title: pombe_delta4dus_noR_2

data_processing:
Library strategy: Rho-seq
Reads were quality- and adaptor-trimmed using trimmomatic 0.36 with options PE ILLUMINACLIP:TruSeq2-PE.fa:2:30:10 HEADCROP:1 SLIDINGWINDOW:4:15 MINLEN:20
The filtered reads were mapped on the spike-in sequence with bowtie2 (options --no-discordant --no-mixed --phred33 -p 4 --un-conc) then on the genome using also bowtie2 for the E.coli libraries or tophat2 for the S. pombe libraries (options--mate-std-dev 150 -N 2 --read-edit-dist 2 --min-intron-length 5 --max-intron-length 3000 --no-discordant --no-coverage-search -p 4 --library-type fr-firststrand).
Properly paired mapped reads were split by strand. Then bedtools (options genomecov -ibam -d -5)  was used to calculate the number of RT termination events for each strand-specific position as the number of 5'end of R2 reads that map at this position. In parallel, the paired reads were computationally extended/merged into fragments that covered the genome from the left end of the left-most read to the right end of the right-most reads with the notable exeption that the fragments were not extended in identified introns. Those spliced fragments where then used to compute a fragment coverage reflecting the number of time a reverse transcriptase passed through a specific position. Then the ratio between the number of RT termination events and fragment coverage at each position (the D-ratio) was calculated.
After independent pre-filtering of the positions unlikely to have significant differences in D-ratio accross conditions (see manuscrit), the number of RT termination events out of the number of RT readthrough were modelised in generalized linear model of the binomial family (function glm in R) according to the effect of the treatment (R+ vs R-), the effect of the strain (wild-type vs delta4dus), and their interaction. The positions were the interaction between the wild-type and the delta4dus lead to a statistically  significant (FDR<0.1) increase of the proportion of RT termination events were retained as putative dihydrouridilation sites.
Genome_build: ASM294v2.26 (pombe) or ASM584v2.38 (coli)
Supplementary_files_format_and_content: Rho-seq_supplementary.xlsx is a spreadsheet describing the dihydrouridilated sites (D-sites) uncovered in our study. The first two sheets describe the D-sites found respectively on the S. pombe and the E. coli transcriptome, while the third sheet contains a legend explaining the column names in the first two sheets.

source_name: S. pombe cells

growth_protocol: 50 mL of S. pombe grown in YES at 32°C (OD595nm ~ 0.5) or E. coli grown in LB at 37°C (OD595nm ~ 0.6) were harvested by centrifugation and washed in DEPC water.

extract_protocol:
The cell pellets were resuspended in 750μL of TES buffer (10mM Tris pH 7.5, 10mM EDTA pH 8, 0.5% SDS) and the total RNA was isolated by hot phenol extraction.
Rhodamine labeling was performed as described in our manuscript. Briefly, 30μg of total RNA were resuspended in 1% sodium borohydride for 60min at 25°C. Mock samples (R-) were treated similarly but without sodium borohydride. The reduced RNA was then precipitated and the dried pellet was resuspended in 0.1M sodium formate pH 4. Rhodamine labeling was performed for 90min at 37°C in dark with 2.2mM of rhodamine chlorine. Labeled RNA was purified by phenol extraction. A synthetic dihydrouridilated RNA spike-in was added to the samples (1:1000) before ribodepletion of 5 μg of the RNA samples. Zinc-mediated fragmentation was performed at 70°C for 15min with 90-125 ng of ribodepleted RNA. Simultaneous DNA digestion and RNA extremities dephosphorylation were performed at 37°C for 30min with 2U of TURBO DNase and 3U of FastAP Thermosensitive Alkaline Phosphatase. 3'-end ligation of the RNA adapter was performed for 90min at 25°C with 39U of T4 RNA ligase. After ligation, 10pmol of DNA primer were added, the sample was denatured for 2min at 70°C and the reverse transcription was performed with Superscript III. The excess of DNA primer was subsequently digested with 4min incubation with 2μL of ExoSAP-IT. The 3'-end ligation of the cDNA with DNA adapter was performed overnight at 25°C with 48U of T4 RNA ligase. Nucleic acid clean-ups were performed between each step by using MyOne SILANE magnetic beads. 13 cycles od PCR amplification was performed in a 50μL-reaction by mixing cDNA, 1μM of barcoded PCR primer, 1μM of universal PCR primer and 25μL of NEBNext High- Fidelity 2X PCR Master Mix (NEB M0541). Finally, two successive rounds of DNA polymer size selection were performed by mixing PCR products with 1.2 and 1.1 volume of AMPure XP beads. The DNA library was quantified, examined on a DNA microchip and sequenced on Illumina HiSeq 2500.

tag: percentage of d in spike-in

value: R-


title: KO-CTR-2

status: Public on Oct 26 2021

type: SRA

city: Bethesda

first: Mark

middle: R

last: Cookson

state: MD

address: NIHBC 35 - PNRC I BG RM 1A-116

country: USA

institute: National Institutue on Aging, NIH

description: KO CTR rep 2

library_source: transcriptomic

data_processing:
Basecalls performed using CASAVA version 1.7.1
STAR_2.4.2a
express-1.5.1
Genome_build: mm10
Supplementary_files_format_and_content: The processed data file includes raw counts of sequencing reads for transcripts that are the output from eXpress, and the processed file is in tab separated text format

molecule: total RNA

organism: Mus musculus

source_name: postnatal mouse brain

extract_protocol:
RNA extractions from primary microglia were performed usining to Trizol/Chloroform isolation method. RNA quality was measured using a Agilent 2100 Bioanalyzer RNA 6000 Nano Chip (Agilent) and samples had a mean RNA integrity number of 9.0.
We purified rRNA depleted RNA starting from 1μg total RNA, then synthesized cDNA libraries using TruSeq stranded Total RNA library prep kit, RiboZeroGold (Illumina, RS-122-9008).Before sequencing, cDNA libraries were quantified by digital-PCR using a ddPCR Library quantification kit (Biorad).
cDNA libraries were multiplexed with 4 samples per pool and 7pM of each pool hybridized to a flow cell following cluster generation using an Illumina cluster station. Libraries were sequenced on Illumina HiSeq2500 (Illumina) to generate ~35 million of 100-bp single end reads per library.

tag: strain

tag: tissue

value: primary microglia

tag: age

value: post natal day 21

tag: genotype

tag: treatment

value: Control


title: KO-CTR-1

description: KO CTR rep 1


title: E13.5_EC_2Runx1_H3K4me1_rep1

city: PHILADELPHIA

first: Kai

last: Tan

state: Pennsylvania

address: 3501 CIVIC CENTER BLVD

institute: Children's Hospital of Philadelphia

library_source: genomic

data_processing:
ATAC-seq: Sequencing reads were demultiplexed using Bcl2Fastq v2.20 then trimmed and filtered for quality using Trim Galore v0.6.4 with the following settings: fastqc, paired, and trim1. Reads were then aligned to the mouse genome (mm10) using bowtie 2.3.5.1. Only uniquely mapped reads with fewer than 2 mismatches were used for downstream analyses. Samtools v1.1 was used to convert SAM files to BAM files, and Sambamba v0.6.6 was used to filter out duplicates, multi-mappers, reads mapped to ChrM or blacklist regions, and unmapped reads. MACS2 2.1.4 was used for peak calling using the following parameters: BAMPE, q: 0.05. . Merged replicates were used to create bigwig files for visualization using Deeptools v3.3.0 and the following parameters: normalized to reads per genomic content (RPGC), effective genome size: 2308125349, ignore for normalization: ChrX, min fragment length: 20, bin size: 10.
RNA-seq: Sequencing reads were demultiplexed using Bcl2Fastq then trimmed and filtered for quality using Trim Galore v0.6.4 with the following settings: fastqc, paired, and trim1. Reads were then aligned to the mouse genome (mm10) using STAR 2.7.3a and the mm10 gene reference file from UCSC. Only uniquely mapped reads with fewer than 2 mismatches were used for downstream analyses. Samtools v1.1 was used to convert to BAM files, and Sambamba v0.6.6 was used to filter out duplicates, multi-mappers, and unmapped reads. The featureCounts function of the Subread v2.0.0 package was used to extract gene-level and transcript level read counts. EdgeR and TMM normalization were used to calculate normalized RPKM. Bigwig files for visualization were created using Deeptools v3.3.0 from merged BAM files. The following parameters were used: normalized to reads per genomic content (RPGC), effective genome size: 2308125349, ignore for normalization: ChrX, min fragment length: 20, bin size: 10.
ChIP-seq: Sequencing reads were demultiplexed using Bcl2Fastq v2.20 then trimmed and filtered for quality using Trim Galore v0.6.4 with the following settings: fastqc, paired, and trim1. Reads were then aligned to the mouse genome (mm10) using bowtie 2.3.5.1. Only uniquely mapped reads with fewer than 2 mismatches were used for downstream analyses. Samtools v1.1 was used to convert SAM files to BAM files, and Sambamba v0.6.6 was used to filter out duplicates, multi-mappers, reads mapped to ChrM or blacklist regions, and unmapped reads. MACS2 2.1.4 was used for peak calling using the following parameters: broad, q: 0.05. Merged replicates were used to create bigwig files for visualization using Deeptools v3.3.0 and the following parameters: normalized to reads per genomic content (RPGC), effective genome size: 2308125349, ignore for normalization: ChrX, min fragment length: 20, bin size: 10, smooth length: 60, extend reads: 150.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: BigWig files provided are normalized tracks of merged replicates.
Supplementary_files_format_and_content: Bed files provided are the output of MACS2 peak calling.
Supplementary_files_format_and_content: RPKM_Norm.txt: Tab-delimited text file for RNA-seq samples includes normalized RPKM.

molecule: genomic DNA

source_name: Endothelial Cells

extract_protocol:
Cells were sorted from mouse fetuses. ChIP reactions were performed using 50,000 FACS-sorted cells per IP. IPed and Input DNA were purified with MinElute PCR Purification Kit.
Libraries were constructed using Rubicom ThruPLEX DNA-Seq Kit. Libraries were size-selected at 100-700 bp by AMPure XP beads. Libraries were quantified with KAPA qPCR and bioanalyzer prior to single-end sequencing.

treatment_protocol: Females were paired with males for timed matings. Females were injected IP with 2mg tamoxifen 24 hours prior to harvesting. Embryos were harvested at the appropriate embryonic day and cells were sorted on the same day as harvest.

tag: cell type

value: Endothelial Cells

tag: isolation markers

value: CD41-CD45-Ter119-CD31+VEC+cKIT lo/+

tag: developmental stage

tag: organ

value: whole fetus

value: +2Runx1 (Cre; CKI/CKI)

tag: chip antibody


title: smRNA-YwxEyG4_prep2

city: Montréal

first: Claudia

middle: L

last: Kleinman

state: Québec

address: 3999 Côte Ste-Catherine Road

department: Human Genetics

country: Canada

institute: Lady Davis Institute for Medical Research

data_processing:
For smRNA samples: smRNA sequencing reads were trimmed using Trimmomatic (v0.32), removing adaptor, other Illumina-specific sequences and low-quality bases at the end of each read, using a 4bp sliding window to trim where average window quality fell below 30 (phred33 < 30). Trimmed reads with less than 15 bases were discarded. The resulting clean set of reads were then aligned to the drosophila reference genome (dm6) using novoalign (v3.02.12) with a score difference of 0 for calling multiple mapping (-R 0), reporting a maximum of 100 alignments per read (-r All 100), setting miRNA mode (-m 100) and using -l 14 and -t 10,5.5 as alignment scoring parameters.
For RNA samples: RNA sequencing reads were trimmed using Trimmomatic (v0.32), removing adaptor and other Illumina-specific sequences as well as the first four bases from the start of each read, and low-quality bases at the end of each read, using a 4bp sliding window to trim where average window quality fell below 30 (phred33 < 30). Trimmed reads with less than 30 bases were discarded. The resulting clean set of reads were then aligned to the drosophila reference genomes (dm6) using STAR (v2.3.0e) with default parameters. Reads mapping to more than 10 locations in the genome (MAPQ < 1) were discarded.
for ChIP samples: For ChIP-seq data, reads were trimmed of TruSeq adaptor sequences using trimmomatic. Trimmed reads were then aligned toBDGP5 using BWA-MEM, PCR duplicates were soft-clipped using Picard. BigWig files were generated using Homer, and consist of uniquely aligned reads without PCR duplicates.
Genome_build: dm6
Supplementary_files_format_and_content: bigwig files were generated by bedtools (v2.27.1) genomeCoverageBed, using the bam generated by STAR (RNA files) or Novoalign (smRNA files) and a normalization factor equal to the number of mapped reads divided by 100 million.

organism: Drosophila melanogaster

source_name: 3rd instar larvae eye discs

extract_protocol:
RNA was extracted from Drosophila 3rd instar larvae eye discs using a Qiagen kit followed by DNAse treatment. For smRNA-seq RNA was extracted from Drosophila 3rd instar eye discs using Qiagen kit with Trizol, spike-in controls added at the beginning of the protocol, and DNAse treatment was added at the end. For crosslinked ChIP, cells were crosslinked (1% formaldehyde, 10mins) and sonicated. Protein:DNA complexes were immunoprecipitated with specific antibodies pre-bound to protein A or goat anti-mouse IgG magnetic beads. Eluted DNA underwent crosslink reversal, and were purified using Qiagen PCR purification columns. For RNA extraction, 1 million TEX cells were pelleted, washed with PBS and resuspended in 350ul RLT buffer (Qiagen-RNAeasy mini kit) with beta-mercaptoethanol. The suspension was then stored at -80oC until frozen. Sample was thawed and RNA extraction was performed using Qiagen's RNAeasy mini kit as per the manufacturer's instructions.
total RNA samples submitted to Genome Quebec facility for quality control assessment and library preparation. Illumina HiSeq 4000 with miRNA size select has been used for smRNAseq and Illumina HiSeq 4000 using mRNA stranded library has been used for RNA-seq. The eluted ChIP DNA undewent adaptor ligation based library construction for single-end 50bp Illumina sequencing on HiSeq 4000. RNA-seq library preparation was performed with ribosomal RNA (rRNA) depletion according to instructions from the manufacturer (Epicentre) to achieve greater coverage of mRNA and other long non-coding transcripts, paired-end sequencing (100 bp) was performed on the Illumina HiSeq 2500 or 4000 platform.

value: 3rd instar larvae eye discs


title: pombe_WT_R_2

city: Namur

first: Carlo

last: Yague-Sanz

address: 61 rue de Bruxelles

department: Medecine

country: Belgium

institute: Namur University

organism: Schizosaccharomyces pombe

value: wild-type

tag: replicate

value: R+


title: pombe_delta4dus_noR_1


title: pombe_WT_noR_2


title: pombe_delta4dus_R_2


title: E13.5_EC_Ctrl_H3K4me1_input

value: Ctrl (CKI/CKI; CKI/+)


title: pombe_WT_noR_1


title: E13.5_EC_Ctrl_H3K4me1_rep1

description:
E13_Ctrl_K4me1_IP.bw
E13_Ctrl_K4me1_IP_peaks.bed

extract_protocol:
Cells were sorted from mouse fetuses. ChIP reactions were performed using 50,000 FACS-sorted cells per IP. Iped and Input DNA were purified with MinElute PCR Purification Kit.
Libraries were constructed using Rubicom ThruPLEX DNA-Seq Kit. Libraries were size-selected at 100-700 bp by AMPure XP beads. Libraries were quantified with KAPA qPCR and bioanalyzer prior to single-end sequencing.


title: wt_mouse6

city: Rennes

first: Brice

last: Laffleur

address: 2 avenue du professeur Léon Bernard

country: France

institute: INSERM

data_processing:
Library strategy: DNA-seq
Data were processed as previously described (PMID: 28416601) / parameters for analysis by the Csreport algorithm are provided in the Material and Methods section of the manuscript

source_name: Spleen

extract_protocol:
DNA was extracted using GenElute Mammalian Genomic DNA miniprep Kit (Sigma Aldrich)
Ion Xpress plus Fragment Library Kit (Thermo Fisher Scientific); Chip 540 on the Ion S5 sequencer (Life Technologies)

value: Primary B cells

value: SRBC immunization Day 17

tag: genotype/variation

value: WT


title: E13.5_EC_Ctrl_H3K4me1_rep2


title: wt_mouse7


title: pombe_delta4dus_R_1


title: Liver_EC_2Runx1_RNA_rep2

description:
Liver_2Runx1_S2
Liver_2Runx1_RNA.bw
RPKM_norm.txt

molecule: polyA RNA

extract_protocol:
Cells were sorted from adult mouse livers. Total RNA samples were isolated using RNeasy Micro Kit (Qiagen).
Illumina Nextera XT library was used for sequencing library preparation. Briefly, cDNA was fragmented, and an adaptor was added using Transposase, followed by limited-cycle PCR to enrich and add an index to the cDNA fragments. The final library was assessed with Qubit 2.0 Fluorometer and Agilent TapeStation. Libraries were sequenced on Illumina HiSeq2500 using a 2x150 Paired End (PE) configuration.

treatment_protocol: Females were given 2mg tamoxifen via oral gavage prior to harvesting of the liver and cell sorting.

value: Adult (4-6 weeks old)

value: Liver


title: smRNA-YwxEyG4_prep1


title: pombe_WT_R_1


title: smRNA-WTxEyG4_prep2


title: AID-deficient_mouse8

value: AID-deficient


title: smRNA-K36MxEyG4_prep3


title: delta4dus_2

data_processing:
Reads were quality- and adaptor-trimmed using trimmomatic 0.36 with options PE ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 HEADCROP:1 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36.
The filtered reads were mapped on S.pombe genome using tophat2 with the options --no-sort --mate-std-dev 150 -N 2 --read-edit-dist 2 --min-intron-length 5 --max-intron-length 3000 --max-multihits 4 --no-discordant --no-coverage-search -p 4 --library-type fr-firststrand
Mapped reads were summarized at the gene level using featurecounts.
Differential gene expression analysis was performed using the R package DESeq2 .
Genome_build: ASM294v2.26
Supplementary_files_format_and_content: reads_count_per_gene.txt contains featureCounts output (read count per gene and per RNA-seq library). delta4dus_vs_WT.txt contains DESeq2 results() output including the fold change of expression upon 4dus deletion and its associated pvalue.

growth_protocol: 50 mL of S. pombe (OD595nm ~ 0.5) grown in YES at 32°C were harvested by centrifugation and washed in DEPC water.

extract_protocol:
The cell pellets were resuspended in 750μL of TES buffer (10mM Tris pH 7.5, 10mM EDTA pH 8, 0.5% SDS) and the total RNA was isolated by hot phenol extraction.
1μg of total RNA was ribodepleted and analyzed by Bioanalyzer microchip electrophoresis to ensure its good quality (RIN > 8.5). 125ng of ribodepleted samples were prepared for strand-specific NGS with the TruSeq Stranded Total RNA Sample Preparation Protocol (Illumina).


title: AID-deficient_mouse10


title: Liver_EC_Ctrl_RNA_rep2

description:
Liver_Ctrl_S2
Liver_Ctrl_RNA.bw
RPKM_norm.txt


title: smRNA-K36MxEyG4_prep2


title: AID-deficient_mouse7


title: AID-deficient_mouse9


title: Liver_EC_2Runx1_RNA_rep1

description:
Liver_2Runx1_S1
Liver_2Runx1_RNA.bw
RPKM_norm.txt


title: smRNA-WTxEyG4_prep1


title: smRNA-K36MxEyG4_prep1


title: smRNA-WTxEyG4_prep3


title: E9.5_EC_1Runx1_RNA_rep1

description:
E09_1Runx1_S1
E9_1Runx1_RNA.bw
RPKM_norm.txt

extract_protocol:
Cells were sorted from mouse embryos. Total RNA samples were isolated using RNeasy Micro Kit (Qiagen).
Illumina Nextera XT library was used for sequencing library preparation. Briefly, cDNA was fragmented, and an adaptor was added using Transposase, followed by limited-cycle PCR to enrich and add an index to the cDNA fragments. The final library was assessed with Qubit 2.0 Fluorometer and Agilent TapeStation. Libraries were sequenced on Illumina HiSeq2500 using a 2x150 Paired End (PE) configuration.

treatment_protocol: Females were superovulated by administering 5 IU of Pregnant Mare Serum Gonadotrophin and 5 IU human chorionic gonadotrophip at 48 and 0 hours prior to timed mating with males. Females were injected with 2mg tamoxifen 24 hours prior to harvesting. Embryos were harvested at the appropriate embryonic day and cells were sorted on the same day as harvest.

value: whole embryo

value: +1Runx1 (Cre; CKI/+)


title: WT_2


title: smRNA-K27MxEyG4_prep2


title: AID-deficient_mouse6


title: delta4dus_1


title: smRNA-K27MxEyG4_prep1


title: E9.5_EC_Ctrl_RNA_rep2

description:
E09_Ctrl_S2
E9_Ctrl_RNA.bw
RPKM_norm.txt

value: Ctrl (CKI/+)


title: E9.5_EC_1Runx1_RNA_rep2

description:
E09_1Runx1_S2
E9_1Runx1_RNA.bw
RPKM_norm.txt

value: Endothelial Cells


title: J-Lat 8.4-ATAC_TNF_rep1

city: ATLANTA

first: Stefan

middle: G.

last: Sarafianos

state: GA

address: 1760 Haygood Drive NE

institute: Emory University School of Medicine

data_processing:
ATAC-seq reads were aligned to the hg38 and custom hg38-HIV reference genome using Bowtie2
PCR duplicates were removed using Picard Tools and reads were filtered for subnucleosomes
Peak calling was performed using Macs2
Genome_build: hg38 and custom hg38-HIV genome
Supplementary_files_format_and_content: bigwig files

organism: Homo sapiens

source_name: T cells

growth_protocol: Jurkat and Jurkat-derived T cell lines were cultured in RPMI 1640 medium (Gibco, Waltham, MA, USA), supplemented with 10% heat-inactivated fetal bovine serum (FBS) and 2 mM L-glutamine (Gibco), in a humidified incubator at 37 C with 5% CO2.

extract_protocol:
50,000 suspension cells were collected per sample and input for ATAC-seq library preparation.
ATAC-seq was performed using the OMNI-ATAC protocol (Corces et al.). After counting 50,000 cells/library, nuclei were isolated with Lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2) containing 0.1% NP40, 0.1% Tween-20, and 0.01% digitonin. The purified Jurkat or J-Lat nuclei were then resuspended in a transposase reaction containing 0.05% digitonin and incubated for 30 min at 37 °C. Following incubation, samples were treated with Proteinase K at 55 °C for 2 hr, and genomic DNA was isolated via phenol:chloroform:isoamyl alcohol and EtOH precipitation. Library amplification was done with 2x KAPA HiFi mix (Kapa Biosystems) and 1.25 µM indexed Illumina primers using the following PCR conditions: 72 °C for 5 min; 98 °C for 30 s; and 10-11 cycles at 98 °C for 10s, 63 °C for 30 s, and 72 °C for 1 min. Libraries were generated with two biological replicates per condition sampled.

treatment_protocol: Cells +/- treatment with TNF-alpha for 24 hours

value: Lymphocytic T cell line

tag: origin

value: Jurkat T cell-derived

value: TNF-alpha for 24 hours


title: Liver_EC_Ctrl_RNA_rep1

description:
Liver_Ctrl_S1
Liver_Ctrl_RNA.bw
RPKM_norm.txt

value: CD41-CD45-Ter119-CD31+VEC+cKIT lo/+


title: smRNA-K27MxEyG4_prep3

value: 3rd instar larvae eye discs


title: J-Lat 8.4-ATAC_TNF_rep2


title: AID-deficient_mouse3


title: E13.5_EC_2Runx1_RNA_rep1

description:
E13_2Runx1_S1
E13_2Runx1_RNA.bw
RPKM_norm.txt

extract_protocol:
Cells were sorted from mouse fetuses. Total RNA samples were isolated using RNeasy Micro Kit (Qiagen).
Illumina Nextera XT library was used for sequencing library preparation. Briefly, cDNA was fragmented, and an adaptor was added using Transposase, followed by limited-cycle PCR to enrich and add an index to the cDNA fragments. The final library was assessed with Qubit 2.0 Fluorometer and Agilent TapeStation. Libraries were sequenced on Illumina HiSeq2500 using a 2x150 Paired End (PE) configuration.

value: whole fetus

value: +2Runx1 (Cre; CKI/CKI)


title: J-Lat 8.4-ATAC_rep1

value: untreated


title: WT_1

value: wild-type


title: E9.5_EC_Ctrl_RNA_rep1

description:
E09_Ctrl_S1
E9_Ctrl_RNA.bw
RPKM_norm.txt


title: J-Lat 10.6-ATAC_TNF_rep2


title: wt_mouse5

value: Primary B cells

value: SRBC immunization Day 17

value: WT


title: AID-deficient_mouse4

value: AID-deficient


title: piRNA plasmid circular, rep2, 5’mono-Pi dependent sRNA-seq

city: Piscataway

first: Sam

middle: Guoping

last: Gu

state: New Jersey

address: 604 Allison Road

department: Molecular Biology and Biochemistry

institute: Rutgers University

data_processing:
Genomic alignment was performed by using Bowtie 1.2.3
Genome_build: WS235(ce11)

organism: Caenorhabditis elegans

source_name: Mixed stage animals

extract_protocol: RNA-seq libraries were prepared by Novogene using NEB Next Multiplex Small RNA Library Prep Set for Illumina

value: Ex[pMNK54, pCFJ90, pCFJ782, 1 kb ladder]

tag: pirnai target gene

tag: rna-seq method

value: Ligation-based sRNA-seq, 5’-linker ligation is dependent of the 5’-mono phosphate of the small RNAs


title: J-Lat 8.4-ATAC_rep2


title: E13.5_EC_1Runx1_RNA_rep2

description:
E13_1Runx1_S2
E13_1Runx1_RNA.bw
RPKM_norm.txt

value: +1Runx1 (Cre; CKI/+)


title: piRNA plasmid linear, rep1, 5’mono-Pi dependent sRNA-seq


title: E13.5_EC_2Runx1_RNA_rep2

description:
E13_2Runx1_S2
E13_2Runx1_RNA.bw
RPKM_norm.txt

value: Endothelial Cells


title: piRNA plasmid linear, rep2, 5’mono-Pi dependent sRNA-seq


title: wt_mouse3


title: AID-deficient_mouse1


title: E13.5_EC_Ctrl_RNA_rep1

description:
E13_Ctrl_S1
E13_Ctrl_RNA.bw
RPKM_norm.txt

value: Ctrl (CKI/CKI; CKI/+)


title: WT and Cd226-/- CD45+ cells from naïve mice

city: tsukuba

first: Yuho

last: Nakamura-Shinya

state: ibaraki

address: Ibaraki, tuskuba city, tennodai1-1-1

country: Japan

institute: univesity oftsukuba

data_processing:
Read alignment and estimation of cell-containing partitions and associated UMIs using Cell Ranger 3.1.0.
Genome_build: mm10
Supplementary_files_format_and_content: mtx: count matrix in sparse matrix format; barcodes.tsv: barcode ids per sample; genes.tsv: gene ids per sample

source_name: skin cells

extract_protocol:
Skin tissue (2 cm × 2 cm) was cut into small pieces of 1-2 mm and transferred to gentle MACS C-tubes (Miltenyi Biotec, Bergisch Gladbach, Germany) in 2.5 mL of complete RPMI medium with 2.5 mg collagenase type IV (Sigma-Aldrich) and 1.25 μl DNase I (Deoxyribonuclease Ⅰ, DP, Worthington Biochemical Corp, Lakewood, New Jersey, USA) at 37 ℃ for 1 h. Samples were filtered through a 70 μm cell strainer and spun down at 2,500 rpm for 5 minutes.
10X Genomics, Chromium Single Cell 3’ Library and Gel Bead Kit v3.1.

treatment_protocol: A dorsal area of skin (4 cm × 2 cm) was shaved, and 25 μg of DMBA (Sigma-Aldrich, St. Louis, Missouri, USA) dissolved in 200 μl acetone (Sigma-Aldrich) was administered by a micropipette. One week later, 5 μg TPA (Sigma-Aldrich) dissolved in 200 μl acetone was applied to the same area of the skin once weekly for 3 weeks.

value: CD45+ cells

value: skin cells

value: Balb/c

value: WT and Cd226-/- CD45+ cells from naive mice


title: AID-deficient_mouse2


title: Cd226-/- skin cells (CD45+ and CD45- cells) from DMBA-TPA treated mice

value: CD45+ and CD45- cells


title: J-Lat 10.6-ATAC_rep1

value: Lymphocytic T cell line

value: Jurkat T cell-derived


title: AID-deficient_mouse5


title: J-Lat 10.6-ATAC_TNF_rep1

value: TNF-alpha for 24 hours


title: piRNA plasmid circular, rep1, 5’mono-Pi dependent sRNA-seq


title: wt_mouse2

value: Primary B cells


title: E13.5_EC_1Runx1_RNA_rep1

description:
E13_1Runx1_S1
E13_1Runx1_RNA.bw
RPKM_norm.txt

value: CD41-CD45-Ter119-CD31+VEC+cKIT lo/+

value: whole fetus


title: SCA_26

city: Rozzano (MI)

first: Daniele

last: Braga

address: Via Manzoni 56

country: Italy

institute: Humanitas Clinical and Research Center

data_processing:
Quality filtering and adapter trimming (trimmomatic v0.39)
Alignment (STAR version 2.6.1b)
Count (featureCounts version 1.6.4 - gencode.vM22.annotation.gtf )
Genome_build: GRCm38 primary assembly genome
Supplementary_files_format_and_content: "GEO_SCA_RNASeq_plexus_raw_counts.txt" contains raw count data (row: ensembl_gene_id, column: samples)

source_name: Choroid Plexus - T5

extract_protocol:
Total RNA from the whole CP tissue dissected from lateral ventricles was extracted using Direct-zol RNA MiniPrep Plus (Zymo, R2072) following manufacturer’s instruction.
SMART-Seq v4 Ultra Low Input RNA Kit (Clontech-Takara)

value: Choroid Plexus

tag: dss treatment timepoint


title: Jurkat T cells-ATAC_TNF_rep1


title: wt_mouse4

value: SRBC immunization Day 17

value: WT


title: WT and Cd226-/- CD45- cells from naïve mice

value: CD45- cells

value: WT and Cd226-/- CD45- cells from naive mice


title: Jurkat T cells-ATAC_TNF_rep2


title: WT skin cells (CD45+ and CD45- cells) from DMBA-TPA treated mice


title: Jurkat T cells-ATAC_rep2

value: untreated


title: J-Lat 10.6-ATAC_rep2


title: SCA_32

source_name: Choroid Plexus - T3


title: Mettl3-WT-IP-ST-1

city: Wuhan

first: jiwei

last: chang

state: Hubei

address: No.185, East Lake Road, Wuchang District,

department: Medical Research Institute,  School of Medicine,

country: China

institute: Wuhan University

data_processing:
fastp/trimmomatic trimming raw fastq files
kallisto mapping to GRCm38 cDNA sequences
SLAM-seq mapping NextGenMap
Genome_build: GRCm38
Supplementary_files_format_and_content: normalized gene counts or raw gene counts:
Sample-IP-gene-counts-16cell_types.tsv (raw counts)
normalized-Sample-input-counts-gene-16cell_type.tsv (normalized counts)
Mettl3-normalized-gene-counts-input.tsv (normalized counts)
Mettl3-gene-counts-IP.tsv (raw counts)
Igf2bp2-LT.HSC-gene-counts.tsv (raw counts)
RNA-Ratio-T2C-6cell_type.tsv (T>C transition ratio)
RNA-T2C-ratio-average-LT.HSC.tsv (T>C transition ratio)
RNA-T2C-ratio-average-MkP.tsv (T>C transition ratio)

extract_protocol:
Total RNA was isolated using Tirzol reagent (Takara). Anti-m6A antibody (0.5 μg per sample) (ab15320, Abcam) was pre-bound to Protein A magnetic beads (Thermo Fisher Scientific) in IP buffer (10mM Tris-HCl pH 7.4, 100mM NaCl,0.1% NP40, , 0.4 U/μl RNasin) with head-to-tail mixing at 4 °C for 2 h. Total RNA (100 ng per sample) was added and incubated at 4°C for another 2 h. Beads were washed twice with 200 μl IP buffer, twice with 200 μl low-salt buffer (10mM Tris-HCl pH 7.4, 50 mM NaCl, 0.1% NP-40, 0.4 U/μl RNasin), twice with 200 μl high-salt buffer (10mM Tris-HCl pH 7.4, 500mM NaCl, 0.1% NP40, 0.4 U/μl RNasin) and once with 200 μl 1× IP buffer.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: wild type

tag: rip antibody

value: Anti-m6A antibody ,ab15320, Abcam (0.5 μg per sample)


title: SCA_24

tag: strain


title: SCA_25

tag: tissue


title: wt_mouse1


title: SCA_23


title: Jurkat T cells-ATAC_rep1


title: SCA_21


title: SCA_20


title: Mettl3-WT-IP-Mkp-2

source_name: MkP

value: MkP


title: Mettl3-WT-IP-ST-2


title: Mettl3-WT-IP-MPP-2

source_name: MPP

value: MPP


title: AN_input_SSDS

first: Kevin

last: Brick

address: 5/205 Memorial Drive

department: GBB

institute: NIDDK

data_processing:
Basecalling was performed using Illumina HCS 1.5.15.1
The pipeline described in Khil et al. Genome Res. 2012 was used to align SSDS reads to the genome (https://github.com/kevbrick/SSDSpipeline.git). Uniquely mapping fragments unambiguously derived from ssDNA (ssDNA type 1) and having both reads with a mapping quality score ≥ 30 were used for identifying hotspot locations (peak calling). NCIS was used to estimate the background fraction for each library. Peak calling was performed using MACS (v.2.1.0.20150420) with the following parameters : --ratio [output from NCIS]  -g mm --bw 1000 --keep-dup all --slocal 5000. (https://github.com/kevbrick/callHotspotsSSDS.git) and using the matching input dlibrary as a control. DSB hotspots within regions previously blacklisted were removed and hotspot strength was calculated as described previously (Brick & Pratto et al., Meth. Enzym. 2019).
BIGWIG files were generated from ssDNA type1 data using the deeptools3.0.1 bamCoverage function and the following arguments: --binSize 150 --normalizeUsing RPKM --ignoreDuplicates
Genome_build: hg38
Supplementary_files_format_and_content: BIGWIG: Genomic coverage
Supplementary_files_format_and_content: BAM: Processed ssDNA aligned to reference genome
Supplementary_files_format_and_content: BAI: Index files for BAMs
Supplementary_files_format_and_content: BEDGRAPH: DMC1-SSDS peaks with associated strength
Supplementary_files_format_and_content: HOTSPOTS TABLE: SSDS peaks in each individual
Supplementary_files_format_and_content: HAPLOTYPES TABLE: PRDM9 genotyping information for all individuals

source_name: Human testes

extract_protocol:
Samples were obtained frozen and were directly thawed in 1% paraformaldehyde and gently dissociated. Sequencing libraries for anti-DMC1 were prepared following the method described in (Khil et al., 2012).
Sequencing libraries were prepared following the method described in (Khil et al., 2012).

tag: population

tag: Sex

value: Male

tag: sequencing technique

value: ChIP-Single Stranded DNA Sequencing (SSDS)

tag: antibody


title: Mettl3-WT-IP-MPP-1

tag: genotype

tag: cell type

tag: treatment


title: AN_dmc1_SSDS

value: Anti-DMC1 Santa Cruz (C-20, sc 8973)


title: CL4_dmc1_SSDS [re-analysis]

description:
GSM4460466
CL4_dmc1_SSDS


title: CL4_input_SSDS [re-analysis]

description:
GSM4460467
CL4_input_SSDS


title: AC_input_SSDS [re-analysis]

description:
GSM1447339
AC_input_SSDS


title: Mettl3-WT-IP-Mkp-1


title: SCA_30

source_name: Choroid Plexus - T1


title: Mettl3-WT-IP-MEP-2

source_name: MEP

value: MEP


title: SCA_29


title: SCA_16


title: SCA_28


title: Mettl3-WT-IP-LT-2


title: AC_dmc1_SSDS [re-analysis]

description:
GSM1447338
AC_dmc1_SSDS


title: Mettl3-WT-IP-MEP-1


title: AB1_dmc1_SSDS [re-analysis]

description:
GSM1447331
AB1_dmc1_SSDS


title: AB1_input_SSDS [re-analysis]

description:
GSM1447332
AB1_input_SSDS


title: Mettl3-WT-IP-LT-1


title: SCA_09


title: Mettl3-WT-IP-GMP-2

source_name: GMP

value: GMP


title: Heat stress (HS) replicate 3 grains

city: Valdivia

first: Javier

last: Canales

state: Los Ríos

address: Campus Isla Teja s/n

department: Instituto de Bioquimica y Microbiologia

country: Chile

institute: Universidad Austral de Chile

data_processing:
Sequenced reads were pseudo-aligned to the publicly available Triticum turgidum transcriptome obtained from Ensembl Plants using kallisto (v0.46)
RNA-seq data was normalized using the R package sleuth
Genome_build: Svevo.v1
Supplementary_files_format_and_content: tab-delimited text file includes tpm values for each sample

organism: Triticum turgidum subsp. durum

growth_protocol: A glasshouse experiment  was carried out at the Austral Farming Experimental Station in Valdivia, Chile (39° 47’ S., 73° 14’ W.). In this experiment tetraploid wheat (Triticum turgidum spp. durum) genotype Queule-INIA was grown under standard glasshouse conditions. Three seeds per pots were sowing and fertilized with 150 kg ha-1 of nitrogen (N) and 300 kg ha-1 P2O5. In addition, 150 kg ha-1 N were applied averaging tillering. Pots were periodically surface irrigated to avoid water shortages.  The crop phenophases were followed every five days starting at heading using the decimal code scale (Zadoks et al., 1974). At flowering (Zadok 65), three principal spikes/pot with similar development and size were tagged. Two thermal treatments were performed: control treatment (to ambient glasshouse temperature) and a heat stress (HS), which consisted of increasing the temperature in a range of moderately high temperatures (20 to 32 ºC). The thermal treatments were set at 10 days after flowering.  To perform the thermal increase, chambers of transparent polyethylene (0.15 microns) were build up. Each chamber (1.2 × 1.0 × 1.2 m) was equipped with thermostatically controlled electric heaters as in previous experiments (Lizana and Calderini, 2013: doi:10.1017/S0021859612000639). The thermal regime was controlled by thermal sensors placed at the height of the spikes and connected to a temperature regulator (Cavadevices, Buenos Aires, Argentina). The air temperature was recorded both within and outside the chambers using data loggers (Extech Instruments SDL200 FLIR System, Inc.).

extract_protocol:
The RNA extraction protocol was based in Yaffe et al., (2012); https://doi.org/10.1186/1756-0500-5-45)), with modifications for  wheatgrain, with 100 mg of each sample and using NucleoSpin® Gel and PCR columns
RNA quality analysis, libraries construction and sequencing were performed by by the sequencing service unit of the Faculty of Sciences in the Pontifical Catholic University of Chile (Santiago, Chile), using standard Illumina protocols

tag: time

value: 10 days after flowering

value: Heat stress (HS)


title: SCA_08

source_name: Choroid Plexus - CTRL

value: Choroid Plexus

value: CTRL


title: Heat stress (HS) replicate 2 grains

treatment_protocol: Two thermal treatments were performed: control treatment (to ambient glasshouse temperature) and a heat stress (HS), which consisted of increasing the temperature in a range of moderately high temperatures (20 to 32 ºC). The thermal treatments were set at 10 days after flowering.  To perform the thermal increase, chambers of transparent polyethylene (0.15 microns) were build up. Each chamber (1.2 × 1.0 × 1.2 m) was equipped with thermostatically controlled electric heaters as in previous experiments (Lizana and Calderini, 2013: doi:10.1017/S0021859612000639).

tag: replicate


title: AA4_input_SSDS


title: SCA_06


title: Heat stress (HS) replicate 1 grains


title: Mettl3-WT-IP-GMP-1


title: AA4_dmc1_SSDS


title: SCA_05


title: Control replicate 2 grains

value: Control


title: SCA_03


title: AA3_dmc1_SSDS


title: Mettl3-WT-IP-CMP-1

source_name: CMP

value: CMP


title: Control replicate 1 grains


title: SCA_01


title: Mettl3-WT-IN-ST-2


title: Cell from adult ovary follicle, OVA92-F4-11_8

city: Leiden

first: Susana

last: Chuva de Sousa Lopes

address: Einthovenweg 20

department: Anatomy and Embryology

country: Netherlands

institute: Leiden University Medical Center

data_processing:
Read QC with Cutadapt v2.10
Read alignment with STAR v2.7.5a
Read counting with HTSeq v012.4
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix with raw gene counts for every gene and every cell

source_name: Adult ovary follicle

extract_protocol:
For single-cell RNA-sequencing, the small antral follicles (1-8 mm) were collected in saline solution (0.9% NaCl, Fresenius Kabi, Bad Homburg, Germany). The follicles were mechanically ruptured with tungsten needles and the region with the cumulus GCs and oocyte was trimmed and transferred into a clean dish. Individual follicular cells were manually picked up using a pulled glass-capillary under a stereo microscope (Zeiss). Oocytes were denuded by pipetting up and down. None of the collected oocytes contained a polar body. Each cell was transferred into a cold PCR tube contain 1.9 ml 0.2% TritonX-100 in DEPC water and 0.1 ml Recombinant RNase inhibitor (2313A, 40U/ml, TaKaRa), snap-frozen on dry ice and stored at -80°C.
Sequencing libraries were prepared according to the user guide of the Nextera XT (illumina)

value: Follicular cell

tag: follicle id

tag: batch

tag: patient id


title: Mettl3-WT-IN-ST-1

value: untreated


title: AA2_input_SSDS [re-analysis]

description:
GSM1447329
AA2_input_SSDS


title: D6_BRMKO_REST_ChIPseq

city: San Francisco

first: Benoit

last: Bruneau

state: CA

address: 1650 Owens Street

institute: Gladstone Institute of Cardiovascular Disease

data_processing:
Libraries were sequenced on Nextseq 500 using V75 high poutput kit
Raw sequencing reads were converted to FASTQ files using bcl2fastq
Reads were aligned to mm9  using Bowtie2
Genome_build: mm9
Supplementary_files_format_and_content: bigwig

source_name: mouse ES cell derived cardiac precursors

growth_protocol: mouse ESCs were maintained in DMEM media supplemented with LIF and serum

extract_protocol:
Cells were lysed, lysates were clarified and incubated with REST antibody(Sigma, 17-10456) for O/N, captured with IgG coated magnetic beads, washed, and ChIPed DNA eluted. Protein-DNA complexes were reverse crosslinked, proteinase digested and ampure bead purified
To prepare libraries DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (3 to 5 exo minus) and dATP  and ligated of Illumina adapters. Adapter ligated DNA was PCR amplified with Illumina primers for 14 cycles and library fragments of 200 - 500bp bp were band isolated from an agarose e-gel (invitrogen).  The purified libraries were quantified, and libraries were pooled before sequencing on Illumina NextSeq 500 system

treatment_protocol: mouse ESC lines were differentiated to cardiac mesoderma dn cardiac precursors using the Kattman et al 2011 Cardiomyocyte Differentiation protocol.

tag: timepoint

value: Day 6

value: REST


title: AA2_dmc1_SSDS [re-analysis]

description:
GSM1447328
AA2_dmc1_SSDS


title: D6_BRMKO_Input


title: Cell from adult ovary follicle, OVA92-F3-9_8


title: Mettl3-WT-IN-MPP-2

value: wild type


title: Cell from adult ovary follicle, OVA92-F3-9_7


title: D6_WT_REST_ChIPseq


title: AA1_input_SSDS [re-analysis]

description:
GSM1447326
AA1_input_SSDS


title: Mettl3-WT-IN-MPP-1

value: MPP


title: Cell from adult ovary follicle, OVA92-F3-9_6


title: D6_WT_Input


title: Mettl3-WT-IN-MkP-2

value: MkP


title: D4_BRMKO_REST_ChIPseq

source_name: mouse ES cell derived cardiac mesoderm

value: Day 4


title: EWS894 Xenograft Tissue, Block 2 - Rep 3

city: Chapel Hill

first: Ian

middle: Jonathan

last: Davis

state: NC

address: 450 West Drive

institute: University of North Carolina-Chapel Hill

data_processing:
Basecalls performed using Illumina
Reads quality assessed using fastqc/0.11.5
Adapter sequences removed using cutadapt/1.12
Reads of poor base quality removed using fastx_toolkit/0.0.14 (-Q 33 -p 90 -q 20)
Duplicate reads removed
Reads aligned to hg19 genome using star/2.5.2b (--outFilterScoreMin 1 --outFilterMultimapNmax 1 --alignMatesGapMax 1000 --outFilterMismatchNmax 2 --chimJunctionOverhangMin 15 --chimSegmentMin 15)
Multimapping reads removed (samtools view -f 256) and reads aligning to blacklisted regions of genome removed
Bam files converted to bed files using bedtools/2.26 bamtobed
Reads shift extended to 150bp
Genome_build: hg19/mm9
Supplementary_files_format_and_content: Bed files converted to bedgraphs using bedtools/2.26 genomecov, scaling by the total number of reads aligned
Supplementary_files_format_and_content: Bedgraphs converted to bigwigs using bedGraphToBigWig

source_name: EWS894 tissue

growth_protocol: Cells were cultured in standard conditions at 37˚C with 5% CO2

extract_protocol:
FOR CELLS: 5 million cells (EWS894, UM-RC-2, MCF-7, HUVEC) were crosslinked in 1% formaldehyde   in biological triplicate and nuclei were prepared using the Active Motif Chromatin Preparation kit (53046) according to manufacturer’s instructions. 0.25 million formaldehyde crosslinked Drosophila S2 cells were mixed with the human tumor cells just prior to nuclei preparation   . Nuclei were resuspended at a concentration of 1 million nuclei per 90 µL of Lysis Buffer A (7) and 10 µL of nanodroplets (prepared as described in Kasoji et al. (23), available from Triangle Biotechnology, Inc.) was added to each tube prior to sonication. Sonication was performed in a Covaris E110 instrument using conditions described in (22) with nanodroplets (EWS89445 seconds; UM-RC-2 30 seconds; MCF-7 1.5 minutes; HUVEC 2 minutes) or without nanodroplets (EWS894and MCF-7 16 minutes; UM-RC-2 10 minutes, HUVEC sonicated with a probe sonicator as described in (51)). Following sonication, insoluble debris was removed by centrifugation and samples were digested with 200 µg RNase (Qiagen) at 37˚C for 30 minutes. Ten µL of sample was removed for input and digested with 40 mg Proteinase K (Worthington) for 1 hour at 55˚C, followed by 2 hours at 80˚C to reverse the crosslinks, then purified using a silica matrix column (Zymo Research, ChIP DNA Clean and Concentrate kit, D5201). FAIRE was performed on the remaining 90 µL of sonicated chromatin by purification on a silica matrix column as described in (51). DNA was quantified by fluorometry (Qubit dsDNA High Sensitivity Assay Kit, Invitrogen). Average peak fragment size of input and FAIRE DNA was confirmed using Agilent TapeStation. FOR TISSUE: FFPE tissue blocks were sectioned (UNC Translational Pathology Laboratory) to 10 µm thickness and each section was mounted on a charged glass slide. The top and bottom sections from the first sectioning of each block were stained with Haemotoxylin and Eosin (H&E), visualized on an Aperio ScanScope AT2 and nuclei counted using the Aperio ImageScope software. The slides were deparaffinized and hydrated in xylene, 100%,  85% and 70% ethanol followed by double deionized water. Tissue sections were scraped from the slide with a razor blade and transferred to a 100 µL glass borosilicate vial (Triangle Biotechnology, Inc.) containing 90 µL of Lysis Buffer A (7). Just prior to sonication, 10 µL of nanodroplets (Triangle Biotechnology, Inc. ) was added to each tube. Sonication and FAIRE were performed as described for fixed cells. For Fig. 3C, chromatin was extracted (Active Motif, 53045) from eight, 10 µm EWS894 FFPE tissue sections according to manufacturer instructions. For the nanodroplet extraction method, chromatin was extracted from one, 10 µm tissue section using protocol described above. Each FFPE FAIRE-seq sample consisted of FAIRE DNA extracted from 4 adjacent 10 µM tissue sections per tumor (see Supplemental Table 1 for nuclei count from FFPE tumors).
Sequencing libraries were prepared (Kapa HyperPrep) according to manufacturer instructions.

value: EWS894 tissue

tag: sonication method

value: + nanodroplets


title: Mettl3-WT-IN-Mkp-1

tag: rip antibody


title: Cell from adult ovary follicle, OVA92-F3-9_4


title: D4_BRMKO_Input


title: Mettl3-WT-IN-MEP-2

value: MEP


title: Cell from adult ovary follicle, OVA92-F3-9_3


title: D4_WT_REST_ChIPseq


title: Control replicate 3 grains

value: 10 days after flowering


title: Mettl3-WT-IN-MEP-1


title: EWS894 Xenograft Tissue, Block 1 - Rep 3

value: EWS894 cells


title: Cell from adult ovary follicle, OVA92-F1-4_7


title: D4_WT_Input


title: EWS894 Xenograft Tissue, Block 2 - Rep 2


title: EWS894 Xenograft Tissue, Block 1 - Rep 2


title: Cell from adult ovary follicle, OVA92-F3-9_5


title: Mettl3-WT-IN-LT-1


title: BrmKO_D2_Rep3 ATAC-seq

data_processing:
Libraries were sequenced on Nextseq 500
Raw sequencing reads were converted to FASTQ files using bcl2fastq
Reads were aligned to mm9  using the bowtie
Genome_build: mm9

source_name: mouse ES cell differentiated to embryoid bodies

growth_protocol: Es cell were differentiated following Katman et al., 2011 and Wamstad et al., 2012 papers

extract_protocol:
We followed Corces et al., 2017 paper to perform ATACSeq
Lysed nuclei were tagmented at 37C for 45 mins for ESC and D2 differentiated embryoid bodies samples , before tagmented and purified and PCR amplified with Ad1 and Ad2 primers (corces et al., 2017)

treatment_protocol: ES cells were differentiated to embryoid  before harvested for ATACseq

value: Brg1-3xFLAG; Brm::Puro

value: Day 2


title: Cell from adult ovary follicle, OVA92-F1-4_5


title: Mettl3-WT-IN-GMP-2

value: GMP


title: EWS894 Xenograft Tissue, Block 2 - Rep 1


title: Cell from adult ovary follicle, OVA92-F1-4_6


title: Nanodroplet FAIRE in EWS894 cells - Rep 2

source_name: EWS894 cells


title: Cell from adult ovary follicle, OVA92-F1-4_1


title: BrmKO_D2_Rep1 ATAC-seq


title: PHHs-3

type: genomic

city: Beijing

first: Bingqing

last: Xie

address: Peking University, No.5 Yiheyuan Road Haidian District, Beijing, P.R.China

institute: Peking University

description: DNA Methylation

hyb_protocol: The BeadChips were imaged using the Illumina iScan System. Using default parameters, all Illumina array raw data were processed using the Methylation Module of GenomeStudio v1.9 software.

scan_protocol: Infinium Human methylation EPIC arrays (Illumina) was processed according to manufacturer’s instructions.

data_processing: Raw 850K data for all sample sets were normalized by the SWAN method with background subtraction using RnBeads software package. Default parameters and procedures are used. Probes with the last 3 bases in its target sequence overlap with SNP and the X and Y chromosomes were removed.

label: Cy5 and Cy3

source_name: primary human hepatocytes

label_protocol: The Illumina Infinium Methylation Assay protocol was employed to process around 500 ng of bisulfate-converted DNA (bisulfite treatment results in the conversion of cytosine (C) nucleotides that are unmethylated into uracil/thymine (U/T) nucleotides).

growth_protocol: Human embryonic fibroblasts were isolated and cultured in HEF medium (DMEM + 10% FBS + 1% P.S.). hiHeps were cultured in 2C medium. Primary human hepatocytes were not cultured

extract_protocol: Total DNA was extracted using QIAamp DNA Mini Kit (QIAGEN) according to the manufactures’instructions.

treatment_protocol: No further treatment was processed before extract protocol.

value: Freshly isolated

value: primary human hepatocytes


title: BrmKO_D2_Rep2 ATAC-seq


title: Nanodroplet FAIRE in EWS894 cells - Rep 1


title: Mettl3-WT-IP-CMP-2

value: CMP

value: Anti-m6A antibody ,ab15320, Abcam (0.5 μg per sample)

value: untreated


title: Mettl3-WT-IN-CMP-2

value: wild type


title: Mettl3-WT-IN-GMP-1


title: WT_D2_Rep2 ATAC-seq


title: Traditional FAIRE in EWS894 cells - Rep 2

value: - nanodroplets


title: Methylome capture of HG004 using EMSeq [EMSeq_HG004_LAB01_REP02]

city: Uppsala

first: Jessica

last: Nordlund

address: Box 1432, BMC

department: Department of Medical Sciences

country: Sweden

institute: Uppsala University

description: Whole Genome Enzymatic Deamination

data_processing:
Library strategy: enzymatic deamination sequencing
Base-calling software: RTA v3.4.4
Adapter trimming: fastp v0.20.1
Alignment: bwa-meth v02.1
Sorting and indexing: sambamba
Duplicate marking: Picard MarkDuplicates v2.10.10-SNAPSHOT
Methylation calling: MethylDackel v0.3.0-3-g084d926
Genome_build: genome build: GRCh38
Supplementary_files_format_and_content: Bedgraph

source_name: Cell line

extract_protocol:
NEB Enzymatic Methyl-Seq
DNA (gDNA) was purchased from the Coriell Institute for Medical Research

tag: cell line


title: Mettl3-WT-IN-CMP-1


title: WT_D2_Rep3 ATAC-seq


title: WT_D2_Rep1 ATAC-seq


title: Methylome capture of HG004 using EMSeq [EMSeq_HG004_LAB02_REP02]

description: Whole Genome Enzymatic Deamination


title: Methylome capture of HG004 using EMSeq [EMSeq_HG004_LAB02_REP01]

description: Whole Genome Enzymatic Deamination


title: Cell from adult ovary follicle, S_3H

value: Oocyte


title: Mettl3-KO-IP-ST-1

value: Mettl3 -/-


title: hiHeps-2

description: DNA Methylation

source_name: human induced hepatocytes

value: 2C medium

value: human induced hepatocytes


title: Cell from adult ovary follicle, S_92_10C

value: Follicular cell


title: BrmKO_D0_Rep3 ATAC-seq

source_name: mouse ES cells

value: Day 0


title: Traditional FAIRE in EWS894 cells - Rep 1

value: EWS894 cells


title: AA3_input_SSDS

value: Male

value: ChIP-Single Stranded DNA Sequencing (SSDS)


title: Methylome capture of HG005 using EMSeq [EMSeq_HG005_LAB01_REP01]

description: Whole Genome Enzymatic Deamination


title: PHHs-2

description: DNA Methylation


title: Mettl3-KO-IP-MPP-2

source_name: MPP

value: MPP


title: PHHs-1

description: DNA Methylation

value: Freshly isolated


title: Mettl3-KO-IP-MPP-1


title: Targeted methylome capture of HG002 using TruSeq Methyl Capture EPIC [EPIC_HG002_LAB01_REP01]

description: Targeted Bisulfite

data_processing:
Base-calling software: RTA v3.4.4
Adapter trimming: fastp v0.20.1
Alignment: bwa-meth v02.1
Sorting and indexing: sambamba
Duplicate marking: Picard MarkDuplicates v2.10.10-SNAPSHOT
Methylation calling: MethylDackel v0.3.0-3-g084d926
Genome_build: genome build: GRCh38
Supplementary_files_format_and_content: Bedgraph

extract_protocol:
Illumina Methyl Capture EPIC
DNA (gDNA) was purchased from the Coriell Institute for Medical Research


title: Cell from adult ovary follicle, S_92_10A


title: Methylome capture of HG005 using EMSeq [EMSeq_HG005_LAB02_REP01]

description: Whole Genome Enzymatic Deamination


title: hiHeps-3

description: DNA Methylation


title: BrmKO_D0_Rep1 ATAC-seq


title: Mettl3-WT-IN-LT-2


title: Cell from adult ovary follicle, S_92_10B


title: WT_D0_Rep3 ATAC-seq


title: BrmKO_D0_Rep2 ATAC-seq


title: Methylome capture of HG006 using EMSeq [EMSeq_HG006_LAB01_REP01]

description: Whole Genome Enzymatic Deamination


title: Mettl3-KO-IP-Mkp-2

source_name: MkP

value: MkP


title: Targeted methylome capture of HG002 using TruSeq Methyl Capture EPIC [EPIC_HG002_LAB01_REP02]

description: Targeted Bisulfite


title: Mettl3-KO-IP-Mkp-1


title: hiHeps-1

description: DNA Methylation


title: WT_D0_Rep1 ATAC-seq


title: WT_D0_Rep2 ATAC-seq


title: Methylome capture of HG002 using TrueMethyl oxidative bisulite sequencing, mockBS [TrueMethylBS_HG002_LAB01_REP01]

description: Whole Genome Bisulfite

extract_protocol:
NuGEN TrueMethyl oxBS-Seq
DNA (gDNA) was purchased from the Coriell Institute for Medical Research


title: Cell from adult ovary follicle, OVA92_verysmall_G


title: Cell from adult ovary follicle, OVA92_verysmall_B


title: Mettl3-KO-IP-MEP-2

value: MEP


title: Cell from adult ovary follicle, S_92_12E


title: D0_BRM KO_Rep2 scRNA-seq

data_processing:
Libraries were sequenced on NextSeq 500
Raw sequencing reads were converted to FASTQ files using Cellranger 2.0.2 mkfastq
Reads were aligned to mm9  using the Cellranger 2.0.2 count
Cellranger 2.0.2 aggr was used to aggregate libraries from WT and BRMKO cells
Aggregated gene expression matrix was processed in Seurat 2.3.4. Briefly, cells with UMI counts between 10,000 and 80,000 were retained. Gene expression was normalized, scaled and mitochondrial reads and cell cycle genes were regressed. Cells were clustered based on the top 25-30 prinicipal components.
Genome_build: mm9
Supplementary_files_format_and_content: Processed Seurat expression matrix as a csv file, with columns as cell barcodes and rows as genes

extract_protocol:
ES Cells were singularized using Trypsin 0.25% and 10,000 cells were loaded on a 10X Chromium chip
Chromium Single Cell 3′ GEM, Library & Gel Bead Kit v2 was used to construct libraries


title: Methylome capture of HG003 using TrueMethyl oxidative bisulite sequencing, mockBS [TrueMethylBS_HG003_LAB01_REP01]

description: Whole Genome Bisulfite


title: D0_BRM KO_Rep1 scRNA-seq


title: Mettl3-KO-IP-LT-2

value: Anti-m6A antibody ,ab15320, Abcam (0.5 μg per sample)


title: Methylome capture of HG003 using TrueMethyl oxidative bisulite sequencing, mockBS [TrueMethylBS_HG003_LAB01_REP02]

description: Whole Genome Bisulfite


title: D0_WT_Rep2 scRNA-seq


title: HEFs-2

description: DNA Methylation

source_name: human embryonic fibroblasts

value: DMEM + 10%FBS + 1% P.S.

value: human embryonic fibroblasts


title: Methylome capture of HG002 using TrueMethyl oxidative bisulite sequencing, mockBS [TrueMethylBS_HG002_LAB01_REP02]

description: Whole Genome Bisulfite


title: Cell from adult ovary follicle, OVA92_verysmall_E


title: Cell from adult ovary follicle, OVA92_verysmall_C


title: Mettl3-KO-IP-MEP-1

source_name: MEP

value: untreated


title: Mettl3-KO-IP-LT-1


title: Mettl3-KO-IP-GMP-2

source_name: GMP

value: GMP


title: D0_WT_Rep1 scRNA-seq


title: Methylome capture of HG004 using TrueMethyl oxidative bisulite sequencing, mockBS [TrueMethylBS_HG004_LAB01_REP01]

description: Whole Genome Bisulfite


title: Cell from adult ovary follicle, OVA92_verysmall_F


title: HEFs-1

description: DNA Methylation


title: Cell from adult ovary follicle, OVA92_verysmall_H

value: Oocyte


title: Methylome capture of HG004 using TrueMethyl oxidative bisulite sequencing, mockBS [TrueMethylBS_HG004_LAB01_REP02]

description: Whole Genome Bisulfite


title: Liver_EC_2Runx1_ATAC_rep2

description:
Liver_2Runx1_ATAC.bw
Liver_2Runx1_ATAC_peaks.bed

data_processing:
ATAC-seq: Sequencing reads were demultiplexed using Bcl2Fastq v2.20 then trimmed and filtered for quality using Trim Galore v0.6.4 with the following settings: fastqc, paired, and trim1. Reads were then aligned to the mouse genome (mm10) using bowtie 2.3.5.1. Only uniquely mapped reads with fewer than 2 mismatches were used for downstream analyses. Samtools v1.1 was used to convert SAM files to BAM files, and Sambamba v0.6.6 was used to filter out duplicates, multi-mappers, reads mapped to ChrM or blacklist regions, and unmapped reads. MACS2 2.1.4 was used for peak calling using the following parameters: BAMPE, q: 0.05. . Merged replicates were used to create bigwig files for visualization using Deeptools v3.3.0 and the following parameters: normalized to reads per genomic content (RPGC), effective genome size: 2308125349, ignore for normalization: ChrX, min fragment length: 20, bin size: 10.
RNA-seq: Sequencing reads were demultiplexed using Bcl2Fastq then trimmed and filtered for quality using Trim Galore v0.6.4 with the following settings: fastqc, paired, and trim1. Reads were then aligned to the mouse genome (mm10) using STAR 2.7.3a and the mm10 gene reference file from UCSC. Only uniquely mapped reads with fewer than 2 mismatches were used for downstream analyses. Samtools v1.1 was used to convert to BAM files, and Sambamba v0.6.6 was used to filter out duplicates, multi-mappers, and unmapped reads. The featureCounts function of the Subread v2.0.0 package was used to extract gene-level and transcript level read counts. EdgeR and TMM normalization were used to calculate normalized RPKM. Bigwig files for visualization were created using Deeptools v3.3.0 from merged BAM files. The following parameters were used: normalized to reads per genomic content (RPGC), effective genome size: 2308125349, ignore for normalization: ChrX, min fragment length: 20, bin size: 10.
ChIP-seq: Sequencing reads were demultiplexed using Bcl2Fastq v2.20 then trimmed and filtered for quality using Trim Galore v0.6.4 with the following settings: fastqc, paired, and trim1. Reads were then aligned to the mouse genome (mm10) using bowtie 2.3.5.1. Only uniquely mapped reads with fewer than 2 mismatches were used for downstream analyses. Samtools v1.1 was used to convert SAM files to BAM files, and Sambamba v0.6.6 was used to filter out duplicates, multi-mappers, reads mapped to ChrM or blacklist regions, and unmapped reads. MACS2 2.1.4 was used for peak calling using the following parameters: broad, q: 0.05. Merged replicates were used to create bigwig files for visualization using Deeptools v3.3.0 and the following parameters: normalized to reads per genomic content (RPGC), effective genome size: 2308125349, ignore for normalization: ChrX, min fragment length: 20, bin size: 10, smooth length: 60, extend reads: 150.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: BigWig files provided are normalized tracks of merged replicates.
Supplementary_files_format_and_content: Bed files provided are the output of MACS2 peak calling.
Supplementary_files_format_and_content: RPKM_Norm.txt: Tab-delimited text file for RNA-seq samples includes normalized RPKM.

source_name: Endothelial Cells

extract_protocol:
50,000 cells were FACS sorted then washed with cold PBS. Cell pellet were resuspended in 50 µl of cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% (v/v) Igepal CA-630) and immediately applied to centrifugation at 1,600g, 4 °C for 10 min. Nuclei pellet was resuspended in 50 µl of transposition reaction mix (1× tagment DNA Buffer, 2.5 µl of Tagment DNA Enzyme 1) and incubated for 30 min at 37 °C.
Libraries were purified using a Qiagen MinElute Gel Purification kit and the concentrations were measured using both Qubit and KAPA qPCR. 2100 Bioanalyzer was used to check the quality of libraries. Libraries were sequenced on the Illumina NextSeq 500, with 75-bp paired-end reads.

value: Endothelial Cells

tag: isolation markers

value: CD41-CD45-Ter119-CD31+VEC+cKIT lo/+

tag: strain

tag: developmental stage

value: Adult (4-6 weeks old)

tag: organ

value: Liver

value: +2Runx1 (Cre; CKI/CKI)


title: Mettl3-KO-IP-GMP-1

value: Mettl3 -/-


title: Cell from adult ovary follicle, OVA92_verysmall_D

value: Follicular cell


title: Methylome capture of HG005 using TrueMethyl oxidative bisulite sequencing, mockBS [TrueMethylBS_HG005_LAB01_REP01]

description: Whole Genome Bisulfite


title: Mettl3-KO-IP-CMP-2

source_name: CMP

value: CMP


title: Liver_EC_2Runx1_ATAC_rep1


title: Liver_EC_Ctrl_ATAC_rep2

description:
Liver_Ctrl_ATAC.bw
Liver_Ctrl_ATAC_peaks.bed

value: Ctrl (CKI/CKI; CKI/+)


title: Cell from adult ovary follicle, OVA92_verysmall_A

source_name: Adult ovary follicle


title: Mettl3-KO-IP-CMP-1


title: Methylome capture of HG005 using TrueMethyl oxidative bisulite sequencing, mockBS [TrueMethylBS_HG005_LAB01_REP02]

description: Whole Genome Bisulfite


title: HEFs-3

description: DNA Methylation


title: Cell from adult ovary follicle, OVA92_LARGE_G


title: Mettl3-KO-IN-ST-2


title: Methylome capture of HG006 using TrueMethyl oxidative bisulite sequencing, mockBS [TrueMethylBS_HG006_LAB01_REP02]

description: Whole Genome Bisulfite


title: Methylome capture of HG006 using TrueMethyl oxidative bisulite sequencing, mockBS [TrueMethylBS_HG006_LAB01_REP01]

description: Whole Genome Bisulfite


title: EWS894 Xenograft Tissue, Block 1 - Rep 1

value: EWS894 cells

value: + nanodroplets


title: Cell from adult ovary follicle, OVA92_LARGE_E


title: E9.5_EC_1Runx1_ATAC_rep2

description:
E9_1Runx1_ATAC.bw
E9_1Runx1_ATAC_peaks.bed

value: whole embryo

value: +1Runx1 (Cre; CKI/+)


title: E9.5_EC_Ctrl_ATAC_rep2

description:
E9_Ctrl_ATAC.bw
E9_Ctrl_ATAC_peaks.bed

value: Ctrl (CKI/+)


title: Cell from adult ovary follicle, OVA92_LARGE_F


title: Mettl3-KO-IN-MPP-2

value: MPP

value: untreated


title: Methylome capture of HG007 using TrueMethyl oxidative bisulite sequencing, mockBS [TrueMethylBS_HG007_LAB01_REP01]

description: Whole Genome Bisulfite


title: Cell from adult ovary follicle, OVA92_LARGE_B


title: Mettl3-KO-IN-MPP-1


title: Cell from adult ovary follicle, OVA92_LARGE_C


title: E9.5_EC_Ctrl_ATAC_rep1

description:
E9_Ctrl_ATAC.bw
E9_Ctrl_ATAC_peaks.bed


title: Mettl3-KO-IN-Mkp-2

value: MkP


title: Methylome capture of HG001 using TrueMethyl oxidative bisulite sequencing, oxidative [TrueMethylOX_HG001_LAB01_REP02]

description: Whole Genome Oxidative Bisulfite

data_processing:
Library strategy: oxidative bisulfite sequencing
Base-calling software: RTA v3.4.4
Adapter trimming: fastp v0.20.1
Alignment: bwa-meth v02.1
Sorting and indexing: sambamba
Duplicate marking: Picard MarkDuplicates v2.10.10-SNAPSHOT
Methylation calling: MethylDackel v0.3.0-3-g084d926
Genome_build: genome build: GRCh38
Supplementary_files_format_and_content: Bedgraph


title: Cell from adult ovary follicle, OVA92_LARGE_D


title: E13.5_EC_2Runx1_ATAC_rep2

description:
E13_2Runx1_ATAC.bw
E13_2Runx1_ATAC_peaks.bed

value: Endothelial Cells

value: whole fetus


title: Liver_EC_Ctrl_ATAC_rep1

value: CD41-CD45-Ter119-CD31+VEC+cKIT lo/+

value: Adult (4-6 weeks old)


title: Mettl3-KO-IN-Mkp-1


title: E13.5_EC_2Runx1_ATAC_rep1

value: +2Runx1 (Cre; CKI/CKI)


title: Mettl3-KO-IN-MEP-2

value: Mettl3 -/-

value: MEP


title: Mettl3-KO-IN-ST-1


title: Cell from adult ovary follicle, OVA92_LARGE_H

value: Oocyte


title: Cell from adult ovary follicle, OVA92_LARGE_A

value: Follicular cell


title: E9.5_EC_1Runx1_ATAC_rep1


title: E13.5_EC_1Runx1_ATAC_rep2

description:
E13_1Runx1_ATAC.bw
E13_1Runx1_ATAC_peaks.bed


title: Cell from adult ovary follicle, S_92_1G


title: Mettl3-KO-IN-MEP-1


title: Methylome capture of HG001 using TrueMethyl oxidative bisulite sequencing, oxidative [TrueMethylOX_HG001_LAB01_REP01]

description: Whole Genome Oxidative Bisulfite


title: Cell from adult ovary follicle, S_92_1D


title: Mettl3-KO-IN-LT-2


title: Methylome capture of HG007 using TrueMethyl oxidative bisulite sequencing, mockBS [TrueMethylBS_HG007_LAB01_REP02]

description: Whole Genome Bisulfite


title: Methylome capture of HG003 using TrueMethyl oxidative bisulite sequencing, oxidative [TrueMethylOX_HG003_LAB01_REP01]

description: Whole Genome Oxidative Bisulfite


title: Mettl3-KO-IN-GMP-2

value: GMP


title: Methylome capture of HG002 using TrueMethyl oxidative bisulite sequencing, oxidative [TrueMethylOX_HG002_LAB01_REP01]

description: Whole Genome Oxidative Bisulfite


title: Methylome capture of HG004 using TrueMethyl oxidative bisulite sequencing, oxidative [TrueMethylOX_HG004_LAB01_REP01]

description: Whole Genome Oxidative Bisulfite


title: Mettl3-KO-IN-LT-1


title: E13.5_EC_Ctrl_ATAC_rep1

description:
E13_Ctrl_ATAC.bw
E13_Ctrl_ATAC_peaks.bed

value: Ctrl (CKI/CKI; CKI/+)


title: Cell from adult ovary follicle, S_92_1F


title: Methylome capture of HG003 using TrueMethyl oxidative bisulite sequencing, oxidative [TrueMethylOX_HG003_LAB01_REP02]

description: Whole Genome Oxidative Bisulfite


title: MCF7_RNAseq_EV_EtOH_Rep3

first: Gilles

last: Salbert

address: 263 Av. Gal. Leclerc

department: IGDR UMR6290

institute: University Rennes 1

data_processing:
All ChIP-seq and SCL-exo-seq sequencing reads were mapped to hg19 with using Bowtie (Langmead et al., Genome Biol. 2009). SAMtools (Li et al., Bioinformatics 2009) generated bam files which were processed with MACS (Zhang et al., Genome Biol. 2008) to generate wig files. Peak calling followed the procedure descibed in Sérandour et al (Nucleic Acids Res., 2012).
RNA-seq reads were mapped to hg19 with Bowtie (Langmead et al., Genome Biol. 2009) and transcripts were quantified with RSEM (Li and Dewey, Bioinformatics 2011). Differentially expressed genes were identified from RNA-seq data by the R package DESeq2 (Love et al., Genome Biol. 2014) after filtering of the raw data using the R package HTSFilter (Rau et al., Bioinformatics 2013).
SCL-exo-seq reads were treated as descibed (Sérandour et al., Bio-Protoc. 2018) using the python script available at https://mycore.core-cloud.net/index.php/s/4gyZ9dLTqgo86dt on SAM files.
Genome_build: hg19

source_name: EV cells

growth_protocol: Cells were grown in high glucose and pyruvate containing DMEM (Gibco 41966) supplemented with 10% fetal calf serum (Eurobio S116365181H), non-essential amino acids (Gibco 11140035), Penicillin-Streptomycin (Gibco 15240) and Geneticin (Gibco 11811064) at 37°C and 5% CO2.

extract_protocol:
For ChIP-seq assays, cells were fixed in 1.5% formaldehyde (Sigma F8775) for 10 min at room temperature, the reaction was stopped by the addition of glycine (100 mM). Cells were lysed in lysis buffer (150 mM Tris-HCl pH 8.1, 10 mM EDTA, 0.5% Empigen BB, 1% SDS, protease inhibitor cocktail (Roche 5056489) and sonicated using a bioruptor (Diagenode, 15 min 30 sec ON /30 sec OFF). Sonicated chromatin was incubated at 4°C overnight with antibodies (ERa: mix of TE111.5D11 from Abcam and HC-20 from Santa Cruz Biotechnology, H3K4me3: 04-745 from Millipore, H3K27me3: 07-449 from Millipore) in IP buffer (2.8 ng/mL yeast tRNA, 20 mM Tris-HCl, 2 mM EDTA, 150 mM NaCl, 1% Triton X-100, proteases inhibitor cocktail). Complexes were recovered after 4h incubation with 45 mL protein A- and 15 mL protein G-conjugated sepharose beads slurry at 4°C. Beads were washed in washing buffers WB1 (20 mM Tris-HCl pH 8, 2 mM EDTA, 150 mM NaCl, 0.1% SDS, 1 % Triton X-100), WB2 (20 mM Tris-HCl pH 8, 2 mM EDTA, 500 mM NaCl, 0.1% SDS, 1 % Triton X-100), WB3 (10 mM Tris-HCl pH 8, 1 mM EDTA, 250 mM LiCl, 1 % deoxycholate, 1 % NP-40), WB4 (10 mM Tris-HCl pH 8, 1mM EDTA) and DNA fragments were eluted in extraction buffer (1% SDS, 0.1 M NaHCO3). For RNA-seq, total RNAs were extracted with the RNeasy Plus kit from QIAGEN including a DNase digestion step, and mRNA were enriched by selection with poly-dT beads. For SCL-exo-seq, genomic DNA was extracted using reagents from the DNeasy Blood and Tissue kit (QIAGEN).
ChIP-seq libraries (2 replicates) were generated with DNA fragments from 6 to 9 pooled individual ChIP experiments and the TruSeq kit from Illumina according to the manufacturer's protocol. For RNA-seq, three replicate libraries of each condition (TruSeq stranded mRNA, Illumina) were prepared and sequenced (single reads of 75 bases) at the Genomic Paris Center facility (Paris, France). For each SCL-exo experiment, 8 micrograms of gDNA were sonicated two times 7 min (30 sec ON /30 sec OFF) and two times 14 min (30 sec ON /30 sec OFF) with a bioruptor (Diagenode). Glucosylation and biotinylation of 5hmC were performed with the Hydroxymethyl Collector kit (Active Motif), followed by on beads-exonuclease digestion of the captured fragments and library preparation (TrueSeq library preparation kit, Ilumina). For normalization purpose, 400 pg of 5hmC Control DNA provided by the Hydroxymethyl Collector kit were added to each sample as spike-in. Libraries from 3 independent SCL-exo experiments were sequenced with a HiSeq 1500 (Illumina) by the GEH facility (Rennes, France).

treatment_protocol: For RNA-seq, ChIP-seq and SCL-exo-seq, cells were kept for 48h in phenol-red-free DMEM (Gibco 31052) supplemented with 2.5% dextran-charcoal-treated fetal calf serum (Eurobio S116365181W), glutamine, sodium pyruvate, non-essential amino acids, Penicillin-Streptomycin and Geneticin at 37°C and 5% CO2 before treatment with 10 nM estradiol or 0.1% EtOH.

value: MCF-7-derived breast cancer cells

tag: genotype/variation

value: EV

value: 0.1% EtOH for 4 hours


title: Methylome capture of HG002 using TrueMethyl oxidative bisulite sequencing, oxidative [TrueMethylOX_HG002_LAB01_REP02]

description: Whole Genome Oxidative Bisulfite


title: Cell from adult ovary follicle, S_92_1C


title: Cell from adult ovary follicle, S_92_1E


title: E13.5_EC_1Runx1_ATAC_rep1

first: Kai

last: Tan

address: 3501 CIVIC CENTER BLVD

institute: Children's Hospital of Philadelphia

tag: genotype

value: +1Runx1 (Cre; CKI/+)


title: Mettl3-KO-IN-GMP-1

tag: cell type

value: untreated


title: Methylome capture of HG005 using TrueMethyl oxidative bisulite sequencing, oxidative [TrueMethylOX_HG005_LAB01_REP01]

description: Whole Genome Oxidative Bisulfite


title: Cell from adult ovary follicle, S_92_1H


title: MCF7_RNAseq_EV_EtOH_Rep2

tag: treatment


title: Mettl3-KO-IN-CMP-2

value: CMP


title: Mettl3-KO-IN-CMP-1


title: MCF7_RNAseq_EV_E2_Rep3

value: 10 nM estradiol for 4 hours


title: MCF7_RNAseq_EV_EtOH_Rep1


title: Cell from adult ovary follicle, S_92_1A


title: IP-ST.HSC-rep2

value: wild type

value: Anti-m6A antibody ,ab15320, Abcam (0.5 μg per sample)


title: E13.5_EC_Ctrl_ATAC_rep2

value: Endothelial Cells

value: CD41-CD45-Ter119-CD31+VEC+cKIT lo/+

value: whole fetus


title: Cell from adult ovary follicle, S_92_1B


title: Methylome capture of HG005 using TrueMethyl oxidative bisulite sequencing, oxidative [TrueMethylOX_HG005_LAB01_REP02]

description: Whole Genome Oxidative Bisulfite


title: MCF7_RNAseq_EV_E2_Rep2


title: Methylome capture of HG006 using TrueMethyl oxidative bisulite sequencing, oxidative [TrueMethylOX_HG006_LAB01_REP02]

description: Whole Genome Oxidative Bisulfite


title: Methylome capture of HG004 using TrueMethyl oxidative bisulite sequencing, oxidative [TrueMethylOX_HG004_LAB01_REP02]

description: Whole Genome Oxidative Bisulfite


title: Cell from adult ovary follicle, S_3D


title: IP-ST.HSC-rep1


title: MCF7_RNAseq_EV_E2_Rep1


title: Cell from adult ovary follicle, S_3C


title: IP-Neutrophil-rep2

source_name: Neutrophil

value: Neutrophil


title: MCF7_RNASeq_TET2_mCD_EtOH_Rep3

source_name: TET2 mCD cells

value: TET2 mCD


title: IP-Neutrophil-rep1


title: Methylome capture of HG006 using TrueMethyl oxidative bisulite sequencing, oxidative [TrueMethylOX_HG006_LAB01_REP01]

description: Whole Genome Oxidative Bisulfite


title: Cell from adult ovary follicle, S_3B

value: Follicular cell


title: MCF7_RNASeq_TET2_mCD_EtOH_Rep2


title: IP-MPP-rep2

value: MPP


title: Methylome capture of HG007 using TrueMethyl oxidative bisulite sequencing, oxidative [TrueMethylOX_HG007_LAB01_REP02]

description: Whole Genome Oxidative Bisulfite


title: Cell from adult ovary follicle, S_3G

value: Oocyte


title: MCF7_RNASeq_TET2_mCD_EtOH_Rep1

value: MCF-7-derived breast cancer cells


title: Methylome capture of HG001 using EMSeq [EMSeq_HG001_LAB01_REP01]

description: Whole Genome Enzymatic Deamination


title: Methylome capture of HG001 using EMSeq [EMSeq_HG001_LAB02_REP02]

description: Whole Genome Enzymatic Deamination


title: Cell from adult ovary follicle, S_3A


title: MCF7_RNASeq_TET2_mCD_E2_Rep3


title: IP-MPP-rep1


title: Cell from adult ovary follicle, S_3F


title: Methylome capture of HG001 using EMSeq [EMSeq_HG001_LAB02_REP01]

description: Whole Genome Enzymatic Deamination


title: Methylome capture of HG001 using EMSeq [EMSeq_HG001_LAB01_REP02]

description: Whole Genome Enzymatic Deamination


title: IP-Monocyte-rep1

source_name: Monocyte

value: Monocyte


title: Methylome capture of HG007 using TrueMethyl oxidative bisulite sequencing, oxidative [TrueMethylOX_HG007_LAB01_REP01]

description: Whole Genome Oxidative Bisulfite


title: Cell from adult ovary follicle, S_3E


title: Methylome capture of HG002 using EMSeq [EMSeq_HG002_LAB01_REP01]

description: Whole Genome Enzymatic Deamination


title: Methylome capture of HG002 using EMSeq [EMSeq_HG002_LAB01_REP02]

description: Whole Genome Enzymatic Deamination


title: MCF7_RNASeq_TET2_mCD_E2_Rep1


title: IP-MkP-rep2

value: MkP


title: MCF7_RNASeq_TET2_CD_EtOH_Rep3

source_name: TET2 CD cells

value: TET2 CD

value: 0.1% EtOH for 4 hours


title: Cell from adult ovary follicle, Vanessa_H


title: Mettl3-KO-IP-ST-2

value: Mettl3 -/-

value: untreated


title: IP-MkP-rep1

value: wild type


title: Methylome capture of HG002 using EMSeq [EMSeq_HG002_LAB02_REP01]

description: Whole Genome Enzymatic Deamination


title: IP-Monocyte-rep2

value: Anti-m6A antibody ,ab15320, Abcam (0.5 μg per sample)


title: Cell from adult ovary follicle, Vanessa_G


title: IP-MEP-rep2

value: MEP


title: MCF7_RNASeq_TET2_CD_EtOH_Rep2


title: Cell from adult ovary follicle, Vanessa_F


title: IP-MEP-rep1


title: MCF7_RNASeq_TET2_mCD_E2_Rep2

value: 10 nM estradiol for 4 hours


title: MCF7_RNASeq_TET2_CD_EtOH_Rep1


title: Methylome capture of HG002 using EMSeq [EMSeq_HG002_LAB02_REP02]

description: Whole Genome Enzymatic Deamination


title: Methylome capture of HG003 using EMSeq [EMSeq_HG003_LAB01_REP02]

description: Whole Genome Enzymatic Deamination


title: Cell from adult ovary follicle, Vanessa_E


title: Cell from adult ovary follicle, Vanessa_C


title: MCF7_RNASeq_TET2_CD_E2_Rep1


title: MCF7_RNASeq_TET2_CD_E2_Rep3


title: Methylome capture of HG003 using EMSeq [EMSeq_HG003_LAB01_REP01]

description: Whole Genome Enzymatic Deamination


title: IP-LT.HSC-rep2


title: Cell from adult ovary follicle, Vanessa_D


title: MCF7_RNASeq_TET2_CD_E2_Rep2


title: Cell from adult ovary follicle, OVA88_F


title: IP-LMPP-rep2

source_name: LMPP

value: LMPP


title: Tumor-infiltrating empty vector-overexpressing Pmel CD8 T cells, 5

city: Chicago

first: Weiguo

last: Cui

state: IL

address: 303 E Chicago Ave

department: Pathology

institute: Northwestern University

data_processing:
Reads were aligned to mouse reference genome mm10
Genome_build: mm10
Supplementary_files_format_and_content: Quant files were generated using Salmon

source_name: Tumor-infiltrating CD8 T cells

growth_protocol: Splenocytes from Pmel Thy1.2/Thy1.2 mice were activated with gp100 peptide and 10 IU/mL IL-2 for 24 hours, followed by transduction with the MSCV-IRES-Thy1.1 (MIT) retroviral vector (RV) containing Mouse BATF ORF or empty vector control. Following transduction with either empty vector ("MIT") or MIT-BATF ("BATF"), cells were cultured for 24 hours, followed by subculture with 50 IU/mL IL-2, 10 ng/mL IL-7, and 10ng/mL IL-15. Expression of Thy1.1 by positively-transduced cells (either MIT-Empty or MIT-BATF) was confirmed by flow cytometry.

extract_protocol:
At day 7 post-adoptive transfer, immune cells were isolated from the tumors. For each biological replicate, 2000 positively transduced (Thy1.1+) live (7AAD-) Pmel T cells from each mouse were directly sorted into lysis buffer containing Protector RNase Inhibitor.
RNA-seq libraries were prepared using a modified SMART-Seq2 protocol and sequenced with a NextSeq 500 sequencer using a high output V2 75 cycle kit (Illumina) in a 37 bp paired-end mode.

treatment_protocol: Five million Thy1.1+ cells (either MIT or BATF) were adoptively transferred by retroorbital injection per B16-F10 tumor-bearing Ly5.1 mouse.

value: Pmel-Thy1.2 mice

tag: disease

value: cancer

tag: tissue

value: Tumor


title: IP-LT.HSC-rep1


title: Cell from adult ovary follicle, OVA88_E

value: Follicular cell

tag: follicle id


title: IP-GMP-rep2

value: GMP


title: Cell from adult ovary follicle, OVA88_C

tag: batch


title: Methylome capture of HG003 using EMSeq [EMSeq_HG003_LAB02_REP01]

description: Whole Genome Enzymatic Deamination

source_name: Cell line


title: Tumor-infiltrating empty vector-overexpressing Pmel CD8 T cells, 3


title: Cell from adult ovary follicle, OVA88_B

tag: patient id


title: IP-GMP-rep1


title: Tumor-infiltrating empty vector-overexpressing Pmel CD8 T cells, 2


title: Methylome capture of HG006 using EMSeq [EMSeq_HG006_LAB02_REP01]

description: Whole Genome Enzymatic Deamination


title: IP-LMPP-rep1


title: Methylome capture of HG003 using EMSeq [EMSeq_HG003_LAB02_REP02]

description: Whole Genome Enzymatic Deamination


title: Tumor-infiltrating empty vector-overexpressing Pmel CD8 T cells, 4


title: IP-Erythroid-rep2

source_name: Erythroid

value: Erythroid


title: Tumor-infiltrating empty vector-overexpressing Pmel CD8 T cells, 1


title: Targeted methylome capture of HG003 using TruSeq Methyl Capture EPIC [EPIC_HG003_LAB01_REP01]

description: Targeted Bisulfite


title: Cell from adult ovary follicle, OVA88_D


title: Tumor-infiltrating BATF-overexpressing Pmel CD8 T cells, 5


title: IP-Erythroid-rep1


title: Cell from adult ovary follicle, OVA88_H


title: Cell from adult ovary follicle, OVA88_A


title: Methylome capture of HG007 using EMSeq [EMSeq_HG007_LAB01_REP01]

description: Whole Genome Enzymatic Deamination


title: Methylome capture of HG007 using EMSeq  [EMSeq_HG007_LAB02_REP01]

description: Whole Genome Enzymatic Deamination


title: IP-DC-rep2

source_name: DC

value: DC


title: IP-DC-rep1


title: Cell from adult ovary follicle, OVA88_G


title: Targeted methylome capture of HG001 using TruSeq Methyl Capture EPIC [EPIC_HG001_LAB01_REP01]

description: Targeted Bisulfite


title: Tumor-infiltrating BATF-overexpressing Pmel CD8 T cells, 4


title: Targeted methylome capture of HG003 using TruSeq Methyl Capture EPIC [EPIC_HG003_LAB01_REP02]

description: Targeted Bisulfite


title: IP-CMP-rep2

value: CMP


title: Tumor-infiltrating BATF-overexpressing Pmel CD8 T cells, 3


title: Targeted methylome capture of HG004 using TruSeq Methyl Capture EPIC [EPIC_HG004_LAB01_REP01]

description: Targeted Bisulfite


title: Cell from adult ovary follicle, S_9F


title: Cell from adult ovary follicle, S_9D


title: Targeted methylome capture of HG001 using TruSeq Methyl Capture EPIC [EPIC_HG001_LAB01_REP02]

description: Targeted Bisulfite


title: IP-CLP-rep2

source_name: CLP

value: CLP


title: Targeted methylome capture of HG004 using TruSeq Methyl Capture EPIC [EPIC_HG004_LAB01_REP02]

description: Targeted Bisulfite


title: Methylome capture of HG004 using EMSeq [EMSeq_HG004_LAB01_REP01]

description: Whole Genome Enzymatic Deamination


title: IP-CLP-rep1


title: IP-CMP-rep1


title: Tumor-infiltrating BATF-overexpressing Pmel CD8 T cells, 2


title: D10_BRG1cKO

data_processing:
Libraries were sequenced on Illumina Novaseq
Raw sequencing reads were converted to FASTQ files using Cellranger 2.0.2 mkfastq
Reads were aligned to mm9  using the Cellranger 2.0.2 count
Cellranger 2.0.2 aggr was used to aggregate libraries from WT and BRM KO cells at normal BMP4 concentration or combined with high BMP4 concentrations
Aggregated gene expression matrix was processed in Seurat 2.3.4. Briefly, cells with UMI counts between 10,000 and 80,000 were retained. Gene expression was normalized, scaled and mitochondrial reads and cell cycle genes were regressed. Cells were clustered based on the top 25-30 prinicipal components.
URD (v1.0.2) was used for trajectory analysis. Seurat matrix was converted to an URD object, cell-to-cell transition probabilities were calculated by setting number of nearest neighbors to 211 and sigma of 8.
Pseudotime was then calculated by running 80 flood simulations with POU5F1+ clusters as the ‘root’ cells. Next, all day 10 clusters were set as ‘tip’ cells and biased random walks were simulated from each tip to build an URD tree.
Genome_build: mm9
Supplementary_files_format_and_content: Processed Seurat expression matrix as a csv file, with columns as cell barcodes and rows as genes

source_name: mouse ES cell derived cardiac myocytes

extract_protocol:
Cells on day 4 and day 10 were singularized using Trypsin 0.25% and 10,000 cells were loaded on a 10X Chromium chip
Chromium Single Cell 3′ GEM, Library & Gel Bead Kit v2 was used to construct libraries

treatment_protocol: mouse ESC lines were differentiated to cardiomyocytes using the Kattman et al 2011 Cardiomyocyte Differentiation protocol. Brg1 was conditionally deleted at D2 by inducing with 4-hydroxytamoxifen and cell were coolected at D4 or D10 for scRNAseq

value: mouse ES cell derived cardiac myocytes

value: Brg1fl/fl;ActinCRE ERT2

tag: timepoint

value: Day 10

value: 4OHT treated


title: Cell from adult ovary follicle, S_9E


title: D10_WT

value: THF treated


title: Targeted methylome capture of HG005 using TruSeq Methyl Capture EPIC [EPIC_HG005_LAB01_REP01]

description: Targeted Bisulfite


title: Cell from adult ovary follicle, S_9H


title: Targeted methylome capture of HG006 using TruSeq Methyl Capture EPIC [EPIC_HG006_LAB01_REP01]

description: Targeted Bisulfite


title: D4_BRG1cKO

source_name: mouse ES cell derived cardiac mesoderm

value: mouse ES cell derived cardiac mesoderm

value: Day 4


title: Tumor-infiltrating BATF-overexpressing Pmel CD8 T cells, 1


title: IP-CD8-rep1

source_name: CD8 cell

value: wild type

value: CD8 cell

value: Anti-m6A antibody ,ab15320, Abcam (0.5 μg per sample)

value: untreated


title: IP-CD8-rep2


title: Targeted methylome capture of HG005 using TruSeq Methyl Capture EPIC [EPIC_HG005_LAB01_REP02]

description: Targeted Bisulfite


title: IP-CD4-rep2

source_name: CD4 cell

value: CD4 cell


title: Cell from adult ovary follicle, S_9C

value: Follicular cell


title: D4_WT


title: Cell from adult ovary follicle, S_9G


title: Targeted methylome capture of HG006 using TruSeq Methyl Capture EPIC [EPIC_HG006_LAB01_REP02]

description: Targeted Bisulfite


title: D10_BrmKO_H3K27me3_ChIP_rep2

description: input sample: D10_BrmKO_Input_rep2

data_processing:
Libraries were sequenced on Illumina NextSeq 500 system
Raw sequencing reads were converted to FASTQ files using bcl2fastq
Reads were aligned to mm9  using Bowtie
Genome_build: mm9
Supplementary_files_format_and_content: bigwig

extract_protocol:
Cells were lysed, lysates were clarified and incubated with anti-H3K27ac or anti-H3K27me3 antibodies for O/N, captured with IgG coated magnetic beads, washed, and ChIPed DNA eluted. Protein-DNA complexes were reverse crosslinked, proteinase digested and ampure bead purified
To prepare libraries DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (3 to 5 exo minus) and dATP  and ligated of Illumina adapters. Adapter ligated DNA was PCR amplified with Illumina primers for 14 cycles and library fragments of 200 - 500bp bp were band isolated from an agarose e-gel (invitrogen).  The purified libraries were quantified, and libraries were pooled before sequencing on Illumina NextSeq 500 system

treatment_protocol: mouse ESC lines were differentiated to cardiomyocytes using the Kattman et al 2011 Cardiomyocyte Differentiation protocol.

value: Brg1-3xFLAG; BRM::Puro


title: Cell from adult ovary follicle, S_9B


title: Cell from adult ovary follicle, S_88_7C


title: IP-CD4-rep1

data_processing:
fastp/trimmomatic trimming raw fastq files
kallisto mapping to GRCm38 cDNA sequences
SLAM-seq mapping NextGenMap
Genome_build: GRCm38
Supplementary_files_format_and_content: normalized gene counts or raw gene counts:
Sample-IP-gene-counts-16cell_types.tsv (raw counts)
normalized-Sample-input-counts-gene-16cell_type.tsv (normalized counts)
Mettl3-normalized-gene-counts-input.tsv (normalized counts)
Mettl3-gene-counts-IP.tsv (raw counts)
Igf2bp2-LT.HSC-gene-counts.tsv (raw counts)
RNA-Ratio-T2C-6cell_type.tsv (T>C transition ratio)
RNA-T2C-ratio-average-LT.HSC.tsv (T>C transition ratio)
RNA-T2C-ratio-average-MkP.tsv (T>C transition ratio)

extract_protocol:
Total RNA was isolated using Tirzol reagent (Takara). Anti-m6A antibody (0.5 μg per sample) (ab15320, Abcam) was pre-bound to Protein A magnetic beads (Thermo Fisher Scientific) in IP buffer (10mM Tris-HCl pH 7.4, 100mM NaCl,0.1% NP40, , 0.4 U/μl RNasin) with head-to-tail mixing at 4 °C for 2 h. Total RNA (100 ng per sample) was added and incubated at 4°C for another 2 h. Beads were washed twice with 200 μl IP buffer, twice with 200 μl low-salt buffer (10mM Tris-HCl pH 7.4, 50 mM NaCl, 0.1% NP-40, 0.4 U/μl RNasin), twice with 200 μl high-salt buffer (10mM Tris-HCl pH 7.4, 500mM NaCl, 0.1% NP40, 0.4 U/μl RNasin) and once with 200 μl 1× IP buffer.
RNA libraries were prepared for sequencing using standard Illumina protocols


title: Cell from adult ovary follicle, S_9A


title: Cell from adult ovary follicle, S_88_7A


title: Cell from adult ovary follicle, S_88_7D


title: Targeted methylome capture of HG007 using TruSeq Methyl Capture EPIC [EPIC_HG007_LAB01_REP01]

description: Targeted Bisulfite


title: input-ST.HSC-rep1

description: normalized-Sample-input-counts-gene-16cell_type.tsv


title: D10_BrmKO_H3K27me3_ChIP_rep1

description: input sample: D10_BrmKO_Input_rep1


title: D10_WT_H3K27me3_ChIP_rep2

description: input sample: D10_WT_Input_rep2


title: D6_BrmKO_H3K27me3_ChIP_rep2

description: input sample: D6_BrmKO_Input_rep2

value: mouse ES cell derived cardiac precursors

value: Day 6


title: Methylome capture of HG001 using Accel-NGS Methyl-Seq [MethylSeq_HG001_LAB01_REP01]

description: Whole Genome Bisulfite

extract_protocol:
Swift Biosciences Accel-NGS Methyl-Seq
DNA (gDNA) was purchased from the Coriell Institute for Medical Research


title: Targeted methylome capture of HG007 using TruSeq Methyl Capture EPIC [EPIC_HG007_LAB01_REP02]

description: Targeted Bisulfite


title: IP-B_cell-rep2


title: IP-B_cell-rep1


title: Cell from adult ovary follicle, S_88_7H


title: D10_WT_H3K27me3_ChIP_rep1

description: input sample: D10_WT_Input_rep1


title: input-ST.HSC-rep2


title: Methylome capture of HG001 using Accel-NGS Methyl-Seq [MethylSeq_HG001_LAB01_REP02]

description: Whole Genome Bisulfite


title: Cell from adult ovary follicle, S_88_7B


title: Methylome capture of HG002 using Accel-NGS Methyl-Seq [MethylSeq_HG002_LAB01_REP01]

description: Whole Genome Bisulfite


title: D6_WT_H3K27me3_ChIP_rep1

description: input sample: D6_WT_Input_rep1


title: input-MPP-rep2

source_name: MPP

value: MPP


title: input-Neutrophil-rep2

value: Neutrophil


title: D6_BrmKO_H3K27me3_ChIP_rep1

description: input sample: D6_BrmKO_Input_rep1


title: input-MPP-rep1


title: Methylome capture of HG002 using Accel-NGS Methyl-Seq [MethylSeq_HG002_LAB01_REP02]

description: Whole Genome Bisulfite


title: D6_WT_H3K27me3_ChIP_rep2

description: input sample: D6_WT_Input_rep2


title: input-Neutrophil-rep1


title: Cell from adult ovary follicle, S_88_7F

source_name: Adult ovary follicle


title: Cell from adult ovary follicle, S_5F


title: Cell from adult ovary follicle, S_88_7G


title: D4_BrmKO_H3K27me3_ChIP_rep2

description: input sample: D4_BrmKO_Input_rep2


title: Methylome capture of HG003 using Accel-NGS Methyl-Seq [MethylSeq_HG003_LAB01_REP02]

description: Whole Genome Bisulfite


title: Cell from adult ovary follicle, S_88_7E


title: Cell from adult ovary follicle, S_5D


title: Methylome capture of HG005 using Accel-NGS Methyl-Seq [MethylSeq_HG005_LAB01_REP01]

description: Whole Genome Bisulfite


title: Cell from adult ovary follicle, S_5G


title: Methylome capture of HG003 using Accel-NGS Methyl-Seq [MethylSeq_HG003_LAB01_REP01]

description: Whole Genome Bisulfite


title: D4_BrmKO_H3K27me3_ChIP_rep1

description: input sample: D4_BrmKO_Input_rep1


title: Methylome capture of HG005 using Accel-NGS Methyl-Seq [MethylSeq_HG005_LAB01_REP02]

description: Whole Genome Bisulfite


title: D4_WT_H3K27me3_ChIP_rep2

description: input sample: D4_WT_Input_rep2


title: Methylome capture of HG004 using Accel-NGS Methyl-Seq [MethylSeq_HG004_LAB01_REP01]

description: Whole Genome Bisulfite


title: D10_BrmKO_Input_rep2

value: mouse ES cell derived cardiac myocytes


title: Cell from adult ovary follicle, S_5H

value: Oocyte


title: input-Monocyte-rep2

value: Monocyte


title: input-MEP-rep1

source_name: MEP

value: MEP


title: input-Monocyte-rep1


title: input-MkP-rep2

source_name: MkP

value: MkP


title: Methylome capture of HG006 using Accel-NGS Methyl-Seq [MethylSeq_HG006_LAB01_REP01]

description: Whole Genome Bisulfite


title: input-MkP-rep1


title: input-MEP-rep2


title: D10_BrmKO_H3K27Ac_ChIP_rep2

description: input sample: D10_BrmKO_Input_rep2

value: Day 10


title: D4_WT_H3K27me3_ChIP_rep1

description: input sample: D4_WT_Input_rep1

value: mouse ES cell derived cardiac mesoderm

value: Day 4


title: input-LT.HSC-rep2

value: wild type


title: Cell from adult ovary follicle, S_5E


title: D10_WT_Input_rep2


title: D10_WT_H3K27Ac_ChIP_rep2

description: input sample: D10_WT_Input_rep2


title: D10_BrmKO_Input_rep1


title: Methylome capture of HG004 using Accel-NGS Methyl-Seq [MethylSeq_HG004_LAB01_REP02]

description: Whole Genome Bisulfite


title: Methylome capture of HG006 using Accel-NGS Methyl-Seq [MethylSeq_HG006_LAB01_REP02]

description: Whole Genome Bisulfite


title: input-LMPP-rep2

value: LMPP

value: untreated


title: input-LT.HSC-rep1


title: Cell from adult ovary follicle, S_88_1B

value: Follicular cell


title: Methylome capture of HG007 using Accel-NGS Methyl-Seq [MethylSeq_HG007_LAB01_REP02]

description: Whole Genome Bisulfite


title: Methylome capture of HG001 using SPlinted Ligation Adapter Tagging (SPLAT) [SPLAT_HG001_LAB01_REP01]

description: Whole Genome Bisulfite

extract_protocol:
SPlinted Ligation Adapter Tagging (SPLAT)
DNA (gDNA) was purchased from the Coriell Institute for Medical Research


title: Methylome capture of HG001 using SPlinted Ligation Adapter Tagging (SPLAT) [SPLAT_HG001_LAB01_REP02]

description: Whole Genome Bisulfite


title: Cell from adult ovary follicle, S_5B

extract_protocol:
For single-cell RNA-sequencing, the small antral follicles (1-8 mm) were collected in saline solution (0.9% NaCl, Fresenius Kabi, Bad Homburg, Germany). The follicles were mechanically ruptured with tungsten needles and the region with the cumulus GCs and oocyte was trimmed and transferred into a clean dish. Individual follicular cells were manually picked up using a pulled glass-capillary under a stereo microscope (Zeiss). Oocytes were denuded by pipetting up and down. None of the collected oocytes contained a polar body. Each cell was transferred into a cold PCR tube contain 1.9 ml 0.2% TritonX-100 in DEPC water and 0.1 ml Recombinant RNase inhibitor (2313A, 40U/ml, TaKaRa), snap-frozen on dry ice and stored at -80°C.
Sequencing libraries were prepared according to the user guide of the Nextera XT (illumina)


title: Methylome capture of HG007 using Accel-NGS Methyl-Seq [MethylSeq_HG007_LAB01_REP01]

description: Whole Genome Bisulfite


title: Methylome capture of HG002 using SPlinted Ligation Adapter Tagging (SPLAT) [SPLAT_HG002_LAB01_REP01]

description: Whole Genome Bisulfite


title: Cell from adult ovary follicle, S_5C


title: Cell from adult ovary follicle, S_88_4H


title: D6_BrmKO_Input_rep2

value: Brg1-3xFLAG; BRM::Puro


title: Methylome capture of HG002 using SPlinted Ligation Adapter Tagging (SPLAT) [SPLAT_HG002_LAB01_REP02]

description: Whole Genome Bisulfite


title: Cell from adult ovary follicle, S_5A


title: D10_BrmKO_H3K27Ac_ChIP_rep1

description: input sample: D10_BrmKO_Input_rep1


title: Cell from adult ovary follicle, S_88_1C


title: input-GMP-rep2

source_name: GMP

value: GMP


title: input-GMP-rep1


title: input-LMPP-rep1


title: Cell from adult ovary follicle, S_88_4B


title: Methylome capture of HG003 using SPlinted Ligation Adapter Tagging (SPLAT) [SPLAT_HG003_LAB01_REP02]

description: Whole Genome Bisulfite


title: D6_BrmKO_Input_rep1

value: mouse ES cell derived cardiac precursors

value: Day 6


title: D10_WT_Input_rep1


title: input-DC-rep2

value: DC


title: D6_BrmKO_H3K27Ac_ChIP_rep1

description: input sample: D6_BrmKO_Input_rep1


title: Cell from adult ovary follicle, S_88_4C


title: D6_WT_Input_rep2


title: Cell from adult ovary follicle, S_88_4D


title: Cell from adult ovary follicle, S_88_4E


title: Methylome capture of HG004 using SPlinted Ligation Adapter Tagging (SPLAT) [SPLAT_HG004_LAB01_REP02]

description: Whole Genome Bisulfite


title: Methylome capture of HG005 using SPlinted Ligation Adapter Tagging (SPLAT) [SPLAT_HG005_LAB01_REP01]

description: Whole Genome Bisulfite


title: D6_BrmKO_H3K27Ac_ChIP_rep2

description: input sample: D6_BrmKO_Input_rep2


title: input-CMP-rep2

source_name: CMP

value: CMP


title: input-Erythroid-rep1

value: Erythroid


title: Cell from adult ovary follicle, S_88_1A


title: input-DC-rep1


title: Methylome capture of HG003 using SPlinted Ligation Adapter Tagging (SPLAT) [SPLAT_HG003_LAB01_REP01]

description: Whole Genome Bisulfite


title: D10_WT_H3K27Ac_ChIP_rep1

description: input sample: D10_WT_Input_rep1

value: mouse ES cell derived cardiac myocytes


title: Methylome capture of HG004 using SPlinted Ligation Adapter Tagging (SPLAT) [SPLAT_HG004_LAB01_REP01]

description: Whole Genome Bisulfite


title: D4_BrmKO_Input_rep2


title: input-Erythroid-rep2


title: Cell from adult ovary follicle, S_88_1G


title: Methylome capture of HG006 using SPlinted Ligation Adapter Tagging (SPLAT) [SPLAT_HG006_LAB01_REP02]

description: Whole Genome Bisulfite


title: Cell from adult ovary follicle, S_88_1E


title: D6_WT_H3K27Ac_ChIP_rep2

description: input sample: D6_WT_Input_rep2


title: D4_BrmKO_Input_rep1


title: Methylome capture of HG006 using SPlinted Ligation Adapter Tagging (SPLAT) [SPLAT_HG006_LAB01_REP01]

description: Whole Genome Bisulfite


title: input-CLP-rep2

value: CLP


title: input-CD8-rep1

value: CD8 cell


title: D6_WT_Input_rep1


title: input-CMP-rep1


title: Methylome capture of HG007 using SPlinted Ligation Adapter Tagging (SPLAT) [SPLAT_HG007_LAB01_REP02]

description: Whole Genome Bisulfite


title: Cell from adult ovary follicle, S_88_4A


title: input-CLP-rep1


title: D6_WT_H3K27Ac_ChIP_rep1

description: input sample: D6_WT_Input_rep1


title: Methylome capture of HG007 using SPlinted Ligation Adapter Tagging (SPLAT) [SPLAT_HG007_LAB01_REP01]

description: Whole Genome Bisulfite


title: Cell from adult ovary follicle, S_88_1H

value: Oocyte


title: D4_BrmKO_H3K27Ac_ChIP_rep2

description: input sample: D4_BrmKO_Input_rep2

value: mouse ES cell derived cardiac mesoderm


title: Cell from adult ovary follicle, S_88_4F


title: D4_BrmKO_H3K27Ac_ChIP_rep1

description: input sample: D4_BrmKO_Input_rep1

value: Day 4


title: input-CD8-rep2

value: wild type


title: Methylome capture of HG005 using SPlinted Ligation Adapter Tagging (SPLAT) [SPLAT_HG005_LAB01_REP02]

description: Whole Genome Bisulfite


title: Cell from adult ovary follicle, S_88_1D


title: Cell from adult ovary follicle, S_88_1F


title: Cell from adult ovary follicle, S_88_4G


title: D4_WT_Input_rep1


title: Methylome capture of HG001 using TruSeq [TruSeq_HG001_LAB01_REP02]

description: Whole Genome Bisulfite

extract_protocol:
Illumina TruSeq DNA Methylation
DNA (gDNA) was purchased from the Coriell Institute for Medical Research


title: Methylome capture of HG001 using TruSeq [TruSeq_HG001_LAB01_REP01]

description: Whole Genome Bisulfite


title: input-CD4-rep2

value: CD4 cell


title: Methylome capture of HG002 using TruSeq [TruSeq_HG002_LAB01_REP01]

description: Whole Genome Bisulfite


title: input-B_cell-rep2

value: untreated


title: D4_WT_Input_rep2


title: Cell from adult ovary follicle, S_4H

value: Follicular cell


title: D10_highSDS_FLAG_65C_eluted_ChIP-Seq

data_processing:
Libraries were sequenced on Illumina Novaseq
Raw sequencing reads were converted to FASTQ files using bcl2fastq
Reads were aligned to mm9  using Bowtie2
Genome_build: mm9
Supplementary_files_format_and_content: bigwig

extract_protocol:
Cells were lysed, lysates were clarified and incubated with anti-FLAG antibody(Sigma, F1806) for O/N, captured with IgG coated magnetic beads, washed, and ChIPed DNA eluted. Protein-DNA complexes were reverse crosslinked, proteinase digested and ampure bead purified
To prepare libraries DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (3 to 5 exo minus) and dATP  and ligated of Illumina adapters. Adapter ligated DNA was PCR amplified with Illumina primers for 14 cycles and library fragments of 200 - 500bp bp were band isolated from an agarose e-gel (invitrogen).  The purified libraries were quantified, and libraries were pooled before sequencing on Illumina NextSeq 500 system

value: Day 10


title: input-B_cell-rep1


title: Methylome capture of HG002 using TruSeq [TruSeq_HG002_LAB01_REP02]

description: Whole Genome Bisulfite


title: D4_WT_H3K27Ac_ChIP_rep2

description: input sample: D4_WT_Input_rep2


title: Cell from adult ovary follicle, S_4D


title: D4_WT_H3K27Ac_ChIP_rep1

description: input sample: D4_WT_Input_rep1