title: Mutant (HCT116-CTNNB1-/Δ45) Rep2

city: Southampton

first: Rob

last: Ewing

address: Building 85, Life Sciences, Highfield Campus

institute: University of Southampton

description:
K_2
WT Beta-catenin allele disrupted

data_processing:
Casava v1.8.2 illumina HiScan control software
Reads were mapped to human genome hg19 using TopHat2 version 2.1.0 (Kim et al, 2013) with default settings and reads summarized by gene feature using htseq-count (Anders et al, 2014). Differential expression analysis was performed and p-values adjusted for fdr computed DeSeq (Anders et al, 2010).
Genome_build: hg19
Supplementary_files_format_and_content: gene-symbols with normalized raw read counts for each sample

source_name: Colorectal cancer cells

growth_protocol: Colorectal cancer cell lines HCT116-CTNNB1-/Δ45  and HCT116-CTNNB1WT/- were regularly maintained in McCoy-5A media (Life Technologies, 16600-108, Carlsbad, CA) containing 10% fetal bovine serum (Life Technologies, 10438-026, Carlsbad, CA) and 1% streptomycin-penicillin (Life Technologies, 15140-148, Carlsbad, CA) at 37°C  in CO2 incubator (5% CO2, 100% H2O). Cells were harvested by scraping the cells off plates and then washed with cold PBS twice for immediate use or storage (-80°C).

extract_protocol:
The quantity of total RNA in each sample was collected using Qubit (Invitrogen)
For library preparation, the Illumina TruSeq Total RNA v2 kit with Ribo Zero Gold for rRNA removal was used. This protocol starts by using the Ribo-Zero kit to remove ribosomal RNA (rRNA) from1 µg of Total RNA using a hybridization/bead capture procedure that selectively binds rRNA species using biotinylated capture probes. The resulting purified mRNA is used as input for the Illumina TruSeq kit in which libraries are tagged with unique adapter-indexes. Final libraries were validated using the Agilent High Sensitivity DNA kit (Agilent), quantified via Qubit, and diluted and denatured per Illumina's standard protocol.

tag: genotype/variation

value: Mutant (HCT116-CTNNB1-/delta 45)


title: Wild-type (HCT116-CTNNB1 WT/-) Rep3

status: Public on Jul 17 2018

type: SRA

country: United Kingdom

description:
D_3
Mutant Beta-catenin allele disrupted

library_source: transcriptomic

molecule: polyA RNA

organism: Homo sapiens

value: Wild-type

tag: cell line


title: Mutant (HCT116-CTNNB1-/Δ45) Rep3

description:
K_3
WT Beta-catenin allele disrupted


title: Wild-type (HCT116-CTNNB1 WT/-) Rep2

description:
D_2
Mutant Beta-catenin allele disrupted


title: Fig2B_Scc2PK_METScc1_30min_WCE

city: Oxford

first: Kim

last: Nasmyth

address: South Parks Road

department: Biochemistry

institute: University of Oxford

description: MET-Scc1 strain 30 min after release from G1 in the presence of methionine (K25222)

library_source: genomic

data_processing:
Library sequencing was carried out on the Ion Torrent Proton
The quality of the raw sequence data was examined using FastQC (Galaxy tool version 1.0.0) and trimming of reads was carried out using “trim sequences” (Galaxy tool version 1.0.0)
Any reads smaller than 50bp were removed using ‘Filter FASTQ’
The final reads were aligned to the Saccharomyces cerevisiae genome (sacCer3, SGD) or Candida glabrata genome (CBS138, genolevures) using Bowtie2 (Galaxy tool version 0.2) with the default (--sensitive) parameters
To generate an alignment in which all the sequences exclusively align to the Saccharomyces cerevisiae genome, the whole reads were first aligned to Candida glabrata genome and the unaligned reads were retrieved as a separate Fastq file. Subsequently, these unaligned reads were re-aligned to Saccharomyces cerevisiae genome and the resulting aligned BAM file therefore contained reads that were unique to Saccharomyces cerevisiae. A same strategy was used to generate alignments unique to Candida glabrata.
Genome_build: SacCer3 or Candida glabrata (ASM254v2)
Supplementary_files_format_and_content: fastq files contain reads from both organisms (S. cerevisiae and C. glabrata) but the BigWig files are S. cerevisiae only

molecule: genomic DNA

organism:
Saccharomyces cerevisiae
Nakaseomyces glabratus

growth_protocol: Yeast cells were grown in YPD to reach a density of 0.3-0.6 OD600.

extract_protocol:
To crosslink cells, 45ml of yeast culture was mixed with 4.2ml of fixation solution (50mM Tris-HCl pH 8.0, 100mM NaCl, 0.5mM EGTA, 1mM EDTA, 30% Formaldehyde) and incubated at 18°C for 30 minutes. The crosslinking reaction was quenched by incubating with 2ml of 2.5M Glycine for 5 min. Fixed cells were harvested, washed with ice-cold PBS and re-suspended in 1ml of ChIP lysis buffer (50mM Hepes-KOH pH 8.0, 140mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% Sodium deoxycholate, 1mM PMSF, Roche protease inhibitor). For each ChIP, 10 OD600 units of Saccharomyces cerevisiae cells mixed with 5 OD600 units of Candida glabrata cells were pelleted and re-suspended in 0.3ml of ChIP lysis buffer. Cells were mixed with glass beads and disrupted by FastPrep®-24 (MP Biomedicals, USA). The entire lysis was collected and sonicated at 4°C for 40 minutes using a Bioruptor (Diagenode, Belgium). The cell debris were removed by centrifugation and supernatants containing sheared chromatin with a size range from 100-800bp were adjusted to a final volume of 1ml with ChIP lysis buffer. Extracts were pre-cleared for 1 hour at 4°C with 30µl of Protein G Dynabeads (Invitrogen). 80µl of supernatant was taken as whole cell extract (W) and stored at -80°C. Five µg of anti-PK antibody (Bio-Rad) and 50 µl of Protein G Dynal beads (Invitrogen) was used for immunoprecipitation (6 hours-overnight, rotation at 4°C). The beads were subsequently washed for 5 minutes with the following buffers: 2Ã—ChIP lysis buffer; 3x ChIP high-salt lysis buffer (50mM Hepes-KOH pH 8.0, 500mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% Sodium deoxycholate, 1mM PMSF); 2Ã—ChIP wash buffer (10mM Tris-HCl pH 8.0, 0.25M LiCl, 0.5% NP-40, 0.5% sodium deoxycholate, 1mM EDTA, 1mM PMSF) and 1x TE buffer (10mM Tris-HCl pH 8.0, 1mM EDTA, 50mM NaCl). The immunoprecipitated chromatin was eluted by incubation of beads with 120µl of TES buffer (50mM Tris-HCl pH 8.0; 10mM EDTA; 1% SDS) at 65°C for 15 minutes. The supernatants were collected and termed the IP sample. The whole cell extract sample (W) was mixed with 40µl of TES3 buffer (50mM Tris-HCl pH 8.0; 10mM EDTA; 3% SDS). Both samples were de-crosslinked at 65°C overnight. RNA was degraded by incubating with 2-µl of RNAse A (10mg/ml, Roche) at 37°C for 1 hour and protein was subsequently removed by incubation with 10µl of Proteinase K (18mg/ml, Roche) at 65°C for 2 hours. DNA was purified using ChIP DNA Clean & Concentrator kit (Zymo Research, USA).
NEBNext Fast DNA Library Prep set for Ion Torrent, E6270

tag: tissue

tag: sac_cer strain

tag: can_gla strain

tag: antibody

value: none (input)


title: Wild-type (HCT116-CTNNB1 WT/-) Rep1

description:
D
Mutant Beta-catenin allele disrupted


title: Fig2B_Scc2PK_METScc1_45min_IP

description: MET-Scc1 strain 45 min after release from G1 in the presence of methionine (K25222)

source_name: 10 OD600 units of Saccharomyces cerevisiae cells mixed with 5 OD600 units of Candida glabrata cells

value: anti-PK antibody (Bio-Rad)


title: Fig2B_Scc2PK_METScc1_30min_IP

value: 10 OD600 units of Saccharomyces cerevisiae cells mixed with 5 OD600 units of Candida glabrata cells


title: Fig2B_Scc2PK_60min_WCE

description: Wild type strain 60 min after release from G1 in the presence of methionine (K21388)


title: Fig2B_Scc2PK_45min_WCE

description: Wild type strain 45 min after release from G1 in the presence of methionine (K21388)


title: Fig2B_Scc2PK_60min_IP


title: Mutant (HCT116-CTNNB1-/Δ45) Rep1

description:
K
WT Beta-catenin allele disrupted


title: Fig2A4DS2EFGH_Untagged_WCE

description: exponentially growing untagged wild type strain (K699)


title: Fig2B_Scc2PK_30min_WCE

description: Wild type strain 30 min after release from G1 in the presence of methionine (K21388)


title: Fig2AS2EFGH_Scc2PK_Cycling_IP

description: exponentially growing wild type strain (K21388)


title: Fig2B_Scc2PK_30min_IP


title: Fig2B_Scc2PK_45min_IP


title: FigS7C_V137K_WCE

description: exponentially growing scc1V137K strain (K17189)

organism: mixed sample

source_name: Saccharomyces cerevisiae cells


title: Fig2AS2EFGH_Scc2PK_Cycling_WCE


title: FigS7C_WT_IP

description: exponentially growing scc1WT strain (K17189)

value: anti-HA antibody (Roche)


title: Fig2AS2EFGH_Scc2PK_G1_WCE

description: wild type strain arrested in G1 with pheromone (K21388)


title: Fig2AS2EFGH_Scc2PK_G1_IP


title: Fig2A4DS2EFGH_Untagged_IP


title: FigS7C_WT_WCE


title: FigS7C_Untagged_WCE

description: exponentially growing untagged strain (K699)


title: FigS7C_V137K_IP


title: FigS7C_Untagged_IP


title: Roemerine

city: İstanbul

first: Fatma

middle: Gizem

last: Avci

address: Marmara Uni, Bioengineering  Dep., No:404  Kadıköy

department: Bioengineering

country: Turkey

institute: Marmara University

data_processing:
The raw reads were filtered. Data filtering includes removing adapter sequences, contamination and low-quality reads from raw reads
Sequencing reads were aligned to B. subtilis 168 genome using the quantify and annotate short reads (QuasR) package in R
Differential expression analyses were performed in R version 3.3.3 R using the package DESeq2
Genome_build: RefSeq accession number NC_000964.3
Supplementary_files_format_and_content: txt files (DESeq2 output) including log2 values of differentially expressed genes.

organism: Bacillus subtilis subsp. subtilis str. 168

source_name: Bacillus subtilis

growth_protocol: Cells were grown in nutrient broth at 37oC and 180 rpm.

extract_protocol:
One-hour alkaloid and DMSO treated cells were placed in RNAprotect Bacteria Reagent (Qiagen, Germany) and incubated for 5 minutes at room temperature. Cell suspensions were centrifuged at 5,000xg for 10 minutes. Total RNA isolation was achieved using RNeasy Mini Kit (Qiagen, Germany) according to manufacturer’s protocol with mechanical disruption at 6 m/s for 40 seconds (FastPrep Instrument, MP Biomedicals, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were treated with 75 mg/ L of alkaloids (berberine chloride hydrate, boldine, (+)-bulbocapnine hydrochloride or (-)-roemerine) as OD600 reached 0.55±0.05.

tag: strain


title: Bulbocapnine


title: Mybl2 overexpression replicate 2

city: Birmingham

first: Carl

last: Ward

address: Edgbaston

institute: University of Birmingham

data_processing:
CASAVA v1.8 was used to call bases
bcl2fastq-1.8.4 was used to convert
FASTQC v0.11.5 was used to trim low quality reads
TopHat v2.0.10 was used to align reads to genome using options: -r 100  --library-type=fr-firststrand
Cufflinks v2.2.1 was used to assembly transcripts using options: --library-type=fr-firststrand
Cuffmerge v2.2.1 was used to merge transcript assemblies
Cuffdiff v2.2.1 was used to quantify gene expression using options:  --library-type=fr-firststrand
Genome_build: mm10
Supplementary_files_format_and_content: gene_exp.diff, cuffidff output; A = control, B = Treatment

molecule: total RNA

organism: Mus musculus

source_name: Mouse embryonic fibroblasts

growth_protocol: DMEM with 1% Penicillin/Streptomycin, 2mM L-glutamine, 15% ESC qualified FBS, 1% non-essential amino acids, 0.1mM 2-mercaptoethanol, 0.01% LIF and 10μg/ml vitamin C. 200ng/ul Doxycycline was added to induce reprogramming.

extract_protocol:
RNA was extracted from cells using Trizol reagent by following the manufactorers guidelines. Purified RNA was treated with DNAse I to remove contaminating genomic DNA and then purified again using Qiagen minelute RNA-purification columns before library construction.
TruSeq Stranded mRNA with Ribo-Zero human/mouse/rat assay (Illumina) following the manufacturers protocol

treatment_protocol: Trasgenic (Tg) MEFs carrying doxycycline-inducible Yamanaka factors were transduced with lentiviral particles encoding AmCyan or Mybl2-AmCyan and then reprogramming was induced by addition of doxycycline. Cells were collected after 3 days of reprogramming.

tag: cell type

value: embryonic fibroblast


title: Control replicate 1

value: Control (AmCyan)


title: DMSO


title: Boldine


title: Control replicate 2


title: Mybl2 overexpression replicate 1


title: GFP_8

city: Minato-ku

first: Hideto

last: Koso

state: Tokyo

address: 4-6-1 Shirokanedai

country: Japan

institute: Institute of Medical Science, The University of Tokyo

data_processing:
bcl2fastq-1.8.4 software used for basecalling with default parameters.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the mouse mm9 reference genome assembly with the option (--coverage-search --max-multihits 50).
FPKM (Fragments Per Kilobase of transcript per Million mapped reads) with Cufflinks ver. 2.1.1 with the default option.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

source_name: Infiltrating macrophages

extract_protocol:
RNA was harvested retinas using Sepazol reagent. The RNA-seq library was constructed using the mRNA-seq sample preparation kit (Illumina).
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: strain background

value: C57BL/6; 129 mixed

tag: age

value: ~5 months of age

value: Msi1-CreERT2/+; R26R-DTA/+

value: retina

tag: time point

value: day 7 post-injury

tag: tissue subtype

value: Infiltrating macrophages


title: GFP_7


title: GFP_6


title: GFP_5


title: 6_48 control [miRNA-seq]

status: Public on Jul 16 2018

city: Taipei

first: Ting-Shuan

last: Wu

address: 5F ,No 1, Sec 1, Jen-Ai Rd

country: Taiwan

institute: ntu

description: mRNA expression after 0 mM ochratoxin A treated embryos from 6-48 hpf

data_processing:
Initially, the sequences generated went through a filtering process to obtain qualified reads. ConDeTri was implemented to trim or remove the reads according to the quality score.
Qualified reads after filtering low-quality data were analyzed using miRDeep2 to clip the 3′ adapter sequence and discarding reads shorter than 18 nucleotides, before aligning reads to the _Zebrafish_ genome from UCSC.
Only reads that mapped perfectly to the genome five or less times were used for miRNA detection, since miRNAs usually map to few genomic locations. MiRDeep2 estimates expression levels of known miRNAs, and also identifies novel miRNAs.
Genome_build: GCF_000002035.4
Supplementary_files_format_and_content: bed file for the location of miRNA mapped to chromosome

organism: Danio rerio

growth_protocol: zebrafish embryos were selected at 6 hph with normal development.

extract_protocol:
Total RNA was extracted by Trizol® Reagent (Invitrogen, USA) according to the instruction manual. RNA purified was quantified at OD260nm by using a ND-1000 spectrophotometer (Nanodrop Technology, USA) and qualitated by using a Bioanalyzer 2100 (Agilent Technology, USA) with RNA 6000 labchip kit (Agilent Technologies, USA).
The small RNA library construction and deep sequencing was carried out at biotechnology company (Welgene, Taipei, Taiwan). Samples were prepared using Illumina sample preparation kit according to the TruSeq Small RNA Sample Preparation Guide.The 3′ and 5′ adaptors were ligated to total RNA and reverse transcription followed by PCR amplification. The enriched cDNA constructs were size-fractionated and purified on a 6% polyacrylamide gel electrophoresis and the bands containing the 18-40 nucleotide RNA fragments (140-155 nucleotide in length with both adapters).  Libraries were sequenced on an Illumina GAIIx instrument (50 cycle single read ). Sequencing data was processed with the Illumina software

treatment_protocol: 6 hpf embryos  were treated with ochratoxin A (0.5 mM) till 48 hpf.

value: Wild Type AB line

tag: developemental stage

value: 6 hpf embryos

tag: exposed to

value: none (control)


title: 6_48 0.5µM OTA [miRNA-seq]

description: mRNA expression after 0.5 mM ochratoxin A treated embryos from 6-48 hpf

value: 0.5 µM ochratoxin A from 6 hpf to 48 hpf


title: cont_3

source_name: Microglia

value: Microglia


title: cont_4


title: cont_2


title: Berberine


title: YWT-HC-1905

city: Irvine

first: Christophe

middle: Nicolas

last: Magnan

state: CA

address: Institute for Genomics and Bioinformatics 236, Info & Computer Science Building 2

country: USA

institute: University of California, Irvine

description:
Tissue harvested directly from home cage
RPKM_Values.xlsx
Differential_Analysis.xlsx

data_processing:
Basecalling performed using RTA version 1.13.48
Demultiplexing performed using CASAVA version 1.8.2
Alignments to reference assembly mm10 performed using ELAND v2e and Bowtie2
Mapping results filtering and selection performed using in-house tools
Expression analysis performed using CASAVA version 1.8.2
Differential analysis performed using CyberT: http://cybert.ics.uci.edu
Genome_build: mm10
Supplementary_files_format_and_content: RPKM values for each replicate have been combined in a single excel file (RPKM_Values.xlsx), the differential analysis results from CyberT have been summarized and annotated in a single excel file (Differential_Analysis.xlsx)

source_name: dorsal hippocampal tissue

extract_protocol:
RNA was isolated from bilateral, dorsal hippocampus using the RNeasy minikit (Qiagen, 74104)
cDNA libraries for each group were prepared as described in the TruSeq RNA Sample Preparation v2 Guide (Illumina)
Samples were multiplexed so that each behavioral group was represented in each flow cell of the sequencer. 10nM of each library was pooled together in four multiplex libraries and sequenced on an IlluminaHiSeq 2500 instrument by the Genomics High-Throughput Facility (GHTF) at the University of California, Irvine.

value: Wild Type

value: 2-4 months

value: directly from home cage


title: YWT-BV-1923

description:
Tissue harvested 60min following behavior
RPKM_Values.xlsx
Differential_Analysis.xlsx

value: 60min following behavior


title: YWT-HC-1873


title: YWT-BV-1915


title: YWT-HC-1940


title: YWT-BV-1924


title: YWT-HC-1907


title: YWT-BV-1906


title: OWT-HC-129A

value: 18-20 months


title: OWT-HC-131A


title: YWT-BV-1913


title: OWT-HC-110A


title: OWT-HC-126A


title: OWT-HC-114A


title: OWT-HC-107A


title: cont_1


title: OWT-BV-116C


title: OWT-BV-109C


title: Fig5AB_Scc1PK_WT_IP

description: WT strain 75 min after release from G1 at 37°C (K22005)

value: 10 OD600 units of Saccharomyces cerevisiae cells mixed with 5 OD600 units of Candida glabrata cells

value: anti-PK antibody (Bio-Rad)


title: OWT-BV-106C


title: H3F-HC-124B


title: OWT-BV-103C


title: OWT-BV-104C


title: H3F-HC-121B


title: YWT-BV-1935


title: H3F-HC-117B


title: YWT-HC-1931


title: H3F-HC-111B


title: H3F-HC-115B


title: H3F-HC-101B


title: H3F-BV-128D


title: H3F-HC-105B


title: H3F-HC-112B


title: H3F-BV-123D


title: YWT-HC-1908


title: H3F-BV-119D


title: H3F-BV-125D


title: TSS TEX not treated

city: Yuseong-gu

first: Yoseb

last: Song

state: Daejeon

address: 291 Daehak-ro

country: South Korea

institute: KAIST

description: RNA 5'-polyphosphatase treated total RNA

data_processing:
Using CLC Genomics Workbench, the trimmed reads were aligned to the assembled E. limosum ATCC 8486 genome with following parameters (mismatch cost = 2, deletion cost = 3, insertion cost = 3, length fraction = 0.8, and similarity fraction = 0.8), and the uniquely mapped reads were retained.
For RNA-seq and Ribo-seq, the gene expressions were normalized using DESeq2 package in R with default parameters
Genome_build: Eubacterium limosum ATCC 8486
Supplementary_files_format_and_content: tab-delimited text files with mapped reads on genes

organism: Eubacterium limosum

source_name: Cell culture

growth_protocol: Eubacterium limosum ATCC 8486 was obtained from Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures (DSMZ, Germany) and cultivated anaerobically at 37 °C in DSM 135 media supplemented with 5 g l-1 glucose or H2/CO2 (80:20) at a pressure of 200 kPa for the heterotrophic and the autotrophic growth conditions, respectively.

extract_protocol:
For total RNA extraction, the cells were resuspended in 500 µl of lysis buffer composed of 20 mM Tris-HCl (pH 7.4), 140 mM NaCl, 5 mM MgCl2, and 1% Triton X-100. Resuspended cells were frozen in liquid nitrogen and then ground with pestle and mortar. The powdered cells were thawed and the cell debris was removed by centrifugation at 4,000g for 15 min at 4 °C. Total RNA was then isolated using Trizol (Thermo Scientific, Waltham, USA) according to the manufacturer’s instruction. To remove remaining genomic DNA in the purified RNA sample, 4 U of rDNase I (Ambion, Waltham, USA) was treated to the isolated RNA for 1 h at 37 °C, followed by the incubation at 75 °C for 10 min. For ribosome profiling, the CM treated cells were washed using 500 µl polysome buffer that composed of 20 mM Tris-HCl (pH 7.4), 140 mM NaCl, 5 mM MgCl2, and 100 µM CM. The cells were resuspended in lysis buffer that composed of 20 mM Tris-HCl (pH 7.4), 140 mM NaCl, 5 mM MgCl2, 100 µM CM, and 1% Triton X-100. The resuspended cells were frozen in liquid nitrogen and ground with pestle and mortar. The powdered cells were recovered by centrifugation at 4,000g for 15 min at 4 °C, then the supernatant was transferred to a new tube. For further clarification, the supernatant was additionally centrifuged at 16,000g for 10 min at 4 °C. To degrade RNA that unprotected by ribosome, 400 U of MNase (NEB, Ipswich, USA), 2 µl of BSA (1 mg ml-1), 20 µl of 10× MNase buffer were added and incubated at 37 °C for 2 h with gentle rotation. For inactivation of the reaction, 10 µl of EGTA (0.5 M) was added to the sample. Monosome fraction was recovered using Microspin S-400 HR (GE, Pittsburgh, USA) in accordance to the manufacturer’s instruction. The recovered ribosome bound RNA was isolated by using Trizol
For RNA-seq, Ribosomal RNAs (rRNA) were removed by using Ribo-ZeroTM rRNA Removal Kit for Meta-bacteria (Epicentre, Madison, USA) according to the manufacturer’s instruction, and the rRNA-depleted RNA quality was checked with Agilent 2200 TapeStation system (Agilent Technologies, Santa Clara, USA). Using TrueSeq Stranded mRNA Library Prep Kit (Illumina, San Diego, USA). For ribosome profiling seq, the remaining rRNAs were removed by using Ribo-ZeroTM rRNA Removal Kit for Meta-bacteria. For phosphorylation reaction, samples were denatured at 80 °C for 90 s, equilibrated to 37 °C, and incubated at 37 °C for 1 h with 5 µl of 10× T4 PNK buffer (NEB, Ipswich, USA), 20 U of SUPERase In RNase Inhibitor, and 10 U of T4 PNK (NEB, Ipswich, USA). After purification of the RNA samples using RNeasy MinElute Column, the concentration of the purified RNA was measured using Qubit RNA HS assay kit (Invitrogen, Waltham, USA). For library construction, small RNA library prep kit for Illumina (NEB, Ipswich, USA) was used. For differential RNA-seq, the rRNA-depleted RNA was split into three samples for the construction of three different libraries (TEX, TEX, and TAP). For the preparation of TEX library, TerminatorTM 5’-Phosphate-Dependent Exonuclease (Epicentre, Madison, USA) was treated with 2 µl of 10× TerminatorTM Reaction Buffer A (Epicentre, Madison, USA) and 20 U of SUPERase In RNase Inhibitor (Thermo Scientific, Waltham, USA). For the preparation of TEX and TAP libraries, TEX treatment was omitted but 2 µl of 10× TerminatorTM Reaction Buffer A and 20 U of SUPERase In RNase Inhibitor were added. All of the samples were incubated at 30 °C for 1 h, and then the reaction was terminated by adding 1 µl of 100 mM EDTA (pH 8.0). To ligate 5 RNA adaptor, 20 U of RNA 5-polyphosphatase (Epicentre, Madison, USA) was treated to TEX and TEX samples. For TAP sample, the RNA 5-polyphosphatase treatment was omitted. 2 µl of 10× RNA 5’-phosphatase Reaction buffer (Epicentre, Madison, USA) was added to all samples with 20 U of SUPERase In RNase Inhibitor and incubated at 37 °C for 1 h. The samples were purified by phenol-chloroform extraction and ethanol precipitation. 10 pM of 5 RNA adaptor (5’- GUUCAGAGUUCUACAGUCCGACGAUC-3’) was added to the purified mRNA with 2 µl of T4 RNA ligase buffer (Thermo Scientific, Waltham, USA), 2 µl of BSA (1 mg ml-1) (Thermo Scientific, Waltham, USA), 20 U T4 RNA ligases (Thermo Scientific, Waltham, USA), and 20 U of SUPERase In RNase Inhibitor (Epicentre, Madison, USA). The samples were then incubated at 37 °C for 90 min, followed by incubating at 70 °C for 10 min. For cDNA synthesis, 10 pM of the random hexamer 3’ overhanging primer (5’-GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTNNNNNN-3’) was added to the purified sample with 1 µl of 10 mM dNTPs (Invitrogen, Waltham, USA) and incubated at 65 °C for 10 min. Subsequently, 2 µl of 10× RT buffer, 2 µl of 100 mM DTT, 4 µl of 25 mM MgCl2, 20 U of SUPERase In RNase Inhibitor (Epicentre, Madison, USA), and 200 U of SuperScript III Reverse Transcriptase (Invitrogen, Waltham, USA) were added. The reaction was incubated at 25 °C for 10 min, at 50 °C for 60 min, 85 °C for 5 min, and cooled down to 4°C. To remove remaining RNA, 2 U of RNase H (Invitrogen, Waltham, USA) was added and incubated at 37 °C for 20 min. The cDNA fraction at a size range between 120 bp and 400 bp was purified on 2% agarose gel using MinElute Gel Extraction kit (Qiagen, Hilden, Germany). The purified library was amplified with indexed primer for Illumina sequencing platform and monitored by CFX96TM Real-Time PCR Detection System (Bio-Rad, Hercules, USA) with stopping the amplification at the beginning of the saturation point. The amplified cDNA was size-selected at a range between 150 bp and 400 bp, which was then sequenced using the 100 bp read recipe on Illumina Hiseq2500.
RNA-seq, Ribosome profiling seq, differential RNA-seq

treatment_protocol: Only for ribosome profiling samples, at the sampling time, 100 µM chloramphenicol (CM) was added to the cultures and further incubated at 37 °C for 10 min.

value: ATCC 8486


title: H3F-BV-118D


title: H3F-BV-113D


title: H3F-BV-108D


title: OWT-BV-127C


title: TSS TEX treated

description: Terminator 5' phosphate dependent exonuclease and RNA 5'-polyphosphatase treated total RNA


title: Autotrophic RNA rep1

description: total RNA


title: Heterotrophic Ribo rep2

description: ribosome bound RNA


title: H3F-BV-102D


title: Heterotrophic RNA rep2

description: total RNA


title: Heterotrophic Ribo rep1

description: ribosome bound RNA


title: Heterotrophic RNA rep1

description: total RNA


title: CPPU 5 ppm

status: Public on Jul 15 2018

city: nanjing

first: wu

last: wang

address: Weigang1 hao

country: China

institute: Nanjing Agricultural University

data_processing:
The primary raw reads obtained by Illumina HiSeqTM2000 were filtered to remove low quality reads which were low complexity or containing adaptor sequence
The cleaned reads were aligned to the reference genome of Vitis using HISAT software.
GO functional enrichment analysis and KEGG pathway analysis was continued with Blast2Go. KEGG pathway analysis is also used for the target gene candidates. In organisms, genes usually interact with each other to play different roles in certain biological function. The analysis based on pathways could facilitate the understanding of biological functions of genes. KEGG is the major public pathway-related database[8]. KEGG pathway analysis identifies significantly enriched metabolic pathways or signal transduction pathways in target gene candidates comparing with the whole reference gene background. The calculating formula is the same as that in GO analysis. Here N is the number of all genes with KEGG annotation, n is the number of target gene candidates in N, M is the number of all genes annotated to a certain pathway, and m is the number of target gene candidates in M. Genes with FDR<=0.05 are considered as significantly enriched in target gene candidates
DEGseq2 was used for gene expression analysis.
Genome_build: ftp://ftp.ncbi.nlm.nih.gov/genomes/Vitis_vinifera/
Supplementary_files_format_and_content: text file with gene IDs, expression values, and gene sequences

organism: Vitis vinifera

source_name: fruit

growth_protocol: All plants were grown under standard cultivation condition

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

treatment_protocol: Selected clusters were treated with CPPU 0.5ppm and 10 ppm respectively.

value: 110 days

value: fruit

tag: cultivar

value: Shine Muscat


title: CPPU 0 ppm


title: WGBS from WT system, Day4

city: Rehovot

first: Noa

last: Novershtern

address: Weizmann Institute

department: Molecular Genetics

country: Israel

institute: Weizmann Institute of Science

data_processing:
We used Illumina CASAVA 1.8.2 software to generate fastq files.
Reads were aligned to mm10 reference genome using proprietary software, which is based on bowtie2, and is available for download here: https://tanaylab.bitbucket.io/misha/. In  cases  where  the  two  reads  were  not  aligned  in  a concordant manner, the reads were discarded.
for each CpG site, the numbers of methylated and unmethylated reads were counted.
Genome_build: mm10
Supplementary_files_format_and_content: The tab file is the output of misha software. Each file consists of chromosomal location (like a bed file), the number of methylated reads and number of unmethylated reads in each location.

source_name: WT cell line, Day4 post DOX induction

growth_protocol: Maintenance and reprogramming (Day 3 and beyond) of murine naïve pluripotent cells were conducted in bovine serum-free N2B27-based media or KSR media:   N2B27- based media: 500ml KO-DMEM (Invitrogen), 5ml N2 supplement (Invitrogen; 17502048), 5ml B27 supplement (Invitrogen; 17504044), 15% knockout serum replacement (Invitrogen – 10828), 1mM glutamine (Invitrogen), 1% nonessential amino acids (Invitrogen), 0.1mM β-mercaptoethanol (Sigma), penicillin-streptomycin (Invitrogen), 5mg/ml BSA (Sigma).   KSR media: 500 ml DMEM (Invitrogen), 1mM glutamine (Invitrogen), 1% nonessential amino acids (Invitrogen), 0.1mM β-mercaptoethanol (Sigma), penicillin- streptomycin (Invitrogen).   Naïve conditions for murine PSCs included 10μg recombinant human LIF (Millipore; LIF1005). Where indicated 2i was added 48 hours after OSKM induction: small-molecule inhibitors CHIR99021 (CH, 3μM- Axon Medchem) and PD0325901 (PD 0.2 or 1μM - Axon Medchem).

extract_protocol:
Cells were harvested at different time points according to the protocol. DNA was then isolated from cells using the Quick-gDNA mini prep kit (Zymo), followed by bisulfite convertion using the EZ DNA Methylation-Gold kit (Zymo).
Sequencing libraries were created using the EpiGnome Methyl-Seq (Epicentre) .

treatment_protocol: Reprogramming dynamics samples were generated by adding Dox to Secondary MEF. iPSC samples were harvested after 3-4 days of growth in N2B27 2i\LIF medium. Reprogramming samples of days 3-8, and iPSC samples were plated on irradiated human foreskin fibroblasts (HFF).

value: WT cell line

tag: genotype

value: WT-2, isogenic to Gatad2a-/-

tag: stage of reprogramming


title: CPPU 10ppm


title: WGBS from Gatad2a-/- system, Day8

source_name: Gatad2a-/- cell line, Day8 post DOX induction

value: Gatad2a-/- cell line


title: WGBS from WT system, MEF

source_name: WT Mouse embryonic fibroblasts

value: MEF


title: WGBS from Gatad2a-/- system, Day4

source_name: Gatad2a-/- cell line, Day4 post DOX induction


title: Autotrophic Ribo rep1

description: ribosome bound RNA


title: WGBS from Gatad2a-/- system, Day2

source_name: Gatad2a-/- cell line, Day2 post DOX induction


title: Autotrophic Ribo rep2

description: ribosome bound RNA


title: WGBS from Gatad2a-/- system, Day6

source_name: Gatad2a-/- cell line, Day6 post DOX induction


title: ATAC-seq from Gatad2a system, MEF

data_processing:
We used Illumina CASAVA 1.8.2 software to generate fastq files.
Reads were aligned to mm10 mouse genome using Bowtie2 with the parameter -X2000 (allowing fragments up to 2 kb to align).
Duplicated aligned reads were removed using Picard MarkDuplicates tool with the command REMOVE_DUPLICATES=true.
To identify chromatin accessibility signal we considered only short reads (≤ 100bp) that correspond to nucleosome free region.
To detect and separate accessible loci in each sample, we used MACS version 1.4.2-1 with --call-subpeaks flag (PeakSplitter version 1.0).
93,137 enhancers with co-localized ATAC-seq and H3K27ac peaks were identified.
For each promoter and each enhancer we report here the read depth in a 50-bp bins, 1 Kb around the TSS or 300 bp around the enhancer summit.
Genome_build: mm10
Supplementary_files_format_and_content: Promoter "matrix" files contain for each TSS, the number of reads in 50bp bins, spanning 1Kb window around the TSS. 1st column - gene esemble ID, columns 2-21 - read num  in 50bp bins. Enhancer "matrix" files contain for each identified enhancer, the number of reads in 50bp bins, spanning 300bp window around the enhancer summit. 1st column - enhaner genomic interval. 2nd column - enhancer ID number, columns 3-8 - read num in 50bp bins.

source_name: Gatad2a cell line, MEF post DOX induction

growth_protocol: Maintenance and reprogramming (Day 3 and beyond)  of murine naïve pluripotent cells were conducted in bovine serum-free N2B27-based media or KSR media:   N2B27- based media: 500ml KO-DMEM (Invitrogen), 5ml N2 supplement (Invitrogen; 17502048), 5ml B27 supplement (Invitrogen; 17504044), 15% knockout serum replacement (Invitrogen – 10828), 1mM glutamine (Invitrogen), 1% nonessential amino acids (Invitrogen), 0.1mM β-mercaptoethanol (Sigma), penicillin-streptomycin (Invitrogen), 5mg/ml BSA (Sigma).   KSR media: 500 ml DMEM (Invitrogen) , 1mM glutamine (Invitrogen), 1% nonessential amino acids (Invitrogen), 0.1mM β-mercaptoethanol (Sigma), penicillin- streptomycin (Invitrogen).   Naïve conditions for murine PSCs included 10μg recombinant human LIF (Millipore; LIF1005). Where indicated 2i was added 48 hours after OSKM induction: small-molecule inhibitors CHIR99021 (CH, 3μM- Axon Medchem) and PD0325901 (PD 0.2 or 1μM - Axon Medchem).

extract_protocol:
50,000 cells were centrifuged (500g, 3 minutes), then washed using 50 μL of cold PBS, and centrifuged again (500g for 3 min). Cells were lysed using cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% IGEPAL CA-630). Immediately after lysis, nuclei were spun at 500g for 10 min using a refrigerated centrifuge. Next, the pellet was re-suspended in the transposase reaction mix (25 μL 2× TD buffer, 2.5 μL transposase (Illumina) and 22.5 μL nuclease-free water). The transposition reaction was carried out for 30 minutes at 37 °C and immediately transfered to ice. The sample was then purified using Qiagen MinElute kit.
Following purification, the library fragments were amplified using custom Nextera PCR primers 1 and 2 for a total of 12 cycles. Following PCR amplification the libraries were purified using a Qiagen MinElute Kit.

treatment_protocol: Reprogramming dynamics samples were generated by adding Dox to Secondary MEF. ES and iPSC samples were harvested after 3-4 days of growth in N2B27 2i\LIF medium. Reprogramming samples of days 3-8, ES and iPSC samples were plated on irradiated human foreskin fibroblasts (HFF).


title: ATAC-seq from Gatad2a system, Day8

source_name: Gatad2a cell line, Day8 post DOX induction


title: PolyA_WT-2_Day8

description: PolyA RNA-seq from WT-2 system, Day8

data_processing:
We used Illumina CASAVA 1.8.2 software to generate fastq files.
Tophat software version 2.0.10 was used to align reads to mouse mm10 reference genome
FPKM values were calculated over all genes in mm10 assembly GTF (UCSC, December 2011), using cufflinks version 2.2.1.
Genome_build: mm10

source_name: WT-2 cell line, Day8 post DOX induction

growth_protocol:
Maintenance and reprogramming (Day 3 and beyond)  of murine naïve pluripotent cells were conducted in bovine serum-free N2B27-based media or KSR media:
N2B27- based media: 500ml KO-DMEM (Invitrogen), 5ml N2 supplement (Invitrogen; 17502048), 5ml B27 supplement (Invitrogen; 17504044), 15% knockout serum replacement (Invitrogen – 10828), 1mM glutamine (Invitrogen), 1% nonessential amino acids (Invitrogen), 0.1mM β-mercaptoethanol (Sigma), penicillin-streptomycin (Invitrogen), 5mg/ml BSA (Sigma).
KSR media: 500 ml DMEM (Invitrogen) , 1mM glutamine (Invitrogen), 1% nonessential amino acids (Invitrogen), 0.1mM β-mercaptoethanol (Sigma), penicillin- streptomycin (Invitrogen).
Naïve conditions for murine PSCs included 10μg recombinant human LIF (Millipore; LIF1005). Where indicated 2i was added 48 hours after OSKM induction: small-molecule inhibitors CHIR99021 (CH, 3μM- Axon Medchem) and PD0325901 (PD 0.2 or 1μM - Axon Medchem).

extract_protocol:
Total RNA was isolated from indicated cell lines, and extracted from Trizol pellets by Direct-zol RNA MiniPrep kit (Zymo) according to manufacturer’s manual.
RNA was extracted from Trizol pellets, and utilized for RNA-Seq by TruSeq RNA Sample Preparation Kit v2 (Illumina) according to manufacturer’s instruction.

value: WT-2 cell line


title: WGBS from Gatad2a-/- system, IPS

source_name: Gatad2a-/- cell line, Established induced pluripotent stem cells

value: IPS


title: ATAC-seq from Gatad2a system, Day6

source_name: Gatad2a cell line, Day6 post DOX induction


title: PolyA_WT-2_IPS

description: PolyA RNA-seq from WT-2 system, IPS

source_name: WT-2 cell line, Established induced pluripotent stem cells


title: PolyA_WT-2_Day6

description: PolyA RNA-seq from WT-2 system, Day6

source_name: WT-2 cell line, Day6 post DOX induction


title: PolyA_WT-2_Day2

description: PolyA RNA-seq from WT-2 system, Day2

source_name: WT-2 cell line, Day2 post DOX induction


title: PolyA_WT-2_Day4

description: PolyA RNA-seq from WT-2 system, Day4

source_name: WT-2 cell line, Day4 post DOX induction


title: Autotrophic RNA rep2

description: total RNA

source_name: Cell culture


title: ATAC-seq from Gatad2a system, Day4

source_name: Gatad2a cell line, Day4 post DOX induction


title: PolyA_Gatad2a-/-_IPS

description: PolyA RNA-seq from Gatad2a-/- system, IPS


title: PolyA_Gatad2a-/-_Day8

description: PolyA RNA-seq from Gatad2a-/- system, Day8


title: WGBS from WT system, IPS

source_name: WT cell line,  Established induced pluripotent stem cells


title: PolyA_Gatad2a-/-_Day7

description: PolyA RNA-seq from Gatad2a-/- system, Day7

source_name: Gatad2a-/- cell line, Day7 post DOX induction


title: WGBS from Gatad2a-/- system, MEF

source_name: Gatad2a-/- cell line, Mouse embryonic fibroblasts


title: PolyA_Gatad2a-/-_Day6

description: PolyA RNA-seq from Gatad2a-/- system, Day6


title: PolyA_Gatad2a-/-_Day1

description: PolyA RNA-seq from Gatad2a-/- system, Day1

source_name: Gatad2a-/- cell line, Day1 post DOX induction


title: PolyA_Gatad2a-/-_Day3

description: PolyA RNA-seq from Gatad2a-/- system, Day3

source_name: Gatad2a-/- cell line, Day3 post DOX induction


title: PolyA_Gatad2a-/-_Day2

description: PolyA RNA-seq from Gatad2a-/- system, Day2

source_name: Gatad2a-/- cell line, Day2 post DOX induction


title: PolyA_Gatad2a-/-_Day4

description: PolyA RNA-seq from Gatad2a-/- system, Day4

source_name: Gatad2a-/- cell line, Day4 post DOX induction


title: WGBS from Mbd3f/- system, Day7

source_name: Mbd3f/- cell line, Day7 post DOX induction

value: Mbd3f/- cell line


title: PolyA_Gatad2a-/-_MEF

description: PolyA RNA-seq from Gatad2a-/- system, MEF


title: PolyA_WT-2_MEF

description: PolyA RNA-seq from WT-2 system, MEF

source_name: WT-2 cell line, Mouse embryonic fibroblasts


title: WGBS from Mbd3f/- system, Day6

source_name: Mbd3f/- cell line, Day6 post DOX induction


title: WGBS from Mbd3f/- system, Day5

source_name: Mbd3f/- cell line, Day5 post DOX induction


title: WGBS from Mbd3f/- system, IPS

source_name: Mbd3f/- cell line, Established induced pluripotent stem cells


title: WGBS from Mbd3f/- system, Day8

source_name: Mbd3f/- cell line, Day8 post DOX induction


title: WGBS from Mbd3f/- system, Day2

source_name: Mbd3f/- cell line, Day2 post DOX induction


title: WGBS from Mbd3f/- system, MEF

source_name: Mbd3f/- cell line, Mouse embryonic fibroblasts


title: ATAC-seq from Mbd3f/- system, Day8


title: ATAC-seq from V6.5 WT ES cells

source_name: v6.5 WT Embryonic stem cells

value: V6.5 WT cell line

value: ES

value: V6.5 WT


title: PolyA_Gatad2a-/-_Day5

description: PolyA RNA-seq from Gatad2a-/- system, Day5

source_name: Gatad2a-/- cell line, Day5 post DOX induction


title: WGBS from Mbd3f/- system, Day1

source_name: Mbd3f/- cell line, Day1 post DOX induction


title: WGBS from Mbd3f/- system, Day4

source_name: Mbd3f/- cell line, Day4 post DOX induction


title: WGBS from Mbd3f/- system, Day3

source_name: Mbd3f/- cell line, Day3 post DOX induction


title: ATAC-seq from Mbd3f/- system, IPS


title: ATAC-seq from Mbd3f/- system, Day6


title: ATAC-seq from Mbd3f/- system, Day3


title: ATAC-seq from Mbd3f/- system, Day7


title: ATAC-seq from Mbd3f/- system, Day2


title: ATAC-seq from Mbd3f/- system, Day4


title: ATAC-seq from Mbd3f/- system, Day1


title: ATAC-seq from Mbd3f/- system, MEF


title: P14m6A_cKO1

city: Beijing

first: Xiuying

last: Liu

address: Yard 28, Science Park Road, Changping District

institute: Changping Laboratory

description: cKO m6A-Seq at P14

data_processing:
Raw reads were mapped to mouse reference genome using HISAT2
Construct transcripts using StringTie
Filter transcripts using TACO
Generate bigwig files for visualization
Identify differentially expressed genes using edgeR
Peak calling using PePr
Genome_build: mm10
Supplementary_files_format_and_content: bigwig, processed using bamCoverage from deeptools with RPKM and PePr's scale factor.

source_name: Brain tissue

extract_protocol:
Mouse cerebellums were harvested after cervical dislocation, and were homogenized either by grounding into homogenous powder using mortar and pestle cooled in liquid-nitrogen bath or by mechanical homogenizer using beating beads. Total RNA from mouse cerebella was extracted using TRIzol reagent (Invitrogen). mRNA was purified with Dynabeads mRNA Purification Kit (Thermo) according to the manufacturer’s manual, followed by DNase I (M6101, Promega) treatment to remove genomic DNA. RNA concentration was measured using Nanodrop 1000 (Thermo). Purified mRNA was randomly fragmented to size around 100 nucleotides using Ambion RNA fragmentation reagents, and then subjected to immunoprecipitation (IP) with anti-m6A antibody (202003, Synaptic Systems) and protein-A magnetic beads (88845, Pierce) in MeRIP buffer (150 mM NaCl, 10 mM Tris-HCl pH7.4, 0.1% NP-40) supplemented with RNase inhibitor. m6A-containing mRNA fragments were eluted with N6-methyladenosine in MeRIP buffer and were purified using TRIzol reagent.
Poly (A) RNA from 1 mg total RNA or purified mRNA and purified m6A-containing fragments were used to generate the cDNA libraries, respectively, according to TruSeq RNA Sample Prep Kit protocol.

value: C57BL/6 and DBA2

value: Brain

tag: genotype/variation

value: knockout of Mettl3

tag: developmental stage

value: Postnatal 14 (P14)


title: P14m6A_WT2

description: Ctrl m6A-Seq at P14

tag: tissue

value: WT


title: P7RNA_cKO2

description: cKO RNA-Seq at P7

value: Postnatal 7 (P7)


title: P14RNA_cKO1

description: cKO RNA-Seq at P14


title: P14RNA_WT1

description: Ctrl RNA-Seq at P14


title: P7m6A_cKO2

description: cKO m6A-Seq at P7


title: P7m6A_cKO1

description: cKO m6A-Seq at P7


title: P7m6A_WT2

description: Ctrl m6A-Seq at P7


title: P14RNA_WT2

description: Ctrl RNA-Seq at P14


title: P14m6A_WT1

description: Ctrl m6A-Seq at P14


title: P14RNA_cKO2

description: cKO RNA-Seq at P14


title: P7m6A_WT1

description: Ctrl m6A-Seq at P7


title: ATAC-seq from Gatad2a system, Day2

source_name: Gatad2a cell line, Day2 post DOX induction


title: P7RNA_WT2

description: Ctrl RNA-Seq at P7


title: P7RNA_cKO1

description: cKO RNA-Seq at P7


title: PolyA_WT-1_IPS

description: PolyA RNA-seq from WT-1 system, IPS

source_name: WT-1 cell line, Established induced pluripotent stem cells

tag: cell line

value: WT-1 cell line


title: PolyA_WT-1_ES

description: PolyA RNA-seq from WT-1 system, ES

source_name: WT-1 cell line, Embryonic stem cells


title: ATAC-seq from Mbd3f/- system, Day5


title: P7RNA_WT1

description: Ctrl RNA-Seq at P7


title: PolyA_WT-1_Day8

description: PolyA RNA-seq from WT-1 system, Day8

source_name: WT-1 cell line, Day8 post DOX induction


title: PolyA_WT-1_Day4

description: PolyA RNA-seq from WT-1 system, Day4

source_name: WT-1 cell line, Day4 post DOX induction


title: PolyA_Mbd3f/-_IPS

description: PolyA RNA-seq from Mbd3f/- system IPS


title: PolyA_Mbd3f/-_ES

description: PolyA RNA-seq from Mbd3f/- system ES

source_name: Mbd3f/- cell line, Embryonic stem cells


title: PolyA_Mbd3f/-_Day8

description: PolyA RNA-seq from Mbd3f/- system day8


title: PolyA_WT-1_Day2

description: PolyA RNA-seq from WT-1 system, Day2

source_name: WT-1 cell line, Day2 post DOX induction


title: PolyA_Mbd3f/-_Day7

description: PolyA RNA-seq from Mbd3f/- system day7

source_name: Mbd3f/- cell line, Day7 post DOX induction


title: P14m6A_cKO2

description: cKO m6A-Seq at P14


title: PolyA_Mbd3f/-_Day6

description: PolyA RNA-seq from Mbd3f/- system day6

source_name: Mbd3f/- cell line, Day6 post DOX induction


title: PolyA_Mbd3f/-_Day5

description: PolyA RNA-seq from Mbd3f/- system day5

source_name: Mbd3f/- cell line, Day5 post DOX induction


title: PolyA_Mbd3f/-_Day4

description: PolyA RNA-seq from Mbd3f/- system day4


title: PolyA_Mbd3f/-_Day3

description: PolyA RNA-seq from Mbd3f/- system day3


title: NL-148

city: Cleveland

first: Ernest

middle: R

last: Chan

state: OH

address: 10900 Euclid Ave, Robbins E211

department: PQHS

institute: CWRU

description: FPKMTable.txt

data_processing:
FastQC (Read Quality Assessment)
TrimGalore (Adapter and Quality Trimming)
Tophat (Read Alignment)
Cuffdiff (Differential Expression)
Genome_build: GRCh38
Supplementary_files_format_and_content: Cuffdiff Gene FPKM Table

source_name: colon

growth_protocol: Van Dussen et al Gut

extract_protocol:
intestinal epithelial organoids in Matrigel were flash fozen on dry ice and RNA was harvested using Trizol reagent. Qiagen miRNeasy kit was used wth 1 ug of total RNA for the construction of sequencing libraries
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: status

value: normal

value: intestinal epithelial organoid


title: PolyA_WT-1_MEF

description: PolyA RNA-seq from WT-1 system, MEF

source_name: WT-1 cell line, Mouse embryonic fibroblasts


title: PolyA_WT-1_Day6

description: PolyA RNA-seq from WT-1 system, Day6

source_name: WT-1 cell line, Day6 post DOX induction


title: NL-149

description: FPKMTable.txt


title: NL-156

description: FPKMTable.txt


title: NL-145

description: FPKMTable.txt


title: PolyA_Mbd3f/-_Day1

description: PolyA RNA-seq from Mbd3f/- system day1

source_name: Mbd3f/- cell line, Day1 post DOX induction


title: NL-141

description: FPKMTable.txt


title: NL-147

description: FPKMTable.txt


title: CTd-155

description: FPKMTable.txt

value: ulcerative colitis


title: NL-135

description: FPKMTable.txt


title: NL-137

description: FPKMTable.txt


title: PolyA_Mbd3f/-_MEF

description: PolyA RNA-seq from Mbd3f/- system MEF

source_name: Mbd3f/- cell line, Mouse embryonic fibroblasts

value: MEF


title: CTd-153

description: FPKMTable.txt


title: p65-TNF-30-2

city: Galveston

first: Istvan

last: Boldogh

state: Texas

address: 301 UNIVERSITY BLVD.

department: Microbiology & Immunology

institute: UNIVERSITY OF TEXAS MEDICAL BRANCH

data_processing:
The raw sequence reads were aligned to the latest human genome (hg38) using bowtie2
The Homer program was used to make peak calls (for each sample alone, without control samples).
Data were viewed using IGV or UCSC genome browser
Binding motifs (6-20 bp) were idenfified using Homer software and confirmed with MEME v4.3.0.
Position-dependent letter probability matrices were generated by MEME using WebLogo application.
Genome_build: hg38

source_name: Human Embryonic Kidney 293 cells

growth_protocol: Cells were maintained in  Eagle's Minimum Essential Medium, supplemented with 10% FBS and Pen/Strept in a humidified 5% CO2 incubator at 37 C degrees.

extract_protocol:
Formalin-fixed protein-DNA complexes were sonicated and isolated with antibody.
Libraries were prepared according to Illumina's instructions using 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 Genome Analyzer following the manufacturer's protocols.

treatment_protocol: For ChIP, cells were plated in 10 cm Petri dishes, and exposed to 20 ng/ml TNF when cells were at 70% confluency and harvested at 0, 15, 30 and 60 min thereafter.

value: Hypotriploid human cell line

tag: chip antibody


title: p65-TNF-60-1


title: Flag-OGG1-TNF-30-2

value: anti-FLAG


title: p65-Con-1


title: p65-TNF-15-1


title: PolyA_Mbd3f/-_Day2

description: PolyA RNA-seq from Mbd3f/- system day2

source_name: Mbd3f/- cell line, Day2 post DOX induction

value: Mbd3f/- cell line


title: p65-TNF-30-1


title: INPUT DNA_149i

description: 1172_NL_merge_convert_BAM_to_BigWig_on_data_1170

data_processing:
Fastq.gz convert to fastqsanger (via FastqGroomer)
Adapter trimming using TrimGalore
Bowtie 2 for genomic alignments
Conversion of Bowtie mapped sequences to filtered, indexed, sorted and duplicate removed BAM file (BAM tools)
Peak calling using MACS2 yielding BED files
Blacklist removed using BEDtools
Regions of differential H3K27 ac activities were analyzed for signficance using DESeq2 package
Genome_build: GRCh19
Supplementary_files_format_and_content: Galaxy tools for conversion to BigWig files

source_name: intestinal epithelial organoids

growth_protocol: VanDUssen KL et al Gut 2015 Jun;64(6):911-20

extract_protocol:
2 week old intestinal epithelial organoids (passage 3-5) were pooled (n=12) and snap from prior to processing for chromatin immunoprecipitation and sequencing according to Mack SC et al Nature 2014 Feb 27;506(7489):445-50
Rubicon Genomics ThruPlex DNA-Seq 48S with single indices

treatment_protocol: no treatment

tag: tissue origin

value: organoids cultivated from patient-derived normal colon mucosa

tag: passages

value: 3-5 passages

tag: antibody


title: INPUT DNA_148i


title: Flag-OGG1-TNF-30-1

tag: cell type


title: Flag-OGG1-TNF-15-1


title: Flag-OGG1-Con-1


title: CTd-151

description: FPKMTable.txt


title: CTd-146

description: FPKMTable.txt


title: H3K27ac ChIP-Seq_149a

value: Histone H3K27ac (Active Motif Cat# 39133, Lot# 31814008)


title: CTd-111

description: FPKMTable.txt


title: CTd-139

description: FPKMTable.txt


title: CTd-142

description: FPKMTable.txt


title: Flag-OGG1-TNF-60-1


title: H3K27ac ChIP-Seq_147b


title: H3K27ac ChIP-Seq_148b


title: H3K27ac ChIP-Seq_148a


title: INPUT DNA_143i


title: CTd-140

description: FPKMTable.txt


title: INPUT DNA_141i


title: H3K27ac ChIP-Seq_171a


title: CTd-152

description: FPKMTable.txt


title: TET2WT normal-g 5mC

city: Boston

first: Di

state: MA

address: 221 longwood Ave, EBRC (LMRC) 222A

department: Endocrinology

institute: The Brigham and Women's Hospital

description: MeDIP-seq

data_processing:
Basecalls performed using CASAVA (version 1.8.2).
hMeDIP/MeDIP-seq reads were aligned to the hg19 genome assembly using bowtie (version 1.0.0) with parameters: "-m 1 --sam", which "-m 1" for unique mapping, "--sam" for outputing sam format files.
The same files were converted into bam format files and sorted with samtools (Version: 0.1.18). The sorted bam files were converted into Bed format files with bedtools (v2.17.0).
and then we removed the duplicated reads, and extended 300bp from 5' to 3', which was because the IP fragment size was enriched in about 300bp.
The Input reads were also processed with the same steps.
Peaks were called with  MACS 2 (version 2.0.10.20131216) in default settings.
hMeDIP/MeDIP density was normalized into 20 million reads based on the ratio of corresponding input reads.
Genome_build: hg19
Supplementary_files_format_and_content: bedgraph and narrowpeak (BED6+4 format)

source_name: TET2WT normal-g 5mC

growth_protocol: Cells were cultured in high-g or normal-g for 7 days prior to collection, with splitting every 2-3 days.

extract_protocol:
Genomic DNA was extracted using phenol chloroform extraction
hMeDIP/MeDIP DNA libraries were prepared using standard Illumina protocols

treatment_protocol: Cells were washed with 4-degree PBS, scraped down, and centrifuged into pellets (1000 rpm, 2 min)

value: melanoma cell line

value: TET2WT over-expressing

tag: growth conditions

value: normal glucose

tag: ip antibody


title: H3K27ac ChIP-Seq_141b


title: Input TET2WT Normal

description: Input

source_name: Input TET2WT Normal


title: Input TET2WT High

description: Input

source_name: Input TET2WT High

value: high glucose


title: TET2WT normal-g 5hmC

description: hMeDIP-seq

source_name: TET2WT normal-g 5hmC

value: 5hmC (Active Motif, cat#39769, lot#10310001)


title: CTd-150

description: FPKMTable.txt


title: H3K27ac ChIP-Seq_141a


title: TET2WT high-g 5mC

description: MeDIP-seq

source_name: TET2WT high-g 5mC


title: INPUT DNA_147i


title: H3K27ac ChIP-Seq_149b


title: INPUT DNA_155i

description: 1173_Ctd_merge_convert_BAM_to_BigWig_on_data_1171

value: organoids cultivated from patient-derived colitic colon mucosa


title: INPUT DNA_153i


title: H3K27ac ChIP-Seq_143b


title: INPUT DNA_139i


title: H3K27ac ChIP-Seq_143a


title: H3K27ac ChIP-Seq_155b


title: RRBS from v6.5 ES

data_processing:
FASTQ files were generated using the Illumina CASAVA 1.8.2 software.
The plasmid introduces a CTAGANNNNNNATTGATT prefix at one read and an AATTCAATT prefix on the other read (were NNNNNN is the UMI). These prefixes were removed and the UMI recorded for each fragment. A small fraction of reads include longer prefixes that result from amplicons that did not undergo digestion by XbaI or EcoRI. These reads were identified and the longer prefixes were removed as well.
The reads were aligned to the mm9 reference genome using bismark version 0.7.7 with bowtie 1.0.1. Alignment was performed independently for each read of the read-pair. We expect each read to start at an MspI restriction site. Therefore we discarded reads that failed to align within 1bp of such sites. We also discarded read-pairs where each read aligned to remote MspI sites. On the other hand, in cases where one read uniquely mapped on a restriction site but its pair could not be mapped uniquely or could not be mapped at all, we attempted to re-align the entire read pair to the fragment.
To avoid PCR biases we grouped reads that map to the same MspI restriction site, have the same UMI and were ligated into the plasmid in the same orientation (positive or negative). Only the first such read was maintained and all other reads were dropped.
The methylation state of each CpG was extracted from the bismark output. For each CpG, the number of reads in which it was methylated or unmethylated was counted and recorded.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-separated text files containing CpG methylation values. The files' columns are: Column1: chromosome. Column 2: position of CpG (1-based). Column 3: seen count. Column 4: methylation count. Note that each CpG's coverage is given by column 3, and its methylation value by column4/column3.

source_name: V6.5 cell line, Embryonic stem cells

extract_protocol:
Genomic DNA was extracted from snap-frozen cell pellets (Quick-gDNA MiniPrep, Zymo Research).
300ng of DNA was digested overnight with MspI (NEB R0106) followed by end-repair (NEB E6050) and addition of a 3’ overhang A using Klenow fragment (3'-5' Exo-, NEB M0212). The resulting DNA fragments were size-selected for ones shorter than 500bp using AMPure XP beads (Beckman Coulter A63881). 10ng of size-selected DNA was ligated, using quick T4 ligase (NEB M2200), into a cut and T-tailed plasmid containing a 6bp unique molecular identifier (UMI) sequence. The ligated plasmid was bisulfite converted and cleaned (EZ DNA methylation Gold kit, Zymo Research). The converted DNA was amplified using 25 cycles of PCR with GoTaq Hot Start polymerase (Promega M5005) and primers matching specific locations on the plasmid. The primer sites were cut from the amplicons using XbaI (NEB R0145) end EcoRI-HF (NEB R3101) followed by end-repair (NEB E6050). Further details regarding the protocol and the plasmid are available in Shipony Z et al. Dynamic and static maintenance of epigenetic memory in pluripotent and somatic cells. Nature 2014 Sep 4;513(7516):115-9.  RRBS fragments underwent addition of a 3’ overhang A using Klenow fragment (3'-5' Exo-, NEB M0212). The fragments were then ligated to Illumina compatible adapters using quick T4 ligase (NEB M2200) and amplified using 8 cycles of PCR with GoTaq Hot Start polymerase (Promega M5005) and primers matching the Illumina adapters. The final products underwent gel electrophoresis using NuSieve 3:1 agarose (Lonza 50094). Gel bands matching fragment sizes of 200-500bp were cut and the DNA was extracted (MinElute Gel Extraction Kit, Qiagen 28604).
To improve cluster registration at the Illumina sequencer, paired-end sequencing was performed as following:  1. Sequencing of read 1 was performed with 22 dark cycles and 80 regular cycles (resulting in a read of bases 23-102 of read 1). The bases are included in the R1 files.  2. Sequencing of read 1 was performed with regular dark cycles (resulting in a read of bases 1-22 of read 1). The bases are included in the R2 files.  3. Sequencing of read 2 was performed normally with 80 regular cycles (bases 1-80 of read 2). The bases are included in the R3 files.

value: v6.5 cell line

value: ES

value: v6.5 wildtype


title: H3K27ac ChIP-Seq_155a


title: H3K27ac ChIP-Seq_153b


title: Young pod

city: New Delhi

first: Mukesh

last: Jain

state: New Delhi

address: New Mehrauli Road

country: India

institute: Jawaharlal Nehru University

data_processing:
The sequence data was filtered for adapter sequences and low-quality reads using NGS QC Toolkit (v2.3).
The quality filtered reads from each sample were aligned to the kabuli chickpea genome (v1.0) using Bismark (v0.14.3). Only the uniquely aligned reads were retained.
The mapped reads on the genome were used as input in methylKit (v0.9.2).
Identification of mCs was performed with minimum read coverage of ≥ 5 and P-value ≤ 0.0001.
Genome_build: Chickea genome (v1.0)
Supplementary_files_format_and_content: Methylated cytosines

organism: Cicer arietinum

source_name: Young pod

growth_protocol: For root tissues, plants were grown in a culture-room maintained at a maximum temperature of 22 ± 1 °C and a minimum of 12 ± 1 °C, and relative humidity of 60% under continuous light (200 μE m−2 s−1) for 15 days. Other tissues (leaves, flowers and young pods of cultivated chickpea and leaves of wild chickpea) were harvested from the field-grown mature plants.

extract_protocol: Genomic DNA was isolated using Qiagen DNeasy Minikit. DNA samples were  fragmented via sonication to generate 100-300bp fragments. The fragments  were end repaired, followed by ligation with TruSeq-methylated adapters.  500ng adapter-ligated DNA fragments were used for bisulphite conversion using EZ DNA Methylation-GoldTM kit (Zymo Research Corporation, CA, USA)  according to the manufacturer's instructions. Library quality was analyzed after desalting, size selection and PCR amplification.

value: Young pod


title: H3K27ac ChIP-Seq_153a


title: Root

source_name: Root

value: Root


title: Leaf

source_name: Leaf

value: Leaf


title: RRBS from Mbd3f/- system IPS

source_name: Mbd3f/- cell line, Established induced pluripotent stem cells

value: IPS


title: RRBS from Mbd3f/- system day8

source_name: Mbd3f/- cell line, Day8 post DOX induction

value: Mbd3f/- cell line


title: H3K27ac ChIP-Seq_142b


title: H3K27ac ChIP-Seq_150a


title: Young pod_transcript

data_processing:
The FASTQ files obtained were pre-processed using NGS QC Toolkit (v2.3) to remove adapters and low-quality reads.
Filtered high-quality reads were mapped on the chickpea genome (v1.0) using TopHat2 pipeline (v2.0.0).
A consensus reference-guided assembly of the transcriptome data was generated using Cufflinks (v2.0).
Differential expression of genes was determined by Cuffdiff.
Genome_build: Chickea genome (v1.0)
Supplementary_files_format_and_content: normalised gene expression (FPKM)

growth_protocol: For root tissues, plants were grown in a culture-room maintained at a maximum temperature of 22 ± 1 °C and a minimum of 12 ± 1 °C, and relative humidity of 60% under continuous light (200 μE m−2 s−1) for 15 days. Other tissues (leaves, flowers and young pods of cultivated chickpea and leaves of wild chickpea) were harvested from the field-grown mature plants

extract_protocol:
Total RNA was extracted using TRI Reagent. RNA quantification was performed and quality was assessed using Agilent Bioanalyzer. cDNA libraries were prepared and sequencing was performed on Illumina HiSeq platform.
RNA libraries were prepared for sequencing using standard Illumina protocols.


title: RRBS from Mbd3f/- system day7

source_name: Mbd3f/- cell line, Day7 post DOX induction


title: Flower_transcript

source_name: Flower

value: Flower


title: RRBS from Mbd3f/- system day6

source_name: Mbd3f/- cell line, Day6 post DOX induction


title: INPUT DNA_150i

value: 3-5 passages


title: Root_transcript


title: TET2WT high-g 5hmC

description: hMeDIP-seq

source_name: TET2WT high-g 5hmC


title: H3K27ac ChIP-Seq_139b

value: Histone H3K27ac (Active Motif Cat# 39133, Lot# 31814008)


title: Flower


title: Leaf_transcript


title: RRBS from Mbd3f/- system day5

source_name: Mbd3f/- cell line, Day5 post DOX induction


title: H3K27ac ChIP-Seq_150b

source_name: intestinal epithelial organoids


title: hESC-CM biological replicate 3

city: Cambridge

first: Steven

middle: William

last: Wingett

state: Cambs

address: Francis Crick Avenue, Cambridge Biomedical Campus

department: Cell Biology

institute: MRC Laboratory of Molecular Biology

description: Hi-C ligated DNA

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).)
Capture Hi-C interation calling : CHiCAGO (Cairns, J. et al. CHiCAGO: robust detection of DNA looping interactions in Capture Hi-C data. Genome Biol 17, 127 (2016).)
Genome_build: Human: GRCh37
Supplementary_files_format_and_content: ChiCAGO interaction files list interacting restriction fragments

source_name: Cardiomyocytes differentiated from human embryonic stem cells (hESC-CM)

growth_protocol: hESC line WA09 (H9) was obtained from WiCell, maintained and cultured in monolayers according to WiCell Feeder-Independent Pluripotent Stem Cell Protocols using mTeSR1 Medium (SOP-SH-002).

extract_protocol:
hESC-CM were fixed by 2% formaldehyde (Agar Acientifics; R1026) for 10 min at room temperature, quenched by cold 0.125 M glycine (5 min at room temperature followed by 15 min on ice), flash frozen in liquid nitrogen and stored at -80˚C. Then as dscribed in Javierre, B.M. et al. Lineage-Specific Genome Architecture Links Enhancers and Non-coding Disease Variants to Target Gene Promoters. Cell 167, 1369-1384 (2016).
As dscribed in Javierre, B.M. et al. Lineage-Specific Genome Architecture Links Enhancers and Non-coding Disease Variants to Target Gene Promoters. Cell 167, 1369-1384 (2016).

treatment_protocol: hESC-CM differentiation was performed on WA09 hESC monolayers (passage 32) at 80-100% confluence using PSC Cardiomyocyte Differentiation Kit (Gibco; A2921201). After the treatments of Cardiomyocyte Differentiation Medium A and B (2 days each), the cells were allowed to recover in Cardiomyocyte Maintenance Medium for a day. The cells were then passaged (1:1.5 ratio) into plates coated with fibronectin (12.5 µg/ml in 0.02% gelatin; Sigma) and allowed to grow for 6 days in RPMI1640-B27 minus insulin (Gibco) before changing to RPMI1640-B27 complete (Gibco) for further 2 days. The cardiomyocytes were then enriched in glucose-depleted-lactate-enriched medium (DMEM without glucose [Gibco; 11966025]; 4 mM lactate [Sigma]; non-essential amino acids [Gibco]; GlutaMAX [Gibco]) for 6 days and recovered in Iscove's Modified Dulbecco's Medium (IMDM; Gibco) containing 20% FBS for 2 days. The hESC-CM were cultured in RPMI1640-B27 complete (Gibco) for 7 more days before the quality check (at least 80-90% purity by flow cytometry and qPCR using MYH7 and TNNT2 as markers) and the fixation for PCHi-C.


title: Wild leaf

organism: Cicer reticulatum

source_name: Wild leaf

value: Wild leaf


title: RRBS from Mbd3f/- system day3

description: Due to technical problem in multiplexing, this sample was filtered to exclude reads that originated from an unrelated experiment.

source_name: Mbd3f/- cell line, Day3 post DOX induction


title: H3K27ac ChIP-Seq_142a


title: Wild Leaf

data_processing:
Data obtained in FASTQ files was pre-processed to remove low-quality reads using custom perl script.
After quality control, the identical reads were collapsed into a unique read and read count for each sequence was recorded.
Unique reads from each sample were mapped to the chickpea genome using Bowtie (v1.1.2).
Supplementary_files_format_and_content: FASTA files containing non-redundant reads with read count of unique reads.

growth_protocol: Leaves of wild chickpea PI 489777 were harvested from field-grown plants.

extract_protocol:
RNA was isolated and small RNA library was prepared using TruSeq Small RNA Sample Prep Kit (Illumina Technologies).
Small RNA library was prepared for sequencing using standard Illumina protocols.


title: RRBS from Mbd3f/- system day4

source_name: Mbd3f/- cell line, Day4 post DOX induction


title: hESC-CM biological replicate 2

description: Hi-C ligated DNA

value: Cardiomyocytes differentiated from human embryonic stem cells


title: RRBS from Mbd3f/- system day1

source_name: Mbd3f/- cell line, Day1 post DOX induction


title: INPUT DNA_142i


title: Rroid KO_B3_RNA-seq

status: Public on Jul 14 2018

city: Farmington

first: Asli

last: Uyar

state: CT

address: 10 Discovery Dr

department: Computational Sciences

institute: The Jackson Laboratory

data_processing:
Adapters were removed and reads filtered with Trimmomatic version 0.33 using default parameters.
Data were aligned to the NCBIM37/mm9 genome using Tophat version 2.1.0 using default parameters
Raw transcript read counts were generated with HTSeq version 0.6.1 using default parameters
Normalized read counts and statistics were computed using the DESeq2 package
Genome_build: NCBIM37/mm9
Supplementary_files_format_and_content: Raw read counts from HTSeq on samples record, text file of normalized read counts and statistics obtained from DESeq2 on series record.

source_name: Splenic CD27+ CD11b+ NK cells

extract_protocol:
The aqueous phase from the TRIzol-chloroform extraction was precipitated with ethanol, applied to RNeasy Micro columns and processed according to the manufacturer’s instructions
The RNA-Seq libraries were generated using the Ovation RNA-Seq System V2 (Nugen) and the KAPA Hyper Prep Kit (KAPA Biosystems). 1x100bp sequencing was performed on the HiSeq2500 using the TruSeq Rapid SBS Kit

value: NK cells

value: Spleen

value: Rroid deficient

tag: background strain


title: hESC-CM biological replicate 1

description: Hi-C ligated DNA


title: Rroid KO_B1_RNA-seq


title: Rroid KO_B2_RNA-seq


title: Wildtype_A3_RNA-seq

value: wildtype


title: Wildtype_A2_RNA-seq


title: Wildtype_A1_RNA-seq


title: RRBS from Mbd3f/- system MEF

source_name: Mbd3f/- cell line, Mouse embryonic fibroblasts

value: MEF


title: Wildtype_3 ATAC-Seq

data_processing:
Basecalls performed using bcl2fastq version 2.16.0
Data were filtered using Trimmomatic software version 0.32 with the following setting: TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
ATAC-seq reads were aligned to the mm9 genome assembly using BWA with 'mem' option
Peaks were called using MACS2 version 2.1.0 with the following setting: callpeak -t <ATAC tag file> -f BAMPE -n <output peak file> -g 'mm' --nomodel -B
Genome_build: mm9
Supplementary_files_format_and_content: Consensus peaks and TMM normalized read counts were obtained using DiffBind library in R version 3.1.1. Consensus peaks were annotated using HOMER software.

source_name: Spleen

extract_protocol:
WT and KO NK cells ( CD3-CD5- NK1.1+ NKp46+) were isolated and flow sorted from spleen and 50,000 of each geneotype were used for transposition in triplicate.
ATAC-seq libraries were prepared as described in Buenrostro et al (Buenrostro et al. Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. 2013. Nature Methods 10, 1213-1218, doi:10.1038/nmeth.2688

value: spleen


title: Wildtype_1 ATAC-Seq


title: Rroid KO_3 ATAC-Seq


title: Wildtype_2 ATAC-Seq


title: Rroid KO_1 ATAC-Seq


title: CLF-FLAG

city: Madison

first: Christine

last: Wooddell

state: WI

address: 502 S Rosa Rd

institute: Arrowhead Pharmaceuticals

description: Genomic DNA isolicated from immnuoprecipitated chromatin using FLAG antibody (Sigma)

data_processing:
ChIPseq reads were filtered for average QC score>30. Reads were mapped with Bowtie2 to the TAIR10 genome, with default parameters. Reads mapping to identical positions in the genome were collapsed into one read.bedtools was used to generate bedGraph file; UCSC "bedGraphToBigWig" scipt was used to generate bigwig file.
Genome_build: Arabidopsis TAIR10

organism: Arabidopsis thaliana

source_name: pCLF::EBS-CLF transformed into clf mutant background

growth_protocol: Arabidopsis plants were grown in soil at 22 degree under long day (16 hrs light) or short day (8 hrs light) conditions .

extract_protocol:
ChIP genomic DNA protocols are followed by Zhong et al., Nat Struct Mol Biol, 2012, 19:870-850. FLAG antibody we used were from Sigma company (A8592).
ChIP library and RNA library was construbuted by using the Ovation Ultralow Library Kit (NuGen, Part No. 0330).

tag: ecotype

value: Aerial tissue

value: CLF-FLAG (containing FLAG-tagged transgenic CLF)


title: Rroid KO_2 ATAC-Seq


title: control mouse brain, poly-RIBOseq, P5, rep 1

status: Public on Jul 13 2018

city: Povo

first: Toma

last: Tebaldi

state: Trento

address: via Sommarive n. 9

department: Centre for Integrative Biology

country: Italy

institute: University of Trento

description: ribosome profiling of polysomes from a control mouse brain at P5

data_processing:
Library strategy: RIBO-seq
Raw reads were processed by removing 5’ adapters, discarding reads shorter than 20 nucleotides and trimming the first nucleotide (using Trimmomatic v0.36). Reads mapping on rRNAs and tRNAs (downloaded from the SILVA rRNA and the Genomic tRNA databases respectively) were removed. The remaining reads were aligned to the mouse transcriptome (Ensembl v81, corresponding to GENCODE mouse M6) with Bowtie2 (v2.2.6) employing the default settings. All reads aligning to the very same region were collapsed to avoid potential PCR duplicates, and only strand-specific reads were kept.  The number of ribosome protected fragments was determined with samtools idxstats.
Genome_build: GRCm38.p4
Supplementary_files_format_and_content: tab-delimited text file including a brief annotation and transcript-specific counts of ribosome protected fragments

molecule: cytoplasmic RNA

source_name: control mouse brain, ribosome profiling from polysomes, biological replicate 1

growth_protocol: Heterozygos Taiwanese mice (Smn+/-; SMN2tg/0) were used in this study (Hsieh-Li et al., 2000; Riessland et al., 2010; Somers et al., 2015). All mice were on a congenic FVB background, with colonies at the University of Edinburgh established from breeding pairs purchased from Jackson Labs. Litters were retrospectively genotyped using standard PCR protocols. All mice were housed within the animal care facilities in Edinburgh under standard SPF conditions. All animal procedures and breeding were performed in accordance with University of Edinburgh institutional guidelines and under appropriate project and personal licenses granted by the UK Home Office.

extract_protocol:
Cytoplasmic lysates were prepared pulverizing frozen mouse brains in a pestle and mortar cooled by liquid nitrogen and dissolving the powder in lysis buffer. Lysates were clarified by two following centrifugations. The lysates were loaded in a 15-50% linear sucrose gradient and polysomes separated by ultracentrifugation.
Polysomal fractions were pooled and digested with Rnase I for 2h at 4°C. Ribosome Protected Fragments (RPFs) were extracted with acid-phenol:chloroform:isoamylalcohol and isopropanol precipitation and size selected (25-35 nt) by UREA Page. RPFs were treated to remove 3’ phosphate, ligated to the 3’ adaptor and purified by UREA page. Ligated RPFs were retrotranscribed and the cDNA circularized. Libraries were finally amplified by PCR using Illumina PCR Primer Index. Libraries were sequenced on an Illumina HiSeq2500.

treatment_protocol: Neonatal mice were euthanized at P5 by overdose of anaesthetic, before decapitation to allow the brain to be removed. Following isolation, all tissues were immediately snap-frozen on dry ice and then transferred to -80 °C for storage.

value: Smn+/-; SMN2tg/0

tag: rna fraction

value: Poly-RIBOseq

tag: Stage

tag: replicate

tag: strain

value: FVB


title: Wild leaf_transcript

tag: genotype


title: control mouse brain, poly-RIBOseq, P5, rep 2

source_name: control mouse brain, ribosome profiling from polysomes, biological replicate 2


title: H3K27ac ChIP-Seq_139a

value: organoids cultivated from patient-derived colitic colon mucosa


title: BHF_aWAT [Sample 13]

status: Public on Jul 12 2018

city: Shenyang

first: Zhe

last: Wang

address: 120 Dongling Road

institute: Shenyang Agricultural University

data_processing:
Illumina Casava 1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
The filtered reads were mapped to known reference genomes
Gene annotation were performed using Ensembl mouse gene ID
Abundances of mRNA-Seq reads were reported in FPKM
Genome_build: Reference genome (ftp://ftp.ensembl.org/pub/release-74/fasta/mus_musculus/dna/)
Supplementary_files_format_and_content: The txt file, GeneCounts_FPKM.txt, includes the normalized gene counts of the 20 samples.

organism: Hipposideros armiger

source_name: Intra-abdomminal white adipose tissue

extract_protocol:
Total RNA of adipose tissues was extracted using RNeasy Lipid Tissue Mini Kit
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The bats and mice were treated under 30°C and 10°C for 7 days

tag: strain background

value: wild type bats

tag: treatment

value: 30°C for 1 week

tag: gender

value: Female

tag: tissue

value: intra-abdominal white adipose tissue (aWAT)


title: BHM_iBAT [Sample 18]

source_name: Brown adipose tissue

value: Male

value: interscapular brown adipose tissue (iBAT)


title: BCF_sWAT [Sample 11]

source_name: Subcutaneous white adipose tissue

value: 10°C for 1 week

value: Subcutaneous white adipose tissue (sWAT)


title: BHM_sWAT [Sample 10]


title: BHM_aWAT [Sample 14]


title: BHF_iBAT [Sample 17]


title: BCM_sWAT [Sample 12]


title: BCF_iBAT [Sample 19]


title: BHF_sWAT [Sample 9]


title: BCF_aWAT [Sample 15]


title: HA-GRHL2 ESC H3K27Ac rep2

city: Stanford

first: Amy

last: Chen

address: 279 Campus Drive West

institute: Stanford University

data_processing:
Fastq files were mapped to the genome using Bowtie2 with the following setting: -p 4 -q -D 15 -R 10 -L 22 -i S,1,1.15
Mapped reads were filtered to keep only uniquely mapping, deduplicated reads
MACS2 was used for peak finding using the following settings: --nomodel --extsize 200 -s 50 --bw 200 -f BAM -g mm -B -q 0.05
Genome_build: mm10
Supplementary_files_format_and_content: bigwig format after combining replicates for each condition

source_name: embryonic stem cells

growth_protocol: All cells were grown in Knockout DMEM with 15%FBS, Pen/Strep, L-glutamine and Non-essential amino acids. ESCs were also grown in Lif and 2i (GSKi and MEKi).

extract_protocol:
DNA was extracted using a standard ChIP protocol
Library was constructed using a standard Illumina protocol
ChIP-seq, ATAC-seq

treatment_protocol: Doxycycline was added at 0.5ug/ml for 24hrs

value: ESCs

tag: cell line of origin

value: Rosa-26 M2rtTA; ColA1-TetO-HA-GRHL2 ESCs

tag: chip antibody

value: Lif 2i and doxycycline


title: HA-GRHL2 ESC H3K27Ac rep1


title: HA-GRHL2 ESC SMC1 rep2


title: HA-GRHL2 ESC HA rep1

value: HA


title: BCM_aWAT [Sample 16]


title: HA-GRHL2 ESC SMC1 rep1


title: BCM_iBAT [Sample 20]


title: HA-GRHL2 ESC HA rep2


title: HA-GRHL2 ESC IgG rep2

value: IgG (normal rabbit)


title: HA-GRHL2 ESC IgG rep1


title: ColFRT ESC SMC1 rep2

value: Rosa-26 M2rtTA; ColA1-FRT ESCs


title: ColFRT ESC H3K27Ac rep2


title: ColFRT ESC SMC1 rep1


title: ColFRT ESC H3K27Ac rep1


title: HA-GRHL2 ESC H3K4me1 rep2


title: ColFRT ESC H3K4me1 rep2


title: ColFRT ESC H3K4me1 rep1


title: GRHL2 KO EpiC H3K27Ac rep2

source_name: epiblast cells

value: EpiCs

value: V6.5 ESCs

value: -Lif -2i day 3


title: ColFRT ESC IgG rep2


title: GRHL2 KO EpiC SMC1 rep1


title: GRHL2 KO EpiC H3K4me1 rep2


title: GRHL2 KO EpiC H3K4me1 rep1


title: ColFRT ESC HA rep1


title: GRHL2 KO EpiC GRHL2 rep1


title: GRHL2 KO EpiC H3K27Ac rep1


title: WT EpiC SMC1 rep2


title: ColFRT ESC IgG rep1


title: WT EpiC SMC1 rep1


title: HA-GRHL2 ESC H3K4me1 rep1


title: WT EpiC H3K27Ac rep2


title: WT EpiC H3K4me1 rep2


title: GRHL2 KO EpiC GRHL2 rep2


title: GRHL2 KO EpiC IgG rep1


title: WT EpiC H3K27Ac rep1


title: GRHL2 KO EpiC IgG rep2


title: WT EpiC GRHL2 rep2


title: WT EpiC H3K4me1 rep1


title: WT EpiC IgG rep2


title: WT EpiC GRHL2 rep1


title: ColFRT ESC HA rep2


title: WT EpiC IgG rep1


title: GRHL2 KO EpiC ATAC rep2

value: GRHL2 knockout V6.5 ESCs clone D12


title: GRHL2 KO EpiC ATAC rep1

value: GRHL2 knockout V6.5 ESCs clone D8


title: IMR90 WGBS

city: Bronx

first: Andrew

last: Johnston

state: NY

address: 1301 Morris Park Avenue

department: Genetics

institute: Albert Einstein College of Medicine

data_processing:
FASTQ reads were adapter asked using cutadapt v1.9.1 for bisulfite converted adapter sequences
Masked reads were aligned to hg19 using bwa-meth v0.10 with default parameters
Aligned reads were marked for duplicates using Picard v2.4.1
A custom perl script was used to filter "fill-in" artifact be qc-fail flagging reads with 3 or more methylated CHH's outside the first 11 cycles
Methylation ratios were determined, by CpG, CHG, CHH context, using MethylDackel v0.1.13 with min baseQ >= 20, min mapQ >=20 and excluding the first 11bases of R1 and R2 alignments
Genome_build: hg19
Supplementary_files_format_and_content: Compressed methylKit files were generated which capture CpG CHG, CHH methylation and coverage (https://github.com/al2na/methylKit)

growth_protocol: IMR90 cells were grown in ATCCformulated Eagle's Minimum Essential Medium with 10%FBS and Penicillin-Sterptomycin. The cells were placed in 37 degree humidified incubator containing 5% CO2.

extract_protocol:
NA12878 genomic DNA was purchased from ATCC. IMR90 high molecular weight genomic DNA was extract from cultured cells using SDS+proteinase K lysis/phenol-chloroform treatment. Extracted DNA was treated DNase-free RNase A.
100 ng of genomic DNA was treated with Tn5 transposase for tagmentation, then tagged DNA was filled with methylated dCTP, dATP, dGTP, dTTP mixture. The filled DNA was bisulphite treated using EZ DNA methylation Gold kit (Zymo research). The bisulphite treated samples were amplified with custom and Illumina index adapters. The amplified products were size selected using AMPureXP beads.

value: Female

tag: cell line

value: Fetal lung fibroblast


title: GRHL2 KO EpiC SMC1 rep2

tag: cell type


title: NL-143

description: FPKMTable.txt

source_name: colon

tag: status

value: normal

value: intestinal epithelial organoid


title: NL-144

description: FPKMTable.txt


title: WT EpiC ATAC rep2


title: GRHL2 KO ESC ATAC rep2

value: Lif 2i


title: GRHL2 KO ESC ATAC rep1


title: WT ESC ATAC rep2


title: WT EpiC ATAC rep1


title: Small RNAs from ovaries of yw strain

city: Moscow

first: Sergei

last: Ryazansky

address: Kurchatov sq., 2

department: Department of Molecular Genetics of Cell

country: Russia

institute: Institute of Molecular Genetics

data_processing:
The reads with clipped 3'-adapter (5'-TGGAATTCTCGGGTGCCAAGG) were passed through length (>18 nt), quality (80% of nt should contain >=20 Phred score) and artefacts filters, and mapped by bowtie to dm3 genome assembly with requiring of perfect matching.
Genome_build: dm3 (Release 5)
Supplementary_files_format_and_content: *.collapsed.txt: Tab-delimited text files include the raw counts of clipped read occurrences in each library.

organism: Drosophila melanogaster

source_name: ovaries, yw

growth_protocol: Flies were grown according to standard protocols.

extract_protocol:
Total RNA was isolated by Trizol (Invitrogen) and size-fractioned by PAGE (19-29 nt).
Libraries of small RNAs 19-29 nt were constructed as previously described in (Muerdter et al. 2012).

tag: strain/background

value: yw

value: ovaries


title: Small RNAs from ovaries of EY08176 transgenic strain

source_name: ovaries, EY08176 transgenic strain


title: Small RNAs from ovaries of EY09966 transgenic strain

source_name: ovaries, EY09966 transgenic strain


title: Small RNAs from ovaries of EY00802 transgenic strain

source_name: ovaries, EY00802 transgenic strain


title: 14-15h_dH1

city: Shanghai

first: Jian

last: Hu

address: 1239,Siping Road

institute: Tongji University

data_processing:
ChIP-seq raw reads were cleaned by removing adaptor sequence and low-quality sequences, then mapped to dm3 whole genome using bowtie v0.12.7 with parameters: -p 8 -m 1 -v 2
The uniquely mapped nucleosomal reads were used to identify genome-wide nucleosome positions through the peak-calling tool GeneTrack
Aligned dH1 reads were converted into tdf format use igvtools.
Genome_build: dm3
Supplementary_files_format_and_content: Tab-delimited files for nucleosome positions includes nucleosome name, location (chromatin, start, end), the number of reads aligned on predicted nucleosme (rc), fuzziness of predicted nucleosme (fuzziness, the standard deviation of tag locations around the nucleosome dyad).Tdf files are binary files which represented the dH1 enrichment at genomic loci.

source_name: embryo

growth_protocol: Embryos were collected on grape juice plates with yeast paste from embryo collection cages for 1 hr, and then allowed to develop for 3 and 14 additional hours before being harvested. So the collected embryos are 3-4h and  and 14-15h old, respectively.

extract_protocol:
1.Nucleosome DNA fragment extraction, chromatin are digested by MNase and nucleosome was dissolved through sonication with 3 cycles of 20s duration with at least 40s pauses between cycles at the power setting of 6 (out of 20) on a Misonix sonicators XL-2000. Then nucleosome DNA was extracted by phenol–chloroform and dissolved in ddH2O. 2. H1 binding DNA fragment extraction, generated chromatin fragments between 100 and 500 bp through sonication with 7 cycles and 5 cycles on 3-4h and 14-15h embryonic nuclei, separately. Then immunoprecipitated DNA-H1 complexes were captured by anti-H1 antibody (Active Motif, 39707) dose as specification described in 20-25ug chromatin.Immunoprecipitated DNAs were obtained by extraction with phenol chloroform after incubated on metal bath under the condition of 65 ℃ over night.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit.

treatment_protocol: Embryos were dechorionated with 50% solution of bleach for 3 minutes and were cross-linked in a 1:3 mix of ChIP-fixed buffer with 1.8% formaldehyde and heptane for 15 min on a shaker with speed at 300 rpm. The aqueous and organic phase was replaced with PBST plus 0.25 mM glycine to cease cross-linked reaction, and fixed embryos were rinsed by PBST for 3 times. The cross-linked embryos were homogenized by Douce all-class tissue grinder, and filtered large residual tissue by Miracloth to get nuclei suspension.

value: H1 (Active Motif, catalog# 39575, lot# 05809001)


title: 3-4h_nucleosome_rep2

value: 3-4h AEL

tag: enzyme

value: Mnase (Worthington Biochemical Corporation, catalog# LS004797)


title: 14-15h_nucleosome_rep1


title: 3-4h_dH1

value: 3-4h after egg laying (AEL)


title: 3-4h_nucleosome_rep1


title: Small RNAs from ovaries of EY00453 transgenic strain

source_name: ovaries, EY00453 transgenic strain


title: 14-15h_nucleosome_rep2


title: GM12878_rep1

description: number of cells: 50k

data_processing:
Basecalls were performed using CASAVA v1.8.4
Sequenced reads were trimmmed using trim_galore v0.3.3
Sequenced reads were aligned to Homo sapiens (hg19) reference genome using Burrows-Wheeler Aligner (BWA-MEM v0.7.13)
Reads were filtered for unique alignments and deduplicated using picard-tools v1.92 and samtools v0.1.19
Reads were shifted using bedtools2 v2.24.0
Peaks were called for each replicate using MACS2 v.2.1.0
Peaks with an Irreproducible discovery rate (IDR) of < 0.05 were retained and filtered by consensus blacklisted regions as well as mitchondria homologous regions.
Genome_build: hg19
Supplementary_files_format_and_content: MACS narrowPeak files from peak calling for each replcate and a bed file containing the IDR<0.05, filtered peaks [5th column contains the scaled IDR value; min(int(log2(-125IDR), 1000)]

growth_protocol: GM12878 cells were grown in suspension using RPMI 1640 with 15% FBS in T-75 flasks, cells were maintained between 200,000-800,000 cells/ml.

extract_protocol:
50,000 cells from two biological replicates of GM12878 were harvested during the exponential growth phase. The cells were spun at 500 g for 5 minutes at 4˚C and then washed using 50 μL of cold 1X PBS.  Samples were then centrifuged at 500 g for 5 minutes.  Cells were lysed in cold lysis buffer (10 mM Tris-HCL, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% IGEPAL CA-630) and immediately spun at 500 g for 5 minutes at 4˚C.
The pellet was then resuspended in the transposase reaction mix (25 μL 2x TD buffer, 2.5 μL transposase and 22.5 μL nuclease-free water; Illumina Nextera).  Following a 30-minute incubation at 37˚C, the samples were purified using the Zymo DNA Clean and Concentrator purification kit. Following the purification, the libraries were amplified with the following PCR conditions: 72°C for 5 minutes; 98°C for 30 seconds; and a total of 10 cycles of 98°C for 10 seconds; 63°C for 30 seconds; 1 minute for 72°C.  Subsequently, the libraries were purified using Agencourt AMpure XP beads; large fragments were filtered by using 0.6x (of PCR mixture volume) magnetic bead volume and taking the supernatant. Primer-dimer and short fragments were removed by collecting bead-associated DNA in a 1:1 (bead solution volume:mixture volume) mix.

value: EBV-transformed lymphoblastoid cell line


title: CD4_resting_rep4_TrAC-loop

city: Bethesda

first: Keji

last: Zhao

state: MD

address: 9000 Rockville Pike

department: Systems Biology Center

institute: NHLBI,NIH

description: TrAC-looping

data_processing:
Library strategy: TrAC-looping
Basecalls performed using CASAVA
Reads were aligned to hg19 genome using Bowtie2
Read of PETs <1Kb were used for peakcalling for getting the HSs
The PETs >1Kb were used for identify interaction among the HSs
Calculated the p value of interaction based on Mango
Genome_build: hg19
Supplementary_files_format_and_content: TrAC-looping Interaction file: A is the first anchor and B is the second anchor, each row is one interaction event

source_name: blood

growth_protocol: Human CD4+ T cells were purified from human blood using human CD4 T cell enrichment Kit from Stemcell Technologies (cat# 19052) according to the manufactures manual. The cells were used directly as resting T cells or activated using anti-CD3/CD28 beads (Invitrogen Dynabeads Human T-Activator CD3/CD28, Cat# 11131D) for 16 hours at 37°C.

extract_protocol:
Human CD4+ T cells were purified from human blood using human CD4 T cell enrichment Kit from Stemcell Technologies (cat# 19052) according to the manufactures manual
The eluted DNA was purified by phenol-chloroform extraction and ethanol precipitation. For intramolecular circulization, the DNA was incubated in the presence of T7 DNA ligase in 50ml of ligation buffer (66 mM Tris-HCl pH 7.4, 10 mM MgCl2, 1 mM ATP, 1 mM DTT, 7.5% Polyethylene glycol (PEG 6000) at room temperature for overnight. The ligated DNA was precipitated by ethanol and then resuspended in 55μl sampling buffer from templify100 kit (GE Hearlthcare cat# 25-6400-10). The DNA was denatured at 97°C for 3min and then chilled on ice. RCA was performed by adding 50μl Reactions buffer +2μl enzyme mix to the denatured DNA mix and incubated at 30°C for overnight. Use 1μl of RCA product for PCR by mixing with 25μl NEB Phusion HF master mix, 23μl H2O, 1μl 10μM PCR primer N501, 1 μl 10μM PCR primer N701 with the cycling conditions: 98 °C for 30 s; 11 cycle of 98 °C for 10 s, 65 °C for 30 s and 72 °C for 8 s; 72 °C for 5 min; 4C hold. The PCR products were resolved on E-gel and the DNA with a size range of 250-650bp was isolated and sequenced by paired-end sequencing on Illumina Hiseq 2500.

treatment_protocol: The resting CD4+ T cells were activated using anti-CD3/CD28 beads (Invitrogen Dynabeads Human T-Activator CD3/CD28, Cat# 11131D) for 16 hours at 37°C.

value: blood

value: Resting CD4+ T cells


title: CD4_resting_rep3_TrAC-loop

description: TrAC-looping


title: CD4_unfixed_cell_ATAC_seq

data_processing:
Basecalls performed using CASAVA
Reads were aligned to hg18 genome using Bowtie2
Redudant reads or PETs were removed from further analysis
For Capture-C datasets, only PETs with bait at promoter of IL2RA were reteined. Reads from replicates were combined. Normalized read count mean value in 21 running window (500 bp) were calucated.
Normalized read count were calculated and uploaded to UCSC genome browser.
Genome_build: hg18
Supplementary_files_format_and_content: HiC/Capture-C Interaction file: A is the first anchor and B is the second anchor, each row is one interaction event detected by paired-end tag (PET); bedgraph file: First 3 columns indicate genomic coordinate, Column 4 indicates RPBM value.

extract_protocol:
A total of 100k human CD4+ T resting cells, fixed or native (not fixed) were washed with PBS.  The cell pellets were washed with RSB buffer (10mM Tris-HCl, pH 7.5, 10mM NaCl, 3mM MgCl2) once and resuspended in 52 μl  cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.5% IGEPAL CA-630) and incubated on ice for 15min. add 6 ul 10x reaction buffer and 2ul ATAC-seq Tnp complex. Put in PCR machine for 37 °C 30 min. Add  3 μl 0.5M EDTA to stop the reaction. Add 40 μl H2O + 3 μl 10% SDS +5 μl proteinase K. put the samples in a 65 °C incubator overnight. Transfer samples to a new Eppendorf and extract DNA by phenol-chloroform extraction and ethanol precipitation.
The libraries were processed same as Hi-C protocol (Lieberman-Aiden et al., 2009, Science. 2009 Oct 9;326(5950):289-93)
The ATAC-seq Tnp comple-tagmented DNA pellets were resuspended in 10 μl of elution buffer (EB). Set up PCR by adding 25 μl of master Phusion HF mix, 22 μl H2O, 1 μl of one of the 10uM N501-N508 and 1 μl of one of the 10uM N701-N712. PCR: 72°C for 5min, 98°C for 45 sec. 19 cycles of ( 98°C, 15”; 65°C, 30”; 72°C, 30”), 72°C 5min. 4°C hold. Gel purify the 200-500 bp smear/fragments for sequencing.

value: CD4+ T cells

value: resting

tag: fixation

value: unfixed


title: GM12878_rep2

description: number of cells: 50k


title: NA12878 WGBS

value: Female


title: CD4_unfixed_cell_ATAC_seq_rep


title: CD4_fixed_cell_ATAC_seq

value: fixed


title: CD4_stimulated_HiC_rep

extract_protocol:
Cells were cross-linked with 1% formaldehyde for 10 minutes at RT. 10 X 106 cells were lysed in 10 ml lysis buffer (10 mM Tris-HCl pH8.0, 10 mM NaCl, 0.2% NP40; 10 μl protease inhibitors (Sigma)) with rotation at 4°C for 60 minutes. The cells were then treated with 400 μl 1X NEB cutsmart buffer with 0.1% SDS at 65°C for 10 minutes, followed by addition of 44 μl 10% Triton X-100 to quench SDS. Chromatin was subsequently digested with 20 Units 4 cutters (NEB). The reaction was stopped by washing the cells twice with 600 ml wash buffer. After reversing crosslink, the purified DNA were ready for the library preparation.
The libraries were processed same as Hi-C protocol (Lieberman-Aiden et al., 2009, Science. 2009 Oct 9;326(5950):289-93)

value: stimulated


title: WT ESC ATAC rep1

value: ESCs

value: V6.5 ESCs


title: 3-4h_AEL_RNA-seq

data_processing:
mRNA-Seq raw reads were cleaned by removing adaptor sequence and low-quality sequences, aligned to the Drosophila genome (dm3) using Bowtie/Tophat (v1.3.1) with default parameters.
Uniquely mapped reads were assembled into transcripts guided by reference annotation (FlyBase r5.57) with Cufflinks (v1.3.0) to calculate gene expression levels which measured as Fragment Per Kilobase per Million mapped fragments (FPKM).
Genome_build: dm3
Supplementary_files_format_and_content: tab-delimited file includes FPKM values for each gene

extract_protocol:
RNA was prepared using the TRIzol following the manufacturer’s instructions. The quality of the resulting RNA was verified by the relative intensity of rRNA bands using a Agilent 2100 Bioanalyzer, and RNA was quantified using a Nanodrop ND-1000 spectrophotometer
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Embyro homogenizied by by Douce all-class tissue grinder, and used lysis buffer to lysis cell.

value: 3-4hr AEL(after egg laying)


title: CD4_resting_HiC_rep


title: CD4_stimulated_HiC


title: CD4_resting_HiC


title: CD4_stimulated_Biotin-4C IL2RA_Dpn_II_rep

data_processing:
Library strategy: Capture-C
Basecalls performed using CASAVA
Reads were aligned to hg18 genome using Bowtie2
Redudant reads or PETs were removed from further analysis
For Capture-C datasets, only PETs with bait at promoter of IL2RA were reteined. Reads from replicates were combined. Normalized read count mean value in 21 running window (500 bp) were calucated.
Normalized read count were calculated and uploaded to UCSC genome browser.
Genome_build: hg18
Supplementary_files_format_and_content: HiC/Capture-C Interaction file: A is the first anchor and B is the second anchor, each row is one interaction event detected by paired-end tag (PET); bedgraph file: First 3 columns indicate genomic coordinate, Column 4 indicates RPBM value.

extract_protocol:
The DNA is extracted by phenol-chloroform extraction and ethanol precipitation as routine molecular biology precedue. The restriction enzymes used are DpnII and NlaIII.
The libraries are prepared according to reference: Davies, J. O., et al. (2016). "Multiplexed analysis  of chromosome conformation at vastly improved sensitivity." Nat Methods 13(1): 74-80.) with the following differences: we fixed the cells with 1% formaldehyde (Thermo Scientific prod# 28908)-containing culture media at room temperature for 5 minutes with gentle shaking, followed by adding glycine to 0.125M to quench the reaction for 5min and washing twice with PBS. The hybridization is done without using the blockers.


title: CD4_stimulated_Biotin-4C IL2RA_Nla_III_rep


title: CD4_resting_Biotin-4C IL2RA_Nla_III_rep


title: CD4_resting_Biotin-4C IL2RA_Dpn_II_rep


title: CD4_resting_Biotin-4C IL2RA_Nla_III


title: CD4_stimulated_Biotin-4C IL2RA_Dpn_II


title: CD4_resting_Biotin-4C IL2RA_Dpn_II


title: CD4_fixed_cell_ATAC_seq_rep


title: CD4_stimulated_Biotin-4C IL2RA_Nla_III