title: N2, UV, 3d/30 (time/dose) vs. control

first: Liang

address: 1150 St. Nicholas Avenue

institute: Columbia University

description:
N2DASH7
control sample: N2 control

data_processing:
We used RTA (Illumina) for base calling and bcl2fastq (version 1.8.4) for converting BCL to fastq format, coupled with adaptor trimming. We mapped the reads to the human reference genome (NCBI/build37.2) using Tophat (version 2.0.4).
We calculated the relative gene expression level using cufflinks (version 2.0.2) with default settings. We determined differentially expressed genes under various conditions using the DEseq software.
Genome_build: NCBI/build37.2
Supplementary_files_format_and_content: csv files include normalized gene expression values and differential gene expression levels in the UVR-treated versus no-UVR control samples.

source_name: neonatal foreskin

growth_protocol: Primary human keratinocytes were isolated from neonatal foreskins and were cultured in 154CF medium supplemented with human keratinocyte growth supplement.

extract_protocol:
Total RNA was isolated from cultured keratinocytes using the QIAGEN RNeasy Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were irradiated in approximately 0.5 ml PBS in each 10 cm dish with 3 different doses: 10, 20, or 30 mJ/cm2. Control and irradiated cells were collected at 4 hours, 1 day or 3days after UV radiation.

value: neonatal foreskin

value: Cultured primary keratinocytes

value: UVR


title: N2, UV, 1d/30 (time/dose) vs. control

status: Public on Dec 01 2018

type: SRA

city: New York

last: Liu

state: NY

country: USA

description:
N2DASH4
control sample: N2 control

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: tissue

tag: cell type

tag: treatment


title: N2, UV, 3d/10 (time/dose) vs. control

description:
N2DASH5
control sample: N2 control


title: N2, UV, 3d/20 (time/dose) vs. control

description:
N2DASH6
control sample: N2 control


title: N2, UV, 1d/10 (time/dose) vs. control

description:
N2DASH2
control sample: N2 control


title: E1_R2

city: Singapore

first: Phillip

middle: H

last: Koeffler

address: 14 Medical Drive

country: Singapore

institute: Cancer Science Institute

library_source: genomic

data_processing:
The long-range genomic interaction regions generated by the 4C-Seq experiment were analyzed by using the R package r3CSeq v1.22.0 (Thongjuea et al., Nucleic Acids Res., 2013). Briefly, for each replicate the raw reads were aligned to the masked version of the reference human genome (masked for the gap, repetitive and ambiguous sequences) downloaded from the R Bioconductor repository (BSgenome.Hsapiens.UCSC.hg19.masked). The chromosome 9 was selected as the viewpoint chromosome and HindIII was used as the restriction enzyme to digest the genome. A non-overlapping window size of 2 kb was selected to identify the interaction regions. The number of mapped reads for each window were counted and then normalized to obtain RPM (the reads per million per window) values to perform the statistical analysis. The interaction regions were then plotted based on the significance level and visualized on the UCSC Genome Browser as custom tracks.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include interactions regions with associated statistical values and genes

molecule: genomic DNA

source_name: Esophageal squamous carcinoma cells

growth_protocol: cells were cultured in Dulbecco's Modified Eagle Medium supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Standard Illumina library preparation protocol
4C-Seq

tag: cell line


title: E2_R1


title: E1_R1


title: N2 control

value: no UVR


title: N1, UV, 3d/30 (time/dose) vs. control

description:
N17
control sample: N1 control


title: LaminB1_ChIPSeq_Heart_E9.5_2

city: Philadelphia

first: Michael

middle: Patrick

last: Morley

state: PA

address: 3400 Civic Center Blvd, Bldg 421

department: Penn Cardiovascular Institute

institute: Perelman School of Medicine at the University of Pennsylvania

description: ChIP protocol as previously described (PMID:23934658)

data_processing:
Illumina Casava1.8 software used for basecalling.
ChIP-seq Reads were aligned to mouse reference genome (mm9) using bowtie with the followingparameters '-k 1 -m 1 --best –strata'
Genome_build: mm9
Supplementary_files_format_and_content: BED: LADs called by custom peak software
Supplementary_files_format_and_content: WIG: A signal .wig file is computed with an input file and a laminB file with  an adjustment parameter.  The name gives the embryonic stage (e12.5 or e9.5),  then the adjustment (between 0.12 and 0.17) and the indication which input  and which ChIP files were used

organism: Mus musculus

source_name: Heart

growth_protocol: Timed pregnant CD1 females purchased from Charles River.

extract_protocol:
Protocol as previously described (PMID: 23934658). Briefly, whole hearts microdissected on ice, fixed in 1.1% formaldehyde x 10 min, pooled in lysis buffer (10mM Tris-HCl, 10mM NaCl, 3mM MgCl2, 1% NP-40, 1% SDS, 0.5% DOC), sheared with Diagenode Bioruptor, IP overnight with Protein G Dynabeads, 2ug antibody, washed 5x in RIPA, eluted into TE, incubated at 65°C x 16hr and DNA purified by phenol-chloroform extraction.
Library prepared with NEBNext Ultra DNA Library Prep kit for Illumina according to manufacturer instructions

tag: background strain

tag: age

value: Embryonic day 9.5

value: Whole Heart, pooled 3 litters

tag: chip antibody

value: Lamin B1 (Abcam, ab16048, Lot GB95643-1)


title: N1, UV, 3d/20 (time/dose) vs. control

description:
N16
control sample: N1 control


title: N1, UV, 3d/10 (time/dose) vs. control

description:
N15
control sample: N1 control


title: N1, UV, 1d/20 (time/dose) vs. control

description:
N13
control sample: N1 control


title: IFI6 Rep 3

city: Dallas

first: John

last: Schoggins

state: Texas

address: 5323 Harry Hines Blvd

department: Department of Microbiology

institute: UT Southwester Medical Center

description: Cells expressing IFI6 vector for 16 passages

data_processing:
Single-end 50 bp read length Fastq files were checked for quality using fastqc and fastq_screen
Reads were quality trimmed using fastq-mcf (ea-utils).
Trimmed fastq files were mapped to human genome using TopHat
Duplicates were marked using picard-tools
Read counts were generated using featureCounts (subread) for coding genes from gencode (v19)
Normalized read counts generated using edgeR
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited txt files that includes normalized read counts for each sample per gene

source_name: STAT1-/- fibroblasts

growth_protocol: STAT1-/- fibroblasts were grown in RPMI supplemented with 10% FBS, 1X non-essential amino acids, and 4 ug/mL puromycin.

extract_protocol:
RNA was harvested using RNeasy Mini Kit (Qiagen #74106) following the manufacturer's instructions. Integrity was verified using the Agilent 2100 Bioanalyzer. All samples had a RIN score of 8 or higher.
Four micrograms of total DNAse-treated RNA were then prepared with the TruSeq Stranded Total RNA LT Sample Prep Kit from Illumina (Illumina  #RS-122). Poly-A RNA was purified and fragmented before strand specific cDNA synthesis.  cDNA were then A-tailed and indexed adapters were ligated. After adapter ligation, samples were PCR amplified and purified with AmpureXP beads, then validated again on the Agilent 2100 Bioanalyzer. Before being normalized and pooled, samples were quantified by Qubit then run on the Illumina Hiseq 2500 using SBS v3 reagents.

treatment_protocol: Naïve STAT1-/- fibroblasts were spinoculated with lentivirus containing CMV-driven IFI6 or empty control vector. The plasmid backbone also contains TagRFP and a puromycin-resistance cassette. Two days after spinoculation, cells were split into media containing 4 ug/mL puromycin. Cells were passaged at a 1:4 split for the indicated number of passages, No additional manipulations occurred prior to processing cells for RNA extraction.

value: Skin

tag: genotype

tag: expression

value: IFI6 vector


title: IFI6 Rep 1

description: Cells expressing IFI6 vector for 13 passages


title: Empty control Rep 2

description: Cells stably expressing empty control vector for 10 passages

value: empty control vector


title: IFI6 Rep 2


title: Empty control Rep 3


title: Empty control Rep 1

description: Cells stably expressing empty control vector for 7 passages


title: N1, UV, 1d/10 (time/dose) vs. control

description:
N12
control sample: N1 control


title: KYSE140_Input

data_processing:
Raw fastq files were aligned to human gneome using bowtie (VN:1.1.2) and duplicates were removed using picard.
Peaks were called using MACS2 with parameters -g hs --keep-dup 1 --bdg --SPMR --nomodel --extsize 200 -q 0.01
Bedgraph files generated by MACS2 were converted to bigWig files using ucsc bedGraphToBigWig tool.
pipeline: https://github.com/PoisonAlien/chiptk
Genome_build: hg19
Supplementary_files_format_and_content: bw files indicating pileup signal normalized to Reads Per Million. NarrowPeak files indicating peaks detected by MACS2

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Standard Illumina library preparation protocol

tag: antibody (catalog)


title: N1 control


title: N0, UV, 3d/30 (time/dose) vs. control

description:
RL009
control sample: N0 control


title: N0, UV, 3d/10 (time/dose) vs. control

description:
RL007
control sample: N0 control


title: N2, UV, 1d/20 (time/dose) vs. control

description:
N2DASH3
control sample: N2 control


title: N0, UV, 1d/30 (time/dose) vs. control

description:
RL006
control sample: N0 control


title: SS299dc

city: Edmonton

first: Ou

last: Wang

state: AB

address: 410 Agriculture/Forestry Centre, University of Alberta

department: AFNS

country: Canada

institute: University of Alberta

description:
super-shedder
sample_id: I7

data_processing:
sRNAbench: expression profiling of microRNAs based on genome mappings generated by Bowtie aligner
edgeR: differntially expressed microRNA identification, differentially expressed microRNA were defined from edgeR output table with FDR < 10%
miRanda and PITA: consensus microRNA target prediction, using miRanda and PITA
Functional anlaysis for target genes with Ingenuity Pathway Anlaysis
Genome_build: BosTau7
Supplementary_files_format_and_content: excel file including counts of each microRNA identified in each tissue of each animal

organism: Bos taurus

source_name: Descending colon tissue

extract_protocol:
Two 2 cm2 biopsies of intestinal tissues were collected from each animal and immediately snap frozen in liquid nitrogen within 10 min after death of the animal. Samples were stored at -80 °C until RNA was extracted. 100 mg of powdered rectal tissue was used for RNA extraction using a mirVana total RNA Isolation Kit
Illumina TruSeq Small RNA Sample Preparation kit

treatment_protocol: Cattle with two phenotypes, control group was catlle negative for fecal E. coli O157, experimental group was cattle shedding > 104 CFU E. coli O157/g of feces

value: Descending colon

tag: phenotype

value: E. coli O157 super-shedder


title: N0, UV, 4h/10 (time/dose) vs. control

description:
RL001
control sample: N0 control


title: N0, UV, 4h/30 (time/dose) vs. control

description:
RL003
control sample: N0 control


title: N0, UV, 4h/20 (time/dose) vs. control

description:
RL002
control sample: N0 control


title: SS310dc

description:
super-shedder
sample_id: J7


title: N0, UV, 1d/10 (time/dose) vs. control

description:
RL004
control sample: N0 control


title: N0 control


title: N1, UV, 1d/30 (time/dose) vs. control

description:
N14
control sample: N1 control


title: SS294dc

description:
super-shedder
sample_id: H7


title: SS287dc

description:
super-shedder
sample_id: G7


title: NS745dc

description:
negative for E. coli O157
sample_id: E7

value: E. coli O157 non-shedder


title: NS242dc

description:
negative for E. coli O157
sample_id: D7


title: N0, UV, 3d/20 (time/dose) vs. control

description:
RL008
control sample: N0 control


title: NS165dc

description:
negative for E. coli O157
sample_id: C7


title: NS152dc

description:
negative for E. coli O157
sample_id: B7


title: SS294sc

description:
super-shedder
sample_id: H6

source_name: Spiral colon tissue

value: Spiral colon


title: NS108dc

description:
negative for E. coli O157
sample_id: A7


title: SS299sc

description:
super-shedder
sample_id: I6


title: SS274sc

description:
super-shedder
sample_id: F6


title: SS287sc

description:
super-shedder
sample_id: G6


title: NS745sc

description:
negative for E. coli O157
sample_id: E6


title: SS310sc

description:
super-shedder
sample_id: J6


title: NS242sc

description:
negative for E. coli O157
sample_id: D6


title: NS165sc

description:
negative for E. coli O157
sample_id: C6


title: N0, UV, 1d/20 (time/dose) vs. control

description:
RL005
control sample: N0 control


title: NS152sc

description:
negative for E. coli O157
sample_id: B6


title: NS108sc

description:
negative for E. coli O157
sample_id: A6


title: SS274dc

description:
super-shedder
sample_id: F7


title: SS310dj

description:
super-shedder
sample_id: J5

source_name: Distal jejunum tissue

value: Distal jejunum


title: SS310pj

description:
super-shedder
sample_id: J3

source_name: Proximal jejunum tissue

value: Proximal jejunum


title: NS165dj

description:
negative for E. coli O157
sample_id: C5


title: SS274dj

description:
super-shedder
sample_id: F5


title: SS287dj

description:
super-shedder
sample_id: G5


title: SS294dj

description:
super-shedder
sample_id: H5


title: NS108dj

description:
negative for E. coli O157
sample_id: A5


title: 0.2mg/L triclosan treated wild-type control

city: Brisbane

first: Jianhua

last: Guo

address: Research Road, Level 4 Gehrmann Building

department: Australian Centre for Water and Environmental Biotechnology

country: Australia

institute: University of Queensland

description: control 0.2T

data_processing:
base calling through an integrated primary analysis software called RTA (Real Time Analysis. v1.18).
The NGS QC toolkit (version 2.3.3) was used to treat the raw sequence reads to trim the 3’-end residual adaptors and primers, and the ambiguous characters in the reads were removed. Then, the sequence reads consisting of at least 85% bases were progressively trimmed at the 3’-ends until a quality value ≥ 20 were kept. Downstream analyses were performed using the generated clean reads of no shorter than 75 bp.
The clean reads of each sample were aligned to the E. coli reference genome (NC_000913) using SeqAlto (version 0.5). Cufflinks (version 2.2.1) was used to calculate the strand-specific coverage for each gene, and to analyze the differential expression in triplicate bacterial cell cultures. The statistical analyses and visualization were conducted using CummeRbund package in R (http://compbio.mit.edu/cummeRbund/).
Gene expression was calculated as fragments per kilobase of a gene per million mapped reads (FPKM, a normalized value generated from the frequency of detection and the length of a given gene.
Genome_build: NC_000913.3
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

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

source_name: E. coli bacteria

growth_protocol: liquid LB culture at 37 °C

extract_protocol:
Bacterial cells were then harvested by centrifugation at 8000 × g for 10 min. Total RNA was extracted from the mutants using the QIAGEN miRNeasy Mini Kit (QIAGEN, Germany) manufacturer’s protocol with one extra bead-beating step to completely lyse the bacterial cells.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: resistant strains as well as the wild-type strain E. coli K-12 MG1655 were cultured in  triplicate in 10 mL liquid LB with 0.2 mg/L TCS at 37 °C for 8 h, shaken at 150 rpm.

value: Wild-type

tag: agent

value: TCS


title: NS242dj

description:
negative for E. coli O157
sample_id: D5


title: NS745dj

description:
negative for E. coli O157
sample_id: E5


title: SS299dj

description:
super-shedder
sample_id: I5


title: NS152dj

description:
negative for E. coli O157
sample_id: B5


title: SS299pj

description:
super-shedder
sample_id: I3


title: SS294pj

description:
super-shedder
sample_id: H3


title: Tet resistant mutant-1

value: Tet resistant mutant


title: CHL resistant mutant-3

value: CHL resistant mutant


title: CHL resistant mutant-2


title: AMX resistant mutant-3

value: AMX resistant mutant


title: AMX resistant mutant-2


title: AMX resistant mutant-1


title: Wild-type-3


title: Tet resistant mutant-2


title: Wild-type-1


title: Wild-type-2


title: SS310ce

description:
super-shedder
sample_id: J2

source_name: Cecum tissue

value: Cecum


title: SS299ce

description:
super-shedder
sample_id: I2


title: SS287pj

description:
super-shedder
sample_id: G3


title: NS242pj

description:
negative for E. coli O157
sample_id: D3


title: NS165pj

description:
negative for E. coli O157
sample_id: C3


title: NS745pj

description:
negative for E. coli O157
sample_id: E3


title: SS287ce

description:
super-shedder
sample_id: G2


title: SS294ce

description:
super-shedder
sample_id: H2


title: SS274ce

description:
super-shedder
sample_id: F2


title: NS152pj

description:
negative for E. coli O157
sample_id: B3


title: SS274pj

description:
super-shedder
sample_id: F3


title: NS242ce

description:
negative for E. coli O157
sample_id: D2


title: NS165ce

description:
negative for E. coli O157
sample_id: C2


title: NS745ce

description:
negative for E. coli O157
sample_id: E2


title: NS152ce

description:
negative for E. coli O157
sample_id: B2


title: NS108ce

description:
negative for E. coli O157
sample_id: A2


title: SS310du

description:
super-shedder
sample_id: J1

source_name: Duodenum tissue

value: Duodenum


title: SS287du

description:
super-shedder
sample_id: G1


title: SS294du

description:
super-shedder
sample_id: H1


title: NS745du

description:
negative for E. coli O157
sample_id: E1


title: CHL resistant mutant-1


title: SS299du

description:
super-shedder
sample_id: I1


title: SS274du

description:
super-shedder
sample_id: F1


title: NS242du

description:
negative for E. coli O157
sample_id: D1


title: NS108pj

description:
negative for E. coli O157
sample_id: A3


title: NS165du

description:
negative for E. coli O157
sample_id: C1


title: NS108du

description:
negative for E. coli O157
sample_id: A1


title: NS152du

description:
negative for E. coli O157
sample_id: B1


title: ChIP-seq_LNCaP EZH2-HA HA rep2

city: Atlanta

first: Jindan

last: Yu

state: GA

address: E330, 1760 Haygood Dr NE

department: Urology

institute: Emory University

description: Chromatin IP against HA

data_processing:
Reads were aligned to the hg19 reference human genome using bwa v0.6.1
Peak-calling by HOMER v4.1
Genome_build: hg19
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph file and peak txt file

source_name: prostate tumor

growth_protocol: Cell lines were maintained in RPMI supplemented with 10% FBS.

extract_protocol: Chromatin in nuclear fraction were sheared to 200-500bp using anCovaris M220 Focused-ultrasonicator, Lysates were clarified from sonicated nuclei and protein-DNA complexes were immunoprecipitated using the indicated antisera.  DNA was then uncrosslinked from protein, purified and sequenced using Illumina Genome Analyzers followig protocols recommended by the manufacturer. Libraries were prepared according to Illumina's instructions.

treatment_protocol: LNCaP cells were infected with EZH2 knockdown lentivirus and maintained for 2-3 days before fixation by 1% paraformaldehyde. LNCaP cells were stably overexpressed with EZH2-HA lentivirus and maintained for 2-3 days before fixiation by 1% paraformaldehyde.

value: LNCaP

value: EZH2-HA Plko

value: HA

tag: chip antibody vendor

value: abcam

tag: chip antibody cat. #

tag: chip antibody log #


title: 11pre

city: Essen

first: Susanne

last: Horn

address: Hufelandstr. 55

department: Klinik für Dermatologie

country: Germany

institute: Universitätsklinikum Essen

description: Poly-dT enriched mRNA

data_processing:
Illumina Casava1.8.4 software was used for basecalling.
Sequenced reads were trimmed for adaptor sequences and read mapping was performed using Gsnap and the diploid amphibian reference genome of Xenopus tropicalis (November 2009 draft assembly GCA_000004195.1).
Transcript quantification was performed creating a matrix of read counts per transcript and differential gene expression was analyzed using the DESeq2 package in R.
Genome_build: Xenopus tropicalis GCA_000004195.1 xenTro3
Supplementary_files_format_and_content: DESeq normalized read counts in tab separated file format

organism: Ambystoma mexicanum

source_name: Jaw bone

growth_protocol: Individuals of Ambystoma mexicanum (axolotls) albino type were obtained from the colony of the Center for Regenerative Therapies TU Dresden (CRTD). Animals were kept in 18°C Dresden tap water and were fed with Artemia and fish pellets. For surgery animals were anesthetized in 0.01% ethyl-p-aminobenzoate (SIGMA).

extract_protocol:
Samples were disrupted and homogenized using the TissueLyser (Qiagen), lysed in 600ul RLT Buffer and DTT (RNeasy Kit, Qiagen). Per sample one sterilized steel ball (Qiagen) was used in a 2 ml LoBind Tube (Eppendorf) at 30 Hz for 2 x 3 min. After homogenization and a short centrifugation the mix was transferred to a new tube and processed according to the RNeasy Kit (Qiagen) protocol for Animal Tissue (Handbook 06/2012).
RNA sequencing libraries were prepared using mRNA Library Prep for Illumina RNA-Seq (Beckman Coulter) with an estimated fragment size of 300bp. SeraMag Poly-dT mRNA (GE health care life sciences) enrichment of mRNA was performed before sequencing 75bp single end reads on an Hiseq 2000 (Illumina).

treatment_protocol: All surgeries were performed in 5 cm long juvenile axolotls (snout to tail). Axolotls were placed in agar dishes filled with 0.01% ethyl- p- aminobenzoat (SIGMA). Anesthetized individuals were fixed with needles and jaw was removed at a length of 5mm from the midline. The amputated jaws were incubated in RNA- later (SIGMA) and freezed to -80°C. After surgery the weight of the individuals was controlled all 3 days. After five weeks of regeneration the regenerated jaw was removed, incubated in RNA- later (SIGMA) and freezed to -80°C.

value: Normal jaw tissue

tag: animal size

value: 5cm (snout to tail)

tag: library

tag: library idex

tag: library index sequence

value: GTAGAG


title: RNA-seq_C4-2B ENZ 2#

data_processing:
Sequenced reads were mapped to hg38 human genome using STAR
raw counts were calculated by STAR, FPKM values were calculated by perl script
Genome_build: hg38
Supplementary_files_format_and_content: txt file of FPKM values for each Sample ...

source_name: Derived from metastatic site: Left supraclavicular lymph node [PMID 8168083]

growth_protocol: Cells were maintained in RPMI supplemented with 10% FBS and 1% PS.

extract_protocol:
For RNA-seq, total RNA was isolated from cells using PureLinkTM RNA Mini Kit (Life Tech). RNA-seq libraries were prepared from 0.5μg high-quality DNA-free total RNA by using NEBNext Ultra™ RNA Library Prep Kit, according to the manufacturer's instructions.
RNA-Seq sample were sequenced on an Illumina HiSEQ4000 using Illumina provided reagents and protocols.

treatment_protocol: C4-2B cells were treated with DMSO, ENZ ((1uM for LNCaP and 10uM for C4-2B), EPZ6438 (1uM) or combination of ENZ+EPZ for 7 days.

tag: tissue source

value: prostate

tag: treatment/infection

value: ENZ 10 uM


title: ChIP-seq_LNCaP shEZH2 H3K27ac

description: Chromatin IP against H3K27ac

tag: cell line


title: ChIP-seq_LNCaP plko.1 H3K27ac

description: Chromatin IP against H3K27ac


title: ChIP-seq_LNCaP plko.1 H3K27me3

description: Chromatin IP against H3K27me3

value: CST


title: ChIP-seq_LNCaP plko.1 EZH2(CST)

description: Chromatin IP against EZH2(CST)


title: BDP1-FRB rep 2

city: Los Angeles

first: Kevin

last: Roy

state: CA

address: 607 Charles E. Young Drive East

department: Chemistry and Biochemistry

institute: UCLA

description: RNA extracted from yeast cultures and Dnase I-treated

data_processing:
Reads were trimmed with TrimGalore v0.4.0 requiring a minimum final length of 15 nucleotides.
Trimmed reads were mapped using RNA-STAR v2.4.0k to the R64-2-1 version of the S.cerevisiae genome obtained from the Saccharomyces genome database (SGD) using default mapping parameters and allowing only uniquely mapped reads (Dobin et al., 2013).
RNA-STAR generated bedgraph files which were normalized to 1 million reads.
Genome_build: R64-2-1 version of the S288C genome of S.cerevisiae (Saccharomyces genome database)
Supplementary_files_format_and_content: bedgraph with each strand separate

organism: Saccharomyces cerevisiae

source_name: yeast cultures

growth_protocol: cultures were grown in YPD (1% yeast extract, 2% bacto-peptone, 2% dextrose) at 30°C at 200 rpm and harvested at OD 0.4 to 0.6

extract_protocol:
All cultures were harvested by centrifugation at 4000 rpm for 2 minutes, washed in deionized water, and spun down in microcentrifuge tubes. The supernatant was removed and pellets were flash-frozen in liquid nitrogen and stored at -80°C. RNA was extracted by standard phenol/chloroform extraction and DNase I-treated.
Libraries were constructed using the Illumina TruSeq stranded mRNA sample prep kit per manufacturer's instructions.
RNA-sequencing of poly(A)+ RNA

treatment_protocol: WT HHY168 and FRB-tagged strains were treated for one hour with 0.1% v/v 1 mg/mL rapamycin (in 90% ethanol, 10% Tween-20) to yield a final concentration of 1 μg/mL.

tag: strain genotype

tag: genetic background

value: W303 derivative

tag: mating type

value: alpha


title: WT HHY168 rep 1

value: HHY168 fpr1delta::hphMX4


title: ChIP-seq_LNCaP shEZH2 EZH2

description: Chromatin IP against EZH2

tag: genotype

tag: chip antibody


title: ChIP-seq_LNCaP shEZH2 H3K27me3

description: Chromatin IP against H3K27me3


title: REB1-FRB rep 2


title: WT HHY168 rep 2


title: ChIP-seq_LNCaP CTRL R1881

description: Chromatin IP against EZH2

value: CTRL R1881

value: millipore


title: RNA-seq_C4-2B DMSO 2#

value: control DMSO


title: BDP1-FRB rep 1


title: RNA-seq_C4-2B EPZ 1#

value: EPZ6438 1 uM


title: RNA-seq_C4-2B EPZ 2#


title: RNA-seq_C4-2B EPZ+ENZ 2#

value: Combination


title: RNA-seq_C4-2B ENZ 1#


title: CIVIT_seq_80S_3

city: Baltimore

first: Boris

last: Zinshteyn

state: Maryland

address: 725 N Wolfe St, PCTB 714

department: Molecular Biology and Genetics

institute: Johns Hopkins University School of Medicine

description: ribosome-associated RNA pool

data_processing:
the first 7 and 21 nt were trimmed from the forward and reverse reads, respectively, low-quality nts (phred=10) were trimmed from the forward read, and the RT primer sequence was trimmed from the forward reads with Cutadapt(Martin, 2011). Any read pairs where both members were <30nt long after trimming were discarded. The remaining reads were mapped, using bowtie2 (Langmead and Salzberg, 2012) to a “genome” of the input sequences used to make the oligo pool, with the T7 promoter and RT binding site stripped, but the identifier barcodes maintained. The identifier barcodes allow reads to map uniquely, even when the mutation sites that differentiate TLs are not covered by the paired reads. The number of reads for each TL variant were normalized by the number of reads mapping to all TL variants in a dataset to generate reads per million (RPM) values. Monosome recruitment scores were computed as the ratio (monosome RPM)/(monosome RPM + mRNP RPM).
Library strategy: Ribosome-association measurements (CIVIT-seq)
Genome_build: SacCer3
Supplementary_files_format_and_content: CIVIT_seq_RPM.tsv: tab-seperated text of CIVIT-seq RPM values (reads per million)
Supplementary_files_format_and_content: CIVIT_Seq_monosome_recruitment.tsv: tab-seperated text of CIVIT-seq monosome recruitment scores, and pool sequences
Supplementary_files_format_and_content: CIVIT_seq_monosome_recruitment_change.tsv: tab-seperated text of changes in CIVIT-seq monosome recruitment scores between WT and mutant transcript leader variants

source_name: YWG3 translation extract

growth_protocol: Biotinylated mRNA was added to a 2ml yeast in vitro translation reaction, and incubated with shaking for 30 minutes at 25°C,  in the presence of 0.5mg/ml CHX. 200μl of the completed reaction was set aside (Total sample), and the rest of the reaction was sedimented on a linear 10-50% sucrose density gradient (containing polysome buffer, 0.5mg/ml CHX and 3mM DTT) for 3 hours at 27,000RPM in a SW28 rotor. The gradients were fractionated using a BiocComp gradient station, and the mRNP and 80S ribosome fractions collected separately. RNA was extracted from each fraction using the hot phenol method. RNA pellets were resuspended in 5ml (8M GuHCl, 20mM EDTA and 20mM MES), and ethanol added to 33%. The mixture was passed through a Zymo VI column (C1013-10, 500μg capacity) to bind large RNA. The flowthrough was passed through a Zymo V-E column with midi filter (C1021-25) to collect smaller RNAs. The column was washed twice with 200μl 80% ethanol, eluted with 400ul Tris-Cl pH 8.0, and NaCl and EDTA were added to 0.5M. and 1mM, respectively.  Pool RNA was further enriched with streptavidin pulldown using a modification of the manufacturer’s protocol. RNA was heated to 65°C for 5’, kept on ice for 3’, and added to 125μl washed streptavidin magnetic beads (NEB S1420). After 10’ incubation at 25°C, beads were washed with 1ml wash/binding buffer (NEB) + 0.1% NP40, then 3x with 1ml elution buffer. RNA was eluted by adding 50ul 95% formamide, 10mM EDTA, and incubating at 70C for 5’, followed by dilution and ethanol precipitation.

extract_protocol: For reverse transcription(RT), primer oBZ181 and RNA were denatured and annealed in (50 mM Tris-Cl pH 8.6, 60 mM NaCl, 10 mM DTT). dNTPs (4mM each final) and MgCl2 (20 mM final), RNAsin Plus (Promega; N2611), and AMV RT (Promega; M5108) were added, and RT was carried out at 42 °C for 1h. RT product was ethanol precipitated and resuspended in water, then treated with RNase T1 and RNase A in (50mM Tris pH7.5, 150mM NaCl) for 1h at 37°C. Full length RT products were purified on an 8% TBE-urea PAGE gel. cDNA was circularized with circLigase (Epicenter) and PCR amplified using oRP1 and barcoded reverse primers. Pooled barcoded libraries were sequenced with 40nt paired-end reads on an Illumina NextSeq.

tag: strain


title: CIVIT_seq_total_2

description: ribosome-associated RNA pool


title: CIVIT_seq_mRNP_3

description: ribosome-associated RNA pool


title: REB1-FRB rep 1


title: RNA-seq_C4-2B EPZ+ENZ 1#


title: CIVIT_seq_80S_2

description: ribosome-associated RNA pool


title: CIVIT_seq_total_1

description: ribosome-associated RNA pool


title: ChIP-seq_LNCaP EZH2-HA HA rep1

description: Chromatin IP against HA

value: LNCaP

value: EZH2-HA Plko


title: CIVIT_seq_80S_1

description: ribosome-associated RNA pool


title: CIVIT_seq_input

description: ribosome-associated RNA pool


title: RNA-seq_C4-2B DMSO 1#


title: LS3

city: Beijing

first: Conglong

last: Lian

address: 35 Tsinghua Eastern Road

country: China

institute: Beijing Forestry University

data_processing:
The  clustering  of  the  index-coded  samples  was  performed  on  a  cBot  Cluster Generation System using TruSeq SR Cluster Kit v3-cBot-HS (Illumia) according to  the  manufacturer’s  instructions.  After  cluster  generation,  the  library preparations were sequenced on an Illumina Hiseq 2500/2000 platform and 50bp single-end reads were generated.
Low quality reads were removed, and 10 - 30 nt sRNAs were purified without more than 10 nt single nucleotide repeats, or more than 10% poly N, or these with 5’ adapter contaminants, or with 3’ adapter or the insert tag. And then bowtie software were used to mapped the remaining sequences to the genome of P. euphratica
Mapped small RNA tags were used to looking for known miRNA. The characteristics  of  hairpin  structure  of  miRNA  precursor  can  be  used  to predict  novel  miRNA.
miRNA expression levels were estimated by TPM (transcript per million) through the following criteria (Zhou et al., 2010):
Small RNA annotation and Target gene prediction
Genome_build: NCBI Populus euphratica unplaced genomic scaffold, PopEup_1.0 scaffold1.1, whole genome shotgun sequence; https://www.ncbi.nlm.nih.gov/assembly/GCF_000495115.1/
Supplementary_files_format_and_content: abundance measurements of novel miRNAs found in the current  study and known ptc-miRNAs in the miRBase at http://www.mirbase.org/

organism: Populus euphratica

source_name: Stem collected 4 day after ABA-3

growth_protocol: 1-year-old P. euphratica plantlets with uniformly grown were planted in individual 5 L pots containing loam soil with similar height and placed in the greenhouse at Beijing Forestry University.

extract_protocol:
Total RNA was extracted from 18 collections of CSs, SSs and LSs using CTAB method (Jaakola et al., 2001; Zhou et al., 2009).
Sequencing libraries were generated using NEBNext® Multiplex Small RNA Library Prep Set for Illumina® (NEB, USA.) according to manufacturer’s specifications.

treatment_protocol: For the treated groups, 1L 300 μM ABA solutions were irrigated to each pot to make sure sufficiently watered, and for the control group, pure water instead of ABA solution was applied.

tag: age

value: one year

tag: treated with

value: ABA for 4 day

tag: tissue

value: stem


title: CS2

source_name: Stem control2

value: none (control)


title: CS1

source_name: Stem control1


title: LS1

source_name: Stem collected 4 day after ABA-1


title: LS2

source_name: Stem collected 4 day after ABA-2


title: CIVIT_seq_mRNP_1

description: ribosome-associated RNA pool


title: SS3

source_name: Stem collected 1 day after ABA-3

value: ABA for 1 day


title: SS1

source_name: Stem collected 1 day after ABA-1


title: SS2

source_name: Stem collected 1 day after ABA-2


title: CS3

source_name: Stem control3


title: CR3

source_name: Root control3

extract_protocol:
Total RNA was extracted from 18 collections of  CRs, SRs, and LRs using CTAB method (Jaakola et al., 2001; Zhou et al., 2009).
Sequencing libraries were generated using NEBNext® Multiplex Small RNA Library Prep Set for Illumina® (NEB, USA.) according to manufacturer’s specifications.

value: Root


title: LR1

source_name: Root collected 4 day after ABA-1


title: SR1

source_name: Root collected 1 day after ABA-1


title: SR3

source_name: Root collected 1 day after ABA-3


title: LR3

source_name: Root collected 4 day after ABA-3


title: SR2

source_name: Root collected 1 day after ABA-2


title: CK

city: Zhenjiang

first: Xiangfeng

last: Zheng

state: Jiangsu

address: 301, Xuefu Road

department: Food school

institute: Jiangsu university

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm8
Supplementary_files_format_and_content: FPKM

organism: Rhodotorula mucilaginosa

source_name: Yeast cell

growth_protocol: Rhodotorula mucilaginosa  was inoculated in NYDB medium, an was incubated at 28℃， 180 rpm. For 24 h.

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

treatment_protocol: The sample  of CK is the control which no treatment with patulin, sample PAT was treated with 20mg/mL patulin

tag: treatment

value: Rhodotorula mucilaginosa cell cultured  in NYDB medium

tag: incubation time

tag: incubation conditions


title: PAT

value: Rhodotorula mucilaginosa cell cultured  in NYDB medium which contained 20mg/mL patulin


title: CIVIT_seq_mRNP_2

description: ribosome-associated RNA pool

source_name: YWG3 translation extract


title: activated Ras rep3 [S-37]

status: Public on Nov 30 2018

city: varanasi

first: subhas chandra

last: lakhotia

state: uttar pradesh

address: cytogenetics lab, department of Zoology BHU

department: Department of Zoology

country: India

institute: Brown University

data_processing:
The resulting sequencing FastQ files were mapped to the Drosophila genome (dm6) using Tophat with Bowtie.
The aligned SAM/BAM file for each was processed for guided transcript assembly using Cufflink 2.1.1 and gene counts were determined.
Mapped reads were assembled using Cufflinks. Transcripts from all samples were subjected to Cuffmerge to get final transcriptome assembly across samples.
In order to ascertain differential expression of gene transcripts between different samples, Cuffdiff 2.1.1 was used (Trapnell et al., 2012). A P-value <0.05 was taken to indicate significantly differentially expressing genes between different groups compared.
Genome_build: dm6
Supplementary_files_format_and_content: Cuffdiff 2.1.1 result showing differential gene expression between different samples in excel sheet

organism: Drosophila melanogaster

source_name: eye disc_activated Ras

extract_protocol:
RNA was isolated from 30 pairs of eye discs dissected out from wandering third instar larvae in PBS  using Trizol (Invitrogen, USA) reagent as per manufacture’s protocol. 1µg of the isolated RNA was subjected to DNAase treatment using 2U of TurboTM DNase (Ambion, Applied Biosystem) enzyme for 30 min at 37°C. The reaction was stopped using 15mM EDTA followed by incubation at 65°C for 5-7 min and purification on RNAeasy column (Qiagen). The purified RNA samples were processed for preparations of cDNA libraries using the TruSeq Stranded Total RNA Ribo-Zero H/M/R (Illumina) and sequenced on HiSeq-2500 platform (Illumina) using 50bp pair-end reads, 12 samples per lane and each sample run across 2 lanes.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype/variation

value: wandering third instar

value: eye disc


title: activated Ras down hsrω rep3 [S-38]

source_name: eye disc_activated Ras down hsrω


title: activated Ras up hsrω rep3 [S-39]

source_name: eye disc_activated Ras up hsrω


title: LR2

source_name: Root collected 4 day after ABA-2


title: activated Ras up hsrω rep 2 [S-35]


title: CR2

source_name: Root control2


title: control rep3 [S-36]

source_name: eye disc_control

value: w1118; sev-GAL4/UAS-GFP; dco2/+


title: activated Ras rep2 [S-33]


title: control rep2 [S-32]


title: activated Ras down hsrω rep 2 [S-34]


title: activated Ras up hsrω rep 1 [S-31]


title: T65_12.2-37_12 Days in Short Day

city: Milano

first: Fabio

last: Fornara

address: Via Celoria 26

department: Department of Biosciences

country: Italy

institute: University of Milan

data_processing:
Cleaned raw reads were generated by the Illumina HiSeq 2000 system at GATC Biotech
Sequenced reads were mapped to rice genome v.7 using bowtie2 and TopHat2 with default parameters
Reads were uniquely mapped and counted by HTSeq with parameters -s no -a 10 -t gene -i ID
Gene-level differential expression analysis was performed using the R software (version 3.1.0) for statistical computing and edgeR package version 3.6.4 from bioconductor
Genome_build: O. sativa Japonica group cultivar Nipponbare genome version 7.0. Available at: ftp://ftp.plantbiology.msu.edu/pub/data/Eukaryotic_Projects/o_sativa/annotation_dbs/pseudomolecules/version_7.0/all.dir/
Supplementary_files_format_and_content: Count files contain the number of reads per feature uniquely mapped by HTSeq python package (Anders et al. 2015).  ChrUn and ChrSy have loci and gene models without an assigned LOC_OsXXgXXXXX identifiers and are publicly available in the official rice genome release.

organism: Oryza sativa

source_name: Shoot Apical Meristems

growth_protocol: Oryza sativa cv. Nipponbare (NB) and Taichung 65 (T65) seeds were grown in Conviron PGR15 chambers set on temperature/relative humidity cycles of 28ºC/80% during the day and 24ºC/90% during the night. Light was provided by fluorescent tubes and metal halide bulbs (intensity of ~450μE/m-2sec-1).

extract_protocol:
Shoot apices were sampled under the microscope using scalpels and total RNA was isolated using the NucleoSpin RNA Plant kit (Macherey-Nagel).
RNA libraries were prepared at GATC Biotech (Germany).

treatment_protocol: 6-week-old plants were shifted from chambers with 16 hours light and 8 hours dark to chambers with 10 hours light and 14 hours dark.

tag: cultivar

value: Taichung 65

value: Shoot Apical Meristems

tag: days after shift

tag: sample number used in data processing

value: 37,38,39 (data merged for analysis)


title: CR1

source_name: Root control1


title: T65_12.2-39_12 Days in Short Day

description: processed data for this sample is available on GSM2402847


title: T65_12.1_12 Days in Short Day


title: T65_8.3_8 Days in Short Day


title: T65_12.2-38_12 Days in Short Day


title: T65_8.1_8 Days in Short Day


title: T65_4.3_4 Days in Short Day


title: SHSY5Y_ARMC12

city: Wuhan

first: Qiangsong

last: Tong

state: Hubei

address: 1277 Jiefang Avenue

department: Department of Surgery

institute: Union Hospital of Tongji Medical College

description: Gene expression after stable transfection of ARMC12.

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. All the downstream analyses were based on the clean data with high quality.
Index of the reference genome was built using Bowtie v2.0.6 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.9.
RPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene, considering the effect of sequencing depth and gene length for the reads count at the same time (Mortazavi et al., 2008).
Genome_build: hg38
Supplementary_files_format_and_content: *txt: Tab-delimited text files include RPKM values for each Sample.

source_name: SH-SY5Y stably transfected with ARMC12

growth_protocol: Human neuroblastoma cell line SH-SY5Y was grown in RPMI1640 medium supplemented with 10% fetal bovine serum, penicillin (100 U/ml) and streptomycin (100 μg/ml), and maintained at 37°C in a humidified atmosphere of 5% CO2.

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

treatment_protocol: The ARMC12 expression or empty vectors were transfected into tumor cells, and stable cell lines were screened by administration of neomycin.

tag: cell line

tag: cell type

value: neuroblastoma

tag: passages

tag: stable transfection


title: activated Ras rep1 [S-29]


title: T65_8.2_8 Days in Short Day


title: T65_4.2-30_4 Days in Short Day

value: 30,31 (data merged for analysis)


title: T65_0.3_0 Days in Short Day


title: T65_0.2_0 Days in Short Day


title: T65_0.1_0 Days in Short Day


title: SHSY5Y_mock

description: Gene expression after stable transfection of empty vector.

source_name: SH-SY5Y stably transfected with empty vector

value: empty vector


title: T65_4.1_4 Days in Short Day


title: activated Ras down hsrω rep 1 [S-30]


title: NB_12.2_12 Days in Short Day

value: Nipponbare


title: NB_12.3_12 Days in Short Day


title: control rep1 [S-28]


title: NB_8.3_8 Days in Short Day


title: NB_12.1_12 Days in Short Day


title: NB_8.1-17_8 Days in Short Day

description: processed data for this sample is available on GSM2402828

value: 15,16,17 (data merged for analysis)


title: NB_8.2_8 Days in Short Day


title: NB_4.3-14_4 Days in Short Day

description: processed data for this sample is available on GSM2402826

value: 12,14 (data merged for analysis)


title: T65_4.2-31_4 Days in Short Day

description: processed data for this sample is available on GSM2402840


title: NB_8.1-15_8 Days in Short Day


title: NB_4.3-12_4 Days in Short Day


title: NB_4.1-9_4 Days in Short Day

description: processed data for this sample is available on GSM2402823

value: 7,9 (data merged for analysis)


title: NB_4.1-7_4 Days in Short Day


title: NB_0.1_0 Days in Short Day


title: NB_0.2_0 Days in Short Day


title: NB_4.2_4 Days in Short Day


title: BLaER1__control__rep1

city: Barcelona

first: Roderic

last: Guigó

state: Catalonia

address: doctor aiguader 88

department: Bioinformatics and Genomics

country: Spain

institute: Center for Genomic Regulation (CRG)

data_processing:
Reads were mapped to the hg19 reference genome using Bowtie v2.2.5 and TopHat v2.0.14 with the following options: --no-coverage-search; --transcriptome-index with an index built from Gencode v19.
Gene expression levels were estimated using Cuffdiff v2.2.1 with default options, against a reference transcriptome based on Gencode v19.
Genome_build: hg19
Supplementary_files_format_and_content: gene_expression.txt contains per-replicate gene expression levels (FPKM). gene_exp.diff contains raw Cuffdiff output, including: gene-level expression estimates (average FPKM across replicates), log2 fold change between relevant conditions, and associated FDR values.

molecule: polyA RNA

growth_protocol: BLaER1 cells were grown in complete RPMI media +10% FBS + Pen-Strep + L-Glutamine

extract_protocol:
Total RNA was extracted from cells using RNeasy kit (Qiagen, Netherlands).
Libraries were prepared with 1 ug of total RNA and using TruSeq mRNA Sample Prep Kit (Illumina, USA) according to manufacturer’s protocol. Libraries were analyzed using Agilent DNA 1000 chips to determine the quantity and size distribution

treatment_protocol: Three LNA longRNA GapmeR antisense oligonucleotides complementary to the human lncRNA HAL7 (ENSG00000228427.1, RP5-1091N2.9) were added directly to cell media, rather than transfected.

value: control


title: Input DNA for Tnm2 with DMSO Rep_2

first: Hideo

last: Watanabe

address: One Gustave L. Levy Place

department: Department of Medicine, Division of Pulmonary, Critical Care and Sleep Medicine

institute: Icahn School of Medicine at Mount Sinai

data_processing:
ChIP-seq reads were aligned to the mm10 genome assembly using Bowtie2 with -k 1 option
Resequenced and duplicate sample files are aggregated with merge function of Samtools
H3K27Ac peaks were called using MACS (v1.4.2) at p-value threshould of 1E-05 with no-ChIP input sample as control.
Wiggle files with a 1000bp resolution for H3K9me2 enrichment were regenerated from size shifted wiggle files by MACS v1.4.2 and then rescaled with wigmath.Scale function of Java-Genomics-Toolkit.
Genome_build: mm10
Supplementary_files_format_and_content: bed and wig

source_name: Lung adenocarcinoma cells

growth_protocol: CK1750 and Tnm2 cells were cultured in DMEM supplemented with 10% fetal bovine serum.

extract_protocol:
Lysates were clarified from sonicated nuclei with Covaris M220 and histone-DNA complexes were isolated with antibody.
Libraries were prepared using NEBNext Ultra DNA Library preparation kits from 2-10 ng immunoprecipitated DNA according to manufacturer’s protocol. The finished double strand DNA (dsDNA) libraries were quantified by PicoGreen and Agilent Bioanalyzer according to manufacturer’s protocols. Uniquely indexed libraries were pooled in equimolar ratios and sequenced on an Illumina NextSeq500 with single or paired-end 75bp reads.

treatment_protocol: CK1750 or Tnm2 cells were cultured in the presence of DMSO or  1 μM UNC0638 in DMEM supplemented with 10% FBS

tag: drugs treated

value: DMSO


title: Input DNA for Tnm2 with UNC0638 Rep_2


title: BLaER1__KD__rep0

value: HAL7 knockdown


title: BLaER1__KD__rep1


title: Input DNA for Tnm2 with DMSO Rep_1 Seq_1


title: Input DNA for CK1750 with UNC0638 Rep_2


title: Input DNA for CK1750 with UNC0638 Rep_1 Seq_1


title: H3K9me2 for Tnm2 with UNC0638 Rep_1 Seq_2

description: tnm2_unc0638_merged34_k9me2_swig_treat_afterfiting_all.1k.scaled.wig

tag: chip-antibody

value: H3K9 dimethylation (Abcam, ab1220)


title: Input DNA for CK1750 with DMSO Rep_2


title: Input DNA for CK1750 with DMSO Rep_1 Seq_1


title: H3K9me2 for Tnm2 with UNC0638 Rep_2


title: Input DNA for CK1750 with DMSO Rep_1 Seq_2


title: H3K9me2 for Tnm2 with UNC0638 Rep_1 Seq_1


title: H3K9me2 for Tnm2 with DMSO Rep_2

description: tnm2_dmso_merged34_k9me2_swig_treat_afterfiting_all.1k.scaled.wig


title: NB_0.3_0 Days in Short Day


title: H3K9me2 for Tnm2 with DMSO Rep_1 Seq_2


title: H3K9me2 for Tnm2 with DMSO Rep_1 Seq_1


title: H3K9me2 for CK1750 with UNC0638 Rep_2

description: ck1750_unc0638_merged34_k9me2_swig_treat_afterfiting_all.1k.scaled.wig


title: H3K9me2 for CK1750 with UNC0638 Rep_1 Seq_1


title: H3K9me2 for CK1750 with DMSO Rep_1 Seq_2

description: ck1750_dmso_merged34_k9me2_swig_treat_afterfiting_all.1k.scaled.wig


title: H3K27Ac for Tnm2 with UNC0638 Rep_1 Seq_1

description: tnm2_unc0638_merged34_k27ac_swig_peaks.bed.gz

value: 1uM UNC0638

value: H3K27 acetylation (Abcam, ab4729)


title: H3K27Ac for Tnm2 with UNC0638 Rep_2


title: H3K9me2 for CK1750 with DMSO Rep_1 Seq_1


title: H3K9me2 for CK1750 with UNC0638 Rep_1 Seq_2


title: H3K27Ac for Tnm2 with DMSO Rep_2

description: tnm2_dmso_merged34_k27ac_swig_peaks.bed.gz


title: Input DNA for Tnm2 with UNC0638 Rep_1 Seq_1


title: H3K27Ac for CK1750 with UNC0638 Rep_2 Seq_1

description: ck1750_unc0638_merged34_k27ac_swig_peaks.bed.gz


title: H3K27Ac for CK1750 with UNC0638 Rep_2


title: H3K27Ac for CK1750 with DMSO Rep_1 Seq_2

description: ck1750_dmso_merged34_k27ac_swig_peaks.bed.gz


title: H3K27Ac for CK1750 with DMSO Rep_1 Seq_1


title: H3K27Ac for Tnm2 with DMSO Rep_1 Seq_1


title: BLaER1__control__rep0


title: gastroc-Chow-KO-rep7

city: Baton Rouge

first: Jaycob

middle: D

last: Warfel

state: Louisiana

address: 6400 Perkins Road

department: RNA Homeostasis

institute: PBRC

data_processing:
conversion of SOLiD 5500 XSQ files to csfasta/qual files was performed using perl and bash shell scripts that were developed in-house. These scripts make use of Life Technologies XSQ conversion tools, version 1.5.
alignment of sequence tags back to a mouse reference genome was performed using a modified version of the Applied Biosystems SOLiD™ SAGE™ Analysis Software v1.10 that was developed in-house.
filtering non-unique tags, and establishing counts per RefSeq gene was performed using a modified version of the Applied Biosystems SOLiD™ SAGE™ Analysis Software v1.10 that was developed in-house.
The raw data set was filtered to remove genes where the sum of counts was less than 5  across each group.  The dataset was normalized and differential expression calculated using DESeq2 (Bioconductor.org) version 1.8.3.  JMP Genomics version 6.0 was used for principal components analysis, heatmaps, and Venn diagrams.
Genome_build: mm10/GRCm38.p1
Supplementary_files_format_and_content: Tall fomatted text files containing raw data counts and DESeq2 normalized datacounts.

source_name: gastrocnemius

extract_protocol:
Total RNA was prepared using Trizol, RNA concentration was determined usign a nanodrop UV spectrophotometer, and 500ng RNA per sample was given for sequencing library construction.
Libraries were prepared using the Applied Biosystems SOLiDSAGE kit, according to AB's instructions for the SOLiD 4 System (except a 1:100 of Adaptor B dilution was used).
SOLiD SAGE Kit with Barcoding Adaptor Module (#4452811) and SOLiD RNA Barcode Kit (#4427046)

treatment_protocol: Gastrocnemius muscles were dissected from 8 male wild-type and 7 male skeletal muscle-specific Cpt1b knockout mice after chow feeding for 12-14 weeks.

value: gastrocnemius

tag: Sex

value: male

tag: genotype

value: Cpt1b skeletal muscle knockout

tag: diet

value: 45% HFD


title: gastroc-Chow-KO-rep1

tag: tissue


title: gastroc-Chow-KO-rep3


title: gastroc-Chow-KO-rep2


title: gastroc-Chow-KO-rep5


title: gastroc-Chow-control-rep7

value: wild type (floxed)


title: gastroc-Chow-KO-rep4


title: gastroc-Chow-KO-rep6


title: gastroc-Chow-control-rep4


title: gastroc-Chow-control-rep8


title: gastroc-Chow-control-rep5


title: gastroc-Chow-control-rep6


title: gastroc-Chow-control-rep3


title: H3K9me2 for CK1750 with DMSO Rep_2

city: New York


title: gastroc-Chow-control-rep2


title: H3K27Ac for CK1750 with DMSO Rep_2


title: gastroc-Chow-control-rep1


title: NB_8.1-16_8 Days in Short Day

value: Shoot Apical Meristems


title: a4.wt

first: Paula

last: Mera

department: Genetics and Develoment

institute: Columbia University

data_processing:
Bases were called with RTA (Illumina).
Adaptors were trimmed and reads were converted from BCL to Fasta format with bcl2fastq (version 1.8.4).
Reads were mapped to the genome with bowtie version 0.12.7 and Tophat HTSeq-0.6.1 .
Reads in each gene were counted with HTSeq-0.6.1 .
Genome_build: mm9
Supplementary_files_format_and_content: Xlsx file with raw counts for each gene

source_name: gastrocnemius muscles of 3 month old mice after exercise

extract_protocol: RNA was extracted from each group using RNAqueous®-Micro Total RNA Isolation Kit (ThermoSci,catalog no. AM1931) and the quality of purified RNA samples was determined using aBioanalyzer 2100 (Agilent) with an RNA Pico kit. RNAs with RNA Integrity Number (RIN)values greater than or equal to 6.7 were used to generate sequencing libraries. Extracted RNA sampleswere amplified by Ovation® RNA-Seq System V2 (NuGEN) Kit.Amplified cDNA was labeled with Encore biotin module Kit (NuGEN) for RNA-Seq applicationsIllumina Truseq RNA Sample Prep v2 using the LT protocol.

tag: backround strain

value: gastrocnemius muscles


title: a5.wt


title: a1.wt


title: b3Gprc5a-/-


title: b2.Gprc5a-/-


title: AL1B7_pre_saline6hr

city: Lancaster

first: Barbara

middle: Bo-Ju

last: Shih

address: Bailrigg

department: Biomedical and Life Sciences

country: United Kingdom

institute: Lancaster University

description:
gene_count.csv
pAL1B7S6_S10

data_processing:
RNA-seq data was aligned to GRCh38 genome assembly using hisat2 using the parameters --known-splicesite-infile and --dta
Samtools was used to select for reads paired mates.
Gene level count was generated using Stringtie.

source_name: skin biopsy

extract_protocol:
Skin biopsy specimens were collected from the injection site 6 or 72 hours after injection with VZV antigen or normal saline. Normal (uninjected) skin from the same site was collected as a control. Frozen tissue was homogenized, and total RNA was extracted from bulk tissue homogenates by using the RNeasy Mini Kit (Qiagen, Hilden, Germany)
Kappa Hyperprep kit (Roche Diagnostics)

value: skin

tag: losmapimod status

value: pre

tag: treatment

value: 6 hours after saline injection


title: a2.wt

tag: genotype/variation


title: b1.Gprc5a-/-


title: b4.Gprc5a-/-


title: a3.wt


title: AL1B6_pre_saline6hr

description:
gene_count.csv
pAL1B6S6_S2


title: AL1B29_pre_saline6hr

description:
gene_count.csv
pAL1B29S6_S10


title: AL1B30_pre_saline6hr

description:
gene_count.csv
pAL1B30S6_S10


title: AL1B31_pre_saline6hr

description:
gene_count.csv
pAL1B31S6_S2


title: AL1B26_pre_saline6hr

description:
gene_count.csv
pAL1B26S6_S2


title: AL1B25_pre_saline6hr

description:
gene_count.csv
pAL1B25S6_S10


title: AL1B24_pre_saline6hr

description:
gene_count.csv
pAL1B24S6_S2


title: AL1B23_pre_saline6hr

description:
gene_count.csv
pAL1B23S6_S10


title: AL1B18_pre_saline6hr

description:
gene_count.csv
pAL1B18S6_S2


title: AL1B22_pre_saline6hr

description:
gene_count.csv
pAL1B22S6_S2


title: AL1B15_pre_saline6hr

description:
gene_count.csv
pAL1B15S6_S9


title: AL1B13_pre_saline6hr

description:
gene_count.csv
pAL1B13S6_S2


title: AL1B19_pre_saline6hr

description:
gene_count.csv
pAL1B19S6_S10


title: AL1B7_post_saline6hr

description:
gene_count.csv
AL1B7S6_S14

value: post


title: AL1B12_pre_saline6hr

description:
gene_count.csv
pAL1B12S6_S10


title: AL1B29_post_saline6hr

description:
gene_count.csv
AL1B29S6_S14


title: AL1B31_post_saline6hr

description:
gene_count.csv
AL1B31S6_S6


title: AL1B6_post_saline6hr

description:
gene_count.csv
AL1B6S6_S6


title: AL1B25_post_saline6hr

description:
gene_count.csv
AL1B25S6_S14


title: AL1B26_post_saline6hr

description:
gene_count.csv
AL1B26S6_S6


title: AL1B30_post_saline6hr

description:
gene_count.csv
AL1B30S6_S14


title: AL1B15_post_saline6hr

description:
gene_count.csv
AL1B15S6_S11


title: AL1B22_post_saline6hr

description:
gene_count.csv
AL1B22S6_S6


title: AL1B19_post_saline6hr

description:
gene_count.csv
AL1B19S6_S14


title: AL1B18_post_saline6hr

description:
gene_count.csv
AL1B18S6_S6


title: AL1B13_post_saline6hr

description:
gene_count.csv
AL1B13S6_S6


title: CTRL_input_DNA

status: Public on Nov 29 2018

city: Warsaw

first: Katarzyna

last: Lukasiuk

address: 3 Pasteur Street

department: Department of Molecular and Cellular Neurobiology

country: Poland

institute: Nencki Institute of Experimental Biology Polish Academy of Sciences

description: input for Sham-operated

data_processing:
The fastq files were filtered with fastq_quality_filter (FASTX-Toolkit version 0.0.14) to obtain reads for which 90% of the sequence was sequenced with a sequencing error ≤ 1%.
Adapter contamination was removed with cutadapt 1.7.1.
Reads were mapped to the rat genome version RN5 using Bowtie 1.0.0 47 with options -a -v 3 -m 1 --best –strata.
MBD3 peaks were detected with MACS2 2.1.0.20141030 with a fixed extension size of 150 bp and a significance cut-off at FDR equal to 1e-1 and effective genome size of 1.87e9 and post-processing option --call-summits. Each sham sample was tested against the common for sham samples input DNA obtained from one of the sham animals, and each stimulated sample was tested against the common for stimulated samples input DNA obtained from one of the stimulated animals.
Genome_build: RN5
Supplementary_files_format_and_content: Peaks detected with MACS2

organism: Rattus norvegicus

growth_protocol: Male Sprague-Dawley (Medical Research Centre, Warsaw, Poland) weight 290-320 g were housed in a controlled enviroment (21-23 °C, 12h dark/light cycles) with drinking and feeding ad libitum.

extract_protocol:
Tissue that contained entorhinal, perirhinal, and piriform cortices and the amygdala, dissected as described previously 43 , were sliced into 1 mm pieces and crosslinked with a 1% formaldehyde solution for 15 min at room temperature. Fixation was quenched by 125 mM glycine. The tissue was washed twice with ice-cold PBS and stored at -80°C. Samples were thawed on ice, resuspended in 1 ml of PBS that contained protease inhibitor cocktail (11697498001, Roche Diagnostics, Basel, Switzerland) and 1 mM PMSF, and homogenized using TissueRuptor (Qiagen, Venlo, Netherlands). The homogenates were centrifuged at 2300 × g for 5 min at 4°C. The supernatant was removed, and the pellet was resuspended in 1.8 ml of lysis buffer (50 mM Tris-HCl, 10 mM ethylenediaminetetraacetic acid, and 1% SDS, pH 8.1) that contained protease inhibitor cocktail. After 1-h incubation at 4°C with rotation, cells were physically ground in an ice-cold Dounce homogenizer (Wheaton, NJ, USA) with 30 strokes to release nuclei. Samples were sonicated with Bioruptor Plus UCD-300 (Diagenode, Seraing, Belgium) for 105 min in seven cycles of 30 s on and off at the high setting. Sheared chromatin was centrifuged at 12000 × g for 15 min at 4°C, and the supernatant was collected and stored at -80°C. Next, 420 μl of the supernatant (25 μg chromatin) was diluted 10 times in Chip Buffer 1 and incubated with 26 μl of protein G magnetic beads and 4 μg anti-MBD3 antibody (A302-528A, Bethyl Laboratories, Montgomery, TX, USA) at 4°C overnight with rotation according to the manufacturer’s instructions (53008, Active Motif, Carlsbad, CA, USA). The beads were washed once with 800 μl of Chip Buffer 1 and twice with 800 μl of Chip Buffer 2 and resuspended with 50 μl of Elution Buffer AM2. The samples were incubated for 15 min at room temperature on an end-to-end rotator, and 50 μl of Reverse Cross-linking Buffer was added to the eluted chromatin. Eluted DNA was incubated at 65°C overnight, followed by incubation for 30 min at 37°C with 1 μl of RNase A (Thermo Fisher Scientific, Waltham, MA, USA). The samples were then treated with proteinase K (03 115887 001, Roche Diagnostics, Basel, Switzerland) for 1.5 h at 42°C. DNA was then purified by phenol-chloroform extraction and ethanol precipitation.
Chip-Seq libraries were prepared using custom inline bar-coded adaptors (NEBNext Multiplex Oligos for Illumina, New England BioLabs, Ipswich, MA, USA) and sequenced on the Illumina HiSeq2000 platform at the European Molecular Biology Laboratory (Heidelberg, Germany).

treatment_protocol: Stimulation and recording bipolar electrodes (Plastics One, Roanoke, VA, USA) were implanted in the left lateral nucleus of the amygdala under isoflurane anesthesia (2% in 100% oxygen). A surface recording electrode was implanted in the skull over the right frontal cortex. To evoke SE, the animals were electrically stimulated via the intra-amygdala electrode for 20 min with a 100-ms train of 1-ms biphasic square-wave pulses (400 μA peak to peak) delivered at 60 Hz every 0.5 s (Master-8 Stimulator connected to an ISO-Flex stimulus isolation unit; A.M.P.I., Israel). Status epilepticus was stopped 1.5 h after stimulation with an intraperitoneal injection of diazepam (20 mg/kg; Relanium, Polfa SA, Warsaw, Poland). The rats were continuously monitored by video electroencephalography to detect spontaneous epileptic seizures (Comet EEG, Grass Technologies, West Warwick, RI, USA). Sham-operated control animals had electrodes implanted but did not receive electrical stimulation. Stimulated and sham-operated animals were sacrificed 14 days after stimulation.

value: sham operated

tag: chip-seq antibody

tag: gender

tag: strain

value: Sprague-Dawley


title: RatID_2_MBD3

source_name: entorhinal, perirhinal, and piriform cortices and the amygdala

value: Anti-MBD3 (A302-528A, Bethyl Laboratories, Montgomery, TX, USA)


title: RatID_12_MBD3

value: entorhinal, perirhinal, and piriform cortices and the amygdala

value: amygdala stimulated


title: RatID_14_MBD3


title: RatID_5_MBD3


title: RatID_11_MBD3


title: RatID_1_MBD3


title: HeLa_CSC_H3K27Ac

city: Suita, Osaka

first: Keisuke

last: Tamari

address: 2-2 Yamadaoka

department: Radiation Oncology

country: Japan

institute: Osaka University Graduate School of Medicine

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie2.
ChIP-seq peaks were called using MACS1.4.
Genome_build: hg19
Supplementary_files_format_and_content: Wig files were generated using MACS1.4.

source_name: HeLa, CSC, H3K27Ac

growth_protocol: HeLa cells transfected with ZsGreen-cODCdegron were cultured in DMEM supplemented with 10% FBS and 1% P/S.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the TruSeq ChIP Sample Prep Kit (Part# 15023092 Rev. B).

tag: chip antibody

value: H3K27Ac (abcam, ab4729)


title: SE_input_DNA

description: input for Amygdala Stimulated


title: RatID_3_MBD3


title: HeLa_CSC_H3K4me3

source_name: HeLa, CSC, H3K4me3

tag: cell type

value: HeLa cells transfected with ZsGreen-cODCdegron


title: HeLa_CSC_Pol2

source_name: HeLa, CSC, Pol2

value: Pol2 (abcam, ab5131)


title: HeLa_nonCSC_Pol2

source_name: HeLa, nonCSC, Pol2


title: HeLa_nonCSC_H3K4me3

source_name: HeLa, nonCSC, H3K4me3


title: AL1B24_post_saline6hr

description:
gene_count.csv
AL1B24S6_S6


title: AL1B12_post_saline6hr

description:
gene_count.csv
AL1B12S6_S14


title: 100_input

city: Edinburgh

first: Robin

last: Allshire

state: Midlothian

address: Max Born Cresent

institute: The University of Edinburgh

data_processing:
ChIP-seq reads were aligned to ASM294v2.20 build using Bowtie2
Polymerase II ChIP-seq data were filtered pombe only reads;
Genome_build: ASM294v2.20
Supplementary_files_format_and_content: bigwig files were generated using bedtools and wigToBigWig from UCSC

organism: Schizosaccharomyces pombe

source_name: cell

growth_protocol: Schizosaccharomyces pombe cell were gwon in rich medium (1X or 4X YES). Cell cycle synchronisation were performed using cdc25-22 temperature dependent block release.

extract_protocol:
Lysates were prepared using standard bead beating procedure, sonicated to achieve fragmements of 200-400bp andclarified by centrifugation at 17000g.
Libraries were prepared using standard Illumina pipeline. Briefly, DNA was end-repaired using NEB Quick blunting kit (E1201L).  The blunt, phosphorylated ends were treated with Klenow fragment (3' to 5' exo minus) and dATP to yield a protruding 3- 'A' base for ligation of NEXTflex adapters (Bioo Scientific) which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 13-15 cycles and library fragments of ~300 bp (insert plus adaptor and PCR primer sequences) were selected using Ampure XP beads. The purified DNA was captured on an Illumina flow cell for cluster generation.

treatment_protocol: For Recombination Induced Tag Exchange experiment (RITE), cells were treated with 1 mM b-estradiol.

value: wild type


title: AL1B23_post_saline6hr

description:
gene_count.csv
AL1B23S6_S14


title: 75_input


title: 125_input


title: 175_input


title: 150_input


title: 50_input


title: 200_input


title: 25_input


title: HA-125_CENPA

value: HA tag CENPA


title: HA-150_CENPA


title: HA-200_CENPA


title: HA-175_CENPA


title: HeLa_nonCSC_H3K27Ac

source_name: HeLa, nonCSC, H3K27Ac


title: HA-100_CENPA


title: T7-125_CENPA

value: T7 tag CENPA


title: HA-75_CENPA


title: HA-25_CENPA


title: T7-150_CENPA


title: T7-100_CENPA


title: B324_T7_RNAPIIS2P


title: B324_T9_input


title: T7-175_CENPA


title: HA-50_CENPA


title: T7-200_CENPA


title: T7-50_CENPA


title: T7-75_CENPA


title: B324_T5_input


title: B324_T6_RNAPIIS2P


title: B324_T6_input


title: T7-25_CENPA


title: B324_T5_RNAPIIS2P


title: B324_T3_RNAPIIS2P


title: B324_T2_RNAPIIS2P


title: B324_T1_RNAPIIS2P


title: B324_T7_input


title: B324_T3_input


title: B324_T4_RNAPIIS2P


title: B324_T4_input


title: B324_T1_input


title: B324-H3_ChiP-Nexus

data_processing:
ChIP-seq reads were aligned to ASM294v2.20 build using Bowtie2, trimmed first 15bp;
Data were analysis using MACE
Genome_build: ASM294v2.20
Supplementary_files_format_and_content: bigwig files were generated using bedtools and wigToBigWig from UCSC

growth_protocol: Schizosaccharomyces pombe cell were gwon in rich medium (1X YES).

extract_protocol:
Lysates were prepared using standard bead beating procedure, sonicated to achieve fragmements of 200-400bp andclarified by centrifugation at 17000g.
ChIP-Nexus libraries were prepared essentially as described in He et al., 2015, Briefly, protein G-dynabeads bound DNA-protein-complexes were affinity selected using specific antibodies . DNA was end repaired using T4 DNA polymerase, DNA polymerase I large fragment and T4 polynucleotide kinase. A single 3'-A overhang was added using Klenow 3'-5' exo- polymerase. Adapters were ligated and blunted again by Klenow 3'-5' exo- polymerase to fill in the 5’ overhang first and then by T4 DNA polymerase to trim possible 3’ overhangs. Blunted DNA was then sequentially digested by lambda exonuclease and RecJf. Digested single strand DNA was then eluted, reverse cross-linked and phenol-chloroform purified. Fragments were  then self-circularized by Circligase. An oligonucleotide was hybridized to circularized single DNA for subsequent BamHI digestion in order to linearize the DNA. This linearized single strand DNA was then PCR-amplified using adapter sequences and library was purified and size selected using Ampure XP beads. The sequencing libraries were sequenced following Illumina's work flow.
ChiP-Nexus


title: 501Mel R+T1

city: Valbonne - Sophia-Antipolis

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

data_processing:
Mapping with STAR_2.4.0a versus hg19 with default parameters
Gene counting with featureCounts (subread-1.5.0-p3-Linux-x86_64) with "--primary -g gene_name -p -s 1" options.
Genome_build: hg19
Supplementary_files_format_and_content: tablecount.txt: tab-delimited text files include counts values for each sample

source_name: 501Mel cells treated with Resveratrol (5E-6) + TCDD (1E-9) during 48h

growth_protocol: Cell lines were grown in RPMI-1640 medium (Gibco BRL, Invitrogen, Paisley, UK) supplemented with 10% Fetal Bovine Serum (PAA cell culture company, Pasching, Austria) and 1% Penicillin-Streptomycin antibiotics (Gibco BRL, Invitrogen, Paisley, UK).

extract_protocol:
RNA extraction with the miRVana kit (Thermo Fisher Scientific)
Libraries were generated from 1µg of total RNA using Truseq Stranded mRNA kit (Illumina). Libraries were then quantified with KAPA library quantification kit (Kapa biosystems) and pooled. 4nM of this pool were loaded on a Nextseq 500 high output flowcell and sequenced on a NextSeq 500 platform (Illumina) with 2×75bp paired-end chemistry.

treatment_protocol: 501Mel cells have been treated for 48h respectively with DMSO, Vemurafenib (1uM), Resveratrol (5uM), Resveratrol (5uM)+Vemurafenib (1uM), TCDD (10nM), Resveratrol (5uM) + TCDD (10nM)

value: Skin

value: Melanoma cells

tag: cell line

tag: rin number


title: 1645-H3_ChiP-Nexus


title: B324_T9_RNAPIIS2P


title: 501Mel R+T2


title: 501Mel R+V1

source_name: 501Mel cells treated with Resveratrol (5E-6) + vemurafnib (1E-6) during 48h


title: 501Mel R+V2


title: 501Mel T2

source_name: 501Mel cells treated with TCDD (10E-9) during 48h


title: B324_T2_input


title: 501Mel R2

source_name: 501Mel cells treated with Resveratrol (5E-6) during 48h


title: 501Mel V1

source_name: 501Mel cells treated with Vemurafenib (1E-6) during 48h


title: 501Mel Ctrl1

source_name: 501Mel cells treated with DMSO during 48h


title: 501Mel V2


title: 501Mel Ctrl2


title: XEN cell 1 Male Technical Replicate 1

city: Rotterdam

first: Catherine

last: Dupont

address: Wytemaweg 80

country: Netherlands

institute: Erasmus MC

description:
Sample name in processed data file: XEN_M1_r1
[processed data files:]
Nanog_CDupont_allsamples_gene_counts.txt
Nanog_regulated_genes_list.txt

data_processing:
Sequencing: Illumina HiSeq2000, single read 36bp + 7bp index, using Illumina TruSeq v2 sequencing chemistry
Demultiplexing: Narwhal [Brouwer, R.W., et al., NARWHAL, a primary analysis pipeline for NGS data. Bioinformatics, 2012. 28(2): p. 284-5.]
Alignment against the mm9 reference genome: tophat version 1.3.1
ReadCounting: custom R script, based on IRanges package
Differential expression has been determined using the edgeR package on TMM normalized counts as input
Genome_build: mm9
Supplementary_files_format_and_content: Nanog_CDupont_allsamples_gene_counts.txt: tab separated text file, one gene per line, one column per sample,
Supplementary_files_format_and_content: Nanog_regulated_genes_list.txt: text file, list of FPKM values of the selected up and down regulated genes. The table includes genes that are selected as described in the material and methods. In short, genes were selected when FDR < 0.05, logFC > 2.5, expression in all three Nanog negative embryo's with average expression > 0.49 FPKM or expression in all four Nanog positive embryo's with average expression > 0.49, not specifically expressed in XEN and/or TS cells and published to be bound by NANOG. Upregulated genes are annotated with "UP" and downregulated genes with "DOWN".

source_name: XEN cell line

growth_protocol: Standard Culture protocol as described in Materials and Methods

extract_protocol:
Stem cells each from two different passages (technical replicates), were collected in PCR tubes and stored in lysis buffer (Absolutely RNA Miniprep Kit, Stratagene #400800) at -80°C until further processed according to manufacturer’s instructions
Libraries have been prepared for the 14 stem cell samples with the Illumina TruSeq RNA kit, according to manufacturer’s protocol

value: XEN cell line

value: Wildtype

value: Male


title: TS cell 3 Male Technical Replicate 2

description:
Sample name in processed data file: TS_M3_r2
[processed data files:]
Nanog_CDupont_allsamples_gene_counts.txt
Nanog_regulated_genes_list.txt

source_name: TS cell line

value: TS cell line


title: B324-H4_ChiP-Nexus


title: XEN cell 1 Male Technical Replicate 2

description:
Sample name in processed data file: XEN_M1_r2
[processed data files:]
Nanog_CDupont_allsamples_gene_counts.txt
Nanog_regulated_genes_list.txt


title: XEN cell 2 Male Technical Replicate 1

description:
Sample name in processed data file: XEN_M2_r1
[processed data files:]
Nanog_CDupont_allsamples_gene_counts.txt
Nanog_regulated_genes_list.txt


title: TS cell 1 Female Technical Replicate 2

description:
Sample name in processed data file: TS_F1_r2
[processed data files:]
Nanog_CDupont_allsamples_gene_counts.txt
Nanog_regulated_genes_list.txt

value: Female


title: TS cell 2 Female Technical Replicate 1

description:
Sample name in processed data file: TS_F2_r1
[processed data files:]
Nanog_CDupont_allsamples_gene_counts.txt
Nanog_regulated_genes_list.txt


title: TS cell 3 Male Technical Replicate 1

description:
Sample name in processed data file: TS_M3_r1
[processed data files:]
Nanog_CDupont_allsamples_gene_counts.txt
Nanog_regulated_genes_list.txt


title: TS cell 1 Female Technical Replicate 1

description:
Sample name in processed data file: TS_F1_r1
[processed data files:]
Nanog_CDupont_allsamples_gene_counts.txt
Nanog_regulated_genes_list.txt


title: TS cell 2 Female Technical Replicate 2

description:
Sample name in processed data file: TS_F2_r2
[processed data files:]
Nanog_CDupont_allsamples_gene_counts.txt
Nanog_regulated_genes_list.txt


title: ES cell 2 Male Serum Free Technical Replicate 2

description:
Sample name in processed data file: ES_M2_r2
[processed data files:]
Nanog_CDupont_allsamples_gene_counts.txt
Nanog_regulated_genes_list.txt

source_name: ES cell line

value: ES cell line


title: ES cell 1 Female Serum Free Technical Replicate 2

description:
Sample name in processed data file: ES_F1_r2
[processed data files:]
Nanog_CDupont_allsamples_gene_counts.txt
Nanog_regulated_genes_list.txt


title: 1645-H4_ChiP-Nexus


title: ES cell 1 Female Serum Free Technical Replicate 1

description:
Sample name in processed data file: ES_F1_r1
[processed data files:]
Nanog_CDupont_allsamples_gene_counts.txt
Nanog_regulated_genes_list.txt


title: Male Wildtype Nanog

description:
Sample name in processed data file: Emb_WT_M
[processed data files:]
Nanog_CDupont_allsamples_gene_counts.txt
Nanog_regulated_genes_list.txt

source_name: embryo E3.5

extract_protocol:
Embryos were collected in 0,2ml PCR tubes and stored in lysis buffer (Absolutely RNA Nanoprep Kit, Stratagene #400753) at -80°C until further processed. Following thawing and according to the manufacturer's instructions, RNA from the E3.5 embryos was extracted using the Absolutely RNA Nanoprep Kit (Stratagene, #400753) and eluted in 5µl water
For the 8 embryos, cDNA has been generated by SMARTer UltraLow from Clontech, according to manufacturer’s protocol. We started with all available 3.5 µL total RNA per sample. cDNA fragment distribution and quantity has been assessed on the DNA HiSense chip on the 2100 Bioanalyzer (Agilent Technologies). Sequencing libraries have been prepared with the Illumina TruSeq DNA kit, according to manufacturer’s protocol.

value: embryo


title: 501Mel R1


title: Female Wildtype Nanog

description:
Sample name in processed data file: Emb_WT_F
[processed data files:]
Nanog_CDupont_allsamples_gene_counts.txt
Nanog_regulated_genes_list.txt


title: Male Knockout 2 Nanog

description:
Sample name in processed data file: Emb_KO_M2
[processed data files:]
Nanog_CDupont_allsamples_gene_counts.txt
Nanog_regulated_genes_list.txt

value: Knockout


title: Female Knockout 2 Nanog

description:
Sample name in processed data file: Emb_KO_F2
[processed data files:]
Nanog_CDupont_allsamples_gene_counts.txt
Nanog_regulated_genes_list.txt


title: XEN cell 2 Male Technical Replicate 2

description:
Sample name in processed data file: XEN_M2_r2
[processed data files:]
Nanog_CDupont_allsamples_gene_counts.txt
Nanog_regulated_genes_list.txt


title: Female Knockout 1 Nanog

description:
Sample name in processed data file: Emb_KO_F1
[processed data files:]
Nanog_CDupont_allsamples_gene_counts.txt
Nanog_regulated_genes_list.txt


title: Male Heterozygous Nanog

description:
Sample name in processed data file: Emb_Het_M
[processed data files:]
Nanog_CDupont_allsamples_gene_counts.txt
Nanog_regulated_genes_list.txt

value: Heterozygous


title: AlphaTC_ARXS174A_4

city: Adelaide

first: Cheryl

last: Shoubridge

state: SA

address: North Tce

institute: The University of Adelaide

data_processing:
Aligened using STAR aligner to  Mus musculus/mm10
Aligned samples were analysed for differential expression using DESeq2 v1.1.0 through pairwise differential expression analysis between biological replicate groups.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include count data for each sample

source_name: Alpha TC cells

extract_protocol:
RNA was isolated using Trizol (Invitrogen) and RNeasy Mini Kit (QIAGEN)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: transfection

value: Alpha TC cells


title: AlphaTC_ARXS37AS67A_3


title: AlphaTC_ARXS174A_1


title: AlphaTC_ARXS174A_2


title: AlphaTC_ARXS174A_3


title: AlphaTC_ARXS37AS67A_2


title: AlphaTC_ARXS37AS67A_4


title: AlphaTC_ARXS37AS67A_1


title: ES cell 2 Male Serum Free Technical Replicate 1

description:
Sample name in processed data file: ES_M2_r1
[processed data files:]
Nanog_CDupont_allsamples_gene_counts.txt
Nanog_regulated_genes_list.txt


title: AlphaTC_ARXWT_3

value: ARX-WT


title: AlphaTC_ARXWT_2


title: AlphaTC_ARXWT_4


title: AlphaTC_UT_4

value: untransfected


title: AlphaTC_UT_2


title: AlphaTC_UT_3


title: Male Knockout 1 Nanog

description:
Sample name in processed data file: Emb_KO_M1
[processed data files:]
Nanog_CDupont_allsamples_gene_counts.txt
Nanog_regulated_genes_list.txt


title: AlphaTC_UT_1


title: AML_3

city: Duesseldorf

first: Thomas

last: Schroeder

address: Moorenstr. 5

department: Department of Hematology, Oncology and Clinical Immunology

institute: University of Duesseldorf, Medical Faculty

data_processing:
Reads were trimmed by removing stretches of bases with a quality score <30 at their ends.
Reads were mapped using Tophat2.0.6 against the hg19 assembly of the human genome.
Differential expression was quantified using DESeq2 and Cuffdiff 2.0 and subjected to diverse testing corrections (Love at al. Genome Biol. 2014;15(12):550; Trapnell et al. Nat Biotechnol. 2013;31(1):46-53)
Genome_build: hg19
Supplementary_files_format_and_content: txt containing count data produced by htseq-count

source_name: MSCs from bone marrow

extract_protocol:
Bone marrow samples were obtained from patients with newly-diagnosed MDS and AML (median age 60 years, range 25-89 years) and age- and sex-matched healthy controls (HC, median age 64 years, range: 39-83 years, p=0.52). MSC were derived from the mononuclear cell (MNC) fraction of these specimens and cultured as previously described (Gey et al. Leukemia. 2013;27(9):1841-51; Gey et al. Leukemia. 2016;30(3):683-91). All experiments were carried out using MSC derived from passages 3–4.
Transcriptome-sequencing libraries were prepared from total RNA isolations using the TruSeq RNA sample preparation kit (Illumina, San Diego, CA, USA), and single-read 50 bp sequencing was performed in a HiSeq-2000 device (Illumina, San Diego, CA, USA)

tag: syndrome

value: AML

tag: myelodysplastic syndromes stage

value: Mesenchymal stromal cells (MSC)


title: RAEB_2

value: RAEB

value: late MDS


title: RAEB_3


title: AML_2


title: 501Mel T1

first: Kevin

value: Skin

value: Melanoma cells


title: Female Heterozygous Nanog

description:
Sample name in processed data file: Emb_Het_F
[processed data files:]
Nanog_CDupont_allsamples_gene_counts.txt
Nanog_regulated_genes_list.txt

tag: Sex


title: RAEB_1


title: RCMD_3

value: RCMD

value: early MDS


title: RCMD_1


title: RCMD_2


title: Healthy_3

value: healthy


title: Healthy_1


title: Healthy_2


title: AlphaTC_ARXWT_1


title: DIP_8oxodG_exp2_MCF10A

status: Public on Nov 28 2018

city: Naples

first: Stefano

last: Amente

address: via pansini, 5

department: Department of  Molecular Medicine and Medical Biotechnologies

institute: University of Naples "FEDERICO II"

description: Normal growing MCF10A cells

data_processing:
Alignments were performed with BWA  to hg18 or mm9 using default parameters.
The 8-oxodG peaks were identified from uniquely mapped reads without duplicates using MACS and the p-value cutoff used for peak detection was 1e-5. The gH2AX peaks were identified from uniquely mapped reads without duplicates using SICER and FDR 0.01 was used as cutoff.
Genome_build: hg18 and mm9
Supplementary_files_format_and_content: SAMtools and BEDtools were used for filtering steps and file formats conversion.

source_name: normal breast cells

growth_protocol: MCF10A cells were cultured in 1:1 mixture DMEM-F12 supplemented with 5% horse serum, 10 µg/ml insulin, 0,5 µg/ml hydrocortisone, 100 ng/ml cholera enterotoxin, and 20 ng/ml epidermal growth factor, and incubated at 37°C in humidified atmosphere with 5% CO2. Mouse embryonic fibroblasts MEF (3T9-MycER) were grown in DMEM medium supplemented with 10% serum, penicillin/streptomycin and 2 mM L-Gln.

extract_protocol:
Genomic DNA from MCF10A cells or from growing MEFs was extracted by using Dneasy Blood&Tissue kit. Genomic DNA were sonicated and immunoprecipitated with antibodies anti 8-oxodG O/N. Eluted DNA was processed for library preparation. For ChIp_Seq anti gH2AX, lysates were clarified from sonicasted nuclei and histone-DNA complexes were isolated with specific antibody.
Libraries were prepared according to Illumina's instructions

value: normal breast cells


title: DIP_8oxodG_exp1_MCF10A

description: Normal growing MCF10A cells


title: Input_MCF10A

description: Normal growing MCF10A cells


title: Atria1

city: Stanford

first: Jared

last: Churko

address: 265 Campus Dr G1105 SIM1

department: Radiology

institute: Stanford

description:
Processed data file: heart_genes.txt
Bulk RNA-seq

data_processing:
RNA-seq: reads were deduplicated using prinseq, mapped to reference Ensembl GRCh38 genome using Tophat and RPKM values were obtained using AltAnalyze 2.0.9.3
ChIP-seq: reads were deduplicated using prinseq, mapped to reference Ensembl GRCh38 genome using Bowtie, Bedtools 2.19.1  was used to generate bigwig files
AltAnalyze 2.0.9.3 was used to generated a table of RPKM values
Genome_build: Ensembl GRCh38, UCSC hg19
Supplementary_files_format_and_content: RNA-Seq: RPKM files
Supplementary_files_format_and_content: ChIP-Seq: bw files

source_name: Heart Tissue

growth_protocol: hiPSCs and hESCs were grown in E8 media on  Matrigel

extract_protocol:
RNA-seq: mRNA was extracted using the miRNEASY kit from Qiagen.  ChIP-seq: Cells were crosslinked with formalin.
Bulk RNA-seq: Ovation® RNA-Seq System V2 kit (NuGEN) and NEBNext DNA Library Prep Master Mix Set for Illumina.  Single-cell RNA-seq: SMARTer Ultra Low RNA Kit for the Fluidigm C1 Nextera XT DNA Sample Preparation Kit.  Gene edited lines RNA-seq: Ion AmpliSeq™ Transcriptome Human Gene Expression Kit, the Ion PI™ Hi-Q™ Sequencing 200 Kit.   ChIP-seq: NEBNext DNA Library Prep Master Mix Set for Illumina or NEBNext® Ultra™ DNA Library Prep.

treatment_protocol: no treatment

value: Heart Tissue

tag: Stage

tag: replicate


title: C93

description:
Processed data file: Single_cell genes.txt
Single-cell RNA-seq

source_name: fibroblasts

value: hiPSCs-CMs

value: day 30


title: C84


title: C87


title: Atria2

tag: tissue


title: C90


title: C42


title: C76


title: Ventricle2


title: Ventricle1


title: C18


title: C88


title: C25


title: C81


title: C79


title: C66


title: C68


title: C69


title: C77


title: C78


title: C63


title: C60


title: C64


title: C62


title: C57


title: C54


title: C50


title: C40


title: C41


title: C12


title: C14


title: C36


title: C11


title: C17


title: C30


title: C23


title: AML_1


title: C58


title: C37


title: C06


title: TBX5

description: ChIP-seq

source_name: blood

value: Sigma, SAB1411331


title: F4D9

description:
Processed data file: CMdiffgenes.txt
Bulk RNA-seq

value: day 9


title: F4D10

value: day 14


title: NR2F2

description: ChIP-seq

value: Active Motif, 61213


title: C01


title: HEY2

description: ChIP-seq

value: Proteintech, 10597-1-AP


title: C56


title: F4D8

value: hiPSCs

value: day 8


title: C55


title: F4D6

value: day 6


title: F4D5

value: day 5


title: F4D4

value: day 4


title: C08


title: C26


title: F4D2

value: day 2


title: F4D1

value: day 1


title: F4D11


title: F4D3

value: day 3


title: F3D11


title: F4D7

value: day 7


title: F4D0

value: hiPSCs (day 0)


title: F3D7


title: F3D4


title: F3D10

value: hiPSCs-CMs


title: F3D9


title: F3D8


title: F3D3


title: F3D5


title: F3D2


title: F1D10


title: F1D8


title: F3D0


title: F1D9


title: F1D4


title: F1D6


title: F1D5


title: F1D7


title: F1D3


title: F1D2


title: F1D1


title: F1D0


title: F3D6


title: 3mon1-R

value: day 90


title: 3mon2-R


title: 3mon3-R


title: NR2F2CL17

description:
Processed data file: Gene_edited_lines.txt
Gene edited lines RNA-seq

value: hiPSCs-CMs (NR2F2 CRISPR edited)

value: day 30


title: F1D11


title: F3D1


title: NR2F2CL16


title: NR2F2CL1


title: HEY2CL3

value: hiPSCs-CMs (HEY2 CRISPR edited)


title: HEY2CL4


title: HEY2CL7


title: Cont1


title: Treatment 100ug mAb/Dose Repeat1

city: Gainesville

first: Jianping

last: Huang

state: FL

address: 1149 Newell Dr

department: neurosurgery

institute: UF

data_processing:
Bustard  used for basecalling.
Illumina basespace sequence hub used for alignment.Read mapped using STAR aligner. FPKM estimated of reference genes and transcripts using Cufflinks 2. Novel transcripts assembled with Cufflinks 2. Mus musculus UCSC mm10 (RefSeq gene annotation)
Genome_build: Mus musclus UCSC mm10 (RefSeq gene annotation)
Supplementary_files_format_and_content: gtf files outputted from Cufflinks for each Sample.

source_name: GL261 tumor tissue, VEGF-A blockade,100ug mAb/ dose

extract_protocol:
Tumors were harvested after PBS perfusion and, flash frozen on dry ice, and RNA was harvested using Trizol method.NEB Next Ultra RNA Library Prep Kit(Catalog # E7530L) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The GL261 burden mice were treated with VEGF-A mAb(B20.4.1.1, Genentech), every 3 days, starting Day10 after tumor implantation to the endpoint. The treatment doses are0ug, 50ug,100ug and 200ug/dose.

value: Brain tumor

tag: agent

value: 100ug mAb/Dose


title: Treatment 200ug mAb/Dose Repeat3

source_name: GL261 tumor tissue, VEGF-A blockade,200ug mAb/ dose


title: Treatment 200ug mAb/Dose Repeat2

value: 200ug mAb/Dose


title: Treatment 100ug mAb/Dose Repeat2


title: Treatment 50ug mAb/Dose Repeat3

source_name: GL261 tumor tissue, VEGF-A blockade,50ug mAb/ dose


title: Treatment 100ug mAb/Dose Repeat3


title: No Treatment Repeat3

source_name: GL261 tumor tissue, No treat control

value: 50ug mAb/Dose


title: Treatment 50ug mAb/Dose Repeat1


title: No Treatment Repeat2


title: Treatment 50ug mAb/Dose Repeat2


title: No Treatment Repeat1


title: Healthy brain Repeat 3

source_name: Healthy brain control

value: Healthy Brain


title: Healthy brain Repeat 2


title: NR2F2-1OE

description: Processed data file: OEandGEexp.txt

data_processing:
RNA-seq: reads were deduplicated using prinseq, mapped to reference Ensembl GRCh38 genome using Tophat and RPKM values were obtained using AltAnalyze 2.0.9.3
ChIP-seq: reads were deduplicated using prinseq, mapped to reference Ensembl GRCh38 genome using Bowtie, Bedtools 2.19.1  was used to generate bigwig files
Supplementary_files_format_and_content: AltAnalyze 2.0.9.3 was used to generated a table of RPKM values
Genome_build: Ensembl GRCh38, UCSC hg19
Supplementary_files_format_and_content: RNA-Seq: RPKM files
Supplementary_files_format_and_content: ChIP-Seq: bw files

source_name: Fibroblasts

extract_protocol:
RNA-seq:mRNA was extracted using the miRNEASY kit from Qiagen ChIP-seq:Cells were crosslinked with formalin
Bulk RNA-seq: Ovation® RNA-Seq System V2 kit (NuGEN) and NEBNext DNA Library Prep Master Mix Set for Illumina, OEandGE RNA-seq:  Novogene protocol, 1. mRNA enriched using oligo(dT) beads, 2. fragmented using fragmentation buffer, 3. cDNA synthesis using random hexamer, 4. adapter ligation, 5. Illumina Hiseq 4000 2x150 Single-cell RNA-seq: SMARTer Ultra Low RNA Kit for the Fluidigm C1 Nextera XT DNA Sample Preparation Kit, Gene edited lines RNA-seq: Ion AmpliSeq™ Transcriptome Human Gene Expression Kit, the Ion PI™ Hi-Q™ Sequencing 200 Kit ChIP-seq: NEBNext DNA Library Prep Master Mix Set for Illumina or NEBNext® Ultra™ DNA Library Prep

value: hiPSC-CMs (NR2F2 Overexpression)


title: Healthy brain Repeat 1


title: NR2F2GE2-4

description: Processed data file: OEandGEexp.txt

value: hiPSC-CMs (NR2F2 Gene-editedl)


title: NR2F2GE2-3

description: Processed data file: OEandGEexp.txt


title: Cont2


title: Treatment 200ug mAb/Dose Repeat1


title: TBX5-1OE

description: Processed data file: OEandGEexp.txt

value: hiPSC-CMs (TBX5 Overexpression)


title: NR2F2-1

description: Processed data file: OEandGEexp.txt


title: TBX5GE2-2

description: Processed data file: OEandGEexp.txt

value: hiPSC-CMs (TBX5 Gene-editedl)


title: NR2F2GE2-2

description: Processed data file: OEandGEexp.txt


title: NR2F2GE2-1

description: Processed data file: OEandGEexp.txt


title: TBX5GE2-1

description: Processed data file: OEandGEexp.txt


title: TBX5-2OE

description: Processed data file: OEandGEexp.txt


title: TBX5GE2-3

description: Processed data file: OEandGEexp.txt


title: TBX5-2

description: Processed data file: OEandGEexp.txt


title: HEY2-1OE

description: Processed data file: OEandGEexp.txt

value: hiPSC-CMs (HEY2 Overexpression)


title: HEY2GE2-1

description: Processed data file: OEandGEexp.txt

value: hiPSC-CMs (HEY2 Gene-editedl)


title: TBX5-1

description: Processed data file: OEandGEexp.txt


title: HEY2-2OE

description: Processed data file: OEandGEexp.txt


title: HEY2-2

description: Processed data file: OEandGEexp.txt


title: HEY2GE2-2

description: Processed data file: OEandGEexp.txt


title: GFP-1OE

description: Processed data file: OEandGEexp.txt

value: hiPSC-CMs (Overexpression Control)


title: EPI

description: Processed data file: OEandGEexp.txt

value: hiPSC-CMs (Gene-edited Control)


title: HEY2-1

description: Processed data file: OEandGEexp.txt


title: DIP_8oxodG_exp2_MEF

description: Normal growing MEF cells

source_name: mouse embryonic fibroblast

value: MEF

value: mouse embryonic fibroblast


title: DIP_8oxodG_exp1_MEF

description: Normal growing MEF cells


title: Cont

description: Processed data file: OEandGEexp.txt

value: day 30


title: NR2F2-2

description: Processed data file: OEandGEexp.txt


title: ProB_WT_rep1

first: Richard

last: Koche

state: New York

institute: Memorial Sloan Kettering Cancer Center

description: wildtype

data_processing:
Reads were quality and adapter trimmed before aligning to mouse assembly mm9 with STAR v2.4.
Read count tables were created using HTSeq v0.6.1.
Normalization and differential expression analysis was performed with DESeq2.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text file with read counts over all genes.

source_name: wildtype ProB cells (B220+CD43+IgM-)

growth_protocol: Whole bone marrow from Mll-Af4 mice 6-8 weeks of age was obtained, and lineage depletion was performed.  Double positive c-Kit+ and Sca1+ cells were FACS sorted and grown overnight in lymphoid-promoting media culture conditions (IMDM media containing 15% FBS, supplemented with murine cytokines, mIL7, mSC7, mFL at 20 ng/uL, PeproTech) before retroviral transduction with virus containing MSCV-cre-IRES-TdTomato.  These “pre-leukemic cells” were sorted for Tomato positivity and subsequently retrovirally transduced with either empty vector MSCV-IRES-GFP or vector containing N-RasG12D.   Primary leukemias were generated by injecting 250,000 sorted, pre-leukemic Mll-Af4/ N-RasG12D cells into lethally irradiated recipients (900 rads) with wildtype helper cells by intravenous tail vein injection (200,000 red blood cell lysed total whole bone marrow).

extract_protocol:
RNA was extracted using Qiagen RNeasy kit and DNAse treated.
Libraries were prepared according to Illumina's instructions accompanying the TruSeq RNA Sample Preparation Kit

value: ProB cells

value: bone marrow

tag: genotype

value: wildtype


title: MA4NRAS_Leuk_92_rep2

description: mouse model of acute lymphoblastic leukemia

source_name: MLL-AF4/NRAS primary leukemia cells

value: primary leukemia cells

value: Mll-Af4/ N-RasG12D


title: ProB_WT_rep2

description: wildtype


title: MA4NRAS_Leuk_92_rep1


title: 15: Chic_control_rep1

city: La Jolla

first: Ramya

last: Raviram

address: 9500 Gilman Drive

institute: University of California San Diego

data_processing:
Library strategy: Capture Hi-C
Data was processed using Hicup and loops were called using Chicago
Genome_build: hg19
Supplementary_files_format_and_content: .hic file (Juicebox)

source_name: HeLa control

growth_protocol: HeLa F2 cells were generous gifts from Cedric Feschotte and Edward Chuong.

extract_protocol:
Following treatment cells were fixed with Formaldehyde for 4Tran-Capture.
Nuclei were obtained after lysis on ice for 30 minutes with 10 mM Tris-HCl pH8, 10 mM NaCl, 0.2% Igepal CA-630 and 1 Roche Complete EDTA-free tablet. After 10 minutes treatment with 0.1% SDS at 37°C, nuclei were incubated with Triton 10% for 10 minutes also at 37°C. Nuclei were then suspended in 1X DpnII buffer (NEB) and chromatin digested overnight with 400U of DpnII (NEB) at 37°C. Following an additional 4-hour incubation with extra 400U of DpnII, digestion was stopped by 65°C incubation for 30 minutes. DNA ends were then filled in with dATP-Biotin using polymerase klenow for 60 minutes at 37°C. Ligation was performed in-situ overnight (with nuclei intact) using 2000U of T4 DNA ligase from NEB (M0202) at 16°C. Decrosslinking was performed overnight with Proteinase K at 65°C. 40 mg of unligated biotin ends were removed by incubation with T4 DNA polymerase for 4 hours at 20°C. DNA fragments were then sonicated using an LE Covaris 220 instrument using 450 PIP, 30% duty factor, 200 cycles per burst for 60 seconds. Following sonication, DNA fragments were end-repaired using T4 DNA polymerase, T4 PNK and Klenow polymerase (all from NEB). DNA fragments were then bound to Streptavidin C1 beads and washed following manufacturer’s instructions and using 150 ml per 2.5 mg of sonicated DNA. A-tailing and adaptor ligation was then performed with DNA fragments bound to beads. A-tailing was done using Klenow polymerase without 3’ exonuclease activity. For ligation, adaptors from the NEBNext DNA library prep reagent set (E6040) were used and ligated overnight. Following ligation, enzyme USER treatment was used to open the stem loop. Hi-C library amplification was then amplified using 7 PCR cycles, with Phusion polymerase and PCR primers from NEBNext Multiplex Oligos for Illumina (E7335) and resulted in approximately 1 mg of Hi-C material. For Capture, we used the Nimblegen SeqCap EZ hybridization and wash kit (05634261001), Nimblegen SeqCap EZ accessory kit v2 and Nimblegen SeqCap EZ HE-oligo kit. Briefly, 1 mg of Hi-C material was incubated at 42°C for 48 hours with 2.89 mmoles of a MER41 biotinylated DNA oligo according to Nimblegen’s instructions. Following recommended washes, beads were amplified using 8 cycles, with the Post-LM-PCR Oligos 1 & 2 oligos described in Nimblegen’s kit and Kappa 2X PCR master mix. This yielded approximately 700ng of DNA, which were used for a second round of capture as described above for 24 hours. Final amplification of libraries following second capture was done using 5 PCR cycles. In total 20 PCR cycles were used to amplify the libraries and approximately 100ng of material were prepared for sequencing using Illumina Nextseq paired-end 50 base pair reads.

treatment_protocol: Cells were treated for 24 hours with 1000 U/ml of recombinant human IFNg (cat# 11500-2, PBL assay science).

value: HeLa F2 cells


title: MA4NRAS_Leuk_1_rep1


title: MA4NRAS_Leuk_1_rep2


title: 16: Chic_control_rep2


title: 17: Chic_IFNG_rep1

source_name: HeLa IFNg treated


title: 18: Chic_IFNG_rep2


title: GFP-2OE

description: Processed data file: OEandGEexp.txt