Viable cells (mean 83.4 ± 9.9%, n = 5) in suspensions averaging 995 ± 267 cell/µl were loaded into wells of a 10X Chromium single-cell capture chip targeting a cell recovery rate of 2,000 – 3,000 cells. Single-cell gel beads in emulsion (GEMs) were created on a Chromium Single Cell Controller and scRNA-seq libraries were prepared using the Chromium Single Cell 3’ Library and Gel Bead kit according to the manufacturer's protocol (10× Genomics).
Single-cell gel beads in emulsion (GEMs) were created on a Chromium Single Cell Controller and scRNA-seq libraries were prepared using the Chromium Single Cell 3’ Library and Gel Bead kit according to the manufacturer's protocol (10× Genomics) - following these steps: (1) end repair and A-tailing; (2) adapter ligation; (3) post-ligation cleanup with SPRIselect; (4) sample index PCR and cleanup.  The barcode sequencing libraries were quantified using the Qubit 3.0 (Thermo Fisher, USA) and Agilent 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: Mice were treated with CLF or vehicle intraperitoneally every other day at human equivalent dose starting at day 1 (CR) or day 14 (TC). Human biopsies were incubated for 18 hours in CLF at 1 uM or vehicle at 37F in media and stimulated with 5 ng/ml PMA and 1 uM Ionomycin prior to extraction.

tag: model disease

value: T cell transfer colitis

value: Rag1-/- with Rorc gfp/+ transferred cells both on C57BL/6 background

value: pooled male and female

value: 8-12 Weeks


title: Input, RH30, for H3K27ac, rep1


title: Veh_CR

value: Citrobacter rodentium infection

value: Rorc gfp/+ on C57BL/6 background


title: H3K27ac, RH4, rep1


title: CLF_CR

value: Rorc gfp/+C57BL/6 background


title: Input, RH4, for H3K27ac, rep1


title: H3K9me3, RH4, rep2

value: Active Motif, 39062


title: ChIP-seq RARaa 80% epiboly stage, atRA, replicate 2

value: wild-type

value: RARaa (GeneTex, #GTX124492)

value: atRA


title: AOM PN, replicate 3

city: Glasgow

first: Kathryn

last: Gilroy

address: Garscube

country: United Kingdom

institute: CRUK Scotland Institute

description: 10x Genomics

data_processing:
Demultiplexing, barcode processing and gene counting were performed using Cell Ranger software v6.1.2
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Colon

extract_protocol:
Samples were homogenized and digested using a McIlwain Tissue CHopper and the GentleMACS Octo Dissociator in combination with the Mouse tumor dissociation kit (Miltenyi Biotec). Debris was removed, and then cells were sorted using a FACSAria sorter (BD Biosciences) and DAPI to remove dead cells.
Cells were loaded into a Chromium Chip G using a 10x Chromium Single-Cell 3’ v3 Gel Bead kit and Library (10x Genomics), then libraries were analysed using the Bioanalyzer High Sensitivity DNA kit (Agilent technologies). Sequencing was performed on an Illumina NovaSeq 6000 with paired-end 150-base reads.

treatment_protocol: Recombination of floxed genes was induced with 2mg tamoxifen, administered via intraperitoneal injection. AOM treatment started 4 days post tamoxifen injection, with 10mg/kg administered once weekly for 6 weeks. For intracolonic induction of Apc deficient mice, a single injection of 70ul of 100uM 4-OH tamoxifen was administered into the colonic submucosa. Mice were culled at clinical endpoint, and tumors harvested.

value: whole Colon Tumor

value: VilcreER P53fl/fl Notch1Tg

value: Male

value: AOM

tag: group

value: Ageing Tumor


title: AOM PN, replicate 2

description: 10x Genomics


title: H3K9me3, RH4, rep1


title: MYOD, RD, rep2

value: RD

value: MYOD

value: Cell Signaling, 13812 (D8G3)


title: Input, RH4, for H3K9me3, rep1

value: Input


title: Apc ICI, replicate 2

description: 10x Genomics

value: VilCreER Apcfl/fl

value: Intracolonic Induction


title: PNCCR Tumor Rep2 (iCcr-/-)

data_processing:
Raw sequence quality was assessed using FastQC version 0.11.8, then sequences were trimmed to remove adaptor sequences and low-quality base calls, defined as those with a Phred score of less than 20, using Trim Galore version 0.6.4.
Trimmed sequences were aligned to mouse genome build GRCm38.98 using HISAT2 version 2.1.0
Raw counts per gene were determined using FeatureCounts version 1.6.4 with the following options: --primary -C -t exon -g gene_id.
Assembly: GRCm38.98
Supplementary files format and content: matrix of raw counts

extract_protocol:
RNA was isolated using the Rneasy Micro Kit (Qiagen) according to the manufacturer’s protocol.
Libraries for cluster generation and DNA sequencing were prepared using an Illumina TruSeq RNA sample kit, then run on an Illumina NextSeq 500 (2x36 cycles, paired end, single index).

treatment_protocol: Induction of genetic recombination was performed by 1 x 2mg intraperitoneal injection of Tamoxifen. For intracolonic inductions, a single injection of 70 ul of 100uM 4-OH taxmofen was injected into the colonic submucosa. For AOM-treated mice, AOM treatment was started 4 days post tamoxifen induction, with a 10mg/kg dose given once weekly for 6 weeks. AZD7507 treatment (a CSF1R inhibitor) was administered at 100mg/kg twice daily. Colon tissue was harvested at day 5 or day 14, and tumor samples were harvested at clinical end point.

value: Female

value: VilCreER p53fl/fl Notch1Tg/+ iCcr-/-

value: Primary Colon Tumor


title: MYOD, RH30, rep2


title: Apc ICI, replicate 3

description: 10x Genomics


title: Apc ICI, replicate 1

description: 10x Genomics


title: PNCCR Tumor Rep1 (iCcr-/-)


title: MYOD, RH4, rep2


title: WT Colon Rep4

value: VilCreER

value: Colon Tissue


title: Input, RD, for MYOD, rep2


title: WT Colon Rep5


title: CLF_TC

value: T cell transfer colitis

value: Rag1-/- with Rorc gfp/+ transferred cells both on C57BL/6 background

value: pooled male and female

value: 8-12 Weeks


title: Input, SMS-CTR, for MYOD, rep2

value: SMS-CTR


title: Input, RH4, for H3K9me3, rep2


title: Input, RH30, for MYOD, rep2


title: ChIP-seq RARaa 5 somites stage, control, replicate 2

value: whole embryo

value: 5 somites

value: wild-type

value: RARaa (GeneTex, #GTX124492)

value: control


title: Input, RH4, for MYOD, rep2

value: Input


title: WT Colon Rep2


title: KPNT Tumor Rep3

value: Male

value: vilCreER KrasG12D/+ p53fl/fl Notch1Tg/+ Alk5l/fl


title: RH30, HiC, rep2

data_processing:
fastq-files are aligned to hg38 with bwa mem (version 0.7.17-r1188).
Mapped reads are then tagged for PCR duplications, parsed for ligation junction, merged, and then sorted into binned matrix using pairtools (v0.3.0).
Matrix aggregation and normalization (ICE) were carried out with cooltools (v0.4.0).
Compartments are called at 100kb using cooltools call-compartments, using H3K27ac as reference track.
TADs are called with R package TopDom (v0.10.1). Differential TAD analysis is carried out with R package diffHic (v1.22.0).
Assembly: hg38
Supplementary files format and content: HiC interaction matrix, mcool format
Supplementary files format and content: TAD calls, BED format

growth_protocol: RD, SMS-CTR and C2C12 myoblasts were cultured in DMEM with 10%FBS, Rh30 and Rh41 cells were grown in RPMI with 10% FBS.

extract_protocol:
RD, SMS-CTR, Rh30 and Rh41 cells were fixed for 10 minutes at room temperature (23 °C) and was spiked in with 20% mouse myoblasts (C2C12) and lysed gently with HiC buffer to release nuclei, permeabilized in 0.5% SDS for 10 minutes at 62 °C, quenched with 10% Triton X-100, and digested with MboI (200 U, 2h at 37 °C) which was then heat inactivated (20 min, 62 °C). Biotin incorporation was done with biotin-14-dATP (Thermo, Cat# 19524-016) and DNA Polymerase I, Large (Klenow) Fragment (NEB, Cat# M0210) for 1 hour at 37 °C.  Then we performed in situ ligation with T4 DNA ligase (4h room temperature). Nuclei were resuspended in TE and sonicated (5 cycles with shearing ‘on’ time with 30 seconds ‘on’ 30 seconds off, using the Active Motif Epi-shear probe sonicator, 30% power. The sheared DNA was reverse crosslinked with SDS and ProteinaseK O/N and pulled down with M-280 Streptavidin Dynabeads (Thermo, Cat#11205D), washed and eluted.
End-Repair: Resuspend the bead-bound sample from with 34 μl of TE pH 7.4, and use for the subsequent experimental steps. Add the reagent from End-It DNA End-Repair Kit to make the End-Repair reaction mix. Mix well by pipetting and incubate for 1 h @ RT with slow agitation in a Thermomixer. Resuspend to wash once with 500 μl of Tween Wash Buffer and then once with 500 μl of TE pH 7.4, keeping beads on the magnet throughout washes.   A-tailing to 3′ ends of DNA fragments: Resuspend the bead-bound sample from Step 45 with 32 μl of TE pH 7.4 and add the 3-5'Klenow and buffer to make the A-tailing reaction mix. Incubate for 45 min at 37 °C. Resuspend to wash once with 500 μl of Tween Wash Buffer and then once with 500 μl of TE pH 7.4, keeping beads on the magnet throughout washes.   Linker ligation : Resuspend the bead-bound sample from Step 46 with 22 μl of TE pH 7.4 and add the ligase and adapter to make the Adaptor ligation reaction mix. Incubate for a minimum of 1 h at room temperature with gentle rotation. Resuspend to wash once with 500 μl of Tween Wash Buffer and then once with 500 μl of TE pH 7.4, holding beads magnetically.   Amplify SPICE-C sequencing libraries with unique indexes: Resuspend beads from above step in 50 μl of water, and use 5μL for the following amplification steps. Add 1 μl of Multiplexing PCR FWD (forward) Primer and 1 μl of a REV (reverse) Primer M1-12, with unique barcode. Mix well with quick vortex and table-top centrifugation for several seconds. Add 25 μl of Phusion High-Fidelity PCR Master Mix with HF Buffer and pipette to mix. Remove 25 μl of sample and place in a 200-μl PCR strip tube to prepare for amplification. Run the PCR program for on-bead PCR amplification with 25 μl (half of the total material, after thorough mixing). Check library amplicon fragment lengths with aliquots of 2 μl diluted in 10 μl of water and run with E-Gel EX after 10, 12 and 14 cycles. Desired fragment length should be in the range of 300–800 bp.   library prep. Add 25-μl PCR reaction mix to 25 μl of AMPure beads (1:1 ratio to purify sample from unreacted PCR primers). Mix well and let stand 5 min with beads. Put on a magnet for 5 min. Then, remove the supernatant and wash quickly two times with 80% ethanol with gentle pipette aspiration. Let stand to dry on a magnet for 10–15 min. Add 20 μl of ultrapure water. Mix well and incubate for 5 min. Put on a magnet for 3 min.   Remove the 18 μl of purified indexed SPICE-HiC DNA. Indexed SPICE-C DNA can be stored at−20°C until ready for sequencing. (Modified from Gryder et al. Nat. Protoc., 2020)

treatment_protocol: No treatment conditions were used


title: KPNT Tumor Rep2


title: RH4, HiC, rep2


title: MYOD, SMS-CTR, rep2

value: MYOD

value: Cell Signaling, 13812 (D8G3)


title: AOM PN, replicate 1

description: 10x Genomics

value: whole Colon Tumor

value: VilcreER P53fl/fl Notch1Tg

value: AOM

value: Ageing Tumor


title: WT Colon Rep1

value: VilCreER

value: Colon Tissue


title: SMS-CTR, HiC, rep2

value: SMS-CTR


title: BPNT Tumor Rep3

value: vilCreER BrafV600E/+ p53fl/fl Notch1Tg/+ Alk5fl/fl

value: Primary Colon Tumor


title: H3K27ac, SMS-CTR, rep1

value: Active Motif, 39133


title: BPNT Tumor Rep2


title: RH4, HiC, rep1


title: RH30, HiC, rep1


title: KPNT Tumor Rep1


title: BPNT Tumor Rep1


title: SMS-CTR, HiC, rep1


title: BPT Tumor Rep2

value: vilCreER BrafV600E/+ p53fl/fl Alk5fl/fl


title: RD, HiC, rep1

value: RD


title: BPT Tumor Rep1


title: Histone H3 MNase ChIP-seq mononucleosomes (11) replicate 2

city: Gif-sur-yvette

first: Matthieu

last: Gerard

address: Route Nationale

country: France

institute: CEA

description: Melanoma cell chromatin was fragmented by micrococcal nuclease digestion and centrifugated for 16 hours through a 10-30 % sucrose gradient at 197,000 g, using a Beckman Coulter SW 41 swinging-bucket rotor. After centrifugation, 20 fractions were collected from top to bottom of the tube. ChIP-seq of a fraction containing canonical nucleosomes (fraction 11) was performed using antibodies against histone H3 (Abcam ab1791).

data_processing:
Cleaning with fastp=0.20.1, parameters: --length_required 25 --detect_adapter_for_pe --cut_front --cut_tail --cut_window_size 6 --cut_mean_quality 10 --unqualified_percent_limit 40 --n_base_limit 7 --average_qual 0 –overrepresentation_analysis --trim_poly_g
Alignment with bowtie2=2.4.2, default parameters
Marking duplicates reads with picard=2.23.8, parameters: CREATE_INDEX=true VALIDATION_STRINGENCY=STRICT
Filtring with samtools=1.11, parameters : -h -f 1 -F 3852 -q 30
Coverage with deeptools=3.5.0, parameters: bamCoverage --outFileFormat bigwig --binSize 1 --numberOfProcessors 5 --effectiveGenomeSize 2652783500 --normalizeUsing RPKM --MNase --minFragmentLength 10 --extendReads --centerReads --maxFragmentLength 500 --ignoreForNormalization chrX chrY chrM --blackListFileName hg38-blacklist.bed.gz
Assembly: Hg38
Supplementary files format and content: bigWig

growth_protocol: Human melanoma 501Mel cell line was grown in RPMI 1640 medium (Sigma) supplemented with 10% foetal calf serum and 1X penicillin/streptomycin.

extract_protocol:
Chromatin preparation: 501Mel cells were treated with trypsin and fixed in D15 culture medium containing 1 % formaldehyde (Sigma) for 10 min at 20°C . We stopped fixation by adding glycine to 125 mM, and the cells were centrifugated and washed three times with PBS. Cells were then permeabilized in Tris-HCl pH 7.5 15 mM, NaCl 15 mM, MgCl2 5 mM, EGTA 0.1 mM, KCl 60 mM, Sucrose 0.3 M, 0.4% IGEPAL CA-630 (I3021, Sigma) during 15 min on ice. We next diluted the cells with two volumes of MNase buffer (Tris-HCl pH 7.5 20 mM, NaCl 20 mM, CaCl2 2 mM, MgCl2 4 mM, KCl 15 mM, 0.1 M sucrose), and chromatin was digested during 10 min at 37 °C with 6 Kunitz units of MNase (New England Biolabs, 200 Kunitz units/µl) per 1 million cells. We stopped MNase digestion by adding a final concentration of 10 mM EDTA. We released chromatin from MNase-treated cells by passing the cell suspension 13 times through a 26G syringe. Next, we centrifuged the samples, and the supernatants containing the solubilized chromatin were used directly for ChIP-seq experiments or sucrose gradient centrifugation.
DNA libraries were prepared using MicroPlex Library Preparation Kit v2 or v3 (Diagenode)

treatment_protocol: untreated

value: Melanoma cell line

value: untreated

value: histone H3 (Abcam ab1791)


title: PNCCR Tumor Rep3 (CCRko/ko)

value: Male

value: VilCreER p53fl/fl Notch1Tg/+ CCRko/ko


title: Histone H3 MNase ChIP-seq mononucleosomes (11) replicate 1


title: Histone H3 MNase ChIP-seq low sedimentation rate (4-5-6-7) replicate 2

description: Melanoma cell chromatin was fragmented by micrococcal nuclease digestion and centrifugated for 16 hours through a 10-30 % sucrose gradient at 197,000 g, using a Beckman Coulter SW 41 swinging-bucket rotor. After centrifugation, 20 fractions were collected from top to bottom of the tube. ChIP-seq of low sedimentation rate fractions (pool of fractions 4, 5, 6 and 7) was performed using antibodies against histone H3 (Abcam ab1791).


title: PNCCR Tumor Rep2 (CCRko/ko)


title: PN Tumor AZD7507 Rep4

value: vilCreER p53fl/fl Notch1Tg/+


title: RD, HiC, rep2


title: PNCCR Tumor Rep1 (CCRko/ko)


title: WT Colon Rep3

value: Female


title: Flag-Brg1 MNase ChIP-seq total chromatin replicate 2

description: ChIP-seq of total ES cell chromatin fragmented by micrococcal nuclease (6 Kunitz units per million cells) was performed using antibodies against Flag (Sigma-Aldrich F1804)

data_processing:
Cleaning with fastp=0.20.1, parameters: --length_required 25 --detect_adapter_for_pe --cut_front --cut_tail --cut_window_size 6 --cut_mean_quality 10 --unqualified_percent_limit 40 --n_base_limit 7 --average_qual 0 –overrepresentation_analysis --trim_poly_g
Alignment with bowtie2=2.4.2, default parameters
Marking duplicates reads with picard=2.23.8, parameters: CREATE_INDEX=true VALIDATION_STRINGENCY=STRICT
Filtring with samtools=1.11, parameters : -h -f 1 -F 3852 -q 30
Coverage with deeptools=3.5.0, parameters: bamCoverage --outFileFormat bigwig --binSize 1 --numberOfProcessors 5 --effectiveGenomeSize 2652783500 --normalizeUsing RPKM --MNase --minFragmentLength 10 --extendReads --centerReads --maxFragmentLength 500 --ignoreForNormalization chrX chrY chrM --blackListFileName mm9-blacklist.bed.gz
Assembly: mm9
Supplementary files format and content: bigWig

growth_protocol: Mus musculus ES cells were grown on mitomycin C-inactivated Mus musculus embryonic fibroblasts at 37 °C, 5 % CO2, in DMEM (Sigma) supplemented by leukaemia inhibitory factor (LIF), 1X non-essential amino acids (Invitrogen), 15 % foetal calf serum (Invitrogen), 0.2 % β-mercaptoethanol (Sigma) and 1X penicillin/streptomycin (Invitrogen).

extract_protocol:
Chromatin preparation: ES cells were collected and fixed in D15 culture medium containing 1 % formaldehyde (Sigma) for 10 min at 20°C. We stopped fixation by adding glycine to 125 mM, and the cells were centrifugated and washed three times with PBS. Cells were then permeabilized in Tris-HCl pH 7.5 15 mM, NaCl 15 mM, MgCl2 5 mM, EGTA 0.1 mM, KCl 60 mM, Sucrose 0.3 M, 0.4% IGEPAL CA-630 (I3021, Sigma) during 15 min on ice. We next diluted the cells with two volumes of MNase buffer (Tris-HCl pH 7.5 20 mM, NaCl 20 mM, CaCl2 2 mM, MgCl2 4 mM, KCl 15 mM, 0.1 M sucrose), and chromatin was digested during 10 min at 37 °C with 6 Kunitz units of MNase (New England Biolabs, 200 Kunitz units/µl) per 1 million cells. We stopped MNase digestion by adding a final concentration of 10 mM EDTA. We released chromatin from MNase-treated ES cells by passing the cell suspension 13 times through a 26G syringe. Next, we centrifuged the samples, and the supernatants containing the solubilized chromatin were used directly for ChIP-seq experiments or sucrose gradient centrifugation.
DNA libraries were prepared using MicroPlex Library Preparation Kit v2 or v3 (Diagenode)

value: embryonic stem cells

value: Flag M2 (Sigma-Aldrich F1804)


title: Histone H3 MNase ChIP-seq low sedimentation rate (4-5-6-7) replicate 1


title: TBP MNase ChIP-seq total chromatin replicate 2

description: ChIP-seq of total ES cell chromatin fragmented by micrococcal nuclease (6 Kunitz units per million cells) was performed using antibodies against TBP (Abcam ab51841)

value: TBP (Abcam ab51841)


title: PN Tumor AZD7507 Rep3


title: PN Tumor Rep5


title: PN Tumor AZD7507 Rep1


title: PN Tumor AZD7507 Rep2


title: Sequential Control IgG-H2B MNase ChIP-seq total chromatin replicate 1

description: ES cell chromatin was fragmented by micrococcal nuclease digestion (6 Kunitz units per million cells). Sequential ChIP-seq was performed using in first step antibodies against control IgG (Abcam ab37415), and after an elution by competition with Oct4 peptide, eluate was incubated with antibodies against histone H2B (Abcam ab1790)

growth_protocol: Mus musculus ES cells were grown on mitomycin C-inactivated  Mus musculus embryonic fibroblasts at 37 °C, 5 % CO2, in DMEM (Sigma) supplemented by leukaemia inhibitory factor (LIF), 1X non-essential amino acids (Invitrogen), 15 % foetal calf serum (Invitrogen), 0.2 % β-mercaptoethanol (Sigma) and 1X penicillin/streptomycin (Invitrogen).

value: control IgG (Abcam ab37415) and histone H2B (Abcam ab1790)


title: Sequential Oct4-H2B MNase ChIP-seq total chromatin replicate 2

description: ES cell chromatin was fragmented by micrococcal nuclease digestion (6 Kunitz units per million cells). Sequential ChIP-seq was performed using in first step antibodies against Oct4 (MyBioSource MBS420786), and after an elution by competition with Oct4 peptide, eluate was incubated with antibodies against histone H2B (Abcam ab1790)

value: Oct4 (MBS420786) and histone H2B (Abcam ab1790)


title: Sequential Control IgG-H2B MNase ChIP-seq total chromatin replicate 2


title: PN Tumor Rep3


title: PN Tumor Rep2


title: Sequential Oct4-H2B MNase ChIP-seq total chromatin replicate 1


title: Smc3 MNase ChIP-seq total chromatin

description: ChIP-seq of total ES cell chromatin fragmented by micrococcal nuclease (6 Kunitz units per million cells) was performed using antibodies against Smc3 (Abcam ab9263)

value: Smc3 (Abcam ab9263)


title: PN Tumor Rep1

value: Primary Colon Tumor


title: PN Tumor Rep4


title: H3K27ac MNase ChIP-seq total chromatin replicate 1

description: ChIP-seq of total ES cell chromatin fragmented by micrococcal nuclease (6 Kunitz units per million cells) was performed using antibodies against histone modification H3K27ac (Abcam ab4729)

value: H3K27ac (Abcam ab4729)


title: H3K27ac MNase ChIP-seq total chromatin replicate 2


title: P Tumor Rep5

value: vilCreER p53fl/fl


title: P Tumor Rep4


title: P Tumor Rep3


title: RNA pol II MNase ChIP-seq total chromatin replicate 2

description: ChIP-seq of total ES cell chromatin fragmented by micrococcal nuclease (6 Kunitz units per million cells) was performed using antibodies against RNA polymerase II (Santa Cruz Biotechnology sc-55492)


title: Flag-Brg1 MNase ChIP-seq total chromatin


title: RNA pol II MNase ChIP-seq total chromatin replicate 1

value: RNA polymerase II (Santa Cruz Biotechnology sc-55492)


title: P Tumor Rep2


title: Nanog MNase ChIP-seq total chromatin replicate 3

description: ChIP-seq of total ES cell chromatin fragmented by micrococcal nuclease (6 Kunitz units per million cells) was performed using antibodies against Nanog (Reprocell RCAB-001P)

value: Nanog (Reprocell RCAB-001P)


title: PN Org Rep4

value: Organoid from Colon Tumor


title: PN Org Rep3


title: TBP MNase ChIP-seq total chromatin replicate 1

value: untreated


title: Nanog MNase ChIP-seq total chromatin replicate 2


title: Nanog MNase ChIP-seq total chromatin replicate 1


title: PN Org Rep1

value: Male


title: Sox2  MNase ChIP-seq total chromatin replicate 1

description: ChIP-seq of total ES cell chromatin fragmented by micrococcal nuclease (6 Kunitz units per million cells) was performed using antibodies against Sox2 (Santa Cruz Biotechnology sc-17320)


title: PN Org Rep2


title: Sox2  MNase ChIP-seq total chromatin replicate 2

value: Sox2 (Santa Cruz Biotechnology sc-17320)


title: Oct4 (sc-5279) MNase ChIP-seq total chromatin replicate 3

description: ChIP-seq of total ES cell chromatin fragmented by micrococcal nuclease (6 Kunitz units per million cells) was performed using antibodies against Oct4 (Santa Cruz Biotechnology sc-5279)

value: Oct4 (Santa Cruz Biotechnology sc-5279)


title: P Tumor Rep1

value: Female


title: PNCCR Macrophage Rep3

source_name: Macrophage

value: VilCreER p53fl/fl Notch1Tg/+ CCRko/ko

value: Colon Macrophages


title: PNCCR Macrophage Rep2


title: Oct4 (sc-5279) MNase ChIP-seq total chromatin replicate 1

value: embryonic stem cells


title: Oct4 (sc-5279) MNase ChIP-seq total chromatin replicate 2


title: PNCCR Macrophage Rep1


title: Oct4 (sc-8628) MNase ChIP-seq total chromatin replicate 2

description: ChIP-seq of total ES cell chromatin fragmented by micrococcal nuclease (6 Kunitz units per million cells) was performed using antibodies against Oct4 (Santa Cruz Biotechnology sc-8628)

value: Oct4 (Santa Cruz Biotechnology sc-8628)


title: H3K27ac MNase ChIP-seq total chromatin replicate 3


title: PN Macrophage Rep4

value: VilCreER p53fl/fl Notch1Tg/+


title: Oct4 (sc-8628) MNase ChIP-seq total chromatin replicate 1


title: PN Macrophage Rep3


title: PN Macrophage Rep2


title: PN Macrophage Rep1


title: AKP Intracolonic tumor Rep6

value: vilCreER Apcfl/+ KrasG12D/+ p53fl/fl

value: Intracolonic Colon Tumor


title: Histone H2B MNase ChIP-seq total chromatin control shRNA replicate 1

description: ChIP-seq of total ES cell chromatin fragmented by micrococcal nuclease (6 Kunitz units per million cells) was performed using antibodies against histone H2B (Abcam ab1790)

value: treated with control shRNA

value: histone H2B (Abcam ab1790)


title: AKP Intracolonic tumor Rep5


title: Histone H2B MNase ChIP-seq total chromatin shRNA O7 Brg1 replicate 2

value: treated with Brg1 shRNA O7


title: AKP Intracolonic tumor Rep3


title: AKP Intracolonic tumor Rep4


title: Histone H3 MNase ChIP-seq total chromatin shRNA Chd4 replicate 2

description: ChIP-seq of total ES cell chromatin fragmented by micrococcal nuclease (6 Kunitz units per million cells) was performed using antibodies against histone H3 (Abcam ab1791)

value: treated with Chd4 shRNA

value: histone H3 (Abcam ab1791)


title: AKP Intracolonic tumor Rep2


title: Histone H2B MNase ChIP-seq total chromatin shRNA O7 Brg1 replicate 1


title: Histone H3 MNase ChIP-seq total chromatin control shRNA replicate 6


title: Histone H3 MNase ChIP-seq total chromatin control shRNA replicate 5


title: KPN Intracolonic tumor Rep7

value: vilCreER KrasG12D/+ p53fl/fl Notch1Tg/+


title: Histone H3 MNase ChIP-seq total chromatin control shRNA replicate 4


title: KPN Intracolonic tumor Rep5

value: Male


title: Histone H3 MNase ChIP-seq total chromatin control shRNA replicate 3


title: KPN Intracolonic tumor Rep3


title: AKP Intracolonic tumor Rep1


title: KPN Intracolonic tumor Rep2


title: Histone H3 MNase ChIP-seq total chromatin control shRNA replicate 1


title: Histone H3 MNase ChIP-seq total chromatin shRNA O5 Brg1 replicate 2

value: treated with Brg1 shRNA O5


title: KPN Intracolonic tumor Rep6


title: KPN Intracolonic tumor Rep4


title: KPN Intracolonic tumor Rep1


title: Histone H2B MNase ChIP-seq total chromatin control shRNA replicate 2


title: Histone H3 MNase ChIP-seq total chromatin control shRNA replicate 2


title: OVE4, 72 hour spheroid, biol rep 2

city: London

first: Gabriel

middle: E

last: DiMattia

state: ONTARIO

address: 750 Base Line Rd E

department: Biochemistry

institute: Western University

data_processing:
Galaxy Version 2.0.1
Raw sequencing reads were uploaded to the Galaxy platform at https://usegalaxy.org/52 and tested for quality using FastQC to measure the per base sequence quality, GC content, N content, overrepresented sequences and adapter content.
Reads were mapped to mm10 using HISAT2 using default parameters
Mapped reads were counted using featureCounts (Liao et al. 2013) on the Galaxy Version 2.0.1 server using default parameters with built-in genome (mm10)
Assembly: mm10
Supplementary files format and content: .tabular.txt aligned reads at each Geneid generated by featureCounts

growth_protocol: Cells were maintained as adherent cultures in alpha MEM supplemented with 5% FBS, MEM non-essential amino acids (Gibco), 0.01 mg/mL insulin-transferring-selenium solution (Sigma), 0.01 µM estradiol (Sigma), and 2 ng/mL epidermal growth factor (Sigma)

extract_protocol:
Total RNA was isolated using the RNEasy Spin Column Kit (Qiagen CAT# 74104)
RNA libraries were prepared using VAHTS Total RNA-seq (H/M/R) Library Prep Kit for Illumina (PN NR603) from Vazyme Biotech Co. Ltd.

treatment_protocol: Cells were seeded into Ultra-Low Attachment plates to generate spheroids over 72 hours

value: oviductal epithelial cells

value: WT

value: 72 hour spheroid culture


title: Histone H3 MNase ChIP-seq total chromatin shRNA Chd4 replicate 1


title: Histone H3 MNase ChIP-seq total chromatin shRNA O7 Brg1 replicate 2


title: Histone H3 MNase ChIP-seq total chromatin Brg1-depleted auxin 3h replicate 2

value: treated with auxin for 3 hours


title: OVE4, 72 hour spheroid, biol rep 3


title: Histone H3 MNase ChIP-seq total chromatin Brg1-depleted auxin 3h replicate 1

value: embryonic stem cells


title: Histone H3 MNase ChIP-seq total chromatin Brg1-depleted auxin 20h replicate 3

value: treated with auxin for 20 hours


title: OVE4-p53R175H, 72 hour spheroid, biol rep 2


title: OVE4-p53R175H, 72 hour spheroid, biol rep 1


title: OVE4-p53R175H, 72 hour spheroid, biol rep 3


title: Histone H3 MNase ChIP-seq total chromatin Brg1-depleted auxin 20h replicate 2


title: Histone H3 MNase ChIP-seq total chromatin Brg1-depleted auxin 20h replicate 1


title: Histone H3 MNase ChIP-seq total chromatin 4X MNAse replicate 3

description: ChIP-seq of total ES cell chromatin fragmented by a four-fold dose of micrococcal nuclease (24 Kunitz units per million cells) was performed using antibodies against histone H3 (Abcam ab1791)

value: untreated


title: Histone H3 MNase ChIP-seq total chromatin 4X MNAse replicate 2


title: Histone H3 MNase ChIP-seq total chromatin shRNA O5 Brg1 replicate 1


title: OVE4-Trp53ko, 72 hour spheroid, biol rep 3


title: OVE4-Trp53ko, 72 hour spheroid, biol rep 1


title: OVE16, 72 hour spheroid, biol rep 3


title: Histone H3 MNase ChIP-seq total chromatin shRNA O7 Brg1 replicate 1


title: OVE16, 72 hour spheroid, biol rep 1


title: Histone H3 MNase ChIP-seq total chromatin replicate 3


title: Histone H3 MNase ChIP-seq total chromatin replicate 2


title: OVE16-p53R175H, 72 hour spheroid, biol rep 3


title: OVE16, 72 hour spheroid, biol rep 2


title: OVE4, 72 hour spheroid, biol rep 1


title: OVE16-p53R175H, 72 hour spheroid, biol rep 2


title: MNase-seq medium sedimentation rate (7-8-9) - Brg1-depleted auxin 20h replicate 4

description:
ES cell chromatin was fragmented by micrococcal nuclease digestion and centrifugated for 16 hours through a 10-30 % sucrose gradient at 197,000 g, using a Beckman Coulter SW 41 swinging-bucket rotor. After centrifugation, 20 fractions were collected from top to bottom of the tube. MNase-ChIP-seq of medium sedimentation rate fractions (pool of fractions 7, 8, and 9) was performed.
input_Smarca4_rep4_g7-8-9

data_processing:
Cleaning with fastp=0.20.1, parameters: --length_required 25 --detect_adapter_for_pe --cut_front --cut_tail --cut_window_size 6 --cut_mean_quality 10 --unqualified_percent_limit 40 --n_base_limit 7 --average_qual 0 –overrepresentation_analysis --trim_poly_g
Alignment with bowtie2=2.4.2, default parameters
Marking duplicates reads with picard=2.23.8, parameters: CREATE_INDEX=true VALIDATION_STRINGENCY=STRICT
Filtring with samtools=1.11, parameters : -h -f 1 -F 3852 -q 30
Coverage with deeptools=3.5.0 (for the blacklist : http://mitra.stanford.edu/kundaje/akundaje/release/blacklists/mm9-mouse/mm9-blacklist.bed.gz), parameters: bamCoverage --outFileFormat bigwig --binSize 1 --numberOfProcessors 5 --effectiveGenomeSize 2652783500 --normalizeUsing RPKM --MNase --minFragmentLength 10 --extendReads --centerReads --maxFragmentLength 500 --ignoreForNormalization chrX chrY chrM --blackListFileName mm9-blacklist.bed.gz
Assembly: mm9
Supplementary files format and content: bigWig


title: MNase-seq medium sedimentation rate (7-8-9) - Brg1-depleted auxin 20h replicate 3

description:
ES cell chromatin was fragmented by micrococcal nuclease digestion and centrifugated for 16 hours through a 10-30 % sucrose gradient at 197,000 g, using a Beckman Coulter SW 41 swinging-bucket rotor. After centrifugation, 20 fractions were collected from top to bottom of the tube. MNase-ChIP-seq of medium sedimentation rate fractions (pool of fractions 7, 8, and 9) was performed.
input_Smarca4_rep3_g7-8-9


title: OVE16-p53R175H, 72 hour spheroid, biol rep 1


title: OVE16-Trp53ko, 72 hour spheroid, biol rep 3


title: MNase-seq medium sedimentation rate (7-8-9) - Brg1-depleted auxin 20h replicate 2

description:
ES cell chromatin was fragmented by micrococcal nuclease digestion and centrifugated for 16 hours through a 10-30 % sucrose gradient at 197,000 g, using a Beckman Coulter SW 41 swinging-bucket rotor. After centrifugation, 20 fractions were collected from top to bottom of the tube. MNase-ChIP-seq of medium sedimentation rate fractions (pool of fractions 7, 8, and 9) was performed.
input_Smarca4_rep2_g7-8-9


title: OVE16-Trp53ko, 72 hour spheroid, biol rep 2


title: OVE16-Trp53ko, 72 hour spheroid, biol rep 1


title: MNase-seq medium sedimentation rate (7-8-9) - Brg1-depleted auxin 20h replicate 1

description:
ES cell chromatin was fragmented by micrococcal nuclease digestion and centrifugated for 16 hours through a 10-30 % sucrose gradient at 197,000 g, using a Beckman Coulter SW 41 swinging-bucket rotor. After centrifugation, 20 fractions were collected from top to bottom of the tube. MNase-ChIP-seq of medium sedimentation rate fractions (pool of fractions 7, 8, and 9) was performed.
input_Smarca4_rep1_g7-8-9


title: OVE4-Trp53ko, 72 hour spheroid, biol rep 2


title: ATAC-seq 24 hpf  stage, atRA, replicate 2

data_processing:
Alignment: reads were aligned to the reference genome using Bowtie2 software
Filtering duplicates: duplicated pairs were removed using Samtools software
Localization of the cleavage site: the enzyme cleavage site was determined as the position -4 (minus strand) or +5 (plus strand) from each read start, and this position was extended 5 bp in both directions
Visualization: bigWig files were visualized using UCSC Browser
Assembly: Zebrafish September 2014 (GRCz10/danRer10)
Supplementary files format and content: narrowPeak files with peaks called using MACS2 with q<0.01
Supplementary files format and content: bw files

extract_protocol:
Wild type or mutant embryos were dechorionated, deyolked and lysed
Assay for Transposase-Accessible Chromatin with high throughput sequencing (ATAC-Seq) experiments were performed as described in Buenrostro et al., 2015. Curr. Protoc. Mol. Biol. 109, 21.29.1-9. doi:10.1002/0471142727.mb2129s109

treatment_protocol: Embryos were treated with 0.1 µM atRA or DMSO at 30% epiboly and collected at 80% epiboly, or treated at 80% epiboly and collected at 12 somites or 24 hpf

value: whole embryo

value: 24 hpf

value: wild-type

value: atRA


title: Histone H3 MNase ChIP-seq total chromatin 4X MNAse replicate 1


title: ATAC-seq 24 hpf  stage, control, replicate 2

value: DMSO


title: ATAC-seq 24 hpf  stage, atRA, replicate 1


title: Histone H3 MNase ChIP-seq total chromatin replicate 1


title: ATAC-seq 24 hpf stage, control, replicate 1


title: WT MP cells, d8 H3K27ac C&R

data_processing:
Sequence reads were aligned to GRCm38 (mm10) using STAR v2.5.3a (parameters- default)
CUT&RUN peaks were identified using SEACR (-stringent -norm) with an IgG control. Metaplots were generated using annotatePeaks.pl with parameters -size 2000 and -hist 10. Heatmaps showing overlap of binding sites were generated using mergePeaks in HOMER with flag -matrix, which outputs hypergeometric P values of overlap and the observed/expected ratio of overlap. Peaks sets were annotated with HOMER, and visualizations were created using deepTools.
Assembly: GRCm38 (mm10)
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)
Library strategy: CUT&RUN

source_name: WT

extract_protocol:
Cells were washed in Foxp3/Transcription Factor staining buffer set (eBioscience) permeabilization buffer with 1X EDTA-free protease inhibitor, 0.5mM spermidine, and 2mM EDTA for 1h on ice. Cells were washed twice in buffer 2 (0.05%  (w/v) saponin, 1X EDTA-free protease inhibitors, 0.5mM spermidine in PBS) and resuspended in calcium buffer (buffer 2  containing 2mM CaCl2) to activate the MNase fusion protein. Following a 30 minute incubation on wet ice, 2x stop solution  (20mM EDTA, 4mM EGTA in buffer 2) was added and cells were incubated for 12 minutes in a 37 degree incubator to  release cleaved chromatin fragments. Supernatants were collected by centrifugation and DNA was extracted using a Qiagen  MinElute kit.
CUT&RUN libraries were prepared using the NEBNext Ultra II kit. 10 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 10-12 cycles on the thermocycler. Post amplification libraries were size selected at 150-350bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit.


title: ATAC-seq 12 somites stage, atRA, replicate 2

value: 12 somites


title: WT EEC cells, d8 H3K27ac C&R


title: WT TE cells, d8 H3K27ac C&R


title: ATAC-seq 12 somites stage, control, replicate 2


title: ATAC-seq 12 somites stage, atRA, replicate 1


title: MNase-seq medium sedimentation rate (7-8-9) replicate 4

description:
ES cell chromatin was fragmented by micrococcal nuclease digestion and centrifugated for 16 hours through a 10-30 % sucrose gradient at 197,000 g, using a Beckman Coulter SW 41 swinging-bucket rotor. After centrifugation, 20 fractions were collected from top to bottom of the tube. MNase-ChIP-seq of medium sedimentation rate fractions (pool of fractions 7, 8, and 9) was performed.
input_Tir1_rep4_g7-8-9


title: MNase-seq medium sedimentation rate (7-8-9) replicate 3

description:
ES cell chromatin was fragmented by micrococcal nuclease digestion and centrifugated for 16 hours through a 10-30 % sucrose gradient at 197,000 g, using a Beckman Coulter SW 41 swinging-bucket rotor. After centrifugation, 20 fractions were collected from top to bottom of the tube. MNase-ChIP-seq of medium sedimentation rate fractions (pool of fractions 7, 8, and 9) was performed.
input_Tir1_rep3_g7-8-9


title: WT MP cells, d8 H3K27me3 C&R


title: MNase-seq medium sedimentation rate (7-8-9) replicate 2

description:
ES cell chromatin was fragmented by micrococcal nuclease digestion and centrifugated for 16 hours through a 10-30 % sucrose gradient at 197,000 g, using a Beckman Coulter SW 41 swinging-bucket rotor. After centrifugation, 20 fractions were collected from top to bottom of the tube. MNase-ChIP-seq of medium sedimentation rate fractions (pool of fractions 7, 8, and 9) was performed.
input_Tir1_rep2_g7-8-9


title: ATAC-seq 80% epiboly stage, atRA, replicate 2

value: 80% epiboly


title: MNase-seq medium sedimentation rate (7-8-9) replicate 1

description:
ES cell chromatin was fragmented by micrococcal nuclease digestion and centrifugated for 16 hours through a 10-30 % sucrose gradient at 197,000 g, using a Beckman Coulter SW 41 swinging-bucket rotor. After centrifugation, 20 fractions were collected from top to bottom of the tube. MNase-ChIP-seq of medium sedimentation rate fractions (pool of fractions 7, 8, and 9) was performed.
input_Tir1_rep1_g7-8-9


title: MNase-seq low sedimentation rate (5-6) - Brg1-depleted auxin 20h replicate 3

description:
ES cell chromatin was fragmented by micrococcal nuclease digestion and centrifugated for 16 hours through a 10-30 % sucrose gradient at 197,000 g, using a Beckman Coulter SW 41 swinging-bucket rotor. After centrifugation, 20 fractions were collected from top to bottom of the tube. MNase-ChIP-seq of low sedimentation rate fractions (pool of fractions 5 and 6) was performed.
input_Smarca4_rep3_g5-6


title: MNase-seq low sedimentation rate (5-6) - Brg1-depleted auxin 20h replicate 4

description:
ES cell chromatin was fragmented by micrococcal nuclease digestion and centrifugated for 16 hours through a 10-30 % sucrose gradient at 197,000 g, using a Beckman Coulter SW 41 swinging-bucket rotor. After centrifugation, 20 fractions were collected from top to bottom of the tube. MNase-ChIP-seq of low sedimentation rate fractions (pool of fractions 5 and 6) was performed.
input_Smarca4_rep4_g5-6


title: ATAC-seq 12 somites stage, control, replicate 1


title: WT EEC cells, d8 H3K27me3 C&R


title: ATAC-seq 80% epiboly stage, atRA, replicate 1


title: ATAC-seq 80% epiboly stage, control, replicate 2


title: ATAC-seq 80% epiboly stage, control, replicate 1


title: WT TE cells, d8 H3K27me3 C&R


title: RNA-seq 24 hpf  stage, atRA, replicate 3

data_processing:
Reads were aligned against reference genome using STAR software
Read counts per gene were calculated using htseq-count script from HTSeq tools software package
Assembly: Zebrafish September 2014 (GRCz10/danRer10)
Supplementary files format and content: Individual counts files (reads per gene)
Supplementary files format and content: bw files

extract_protocol: RNA was extracted using TRIsure (Bioline), purified with Direct-zol RNA miniprep kit (Zymo Research) and treated with TURBO DNA free kit (Invitrogen)


title: MNase-seq low sedimentation rate (5-6) - Brg1-depleted auxin 20h replicate 2

description:
ES cell chromatin was fragmented by micrococcal nuclease digestion and centrifugated for 16 hours through a 10-30 % sucrose gradient at 197,000 g, using a Beckman Coulter SW 41 swinging-bucket rotor. After centrifugation, 20 fractions were collected from top to bottom of the tube. MNase-ChIP-seq of low sedimentation rate fractions (pool of fractions 5 and 6) was performed.
input_Smarca4_rep2_g5-6


title: MNase-seq low sedimentation rate (5-6) - Brg1-depleted auxin 20h replicate 1

description:
ES cell chromatin was fragmented by micrococcal nuclease digestion and centrifugated for 16 hours through a 10-30 % sucrose gradient at 197,000 g, using a Beckman Coulter SW 41 swinging-bucket rotor. After centrifugation, 20 fractions were collected from top to bottom of the tube. MNase-ChIP-seq of low sedimentation rate fractions (pool of fractions 5 and 6) was performed.
input_Smarca4_rep1_g5-6


title: RNA-seq 24 hpf  stage, atRA, replicate 2


title: Arid1a KO cells, d5 H3K27ac C&R

source_name: Arid1a KO

value: Arid1a KO


title: RNA-seq 24 hpf  stage, atRA, replicate 1


title: MNase-seq low sedimentation rate (5-6) replicate 4

description:
ES cell chromatin was fragmented by micrococcal nuclease digestion and centrifugated for 16 hours through a 10-30 % sucrose gradient at 197,000 g, using a Beckman Coulter SW 41 swinging-bucket rotor. After centrifugation, 20 fractions were collected from top to bottom of the tube. MNase-ChIP-seq of low sedimentation rate fractions (pool of fractions 5 and 6) was performed.
input_Tir1_rep4_g5-6


title: WT cells, d5 H3K27ac C&R


title: RNA-seq 24 hpf  stage, control, replicate 3


title: RNA-seq 24 hpf  stage, control, replicate 2


title: MNase-seq low sedimentation rate (5-6) replicate 3

description:
ES cell chromatin was fragmented by micrococcal nuclease digestion and centrifugated for 16 hours through a 10-30 % sucrose gradient at 197,000 g, using a Beckman Coulter SW 41 swinging-bucket rotor. After centrifugation, 20 fractions were collected from top to bottom of the tube. MNase-ChIP-seq of low sedimentation rate fractions (pool of fractions 5 and 6) was performed.
input_Tir1_rep3_g5-6


title: Tbet KO cells, d5 ARID1A C&R

source_name: Tbx21 KO

value: Tbx21 KO

value: ARID1A (CST #12354S)


title: RNA-seq 24 hpf stage, control, replicate 1


title: RNA-seq 12 somitesstage, atRA, replicate 3


title: Arid1a KO cells, Tbet-OE, d5 Tbet C&R

value: Tbet (CST #97135S)


title: MNase-seq low sedimentation rate (5-6) replicate 1

description:
ES cell chromatin was fragmented by micrococcal nuclease digestion and centrifugated for 16 hours through a 10-30 % sucrose gradient at 197,000 g, using a Beckman Coulter SW 41 swinging-bucket rotor. After centrifugation, 20 fractions were collected from top to bottom of the tube. MNase-ChIP-seq of low sedimentation rate fractions (pool of fractions 5 and 6) was performed.
input_Tir1_rep1_g5-6


title: RNA-seq 12 somites stage, control, replicate 2


title: MNase-seq low sedimentation rate (5-6) replicate 2

description:
ES cell chromatin was fragmented by micrococcal nuclease digestion and centrifugated for 16 hours through a 10-30 % sucrose gradient at 197,000 g, using a Beckman Coulter SW 41 swinging-bucket rotor. After centrifugation, 20 fractions were collected from top to bottom of the tube. MNase-ChIP-seq of low sedimentation rate fractions (pool of fractions 5 and 6) was performed.
input_Tir1_rep2_g5-6


title: RNA-seq 12 somites stage, atRA, replicate 2


title: MNase-seq top of gradient (2-3-4) - Brg1-depleted auxin 20h replicate 4

description:
ES cell chromatin was fragmented by micrococcal nuclease digestion and centrifugated for 16 hours through a 10-30 % sucrose gradient at 197,000 g, using a Beckman Coulter SW 41 swinging-bucket rotor. After centrifugation, 20 fractions were collected from top to bottom of the tube. MNase-ChIP-seq of top of gradient fractions (pool of fractions 2, 3 and 4) was performed
input_Smarca4_rep4_g2-3-4


title: WT cells, Tbet-OE, d5 Tbet C&R

value: WT


title: MNase-seq top of gradient (2-3-4) - Brg1-depleted auxin 20h replicate 3

description:
ES cell chromatin was fragmented by micrococcal nuclease digestion and centrifugated for 16 hours through a 10-30 % sucrose gradient at 197,000 g, using a Beckman Coulter SW 41 swinging-bucket rotor. After centrifugation, 20 fractions were collected from top to bottom of the tube. MNase-ChIP-seq of top of gradient fractions (pool of fractions 2, 3 and 4) was performed
input_Smarca4_rep3_g2-3-4


title: RNA-seq 80% epiboly stage, atRA, replicate 3


title: MNase-seq top of gradient (2-3-4) - Brg1-depleted auxin 20h replicate 2

description:
ES cell chromatin was fragmented by micrococcal nuclease digestion and centrifugated for 16 hours through a 10-30 % sucrose gradient at 197,000 g, using a Beckman Coulter SW 41 swinging-bucket rotor. After centrifugation, 20 fractions were collected from top to bottom of the tube. MNase-ChIP-seq of top of gradient fractions (pool of fractions 2, 3 and 4) was performed
input_Smarca4_rep2_g2-3-4


title: RNA-seq 80% epiboly stage, control, replicate 3


title: WT cells, d5 Tbet C&R


title: WT cells, d5 ARID1A C&R Rep1


title: MNase-seq top of gradient (2-3-4) - Brg1-depleted auxin 20h replicate 1

description:
ES cell chromatin was fragmented by micrococcal nuclease digestion and centrifugated for 16 hours through a 10-30 % sucrose gradient at 197,000 g, using a Beckman Coulter SW 41 swinging-bucket rotor. After centrifugation, 20 fractions were collected from top to bottom of the tube. MNase-ChIP-seq of top of gradient fractions (pool of fractions 2, 3 and 4) was performed
input_Smarca4_rep1_g2-3-4


title: RNA-seq 80% epiboly stage, control, replicate 2


title: MNase-seq top of gradient (2-3-4) replicate 4

description:
ES cell chromatin was fragmented by micrococcal nuclease digestion and centrifugated for 16 hours through a 10-30 % sucrose gradient at 197,000 g, using a Beckman Coulter SW 41 swinging-bucket rotor. After centrifugation, 20 fractions were collected from top to bottom of the tube. MNase-ChIP-seq of top of gradient fractions (pool of fractions 2, 3 and 4) was performed
input_Tir1_rep4_g2-3-4


title: RNA-seq 80% epiboly stage, control, replicate 1


title: Arid1a KO cells, d5 ETS1 C&R


title: MNase-seq top of gradient (2-3-4) replicate 3

description:
ES cell chromatin was fragmented by micrococcal nuclease digestion and centrifugated for 16 hours through a 10-30 % sucrose gradient at 197,000 g, using a Beckman Coulter SW 41 swinging-bucket rotor. After centrifugation, 20 fractions were collected from top to bottom of the tube. MNase-ChIP-seq of top of gradient fractions (pool of fractions 2, 3 and 4) was performed
input_Tir1_rep3_g2-3-4


title: RNA-seq 12 somites stage, atRA, replicate 1


title: WT cells, d5 ETS1 C&R


title: RNA-seq 12 somites stage, control, replicate 3


title: E3_input

city: Zhengzhou

first: Shuaiyin

last: Chen

address: No. 100 Kexue Avenue, Zhengzhou

institute: Zhengzhou University

description:
Exp_IPVSExp_input_peak.txt
genes_fpkm_expression.txt
isoforms_fpkm_expression.txt

data_processing:
library strategy: MeRIP-Seq
fastp software (https://github.com/OpenGene/fastp) were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases with default parameter. Then sequence quality of IP and Input samples were also verified using fastp.
HISAT2 (http://daehwankimlab.github.io/hisat2) was used to map reads to the reference genomeHomo sapiens(Version: v101). Mapped reads of IP and input libraries were provided for R package exomePeak (https://bioconductor.org/packages/exomePeak), which identifies m6A peaks with bed or bigwig format that can be adapted for visualization on the IGV software (http://www.igv.org).
MEME (http://meme-suite.org) and HOMER (http://homer.ucsd.edu/homer/motif) were used for de novo and known motif finding followed by localization of the motif with respect to peak summit. Called peaks were annotated by intersection with gene architecture using R package ChIPseeker (https://bioconductor.org/packages/ChIPseeker).
StringTie (https://ccb.jhu.edu/software/stringtie) was used to perform expression level for all mRNAs from input libraries by calculating FPKM (total exon fragments /mapped reads (millions) × exon length (kB)).
The differentially expressed mRNAs were selected with log2 (fold change) >1 or log2 (fold change) <-1 and p value < 0.05 by R package edgeR (https://bioconductor.org/packages/edgeR).
Assembly: GRCH38
Supplementary files format and content: tab-delimited file include gene fpkm values for each sample
Supplementary files format and content: tab-delimited file include transcript fpkm values for each sample

organism:
Homo sapiens
Enterovirus A71

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 50μg 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 86℃ 7min. Then the cleaved RNA fragments were incubated for 2h at 4℃ with m6A-specific antibody (No. 202003, Synaptic Systems, Germany) in IP buffer (50 mM Tris-HCl, 750 mM NaCl and 0.5% Igepal CA-630). Then the IP RNA was 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 withE. coliDNA 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.

value: RD cell


title: E2_input


title: Arid1a KO cells, d5 BATF C&R

value: BATF (Brookwood Biomedical #4003)


title: E1_input


title: RNA-seq 12 somites stage, control, replicate 1


title: WT cells, d5 BATF C&R


title: MNase-seq top of gradient (2-3-4) replicate 2

description:
ES cell chromatin was fragmented by micrococcal nuclease digestion and centrifugated for 16 hours through a 10-30 % sucrose gradient at 197,000 g, using a Beckman Coulter SW 41 swinging-bucket rotor. After centrifugation, 20 fractions were collected from top to bottom of the tube. MNase-ChIP-seq of top of gradient fractions (pool of fractions 2, 3 and 4) was performed
input_Tir1_rep2_g2-3-4

value: embryonic stem cells


title: Arid1a KO cells, d5 Tbet C&R


title: E2_IP


title: RNA-seq 80% epiboly stage, atRA, replicate 2


title: MNase-seq top of gradient (2-3-4) replicate 1

description:
ES cell chromatin was fragmented by micrococcal nuclease digestion and centrifugated for 16 hours through a 10-30 % sucrose gradient at 197,000 g, using a Beckman Coulter SW 41 swinging-bucket rotor. After centrifugation, 20 fractions were collected from top to bottom of the tube. MNase-ChIP-seq of top of gradient fractions (pool of fractions 2, 3 and 4) was performed
input_Tir1_rep1_g2-3-4


title: E1_IP


title: R3-240hr-Dans

city: Baltimore

first: Kevin

last: Emmerich

state: MD

address: 400 N Broadway

department: Human Genetics

institute: Johns Hopkins University

description: NTR:Rod fish, 240h post Dan

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: Bioconductor suite in the R statistical software, LIMMA, Carmaweb, and Microsoft Access were used for data processing, differential expression testing and storage

source_name: Transgenic rod fish after Dan treatment (control)

label_protocol: standard Affymetrix protocol

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Embryos were either treated with control Danieau's media or with 2.5 mM Mtz for 24h (unless collected earlier) to induce cell death of either rod or bipolar cells

value: dissected eye

tag: sequencing replicate


title: R3-240hr-MTZ

description: NTR:Rod fish, 240h post mtz

source_name: Transgenic rod fish after mtz treatment (experimental condition)


title: KO cells, d5 IgG C&R


title: RNA-seq 80% epiboly stage, atRA, replicate 1


title: R3-144hr-Dans

description: NTR:Rod fish, 144h post Dan


title: Oct4 (MBS420786) MNase ChIP-seq low sedimentation rate (5-6) replicate 2

description:
ES cell chromatin was fragmented by micrococcal nuclease digestion and centrifugated for 16 hours through a 10-30 % sucrose gradient at 197,000 g, using a Beckman Coulter SW 41 swinging-bucket rotor. After centrifugation, 20 fractions were collected from top to bottom of the tube. ChIP-seq of low sedimentation rate fractions (pool of fractions 5 and 6) was performed using antibodies against Oct4 (myBioSource MBS420786).
EL_PEP_Oct4_5-6_Rep2_C002K7T

value: untreated


title: R3-144hr-MTZ

description: NTR:Rod fish, 144h post mtz


title: WT cells, d5 IgG C&R


title: R3-96hr-MTZ

description: NTR:Rod fish, 96h post mtz


title: R3-96hr-Dans

description: NTR:Rod fish, 96h post Dan


title: WT MP cells, d8 ARID1A C&R


title: Oct4 (sc-5279) MNase ChIP-seq low sedimentation rate (5-6) - Brg1-depleted auxin 20h replicate 2

description:
ES cell chromatin was fragmented by micrococcal nuclease digestion and centrifugated for 16 hours through a 10-30 % sucrose gradient at 197,000 g, using a Beckman Coulter SW 41 swinging-bucket rotor. After centrifugation, 20 fractions were collected from top to bottom of the tube. ChIP-seq of low sedimentation rate fractions (pool of fractions 5 and 6) was performed using antibodies against Oct4 (Santa Cruz Biotechnology sc-5279).
8-SMARCA4-5-6-Oct4_rep2

value: treated with auxin for 20 hours

value: Oct4 (Santa Cruz Biotechnology sc-5279)


title: WT EEC cells, d8 ARID1A C&R


title: R3-72hr-MTZ

description: NTR:Rod fish, 72h post mtz


title: WT TE cells, d8 ARID1A C&R


title: R3-60hr-MTZ

description: NTR:Rod fish, 60h post mtz


title: R3-72hr-Dans

description: NTR:Rod fish, 72h post Dan


title: Arid1a KO cells, d5 ARID1A C&R


title: E3_IP


title: Oct4 (sc-5279) MNase ChIP-seq low sedimentation rate (5-6) - Brg1-depleted auxin 20h replicate 1

description:
ES cell chromatin was fragmented by micrococcal nuclease digestion and centrifugated for 16 hours through a 10-30 % sucrose gradient at 197,000 g, using a Beckman Coulter SW 41 swinging-bucket rotor. After centrifugation, 20 fractions were collected from top to bottom of the tube. ChIP-seq of low sedimentation rate fractions (pool of fractions 5 and 6) was performed using antibodies against Oct4 (Santa Cruz Biotechnology sc-5279).
7-SMARCA4-5-6-Oct4_rep1


title: R3-48hr-MTZ

description: NTR:Rod fish, 48h post mtz


title: R3-48hr-Dans

description: NTR:Rod fish, 48h post Dan


title: Oct4 (sc-5279) MNase ChIP-seq low sedimentation rate (5-6) replicate 2

description:
ES cell chromatin was fragmented by micrococcal nuclease digestion and centrifugated for 16 hours through a 10-30 % sucrose gradient at 197,000 g, using a Beckman Coulter SW 41 swinging-bucket rotor. After centrifugation, 20 fractions were collected from top to bottom of the tube. ChIP-seq of low sedimentation rate fractions (pool of fractions 5 and 6) was performed using antibodies against Oct4 (Santa Cruz Biotechnology sc-5279).
6-TIR1-5-6-Oct4_rep2


title: Oct4 (sc-5279) MNase ChIP-seq low sedimentation rate (5-6) replicate 1

description:
ES cell chromatin was fragmented by micrococcal nuclease digestion and centrifugated for 16 hours through a 10-30 % sucrose gradient at 197,000 g, using a Beckman Coulter SW 41 swinging-bucket rotor. After centrifugation, 20 fractions were collected from top to bottom of the tube. ChIP-seq of low sedimentation rate fractions (pool of fractions 5 and 6) was performed using antibodies against Oct4 (Santa Cruz Biotechnology sc-5279).
5-TIR1-5-6-Oct4_rep1


title: WT cells, d5 ARID1A C&R _Rep2


title: R3-32hr-Dans

description: NTR:Rod fish, 32h post Dan


title: R3-32hr-MTZ

description: NTR:Rod fish, 32h post mtz


title: WT cells, 48h activated in vitro ARID1A C&R _Rep2


title: R3-40hr-MTZ

description: NTR:Rod fish, 40h post mtz


title: R3-40hr-Dans

description: NTR:Rod fish, 40h post Dan


title: Oct4 (MBS420786) MNase ChIP-seq low sedimentation rate (5-6) replicate 1

description:
ES cell chromatin was fragmented by micrococcal nuclease digestion and centrifugated for 16 hours through a 10-30 % sucrose gradient at 197,000 g, using a Beckman Coulter SW 41 swinging-bucket rotor. After centrifugation, 20 fractions were collected from top to bottom of the tube. ChIP-seq of low sedimentation rate fractions (pool of fractions 5 and 6) was performed using antibodies against Oct4 (myBioSource MBS420786).
EL_PEP_Oct4_5-6_Rep1_C002K7S


title: Oct4 (sc-5279) MNase ChIP-seq top of gradient (2-3-4) - Brg1-depleted auxin 20h replicate 2

description:
ES cell chromatin was fragmented by micrococcal nuclease digestion and centrifugated for 16 hours through a 10-30 % sucrose gradient at 197,000 g, using a Beckman Coulter SW 41 swinging-bucket rotor. After centrifugation, 20 fractions were collected from top to bottom of the tube. ChIP-seq of top of gradient fractions (pool of fractions 2, 3 and 4) was performed using antibodies against Oct4 (Santa Cruz Biotechnology sc-5279).
4-SMARCA4-2-3-4-Oct4_rep2


title: Oct4 (sc-5279) MNase ChIP-seq top of gradient (2-3-4) - Brg1-depleted auxin 20h replicate 1

description:
ES cell chromatin was fragmented by micrococcal nuclease digestion and centrifugated for 16 hours through a 10-30 % sucrose gradient at 197,000 g, using a Beckman Coulter SW 41 swinging-bucket rotor. After centrifugation, 20 fractions were collected from top to bottom of the tube. ChIP-seq of top of gradient fractions (pool of fractions 2, 3 and 4) was performed using antibodies against Oct4 (Santa Cruz Biotechnology sc-5279).
3-SMARCA4-2-3-4-Oct4_rep1


title: R3-24hr-MTZ

description: NTR:Rod fish, 24h post mtz


title: R3-16hr-MTZ

description: NTR:Rod fish, 16h post mtz


title: Oct4 (sc-5279) MNase ChIP-seq top of gradient (2-3-4) replicate 2

description:
ES cell chromatin was fragmented by micrococcal nuclease digestion and centrifugated for 16 hours through a 10-30 % sucrose gradient at 197,000 g, using a Beckman Coulter SW 41 swinging-bucket rotor. After centrifugation, 20 fractions were collected from top to bottom of the tube. ChIP-seq of top of gradient fractions (pool of fractions 2, 3 and 4) was performed using antibodies against Oct4 (Santa Cruz Biotechnology sc-5279).
2-TIR1-2-3-4-Oct4_rep2


title: WT cells, Naive ARID1A C&R


title: R3-16hr-Dans

description: NTR:Rod fish, 16h post Dan


title: R3-860hr-Dans

description: NTR:Rod fish, 60h post Dan


title: R3-8hr-MTZ

description: NTR:Rod fish, 8h post mtz


title: Oct4 (sc-5279) MNase ChIP-seq top of gradient (2-3-4) replicate 1

description:
ES cell chromatin was fragmented by micrococcal nuclease digestion and centrifugated for 16 hours through a 10-30 % sucrose gradient at 197,000 g, using a Beckman Coulter SW 41 swinging-bucket rotor. After centrifugation, 20 fractions were collected from top to bottom of the tube. ChIP-seq of top of gradient fractions (pool of fractions 2, 3 and 4) was performed using antibodies against Oct4 (Santa Cruz Biotechnology sc-5279).
1-TIR1-2-3-4-Oct4_rep1


title: WT cells, 48h activated in vitro; IL-12 + BRM014 [IL-12 + BRM014_Rep2]

data_processing:
Sequence reads were aligned to GRCm38 (mm10) using STAR v2.5.3a (parameters- default)
ATAC-seq peaks were identified using the findPeaks program in HOMER with the following options "-style dnase -o auto"
Assembly: GRCm38 (mm10)
Supplementary files format and content: bigwig, bed

extract_protocol:
Cells were lysed in RSB (10mM Tris-HCl (pH 7.4), 10mM NaCl, 3mM MgCl2, 0.1% NP-40) supplemented with 0.1% Tween-20, and 0.01% digitonin for 3 minutes on ice and then washed with RSB supplemeneted with 0.1% Tween-20
Nuclei were then transposed for 30min at 37C with 1000RPM mixing in 50uL transposition mix (25uL 2X TD buffer, 2.5uL Tn5 transposase (100nM final), 16uL PBS, 0.5uL 1% digitonin, 0.5uL 10% Tween-20, 5uL H2O)
DNA was purified with Qiagen MinElute PCR cleanup kit. Libraries were amplified after determining the optimal number of cycles by qPCR. Post amplification libraries were size selected using Agencourt AMPure XP beads from Beckman Coulter.


title: Histone H3 MNase ChIP-seq mononucleosomes (13) replicate 2

description:
ES cell chromatin was fragmented by micrococcal nuclease digestion and centrifugated for 16 hours through a 10-30 % sucrose gradient at 197,000 g, using a Beckman Coulter SW 41 swinging-bucket rotor. After centrifugation, 20 fractions were collected from top to bottom of the tube. ChIP-seq of a fraction containing canonical nucleosomes (fraction 11) was performed using antibodies against histone H3 (Abcam ab1791).
chip_H3_grad2_f13_200727

value: histone H3 (Abcam ab1791)


title: WT cells, 48h activated in vitro; IL-12 + BRM014 [IL-12 + BRM014_Rep1]


title: R2-240hr-Dans

description: NTR:Rod fish, 240h post Dan


title: Histone H3 MNase ChIP-seq mononucleosomes (13) replicate 1

description:
ES cell chromatin was fragmented by micrococcal nuclease digestion and centrifugated for 16 hours through a 10-30 % sucrose gradient at 197,000 g, using a Beckman Coulter SW 41 swinging-bucket rotor. After centrifugation, 20 fractions were collected from top to bottom of the tube. ChIP-seq of a fraction containing canonical nucleosomes (fraction 11) was performed using antibodies against histone H3 (Abcam ab1791).
chip_H3_grad1_f13_200128


title: R2-240hr-MTZ

description: NTR:Rod fish, 240h post mtz


title: R2-144hr-Dans

description: NTR:Rod fish, 144h post Dan


title: R2-144hr-MTZ

description: NTR:Rod fish, 144h post mtz


title: Histone H3 MNase ChIP-seq mononucleosomes (11) replicate  2

description:
ES cell chromatin was fragmented by micrococcal nuclease digestion and centrifugated for 16 hours through a 10-30 % sucrose gradient at 197,000 g, using a Beckman Coulter SW 41 swinging-bucket rotor. After centrifugation, 20 fractions were collected from top to bottom of the tube. ChIP-seq of a fraction containing canonical nucleosomes (fraction 11) was performed using antibodies against histone H3 (Abcam ab1791).
chip_H3_grad2_f11_200727


title: R2-96hr-MTZ

description: NTR:Rod fish, 96h post mtz


title: R2-96hr-Dans

description: NTR:Rod fish, 96h post Dan


title: WT cells, 48h activated in vitro; IL-12 + ACBI1 [IL-12 + ACBI1_Rep2]

value: IL-12 + ACBI1


title: WT cells, 48h activated in vitro; IL-12 + ACBI1 [IL-12 + ACBI1_Rep1]


title: R2-72hr-MTZ

description: NTR:Rod fish, 72h post mtz


title: Histone H3 MNase ChIP-seq mononucleosomes (11) replicate  1

description:
ES cell chromatin was fragmented by micrococcal nuclease digestion and centrifugated for 16 hours through a 10-30 % sucrose gradient at 197,000 g, using a Beckman Coulter SW 41 swinging-bucket rotor. After centrifugation, 20 fractions were collected from top to bottom of the tube. ChIP-seq of a fraction containing canonical nucleosomes (fraction 11) was performed using antibodies against histone H3 (Abcam ab1791).
chip_H3_grad1_f11_200128


title: R3-24hr-Dans

description: NTR:Rod fish, 24h post Dan


title: WT cells, 48h activated in vitro ARID1A C&R _Rep1


title: WT cells, 48h activated in vitro; IL-12 [IL-12_Rep2]


title: R2-72hr-Dans

description: NTR:Rod fish, 72h post Dan


title: Histone H3 MNase ChIP-seq medium sedimentation rate (9-10) replicate 1

description:
ES cell chromatin was fragmented by micrococcal nuclease digestion and centrifugated for 16 hours through a 10-30 % sucrose gradient at 197,000 g, using a Beckman Coulter SW 41 swinging-bucket rotor. After centrifugation, 20 fractions were collected from top to bottom of the tube. ChIP-seq of medium sedimentation rate fractions (pool of fractions 9 and 10) was performed using antibodies against histone H3 (Abcam ab1791).
chip_H3_grad1_f9-10_200128


title: R3-0hr

description: NTR:Rod fish, 0h post mtz

source_name: Transgenic rod fish before ablation


title: R3-8hr-Dans

description: NTR:Rod fish, 8h post Dan


title: Histone H2A MNase ChIP-seq medium sedimentation rate (7-8-9) - Brg1-depleted auxin 20h replicate 2

description:
ES cell chromatin was fragmented by micrococcal nuclease digestion and centrifugated for 16 hours through a 10-30 % sucrose gradient at 197,000 g, using a Beckman Coulter SW 41 swinging-bucket rotor. After centrifugation, 20 fractions were collected from top to bottom of the tube. ChIP-seq of medium sedimentation rate fractions (pool of fractions 7, 8, and 9) was performed using antibodies against histone H2A (Abcam ab18255).
SMARCA4-AID_g7-8-9_rep2_H2A_2020

value: histone H2A (Abcam ab18255)


title: WT cells, 48h activated in vitro; Untreated [Control_Rep1]

value: Untreated


title: R2-60hr-MTZ

description: NTR:Rod fish, 60h post mtz


title: R2-48hr-Dans

description: NTR:Rod fish, 48h post Dan


title: R2-860hr-Dans

description: NTR:Rod fish, 60h post Dan


title: R2-40hr-MTZ

description: NTR:Rod fish, 40h post mtz


title: R2-48hr-MTZ

description: NTR:Rod fish, 48h post mtz


title: Histone H2A MNase ChIP-seq medium sedimentation rate (7-8-9) - Brg1-depleted auxin 20h replicate 1

description:
ES cell chromatin was fragmented by micrococcal nuclease digestion and centrifugated for 16 hours through a 10-30 % sucrose gradient at 197,000 g, using a Beckman Coulter SW 41 swinging-bucket rotor. After centrifugation, 20 fractions were collected from top to bottom of the tube. ChIP-seq of medium sedimentation rate fractions (pool of fractions 7, 8, and 9) was performed using antibodies against histone H2A (Abcam ab18255).
SMARCA4-AID_g7-8-9_rep1_H2A_2020


title: R2-40hr-Dans

description: NTR:Rod fish, 40h post Dan


title: R2-32hr-MTZ

description: NTR:Rod fish, 32h post mtz


title: Histone H2B MNase ChIP-seq medium sedimentation rate (7-8-9) - Brg1-depleted auxin 20h replicate 2

description:
ES cell chromatin was fragmented by micrococcal nuclease digestion and centrifugated for 16 hours through a 10-30 % sucrose gradient at 197,000 g, using a Beckman Coulter SW 41 swinging-bucket rotor. After centrifugation, 20 fractions were collected from top to bottom of the tube. ChIP-seq of medium sedimentation rate fractions (pool of fractions 7, 8, and 9) was performed using antibodies against histone H2B (Abcam ab1790).
SMARCA4-AID_g7-8-9_rep2_H2B_2020

value: histone H2B (Abcam ab1790)


title: R2-32hr-Dans

description: NTR:Rod fish, 32h post Dan


title: R2-24hr-Dans

description: NTR:Rod fish, 24h post Dan


title: Histone H3 MNase ChIP-seq medium sedimentation rate (9-10) replicate 2

description:
ES cell chromatin was fragmented by micrococcal nuclease digestion and centrifugated for 16 hours through a 10-30 % sucrose gradient at 197,000 g, using a Beckman Coulter SW 41 swinging-bucket rotor. After centrifugation, 20 fractions were collected from top to bottom of the tube. ChIP-seq of medium sedimentation rate fractions (pool of fractions 9 and 10) was performed using antibodies against histone H3 (Abcam ab1791).
chip_H3_grad2_f9-10_200727


title: R2-16hr-Dans

description: NTR:Rod fish, 16h post Dan


title: R2-16hr-MTZ

description: NTR:Rod fish, 16h post mtz


title: WT cells, 48h activated in vitro; IL-12 [IL-12_Rep1]


title: Histone H2B MNase ChIP-seq medium sedimentation rate (7-8-9) - Brg1-depleted auxin 20h replicate 1

description:
ES cell chromatin was fragmented by micrococcal nuclease digestion and centrifugated for 16 hours through a 10-30 % sucrose gradient at 197,000 g, using a Beckman Coulter SW 41 swinging-bucket rotor. After centrifugation, 20 fractions were collected from top to bottom of the tube. ChIP-seq of medium sedimentation rate fractions (pool of fractions 7, 8, and 9) was performed using antibodies against histone H2B (Abcam ab1790).
SMARCA4-AID_g7-8-9_rep1_H2B_2020


title: Histone H4 MNase ChIP-seq medium sedimentation rate (7-8-9) - Brg1-depleted auxin 20h replicate 2

description:
ES cell chromatin was fragmented by micrococcal nuclease digestion and centrifugated for 16 hours through a 10-30 % sucrose gradient at 197,000 g, using a Beckman Coulter SW 41 swinging-bucket rotor. After centrifugation, 20 fractions were collected from top to bottom of the tube. ChIP-seq of medium sedimentation rate fractions (pool of fractions 7, 8, and 9) was performed using antibodies against histone H4 (Abcam ab7311).
SMARCA4-AID_g7-8-9_rep2_H4_2020

value: histone H4 (Abcam ab7311)


title: Histone H4 MNase ChIP-seq medium sedimentation rate (7-8-9) - Brg1-depleted auxin 20h replicate 1

description:
ES cell chromatin was fragmented by micrococcal nuclease digestion and centrifugated for 16 hours through a 10-30 % sucrose gradient at 197,000 g, using a Beckman Coulter SW 41 swinging-bucket rotor. After centrifugation, 20 fractions were collected from top to bottom of the tube. ChIP-seq of medium sedimentation rate fractions (pool of fractions 7, 8, and 9) was performed using antibodies against histone H4 (Abcam ab7311).
SMARCA4-AID_g7-8-9_rep1_H4_2020


title: R2-8hr-Dans

description: NTR:Rod fish, 8h post Dan


title: Arid1a KO MP cells, d8 [D8_KO_MP_Exp2_Rep1]

value: Arid1a KO


title: Arid1a KO EEC cells, d8 [D8_KO_EEC_Exp2_Rep1]


title: R2-8hr-MTZ

description: NTR:Rod fish, 8h post mtz


title: Arid1a KO MP cells, d8 [D8_KO_MP_Exp2_Rep2]


title: Arid1a KO EEC cells, d8 [D8_KO_EEC_Exp2_Rep2]


title: R2-0hr

description: NTR:Rod fish, 0h post mtz


title: WT cells, 48h activated in vitro; Untreated [Control_Rep2]


title: Arid1a KO TE cells, d8 [D8_KO_TE_Exp2_Rep2]


title: Histone H3 MNase ChIP-seq medium sedimentation rate (7-8-9) - Brg1-depleted auxin 20h replicate 2

description:
ES cell chromatin was fragmented by micrococcal nuclease digestion and centrifugated for 16 hours through a 10-30 % sucrose gradient at 197,000 g, using a Beckman Coulter SW 41 swinging-bucket rotor. After centrifugation, 20 fractions were collected from top to bottom of the tube. ChIP-seq of medium sedimentation rate fractions (pool of fractions 7, 8, and 9) was performed using antibodies against histone H3 (Abcam ab1791).
SMARCA4-AID_g7-8-9_rep2_H3_2020


title: R1-144hr-MTZ

description: NTR:Rod fish, 144h post mtz