title: KD5 RNA-Seq

city: Pozuelo de Alarcón (Madrid)

first: Daniel

last: Conde

address: Parque Científico y Tecnológico de la U.P.M. Campus de Montegancedo 28223

institute: Centre for Plant Biotechnology and Genomics U.P.M. – I.N.I.A

data_processing:
Pre-processing and assembly of sequence data were conducted using the web-based platform Galaxy at https://usegalaxy.org/which includes tools to remove reads containing N blurs, adapter sequences, and sequences shorter than 15 nucleotides. Quality control of reads was carried out with the FastQC Galaxy tool
Removal of rRNA, if needed, was performed locally with the SortMeRNA tool. The TopHat Galaxy tool was used to map clean reads to the Populus tremula x P. alba INRA clone 717-1B4 genome using the default settings
We used the summarizeOverlaps function (packages GenomicAligments of R) to generate the matrix of read counts for each gene from BAM files
Differentially expressed gene (DEG) lists for KD lines versus WT were obtained using the function exactTest (edgeR package of R)
Genome_build: Populus tremula x P. alba INRA clone 717-1B4 (http://aspendb.uga.edu/s717)
Supplementary_files_format_and_content: "raw_counts.xlsx" with matrix or reads counts in poplar genes and "Dataset S1.xlsx" with log2FC of differentially expressed genes in KD lines in comparisson to WT

organism: Populus tremula x Populus alba

source_name: apices

extract_protocol:
Libraries were prepared using 1 µg of RNA in the NEBNext® Ultra™ Directional RNA Library Prep Kit following the supplier's instructions (New England Biolabs, Ipswich, MA, USA)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: clone

value: INRA clone 717-1B4

value: apices

value: PtaDML10 RNAi


title: KD5 Bisulfite-Seq

status: Public on Mar 08 2018

type: SRA

country: Spain

description: DEG_with_hyperDMR_KDvsWT_promotor/DEG_with_hyperDMR_KDvsWT_transcribed_region

library_source: genomic

data_processing:
The Galaxy platform of the University of Perpignan server was used to performe the quality control of reads and to obtained the read alignment against the Populus tremula x alba INRA clone 717-1B4 genome using Bismark mapper (Krueger and Andrews 2011). Before mapping the last nucleotide of all reads was trimmed because its relative lower quality in sequencing (<28). To identify differentially methylated regions (DMR) in KD2 vs. WT and KD5 vs. WT, the methylkit (Akalin et al. 2012) package of R was used (R studio software in the University of Perpignan server). We calculated the methylation status using a minimum coverture of 10 for cytosines in the sequencing. R was used to identify DMR located in promoter or transcribed region.
Genome_build: Populus tremula x P. alba INRA clone 717-1B4 (http://aspendb.uga.edu/s717)
Supplementary_files_format_and_content: peak

molecule: genomic DNA

extract_protocol:
Genomic DNA was purified from poplar samples using a published method (Causevic et al. 2005; Gourcilleau et al. 2010) employing RNase A digestion, Isopropanol/chloroform extraction, and ethanol precipitation.
Library construction and bisulfite sequencing were performed by Fasteris Company (Switzerland). Having passed quality control, the library is sequenced on Illumina HiSeq 2500.

tag: cell type


title: KD2 RNA-Seq

library_source: transcriptomic

molecule: total RNA

tag: tissue

tag: genotype


title: WT RNA-Seq

value: wild type


title: sperm2A

city: Wuhan

first: Yang

last: Zhou

state: Hubei

address: Shizishanjie #1

department: College of animal science

country: China

institute: Huazhong Agricultural University

description: different lane for sperm2A whole genome bisufite sequencing

data_processing:
Programs FastQC (0.11.2) and Trim Galore (0.4.0) were used to generate sequence quality reports and to trim/filter the sequences, respectively.
The cleaned data for each sample were merged and aligned to the reference genome (Bos taurus UMD3.1) using bowtie2 under the Bismark software (0.14.5)
The methylcytosine information was extracted using the bismark_methylation_extractor after deduplicating the duplication reads.
Genome_build: UMD3.1
Supplementary_files_format_and_content: The data files contain the methylatin information for the CG detected. The column names are: chrmosome, position, position (same as the second column), methylation level, coverage for methylated cytosine, coverage for unmethylated cytosine, total coverage

organism: Bos taurus

source_name: sperm

extract_protocol:
Genomic DNA was isolated according to the QIAamp DNA Mini Kit protocol (QIAGEN, Valencia, CA, USA).
The qualified genomic DNA from somatic tissues and sperm were used to construct libraries. Briefly, 3 μg of genomic DNA spiked with unmethylated lambda DNA were fragmented into 200-300 bp using a Covaris S220 (Covaris, Inc., Woburn, MA, USA), followed by teriminal repairing and A-ligation. Different cytosine methylated barcodes were ligated to sonicated DNA for different samples. The DNA bisufite conversion was performed using the EZ DNA Methylation Gold Kit (Zymo Research, Irvine, CA, USA). Then single-stranded DNA fragments were amplified using the KAPA HiFi HotStart Uracil + ReadyMix (2 X) (Kapa Biosystems, Wilmington, MA, USA). The library concentration was quantified using a Qubit 2.0 fluorometer (Life Technologies, Carlsbad, CA, USA) and qPCR (iCycler, BioRad Laboratories, Hercules, CA, USA), and the insert size was checked using the Agilent 2100.

value: sperm

tag: breed

value: Holstein

tag: developmental stage

value: adult


title: KD2 Bisulfite-Seq


title: WT Bisulfite-Seq


title: sperm1A

description: different lane for sperm1A whole genome bisufite sequencing


title: Young1

status: Public on Mar 07 2018

city: Shanghai

first: Jie

last: Yin

address: 320 Yueyang Road

institute: Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences

data_processing:
Illumina HiSeq 3000 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using using Tophat2 (version 2.0.10) with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Differentially expressed genes were detected using Cuffdiff (version 2.1.1) against RefSeq genes
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Mus musculus

source_name: muscle

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

tag: strain

value: muscle

tag: age

value: 3 month


title: Young2


title: Old1

value: 20 month


title: sperm1B

description: different lane for sperm1B whole genome bisufite sequencing


title: WBC3886

description: different lane for WBC3886 whole genome bisufite sequencing

source_name: blood

value: blood


title: SH cecum mirna

city: Tai’an

first: Chao

last: Tianle

state: Shandong

address: Daizong street, no. 61, 6/5000 Shandong Agricultural University

institute: 6/5000 Shandong Agricultural University

data_processing:
Raw sequencing image data were converted to raw reads via base calling. The following reads were removed: low-quality reads, reads with contaminated 5'-adapters, reads lacking 3'-adapters, reads lacking an insertion sequence, reads containing polyA sequences, and small fragments (<18 nt).
The clean reads were mapped to the genome of O. aries (assembly Oar_v4.0) using Bowtie software, and compared with known sheep precursor and mature miRNAs in the miRBase21.0 database using BLAST.
The reads that were not matched in the databases but were matched to the antisense strand of exons, introns, and intergenic regions in the genome were used to predict novel miRNAs with miRDeep.
Genome_build: Oar_v4.0
Supplementary_files_format_and_content: tab-delimited text files include read count values for known and novel miRNAs

organism: Ovis aries

source_name: cecum

extract_protocol:
The total RNA was extracted using Trizol reagent and the RNA of different fragment size was separated using PAGE. Illumina TruSeq samll RNA Sample Prep Kit (Cat#RS-200-0012) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Small tailed Han sheep

tag: intestinal region

value: cecum

value: intestinal mucosal epithelial tissue


title: SH colon mirna

source_name: colon

value: colon


title: Old2


title: LPS-SGA RNAseq rep2

city: Univeristy Park

first: Gary

middle: H

last: Perdew

state: PA

address: 309A Life Sciences Building

country: USA

institute: The Pennsylvania State University

data_processing:
RNAseq reads were aligned to the mouse genome (mm10) using TopHat version 2.0.13 with default parameters
Reads mapping to genes were counted using HTseq-count version 0.5.4p3 with parameters ‘-s no -a 10’
Genome_build: mm10 mouse genome
Supplementary_files_format_and_content: tag counts (output of the HTseq-count tool) are given for each gene

source_name: peritoenal macrophages

growth_protocol: Wild-type male mice of the C57BL6/J strain were used for all experiments, with adults ranging in age from 6 to 8 weeks.

extract_protocol:
Total RNA from cultured primary macrophages were extracted with trizol. RNAseq libraries were made from polyA enriched toRNA.
Libraries were preapred as described in the Illumina RNAseq cloning kit

treatment_protocol: Cells were pre-treated with 10 uM SGA360 for 1 h, then with 10 ng/ml LPS for 4 h. Cells were harvested at the end of treatment.

tag: expression

value: endogenous

value: C57BL6/J wild-type

tag: treatment

value: 10 µM SGA360 1 h, 10 ng/ml LPS 4 h


title: WBC3842

description: different lane for WBC3842 whole genome bisufite sequencing


title: MAM3886

description: different lane for MAM3886 whole genome bisufite sequencing

source_name: mammary gland

value: mammary gland


title: RRBS_AOS-14_E-n

first: Weisheng

last: Zheng

address: Siping Road, No.1239

department: Department of Bioinformatics

institute: Tongji University

data_processing:
RRBS reads were mapped to mouse mm10 genome by bsmap with parameters: -D C-CGG -s 12 -v 5 -R.
The methylation ratio of each detected CpG site was caculated by mcall from MOABS toolkits.
Genome_build: mm10
Supplementary_files_format_and_content: The processed data file is a bed format file for detected CpG sites methylation ratios.

source_name: mouse haploid embryonic stem cells

growth_protocol: Mouse haploid embryonic stem cells were derived and constructed from mouse AG-haploid embryos by FACS and then cultured in ES cultrure medium.

extract_protocol:
DNA was extracted by PureLink Genomic DNA Mini Kit, then quantified by Nanodrop 2000c and Qubit(Thermo Scientific) according to the manufactor's instruction.
Library preparation was performed with SureSelect Mouse Methyl-Seq Reagent Kit(Agilent Technologies), which could enrich about 100 Mb of mouse genomic regions including CpG island, promoters, Dnase I hypersensitive sites and tissue-specific DMRs. DNA was bisulfite-treated using EZ DNA Methylation-Gold Kit. Sequencing libries were assessed by Bioanalyzer and quantified with KAPA Library Quantification Kits. The libraries were then sequenced on HiSeq 2500 (2X50 bp paired-end reads)

tag: strain background

tag: cell line

value: mouse haploid embryonic stem cells


title: ESC_NKO_CHi-C_Lane3097

city: Cambridge

first: Steven

middle: William

last: Wingett

state: Cambs

address: Francis Crick Avenue, Cambridge Biomedical Campus

department: Cell Biology

country: United Kingdom

institute: MRC Laboratory of Molecular Biology

description:
ESC_NKO_merge_step2_seqmonk.txt.gz
Gene_assignment.xlsx
ROSE_SE.xlsx

data_processing:
Standard Illumina Sequencing Pipeline
Hi-C Processing: HiCUP (Wingett S, Ewels P, Furlan-Magaril M et al. HiCUP: pipeline for mapping and processing Hi-C data (doi: 10.12688) (V0.5.3) with Bowtie (V1.1.0) as the aligner.
Promoter capture interaction calling: CHiCAGO pipeline (Cairns et al., 2016, CHiCAGO: robust detection of DNA looping interactions in Capture Hi-C data', Genome Biol, 17: 127.
ChIP-seq FASTQ files mapped with Bowtie
ChIP-seq peak calls using MACS software
Genome_build: GRCm38/mm10

source_name: embryonic stem cells

growth_protocol: E14Tg2a (129P2/OlaHsd) and RCNβH-B(t) (E14Tg2a-derived Nanog–/–, passages 20-30) ESCs were cultured on gelatin-coated surfaces in standard ESC media (DMEM supplemented with 15% FBS, 1mM sodium pyruvate, 0.1mM 2-mercaptoethanol, 0.1mM non-essential amino acids, 2mM glutamax and 1000 U/ml LIF), and 25µg/ml hygromycin was added during RCNβH-B(t) ESC expansion to select for Nanog–/– cells. Embryo-derived 129S2 (Brons et al. 2007) EpiSC were cultured on fibronectin (10µg/ml) in N2B27 media supplemented with 20ng/ml Activin A and 12ng/ml bFGF.

extract_protocol:
Promoter Capture Hi-C was carried out with SureSelect target enrichment, using a custom-designed biotinylated RNA bait library for mouse promoters and custom paired-end blockers according to the manufacturer’s instructions (Agilent Technologies) (Schoenfelder et al . 2015 The pluripotent regulatory circuitry connecting promoters to their long-range interacting elements, Genome Res, 25: 582-97) and following the protocol detailed in (Nagano et al. 2015 Comparison of Hi-C results using in-solution versus in-nucleus ligation, Genome Biol, 16: 175).     ChIP-seq in EpiSCs was performed according to Schoenfelder et al. 2015, Polycomb repressive complex PRC1 spatially constrains the mouse embryonic stem cell genome, Nat Genet, 47: 1179-86. Cells were fixed in ChIP fixation buffer (1% formaldehyde, 5 μM EGTA, 10 μM EDTA, 1 mM NaCl and 0.5 mM HEPES in PBS) for 10 min at room temperature. Fixation was stopped by the addition of glycine (final concentration of 125 mM). Cells were washed with PBS, buffer A (10 mM HEPES, pH 7.5, 10 mM EDTA, 0.5 mM EGTA and 0.75% Triton X-100) and buffer B (10 mM HEPES, pH 7.5, 200 mM NaCl, 1 mM EDTA and 0.5 mM EGTA). Cells were lysed in lysis buffer (25 mM Tris, pH 7.5, 150 mM NaCl, 5 mM EDTA, 0.1% Triton X-100, 1% SDS, 0.5% deoxycholate and Complete protease inhibitor (Roche)) for 30 min on ice. Sonication was performed using a Biorupter sonicator (Diagenode) to obtain an average DNA fragment size of 300 bp.
Promoter Capture Hi-C was carried out with SureSelect target enrichment, using a custom-designed biotinylated RNA bait library for mouse promoters and custom paired-end blockers according to the manufacturer’s instructions (Agilent Technologies) (Schoenfelder et al . 2015 The pluripotent regulatory circuitry connecting promoters to their long-range interacting elements, Genome Res, 25: 582-97) and following the protocol detailed in (Nagano et al. 2015 Comparison of Hi-C results using in-solution versus in-nucleus ligation, Genome Biol, 16: 175).     ChIP-seq libraries were prepared using the NEBNext DNA Library Preparation kit, following the manufacturer's instructions.  Chromatin was diluted with ChIP dilution buffer (25 mM Tris, pH 7.5, 150 mM NaCl, 5 mM EDTA, 1% Triton X-100, 0.1% SDS, 0.5% deoxycholate and Complete protease inhibitor). Dynabeads Protein G beads (Life Technologies) were blocked for 1 h at 4 °C with 1 mg/ml BSA and 1 mg/ml yeast tRNA (Life Technologies). For each immunoprecipitation, 150 μg of chromatin and 5 μg of antibody were used. Chromatin was precleared with the blocked beads for 1 h at 4 °C. Chromatin was then incubated with antibody overnight at 4 °C with rotation. Protein-antibody complexes were precipitated by the addition of beads for 2 h. Complexes were washed twice with wash buffer A (50 mM Tris, pH 8.0, 150 mM NaCl, 0.1% SDS, 0.5% deoxycholate, 1% NP-40 and 1 mM EDTA), once with wash buffer B (50 mM Tris, pH 8.0, 500 mM NaCl, 0.1% SDS, 0.5% deoxycholate, 1% NP-40 and 1 mM EDTA), once with wash buffer C (50 mM Tris, pH 8.0, 250 mM lithium chloride, 0.5% deoxycholate, 1% NP-40 and 1 mM EDTA) and once with TE. Samples were treated with RNase A and proteinase K, and cross-links were reversed overnight. DNA was purified using a ChIP DNA clean and concentrator column (Zymo Research). Libraries were prepared using the NEB Next Fast DNA Fragmentation and Library Preparation set for the Ion Torrent kit (E6285S), following the manufacturer's instructions. Briefly, 40 ng of ChIP or input DNA was used for library generation. Libraries were size selected for 250-bp fragments using 2% E-gel Size Select agarose gels (Life Technologies) and were amplified with five PCR cycles. Libraries were sequenced on the Ion Proton Sequencer using Ion PI Chip v2 (Life Technologies). Templates were generated using Ion PI Template OT2 200 kit v3 and Ion PI Sequencing 200 kit v3 or the Ion PI IC 200 kit (Life Technologies).

value: embryonic stem cells

value: NANOG knockout


title: ESC_NKO_CHi-C_Lane2769


title: ESC_NKO_CHi-C_Lane1643


title: ESC_CHi-C_Lane3095

description:
ESC_complete_merge_step2_seqmonk.txt.gz
Gene_assignment.xlsx
ROSE_SE.xlsx

value: wild type


title: ESC_CHi-C_Lane3103


title: ESC_CHi-C_Lane2317


title: EpiSC_CHi-C_Lane2049

description:
EpiSC_merge_step2_seqmonk.txt.gz
Gene_assignment.xlsx
ROSE_SE.xlsx

source_name: epiblast-derived stem cells

value: epiblast-derived stem cells


title: EpiSC_CHi-C_Lane2048


title: Tet1-KO Dnmt-TKO mESC RNA-Seq Replicate 2

city: London

first: Peter

last: Hill

address: Kensington

institute: Imperial College London

description:
RNA-Seq of mESCs
mESC_GeneCounts_2.txt

data_processing:
RNA-Seq reads were aligned to the mouse genome (mm9, NCBI build 37) with Bowtie (version 0.12.8) and Tophat (version 2.0.2 with options -N 2 --b2-very-sensitive --b2-L 25. Annotations from Ensembl Gene version 67 were used as gene model with Tophat. Read counts per annotated gene were computed using HTSeq (version 0.5.3p9).
Genome_build: mm9
Supplementary_files_format_and_content: Gene Counts

molecule: polyA RNA

source_name: Tet1-KO Dnmt-TKO mESC

extract_protocol: For study of mESCs, total RNA was isolated using ZR-Duet DNA-RNA MiniPrep kit (Zymo). cDNA synthesis and library prep was performed starting with 500 ng total RNA following manufacturer’s instructions using the NEBNext Ultra Library Prep Kit (NEB) and the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB). All libraries were purified by AMPure XP beads (Beckman-Coulter) and sequenced on the Illumina HiSeq 2500 instrument.

tag: strain (genetic background)

value: J1 129S4/SvJae

value: Tet1-KO Dnmt-TKO

value: mESC


title: J1 mESC RNA-Seq Replicate 2

description:
RNA-Seq of mESCs
mESC_GeneCounts_2.txt

source_name: J1 mESC

value: Wild type


title: Dnmt-TKO mESC RNA-Seq Replicate 1

description:
RNA-Seq of mESCs
mESC_GeneCounts_2.txt

source_name: Dnmt-TKO mESC

value: Dnmt-TKO


title: Dnmt-TKO mESC RNA-Seq Replicate 2

description:
RNA-Seq of mESCs
mESC_GeneCounts_2.txt


title: J1 mESC RNA-Seq Replicate 1

description:
RNA-Seq of mESCs
mESC_GeneCounts_2.txt


title: Tet1-KO Dnmt-TKO mESC RNA-Seq Replicate 1

description:
RNA-Seq of mESCs
mESC_GeneCounts_2.txt


title: Dnmt-TKO mESC + DMSO RNA-Seq Replicate 2

description:
RNA-Seq of mESCs
mESC_GeneCounts_1.txt

source_name: Dnmt-TKO mESC + DMSO

value: DMSO


title: Dnmt-TKO mESC + PRC1 inhibitor RNA-Seq Replicate 2

description:
RNA-Seq of mESCs
mESC_GeneCounts_1.txt

source_name: Dnmt-TKO mESC + PRC1 inhibitor


title: SH duodenum mirna

source_name: duodenum

value: Small tailed Han sheep

value: duodenum

value: intestinal mucosal epithelial tissue


title: Dnmt-TKO mESC + PRC1 inhibitor RNA-Seq Replicate 1

description:
RNA-Seq of mESCs
mESC_GeneCounts_1.txt


title: J1 mESC + PRC1 inhibitor RNA-Seq Replicate 2

description:
RNA-Seq of mESCs
mESC_GeneCounts_1.txt

source_name: J1 mESC + PRC1 inhibitor


title: ESC_NKO_CHi-C_Lane2052


title: RRBS_A129-2_E-n


title: J1 mESC + DMSO RNA-Seq Replicate 1

description:
RNA-Seq of mESCs
mESC_GeneCounts_1.txt

source_name: J1 mESC + DMSO


title: J1 mESC + DMSO RNA-Seq Replicate 2

description:
RNA-Seq of mESCs
mESC_GeneCounts_1.txt


title: J1 mESC + PRC1 inhibitor RNA-Seq Replicate 1

description:
RNA-Seq of mESCs
mESC_GeneCounts_1.txt


title: E14.5 male Tet1-KO PGC RNA-Seq Replicate 1

description:
RNA-Seq of primordial germ cells
processed data file: E10_E12_E14_GeneCounts.txt

data_processing:
For study of Tet1-KO and Tet1-WT PGCs Illumina and Smart-seq adapters from the sequencing reads were first trimmed using Trimmomatic. Trimmomatic produces three fastq output files, one with paired end reads (PE) and two (F and R) with reads whose mate did not pass trimming criteria; PE, F and R fastq files were aligned separately and BAM files were merged at the end. For RNA-Seq libraries derived from PGCs isolated from embryos produced by crossing MF1 females with GOF18ΔPE-EGFP males, fastq files generated from output of next generation sequencing were used directly for alignment. RNA-Seq reads were aligned to the mouse genome (mm9, NCBI build 37) with Bowtie (version 0.12.8) and Tophat (version 2.0.2 with options -N 2 --b2-very-sensitive --b2-L 25. Annotations from Ensembl Gene version 67 were used as gene model with Tophat. Read counts per annotated gene were computed using HTSeq (version 0.5.3p9).
Genome_build: mm9
Supplementary_files_format_and_content: .txt files report gene counts

source_name: E14.5 male Tet1-KO PGC

extract_protocol:
For study of Tet1-KO PGCs, total RNA from sorted PGCs isolated from individual Tet1-KO or wild type embryos was isolated using ZR-Duet DNA-RNA MiniPrep kit (Zymo), and RNA from between two to six embryos (equivalent to 1,000 to 8,000 cells) of the same genotype, stage and sex was pooled and concentrated to 6 µL final volume using the RNA Clean and Concentrator 5 kit (Zymo). For study of wild type PGCs isolated from embryos produced by crossing MF1 females with GOF18ΔPE-EGFP males, total RNA from 600-1,000 sorted E10.5 PGCs was isolated using the Nucleospin RNA XS kit (Macherey-Nagel).
cDNA synthesis and amplification (15 cycles) was performed with the SMARTer Ultra Low Input RNA kit (Clontech) using between 100 pg and 3ng total RNA and following the manufacturer’s instructions. The amplified cDNA was fragmented by a Covaris S2 sonicator (Covaris) and following the manufacturer’s instructions. Sheared cDNA was converted to sequencing libraries using the NEBNext DNA Library Prep kit (NEB), following the manufacturer’s instructions and using 15 cycles of amplification. The libraries were purified by AMPure XP beads (Beckman-Coulter) and sequenced on the Illumina HiSeq 2500 instrument.

tag: genetic background

value: Tet1-het GOF18∆PE-EGFP x Tet1-het GOF18∆PE-EGFP

tag: gender

value: male

value: PGC


title: E14.5 male Tet1-WT PGC RNA-Seq Replicate 1

source_name: E14.5 male Tet1-WT PGC


title: E14.5 male Tet1-KO PGC RNA-Seq Replicate 2


title: E14.5 male Tet1-WT PGC RNA-Seq Replicate 2


title: E14.5 female Tet1-KO PGC RNA-Seq Replicate 2

source_name: E14.5 female Tet1-KO PGC

value: female


title: E14.5 female Tet1-WT PGC RNA-Seq Replicate 2

source_name: E14.5 female Tet1-WT PGC


title: E14.5 female Tet1-WT PGC RNA-Seq Replicate 1


title: E14.5 female Tet1-KO PGC RNA-Seq Replicate 1


title: E10.5 Tet1-WT PGC RNA-Seq Replicate 1

source_name: E10.5 Tet1-WT PGC


title: E10.5 Tet1-WT PGC RNA-Seq Replicate 2


title: E10.5 Tet1-KO PGC RNA-Seq Replicate 1

source_name: E10.5 Tet1-KO PGC


title: Dnmt-TKO mESC + DMSO RNA-Seq Replicate 1

description:
RNA-Seq of mESCs
mESC_GeneCounts_1.txt


title: E14.5 female Tet1-KO PGC RRBS Replicate 2

description: MspI-digested reduced representation bisulphite sequencing of primordial germ cells

data_processing:
Raw RRBS reads were first trimmed using Trim Galore (version 0.3.1, http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) with --rrbs parameter. Alignments were carried out to the mouse genome (mm9, NCBI build 37) with Bismark (version 0.13.0) with the -n 1 parameter. CpG methylation calls were extracted from the mapping output using the Bismark methylation extractor (version 0.13.0) with the –s --comprehensive --merge_non_CpG parameters. The number of methylated and unmethylated cytosines in a CpG context was extracted using bismark2bedGraph (default parameters).
Genome_build: mm9
Supplementary_files_format_and_content: Bismark cov file.  Columns: <chromosome>  <start position>  <end position>  <methylation percentage>  <count methylated> <count unmethylated>

extract_protocol:
Total DNA from FACS-sorted PGCs isolated from individual Tet1-KO or wild type embryos was isolated using ZR-Duet DNA-RNA MiniPrep kit (Zymo), and DNA from between two to six embryos (equivalent to 1,000 to 8,000 cells) of the same genotype, stage and sex was pooled and concentrated to 26 µL final volume using the Savant SpeedVac Concentrator (Thermo) and following the manufacturer’s instructions.
Genomic DNA was digested by 20 units of MspI enzyme (NEB) in NEB buffer 2 at 37°C for 3 hrs, and digested DNA was purified using AMPure XP beads (Beckman-Coulter). Libraries were made following the NEBNext Ultra DNA Library Prep protocol, with the following modifications: 1)  methylated adaptors were diluted 1:10 in nuclease free H2O to a final concentration of 1.5 µM; 2) following adaptor ligation, bisulphite conversion was carried out using the Imprint Modification Kit (Sigma), and following the two step protocol according to the manufacturer’s specifications; and 3) PCR enrichment was carried out for 18 cycles using the KAPA Uracil+ DNA polymerase master mix (KAPA Biosystems) and the NEBNext Library Prep universal and index primers (NEB). The libraries were purified by AMPure XP beads (Beckman-Coulter). Pooled libraries were sequenced on the Illumina HiSeq 2000 instrument.


title: E14.5 male Tet1-WT PGC RRBS Replicate 2


title: E14.5 female Tet1-KO PGC RRBS Replicate 1


title: E14.5 male Tet1-KO PGC RRBS Replicate 2


title: E14.5 male Tet1-KO PGC RRBS Replicate 1


title: E14.5 female Tet1-WT PGC RRBS Replicate 2


title: E14.5 male Tet1-WT PGC RRBS Replicate 1


title: E12.5 male Tet1-KO PGC RRBS Replicate 2

source_name: E12.5 male Tet1-KO PGC


title: E12.5 male Tet1-WT PGC RRBS Replicate 1

source_name: E12.5 male Tet1-WT PGC


title: E12.5 male Tet1-WT PGC RRBS Replicate 2


title: E14.5 female Tet1-WT PGC RRBS Replicate 1


title: E12.5 female Tet1-KO PGC RRBS Replicate 2

source_name: E12.5 female Tet1-KO PGC


title: E12.5 female Tet1-KO PGC RRBS Replicate 1


title: E12.5 female Tet1-WT PGC RRBS Replicate 1

source_name: E12.5 female Tet1-WT PGC


title: E12.5 female Tet1-WT PGC RRBS Replicate 2


title: E12.5 male Tet1-KO PGC RRBS Replicate 1


title: E12.5 male Tet1-KO PGC RNA-Seq Replicate 2


title: E12.5 male Tet1-WT PGC RNA-Seq Replicate 2


title: E12.5 male Tet1-WT PGC RNA-Seq Replicate 1


title: E10.5 Tet1-WT PGC RRBS Replicate 2


title: E10.5 Tet1-WT PGC RRBS Replicate 1


title: E12.5 male Tet1-KO PGC RNA-Seq Replicate 1


title: E12.5 female Tet1-WT PGC RNA-Seq Replicate 1


title: E12.5 female Tet1-WT PGC RNA-Seq Replicate 2


title: E10.5 Tet1-KO PGC RNA-Seq Replicate 2


title: E12.5 female Tet1-KO PGC RNA-Seq Replicate 2


title: E12.5 female Tet1-KO PGC RNA-Seq Replicate 1


title: Ehmt2 wild type DNA methylation

city: Barcelona

first: giovanni

last: iacono

state: Spain

address: Baldiri Reixac, 4

department: single cell sequencing

institute: CNAG,Centro Nacional de Análisis Genómico

data_processing:
FASTQ sequence files generate for BS-seq were aligned to Mus musculus NCBIM37 genome assembly (mm9) using rmapbs-pe (Smith et al., 2009). 5mC level were directly determined using MethPipe (Song et al., 2013).
Genome_build: mm9
Supplementary_files_format_and_content: methylation calls file including 5mC level and coverage

source_name: whole hippocampus

extract_protocol:
DNA was isolated using the Cell Culture DNA Midi Kit from QIAGEN (Cat No 13343) or GenElute™ Mammalian Genomic DNA Miniprep Kit (Cat No G1N350, Sigma).
BS-seq was performed as described previously (Lister et al., 2008).

value: brain

tag: measurement

value: DNA methylation

tag: condition

value: Ehmt2 wild type


title: Ehmt2+/- DNA methylation


title: E10.5 PGC RNA-Seq Replicate 2

description:
RNA-Seq of primordial germ cells
processed data file: E10_MF1_GeneCounts.txt

source_name: E10.5 PGC

value: MF1 x GOF18∆PE-EGFP

tag: cell type


title: E10.5 PGC RNA-Seq Replicate 1


title: Ehmt1+/- DNA methylation

tag: tissue


title: wt_m3

city: Yokohama

first: June-Sik

last: Kim

state: Kanagawa

address: 1-7-22, Suehiro-cho, Tsurumi-ku

country: Japan

institute: RIKEN CSRS

description: the wild-type seedlings treated by the mock condition for 6-hr. repeat 3

data_processing:
Low quality and artificial sequence trimming were achieved by trim_galore (version 0.2.8) with parameters "-f fastq -e 0.1 -q 30 -O 1 -a GCCGTCTTCTGCTTG --paired"
Possible contamination from ribosomal RNA and microbial sources was discarded by helps of SILVA DB (ver. 12.3) and NCBI microorganism concise DB.
The mapping step to the Arabidopsis reference genome was achieved with helps of Tophat software (ver. 2.1.1; Trapnell et al. 2009) with parameters "-r 240 --library-type fr-unstranded --b2-very-sensitive"
The resultant "accepted_hits.bam" file was processed using "samtools view -f 2 -q 4 -b -h" command.
The raw count data collected from the Tophat resultants using htseq-count command from HTSeq (ver. 0.6.0; Anders et al. 2014) with parameters "-m intersection-strict --stranded=no"
Genome_build: Araport11
Supplementary_files_format_and_content: Standard HTSeq output; a tab-delimited text file includes the read count values for each evaluated transcript model.

organism: Arabidopsis thaliana

growth_protocol: The seeds were sterilized and stratified at 4oC for 3 d in the dark, then sown on the a half-strength GM plates. Seedlings were grown in a growth chamber with 16-h fluorescent light time, 22oC, and 65% RH.

extract_protocol:
RNA was extracted from the ground tissues by using RNeasy Plant mini kit (QIAGEN) and Rnase-free Dnase set (QIAGEN). The final product was validated by Agilent Bioanalyzer 2100 (Agilent).
RNA libraries were prepared according to a previous report for the 3'-end sequencing (Townsley et al., 2015).

treatment_protocol: The 12-d-old seedlings were soacked in water containing chemicals for 6-h. The same volume of solvent DMSO was applied as the mock condition. After treatment, whole seedlings were collected and frozen by liquid nitrogen.

value: 12 day-after sowing

value: whole seedling

tag: genotype

value: wild type


title: wt_t3

description: the wild-type seedlings treated by 5 μg ml-1 of tunicamycin for 6-hr. repeat 3


title: wd_d3

description: the wild-type seedlings treated by 2 mM of dithiothreitol for 6-hr. repeat 3


title: wd_d2

description: the wild-type seedlings treated by 2 mM of dithiothreitol for 6-hr. repeat 2


title: wd_d1

description: the wild-type seedlings treated by 2 mM of dithiothreitol for 6-hr. repeat 1


title: wt_t2

description: the wild-type seedlings treated by 5 μg ml-1 of tunicamycin for 6-hr. repeat 2


title: wt_a3

description: the wild-type seedlings treated by 5 mM of azetidine-2-carboxylate for 6-hr. repeat 3


title: wt_a2

description: the wild-type seedlings treated by 5 mM of azetidine-2-carboxylate for 6-hr. repeat 2


title: wt_a1

description: the wild-type seedlings treated by 5 mM of azetidine-2-carboxylate for 6-hr. repeat 1


title: wt_m1

description: the wild-type seedlings treated by the mock condition for 6-hr. repeat 1


title: Ehmt2_F15_wt_k27me3_3T

data_processing:
alignment was done with BWA 0.6.2
read counting was performed with custom C++ script
DEseq2 was used to call the expression changes
Genome_build: mm9

extract_protocol:
Chipping for H3k27me3 (Diagenode A5051-001P) was performed as in http://www.blueprint-epigenome.eu/UserFiles/file/Protocols/Histone_ChIP_July2014.pdf
Library was synthetized with KAPA Hyper prep kit (KK8504) according to manufacturer’s instructions.

tag: antibody


title: F132_wt_k27me3_26T


title: Ehmt1_87H_KO_k27me3_18T


title: Ehmt1_60H_KO_k27me3_31T


title: Ehmt1_73H_KO_k27me3_23T


title: Ehmt1_76H_WT_k27me3_24T

value: Ehmt1 wild type


title: F162_wt_k27me3_21T


title: Ehmt2_F12_wt_k27me3_2T


title: Ehmt1_86H_WT_k27me3_17T


title: c21_t3

description: double knockout seedlings of bZIP17 and bZIP28 treated by 5 μg ml-1 of tunicamycin  for 6-hr. repeat 3


title: Ehmt2_16_ko_k27me3_4T


title: Ehmt1_61H_WT_k27me3_32T


title: Ehmt2_F6_ko_k27me3_1T


title: c21_t2

description: double knockout seedlings of bZIP17 and bZIP28 treated by 5 μg ml-1 of tunicamycin  for 6-hr. repeat 2


title: F161_wt_k27me3_20T


title: wt_t1

description: the wild-type seedlings treated by 5 μg ml-1 of tunicamycin for 6-hr. repeat 1


title: wt_m2

description: the wild-type seedlings treated by the mock condition for 6-hr. repeat 2


title: Ehmt1 wild type DNA methylation


title: Ehmt2_16_ko_k9me2_4D

extract_protocol:
Chipping for H3k9me2 (abcam Ab1220) was performed as in http://www.blueprint-epigenome.eu/UserFiles/file/Protocols/Histone_ChIP_July2014.pdf
Library was synthetized with KAPA Hyper prep kit (KK8504) according to manufacturer’s instructions.


title: Ehmt2_F6_ko_k9me2_1D


title: c21_t1

description: double knockout seedlings of bZIP17 and bZIP28 treated by 5 μg ml-1 of tunicamycin  for 6-hr. repeat 1


title: c21_m3

description: double knockout seedlings of bZIP17 and bZIP28 treated the mock condition for 6-hr. repeat 3


title: c21_m2

description: double knockout seedlings of bZIP17 and bZIP28 treated the mock condition for 6-hr. repeat 2


title: c21_m1

description: double knockout seedlings of bZIP17 and bZIP28 treated the mock condition for 6-hr. repeat 1


title: Ehmt2_F15_wt_k9me2_3D


title: Ehmt1_232_k9me2_ko


title: c18_t3

description: double knockout seedlings of bZIP28 and bZIP60 treated by 5 μg ml-1 of tunicamycin  for 6-hr. repeat 3


title: c18_t2

description: double knockout seedlings of bZIP28 and bZIP60 treated by 5 μg ml-1 of tunicamycin  for 6-hr. repeat 2


title: Ehmt1_221_k9me2_ko


title: Ehmt1_225_k9me2_ko


title: c18_t1

description: double knockout seedlings of bZIP28 and bZIP60 treated by 5 μg ml-1 of tunicamycin  for 6-hr. repeat 1


title: c18_m2

description: double knockout seedlings of bZIP28 and bZIP60 treated the mock condition for 6-hr. repeat 2


title: Ehmt1_223_k9me2_wt


title: Ehmt1_222_k9me2_ko


title: c13_t1

description: double knockout seedlings of S1P and S2P treated by 5 μg ml-1 of tunicamycin  for 6-hr. repeat 1


title: Ehmt1_234_k9me2_wt


title: c13_t3

description: double knockout seedlings of S1P and S2P treated by 5 μg ml-1 of tunicamycin  for 6-hr. repeat 3


title: c18_m1

description: double knockout seedlings of bZIP28 and bZIP60 treated the mock condition for 6-hr. repeat 1


title: F162_wt_k4me1_21O

extract_protocol:
Chipping for H3k4me1 (Diagenode A5051-001P) was performed as in http://www.blueprint-epigenome.eu/UserFiles/file/Protocols/Histone_ChIP_July2014.pdf
Library was synthetized with KAPA Hyper prep kit (KK8504) according to manufacturer’s instructions.


title: Ehmt1_230_k9me2_wt


title: Ehmt1_226_k9me2_wt


title: c13_m2

description: double knockout seedlings of S1P and S2P treated the mock condition for 6-hr. repeat 2


title: F132_wt_k4me1_26O


title: c13_m3

description: double knockout seedlings of S1P and S2P treated the mock condition for 6-hr. repeat 3


title: F161_wt_k4me1_20O


title: c13_m1

description: double knockout seedlings of S1P and S2P treated the mock condition for 6-hr. repeat 1


title: Ehmt2_F6_ko_k4me1_1O


title: c03_t3

description: double knockout seedlings of bZIP17 and bZIP60 treated by 5 μg ml-1 of tunicamycin  for 6-hr. repeat 3


title: Ehmt2_F12_wt_k9me2_2D


title: Ehmt2_F12_wt_k4me1_2O


title: Ehmt2_F2_wt_k4me1_21O


title: Ehmt2_F14_ko_k4me1_22O


title: c03_t1

description: double knockout seedlings of bZIP17 and bZIP60 treated by 5 μg ml-1 of tunicamycin  for 6-hr. repeat 1


title: Ehmt2_F15_wt_k4me1_3O


title: c03_m3

description: double knockout seedlings of bZIP17 and bZIP60 treated the mock condition for 6-hr. repeat 3


title: Ehmt1_87H_KO_k4me1_18O


title: c03_m1

description: double knockout seedlings of bZIP17 and bZIP60 treated the mock condition for 6-hr. repeat 1


title: Ehmt1_76H_WT_k4me1_24O


title: Ehmt1_86H_WT_k4me1_17O


title: Ehmt1_388wt_k4me1


title: Ehmt1_387ko_k4me1


title: c13_t2

description: double knockout seedlings of S1P and S2P treated by 5 μg ml-1 of tunicamycin  for 6-hr. repeat 2


title: c18_m3

description: double knockout seedlings of bZIP28 and bZIP60 treated the mock condition for 6-hr. repeat 3


title: RNA-seq on patient #375 RPCs infected with shRNA #3 against PROM1

city: Groningen

first: Danny

last: Incarnato

state: Netherlands

address: Nijenborgh 7

department: Molecular Genetics

country: Netherlands

institute: University of Groningen

description:
Raw reads were converted to FastQ, and examined using the FastQC tool (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Reads were mapped to the reference human hg19 assembly, using Tophat v2 (parameters: --bowtie1 -a 5).  Processed data file in BEDGraph format were converted to TDF (provided).
P375 shP3

data_processing:
Raw reads were converted to FastQ, and examined using the FastQC tool (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Reads were mapped to the reference human hg19 assembly, using Tophat v2 (parameters: --bowtie1 -a 5). Provided TDF files have been generated using Wiggles and IGVTools.
Genome_build: hg19

organism: Homo sapiens

source_name: Human Renal Progenitor Cells (RPCs)

growth_protocol: CD133+ RPCs were obtained from surgically removed human kidney biopsies (after the approval of ethical committee for the use of human tissue of Molinette Hospital; n. 168/2004), as previously described [13]. In particular, the outer medullary tissue was used. Tissue samples were cut to obtain 3–5mm3 fragments, digested in 0.1% collagenase type I (Sigma-Aldrich) for 30 min at 37°C and subsequently forced through a graded series of meshes for the separation of cell components from stroma and aggregates. The filtrate was then pelleted by centrifugation and cells were resuspended in expansion medium (Endothelial Basal Medium (EBM) plus supplement kit; CambrexBioScience) to be plated at density 1*104 viable cells/cm2. Cells were used until passage  six and maintained their phenotype during the passages.

extract_protocol:
Cells were washed twice in 1X PBS, and lysed by addition of 1ml ice-cold TRIzol (Invitrogen). RNA integrity measurements were performed using Fragment Analyzer™ (Advanced Analytical). All samples had RNA Quality Number (RQN) greater than 9.8.
For RNA-seq library preparation, 2 μg of total RNA were used as input for the TruSeq RNA Library Prep Kit v2 (Illumina), and libraries were prepared following manufacturer instructions

treatment_protocol: The cell line 293T was transfected with constructs using ViraPower Packaging Mix (Life Technologies) for lentiviruses production according to manufacturer’s instructions. After titering the lentiviral stock, CD133+ RPCs, isolated from 12 different nephrectomy specimens, were infected with lentiviral particles following the manufacturer’s instructions. Cells were selected by puromycin (Gibco) (1 μg/ml) and, after six days, antibiotic-resistant cells were expanded. Cell infection was considered effective when the percentage of GFP+ cells was >95%, and the reduction in CD133 protein expression was >70%, as assessed by FACS and Western Blot analysis.

value: shRNA #3 against PROM1

value: CD133+ RPCs


title: RNA-seq on patient #375 RPCs infected with shRNA #1 against PROM1

description:
Raw reads were converted to FastQ, and examined using the FastQC tool (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Reads were mapped to the reference human hg19 assembly, using Tophat v2 (parameters: --bowtie1 -a 5).  Processed data file in BEDGraph format were converted to TDF (provided).
P375 shP1

value: shRNA #1 against PROM1


title: Ehmt2_16_ko_k4me1_4O


title: Ehmt2_16_ko_k36me3_4B

extract_protocol:
Chipping for H3k36me3 (Diagenode A5051-001P) was performed as in http://www.blueprint-epigenome.eu/UserFiles/file/Protocols/Histone_ChIP_July2014.pdf
Library was synthetized with KAPA Hyper prep kit (KK8504) according to manufacturer’s instructions.


title: F161_wt_k36me3_20B


title: F132_wt_k36me3_26B


title: RNA-seq on patient #375 RPCs infected with control shRNA against GFP

description:
Raw reads were converted to FastQ, and examined using the FastQC tool (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Reads were mapped to the reference human hg19 assembly, using Tophat v2 (parameters: --bowtie1 -a 5).  Processed data file in BEDGraph format were converted to TDF (provided).
P375 shGFP

value: control shRNA against GFP


title: Ehmt1_73H_KO_k4me1_23O


title: c03_t2

description: double knockout seedlings of bZIP17 and bZIP60 treated by 5 μg ml-1 of tunicamycin  for 6-hr. repeat 2


title: Ehmt2_F14_ko_k36me3_22B


title: F162_wt_k36me3_21B


title: Ehmt2_F12_wt_k36me3_2B


title: RNA-seq on patient #334 RPCs infected with shRNA #1 against PROM1

description:
Raw reads were converted to FastQ, and examined using the FastQC tool (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Reads were mapped to the reference human hg19 assembly, using Tophat v2 (parameters: --bowtie1 -a 5).  Processed data file in BEDGraph format were converted to TDF (provided).
P334 shP1


title: RNA-seq on patient #334 RPCs infected with control shRNA against GFP

description:
Raw reads were converted to FastQ, and examined using the FastQC tool (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Reads were mapped to the reference human hg19 assembly, using Tophat v2 (parameters: --bowtie1 -a 5).  Processed data file in BEDGraph format were converted to TDF (provided).
P334 shGFP


title: Ehmt2_F15_wt_k36me3_3B


title: c03_m2

description: double knockout seedlings of bZIP17 and bZIP60 treated the mock condition for 6-hr. repeat 2


title: Ehmt2_F2_wt_k36me3_21B


title: 31-7T.RNA.AD

city: Philadelphia

first: Gregory

last: Donahue

address: 3400 Civic Center Blvd, Bldg 421

department: Cell & Developmental Biology

institute: The University of Pennsylvania

data_processing:
Alignment: RNA-seq tags were aligned to the human reference genome (assembly  NCBI37/hg19) using Tophat.
Quantitation: RNA-seq tags were quantified over exons with the HTSeq-count script. For genes that give rise to multiple transcripts, a single representative was chosen for the analysis.
Differential Expression: Differential expression was analyzed at the level of RefSeq transcripts using DESeq in the R statistical environment (www.r-project.org).
Genome_build: hg19
Supplementary_files_format_and_content: Table contains DESeq library size-adjusted tag counts for each gene in each sample plus a pairwise statistical assessment of differential expression in Young:Old, Old:AD, and Young:AD (adjusted to correct for false discovery rate).

source_name: lateral temporal lobe

growth_protocol: Frozen brain tissue samples from lateral temporal lobe (Brodmann area 21 or 20) were obtained from the Center of Neurodegenerative Disease Research (CNDR) biobank at the University of Pennsylvania in accordance with Institutional Review Board approved protocols. A neuropathological diagnosis of AD was established based on the presence of plaques and tangles using the CERAD scores and Braak stages, respectively.  All selected AD cases had high level of AD neuropathological changes (Braak=V/VI and CERAD=C). The Young and Old control brains had no or minimal neuritic amyloid plaques (CERAD=0) or neurofibrillary tangles (CERAD=0). None of the AD cases had other coincident neurodegenerative diseases. Control subjects had no deposits consistent with a frontotemporal lobar degeneration or Lewy body related pathology diagnosis. AD cases with severe neuronal loss were not included. The neuronal loss was originally assessed through semi-quantitative measurements by hematoxylin and eosin (H&E) staining by board-certified neuropathologists of the CNDR. The H&E scoring for neuronal loss ranges from 0-3 where 0 signifies no neuronal loss and 3 is severe neuronal loss. Only cases with neuronal loss of 1 or 2 (mild or moderate) were included.

extract_protocol:
Total RNA was isolated from 100 mg brain tissue by TRIzol solubilization and phenol-chloroform extraction followed by ethanol precipitation.  Purified RNA was subsequently treated with RNase-free DNase (Qiagen).
RNA sequencing libraries were prepared as previously described with a few changes, such as omission of the polyA+ selection step and addition of a double-stranded nuclease (DSN)-mediated step to deplete highly abundant RNA species, such as ribosomal RNA. Briefly, purified RNA was fragmented using RNA Fragmentation Reagent (Thermo Fisher) for 5 min at 70°C and followed by addition of a 5’ phosphate by treating with T4 polynucleotide kinase (NEB). The RNA fragments were then size-selected to 60-250 bp on a 15% TBE-urea gel. Illumina v1.5 RNA adapters were ligated to the 3’ and 5’ ends of the fragmented products using T4 RNA ligase 2, truncated (NEB) and T4 RNA ligase (Promega), respectively. cDNA libraries were generated using Superscript II (Invitrogen) and PCR-amplified using Phusion high-fidelity DNA polymerase (NEB). Libraries were purified on a 6% TBE gel (Invitrogen), treated with DSN and PCR re-amplified. Quality of the resulting sequencing libraries were verified by cloning into Zero Blunt TOPO (Invitrogen) and analyzing 6-10 clones by standard Sanger sequencing to determine the presence of adapters, appropriate size selection, abundance of ribosomal RNA, and the diversity of the library products. The libraries were pooled and sequenced on an Illumina NextSeq 500 using the standard protocols for 75 bp single-read sequencing.

tag: study group

value: Aged, diseased

tag: age (years)

value: lateral temporal lobe


title: 30-9T.RNA.AD


title: 29-6T.RNA.AD


title: Ehmt1_60H_KO_k36me3_31B

tag: age

tag: strain


title: Ehmt1_61H_WT_k36me3_32B


title: 28-8T.RNA.AD


title: 27-5A.RNA.AD


title: Ehmt1_73H_KO_k36me3_23B


title: 23-2A.RNA.AD


title: 24-3T.RNA.AD


title: Ehmt1_86H_WT_k36me3_17B


title: 25-5T.RNA.AD


title: F161_wt_k27ac_20A

extract_protocol:
Chipping for H3k27ac (Diagenode A5051-001P) was performed as in http://www.blueprint-epigenome.eu/UserFiles/file/Protocols/Histone_ChIP_July2014.pdf
Library was synthetized with KAPA Hyper prep kit (KK8504) according to manufacturer’s instructions.


title: F132_wt_k27ac_26A


title: 22-2T.RNA.AD


title: 26-3A.RNA.AD


title: 21-1A.RNA.AD


title: Ehmt2_F6_ko_k36me3_1B


title: Ehmt2_16_ko_k27ac_4A


title: Ehmt2_F14_ko_k27ac_22A


title: Ehmt1_76H_WT_k36me3_24B


title: 20-1T.RNA.AD


title: F162_wt_k27ac_21A


title: Ehmt2_F6_ko_k27ac_1A


title: RNA-seq on patient #334 RPCs infected with shRNA #3 against PROM1

description:
Raw reads were converted to FastQ, and examined using the FastQC tool (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Reads were mapped to the reference human hg19 assembly, using Tophat v2 (parameters: --bowtie1 -a 5).  Processed data file in BEDGraph format were converted to TDF (provided).
P334 shP3


title: 19-11A.RNA.Old

value: Old


title: Ehmt2_F12_wt_k27ac_2A


title: Ehmt1_87H_KO_k36me3_18B


title: Ehmt2_F15_wt_k27ac_3A


title: 17-9A.RNA.Old


title: 16-14T.RNA.Old


title: Ehmt2_F2_wt_k27ac_21A


title: 15-13T.RNA.Old


title: Ehmt1_60H_KO_k27ac_31A


title: 14-7A.RNA.Old


title: Ehmt1_73H_KO_k27ac_23A


title: 18-10A.RNA.Old


title: Ehmt1_387ko_k27ac


title: Ehmt1_61H_WT_k27ac_32A


title: 10-8A.RNA.Old


title: Ehmt2_F6_ko_k9me3_1N

extract_protocol:
Chipping for H3k9me3 (Diagenode A1671-001P) was performed as in http://www.blueprint-epigenome.eu/UserFiles/file/Protocols/Histone_ChIP_July2014.pdf
Library was synthetized with KAPA Hyper prep kit (KK8504) according to manufacturer’s instructions.


title: Ehmt2_16_ko_k9me3_4N


title: 12-6A.RNA.Old


title: 5-18T.RNA.Young

value: Young


title: 7-19T.RNA.Young


title: F132_wt_k9me3_26N


title: 6-14A.RNA.Young


title: 9-16A.RNA.Young


title: 8-15A.RNA.Young


title: Ehmt1_76H_WT_k27ac_24A


title: 11-10T.RNA.Old


title: Ehmt1_388wt_k27ac


title: 3-17T.RNA.Young


title: Ehmt2_F12_wt_k9me3_2N


title: 13-11T.RNA.Old


title: Ehmt2_F15_wt_k9me3_3N


title: 2-12A.RNA.Young


title: Ehmt1_65KO_bulb_k9me3

source_name: whole olfactory bulb


title: 30-9T.Input.AD

description: processed data file: H4K16ac-Input.AD.bw

data_processing:
Alignment: ChIP-seq tags generated with the NextSeq 500 platform were demultiplexed with the bcl2fastq utility and aligned to the human reference genome (assembly  NCBI37/hg19)  using Bowtie v1.1.1 allowing up to two mismatches per sequencing tag (parameters -m 1 --best).
PCR deduplication: Aligned tags were filtered so that when N tags aligned to the same locus, only one representative tag was kept.
Tracks: Generation and visualization of ChIP-seq tracks was conducted as follows. BED files of each pooled study group dataset were converted into coverage maps using the BEDtools utility genomeCoverageBed. Resulting bedGraphs were scaled by using the RPM (reads per million) coefficient, a measure of the millions of tags sequenced per sample to correct for sequencing efficiency biases, and subsequently normalized by subtracting an Input coverage map. Finally, BigWig files were generated and uploaded on the UCSC (University of California Santa Cruz) Genome Browser.
Differential peaks were assessed in the following way. Peaks were first detected using MACS2 (tag size = 75 bp; FDR < 1x10-5) on H4K16ac and input from patient samples pooled over study group. Within each study group, peaks with termini within 150 bp were merged. The MTL method (Chen, X., et al., Cell, 2008. 133(6): p. 1106-17) was then used to compare H4K16ac enrichment across the three study groups. A region of analysis across the three study groups was defined by having at least one peak called in Young, Old or AD. Furthermore, if peaks across the three study groups had their centers within 200 bp distance, the entire area including these peaks (from peak to peak termini) was considered one unique region of analysis. Per-patient H4K16ac enrichment scores were calculated by summing H4K16ac tags overlapping this unique region of analysis and adjusting them by a reads-per-million (RPM) scalar coefficient and by the size of the region of analysis, then subtracting input. AUC values were then transformed in log2(AUC + 1) and statistical significance of differential H4K16ac enrichments was assessed by performing a standard Student's t-test for a pairwise comparisons (i.e., Young vs Old) with alpha 0.05.
Genome_build: hg19
Supplementary_files_format_and_content: BigWig files are created by method described in "Tracks" above.
Supplementary_files_format_and_content: Bed files: ChIP-seq peaks with differential enrichment between the experimental conditions.

extract_protocol:
Briefly, 200 mg brain tissue from each patient was minced on ice and nuclei were prepared by dounce homogenization in nuclei isolation buffer (50 mM Tris-HCl at pH 7.5, 25 mM KCl, 5 mM MgCl2, 0.25 M sucrose) with freshly added protease inhibitors and sodium butyrate, followed by ultracentrifugation on a 1.8 M sucrose cushion. Nuclei pellet was resuspended in 2 ml PBS and crosslinked in 1% formaldehyde for 10 min at room temperature. Crosslinking reactions were quenched with addition of glycine to 125 mM for 5 min followed by two washes in cold PBS. 2 x 106 nuclei were lysed in nuclei lysis buffer (10 mM Tris-HCl at pH 8.0, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Na-deoxycholate, 0.5% N-lauroylsarcosine) with freshly added protease inhibitors and sodium butyrate and chromatin was sheared using a Covaris S220 sonicator to ~250 bp size. Equal aliquots of sonicated chromatin were used per immunoprecipitation reaction with 5 ul H4K16ac antibody (Millipore, #07-329) preconjugated to Protein G Dynabeads (Life Technologies), and 10% of the amount was saved as input. ChIP reactions were incubated overnight at 4°C with rotation and washed three times in wash buffer.
Immunoprecipitated DNA was eluted from the washed beads, purified and used to construct sequencing libraries with 5 ng of DNA (ChIP or Input) using the NEBNext Ultra DNA library prep kit for Illumina (New England Biolabs, NEB). Libraries were multiplexed using NEBNext Multiplex Oligos for Illumina (dual index primers) and single-ended sequenced (75 bp) on the NextSeq 500 platform (Illumina) in accordance with the manufacturer’s protocol.


title: F162_wt_k9me3_21N


title: Ehmt1_87KO_cerebellum_k9me3

source_name: whole cerebellum


title: Ehmt1_65KO_cerebellum_k9me3


title: 31-7T.Input.AD


title: F161_wt_k9me3_20N


title: 4-13A.RNA.Young


title: Ehmt1_87KO_frontcortex_k9me3

source_name: whole frontal cortex


title: 28-8T.Input.AD


title: 25-5T.Input.AD


title: 23-2A.Input.AD


title: 24-3T.Input.AD


title: 27-5A.Input.AD


title: 26-3A.Input.AD


title: Ehmt1_87KO_bulb_k9me3


title: Ehmt1_60KO_frontcortex_k9me3


title: 22-2T.Input.AD


title: 29-6T.Input.AD


title: 21-1A.Input.AD


title: 20-1T.Input.AD


title: Ehmt1_225_k9me3_ko


title: 19-11A.Input.Old

description: processed data file: H4K16ac-Input.Old.bw


title: Ehmt1_P7_1_ko_H_k9me3_37N


title: Ehmt1_232_k9me3_ko


title: Ehmt1_P15_1_ko_H_k9me3_2N


title: Ehmt1_222_k9me3_ko


title: 17-9A.Input.Old


title: Ehmt1_P7_7_ko_H_k9me3_40N


title: 18-10A.Input.Old


title: 16-14T.Input.Old


title: Ehmt1_P1_6_ko_H_k9me3_42N


title: Ehmt1_86WT_cerebellum_k9me3


title: 15-13T.Input.Old


title: Ehmt1_221_k9me3_ko


title: Ehmt1_64WT_cerebellum_k9me3


title: 14-7A.Input.Old


title: Ehmt1_64WT_bulb_k9me3


title: Ehmt1_61WT_frontcortex_k9me3


title: Ehmt1_86WT_frontcortex_k9me3


title: 13-11T.Input.Old


title: Ehmt1_86WT_bulb_k9me3


title: 12-6A.Input.Old


title: 10-8A.Input.Old


title: 8-15A.Input.Young

description: processed data file: H4K16ac-Input.Young.bw


title: Ehmt1_223_k9me3_wt


title: Ehmt1_234_k9me3_wt


title: 6-14A.Input.Young


title: Ehmt1_226_k9me3_wt


title: 9-16A.Input.Young


title: 11-10T.Input.Old


title: Ehmt1_230_k9me3_wt


title: 5-18T.Input.Young


title: Ehmt1_P1_2_ko_k9me3_44N


title: Ehmt1_P15_3_wt_k9me3_46N


title: 3-17T.Input.Young


title: Ehmt1_P7_3_wt_H_k9me3_38N


title: Ehmt1_P7_6_wt_H_k9me3_39N


title: 7-19T.Input.Young


title: 2-12A.Input.Young


title: Ehmt1_P1_5_wt_H_k9me3_41N


title: 1-15T.Input.Young


title: Ehmt1_P1_1_wt_k9me3_43N


title: Ehmt1_P15_2_ko_k9me3_45N


title: F132_wt_k4me3_26F

extract_protocol:
Chipping for H3k4me3 (Diagenode A5051-001P) was performed as in http://www.blueprint-epigenome.eu/UserFiles/file/Protocols/Histone_ChIP_July2014.pdf
Library was synthetized with KAPA Hyper prep kit (KK8504) according to manufacturer’s instructions.


title: 31-7T.H4K16ac.AD

value: Millipore, #07-329


title: Ehmt2_F6_ko_k4me3_1F

value: brain


title: F162_wt_k4me3_21F


title: Ehmt1_P15_6_wt_H_k9me3_3N


title: 4-13A.Input.Young


title: 28-8T.H4K16ac.AD


title: 26-3A.H4K16ac.AD


title: Ehmt2_F12_wt_k4me3_2F


title: 27-5A.H4K16ac.AD


title: Ehmt2_F14_ko_k4me3_22F


title: 24-3T.H4K16ac.AD


title: 23-2A.H4K16ac.AD


title: Ehmt2_F15_wt_k4me3_3F


title: 22-2T.H4K16ac.AD


title: Ehmt1_87KO_cerebellum_k4me3


title: Ehmt1_65KO_cerebellum_k4me3


title: 21-1A.H4K16ac.AD


title: Ehmt2_F2_wt_k4me3_21F


title: Ehmt2_16_ko_k4me3_4F


title: Ehmt1_87KO_bulb_k4me3


title: 18-10A.H4K16ac.Old


title: 19-11A.H4K16ac.Old


title: F161_wt_k4me3_20F


title: 30-9T.H4K16ac.AD


title: Ehmt1_87KO_frontcortex_k4me3


title: 29-6T.H4K16ac.AD


title: Ehmt1_60KO_frontcortex_k4me3


title: 25-5T.H4K16ac.AD


title: 17-9A.H4K16ac.Old


title: Ehmt1_387ko_k4me3_387F


title: 16-14T.H4K16ac.Old


title: Ehmt1_87H_KO_k4me3_18F


title: 14-7A.H4K16ac.Old


title: 15-13T.H4K16ac.Old


title: Ehmt1_73H_KO_k4me3_23F


title: 12-6A.H4K16ac.Old


title: 13-11T.H4K16ac.Old


title: Ehmt1_P15_2_ko_k4me3_45F


title: Ehmt1_P7_1_ko_H_k4me3_37F


title: Ehmt1_P1_2_ko_k4me3_44F


title: 11-10T.H4K16ac.Old


title: 10-8A.H4K16ac.Old


title: 7-19T.H4K16ac.Young


title: 8-15A.H4K16ac.Young


title: Ehmt1_86WT_cerebellum_k4me3


title: 6-14A.H4K16ac.Young


title: Ehmt1_64WT_cerebellum_k4me3


title: 5-18T.H4K16ac.Young


title: Ehmt1_86WT_bulb_k4me3


title: 3-17T.H4K16ac.Young


title: 4-13A.H4K16ac.Young


title: Ehmt1_61WT_frontcortex_k4me3


title: 2-12A.H4K16ac.Young


title: Ehmt1_86WT_frontcortex_k4me3


title: Ehmt1_P15_1_ko_H_k4me3_2F


title: Ehmt1_86H_WT_k4me3_17F


title: Ehmt1_76H_WT_k4me3_24F


title: 1-15T.H4K16ac.Young


title: 9-16A.H4K16ac.Young


title: Ehmt1_388wt_k4me3_388F


title: Ehmt1_P7_7_ko_H_k4me3_40F


title: Ehmt1_P15_3_wt_k4me3_46F


title: Ehmt1_P1_6_ko_H_k4me3_42F


title: VIRMA_Mut_PE_m6A_IP2

city: Chicago

first: Xiaolong

last: Cui

state: IL

address: 680 N Lake Shore Drive

department: Department of Preventive Medicine

institute: Northwestern University

data_processing:
Library strategy: m6A-seq
Sequencing reads were trimmed of low quality nucleotides by trim_galore.
Trimmed reads were mapped to human genome hg19 by HISAT.
Only uniquely mapped reads were kept for down-stream analyses.
M6A enriched regions were called by MACS2.
Genome_build: hg19
Supplementary_files_format_and_content: For each m6A IP sample, narrowPeak files contain m6A enriched peaks.

source_name: HeLa

growth_protocol: Human HeLa cell line was grown in DMEM (Gibco, 11965) media supplemented with 10% FBS and 1% 100× Pen Strep (Gibco, 15140).

extract_protocol:
At 48-h post-transfection, total RNA was isolated from transfected cells with TRIZOL reagent. Poly-adenylated RNA was enriched by using FastTrack MAG Maxi mRNA isolation kit (Invitrogen).
RNA fragmentation, m6A-seq, and library preparation were performed as in Dominissini et al 2013 Nature Protocols.

tag: protocol

value: knockout samples using cas9 and genetically changed

value: HeLa cell

tag: technology


title: Ehmt1_P7_3_wt_H_k4me3_38F


title: VIRMA_Mut_PE_Input2


title: VIRMA_Mut_PE_m6A_IP1


title: Ehmt1_P7_6_wt_H_k4me3_39F


title: VIRMA_Mut_PE_Input1


title: Ehmt1_P1_1_wt_k4me3_43F


title: VIRMA_Mut_m6A_IP2


title: Ehmt1_64WT_bulb_k4me3


title: VIRMA_Mut_Input2


title: VIRMA_Mut_m6A_IP1


title: P30_additional wt_3

data_processing:
alignment was done with GSNAP-gmap-2015-06-23
read counting was performed with custom C++ script
DEseq2 was used to call the expression changes
Genome_build: mm9
Supplementary_files_format_and_content: Table S1: Dscores for P30 Ehmt1 and Ehmt2 epigenomes, developmental Ehmt1 clusters, P30 Ehmt1 deregulated genes clusters, Ehmt1 vs Ehmt2 gene sets.  RNAseq reads counts: Raw reads counts for RNAseq samples.  H3k4me3 peaks: Peak calls and raw reads counts.  H3k4me1 peaks: Peak calls and raw reads counts.  H3k36me3 peaks: Peak calls and raw reads counts.  H3k27ac peaks: Peak calls and raw reads counts.  H3k9me3 peaks: Peak calls and raw reads counts.  H3k9me2 promoters: raw reads counts in promoters (TSS+/-2kb)  H3k27me3 peaks: Peak calls and raw reads counts.

extract_protocol:
Total RNA was Trizol extracted. RNA was treated with DNase (Qiagen, 79254) and purified on the RNeasy MinElute Cleanup Kit (Qiagen, 74204). 2000 ng of total RNA were treated with the Ribo-Zero rRNA Removal Kit (Human/Mouse/Rat; Illumina MRZH11124). Depleted RNA was precipitated 1 h at -80°C in three volumes of ethanol plus 1 µg of glycogen. RNA was then washed and resuspended in 36 µl of RNase free water. RNA fragmentation buffer (NEBNext® Magnesium RNA Fragmentation Module, E6150S) was added to the solution and the RNA was fragmented by incubation at 95°C for 3 minutes. For reverse transcription, cDNA first strand synthesis was performed with random examer primers. cDNA second strand synthesis was performed with dUNTPs, to ensure strand specificity.
The RNA-seq library was synthetized with KAPA Hyper prep kit (KK8504), a treatment with USER enzyme (NEB, M5505L) was added to digest the unspecific strand. The libraries were pooled (4/lane) and sequenced on the illumina HiSeq, which yielded approximately 40 million single-end reads per sample.


title: P30_additional wt_4


title: P30_additional wt_2


title: P30_additional wt_1


title: VIRMA_Mut_Input1


title: Ehmt1_P15_6_wt_H_k4me3_3F


title: siVIRMA_m6A_IP1

tag: sirna

value: siVIRMA


title: siVIRMA_Input2

tag: cell line


title: siVIRMA_m6A_IP2


title: P30_2_ehmt2 ko

value: Ehmt2 +/-


title: P30_3_ehmt2 ko


title: P30_1_ehmt2 ko


title: siCtrl_for_VIRMA_m6A_IP2

value: siCtrl


title: P30_4_ehmt2 ko


title: P30_4_ehmt2 wt

value: Ehmt2 wild type


title: siVIRMA_Input1


title: siCtrl_for_VIRMA_Input2


title: P30_3_ehmt2 wt


title: P30_2_ehmt2 wt


title: P30_1_ehmt2 wt


title: siCtrl_for_VIRMA_m6A_IP1


title: Ehmt1_P1_5_wt_H_k4me3_41F

value: Ehmt1 wild type


title: siCtrl_for_VIRMA_Input1


title: P30_6C ko

value: Ehmt1 +/-


title: P30_6B ko


title: Ctrl_PE_m6A_IP2


title: 20-1T.H4K16ac.AD


title: Ctrl_PE_m6A_IP1


title: P30_5 ko


title: Ctrl_PE_Input2


title: P30_6A ko


title: P30_4 ko


title: P30_3 ko


title: P30_1 ko


title: Ctrl_PE_Input1


title: Ctrl_m6A_IP2


title: P15_2 ko


title: Ctrl_m6A_IP1


title: P15_1 ko


title: P7_3 ko


title: EpiSC_Sox2_Lane3088_CN4_CAGATC

source_name: epiblast-derived stem cells

extract_protocol:
Promoter Capture Hi-C was carried out with SureSelect target enrichment, using a custom-designed biotinylated RNA bait library for mouse promoters and custom paired-end blockers according to the manufacturer’s instructions (Agilent Technologies) (Schoenfelder et al . 2015 The pluripotent regulatory circuitry connecting promoters to their long-range interacting elements, Genome Res, 25: 582-97) and following the protocol detailed in (Nagano et al. 2015 Comparison of Hi-C results using in-solution versus in-nucleus ligation, Genome Biol, 16: 175).     ChIP-seq in EpiSCs was performed according to Schoenfelder et al. 2015, Polycomb repressive complex PRC1 spatially constrains the mouse embryonic stem cell genome, Nat Genet, 47: 1179-86. Cells were fixed in ChIP fixation buffer (1% formaldehyde, 5 μM EGTA, 10 μM EDTA, 1 mM NaCl and 0.5 mM HEPES in PBS) for 10 min at room temperature. Fixation was stopped by the addition of glycine (final concentration of 125 mM). Cells were washed with PBS, buffer A (10 mM HEPES, pH 7.5, 10 mM EDTA, 0.5 mM EGTA and 0.75% Triton X-100) and buffer B (10 mM HEPES, pH 7.5, 200 mM NaCl, 1 mM EDTA and 0.5 mM EGTA). Cells were lysed in lysis buffer (25 mM Tris, pH 7.5, 150 mM NaCl, 5 mM EDTA, 0.1% Triton X-100, 1% SDS, 0.5% deoxycholate and Complete protease inhibitor (Roche)) for 30 min on ice. Sonication was performed using a Biorupter sonicator (Diagenode) to obtain an average DNA fragment size of 300 bp.
Promoter Capture Hi-C was carried out with SureSelect target enrichment, using a custom-designed biotinylated RNA bait library for mouse promoters and custom paired-end blockers according to the manufacturer’s instructions (Agilent Technologies) (Schoenfelder et al . 2015 The pluripotent regulatory circuitry connecting promoters to their long-range interacting elements, Genome Res, 25: 582-97) and following the protocol detailed in (Nagano et al. 2015 Comparison of Hi-C results using in-solution versus in-nucleus ligation, Genome Biol, 16: 175).     ChIP-seq libraries were prepared using the NEBNext DNA Library Preparation kit, following the manufacturer's instructions.  Chromatin was diluted with ChIP dilution buffer (25 mM Tris, pH 7.5, 150 mM NaCl, 5 mM EDTA, 1% Triton X-100, 0.1% SDS, 0.5% deoxycholate and Complete protease inhibitor). Dynabeads Protein G beads (Life Technologies) were blocked for 1 h at 4 °C with 1 mg/ml BSA and 1 mg/ml yeast tRNA (Life Technologies). For each immunoprecipitation, 150 μg of chromatin and 5 μg of antibody were used. Chromatin was precleared with the blocked beads for 1 h at 4 °C. Chromatin was then incubated with antibody overnight at 4 °C with rotation. Protein-antibody complexes were precipitated by the addition of beads for 2 h. Complexes were washed twice with wash buffer A (50 mM Tris, pH 8.0, 150 mM NaCl, 0.1% SDS, 0.5% deoxycholate, 1% NP-40 and 1 mM EDTA), once with wash buffer B (50 mM Tris, pH 8.0, 500 mM NaCl, 0.1% SDS, 0.5% deoxycholate, 1% NP-40 and 1 mM EDTA), once with wash buffer C (50 mM Tris, pH 8.0, 250 mM lithium chloride, 0.5% deoxycholate, 1% NP-40 and 1 mM EDTA) and once with TE. Samples were treated with RNase A and proteinase K, and cross-links were reversed overnight. DNA was purified using a ChIP DNA clean and concentrator column (Zymo Research). Libraries were prepared using the NEB Next Fast DNA Fragmentation and Library Preparation set for the Ion Torrent kit (E6285S), following the manufacturer's instructions. Briefly, 40 ng of ChIP or input DNA was used for library generation. Libraries were size selected for 250-bp fragments using 2% E-gel Size Select agarose gels (Life Technologies) and were amplified with five PCR cycles. Libraries were sequenced on the Ion Proton Sequencer using Ion PI Chip v2 (Life Technologies). Templates were generated using Ion PI Template OT2 200 kit v3 and Ion PI Sequencing 200 kit v3 or the Ion PI IC 200 kit (Life Technologies).

value: epiblast-derived stem cells

tag: chip antibody

value: SOX2 (ab97959, Abcam)


title: EpiSC_Oct4_Lane3088_CN3_TGACCA

value: OCT4 (sc-5279, Santa Cruz)


title: P7_1 ko


title: Ctrl_Input1


title: Saureus_HG003_RNAseq

city: Jouy-en-Josas

first: Tatiana

last: Rochat

address: Domaine de Vilvert

country: France

institute: INRA

description: RNA sequencing of a pool of RNAs extracted in 16 biological conditions

data_processing:
FastQC (v0.10.1) quality control.
Mapping performed on Refseq CP000253.1 by Bowtie2 software with default parameters.
Genome_build: CP000253.1
Supplementary_files_format_and_content: HG003_46_bona_fide_sRNAs.gff (tab separated file containing a manually curated list of 46 bona fide sRNAs found expressed in Staphylococcus aureus HG003)

organism: Staphylococcus aureus

source_name: Bacteria

growth_protocol: Total RNA samples were extracted in 16 different biological conditions as described below. i) 8 samples harvested in the course of growth: Overnight cultures were diluted 2000 times in BHI medium and incubated at 37°C under shaking agitation (180 rpm). Cells were harvested in exponential phase (at OD600nm 0.6, 1.8 and 3.3), transition phase (at OD600nm 4.5 and 7.2), early stationary phase (at OD600nm 9.8 and 12.8) and late stationary phase (24 hours). ii) 6 samples harvested under stress conditions: Exponential growing cells (at OD600nm 0.6) were submitted before RNA extraction to cold shock (15 min at 10°C), heat shock (10 min at 48°C), oxygen limitation (the exponential growing culture was transferred into a 50 mL Falcon tube fully filled and was incubated during 30 min under static condition), alkaline stress (10 min after addition of KOH 30 mM), oxidative stress (10 min after addition of H2O2 10 mM) or disulfide stress (10 min after addition of diamide 1 mM). iii) 1 sample harvested under iron-depleted condition: Overnight culture was diluted in BHI supplemented with 2,2-dipyridyl at 1.4 mM and incubated for growth until OD600nm reached 1. iv) 1 sample from cells grown on BHI-agar plates: Exponential growing cells were diluted at ~5.103 CFU/mL, 100 µl were spread on BHI-agar plates and incubated 16 h at 37°C. Colonies were resuspended in lysis buffer for RNA extraction.

extract_protocol:
Cultures were centrifuged; the pellets were frozen in liquid nitrogen and stored at -80°C until RNA extraction. Cells pellets were resuspended into 400 μL of Lysis buffer (4 M guanidine thiocyanate, 25 mM sodium acetate pH 5.2, 5 g/L N-laurylsarcosinate), transferred into FastPrep tubes containing 0.6 g of glass beads (G4649, Sigma-Aldrich) and 400 µL of acid phenol:chloroform:IAA (25:24:1). Bacteria were mechanically lysed by using the Fastprep apparatus (MP Biomedicals) with 3 cycles of 45 s at speed 6.0 separated by incubation on ice during 5 min. After lysis, tubes were centrifuged 15 min at 17,900 g at 4 °C. The aqueous phase was acid phenol extracted, isopropanol precipitated and the pellet resuspended in RNase-free water.
Strand-specific RNA-seq libraries were generated with the TruSeq RNA-Seq Library Preparation Kit (Illumina), according to the manufacturer's instructions.

treatment_protocol: When cell density reached an OD600 of 0.7, bacteria were harvested by centrifugation for 3 min at 4 °C after addition of ½ volume of frozen killing buffer (20 mM Tris/HCl pH 7.5, 5 mM MgCl2, 20 mM NaN3) to the culture sample. Cell pellets were frozen in liquid nitrogen and stored at -80 °C until RNA extraction.


title: P7_2 ko


title: EpiSC_Nanog_Lane3088_CN2_CGATGT

value: NANOG (ab80892, Abcam)


title: EpiSC_Input_Lane3088_CN1_ATCACG


title: siCtrl_for_HAKAI_IP1

data_processing:
Sequencing reads were trimmed of low quality nucleotides by trim_galore.
Trimmed reads were mapped to human genome hg19 by HISAT.
Only uniquely mapped reads were kept for down-stream analyses.
M6A enriched regions were called by MACS2.
Genome_build: hg19
Supplementary_files_format_and_content: For each m6A IP sample, narrowPeak files contain m6A enriched peaks.


title: siCtrl_for_HAKAI_IP2


title: P1_3 ko


title: ESC_CHi-C_Lane3057

description:
ESC_complete_merge_step2_seqmonk.txt.gz
Gene_assignment.xlsx
ROSE_SE.xlsx

source_name: embryonic stem cells

value: embryonic stem cells

value: wild type


title: siCtrl_for_HAKAI_Input2


title: P1_2 ko


title: ESC_NKO_CHi-C_Lane3058

description:
ESC_NKO_merge_step2_seqmonk.txt.gz
Gene_assignment.xlsx
ROSE_SE.xlsx

value: NANOG knockout


title: P30_2 ko


title: siCtrl_for_HAKAI_Input1


title: P1_1 ko


title: P15_3 ko


title: P30_6C wt


title: ESC_CHi-C_Lane1338


title: siHAKAI_m6A_IP2


title: P30_6B wt


title: P30_6A wt


title: control HL-60_RNA-seq_rep1

city: Beijing

first: Yanjian

last: Li

address: Tsinghua University, Haidian District

institute: Tsinghua University

data_processing:
Sequence adaptors were removed using cutadapt.
The reads were aligned to a transcriptome and quantified using RSEM v1.2.7
Differential gene expression was calculated using the Deseq2 version 1.4.5 package using the mean value of gene-wise dispersion estimates
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: Tab-delimited table showing the log2FC for all genes from DeSeq2 v1.4.5 analysis

source_name: control HL-60 cells

growth_protocol: HL-60 cells were maintained in RPMI-1640 medium (Gibco) supplemented with 10% fetal bovine serum (FBS, Gibco, USA), 50 units/mL penicillin and streptomycin (Gibco, USA), 1X Non-Essential Amino Acids (Gibco, USA).

extract_protocol:
RNA-seq:Total RNA of ATRA treated and control cells were extracted using TRIZOL
mRNA were isolated using poly(A) mRNA magnetic isolation module (NEB, England) and cDNA were got through reverse transcription and second strand synthesis (NEB, England). Then, cDNA were fragmented by S220 Focused-ultrasonicator (Covaris, USA). End repairing, adenine adding and adaptor ligation were performed using Enzymatics kit (Enzymatics, USA). PCR were performed using high-fidelity master mix (NEB, England).

treatment_protocol: 2x10^5/ml HL-60 cells in 100mm dish were treated with 1μM ATRA (1 mM stock in ethanol, Sigma, USA) for 4 days , referred as ATRA group. Cells treated with equal amount of ethanol (10μl added in 10ml medium) were referred as control group. Medium was changed and ATRA/ethanol was added again at day2.

value: HL-60; ATCC CCL-240

tag: tissue origin

value: peripheral blood

tag: disease

value: acute promyelocytic leukemia

tag: treated with

value: ethanol for 4 days


title: siHAKAI_m6A_IP1

value: HeLa cell


title: Ctrl_Input2


title: siHAKAI_Input2


title: control HL-60_RNA-seq_rep2


title: P1_4 ko

value: brain

tag: condition


title: siHAKAI_Input1


title: ATRA treated HL-60 cells_RNA-seq_rep1

source_name: ATRA treated HL-60 cells

value: 1μM ATRA for 4 days


title: P30_5 wt


title: siZC3H13_m6A_IP2


title: ATRA treated HL-60 cells_RNA-seq_rep2


title: P30_4 wt


title: RNA-Seq_WT_3

city: Bethesda

first: Mingan

last: Sun

state: Maryland

address: Building 6B, 6 Center Drive

department: Eunice Kennedy Shriver National Institute of Child Health and Human Development

institute: National Institute of Health

data_processing:
ChIP-Seq data were first processed using Trim Galore  (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore), then aligned to reference genome (dm3, BDGP Release 5) using Bowtie v1.1.2 (Langmead et al. 2009) with parameters: -n 2 -l 28 -k 1 --best. The PCR duplicates for each dataset were removed using the rmdup function of samtools. The reads from biological replicates were pooled together for further analysis. For H3K27me3 domains which could be of dozens to hundreds of kilobases in length, initial peak calling was performed using SICER v1.1 (Zang et al. 2009) with parameter: window size = 500, fragment size = 200, effective genome fraction = 0.7, gap size = 2000. To focus on canonical H3K27me3 domains, only those with FDR < 0.1, length > 5kb and with at least two-fold enrichment were used for further analysis. For other PcG factors which form punctuated peaks, peak calling was performed using MACS v2.1.1 (Zhang et al. 2008) with parameters: -g dm -q 0.05.
The raw data for RNA-Seq were first processed with Trim Galore, then aligned to the reference genome (dm3, BDGP Release 5) using Tophat v2.1.1 (Ghosh and Chan 2016) with parameter: --no-novel-juncs. Finally, the FPKM for each gene was calculated using cufflinks, and normalized between different datasets using cuffnorm (Ghosh and Chan 2016). To identify differentially expressed genes, we first get the read counts for each gene with htseq-count (Anders et al. 2015), then identified differential genes with FDR<0.05 using DESeq2 (Love et al. 2014).
Genome_build: dm3, BDGP Release 5
Supplementary_files_format_and_content: BED files for broad peaks called by SICER for H3K27me3; BED files for narrow peaks called by macs2 for other factors. Tab-delimited text files include normalized FPKM values for each sample.

organism: Drosophila melanogaster

source_name: third instar larval imaginal discs and brains

growth_protocol: Fly stocks were maintained at 25 0C.

extract_protocol:
Total RNA was isolated with Trizol (Invitrogen) followed by purification using a Qiagen RNeasy micro kit followed by PolyA extraction.
Purified mRNAs were constructed to RNA-Seq libraries with specific barcodes using Illumina TruSeq Stranded mRNA Library Prep Kit and all the 12 RNA-Seq libraries were pooled together and sequenced using Illumina HiSeq 2500 with one Rapid run to generate approximately 30 ~ 50 million 2x100 paired-end reads for each sample.


title: siZC3H13_m6A_IP1


title: P30_3 wt


title: siZC3H13_Input2


title: siZC3H13_Input1


title: P30_2 wt


title: P30_1 wt


title: siCtrl_m6A_IP2


title: P15_3 wt


title: RNA-Seq_WT_1

value: third instar larval imaginal discs and brains


title: RNA-Seq_SppsKO_4


title: siCtrl_m6A_IP1


title: P15_2 wt

value: Ehmt1 wild type


title: RNA-Seq_SppsKO_3


title: RNA-Seq_SppsKO_2


title: siCtrl_Input2


title: P15_1 wt


title: RNA-Seq_SppsKO_1


title: P7_3 wt


title: siCtrl_Input1


title: P7_2 wt


title: siCPSF5_m6A_IP2


title: RNA-Seq_PhoKO_3


title: RNA-Seq_PhoKO_1


title: RNA-Seq_WT_2


title: RNA-Seq_PhoKO_2


title: P1_4 wt


title: ChIP-Seq_Input_PhoKO_2

extract_protocol:
Total genomic DNA was extracted from CNS and disc materials using XXX.
Invitrogen Dynabeads (M-280 sheep anti-rabbit IgG) were used for Chromatin immunoprecipitation in place of protein A or G agarose/salmon sperm DNA beads. ChIP reactions were performed with 1:100 dilutions of anti-Pho  (Brown et al., 2003), anti-Spps (Brown and Kassis 2010), anti-Ph (Donna-Arndt-Jovin), 1:200 dilutions of anti-E(z) (rabbit polyclonal raised against bacterially expressed full length E(z)), anti-Psc (Nicole Francis), anti-Pc (Santa Cruz Biotech Inc, sc25762), and anti-H3K27me3 (Millipore, 17-622).


title: siCPSF5_Input1


title: P1_3 wt


title: ChIP-Seq_Input_PhoKO_1


title: METTL14_Mut_IP2


title: ChIP-Seq_Ph_PhoKO_3


title: P1_2 wt


title: Ehmt1_65KO_bulb_k4me3


title: METTL14_Mut_IP1


title: P1_1 wt


title: METTL14_Mut_Input2


title: ChIP-Seq_Ph_PhoKO_2


title: ChIP-Seq_Ph_PhoKO_1


title: ChIP-Seq_H3K27_PhoKO_3


title: METTL3_Mut_IP2


title: METTL14_Mut_Input1


title: ChIP-Seq_H3K27_PhoKO_2


title: P7_1 wt


title: E12.5 female PGC WGBS Replicate 1

description:
Whole genome bisulphite sequencing of primordial germ cells
E12F_MMus_CpG.sorted.symmetric.8x.bed

data_processing:
Raw reads were first trimmed using Trim Galore (version 0.3.1, http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) with the --paired --trim1 options. Alignments were carried out to the mouse genome (mm9, NCBI build 37) with Bismark (version 0.13.0) with the -n 1 parameter; where appropriate, the λ phage genome (1993-04-28) was added as an extra chromosome. Aligned reads were deduplicated with deduplicate_bismark selecting a random alignment for positions that were covered more than once. CpG methylation calls were extracted from the deduplicated mapping output using the Bismark methylation extractor (version 0.13.0) with the --no_overlap --comprehensive --merge_non_CpG parameters for paired end mode. The number of methylated and unmethylated cytosines in a CpG context was extracted using bismark2bedGraph (default parameters) and coverage2cytosine (parameters: --zero_based). Symmetric CpGs were merged with custom R script. For all downstream analysis, only symmetric CpGs with minimum 8x coverage were used. All WGBS analysis was carried out on data from merged biological replicates.
Genome_build: mm9
Supplementary_files_format_and_content: BED file. Columns: <chromosome>  <start position>  <end position>  <context>  <methylation fraction>  <strand>

source_name: E12.5 female PGC

extract_protocol:
Total DNA was isolated from 10,000 sorted PGCs using the QIAamp DNA Micro Kit (Qiagen) with 0.8 µg of carrier RNA and following the “Isolating DNA from small samples of blood” protocol.
In some cases, unmethylated λ phage DNA (Promega) was spiked in following DNA isolation to assess bisulphite conversion rate. DNA was fragmented using a Covaris S2 sonicator (Covaris), as per manufacturer’s instructions. Libraries were made following the NEBNext Library Prep protocol, with the following modifications: 1)  methylated adaptors were diluted 1:10 in nuclease free H2O to a final concentration of 1.5 µM; 2) following adaptor ligation, bisulphite conversion was carried out using the Imprint Modification Kit (Sigma), and following the two step protocol according to the manufacturer’s specifications; and 3) PCR enrichment was carried out for 16 cycles using the NEXTflex Bisulphite-Seq Kit for Illumina Sequencing (Bioo Scientific) master mix and the NEBNext Library Prep universal and index primers (NEB). The libraries were purified by AMPure XP beads (Beckman-Coulter). Libraries were sequenced on the Illumina HiSeq 2000 or 2500 instrument.

tag: genetic background

value: MF1 x GOF18∆PE-EGFP

value: Wild type

tag: cell type

value: PGC


title: E12.5 male PGC WGBS Replicate 1

description:
Whole genome bisulphite sequencing of primordial germ cells
E12M_MMus_CpG.sorted.symmetric.8x.bed

source_name: E12.5 male PGC

tag: genotype

tag: gender

value: female


title: METTL3_Mut_IP1


title: E12.5 male PGC WGBS Replicate 2


title: siCPSF5_m6A_IP1


title: ChIP-Seq_Input_SppsKO_2

tag: tissue


title: siCPSF5_Input2


title: METTL3_Mut_Input2


title: METTL3_Mut_Input1


title: ChIP-Seq_Input_SppsKO_1


title: E11.5 PGC WGBS Replicate 2

description:
Whole genome bisulphite sequencing of primordial germ cells
E11_MMus_CpG.sorted.symmetric.8x.bed

source_name: E11.5 PGC


title: E11.5 PGC WGBS Replicate 1


title: E10.5 PGC WGBS Replicate 1

description:
Whole genome bisulphite sequencing of primordial germ cells
E10_MMus_CpG.sorted.symmetric.8x.bed


title: Wild_Ctrl_m6A_IP1


title: Wild_Ctrl_m6A_IP2


title: ChIP-Seq_Psc_SppsKO_3


title: ChIP-Seq_Psc_SppsKO_2


title: Wild_Ctrl_Input2


title: E12.5 male PGC AbaSeq Replicate 1

description:
AbaSeq of primordial germ cells
E12M_AbaSeq_symmetric_noBlack_realNorm.bed

data_processing:
Library strategy: Aba-Seq
For the uniquely mappable part of the genome, raw sequencing reads were trimmed for adaptor sequences and low quality bases using Trim Galore (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/). The trimmed reads were mapped to the mouse genome (mm9, NCBI build 37) using Bowtie (version 0.12.8) with parameters -n 1 -l 25 --best --strata -m 1. Calling of 5hmC was based on the recognition sequence and cleavage pattern of the AbaSI enzyme (5′-CN11–13↓N9–10G-3′/3′-GN9–10↓N11–13C-5′) using custom Perl scripts. For assessing relative enrichment of 5hmC at repetitive elements and non-repetitive elements, AbaSeq alignments were divided into two groups: unique (single best alignment) and ambiguous (map to multiple locations with equal alignment score).  Both groups were then mapped to the repetitive elements defined by the RepeatMasker track of mm9 (UCSC Genome Browser) separately. For quantification of relative 5hmC levels at symmetric CpGs in the uniquely mappable part of the genome, the number of counts per symmetric CpG for a given sample were normalized to the combined number of uniquely mapped and ambiguously mapped reads for a given library, and then further multiplied by a stage-specific normalization factor based on the mean 5hmC level for each stage as computed by LC/MS (E10.5 = 1.0; E11.5 = 1.13; E12.5F = 0.76; E12.5M = 1.0). All symmetric CpGs falling within genomic intervals blacklisted by the mouse (mm9) ENCODE project were excluded from all further downstream analysis.
Genome_build: mm9
Supplementary_files_format_and_content: BED file. Columns: <chromosome>  <start position>  <end position>  <context>  <normalized read counts>  <strand>

extract_protocol:
Total DNA was isolated from 10,000 sorted PGCs using the QIAamp DNA Micro Kit (Qiagen) with 0.8 µg of carrier RNA and following the “Isolating DNA from small samples of blood” protocol.
AbaSeq libraries for 5hmC profiling were constructed as previously described (23). In brief, genomic DNA was glucosylated with 400 nmol UDP-glucose and 10 units of T4-β-glucosyltransferase (NEB) in NEB buffer 4 overnight at 37°C and was purified afterward by phenol-chloroform extraction and ethanol precipitation. The glucosylated genomic DNA was then digested by four units of AbaSI enzyme (NEB) in NEB buffer 4 at room temperature (25°C) for 1 hr and the enzyme was  inactivated at 65°C for 20 minute. Biotinylated P1 adapters were ligated onto the AbaSI digested DNA by incubating the digested DNA with 50 pmol of P1 and 2 μl of T4 DNA quick ligase (NEB) in the 1X quick ligation buffer in a total volume of 42 μl at room temperature for 30 min. Ligated DNA was then purified by AMPure XP beads (Beckman-Coulter) and was fragmented using a Covaris S2 sonicator (Covaris), following the manufacturer’s instructions. Sheared P1-ligated DNA was then captured by mixing with 12.5 μl of Dynabeads MyOne Streptavidin C1 beads (Life Technologies) according to the manufacturer’s specifications. End repair and dA-tailing were carried out on the beads by using the NEBNext End Repair Module (NEB) and the NEBNext dA-tailing Module (NEB) at 20°C and 37 °C respectively for 30 min. The beads were washed twice with a buffer containing 5 mM Tris-HCl (pH 7.5), 0.5 mM EDTA, and 1 M NaCl between the two reactions and after dA-tailing. P2 adapters were ligated to the random sheared ends of the dA-tailed DNA using NEB T4 DNA quick ligase at room temperature for 30 min. After washing the DNA-bound beads as described above, the entire DNA was amplified using the Phusion DNA polymerase (NEB) with the addition of 300 nM forward primer (PCR_I) and 300 nM reverse primers (PCR_IIpe) for 16 cycles. The beads were then removed from the PCR and the library was purified using AMPure XP beads (Beckman-Coulter). Libraries were sequenced on the Illumina HiSeq 2000 instrument.

value: male


title: E12.5 male PGC AbaSeq Replicate 2


title: Wild_Ctrl_Input1


title: E12.5 female PGC WGBS Replicate 2


title: E12.5 female PGC AbaSeq Replicate 2

description:
AbaSeq of primordial germ cells
E12F_AbaSeq_symmetric_noBlack_realNorm.bed


title: ChIP-Seq_Pho_SppsKO_2


title: E12.5 female PGC AbaSeq Replicate 1


title: VIRMA_RIP_IP1

value: RIP-Seq


title: ChIP-Seq_Pho_SppsKO_1


title: VIRMA_RIP_IP2


title: ChIP-Seq_H3K27_PhoKO_1


title: E11.5 PGC AbaSeq Replicate 2

description:
AbaSeq of primordial germ cells
E11_AbaSeq_symmetric_noBlack_realNorm.bed


title: ChIP-Seq_Ph_SppsKO_2


title: VIRMA_RIP_Input2


title: ChIP-Seq_Ph_SppsKO_1


title: ChIP-Seq_Ph_SppsKO_3


title: VIRMA_RIP_Input1


title: E10.5 PGC AbaSeq Replicate 2

description:
AbaSeq of primordial germ cells
E10_AbaSeq_symmetric_noBlack_realNorm.bed


title: E11.5 PGC AbaSeq Replicate 1


title: ChIP-Seq_Ez_SppsKO_3


title: ChIP-Seq_Ez_SppsKO_2


title: E10.5 PGC AbaSeq Replicate 1


title: ChIP-Seq_Psc_SppsKO_1


title: ChIP-Seq_Ez_SppsKO_1


title: AR_siARV_ChIPSeq_R1881_rep1

city: San Antonio

first: Zhenqing

last: Ye

state: TX

address: 8403 Floyd Curl Dr

department: 6Department of Population Health Sciences

institute: UT Health San Antonio

data_processing:
Basecalls performed using CASAVA version 1.4
Image data were processed using the Illumina Standard Pipeline.
Base-calling and data filtering processed by the Mayo Cliinc sequence core using the pipeline Cassava 1.7
Raw sequences were mapped to reference genome (hg19) using BWA (v0.5.9) with defautl parameters
Peak calling was performed using MASC2 (v2.0.10)
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files were generated from bedGraph files that generated from MACS, Scores represent reads coverage signal

source_name: Prostate cancer 22Rv1 cells

growth_protocol: Prostate cancer cells were cultures (typically 2–3 × 106 cells into a T75 flask) in RPMI 1640 medium (Gibco, Unite State) with charcoal-stripped (steroid depleted) serum (CSS).

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, 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 (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq 2000 following the manufacturer's protocols.

treatment_protocol: 22Rv1 cells were transfected with non-target siRNA (designated as ARFL+/ARVs+), siRNA targeting ARV1/3/4/7 (designated as ARFL+/ARVs-) or siRNA targeting AR exon7 (designated as ARFL-/ARVs+), cultured with charcoal-stripped serum (CSS) medium for 72 hours, then treated with or without androgen (R1881) .

value: prostate cancer cells

tag: treatment

value: AR(N-20, Santa Cruz)


title: AR_total_ChIPSeq_R1881_rep2


title: AR_siARV_ChIPSeq_R1881_rep2


title: AR_siARFL_ChIPSeq_rep1

value: siARFL+EtOH


title: ChIP-Seq_H3K27_SppsKO_3


title: shNcor2 OSKM day9 replicate 2

city: Shenzhen

first: Andrew

middle: P

last: Hutchins

address: 1088 Xueyuan Rd

department: Bioinformatics

institute: Southern University of Science and Technology

data_processing:
rsem v1.2.17/bowtie2 v2.2.0 was used to align to the ensembl transcriptome (mm10, v76)
transcripts with more than 25 sequence tags in 2 or more timepoints were kept for further analysis
mapping tag counts were GC normalised using EDASeq v2.0.0
Genome_build: mm10
Supplementary_files_format_and_content: tab delimeted text file containing ensembl gene accession number, gene name and normalised abundance estimates for each transcript

source_name: Mouse MEFs, OSKM day 9

growth_protocol: Maintenance of mouse ESCs and fully reprogramed iPSCs was conducted in chemically defined N2B27-based medium: DMEM/F12 (HyClone) and Neurobasal (Gibco) mixed 1:1, supplemented with N2 (Invitrogene), B27 (Invitrogene), non-essential amino acids, GlutaMAX, sodium-pyruvate (Gibco), penicillin/streptomycin (HyClone), 0.1 mM β-mercaptoethanol (Sigma), 100 units/ml leukemia inhibitory factor (LIF) (Millipore), small-molecule inhibitors CHIR99021 (3 μM, Selleck), and PD0325901 (1 μM, Selleck)

extract_protocol:
TRIzol
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 15,000 MEFs were transducted once in 12-well plates using virus-containing supernatants generated by PlatE or HEK293T cells. After infection the medium was changed to mouse ESC serum-based medium (DMEM-High glucose supplemented with 15% FBS, non-essential amino acids, GlutaMAX, sodium-pyruvate, penicillin/streptomycin, 0.1 mM β-mercaptoethanol and 100 units/ml LIF or mouse ESC KSR medium (DMEM-High glucose supplemented with 15% Knockout Serum Replacement (Gibco), non-essential amino acids, GlutaMAX, sodium-pyruvate, penicillin/streptomycin, 0.1 mM β-mercaptoethanol, N2, 5 ng/ml basic fibroblast growth factor (bFGF) (Peprotech) and 100 units/ml LIF, and renewed daily.

tag: day

tag: shRNA transfection

value: shRNA Ncor2

tag: transfection

value: OSKM lentiviral transfection

tag: presumed cell type

value: Intermediate pluripotent reprogramed cells


title: shNcor2 OSKM day9 replicate 1

tag: strain


title: ChIP-Seq_H3K27_SppsKO_2


title: shNcor2 OSKM day5 replicate 1

source_name: Mouse MEFs, OSKM day 5


title: shNcor1 OSKM day9 replicate 2

value: shRNA Ncor1


title: ChIP-Seq_Input_WT_2


title: control_Hi-C_rep2

data_processing:
library strategy: HiC-seq
We cleaned illumina primer and adaptor sequence in the paired-end reads and trimed bridge linker by cutadaptor (paramaters: -m -b)
We then mapped each end of these trimed paired-end reads to human genome, GRCh37/hg19 assembly, respectively using BWA. Then we joined mapped reads into pairs by sequenced ID.
To reduce the PCR bias, we removed redundant paired-end reads.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: Tab-delimited table showing the interaction calling results

extract_protocol:
BL-Hi-C:cells are cross-linked with formaldehyde and nucleuses are isolated by lysis buffers. The chromain is then randomly fragmented by 4-bp enzymes (HaeIII, MboI or HindIII) and then two proximal fragments are connected by 20 bp biotinylated bridge linker in nucleus. A whole genome chromatin is extracted and sheared into 400 bp. Then the biotinylated junctions are captured by M-280 streptavidin magnetic beads. After amplification, a BL-Hi-C library is sequenced by illumina sequencer with paired-end strategy.
In house protocol which is similar as NEB library constructions (#7370)

treatment_protocol: 2x105/ml HL-60 cells in 100mm dish were treated with 1μM ATRA (1 mM stock in ethanol, Sigma, USA) for 4 days , referred as ATRA group. Cells treated with equal amount of ethanol (10μl added in 10ml medium) were referred as control group. Medium was changed and ATRA/ethanol was added again at day2.

tag: cell line

value: HL-60; ATCC CCL-240

value: peripheral blood

value: acute promyelocytic leukemia

value: ethanol for 4 days


title: AR_total_ChIPSeq_R1881_rep1

tag: chip antibody


title: ChIP-Seq_H3K27_SppsKO_1

value: third instar larval imaginal discs and brains


title: shNcor1 OSKM day9 replicate 1


title: ChIP-Seq_Input_WT_1


title: AR_siARFL_ChIPSeq_rep2


title: control_Hi-C_rep1

tag: tissue origin


title: ATRA_Hi-C_rep1

tag: disease

value: 1μM ATRA for 4 days


title: control_H3K27ac_ChIP-seq_rep2

data_processing:
Sequence adaptors were removed using cutadapt.
Then reads were aligned to human hg19 assembly using Bowtie with parameter: -n 2 -m 1 .
Histone modification peaks were called by MACS2 with parameter setting ‘-g hs --nomodel --broad’.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: Tab-delimited table showing the MACS peak calling results

extract_protocol:
Cells were treated with 1% formaldehyde to crosslink. Then cell membrane were broken using lysis buffer (50mM HEPES-KOH, 150mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 1% SDS). Chromatin were resuspended using FA lysis buffer (50mM HEPES-KOH, 150mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 0.1% SDS) and fragmented by ultra-sonication processor (cole-parmer, USA). Immunoprecipitation were performed overnight using dynabeads (Thermo Fisher) pre-incubated with anti-H3K4me3 and H3K27ac antibodies (abcam, England).
Library construction was performed using TruePrep DNA Library Prep Kit (Vazyme, China) according to the manufacture's protocol.

tag: treated with

value: H3K27ac (abcam, ab4729)


title: ChIP-Seq_Spps_WT_2


title: ChIP-Seq_Psc_WT_1


title: shNcor1 OSKM day5 replicate 1


title: shNcor1 OSKM day5 replicate 2


title: shNcor2 OSKM day5 replicate 2


title: ChIP-Seq_Psc_WT_2


title: ChIP-Seq_Pho_WT_3


title: shLuc OSKM day9 replicate 1

value: shRNA Luciferase


title: ChIP-Seq_Spps_WT_1


title: ChIP-Seq_Pho_WT_2


title: control_H3K27ac_ChIP-seq_rep1


title: ATRA_H3K27ac_ChIP-seq_rep1


title: shLuc OSKM day5 replicate 2


title: shLuc OSKM day5 replicate 1


title: shLuc OSKM day9 replicate 2


title: OSKM Day 13 HDAC3-YF H3K27ac ChIP-seq

data_processing:
Reads were aligned to the mouse mm10 genome using bowtie2 v2.2.0
Peaks were discovered using MACS 1.4 (NCoR/SMRT)
Peaks were discovered using Dfilter (H3K27ac)
Genome_build: mm10
Supplementary_files_format_and_content: Processed data files are peak bed files and bigWig tracks

source_name: MEFs transfected with OSKM and HDAC3-YF mutant plasmid Day 13

extract_protocol:
Cells were lysed in nuclei extraction buffer (50 mM HEPES KOH (pH 7.5), 140 mM NaCl, 1m M EDTA, 10% glycerol, 0.5% NP-40 alternative, 0.25% Triton X-100) supplemented with protease inhibitor cocktail (Roche) for 10 minutes at 4 °C. Cell pellets were resuspended in protein extraction buffer (10 mM Tris-HCl (pH 8.0), 200 mM NaCl, 1 mM EDTA and 0.5 mM EGTA) supplemented with protease inhibitor cocktail and incubated for 10 minutes at room temperature. For sonication, pellets were resuspended in sonication buffer (10 mM Tris-HCl (pH 8.0), 0.5 mM EGTA, 1% Triton X-100, protease inhibitor cocktail) and then fragmented with a Bioruptor (Diagenode) sonicator at 4°C for 30 cycles using high amplitude and 30 seconds ON and 30 seconds OFF cycles to produce size ranges between 200 and 500 base pairs. 2 mg of each antibody was prebound by incubating with Protein A+G Dynabeads (Invitrogen 100-07D) in blocking buffer (PBS supplemented with 0.5% TWEEN) for 6 hours at 4°C. Washed beads were added to the chromatin lysate and incubated overnight. Samples were washed twice with low salt washing buffer (20 mM Tris-HCl (pH 8.0), 150 mM NaCl, 2 mM EDTA, 0.1% SDS, 1% Triton X-100), twice with high salt washing buffer (20 mM Tris-HCl (pH 8.0), 500 mM NaCl, 2 mM EDTA, 0.1% SDS, 1% Triton X-100) twice with LiCl buffer (10 mM Tris-HCl, 250mM LiCl, 1mM EDTA, 1% NP-40, 1% Na-deoxycholate), twice with TE (10 mM Tris-HCl pH 8.0, 1mM EDTA), supplemented with 50 mM NaCl and eluted in elution buffer (50 mM Tris-HCl, 10 mM EDTA and 1% SDS). Eluates were incubated at 65°C for 20 minutes, followed by de-crosslinking at 65°C for 6-15 hours. Samples were diluted in TE buffer and then treated with RNaseA (Roche) for 60 minutes at 37°C, followed by incubation with proteinase K (Sigma) for 45 minutes at 56°C. DNA was purified with phenol:chloroform:isoamyl alcohol. The following antibodies were used for ChIP experiments: anti-NCoR (ABE251, Millipore), anti-SMRT (ab24551, Abcam), anti-H3K27ac (ab4729, Abcam).
Standard Illumina protocols

treatment_protocol: 15,000 MEFs were transducted once in 12-well plates using virus-containing supernatants generated by PlatE or HEK293T cells. After infection the medium was changed to mouse ESC serum-based medium (DMEM-High glucose supplemented with 15% FBS, non-essential amino acids, GlutaMAX, sodium-pyruvate, penicillin/streptomycin, 0.1 mM β-mercaptoethanol and 100 units/ml LIF or mouse ESC KSR medium (DMEM-High glucose supplemented with 15% Knockout Serum Replacement (Gibco), non-essential amino acids, GlutaMAX, sodium-pyruvate, penicillin/streptomycin, 0.1 mM β-mercaptoethanol, N2, 5 ng/ml basic fibroblast growth factor (bFGF) (Peprotech) and 100 units/ml LIF, and renewed daily. Cells were cross-linked in freshly prepared formaldehyde solution (1% final concentration for 10 minutes at room temperature), and then quenched with 125 mM glycine (5 minutes at room temperature). Fixed cells were washed with PBS, harvested, flash-frozen in liquid nitrogen and store at -80°C for further use.

value: OSKM+HDAC3-YF transfection

tag: antibody

value: ant-H3K27ac Abcam, GR167929-1 Lot# ab4729


title: control_H3K4me3_ChIP-seq_rep2

value: anti-H3K4me3 (abcam, ab8580)


title: control_H3K4me3_ChIP-seq_rep1


title: OSKM Day 13 FLAG H3K27ac ChIP-seq

source_name: MEFs transfected with OSKM and FLAG control plasmid Day 13

value: OSKM+FLAG control transfection


title: ChIP-Seq_Pho_WT_1


title: ChIP-Seq_Ph_WT_1


title: OSKM Day 9 HDAC3-YF H3K27ac ChIP-seq

source_name: MEFs transfected with OSKM and HDAC3-YF mutant plasmid Day 9


title: ATRA_H3K27ac_ChIP-seq_rep2


title: ChIP-Seq_Ph_WT_2


title: ATRA_Hi-C_rep2


title: ATRA_H3K4me3_ChIP-seq_rep2


title: ATRA_H3K4me3_ChIP-seq_rep1


title: ChIP-Seq_Pc_WT_2