title: H3K27Ac ChIP-seq Input PBS rep1

city: La Jolla

first: Nathanael

last: Spann

address: 9500 Gilman Drive CMMW 219A

institute: UCSD

description:
formaldehyde cross-linked
processed data file:
BMDM_ChIP_H3K27Ac_TFmerge.txt, BMDM_ChIP_H3K27Ac_AllMerged.txt

data_processing:
Preprocessing: FASTQ files from sequencing experiments were mapped to the mouse mm10 genome. Bowtie2 with default parameters was used to map ChIP-seq experiments (Langmead and Salzberg, 2012). HOMER was used to convert aligned reads into “tag directories” for further analysis (Heinz et al., 2010).
For p300, SREBP and LXR ChIP-seq experiments peaks were called with HOMER for each tag directory with default peak finding parameters -style factor against the corresponding input directory. Only peaks with > 16 normalized tags (normalized to total tags of 1e7) were kept. Overlapping peak sets were determined using mergePeaks command. The pooled tag directory from two replicates was used for track visualization. To annotate p300 signal in ATAC-seq or LXR,SREBP, p65 ChIP-seq peaks the parameter -size 200 was used. Subsequently, DESeq2 (Love et al., 2014) was used to identify differential p300 signal > 2 fold-change and p-adj < 0.05, unless stated otherwise in the text.
For H3K27ac analysis: To annotate H3K27ac signal around ATAC-seq or LXR,SREBP, p65 ChIP-seq peaks the parameter -size 1000 was used. Subsequently, DESeq2 (Love et al., 2014) was used to identify differential H3K27ac signal or chromatin accessibility with > 2 fold-change and p-adj < 0.05, unless stated otherwise in the text.
For p65 and ATAC-Seq analysis of data from GSE79423 and GSE109965 respectively: Relevant raw FASTQ files were mapped to mm10 genome with Bowtie2 with default parameters (Langmead and Salzberg, 2012). HOMER was used to convert aligned reads into “tag directories” for further analysis (Heinz et al., 2010). For p65 peaks were called with HOMER findPeaks for each tag directory with default peak finding parameters -style factor against the corresponding input directory. Peak files across various timepoints for vehicle and KLA treated timepoints were merged using HOMER mergePeaks. Merged peaks were annotated for H3K27ac and p300 signal as indicated. For ATAC-Seq, mm10 mapped, IDR defined peaks from GSE109965, for both vehicle and KLA treatment conditions, were used. Peaks were merged using HOMER mergePeaks, then merged peak file was used for further analysis as indicated in text.
To identify motifs enriched in peak regions over the background, HOMER’s motif analysis (findMotifsGenome.pl) including known default motifs and de novo motifs was used. The background sequences were either from random genome sequences or from peaks from the comparing condition indicated in the main text and in the figure legends.
Genome_build: mm10
Supplementary_files_format_and_content: Processed files include peak text files (ChIP-Seq peak data, using default HOMER parameters). All genomic coordinates are relative to mm10 mouse assembly.

source_name: H3K27Ac ChIP-seq Input PBS

growth_protocol: Bone marrow derived macrophages (BMDMs): Mouse bone marrow was harvested and washed once with PBS, seeded/cultured in DMEM containing 20 % FCS, 30 % L-cell conditioned media (as source of macrophage colony stimulating factor, M-CSF), and 100 U/ml penicillin/streptomycin in non-tissue culture-treated petri dishes. After 6-8 days of culture, non-adherent cells were washed off with room temperature PBS and macrophages were obtained as a homogeneous population of adherent cells which were scraped and subsequently seeded onto tissue culture-treated petri dishes overnight in RPMI-1640 containing 10% FCS, 100 U/ml penicillin/streptomycin, and 10ng/ml M-CSF.

extract_protocol:
For H3K27ac ChIP-seq, culture media was removed and plates were washed once with PBS and then fixed with 1% formaldehyde (Thermo Fisher Scientific) in PBS for 10 minutes at room temperature. The reaction was quenched by adding glycine (Thermo Fisher Scientific) to 0.125M. For p300, LXR and SREBP ChIP-seq, cells were crosslinked with 3mM DSG (ProteoChem) in PBS for 30 minutes at room temperature, and then fixed with 1% formaldehyde (Thermo Fisher Scientific) in PBS for 10 minutes at room temperature. The reaction was quenched by adding glycine (Thermo Fisher Scientific) to 0.125M. After fixation, cells were washed once with cold PBS and then pelleted at 700 X G for 5 minutes at 4°C. Crosslinked cells were stored at –80°C until ready for ChIP-seq library preparation. Fixed cells were thawed on ice, resuspended in either ice-cold LB3 (10 mM Tris/HCl pH 7.5, 100 mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.1% Na-deoxycholate, 0.5% N-lauroylsarcosine, 1 X protease inhibitor cocktail, 1mM Na-Butyrate, for H3K27ac ChIP) or ice-cold RIPA-NR lysis buffer (20 mM Tris-HCl, pH 7.5, 150 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.4% Na-Deoxycholate, 0.1% SDS, 1% NP-40, 1x protease inhibitors, for p300, LXR, and SREBP ChIP). Frozen crosslinked nuclei were resuspended in wash buffer (10mM HEPES/KOH pH7.9, 85mM KCl, 1mM EDTA, 0.2% IGEPAL CA-630, 1x protease inhibitor cocktail (Sigma), 1 mM PMSF) for 5minutes on ice. Cells were spun down and then resuspended in RIPA-NR lysis buffer. Chromatin was sheared by sonication. Samples were sonicated in a 96 Place microTUBE Rack (Covaris cat#500282) using a Covaris E220 for 12 cycles (samples in LB3) or 18 cycles (samples in RIPA-NR buffer) with the following setting: time, 60 seconds; duty, 5.0; PIP, 140; cycles, 200; amplitude, 0.0; velocity, 0.0; dwell, 0.0. Samples were recovered and spun down at max speed, 4°C for 10 minutes. The LB3 lysate was diluted 1.1-fold with ice-cold 10% Triton X-100 after sonication. One percent of the lysate was kept as ChIP input. For each immunoprecipitation, aliquots of diluted lysate equivalent to 500,000 cells (for H3K27ac ChIP) or 1-2 million cells  (for p300, SREBP ChIP), 20 µl of Dynabeads Protein A (for rabbit polyclonal antibodies) or Dynabeads protein A/G (for p300, LXR, and SREBP ChIP) bound to specific antibodies for H3K27ac (2 μg, Active Motif, 39133), p300 (2 μg, Millipore, cat# 05-257,Diagenode, cat# C15200211), LXR (Santa Cruz Biotechnology: sc-1000X, sc- 133221X, sc-271064X) , and SREBP (2 μg, Santa Cruz Biotechnology: sc-8984X, Thermo Fisher Scientific: PA1-337, R&D Systems: AF7119) were combined and rotated overnight at 4°C. For H3K27ac ChIP, beads were collected on a magnet and washed three times each with wash buffer I (20 mM Tris/HCl pH 7.5, 150 mM NaCl, 1% Triton X-100, 0.1% SDS, 2 mM EDTA), wash buffer III (10 mM Tris/HCl pH 7.4, 250 mM LiCl, 1% Triton X-100, 0.7% Na-Deoxycholate, 1 mM EDTA) and twice with ice-cold TET (10 mM Tris/HCl pH7.5, 1 mM EDTA, 0.2% Tween-20). For p300, LXR and SREBP ChIP, beads were washed three times with RIPA-NR buffer (20 mM Tris-HCl/pH7.5, 150 mM NaCl, 0.1% SDS, 1% NP-40, 0.4 % Na-Deoxycholate, 1 mM EDTA, 0.5mM EGTA, 0.5mM DTT), six times with RIPA-LiCl buffer (10 mM Tris-HCl/pH 7.5, 250 mM LiCl, 1% NP-40, 0.7% Na-Deoxycholate, 1 mM EDTA), three times with ice-cold TET (10 mM Tris/HCl pH7.5, 1 mM EDTA, 0.2% Tween-20), and one time with IDTE (10mM Tris-HCl pH 8.0, 0.1mM EDTA). Bead complexes were resuspended in 25 μl TT (10 mM Tris/HCl pH 8.0, 0.05% Tween-20, 1x protease inhibitor cocktail) and sequencing libraries were prepared on-bead as described below.
ChIP libraries were prepared while bound to Dynabeads using NEBNext Ultra II Library preparation kit with reaction volumes reduced by half, essentially as previously described (Heinz et al., 2018). Libraries were eluted and crosslinks reversed by adding to the 46.5 μl NEB reaction 20 μl water, 4 μl 10% SDS, 4.5 μl 5M NaCl, 3 μl 0.5 M EDTA, and 1 μl 20 mg/ml proteinase K, followed by incubation at 55C for 1 hour and 65C for 30 minutes to overnight in a thermal cycler. Dynabeads were removed from the library using a magnet and libraries cleaned by adding 2 μl SpeedBeads 3 EDAC in 61 μl 20% PEG 8000/1.5 M NaCl, mixing well, then incubating at room temperature for 10 minutes. SpeedBeads were collected on a magnet and washed two times with 150 μl 80% ethanol for 30 seconds. Beads were collected and ethanol removed following each wash. After the second ethanol wash, beads were air dried and DNA eluted in 25 μl 10 mM Tris/HCl pH 8.0 and 0.05% Tween-20. DNA was amplified by PCR for 14 cycles in a 50 μl reaction volume using NEBNext Ultra II PCR master mix and 0.5 μM each Solexa 1GA and Solexa 1GB primers. Libraries were cleaned up with SpeedBeads as above using 36.5 μl 20% PEG 8000/1.5 M NaCl and 2 μl SpeedBeads. After ethanol washing and drying, PCR amplified libraries were eluted from the SpeedBeads using 20 μl 10 mM Tris/HCl pH 8.0 and 0.05% Tween- 20. Next, libraries were size selected 250-500 bp using gel extraction using 10% TBE acrylamide gels. Libraries were single-end sequenced using either a HiSeq 4000 or a NextSeq 500 to a depth of 10-20 million reads.

treatment_protocol: The following day after replating BMDMs, fresh medium containing 0.5% fetal bovine serum was added to the cells and serum starvation was carried overnight. After serum starvation the cells were treated with or without 100 µg/ml 3'SL , with 10 ng/ml of LPS for 1 – 24 hours as indicated. For LXR and SREBP experiments cells were treated with 1uM GW3965.

value: bone marrow derived macrophages

value: vehicle PBS treatment


title: F140509Gastric cancer tumor nest CD68- ROI 6

status: Public on Mar 04 2024

type: SRA

city: South San Francisco

first: Lee

middle: Benjamin

last: Rivera

state: CA

address: 333 Oyster Point Blvd.

department: Biology

country: USA

institute: NGM Bio

description: Spatial transcriptomics by GeoMx Digital Spatial Prolifer

library_source: transcriptomic

data_processing:
Raw fastq files were converted to DCC files by the Nanostring geomxngspipeline software.
The DCC files were uploaded to the DSP software and the read counts file was exported for furthere analysis.
Assembly: hg38
Supplementary files format and content: DCC files generated by the Nanostring geomxngspipeline software
Supplementary files format and content: Read count files exported from Nanostring GeoMx DSP software

molecule: total RNA

organism: Homo sapiens

source_name: tumor

extract_protocol:
Probes (photocleaved oligos containing a readout tag sequence identifier and unique molecule identifier) were aspirated by the GeoMx instrument for library preparation.
Following collection on the GeoMx instrument, the probes were subjected to polymerase chain reaction amplification during which i5 and i7 indexing sequences were added. Following subsequent pooling, purification, and qualtity control, the library was sequenced on an Illumina HiSeq4000.
Spatial Transcriptomics

tag: tissue

value: tumor

tag: cell type

value: CD68 neg


title: H3K27Ac ChIP-seq PBS6h rep1

middle: Judge

department: Cellular and Molecular Medicine

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

source_name: H3K27Ac ChIP-seq PBS6h

tag: strain

tag: treatment

tag: antibody

value: H3K27Ac (Vendor:Active Motif, cat# 39133)


title: IBD, SAMPLE 36

type: RNA

city: Herlev

first: Jaslin

middle: P

last: James

address: Borgmester Ib Juuls vej 1

department: Department of Pathology

country: Denmark

institute: Herlev hospital

hyb_protocol: Genechip Fluidics Station 450

scan_protocol: Affymetrix GeneChip 7G scanner

data_processing: analysis was done using RStudio with R version 4.2.2. Preprocessing were performed using robust multichip average (RMA) algorithm.  Lowly expressed probe sets were removed, and batch correction was performed using ComBat batch correction.

label: biotin

source_name: FFPE IBD

label_protocol: FlashTag Biotin HSR

growth_protocol: Formalin fixed paraffin embedded tissue biopsies stored at room temperature

extract_protocol: Total RNA was extracted using MagMAX™ FFPE DNA/RNA Ultra Kit from Applied Biosystems

tag: disease classification

value: UC

tag: age group

value: Adult

value: Mucosal tissue biopsies


title: F140509 Gastric cancer tumor nest CD68+ ROI 6

value: CD68 pos


title: D2_INF_a1_4h

city: Paris

first: Ludovic

last: Tailleux

state: non-US Resident

address: 25-28 rue du Dr Roux, 75015 Paris, France

country: France

institute: Institut Pasteur

data_processing:
Raw reads derived from the sequencing instrument are clipped for adapter sequence, trimmed for minimum quality (Q30) in 3' and filtered for minimum length of 32 bp using Trimmomatic [PMID: 24695404]. Surviving read pairs were aligned to GRCh38 by the ultrafast universal RNA-seq aligner STAR [PMID: 23104886] using the recommended two passes approach. Aligned RNA-Seq reads were assembled into transcripts and their relative abundance was estimated using Stringtie [PMID: 25690850]. All of the above processing steps were accomplished through the GenPipes framework [PMID 31185495].
Assembly: GRCh38
Supplementary files format and content: The raw counts were generated using Stringtie [PMID: 25690850].

source_name: Blood mononuclear cells - donor 2

growth_protocol: Blood mononuclear cells from 4 healthy volunteers (named D1, D2, D3 and D4; Etablissement Français du Sang, Paris, France) were isolated by Lymphocytes Separation Medium centrifugation (Eurobio). CD14+ monocytes were isolated by positive selection using CD14 microbeads (Miltenyi Biotec). Recovered cells were cultured at 37°C and 5% CO2 in RPMI-1640 medium (Gibco) supplemented with 10% heat-inactivated fetal bovine serum (Dutscher), 2 mM L-glutamine (Gibco) and macrophage colony stimulating factor (M-CSF, 20 ng/mL; Miltenyi Biotec). Cultures were fed every 2 days with complete medium containing full doses of cytokine. Monocytes were allowed to differentiate into macrophages for 6 days at 37°C in 5% CO2 humidified atmosphere.

extract_protocol:
Total RNA was extracted using QIAzol reagent (Life Technologies) and purified over RNeasy columns (Qiagen). The quality of all samples was assessed with an Agilent 2100 bioanalyzer (Agilent Technologies) to verify RNA integrity. Only samples with a good RNA yield and no RNA degradation (ratio of 28S to 18S, > 1.7; RNA integrity number > 9) were used for further experiments. All samples were sequenced two times, in two different lanes (named L001 and L002 in the file names).
cDNA libraries were prepared with the Illumina TruSeq Stranded mRNA and the IDT for Illumina TruSeq UD Indexes, and were sequenced on an Illumina NovaSeq 6000 systems at the CHU Sainte-Justine Integrated Centre for Pediatric Clinical Genomics (Montreal, Canada).

treatment_protocol: Mycobacterium tuberculosis H37Rv (MTB) was grown from a frozen stock to mid-log phase in 7H9 medium (Becton Dickinson), supplemented with albumin-dextrose-catalase (ADC, Becton Dickinson). Before infection, MTB were washed and resuspended in 4 mL PBS. Clumps were eliminated by passing through a 10 µm filter. The density of bacteria in the supernatant was verified by measuring the OD600 and aliquot volumes defined to allow one bacterium-per two cell infections. After 2 h of incubation at 37 °C, infected cells were washed three times in PBS and treated with amikacin (50 µg/ml). After 1 h, cells were washed and incubated in fresh complete medium. After 24h, cells were treated with MC3465 or MC3209 (10 μM) during 4 h and 24 h.

tag: subject

value: Donor 2

value: human monocyte-derived macrophage

tag: infection statut

value: Infected


title: D2_INF_DMSO_4h

value: DMSO


title: H3K27Ac ChIP-seq PBS2h rep1

source_name: H3K27Ac ChIP-seq PBS2h


title: D2_UNF_a1_4h

value: Uninfected


title: IBDU, SAMPLE 31

source_name: FFPE IBDU


title: D2_UNF_40_4h


title: D2_UNF_DMSO_4h


title: H3K27Ac ChIP-seq 3'SL6h rep1

source_name: H3K27Ac ChIP-seq 3'SL6h

value: 3'SL for 6 hours


title: F140509 Gastric cancer tumor nest CD68+ ROI 5


title: H3K27Ac ChIP-seq 3'SL2h rep1

source_name: H3K27Ac ChIP-seq 3'SL2h

value: 3'SL for 1 hours


title: F140509 Gastric cancer tumor nest CD68- ROI 5


title: IBDU, SAMPLE 32


title: H3K27Ac ChIP-seq Input 3SL LPS rep1

source_name: H3K27Ac ChIP-seq Input 3SL LPS

value: 3SL LPS treatment


title: IBDU, SAMPLE 29

value: Pediatric


title: IBDU, SAMPLE 33


title: H3K27Ac ChIP-seq 3'SL LPS6h rep1

source_name: H3K27Ac ChIP-seq 3'SL LPS6h

value: bone marrow derived macrophages

value: 3'SL LPS for 6 hours


title: IBDU, SAMPLE 30


title: IBDU, SAMPLE 28


title: D1_INF_a1_4h

source_name: Blood mononuclear cells - donor 1

value: Donor 1


title: D1_INF_40_4h


title: H3K27Ac ChIP-seq 3'SL LPS2h rep1

source_name: H3K27Ac ChIP-seq 3'SL LPS2h

value: 3'SL LPS for 1 hours

value: H3K27Ac (Vendor:Active Motif, cat# 39133)


title: F140509 Gastric cancer tumor nest CD68- ROI 4

value: tumor

value: CD68 neg


title: IBDU, SAMPLE 26

value: Mucosal tissue biopsies


title: IBDU, SAMPLE 27


title: D1_INF_DMSO_4h


title: F140509 Gastric cancer stroma CD68- ROI 3


title: H3K27Ac ChIP-seq LPS6h rep1

source_name: H3K27Ac ChIP-seq LPS6h

value: LPS for 6 hours


title: F140509 Gastric cancer stroma CD68- ROI 2


title: D1_UNF_DMSO_4h

value: human monocyte-derived macrophage


title: D1_UNF_40_4h


title: H3K27Ac ChIP-seq PBS rep1

source_name: H3K27Ac ChIP-seq PBS

value: vehicle PBS treatment


title: IBDU, SAMPLE 23


title: IBDU, SAMPLE 25


title: F140509 Gastric cancer stroma CD68+ ROI 3

value: CD68 pos


title: p300 ChIP-seq Input rep1

description:
disuccinimidyl glutarate-formaldehyde cross-linked
processed data file:
BMDM_ChIP_p300_TFmerged.txt

source_name: p300 ChIP-seq Input


title: H3K27Ac ChIP-seq LPS2h rep1

source_name: H3K27Ac ChIP-seq LPS2h

value: LPS for 1 hours


title: F140509 Gastric cancer stroma CD68+ ROI 2


title: F140509 Gastric cancer stroma CD68- ROI 1


title: U3

city: Hangzhou

first: Jiang

last: Penglei

address: Yuhangtang Road 866

department: School of basic medicine science

country: China

institute: Zhejiang University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced data were trimmed with trimmomatic and keep reads which length more than 16bp.
Clean data were mapped to rRNA reference (GenBank accession numbers for the rRNA sequences: 28S rRNA: U13369 nts 7935-12969; 18S rRNA: X03205; 5.8S rRNA: U13369 nts 6623-6779) using bowtie2 with parameter “--end-to-end -k 1”.
The sam files obtained from the alignment were converted to the bed files.
5’ and 3’ ends counting was done by bedtools (2.29.0) and combined to calculate RiboMeth score. The scores were normalized to average values for -6 and +6 nucleotides.
Assembly: GRCh38
Supplementary files format and content: BedGraph files with each sample RiboMeth score.

extract_protocol:
The total RNA of WT and FBL KD AML cells was isolated and alkaline hydrolyzed with NaHCO3 solution for 20 min at 95℃. After ethanol/sodium acetate cryoprecipitation, centrifugation and 75% ethanol washing, 25-200nt fragmented RNA was obtained.
Construction of the RNA fragment library was performed by LC Sciences (Hangzhou, China) using TruSeq Small RNA Sample Prep Kits (Illumina, USA) following manufacturer instructions.

tag: cell line

value: AML cells

tag: genotype

value: FBL knockdown


title: F140509 Gastric cancer tumor nest CD68+ ROI 4


title: F140509 Gastric cancer stroma CD68+ ROI 1


title: p300 ChIP-seq PBS6 rep1

source_name: p300 ChIP-seq PBS6

value: p300 (Millipore, cat# 05-257,Diagenode, cat# C15200211)


title: U2


title: Repli-seq-WT-APH-for-URI-S6

city: Beijing

first: Yang

last: Liu

address: Yiheyuan Road, No. 5

institute: School of life sciences, Peking University

data_processing:
Reads are mapped to hg19 with BWA-MEM
Assembly: hg19
Supplementary files format and content: bw files
Library strategy: Repli-seq

growth_protocol: Standard protocols for K562 cells, which has been provided in the ATCC database.

extract_protocol: Standard protocols with Proteinase K

treatment_protocol: It has been described in the experimental design

value: 600nM APH


title: U1


title: p300 ChIP-seq PBS2 rep1

source_name: p300 ChIP-seq PBS2

value: bone marrow derived macrophages


title: p300 ChIP-seq 3'SL6h rep1

source_name: p300 ChIP-seq 3'SL6h

value: 3'SL for 6 hours


title: IBDU, SAMPLE 22

value: Pediatric


title: IBDU, SAMPLE 24


title: Repli-seq-WT-APH-for-URI-S5


title: D1_UNF_a1_4h

value: Donor 1

value: Uninfected


title: CT3

value: WT


title: IBDU, SAMPLE 21


title: IBDU, SAMPLE 20


title: p300 ChIP-seq 3'SL2h rep1

source_name: p300 ChIP-seq 3'SL2h

value: 3'SL for 2 hours


title: Repli-seq-WT-APH-for-URI-S4


title: IBDU, SAMPLE 19

value: Mucosal tissue biopsies


title: p300 ChIP-seq 3'SL LPS2h rep1

source_name: p300 ChIP-seq 3'SL LPS2h

value: 3'SL LPS for 2 hours


title: Repli-seq-WT-APH-for-URI-S3


title: p300 ChIP-seq 3'SL LPS6h rep1

source_name: p300 ChIP-seq 3'SL LPS6h

value: 3'SL LPS for 6 hours


title: CT2


title: Input RNA U2

description: Input RNA

data_processing:
Illumina Casava1.8 software used for basecalling.
Raw reads were trimmed using Trimmomatic (v0.38).
Bowtie2 was then used to align trimmed reads to the human reference genome GRCh38.
HTSeq (v0.11.2) was used to calculate genes counts with parameter “--mode intersection-strict --stranded no --minaqual 1”.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include raw counts for each Sample .

extract_protocol: Cell were lysed in 400 μL MCE buffer (100 mM KCl, 0.1% Triton X-100, 50 mM HEPES, 2 mM MgCl2, 10%  glycerin) supplemented with 1mM DTT (Sigma), 20 unit/mL RNase Inhibitor (EDTA free, Vazyme) and 1× protease inhibitor cocktail (EDTA free, Beyotime). After centrifugation at 15000 rpm for 10 min, the supernatants were harvested. 100 μL of them were used as input, and 290 μL of them were added to the pre-prepared 10%-50% sucrose density gradient solution (by BioCom Gradient Station) and centrifuged at 38000 rpm (SW41 Beckman rotor) for 3 h at 4 ℃. 14 fractions with ribosome and RNA were collected and the absorbance of OD260 was measured using the automatic Density Gradient Separation System (Biocomp).

treatment_protocol: AML cells infected with shCT or shFBL (5 million cells per sample) were treated with cycloheximide (100 μg/mL, Sigma) for 15 min at 37 ℃ to inhibit translational elongation.


title: p300 ChIP-seq LPS6h rep1

source_name: p300 ChIP-seq LPS6h

value: LPS for 6 hours


title: Repli-seq-WT-APH-for-URI-S1


title: Repli-seq-WT-APH-for-URI-S2


title: Input RNA U1

description: Input RNA


title: Input RNA CT2

description: Input RNA


title: p300 ChIP-seq PBS rep1

source_name: p300 ChIP-seq PBS

value: vehicle PBS treatment

value: p300 (Millipore, Diagenode)


title: Repli-seq-WT-for-URI-S6

value: DMSO


title: p300 ChIP-seq LPS2h rep1

source_name: p300 ChIP-seq LPS2h

value: LPS for 2 hours


title: IBDU, SAMPLE 15

source_name: FFPE IBDU

value: Adult


title: Input RNA CT1

description: Input RNA

value: AML cells


title: IBDU, SAMPLE 16


title: p300 ChIP-seq  GW3965 rep1

description:
disuccinimidyl glutarate-formaldehyde cross-linked
processed data file:
BMDM_ChIP_p300_peaks.txt

source_name: p300 ChIP-seq  GW3965

value: bone marrow derived macrophages

value: GW3965 (1uM) for 18 hours


title: IBDU, SAMPLE 14


title: IBDU, SAMPLE 18

value: Pediatric


title: Repli-seq-WT-for-URI-S4


title: IBDU, SAMPLE 12


title: IBDU, SAMPLE 13


title: polysome RNA U2

description: Polysome RNA

value: FBL knockdown


title: LXR ChIP-seq Input GW3965 rep2

description:
disuccinimidyl glutarate-formaldehyde cross-linked
processed data file:
BMDM_ChIP_LXR_peaks.txt

source_name: LXR ChIP-seq Input GW3965


title: IBDU, SAMPLE 17


title: IBDU, SAMPLE 11


title: polysome RNA U1

description: Polysome RNA


title: Repli-seq-WT-for-URI-S3


title: IBDU, SAMPLE 10


title: Repli-seq-WT-for-URI-S2


title: polysome RNA CT2

description: Polysome RNA


title: Srebp ChIP-seq Input GW3965 rep1

description:
disuccinimidyl glutarate-formaldehyde cross-linked
processed data file:
BMDM_ChIP_SREBP_peaks.txt

source_name: Srebp ChIP-seq Input GW3965


title: IBDU, SAMPLE 9


title: Repli-seq-WT-for-URI-S1


title: atalkbh1a1b_str3

city: Changsha

first: Chongsheng

last: He

state: Hunan

address: 27 Tianma road

institute: Hunan university

description: Stratified atalkbh1a/1b seed mRNAs were used to generate the cDNA libraries, respectively, according to NEBNext UltraTM II Directional RNA Library Prep Kit for Illumina

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using cutadapter
Trimmed sequence reads were mapped to TAIR10 using STAR
Differential expression analysis was performed by DESeq2
Assembly: TAIR10
Supplementary files format and content: Excel files include RPKM values for each Sample.

organism: Arabidopsis thaliana

source_name: Seed

extract_protocol:
Total RNA was harvested using Trizol. mRNA was purified by oligo-dT beads
RNA libraries for mRNA-seq were prepared using NEBNext UltraTM II Directional RNA Library Prep Kit for Illumina following manufacturer's protocols

treatment_protocol: Wild type and atalkbh1a/1b seeds were submerged in steried water at 4ºC for stratification

tag: ecotype

value: Seed

value: stritification

tag: time

value: 2 days


title: CELL-RE3

city: Chang Chun

first: Xin

last: Hu

address: 2699 Qianjin road,china

institute: Jilin university

data_processing:
Sequencing adapters were processed using the software Cutadapt(version 2.7) for low-quality, n-rich, short reads smaller than 16bp
The software perl5(version 26) was used to process reads with UMIs less than 12bp and reads without UMI, and identify UMIs
The software Bowtie (version 1.2.2) was used for comparison to miRBase database
Assembly: miRBase database
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: MCF7 cells

growth_protocol: MCF7 cell line was cultured in DMEM (Gibco) supplemented with 10% FBS and streptomycin/penicillin (100 U/mL) at 37˚C in an atmosphere of 5% CO2.

extract_protocol:
The total RNA was harvested using Trizol reagent.The QIAseq miRNA Library Kit was used for the construction of sequencing libraries.
Sequencing libraries were generated using QIAseq® miRNA Library Kit for Illumina (Qiagen)

treatment_protocol: Transient transfection of siRNA and plasmid was performed by using lipofectamine 3000 (Invitrogen).

value: MCF7 cells

value: Breast cancer cells

value: LSD1 Rescue

value: Transient transfection with LSD1-specific siRNAs and LSD1 rescue plasmid


title: polysome RNA CT1

description: Polysome RNA

value: WT


title: LXR ChIP-seq GW3965 rep1

source_name: LXR ChIP-seq GW3965

value: LXR (Santa Cruz Biotechnology:sc-1000X, sc- 133221X, sc-271064X)


title: IBDU, SAMPLE 8

value: Mucosal tissue biopsies


title: Repli-seq-WT-for-URI-S5

value: DMSO


title: IBDU, SAMPLE 7

value: Adult


title: atalkbh1a1b_str2


title: Srebp ChIP-seq  GW3965 rep1

source_name: Srebp ChIP-seq  GW3965

value: SREBP (Santa Cruz Biotechnology:sc-8984X, Thermo Fisher Scientific:PA1-337, R&D Systems:AF7119)


title: LXR ChIP-seq Input GW3965 rep1

value: bone marrow derived macrophages


title: CELL-RE1


title: Ovary-CRS treated- rep5

city: Adelaide

first: Thao

last: Dinh

state: South Australia

address: North Terrace

country: Australia

institute: University of Adelaide

description: mice were injected i.p  eCG on day 22 and hCG on day 24

data_processing:
FASTQ files checked with FastQC.
Quasi-alignment to GRCm38.p6 (M25) transcript assembly and count quanticiation using Salmon.
Differential expression analyses were performed using DESeq2.
Genome_build: Genome Reference Consortium Mouse Build 38 patch release 6
Supplementary_files_format_and_content: Tabular list of raw and normalised (TPM) counts generated from Salmon

source_name: ovary 16h post-hCG

growth_protocol: 21 days old mice; 10-12grams

extract_protocol:
one ovary from each mice was processed for RNA extraction using RNeasy Mini Kit (Qiagen) and Dnase-treated.
Total RNA was converted to strand specific Illumina compatible sequencing libraries using the Nugen Universal Plus mRNA mRNA-Seq library kit from Tecan (Mannedorf, Switzerland) as per the manufacturers instructions (MO1442 v2). 75bp SR sequencing using Illumina NextSeq500 High output mode and v2.5 chemistry. Illumina Protocol 15069765 v06, July 2019.

treatment_protocol: mice were injected i.p either with CRS or 7.5% DMSO vehicle on days 21, 22, 23 and 24

value: CBA x C57BL/6 F1

tag: age

value: 21days old; 10-12 grams

value: CRS @ 50mg/kg


title: CELL-RE2


title: atalkbh1a1b_dry3

description: Dry atalkbh1a/1b seed mRNAs were used to generate the cDNA libraries, respectively, according to NEBNext UltraTM II Directional RNA Library Prep Kit for Illumina

value: Seed

value: control

value: 0 day


title: CELL-KD3

value: MCF7 cells

value: LSD1 Knockdown

value: Transient transfection with LSD1-specific siRNAs


title: LXR ChIP-seq GW3965 rep2

value: GW3965 (1uM) for 18 hours


title: atalkbh1a1b_dry2


title: Ovary-CRS treated- rep2


title: IBDU, SAMPLE 5


title: CELL-KD2

value: Breast cancer cells


title: IBDU, SAMPLE 4


title: IBDU, SAMPLE 3


title: atalkbh1a1b_dry1


title: ATAC_MAC_3

city: Seoul

first: Jin-Hong

last: Kim

address: 1 Gwanak-ro, Gwanak-gu

country: South Korea

institute: Seoul National University

data_processing:
ATAC-seq reads were quality-controlled using FastQC software.
Trimming of Nextera adapters and low-quality bases were conducted using Trimmomatic v0.39.
Trimmed reads were aligned to the mouse reference genome (GRCm39) using the Burrows-Wheeler Aligner-MEM version 0.7.17.
Multi-mapped reads, mitochondrial reads, and duplicate reads were removed with Samtools “view” function and MarkDuplicates.
After peak calling with merged aligned reads with MACS3, downstream analysis were performed with UROPA version 4.0.2 and TOBIAS version 0.13.1.
Assembly: mm39
Supplementary files format and content: Bigwig containing footprint score calculated with merged data

source_name: Articular cartilage

extract_protocol:
Nuclei were extracted using cell lysis buffer (IGEPAL CA-630, 1M Trizma HCl (pH 7.4), 5M NaCl, 1M MgCl2).
The extracted nuclei were used to prepare a library using a Tagment DNA Enzyme and Buffer Small Kit (Illumina).

value: Articular cartilage

value: Primary culture

value: Chondrocyte

value: wild type


title: Ovary-VC treated- rep6

value: 7.5% DMSO


title: CELL-NC3

value: Control

value: Transient transfection with scrambled control siRNAs


title: WT_str3

description: Stratified wild type seed mRNAs were used to generate the cDNA libraries, respectively, according to NEBNext UltraTM II Directional RNA Library Prep Kit for Illumina

value: WT

value: stritification

value: 2 days


title: IBDU, SAMPLE 1

value: Adult

value: Mucosal tissue biopsies


title: atalkbh1a1b_str1

value: Seed


title: Ovary-VC treated- rep5

value: CBA x C57BL/6 F1

value: 21days old; 10-12 grams


title: ATAC_MAC_2


title: IBDU, SAMPLE 6


title: CELL-NC2

value: MCF7 cells


title: Ovary-VC treated- rep4


title: ATAC_MAC_1


title: WT_str2


title: WT_str1


title: CELL-NC1

value: Breast cancer cells


title: Ovary-CRS treated- rep4

value: CRS @ 50mg/kg


title: WT_dry3

description: Dry wild type seed mRNAs were used to generate the cDNA libraries, respectively, according to NEBNext UltraTM II Directional RNA Library Prep Kit for Illumina

value: control

value: 0 day


title: Ovary-VC treated- rep3


title: EXO-RE3

source_name: MCF7 exosomes

growth_protocol: MCF7 cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin at 37°C and 5% CO2.

extract_protocol:
The exosomes were separated and total RNAs were extracted using QIAGEN exoRNeasy Maxi Kit (Qiagen)
Sequencing libraries were generated using QIAseq® miRNA Library Kit for Illumina (Qiagen)

value: scrambled LSD1-specific siRNAs and LSD1 rescue plasmid (RE)


title: CELL-KD1

value: LSD1 Knockdown

value: Transient transfection with LSD1-specific siRNAs


title: Ovary-VC treated- rep2

value: 7.5% DMSO


title: WT_dry2

value: WT


title: EXO-RE2


title: IBDU, SAMPLE 2


title: HS0.5-R36_2

city: jingzhou

first: wu

middle: zi

last: wei

state: Hubei

department: Animal Science

institute: yangtze university

data_processing:
illumina bcl2fastq2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Sus scrofa11.1 whole genome using Hisat2 v2.0.5 with parameters --rna-strandness RF --dta -t -p 4.
Fragments per Kilobase per Million Mapped Fragments of(FPKM) were calculated using a protocol from Trapnell, C. et al, 2010.FPKM method can eliminate the influence of gene length and sequencing amount on the calculated gene expression.
Genome_build: Sus scrofa11.1
Supplementary_files_format_and_content: FPKM

organism: Sus scrofa

source_name: HS0.5-R36 (36h recovery after HS) groups of iSCs

growth_protocol: iSCs were cultured in Minimum Essential Medium (MEM) with Eagle's balanced salt solution (HyClone, USA), supplementing with 10% fetal bovine serum (Clark, Australia) and 1% penicillin-streptomycin (Gibco, USA), in a 5% CO2 incubator at 37°C.

extract_protocol:
Trizol reagent (Sigma) was used to isolate the total RNA of samples collected from three controls (C1, C2 and C3) , three HS0.5 groups (HS0_1, HS0_2 and HS0_3) and three HS0.5-R36(HS36_1, HS36_2, HS36_3) groups of iSCs.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Before treating with heat in a 5% CO2 incubator at 43℃ respectively for 0.5h,  cells were seeded at a density of 1×105 cells/mL to culture for 6h. Then, cells were cultured at 37°C to recover for 36h .

value: 80 to 90 days gestation

value: testis

value: immature sertoli cells (iSCs)

value: HS0.5-R36 (36h recovery after HS)


title: HS0.5-R36_3

value: 80 to 90 days gestation


title: Ovary-VC treated- rep1

value: CBA x C57BL/6 F1


title: WT_dry1

value: Seed


title: HS0.5-R36_1


title: COCs-CRS treated- rep4

description: mice were injected i.p  eCG on day 22

source_name: COCs 10h IVM

growth_protocol: COCs from 21 days old mice; 10-12grams

extract_protocol:
100 pooled COCs per treatment were processed for RNA extraction using RNeasy Mini Kit (Qiagen) and Dnase-treated.
Total RNA was converted to strand specific Illumina compatible sequencing libraries using the Nugen Universal Plus mRNA mRNA-Seq library kit from Tecan (Mannedorf, Switzerland) as per the manufacturers instructions (MO1442 v2). 75bp SR sequencing using Illumina NextSeq500 High output mode and v2.5 chemistry. Illumina Protocol 15069765 v06, July 2019.

treatment_protocol: COCs were treated either with CRS or 0.1% DMSO vehicle for 10h during in vitro maturaion assay

value: 21days old; 10-12 grams

value: 2.5ug/ml CRS


title: HS0.5_3

source_name: HS0.5 (0h after HS) group of iSCs

value: HS0.5 (0h after HS)


title: MUT HiC rep3

city: Guanghzou

first: Zeng

last: Pengguihang

address: No.74, Zhongshan 2nd Road, Guangzhou, Guangdong

institute: Sun Yat-Sen University

data_processing:
Raw fastq files were under adapter trimming and quality control by Trim Galore 0.4.4_dev, using default parameters.
Trimmed reads were mapped to mm9 genome assembly by Bowtie2 2.3.4.1, using default parameters.
HiC data were processed by HiC-Pro softeare version 2.10.0.
Assembly: mm9
Supplementary files format and content: Validpairs and cool files.

source_name: ESC

growth_protocol: ESC lines was cultured in gelatin-coated dish with ESC medium, which consisted of DMEM (Hyclone), 15% (v/v) fetal bovine serum (FBS, Lonsera), 0.1 mM β-mercaptoethanol (Sigma), 2 mM L-glutamine (Thermo Fisher), 0.1 mM nonessential amino acids (Thermo Fisher), 1% (v/v) nucleoside mix (Sigma), 1,000 U/mL recombinant LIF (Millipore).

extract_protocol:
1% formaldehyde in PBS was used to crosslink the cells.
Libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: The MUT_CTCF cells was mutated the CTCF at T668.

value: ESC

value: embryonic stem cells

value: MUT


title: EXO-RE1

value: scrambled LSD1-specific siRNAs and LSD1 rescue plasmid (RE)


title: EXO-KD3

value: scrambled LSD1-specific siRNAs


title: EXO-KD2


title: MUT HiC rep2


title: HS0.5_2


title: HS0.5_1


title: COCs-CRS treated- rep2

description: mice were injected i.p  eCG on day 22


title: COCs-VC treated- rep4

description: mice were injected i.p  eCG on day 22

value: 0.1% DMSO


title: COCs-CRS treated- rep3

description: mice were injected i.p  eCG on day 22


title: WT HiC rep3

value: WT


title: C3

source_name: control group of iSCs

value: Control (before HS)


title: MUT HiC rep1


title: C2

value: 80 to 90 days gestation

value: testis


title: WT HiC rep2


title: EXO-NC3

value: scrambled NC siRNAs


title: EXO-NC1


title: COCs-VC treated- rep2

description: mice were injected i.p  eCG on day 22


title: EXO-NC2


title: WT HiC rep1


title: COCs-VC treated- rep1

description: mice were injected i.p  eCG on day 22


title: siCARM1-1 [lncRNA-seq]

status: Public on Mar 03 2024

city: beijing

first: yan

last: wang

address: 17 panjiayuan nanli, chaoyang district, Beijing, China

country: Zimbabwe

institute: National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences

data_processing:
SOAPnuke (version: v1.5.2) was used for filter reads, parameters: -1 15 -q 0.5 -n 0.1.
Bowtie2 (version: v2.2.5) was used to map clean reads to reference gene, parameters: -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k 200.
HISAT (version: v2.0.4) was used to align clean reads to the mouse genome, parameters: -p 8 --phred64 --sensitive -I 1 -X 10000.
RSEM (version: v1.2.12) was used for abundance measurement, parameters: default.
FPKM method was used in calculated expression level.
Genome_build: hg 38
Supplementary_files_format_and_content: abundance measurements

source_name: Human breast cancer cell line

growth_protocol: MDA-MB-231 cells were maintained in Dulbecco’s modified Eagle’s medium supplemented with 10% fetal bovine serum (FBS), 100 units/ml penicillin, and 100 mg/ml streptomycin.

extract_protocol:
Total RNA was extracted from the MDA-MB-231 cells using Trizol reagent (Invitrogen). RNA quality was checked by Agilent 2100 Bioanalyzer (Agilent Technologies, USA).
RNA libraries were prepared for sequencing using standard BGI protocols

treatment_protocol: siRNA was transfected into MDA-MB-231 cells using Lipofectamine RNAiMAX (Invitrogen).


title: C1

value: 80 to 90 days gestation

value: immature sertoli cells (iSCs)


title: M17 cells, LINC00894 knockdown, B-3

city: jiangsunantong

first: hu

middle: han

last: jing

address: Chongchuan District Xincheng Bridge street

institute: nantonguniversity

data_processing:
HISAT2 is a second-generation sequencing sequence alignment software, which can compare the whole genome, transcriptome and exome data with the reference genome. Using the improved BWT algorithm, the sequencing Reads can be efficiently compared to the reference genome. In this project, the HISAT2 software was used to sequence Clean Reads with a specified genome to obtain information about their location on the reference genome. The HISAT2 algorithm is mainly divided into three parts: (1) The whole sequencing sequence is compared to the single exon of the genome; (2) Segmented alignment of the sequencing sequence to two exons of the genome; (3) Segmenting the sequencing sequence to more than three (including three) exons of the genome.
Assembly: Homo_sapiens_Ensembl_104(http:// may2021.archive.ensembl.org/Homo_sapiens/Info/Index)
Supplementary files format and content: DEG.xlsx
Supplementary files format and content: readcounts.xlsx

source_name: brain

extract_protocol:
Total RNA was extracted by TRIzol(Takara)
After the sample was qualified, eukaryotic mRNA was enriched with magnetic beads with Oligo (dT) connections. mRNA was then randomly interrupted by fragmentation buffer. Using mRNA as template, the first strand of cDNA was synthesized with six-base random primers, then the second strand of cDNA was synthesized by adding buffer, dNTPs and DNA polymerase I, and then the double-stranded cDNA was purified by AMPure XP beads. The purified double-stranded cDNA was then end-repaired, A-tailed and sequenced, and then treated with AMPure XP beads were used for fragment size selection and PCR enrichment to obtain the final cDNA library.

value: brain

value: neuroblast

value: LINC00894 knockdown


title: EXO-KD1


title: siControl-1 [lncRNA-seq]

value: siControl


title: M17 cells, Control, A-1

value: NC


title: M17 cells, LINC00894 knockdown, B-1


title: M17 cells, LINC00894 knockdown, B-2


title: WT-P16-testis-1

city: Wuhan

first: ZHIYI

last: CHEN

address: WuHan

institute: WuHan University

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using cutadapt (minimum read length:40,quality-cutoff 20)
Trimmed sequence reads were mapped to mm39 using bowtie2
Read count extraction and normalization were performed using featureCount
Differential expression analysis using DESeq2
Assembly: mm39
Supplementary files format and content: Differential expression analysis result for four samples we chose

source_name: testis

extract_protocol:
Total RNA was used as input material for the RNA sample preparations.
Sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA, Catalog #: E7530L).

value: wild type


title: WT-P16-testis-3


title: M17 cells, Control, A-3


title: M17 cells, Control, A-2


title: H5-KO-P16-testis-3

value: knock out


title: WT-P16-testis-2


title: COCs-VC treated- rep3

description: mice were injected i.p  eCG on day 22

value: CBA x C57BL/6 F1

value: 21days old; 10-12 grams


title: H5-KO-P16-testis-1


title: Re_3_myoblast

city: Gwangju

first: Dongryeol

last: Ryu

address: 123 Cheomdangwagi-ro

department: Biomedical science and engineering

institute: Gwangju Institute of Science and Technology

data_processing:
Reads were mapped to the GRCh38 reference using STAR (Spliced Transcripts Alignment to a Reference, ver. 2.7.10a). Read counts for each gene were obtained by RSEM (RNA-Seq by Expectation-Maximization, ver. 1.3.1)
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

extract_protocol:
Total RNAs were extracted using Rneasy mini plus kit (Qiagen). 1.5 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq RNA library prep kit (illumina) following manufacturer's protocols.

value: immortalized mouse myoblast

value: Ginsenoside Re


title: Control_3_myoblast

value: DMSO


title: Control_2_myoblast


title: Re_2_myoblast


title: Control_1_myoblast


title: Re_1_myoblast


title: GBC-treated

value: GBC


title: BL_HiC_2i_d21_wild_type_rep1

city: guangzhou

first: xiaotao

last: dong

address: 190 Kai Yuan Avenue

institute: Chinese Academy of Sciences

data_processing:
The BL-Hi-C data were processed with ChIA-PET2 v0.9.2 software with the parameter “-A ACGCGATATCTTATC -B AGTCAGATAAGATAT -s 1 -m 1 -t 4 -k 2 -e 1 -l 15 -S 500” to identify chromatin interactions that annotated with the genome mm10. The biological replicates in each group were merged to perform the A/B compartments and TAD analysis. The interaction matrix was generated by HiC-Pro. Normalization was performed by HiCExplorer hicCorrectMatrix (--correctionMethod KR). TADs and TAD boundaries were defined by HiCExplorer hicFindTADs (--correctForMultipleTesting fdr --thresholdComparisons 0.05 --minDepth 120000 --maxDepth 200000 --step 40000) at 40-kb resolution. Compartments were analyzed using HOMER (v.4.10) tools(Heinz et al., 2010) with the default parameters at 100 kb resolution. APA analysis was performed using juicer tools.The producibility of BL-Hi-C datasets was calculated on pairs of raw Hi-C contact matrices at 100 kb resolution by using HiCRep.
High confidence interactions were defined as those with an FDR < 0.05 for downstream analysis. Differential EP loops mediated by TEAD2 were identified using the diffloop pipeline, with quickAssoc function, which was based on an overdispersed Poisson regression model. Differential loops with high confidence were chosen by applying the following criteria: p value < 0.05 and |log2FC| > 1. The data was further visualized in the WashU Epigenome Browser.
Assembly: mm10

source_name: E14 mESCs

growth_protocol: For serum/LIF culture, DMEM high-glucose media supplemented with 15%FBS, 1 mM sodium pyruvate (Gibco), 1% nonessential amino acids (Gibco), 1% GlutaMAX (Gibco), 0.1 mM β-mercaptoethanol (Life Technologies), 1% penicillin-streptomycin (Gibco)，1000 U/mL LIF (Millipore).  For 2i/LIF culture, mouse ESCs were cultured in 2i medium. In total, 500 mL of 2i medium were prepared with 240 mL of DMEM/F12 (Thermo Fisher Scientific), 240 mL of neurobasal (Thermo Fisher Scientific), 2.5 mL of N2 supplement (Thermo Fisher Scientific), 5 mL of B27 supplement (Thermo Fisher Scientific), 1% GlutaMAX, 1% nonessential amino acids, 0.1 mM β-mercaptoethanol, and 1% penicillin-streptomycin, 1000 U/mL LIF, 3 μM CHIR99021 (Selleck), and 1 μM PD0325901 (Selleck). All cells were maintained at 37°C in an incubator with 5% CO2. The medium was changed every day, and the cells were passaged with 0.25% trypsin-EDTA (Gibco).For interconversion of 2iL-ESCs and SL-ESCs, 2iL-ESCs and SL-ESCs were cultured on gelatinized plates for 3 days, and were digested with 0.25% trypsin. Then 2iL-ESCs or SL-ESCs were plated into gelatinized six-well plates with 6-7 × 104 cells per well in either serum/LIF or 2i medium. The medium was changed daily.

extract_protocol:
The BL-Hi-C experiments were performed as previous described (Dong et al, 2022; Liang et al., 2017)
Cells were treated with 1% formaldehyde at RT for 10 min followed by quenching with 0.2 M glycine. Nuclei were isolated for subsequent experiments, including digestion with HaeIII (NEB), end-plus-A treatment, proximity ligation with biotin-labeled Bridge Linker, DNA purification and enrichment of biotin-labeled DNA with Dynabeads M-280 streptavidin. The enriched bead-bound DNA was subjected to end repair, adapter ligation, PCR amplification and DNA library construction, followed by sequencing on the Illumina NovaSeq platform (Annoroad Gene Technology Co., Ltd.).

treatment_protocol: The CRISPR/Cas9 system was used to generated Tead2-knockout SL-ESC lines

value: E14 mESCs

value: Embryonic stem cells

value: Wild type

value: SL-to-2iL transition day 21


title: DMSO-treated


title: BL_HiC_2i_d0_wild_type_rep1

value: ESCs cultured in serum and leukemia inhibitory factor (serum/LIF)


title: BL_HiC_2i_d0_wild_type_rep2


title: H3K27ac_CUTTag_2iL_ESCs_wild_type_rep2

data_processing:
After trimming the adaptor sequence with Cutadapt, ChIP-seq reads were aligned to mm10 genome using Bowtie2 with the default parameters. Reads mapping to mitochondrial DNA or unassigned sequences were discarded. Finally, concordantly aligned pairs were retained. The peaks were called using MACS2 (Zhang et al, 2008) with the default parameters. Alignment BAM files were converted into read coverage files (bigWig format) using deepTools (Ramírez et al., 2016).  Peak overlap was done by using bedtools (v2.25.0). Differential peaks were called by MACS2 bdgdiff function with the default parameters. Motif analysis of ChIP-seq peaks was performed by using Homer.
Assembly: mm10
Supplementary files format and content: Normalized bigWig and peak file for each sample.
Library strategy: CUT&Tag

growth_protocol: For serum/LIF culture, DMEM high-glucose media supplemented with 15%FBS, 1 mM sodium pyruvate (Gibco), 1% nonessential amino acids (Gibco), 1% GlutaMAX (Gibco), 0.1 mM β-mercaptoethanol (Life Technologies), 1% penicillin-streptomycin (Gibco)，1000 U/mL LIF (Millipore). For 2i/LIF culture, mouse ESCs were cultured in 2i medium. In total, 500 mL of 2i medium were prepared with 240 mL of DMEM/F12 (Thermo Fisher Scientific), 240 mL of neurobasal (Thermo Fisher Scientific), 2.5 mL of N2 supplement (Thermo Fisher Scientific), 5 mL of B27 supplement (Thermo Fisher Scientific), 1% GlutaMAX, 1% nonessential amino acids, 0.1 mM β-mercaptoethanol, and 1% penicillin-streptomycin, 1000 U/mL LIF, 3 μM CHIR99021 (Selleck), and 1 μM PD0325901 (Selleck). All cells were maintained at 37°C in an incubator with 5% CO2. The medium was changed every day, and the cells were passaged with 0.25% trypsin-EDTA (Gibco).For interconversion of 2iL-ESCs and SL-ESCs, 2iL-ESCs and SL-ESCs were cultured on gelatinized plates for 3 days, and were digested with 0.25% trypsin. Then 2iL-ESCs or SL-ESCs were plated into gelatinized six-well plates with 6-7 × 104 cells per well in either serum/LIF or 2i medium. The medium was changed daily.

extract_protocol:
For ChIP, cells stably expressed biotin-alone or biotin-TEAD2 were expanded and crosslinked with 1% formaldehyde. Crosslinked cells were sonicated and diluted tenfold with ChIP dilution buffer, and then incubated with M280 streptavidin dynabeads at 4°C overnight. Streptavidin dynabeads-bound DNA was subsequently washed twice with wash buffer 1 (2% SDS), once with wash buffer 2 (50 mM HEPES (pH 7.5), 1 mM EDTA, 500 mM NaCl, 0.1% sodium deoxycholate, 1% Triton X-100), once with wash buffer 3 (10 mM Tris-HCl (pH 8.0), 1 mM EDTA, 250 mM LiCl, 0.5% NP-40, 0.5% sodium deoxycholate) and then twice with TE wash buffer (10 mM Tris-HCl (pH 8.0), 1 mM EDTA). ChIPed DNA was reverse-crosslinked and purified for DNA library construction followed by sequencing. For CUT&Tag, 100,000 cells were harvested and washed twice with 200 µL of wash buffer. 10 µL concanavalin A beads (Bangs Laboratories) were added per sample and incubated at room temperature for 15 min. Then, 100 µL of dig-wash buffer containing 2 mM EDTA and 1 µg of primary antibody were added. The primary antibody incubation was performed on a rotating platform at 4°C overnight. Two hundred microliters of dig-wash buffer were added to remove the unbound antibodies. Then, the reaction was incubated with pAG-Tn5 (homemade) at 4°C for 2 hr. Two hundred microliters of dig-med buffer were added to remove unbound pAG-Tn5 protein. Next, the cells were resuspended in 100 µL of tagmentation buffer and incubated at 37°C for 1 hr. To stop tagmentation, 2.25 µL of 0.5 M EDTA, 2.75 µL of 10% SDS and 0.5 µL of 20 mg/mL proteinase K were added and incubated at 55°C for 30 min and then at 70°C for 30 min to inactivate proteinase K. Then, DNA was extracted. The antibodies included H3K27ac (Active Motif, 39133), H3K4me1 (Active Motif, 39297).
ChIP-seq libraries were constructed using the VAHTSTM Universal DNA Library Prep Kit for Illumina® V2 (Vazyme Biotech). After PCR library amplification, size selection of adaptor-ligated DNA was performed using Agencourt AMPure XP Beads (Beckman Coulter). The libraries were sequenced on the Illumina NovaSeq or Hiseq X-ten platform (Annoroad Gene Technology Co., Ltd.).  To generate the CUT&Tag libraries, 21 µL DNA were mixed with 2 µL of a universal i5 and a uniquely barcoded i7 primer (Buenrostro et al, 2015a) using a different barcode per sample. A volume of 25 µL of NEBNext high-fidelity 2 × PCR master mix (NEB) was added and mixed. The sample was placed in a thermocycler with a heated lid using the following cycling conditions: 72°C for 5 min (gap filling); 98°C for 30 s; 14 cycles of 98°C for 10 s and 63°C for 30 s; final extension at 72°C for 1 min; and hold at 8°C. Post-PCR clean-up was performed by adding 1 × volume of Ampure XP beads (Beckman Counter), and the libraries were incubated with beads at room temperature for 15 min, washed twice gently with 80% ethanol, and eluted in 25 µL of 10 mM Tris (pH 8.0). The libraries were sequenced on Illumina NovaSeq (Annoroad Gene Technology Co., Ltd.).

treatment_protocol: The CRISPR/Cas9 system was used to genetically generate Tead2-FLAG-AviTag knock-in ESC lines, 2iL-ESC lines with mutation of TEAD2 motifs in the B4galt6 promoter region, and  Tead2-knockout SL-ESC lines

value: ESCs cultured in serum-free medium with LIF and two inhibitors (PD0325901 and CHIR99021) (2i/LIF)


title: BL_HiC_2i_d21_wild_type_rep2


title: BL_HiC_2i_d21_Tead2_knockout_rep2

value: Tead2 Knockout


title: BL_HiC_2i_d21_Tead2_knockout_rep1


title: H3K27ac_CUTTag_2iL_ESCs_wild_type_rep1


title: H5-KO-P16-testis-2

value: testis


title: H3K27ac_CUTTag_2iL_ESCs_Tead2_motif_mutant_rep2

value: TEAD2 motif mutant


title: H3K4me1_CUTTag_2i_d6_wild_type

value: SL-to-2iL transition day 6


title: H3K27ac_CUTTag_2i_d6_Tead2_knockout


title: PSC_old2

city: Shanghai

first: Yiming

state: Shanghai

address: yueyang road

institute: Sibcb

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Aligned reads and gene-barcode matrices were then generated from FASTQ files including Read 1, Read 2 and i7 index using Cell Ranger software package (version 3.0) with default parameters.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Periosteum

extract_protocol:
Freshly collected Bone and periosteum were digested with 1 ml pre-warmed digestion solution (200 U/ml DNase I (Sigma, 11284932001), 2 mg/ml collagenase I (Worthington, LS004197) and 2 mg/ml collagenase IV (Worthington, LS004189) in HBSS(ThermoFisher, 14025134)) and incubated in a shaking water bath at 37°C at a speed of 220 rpm for 30 minutes. After digestion, single-cell suspension was filtered through a 40-µm nylon mesh and washed twice in ice-cold HBSS without Ca2+ and Mg2+ (ThermoFisher, 14170138).Then cells were sorted by Aria sorp(BD)
A single cell library was generated using Chromium Single Cell 3’ Library Kit v2 (10× Genomics). Library sequencing was performed on an Illumina Hiseq PE150 or NovaSeq PE150 platform.

value: Stromal cells

value: Periosteum

value: 10  months old

value: untreated


title: Callus_Frac_4d

description: 10x Genomics

value: 8-10 weeks old

value: Fracture


title: PSC_young

description: 10x Genomics


title: PSC_total

description: 10x Genomics

value: Total periosteum cells


title: BMSC_Frac_6m

description: 10x Genomics

source_name: Bone marrow

value: Bone marrow

value: 8-10 months old


title: PSC_old

description: 10x Genomics


title: 8Cell_RargiTfap2cOE_Tfap2c

first: Gran

last: Young

state: --- Select a state ---

address: 1239th, Siping Road, Yangpu district

institute: Tongji University

description: WT, 8C, Tfap2c, CUT&RUN

data_processing:
Sequencing reads were first trimmed to remove adapters and then mapped to mouse genome (UCSC mm10) using Bowtie2 (v2.3.4.3) with the parameters: -t --no-mixed --no-discordant --no-unal.
Mapped reads with high confidence were kept for further analysis using SAMtools (v1.7) with the parameters: -bf 0x2 -q 20. Duplicated reads were removed using sambamba (v0.6.8)
Genome-wide signals were calculated using a 50-bp window and normalized to the uniquely mapped fragments using ‘bamCoverage’ from deepTools (v2.5.7).
Peaks were identified by macs2 (v2.1.1) with the parameters: -q 0.05 --keep-dup 1 and peaks with signal FPKM > 15 were finally reserved.
For allele specific analysis, reads were separated into paternal or maternal using SNPsplit (v0.4.0).
Assembly: mm10
Supplementary files format and content: bigWig
Library strategy: CUT&RUN

source_name: Mouse embryo

extract_protocol:
After cell immobilization, bead-bound samples were successively incubated with appropriate amount of primary antibodies against protein-of-interest (TFAP2C antibody: Santa Cruz, sc-12762; TEAD4 antibody: Santa Cruz, sc-101184; KLF5 antibody: Proteintech, 21017-1-AP) in 250µL of CUT&RUN antibody buffer and a secondary antibody if necessary (rabbit anti-mouse IgG: Abcam, ab46540) in 250µL of CUT&RUN digitonin buffer for overnight at 4°C. Cell membranes were permeabilized with 0.01% digitonin to allow the specific antibody to find its target. After unbound antibodies were washed away, 700 ng/mL protein A-MNase (pA-MN; a gift from Steven Henikoff lab or purchased from Vazyme Biotech) was added and incubated for 1 hour at 4°C. After washing, CaCl2 was added to a final concentration of 2 mM to activate pA-MN, and the digestion reaction was carried out for 30 min at 0°C and then stopped by adding 150μL 2× CUT&RUN stop buffer. The protein–DNA complex fragments were then released by 20-min incubation at 37°C. After transferring the supernatant to a new tube, 3µL of 10% SDS and 2.5µL of Proteinase K (Thermo) were added and incubated for 30 min at 55°C. DNA was then precipitated by phenol/chloroform/isoamylalcohol followed by ethanol precipitation with glycogen and then dissolved in nuclease-free water.
Sequencing libraries were prepared using KAPA Hyper Prep Kit (KAPA biosystems) following the manufacturer’s instructions with slight modifications. Briefly, end repair was conducted for 30 min at 20°C followed by end-repair/A-tailing for 30 min at 50°C. After adaptor ligation for 30 min at 20°C, the DNA fragments were purified by 1.4× volume of AMPure beads (Beckman Coulter) followed by 18 cycles of PCR amplification with 2× KAPA HiFi HotStart Ready Mix. The final libraries were cleaned up with 1.2× volume of AMPure beads, and all CUT&RUN libraries were sequenced on a NovaSeq6000 (Illumina) platform at Novogene Co., Ltd. with paired-ended 150-bp reads.

value: Mouse embryo

tag: Stage

value: embryo

value: LY2955303 & Tfap2c OE


title: CT1

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced data were trimmed with trimmomatic and keep reads which length more than 16bp.
Clean data were mapped to rRNA reference (GenBank accession numbers for the rRNA sequences: 28S rRNA: U13369 nts 7935-12969; 18S rRNA: X03205; 5.8S rRNA: U13369 nts 6623-6779) using bowtie2 with parameter “--end-to-end -k 1”.
The sam files obtained from the alignment were converted to the bed files.
5’ and 3’ ends counting was done by bedtools (2.29.0) and combined to calculate RiboMeth score. The scores were normalized to average values for -6 and +6 nucleotides.
Assembly: GRCh38
Supplementary files format and content: BedGraph files with each sample RiboMeth score.

extract_protocol:
The total RNA of WT and FBL KD AML cells was isolated and alkaline hydrolyzed with NaHCO3 solution for 20 min at 95℃. After ethanol/sodium acetate cryoprecipitation, centrifugation and 75% ethanol washing, 25-200nt fragmented RNA was obtained.
Construction of the RNA fragment library was performed by LC Sciences (Hangzhou, China) using TruSeq Small RNA Sample Prep Kits (Illumina, USA) following manufacturer instructions.

value: AML cells

value: WT


title: WT, e2C, WGBS

data_processing:
For BS-seq data collected from the double inhibitor model, reads were mapped to SNP-masked mm10 genome using Bismark (version 0.22.1) with parameters: -N 1 --non_directional -un.
PCR duplicates were removed.
To rule out the impact from missing TETs during oogenesis, only read pairs containing PWK SNPs were retained for downstream analysis.
Assembly: mm10
Supplementary files format and content: bed

growth_protocol: DNA extraction and PBAT library construction 100 isolated blastomeres were transferred into lysis buffer using a mouth pipette, and were then lysed for 3 hours at 50°C and then heat-inactivated for 30 minutes at 75°C.

extract_protocol:
The released genomic DNA, together with 1% unmethylated lambda DNA (Thermo Scientific), were sheared into 150 bp to 350 bp by Covaris S2 before subjecting to bisulfite conversion using a MethylCode Bisulfite Conversion Kit (Invitrogen) according to the manufacturer’s instructions.
The bisulfite-converted templates were then used to prepare the sequencing library through EpiArt DNA Methylation Library Kit following the manufacturer’s instructions. The PBAT libraries were also sequenced on Illumina NovaSeq with paired ends and 150-bp read lengths at Nanjing Jiangbei New Area Biophamaceutical Public Service Platform Co., Ltd.

value: early 2Cell

value: Wild type


title: Ly, e2C, WGBS


title: 8Cell_siTfap2c_rep2

data_processing:
Sequencing reads were first trimmed to remove adapters and then mapped to the annotated mouse transcripts (UCSC mm10) using Hisat2 (v2.1.0) with the parameters: --dta-cufflinks --no-unal (Kim et al., 2015).
Mapped reads with high confidence were kept for further analysis using SAMtools (v1.7) with the parameters: -bf 0x2 -q 20.
The retained reads were subsequently assembled into transcripts guided by the UCSC gtf annotation files using Stringtie (v1.3.4) (Pertea et al., 2015).
The expression level of each gene was quantified as FPKM (fragments per kilobase per million mapped reads).
Processed data method: log2 (FPKM + 1)
Assembly: mm10
Supplementary files format and content: csv, log2 (FPKM + 1)
Supplementary files format and content: csv, log2 (FPKM + 1)

source_name: embryo

extract_protocol:
The zona pellucidae of the cleavage-stage embryos were removed with 0.5% pronase E and the embryos were then incubated in Ca2+-free Chatot-Ziomek-Bavister (CZB) medium for 10-20 minutes. Polar bodies were removed by gentle pipetting using a fire-polished glass needle. Single blastomeres were separated and manually picked before subjected to uliCUT&RUN, uliNChIP and total RNA library preparation and sequencing. For ICM and TE isolation (Liu et al., 2016), the zona pellucidae of blastocysts were punched, followed by removal with 0.5% pronase E. The embryos were then incubated in Ca2+-free CZB for 20-30 minutes to disrupt the cell-cell junctions. ICM cells and TE cells were then distinguished and collected according to their sizes and shapes with the aid of a piezo-driven micromanipulator. For epiblast and extraembryonic ectoderm isolation (Wang et al., 2018), embryos were cut at the embryonic/extraembryonic boundary using properly sharpened forceps. A fire-polished glass needle with an inner diameter that is slightly smaller than the width of the embryonic/extraembryonic fragment was used for separating epiblast or extraembryonic ectoderm from the visceral endoderm, and the separated epiblast or extraembryonic ectoderm fragment was then incubated in Ca2+-free CZB medium for 10 minutes.
Embryos with zona pellucida and polar bodies removed were disrupted in TRIzol Reagent (Thermo) and total RNAs were isolated by chloroform extraction, coupled with isopropanol precipitation with 1/10 volume of 3 M NaAc and 1 μL glycogen added to the aqueous phase of each sample. RNAs were washed twice with 75% ethanol before they were eluted with nuclease-free water. Purified RNAs were then subjected to library generation using SMARTer Stranded Total RNA-Seq Kit v2 following the manufacturer’s instructions. Briefly, random primers were used for reverse transcription, and the amplified cDNA was then subjected to ribosomal RNA depletion. Prepared RNA-seq libraries were sequenced on the Illumina NovaSeq 6000 platform with paired ends and 150-bp read lengths at Novogene Co., Ltd.

value: Tfap2c KD


title: HiCuT, E9.5, placenta, c57(m) x pwk(p)

data_processing:
Sequencing reads were first trimmed to remove TN5 adapters and then mapped to SNP-masked mm10 genome.
The reads were processed using HiC-Pro (version 3.1.0)and all valid pairs from two alleles were collected. To compare chromatin interactions between alleles, matrices were converted to cool format (HiCExplorer, version 2.2.1.1) and balanced using cooler [MY3](version 0.9.1) under 1Kb resolution. Interaction loops with: 1) length > 2Kb, 2) both anchors in genebody and promoter regions (TSS-1.5Kb ~ TES+1Kb), 3) one anchor in promoters were defined as valid P-E interactions.
To compare chromatin interactions between alleles, matrices were converted to cool format (HiCExplorer, version 2.2.1.1) and balanced using cooler(version 0.9.1) under 1Kb resolution. Interaction loops with: 1) length > 2Kb, 2) both anchors in genebody and promoter regions (TSS-1.5Kb ~ TES+1Kb), 3) one anchor in promoters were defined as valid P-E interactions.
Interaction loops with: 1) length > 2Kb, 2) both anchors in genebody and promoter regions (TSS-1.5Kb ~ TES+1Kb), 3) one anchor in promoters were defined as valid P-E interactions.
Assembly: mm10
Supplementary files format and content: bedpe
Library strategy: HiCuT

source_name: whole placenta

extract_protocol:
The HiCuT experiments were performed by Wuhan Frasergen Bioinformatics Co., Ltd. according to previous studies (7-9) with minor modifications. Briefly, placenta samples were cross-linked with 1% formaldehyde for 10 minutes at room temperature and quenched with 0.125M final concentration glycine for 5 minutes.
Formaldehyde-fixed cells were subjected to additional cross-linking with 3 mM EGS, freshly prepared for 40 minutes and then quenched with 0.4 M glycine for 10 minutes at room temperature. Formaldehyde and ethylene glycol bis (succinimidylsuccinate) dual cross-linked cells were washed once with PBS supplemented with 0.05% BSA and were subsequently permeated with 0.05% digitonin for minutes at room temperature followed by 0.1% SDS at 65℃ for minutes. SDS were quenched by 1.8% Triton X-100 at 37℃ for minutes. Then chromatin DNA were digested by 50U MboI + 50U DdeI (NEB) at 37℃ for 2 hours, and fill-in with dNTP (Invitrogen) using 15U Klenow (NEB) at 37℃ for 1 hour. Spatial proximal DNA were ligated by 50U T4 DNA ligase (NEB) at 16℃ for 4 hours. Then cells were washed twice in Wash Buffer (20mM HEPES pH 7.5; 150mM NaCl; 0.5mM Spermidine; 1× Protease inhibitor cocktail) by gentle pipetting. Activated concanavalin A-coated bead-bound cells were resuspended in Dig-wash Buffer (Wash Buffer containing 0.05% Digitonin) containing 2mM EDTA and a 1:50 dilution of the primary antibody (H3K27ac antibody: CST, #8173). Primary antibody incubation was performed on a rotating platform at 4℃ overnight. Then the liquid was removed on the magnet stand. Secondary antibody (goat anti-rabbit IgG: Proteintech, B900210) was diluted 1:50 in Dig-Wash buffer and cells were incubated at room temperature for 1 hour. Cells were washed twice in Dig-Wash buffer to remove unbound antibodies. A 1:200 dilution of pG-Tn5 adapter complex (~0.04 μM) was prepared in Dig-300 Buffer (0.01% Digitonin, 20mM HEPES, pH 7.5, 300mM NaCl, 0.5mM Spermidine, 1× Protease inhibitor cocktail). Cells was incubated with pG-Tn5 at room temperature for 1 hour, then were washed twice in Dig-300 Buffer to remove unbound pG-Tn5 protein. Next, cells were resuspended in Tagmentation buffer (10mM MgCl2 in Dig-300 Buffer) and incubated at 37 °C for 1 hour. Tagmentation were stopped by incubating at 55 °C for 1hour containing 16mM EDTA, 0.1% SDS and 0.16 mg/mL Proteinase K. Then DNA was purified using phenol–chloroform–isoamyl alcohol and ethanol, and amplified by PCR reaction as follows: 3 min at 72 °C and 30 s at 98 °C followed by 16 cycles of 15 s at 98 °C and 30 s at 60 °C and 30 s at 72 °C, with a final extension at 72 °C for 3 min. Finally, the amplified DNA was purified using Ampure XP beads. Libraries were sequenced on Illumina NovaSeq platform.

value: whole placenta

tag: chip antibody

value: c57 x pwk


title: 8Cell_siTfap2c_rep1


title: 8Cell_Ctrl_rep2

value: Control


title: 8Cell_siKlf5_rep1

value: Klf5 KD


title: 8Cell_CdxE2_KO_rep2

value: Tfap2c motif KO


title: 8Cell_siKlf5_rep2


title: 8Cell_Arpc1bE_CdxE1_KO_rep2


title: 8Cell_Arpc1bE_CdxE1_KO_rep1


title: H3K27ac_CUTTag_2iL_ESCs_Tead2_motif_mutant_rep1

value: E14 mESCs

value: Embryonic stem cells

value: TEAD2 motif mutant

value: ESCs cultured in serum-free medium with LIF and two inhibitors (PD0325901 and CHIR99021) (2i/LIF)


title: TSC_Tfap2c_5k_rep1

data_processing:
Sequencing reads were first trimmed to remove adapters and then mapped to mouse genome (UCSC mm10) using Bowtie2 (v2.3.4.3) with the parameters: -t --no-mixed --no-discordant --no-unal (Langmead and Salzberg, 2012).
Mapped reads with high confidence were kept for further analysis using SAMtools (v1.7) with the parameters: -bf 0x2 -q 20 (Li et al., 2009). Duplicated reads were removed using sambamba (v0.6.8) (Tarasov et al., 2015).
Genome-wide signals were calculated using a 50-bp window and normalized to the uniquely mapped fragments using ‘bamCoverage’ from deepTools (v2.5.7) (Ramirez et al., 2014).
Promoters were [-1.5k, 0.5k] relative intervals of TSSs. 5’ most TSS selected if multiple TSSs found in one gene. Peaks were identified by macs2 (v2.1.1) (Zhang et al., 2008) with the parameters: -q 0.05 --keep-dup 1 and peaks with signal FPKM > 15 were finally reserved.
For allele specific analysis, reads were separated into paternal or maternal using SNPsplit (v0.4.0) (Krueger and Andrews, 2016).
Assembly: mm10
Supplementary files format and content: bigwig
Library strategy: CUT&RUN-seq

source_name: cell line

extract_protocol:
The zona pellucidae of the cleavage-stage embryos were removed with 0.5% pronase E and the embryos were then incubated in Ca2+-free Chatot-Ziomek-Bavister (CZB) medium for 10-20 minutes. Polar bodies were removed by gentle pipetting using a fire-polished glass needle. Single blastomeres were separated and manually picked before subjected to uliCUT&RUN, uliNChIP and total RNA library preparation and sequencing. For ICM and TE isolation (Liu et al., 2016), the zona pellucidae of blastocysts were punched, followed by removal with 0.5% pronase E. The embryos were then incubated in Ca2+-free CZB for 20-30 minutes to disrupt the cell-cell junctions. ICM cells and TE cells were then distinguished and collected according to their sizes and shapes with the aid of a piezo-driven micromanipulator. For epiblast and extraembryonic ectoderm isolation (Wang et al., 2018), embryos were cut at the embryonic/extraembryonic boundary using properly sharpened forceps. A fire-polished glass needle with an inner diameter that is slightly smaller than the width of the embryonic/extraembryonic fragment was used for separating epiblast or extraembryonic ectoderm from the visceral endoderm, and the separated epiblast or extraembryonic ectoderm fragment was then incubated in Ca2+-free CZB medium for 10 minutes.
uliCUT&RUN was conducted following the published protocols (Patty and Hainer, 2021; Skene et al., 2018) with a few modifications. Briefly, all isolated fresh blastomeres or cells were washed three times with CUT&RUN wash buffer to avoid possible contamination and then transferred into a 1.5 mL low-binding PCR tube (Eppendorf) containing 600 µL of the wash buffer. The samples were then bound to Concanavalin A-coated magnetic beads, which had been activated and resuspended in CUT&RUN binding buffer. After cell immobilization, bead-bound samples were successively incubated with appropriate amount of primary antibodies against protein-of-interest in 250 µL of CUT&RUN antibody buffer and a secondary antibody if necessary in 250 µL of CUT&RUN digitonin buffer for overnight at 4°C. Cell membranes were permeabilized with 0.01% digitonin to allow the specific antibody to find its target. After unbound antibodies were washed away, 700 ng/mL protein A-MNase (pA-MN; a gift from Steven Henikoff lab or purchased from Vazyme Biotech) was added and incubated for 1 hour at 4°C. After washing, CaCl2 was added to a final concentration of 2 mM to activate pA-MN, and the digestion reaction was carried out for 30 min at 0°C and then stopped by adding 150 μL 2× CUT&RUN stop buffer. The protein–DNA complex fragments were then released by 20 min incubation at 37°C. After transferring the supernatant to a new tube, 3 µL of 10% SDS and 2.5 µL of Proteinase K (Thermo) were added and incubated for 30 min at 55°C. DNA was then precipitated by phenol/chloroform/isoamylalcohol followed by ethanol precipitation with glycogen and then dissolved in nuclease-free water. Sequencing libraries were prepared using KAPA Hyper Prep Kit following the manufacturer’s instructions with slight modifications. Briefly, end repair was conducted for 30 min at 20°C followed by end-repair/A-tailing for 30 min at 50°C. After adaptor ligation for 30 min at 20°C, the DNA fragments were purified by 1.4× volume of AMPure beads followed by 18 cycles of PCR amplification with 2× KAPA HiFi HotStart Ready Mix. The final libraries were cleaned up with 1.2× volume of AMPure beads, and all CUT&RUN libraries were sequenced on a NovaSeq6000 (Illumina) platform at Novogene Co., Ltd. with paired-ended 150-bp reads.

value: cell line

value: TSC

value: unknown


title: H3K4me1_CUTTag_2i_d6_Tead2_knockout

value: Tead2 Knockout

value: SL-to-2iL transition day 6


title: 8Cell_CdxE2_KO_rep1

value: embryo


title: PSC_Frac_6m

description: 10x Genomics

value: Stromal cells

value: Periosteum

value: 8-10 months old

value: Fracture


title: H3K27ac_CUTTag_2i_d6_wild_type

value: Wild type


title: TSC_Tfap2c_1k_rep1

value: Control


title: TSC_Tfap2c_10k_rep1


title: TSC_Tfap2c_50k_rep1


title: TSC_Tead4_100k_rep1


title: TSC_Tead4_10k_rep1


title: TE_Tfap2c_rep2

value: TE


title: TSC_Tead4_1k_rep2


title: TSC_Tead4_1k_rep1


title: TE_Tead4_rep1


title: TSC_Tead4_5k_rep1


title: TE_Tfap2c_rep1


title: Morula_Tead4_rep2

value: Morula


title: TE_Tead4_rep2


title: Morula_Tead4_rep1


title: 8Cell_Ctrl_rep1


title: Morula_Tfap2c_rep2


title: Morula_Klf5_rep1


title: Morula_Tfap2c_rep1


title: EXE_E6-5_Tfap2c_rep2

value: ExE


title: EXE_E6-5_Tfap2c_rep1


title: TSC_Tfap2c_1k_rep2


title: 8Cell_Tfap2c_rep2


title: 8Cell_Tfap2c_rep1


title: 8Cell_Tead4_rep1


title: 8Cell_Tead4_rep2


title: EXE_E6-5_Tead4_rep2


title: EXE_E6-5_Tead4_rep1


title: 8Cell_siTfap2c_Tead4_rep1

value: Tfap2c KD


title: 8Cell_siTfap2c_Tead4_rep2


title: 8Cell_siTfap2c_Klf5_rep2


title: 8Cell_siTfap2c_Klf5_rep1


title: 8Cell_Klf5_rep2


title: 8Cell_Klf5_rep1


title: 8Cell_siTfap2c_H3K27ac_rep1

data_processing:
Sequencing reads were first trimmed to remove adapters and then mapped to mouse genome (UCSC mm10) using Bowtie2 (v2.3.4.3) with the parameters: -t --no-mixed --no-discordant --no-unal (Langmead and Salzberg, 2012).
Mapped reads with high confidence were kept for further analysis using SAMtools (v1.7) with the parameters: -bf 0x2 -q 20 (Li et al., 2009). Duplicated reads were removed using sambamba (v0.6.8) (Tarasov et al., 2015).
Genome-wide signals were calculated using a 50-bp window and normalized to the uniquely mapped fragments using ‘bamCoverage’ from deepTools (v2.5.7) (Ramirez et al., 2014).
Promoters were [-1.5k, 0.5k] relative intervals of TSSs. 5’ most TSS selected if multiple TSSs found in one gene. Peaks were identified by macs2 (v2.1.1) (Zhang et al., 2008) with the parameters: -q 0.05 --keep-dup 1 and peaks with signal FPKM > 15 were finally reserved.
For allele specific analysis, reads were separated into paternal or maternal using SNPsplit (v0.4.0) (Krueger and Andrews, 2016).
Assembly: mm10
Supplementary files format and content: bigwig

extract_protocol:
The zona pellucidae of the cleavage-stage embryos were removed with 0.5% pronase E and the embryos were then incubated in Ca2+-free Chatot-Ziomek-Bavister (CZB) medium for 10-20 minutes. Polar bodies were removed by gentle pipetting using a fire-polished glass needle. Single blastomeres were separated and manually picked before subjected to uliCUT&RUN, uliNChIP and total RNA library preparation and sequencing. For ICM and TE isolation (Liu et al., 2016), the zona pellucidae of blastocysts were punched, followed by removal with 0.5% pronase E. The embryos were then incubated in Ca2+-free CZB for 20-30 minutes to disrupt the cell-cell junctions. ICM cells and TE cells were then distinguished and collected according to their sizes and shapes with the aid of a piezo-driven micromanipulator. For epiblast and extraembryonic ectoderm isolation (Wang et al., 2018), embryos were cut at the embryonic/extraembryonic boundary using properly sharpened forceps. A fire-polished glass needle with an inner diameter that is slightly smaller than the width of the embryonic/extraembryonic fragment was used for separating epiblast or extraembryonic ectoderm from the visceral endoderm, and the separated epiblast or extraembryonic ectoderm fragment was then incubated in Ca2+-free CZB medium for 10 minutes.
uliNChIP-seq was performed as previously described (Brind'Amour et al., 2015) to capture the H3K4me3 and H3K27ac status in embryos. Briefly, the harvested blastomeres or cells were subjected to nuclei extraction buffer. The MNase Master mix was then added and the mixture was incubated at 25°C for 10 minutes to allow MNase digestion. The reaction was stopped by 10 mM EDTA, and 0.1% Triton X-100 together with 0.1% DOC was added to lyse the nuclear membrane. The released chromatin was then diluted with ChIP buffer. After 1/20 volume of the reaction was saved as the input, the rest was incubated with H3K4me3 or H3K27ac antibody-coated Dynabeads Protein A/G for overnight at 4°C. The ChIP samples were washed twice with low-salt wash buffer and twice with high-salt wash buffer. The washed beads were then incubated in hot elution buffer for 2 hours at 65°C with shaking. The eluted DNAs were further purified and subjected to sequencing library generation as described above. Paired-end 150-bp sequencing was also performed on ChIP libraries.


title: 8Cell_Ctrl_input


title: 8Cell_siTfap2c_H3K4me3_rep2


title: 8Cell_Ctrl_H3K4me3_rep2


title: 8Cell_Ctrl_H3K4me3_rep1


title: 8Cell_Ctrl_H3K27ac_rep2


title: 8Cell_Ctrl_H3K27ac_rep1


title: L3: Standard feed-fed, Ileum

city: Dongguan

state: Guangdong

address: No.1 Xincheng Blvd, Songshan Lake National High-tech Industrial Development Zone

department: School of Public Health

institute: Guangdong Medical University

data_processing:
The useful Perl script was used to filter adapter,the low quality reads and the reads whose N base more than 5% for total bases. Clean Data was then aligned to the reference genome using HISAT2 v2.1.0.
Reads Count for each gene in each sample was counted by HTSeq v0.6.0, and FPKM (Fragments Per Kilobase Millon Mapped Reads) was then calculated to estimate the expression level of genes in each sample.DEGseq v1.18.0 was used for differential gene expression analysis between two samples with non biological replicates,DESeq2 v1.6.3 was designed for differential gene expression analysis between two samples with biological replicates, Genes with q≤0.05 and |log2_ratio|≥1 are identified as differentially expressed genes.The GO (Gene Ontology, http://geneontology.org/) and KEGG (Kyoto Encyclopedia of Genes and Genomes, http://www.kegg.jp/) enrichment of DEGs were implemented by the hypergeometric test,GO and KEGG terms with q<0.05 were considered to be significantly enriched.
rMATS is a computational tool to detect differential alternative splicing events from RNA-Seq data.
Samtools and bcftools together to call snp and Indel.
Genome_build: ftp://ftp.ensembl.org/pub/release-90/fasta/mus_musculus/dna/
Supplementary_files_format_and_content: tab-delimited text files include count values for each Sample

source_name: Standard feed-fed mice

growth_protocol: The feed for the control group was standard feed for ensuring the nutritional needs of mice. For the test group, to assess the analogbioavailability of arsenic in rice (80%), the arsenical aqueous solution was blended into standard feed material powder and then impacted into granules.The concentration of total arsenic (CtAs) in the feed for the test group was 30 μg g-1, consisting of sodium arsenate (iAsⅤ), sodium arsenite (iAsⅢ), sodium MMA, and sodium DMA (Beijing Century Aoke Biotechnology Co., Ltd. Beijing, China) at proportions of 7.3%, 72.7%, 1.0%, and 19.0%, respectively. The fresh granule feeds weresoon vacuum packaged (50 g per pack for daily use) and stored at –20 °C.

extract_protocol:
A total amount of 2 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext ® Ultra™ RNA Library Prep Kit for Illumina ® (#E7530L, NEB, USA) following the manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads.Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and RNase H. Second strand cDNA synthesis was subsequently performed using buffer, dNTPs, DNA polymerase I and RNase H. The library fragments were purified with QiaQuick PCR kits and elution with EB buffer, then terminal repair,A-tailing and adapter added were implemented. The aimed products were retrieved and PCR was performed, then the library was completed.
The clustering of the index-coded samples was performed on a cBot cluster generation system using HiSeq PE Cluster Kit v4-cBot-HS (Illumina) according to the manufacturer’s instructions. After cluster generation, the libraries were sequenced on an Illumina platform and 150 bp paired-end reads were generated.

treatment_protocol: Six-week-old SPF male C57BL/6 mice were first acclimatized (7 days) and then separated randomly into two groups (10 mice for each group, control 1‒10 and test 1‒10) forpursuant 60-day exposure experiments. Drinking water and food were available ad libitum (control and test groups were fed standard and arsenic-containing standard feed, respectively).

tag: gender

value: male

value: Ileum

value: Standard feed-fed


title: L2: Standard feed-fed, Ileum

tag: tissue


title: L5: Standard feed-fed, Ileum


title: Morula_Klf5_rep2

tag: cell type


title: L13: Standard diet and arsenic-fed, Ileum

source_name: Standard diet and arsenic-fed mice

tag: strain

value: Standard diet and arsenic-fed


title: L11: Standard diet and arsenic-fed, Ileum

tag: treatment


title: L12: Standard diet and arsenic-fed, Ileum


title: C5: Standard feed-fed, Colon

value: Colon


title: L1: Standard feed-fed, Ileum


title: 8Cell_siTfap2c_input


title: C1: Standard feed-fed, Colon


title: C3: Standard feed-fed, Colon


title: C2: Standard feed-fed, Colon


title: RNA-seq_AGO2-WT

first: Jianxiu

last: Yu

address: Room 202, Building 7, 280 South Chongqing Road,

department: Department of Biochemistry and Molecular Cell Biology

institute: Shanghai Jiao Tong University School of Medicine

description:
WT_FPKM
RNA-seq.xlsx

data_processing:
For AGO2-RIP-seq and miRNA-Seq, raw data were generated after sequencing, image analysis, base calling and quality fifiltering on Illumina sequencer and fifinally quality controlled by   Q30. The adaptor sequences were trimmed and the adaptor-trimmed-reads (>= 15 nt) were left by cut adapt software (version 1.9.2). Then the trimmed reads from all samples were pooled, and miRDeep2 software (version 2.0.0.5) was used to predict novel miRNAs. The trimmed reads were aligned to the merged human miRNA databases using Novoalign software (version 3.02.12) with at most one mismatch. The numbers of mature miRNA mapped tags were defifined as the raw expression levels of that miRNA. The read counts were normalized by TPM (tag counts per million aligned miRNAs) approach. Differentially expressed miRNAs between two samples were fifiltered through Fold change. The fold changes in AGO2-bound miRNAs were normalized by input of the miRNAs.
For RNA-Seq, high-quality clean reads were aligned to the reference genome (UCSC hg19) with hisat2 software (version 2.0.4). Then, guided by the Ensembl gtf gene annotation fifile, cuffdiff software (part of cufflflinks) was used to get the gene-level FPKM (Fragments per kilobase of exon per million fragments mapped) as the expression profifiles of mRNA, and fold change and pvalue were calculated based on FPKM, differentially expressed mRNA were identifified.
Assembly: hg19 for RIP-Seq and RNA-Seq, miRBase for miRNA-Seq
Supplementary files format and content: FPKM values for each Sample
Supplementary files format and content: raw tag counts of the mature miRNA for each Sample

growth_protocol: DMEM, 10% fetal bovine serum, 2mM glutamine, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Cells were lysed in RIP lysis buffer and then immunoprecipitated by Flag-AGO2. 1/10 of the lysates was used as input. AGO2-bound RNA, input RNA and total RNAs  from cells were extracted using Trizol by following the manufacturer’s instruction (Thermo Fisher Scientific). MiRNA population was isolated by separating total RNAs on denaturing polyacrylamide gel electrophoresis (PAGE), and cut a portion of the gel corresponding to the size 18-30 nucleotides based standard oligonucleotide markers.
RIP-seq, mRNA and miRNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Untreated

value: lung cancer cell


title: RNA-seq_AGO2-S417A

description:
S417A_FPKM
RNA-seq.xlsx


title: C11: Standard diet and arsenic-fed, Colon


title: C4: Standard feed-fed, Colon


title: 8Cell_siTfap2c_H3K4me3_rep1

value: embryo


title: miRNA-seq_AGO2-S417A

description:
S417A
miRNA-seq.xlsx

tag: molecule subtype

value: miRNA


title: B4: Standard feed-fed, Cecum

value: Cecum


title: C13: Standard diet and arsenic-fed, Colon


title: C12: Standard diet and arsenic-fed, Colon


title: B5: Standard feed-fed, Cecum


title: RIP-seq_input_AGO2-S417A

description:
S417A-Input
AGO2-RIP-seq.xlsx

value: input


title: miRNA-seq_AGO2-WT

description:
WT
miRNA-seq.xlsx


title: RIP-seq_input_AGO2-WT

description:
WT-Input
AGO2-RIP-seq.xlsx


title: C15: Standard diet and arsenic-fed, Colon


title: AGO2-RIP-seq_AGO2-S417A

description:
S417A
AGO2-RIP-seq.xlsx


title: B15: Standard diet and arsenic-fed, Cecum


title: B1: Standard feed-fed, Cecum


title: AGO2-RIP-seq_AGO2-WT

description:
WT
AGO2-RIP-seq.xlsx


title: B2: Standard feed-fed, Cecum


title: L14: Standard diet and arsenic-fed, Ileum


title: L15: Standard diet and arsenic-fed, Ileum


title: B13: Standard diet and arsenic-fed, Cecum


title: B14: Standard diet and arsenic-fed, Cecum


title: B12: Standard diet and arsenic-fed, Cecum


title: NRCFs, Treat.IP

first: Jian

last: Wang

address: Pujian Load 160th, Pudong New Aera

description: Treat_processed data.txt

data_processing:
Briefly, Paired-end reads were harvested from Illumina NovaSeq 6000 sequencer, and were quality controlled by Q30. After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3).
First, clean reads of all libraries were aligned to the reference genome by Hisat2 software (v2.0.4).
Methylated sites on RNAs (peaks) were identified by MACS software. Differentially methylated sites were identified by diffReps.
These peaks identified by both softwares overlapping with exons of mRNA were figured out and chosen by home-made scripts.
Assembly: rn6
Supplementary files format and content: tab-delimited text file includes raw peaks for each sample

organism: Rattus norvegicus

source_name: Heart

extract_protocol:
RNA was harvested using Trjzol (Thermo Fisher). 5ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for IP and input samples were then constructed with GenSeq® Low Input Whole RNA Library Prep Kit(GenSeq, Inc.) by following the manufacturer’s instructions.
MeRIP-seq

value: Heart

value: Cardiac fibroblasts (Primary cells)

value: FTO overexpression

tag: fraction

value: IP


title: NRCFs, Treat.Input

description: Treat_processed data.txt

value: Input


title: NRCFs, Control.Input

description: Control_processed data.txt

value: WT


title: mettl16-/- rep2

first: Yunqiao

last: Han

address: Luoyu Road 1037

institute: Huazhong University of Science and Technology

data_processing:
Illumina Casava 1.8 software used for basecalling.
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by fastp (version 0.18.0). The parameters were as follows: 1) removing reads containing adapters; 2) removing reads containing more than 10% of unknown nucleotides (N); 3) removing low quality reads containing more than 50% of low quality (Q-value≤20) bases.
An index of the reference genome was built, and paired-end clean reads were mapped to the reference genome using HISAT2. 2.4 with “-rna-strandness RF” and other parameters set as a default.
The mapped reads of each sample were assembled by using StringTie v1.3.1 in a reference-based approach.
For each transcription region, a FPKM (fragment per kilobase of transcript per million mapped reads) value was calculated to quantify its expression abundance and variations, using StringTie software.
Assembly: GRCz11
Supplementary files format and content: tab-delimited text files include raw counts values for each gene and each sample

organism: Danio rerio

source_name: the trunk region of zebrafish embryos

extract_protocol:
Total RNA was isolated from the  trunk region including the CHT of zebrafish using RNA isolater Total RNA Extraction Reagent (Invitrogen). RNA quality was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies,) and checked using RNase free agarose gel electrophoresis.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: the trunk region of zebrafish embryos

value: gene knockout


title: mettl16-/- rep1


title: NRCFs, Control.IP

description: Control_processed data.txt


title: mt-input-rep1

data_processing:
Illumina Casava 1.8 software used for basecalling.
fastp software 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 was used to map reads to zebrafish reference genome (Ensembl GRCz11).
Mapped reads of IP and input libraries were provided for R package exomePeak, which identifies m6A peaks with bed or bigwig format that can be adapted for visualization on the IGV 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 by R package edgeR.
Assembly: GRCz11
Supplementary files format and content: BW files include peak files with quantitative data for each gene and each sample

source_name: trunk region of zebrafish embryos

extract_protocol:
Total RNA was isolated from the  trunk region including the CHT of zebrafish using RNA isolater Total RNA Extraction Reagent (Invitrogen). The RNA quality and quantity of each sample was assessed using NanoDrop ND-1000 and Bioanalyzer 2100 (Agilent). Total RNAs (20 μg) was depleted of ribosomal RNA by rRNA Depletion Kits (Thermo Fisher Scientific) and Magnesium RNA Fragmentation Module (NEB, cat.e6150) was used to randomly fragment RNA. Anti-m6A antibody (202003, Synaptic Systems) was applied for m6A immunoprecipitation. Then, the RNA was reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat.1896649).
RNA libraries were prepared for sequencing using standard Illumina protocols
m6A-Seq

value: trunk region of zebrafish embryos

tag: rip antibody


title: mt-IP- rep1


title: mt-input-rep2


title: mt-IP- rep2


title: sibling rep3

value: no treatment


title: sibling-input-rep2


title: mettl16-/- rep3