title: HR2

city: Swansea

first: Tamsyn

last: Uren Webster

address: Wallace Building

country: United Kingdom

institute: Swansea University

data_processing:
The FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit) was used to clip Illumina adapter sequences and to trim the first 12 bp at the 5’ end.
Quality trimming of the 3' end of the reads using a sliding window  trimmer was performed (http://wiki.bioinformatics.ucdavis.edu/index.php/Trim.slidingWindow.pl).
Digital normalisation using khmer (Brown et al. 2012, arXiv:1203.4802 [q-bio.GN]) was performed, and retained reads were paired using a custom script.
De novo transcriptome assembly was performed using Trinity (version R2013-02-25; (Grabherr et al. 2011))
Transcripts were annotated using Blast and all available Ensembl cDNA sequences for zebrafish (Danio rerio), medaka (Oryzias latipes), nile tilapia (Oreochromis niloticus), stickleback (Gasterosteus aculeatus), human and mouse (Release 71), RefSeq RNA, non-redundant nucleotides (nt) and proteins (nr) databases. Top hits with an e-value of < 1e-15 were retained. When no annotation could be found, the Trinity-generated transcript ID was given.
Sequence reads were mapped against the transcriptome assembly using Bowtie2 (version 2.1.0, (Langmead and Salzberg 2012)), using the -k 1 parameter. Count data was extracted using idxstats in samtools (version 0.1.18, (Li et al. 2009)) and differential expression analysis was conducted in edgeR (Robinson et al. 2010).
Genome_build: n/a
Supplementary_files_format_and_content: The edgeR results file for each treatment group versus the control group was merged with the annotation results, and is provided in a tab delimited text file. For each transcript raw count data for each replicate is included together with the log fold change, P values and FDR values from the expression analysis for that treatment.

organism: Salmo trutta

source_name: 10 mg/l Roundup rep 2 liver

extract_protocol:
Liver samples were snap frozen with liquid nitrogen and stored at -80 C. Total RNA was extracted using Quiagen RNeasy columns
Libraries were constructed with Illumina TruSeq RNA sample preparation kit.

treatment_protocol: Fish were exposed to three concentrations of each chemical for 14 days using a flow-through system

value: juvenile female

tag: treatment

value: 10 mg/l Roundup


title: MR6

status: Public on Apr 16 2015

type: SRA

library_source: transcriptomic

molecule: total RNA

source_name: 0.5 mg/l Roundup rep 6 liver

tag: developmental stage

tag: tissue

value: liver

value: 0.5 mg/l Roundup


title: HR1

source_name: 10 mg/l Roundup rep 1 liver


title: HR6

source_name: 10 mg/l Roundup rep 6 liver


title: HR5

source_name: 10 mg/l Roundup rep 5 liver


title: HR3

source_name: 10 mg/l Roundup rep 3 liver


title: MR4

source_name: 0.5 mg/l Roundup rep 4 liver


title: MR2

source_name: 0.5 mg/l Roundup rep 2 liver


title: LR6

source_name: 0.01 mg/l Roundup rep 6 liver

value: 0.01 mg/l Roundup


title: MR1

source_name: 0.5 mg/l Roundup rep 1 liver


title: MR5

source_name: 0.5 mg/l Roundup rep 5 liver


title: H23539/4-5-10_7968_L4.D704

city: Foster City

first: Li

last: Li

address: 333 Lakeside Drive

country: USA

institute: Gilead Sciences

description: Processed data: rsem_gcounts_matrix.txt

data_processing:
Clipping adapters and low-quality bases.
RSEM and BWA.
Genome_build: Marmota monax transcriptome assembly
Supplementary_files_format_and_content: rsem_gcounts_matrix.txt: Tab-delimited text file with raw gene level counts from RSEM output.
Supplementary_files_format_and_content: Trinity.annot.fa: FASTA file with assembled sequences.

organism: Marmota monax

source_name: Liver, placebo, -14 days

extract_protocol:
Total RNA was extracted from liver biopsies.
cDNA libraries were constructed using the TruSeq Stranded Total RNA-RiboZero Gold Sample Prep Kit (Illumina, San Diego, CA).

treatment_protocol: Woodchucks chronically infected with woodchuck hepatitis virus (WHV) were treated with placebo or GS9620 (5mg/kg QW).

tag: disease state

tag: treatment group

value: placebo

value: adult

tag: time (day)

tag: animal id


title: W23708/4-5-10_7972_L1.D709

description: Processed data: rsem_gcounts_matrix.txt

value: chronically infected with woodchuck hepatitis virus (WHV)


title: LR5

source_name: 0.01 mg/l Roundup rep 5 liver


title: LR3

source_name: 0.01 mg/l Roundup rep 3 liver


title: LR2

source_name: 0.01 mg/l Roundup rep 2 liver


title: LR1

source_name: 0.01 mg/l Roundup rep 1 liver


title: LR4

source_name: 0.01 mg/l Roundup rep 4 liver


title: HG6

source_name: 10 mg/l glyphosate rep 6 liver

value: 10 mg/l glyphosate


title: HG5

source_name: 10 mg/l glyphosate rep 5 liver


title: HG4

source_name: 10 mg/l glyphosate rep 4 liver


title: GFP-Tailswap input

city: La Jolla

first: Arshad

last: Desai

state: CA

address: 9500 Gilman Dr

department: Cellular & Molecular Medicine

institute: UCSD/LICR

library_source: genomic

data_processing:
ChIP-seq reads were aligned to the ASM294v2_19 genome assembly using BWA. We used only those reads with a MAPQ of 10 or greater
Genome_build: ASM294v2_19
Supplementary_files_format_and_content: For the wig files, the data was binned into 200 bases

molecule: genomic DNA

organism: Schizosaccharomyces pombe

source_name: Fission yeast strain P415

growth_protocol: Yeast cells were grown at 30C in YES rich medium.

extract_protocol:
DNA was extracted with PCR-purification Qiagen column
Libraries were prepared according to Illumina's instructions

treatment_protocol: Cells were fixed with 1% para-formaldehyde solution, treated with zymolase 100-T and sonicated with Diagenode bioruptor.

tag: chip-antibody

tag: genotype/variation

value: Cnp1 variant tailswap


title: GFP-Cnp1 input

source_name: Fission yeast strain P411

value: wt control in cnp1 deletion


title: HR4

source_name: 10 mg/l Roundup rep 4 liver


title: GFP-Tailswap

value: GFP (Invitrogen A-11122)


title: RNA-seq of PolyA Minus RNA from  Mouse ES cells with Floxed ATRX Allele

city: oxford

first: Jim

last: Hughes

address: Weatherall Institute Of Molecular Me

department: MHU

institute: University of Oxford

description:
PolyA- RNA
An adenoviral packaged eGFP cassette (AdGFP)  used as a negative control

data_processing:
Reads were mapped to the mm9 mouse genome build using TopHat 1.1.4b
Read coverage was calculated genome-wide to produce strand specific  UCSC Wig files
Genome_build: mm9
Supplementary_files_format_and_content: Strand specific  UCSC Wig files of read coverage from tophat  output.

organism: Mus musculus

source_name: ES cells

growth_protocol: Mouse ES cells were cultured according to standard protocols.

extract_protocol:
RNA was isolated with Tri-Reagent (Sigma). The RNA quality was assessed using Agilent Bioanalyser. Only RNA with overall RIN score >9 was used for further procedures. Subsequently, RNA was treated with DNAseI (DNA-free, Ambion) according to the manufacturer’s protocol kit according to the protocol. Good quality and DNA-free RNA was subjected to polyA fractionation using PolyA selection kit (Promega) using the standard kit protocol.  The RNA fraction was precipitated overnight and resuspended with water. The quality of obtained RNA samples was assessed using PicoChip (Agilent). A Paired sequencing library was generated using the standard Illumina prtocol.
Prior to library prep, the polyA- samples were treated with EpiCentre's Ribo-Zero™ Magnetic Kit (Human/Mouse/Rat). All libraries were prepped with the following kit. NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina®. The protocol was modified to make use of our own custom 8bp indexes (Lamble et al. 2013). The prepared libraries then sequenced on a HiSeq2500 in rapid mode (no version number as original chemistry), 50bp paired end.

treatment_protocol: Mouse ES cells were generated from a male Castaneus x female 129 (ATRX Flox) cross.  Castx129 ATRX Flox ES cells were transduced with either an Adenoviral GFP or Adenoviral Cre-recombinase GFP cassette. Cells were sorted in GFP positive fractions at 48 hours post transduction. RNA was extracted at 5 days post-transduction

tag: strain

value: Cast x 129

tag: sample type

value: Strand Specific Library Preparation

value: adGFP


title: RNA-seq of PolyA Minus RNA from  Mouse ES cells  with Floxed ATRX Allele

description:
PolyA-  RNA
An adenoviral packaged Cre-recombinase cassette with a GFP marker (Vector Biolabs 1779) (AdCre) was used to generate ATRX KO ES cells.

value: AdCre


title: MR3

source_name: 0.5 mg/l Roundup rep 3 liver


title: HG3

source_name: 10 mg/l glyphosate rep 3 liver


title: Men1_KO_12m_H3K27me3

city: Boston

first: Wenchu

last: Lin

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana-Farber Cancer Institute

data_processing:
Bowtie alignment
read counts normalization in 100kb window size
Peak calling (MACS 1.4.2)
Processed data are only available for the 2 month timepoint since this was the only timepoint analyzed for the publication.
Genome_build: mm9
Supplementary_files_format_and_content: bed

source_name: pancreatic islet tumor

growth_protocol: Mice were maintained on a mixed 129s6, FVB/N, and C57BL/6 background. All procedures were carried out in in accordance with the National Research Council Guide for the Care and Use of laboratory Animals

extract_protocol:
Crosslinked with 1% formaldehyde, washed with PBS, lysed in lysis buffer (1% SDS, 10mM EDTA, 50mM Tris-HCl, pH 8.0), sonicated with Covaris E210 to shear DNA to 200-1500bp. After immunoprecipitation or without immunoprecipitation for input, beads were washed, RNase A and Proteinase K treated and reverse crosslinked in elution buffer (1% SDS, 0.1M NaHCO3). DNAs were column purified
standard Illumina library construction.

tag: antibody

tag: manufacturer

value: Cell Signaling Technology, catalog no. 9733s, lot no. 6

value: pancreatic islet tumor

tag: genotype

value: Men1 islet-specific knockout

tag: age

value: Harvested at age of 12 months

value: mixed 129s6, FVB/N, and C57BL/6


title: HG1

source_name: 10 mg/l glyphosate rep 1 liver

value: juvenile female

value: liver


title: RNA-seq of mRNA from  Mouse ES cells  with Floxed ATRX Allele

description:
PolyA+ RNA
An adenoviral packaged Cre-recombinase cassette with a GFP marker (Vector Biolabs 1779) (AdCre) was used to generate ATRX KO ES cells.


title: GFP-Cnp1


title: RNA-seq of mRNA from  Mouse ES cells with Floxed ATRX Allele

description:
PolyA+ RNA
An adenoviral packaged eGFP cassette (AdGFP)  used as a negative control


title: D551 Fib STD RNA-seq

city: Montréal

first: Yoshiaki

last: Tanaka

state: Québec

address: 5415 boul. l'Assomption

department: Medicine

country: Canada

institute: Centre de Recherche l'Hôpital Maisonneuve-Rosemont, Université de Montréal

description:
standard RNA-seq in fibroblast
FPKM_table_STD_RNA-seq.txt

data_processing:
Illumina Casava1.8 software used for basecalling.
Reads were aligned to hg19 human genome by Tophat2 (v2.0.10) with SAMtools (v0.1.18) and Bowtie (v2.1.0)
Unmapped reads were trimmed from 3’end and the first 50bp retained to remove error-prone 3’end. These trimmed reads were mapped to the human genome by Tophat again, and results from the first and second round mapping were merged.
FPKM value was calculated Cufflinks (v1.2.1) by using RefSeq genes as reference annotation with "-G" option
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file include RefSeq gene id, gene symbol, chromosome and FPKM value for each sample

organism: Homo sapiens

source_name: Detroit 551

growth_protocol: Fibroblasts were cultured in DMEM high glucose (Gibco) supplemented with 10% FBS and penicillin/streptomycin. Human ESCs and iPSCs were cultured on irradiated murine embryonic feeder cells in medium containing DMEM/F12, 20% knockout serum replacement, and 4ng/ml bFGF.

extract_protocol:
Total RNA was isolated with the protocol described in Pan et al. 2013
library preparation was conducted using standard Tru-Seq Illumina kits.

treatment_protocol: D551 were seeded at 100,000 cells/well of a 6-well plate one day prior to infection. A retrovirus cocktail containing OSKM was added to each well at MOI 5. On day 5-post infection, the cells were trypsinized and transferred to 10-cm culture dishes containing MEFs. Prior to sorting, the cells were detached using accutase, washed, and incubated in 20% FBS in 1X PBS with the following antibodies according to manufacturer’s recommended dilutions: anti-human CD13 (BD cat# 555394), anti-human/mouse SSEA4 (R&D cat# FAB1435A), anti-human TRA160 (BD cat# 560193). Sorting was conducted using a BD FACSAria cell sorter. Then the cells were pelleted and quickly frozen in liquid nitrogen, or sorted directly in RLT + 2-mercaptoethanol lysis buffer (Qiagen).

tag: cell line

value: Detroit 551

tag: gfp


title: D551 Fib eipsomal Amaxa STD RNA-seq

description:
standard RNA-seq at reprogramming day 3
FPKM_table_STD_RNA-seq.txt


title: Men1_KO_12m_H3K4me3

tag: antibody manufacturer

value: Active Motif, catalog no. 36159, lot no. 12613005


title: D551 w4 GFP-SSEA4+TRA160+ rep2

description:
PMA RNA-seq in reprogramming intermediate week 4
FPKM_table_PMA_RNA-seq.txt


title: Men1_KO_12m_input

value: none (input)


title: RIP-Cre_12m_H3K27me3

source_name: pancreatic islets

value: pancreatic islets

value: RIP-Cre


title: D551 Fib empty retrovirus STD RNA-seq


title: D551 w4 GFP-SSEA4+TRA160+ rep1


title: MG2

source_name: 0.5 mg/l glyphosate rep 2 liver

tag: developmental stage

tag: treatment

value: 0.5 mg/l glyphosate


title: MG1

source_name: 0.5 mg/l glyphosate rep 1 liver

tag: tissue


title: D551 w4 GFP-SSEA4+TRA160-


title: D551 w4 GFP+SSEA4+TRA160-


title: RIP-Cre_12m_H3K4me3


title: D551 w4 GFP+SSEA4-TRA160-


title: LG6

source_name: 0.01 mg/l glyphosate rep 6 liver

value: 0.01 mg/l glyphosate


title: RIP-Cre_12m_input


title: D551 w3 GFP-SSEA4+TRA160+ rep2

description:
PMA RNA-seq in reprogramming intermediate week 3
FPKM_table_PMA_RNA-seq.txt


title: LG5

source_name: 0.01 mg/l glyphosate rep 5 liver


title: HG2

source_name: 10 mg/l glyphosate rep 2 liver

value: 10 mg/l glyphosate


title: D551 w3 GFP-SSEA4+TRA160+ rep1


title: D551 Fib empty Amaxa  STD RNA-seq


title: D551 w3 GFP+SSEA4+TRA160-


title: MG3

source_name: 0.5 mg/l glyphosate rep 3 liver


title: D551 w3 GFP-SSEA4+TRA160-


title: Men1_KO_6m_H3K27me3

value: Harvested at age of 6 months


title: Men1_KO_6m_H3K4me3


title: LG4

source_name: 0.01 mg/l glyphosate rep 4 liver


title: Men1_KO_6m_input


title: D551 w2 GFP+CD13+SSEA4+

description:
PMA RNA-seq in reprogramming intermediate week 2
FPKM_table_PMA_RNA-seq.txt


title: LG3

source_name: 0.01 mg/l glyphosate rep 3 liver


title: D551 w2 GFP-CD13-SSEA4+


title: D551 w2 GFP+CD13-SSEA4+


title: LG2

source_name: 0.01 mg/l glyphosate rep 2 liver


title: RIP-Cre_6m_H3K27me3


title: LG1

source_name: 0.01 mg/l glyphosate rep 1 liver


title: D551 w1 GFP+CD13+ rep2

description:
PMA RNA-seq in reprogramming intermediate week 1
FPKM_table_PMA_RNA-seq.txt


title: D551 w2 GFP+CD13-SSEA4-


title: D551 w2 GFP+CD13+SSEA4-


title: D551 w1 GFP+CD13+ rep1


title: RIP-Cre_6m_input


title: D551 w1 GFP+CD13-


title: C12

source_name: control rep 12 liver


title: RyhB

city: SHERBROOKE

first: Eric

last: Massé

address: 3201, Jean Mignault

department: Biochemistry

institute: University of Sherbrooke

data_processing:
Basecalls performed using MCS Version 2.4.1.3
Sequence reads were mapped using CLC Genomic Workbench (version 4, default settings except that reads that could not be uniquely mapped were discarded)
Genomic coverage was calculated using a custom python script that added 1 to each genomic position covered in a single sequence read
Gene scores were calculated using a custom python script and represent a sum of coverage values for each position within a gene.
Genome_build: Escherichia coli K12
Supplementary_files_format_and_content: tab-delimited text file include normalized reads for each sample and MS2-RyhB/RyhB ratio

organism: Escherichia coli K-12

source_name: Bacterium

growth_protocol: The bacterial strains were grown in 100mL of LB medium to an OD600nm of 0.5

extract_protocol:
Cells were resuspended in 2 mL of buffer A and lysed using a French Press (430 psi, three times). Lysate was then cleared by centrifugation. The soluble fraction was subjected to affinity chromatography. The column was prepared by adding 75 µL of amylose resin (New England Biolabs) to Bio-Spin disposable chromatography columns (Bio-Rad). The column was washed with 3 mL of buffer A. Next, 100 pmol of MS2-MPB protein was immobilized on the amylose resin, and the column was washed with 2 mL of buffer A. The cleared lysate was then loaded onto the column, which was washed with 5 mL of buffer A. RNA was eluted from the column with 1 mL of buffer A containing 15 mM maltose. Eluted RNA was extracted with phenol-chloroform, followed by ethanol (3 vol) precipitation of the aqueous phase in the presence of 20 mg of glycogen. RNA samples were treated with TURBO DNA-free (DNase treatment) and precipitated again.
cDNA libraries were prepared with ScriptSeq™ RNA-Seq Library Preparation Kit

treatment_protocol: 0.1% arabinose was added to induce the expression of MS2-RyhB/RyhB during 10 min. Cells were chilled for 10 min on ice. Cells were then centrifuged, resuspended in 1 mL of buffer A (20 mMTris-HCl at pH 8.0, 150 mM KCl, 1 mM MgCl2, 1 mM DTT), and centrifuged again.

value: MG1655 rne131 delta-ryhB

tag: growth phase

value: exponential phase (OD600nm=0.5)


title: C11

source_name: control rep 11 liver


title: MS2-RyhB


title: Men1_KO_2m_H3K27me3

value: Cell Signaling Technology, catalog no. 9733s, lot no. 6

value: Harvested at age of 2 months


title: Men1_KO_2m_H3K4me3

value: Men1 islet-specific knockout


title: D551 w3 GFP+SSEA4-TRA160-


title: Men1_KO_2m_input

value: mixed 129s6, FVB/N, and C57BL/6


title: H9 ESC

description:
PMA RNA-seq in hESC
FPKM_table_PMA_RNA-seq.txt


title: C10

source_name: control rep 10 liver

value: juvenile female


title: C9

source_name: control rep 9 liver

value: liver


title: PGP1 iPSC

description:
PMA RNA-seq in hiPSC
FPKM_table_PMA_RNA-seq.txt


title: H1 ESC


title: C7

source_name: control rep 7 liver


title: RIP-Cre_2m_H3K27me3

source_name: pancreatic islets


title: D551 Fib rep3

description:
PMA RNA-seq in fibroblast
FPKM_table_PMA_RNA-seq.txt

source_name: Detroit 551

value: Detroit 551


title: RIP-Cre_2m_H3K4me3

value: Active Motif, catalog no. 36159, lot no. 12613005


title: C6

source_name: control rep 6 liver


title: RIP-Cre_6m_H3K4me3


title: D551 Fib rep2


title: D551 iPSC


title: C5

source_name: control rep 5 liver


title: RIP-Cre_2m_input

value: none (input)


title: H3.3 Input in  ATRX Knockout Mouse ES Cells

description: Chip-seq Input

data_processing:
Paired-end reads from ChIP-Seq and input samples were aligned to the mouse genome build using Bowtie (version 0.12.3) using standard parameters other than -M option set to 5
Wig files of genomic read distribution were produced using a sliding 300bp window moving at 30 bp increments
Genome_build: MM9
Supplementary_files_format_and_content: Wig files of genomic distribution of aligned reads

source_name: mES Cells ATRX Knockout

extract_protocol:
ChIPs were performed according to the Millipore ChIP protocol, as described previously (De Gobbi et al., 2007). For ChIP-Seq experiments, WT or ATRX KO ES cells were fixed with 1% formaldehyde for 10 minutes at RT and chromatin was sonicated to a size <500 bp. Immunoprecipitations were performed, after an overnight incubation with the appropriate antibody, with protein A agarose (Millipore). A sample containing no antibody was used as a negative control. Input and immunoprecipitated DNA were purified by phenol and chloroform extraction followed by ethanol precipitation. Subsequently the material was analysed by real time PCR (ABI Prism 7000 Sequence Detection System, Applied Biosystems) using a series of PCR amplicons and Sybr green probes at various genomic sites.
Samples were quantified using the High Sensitivity Qubit system (Invitrogen) and distribution of fragments was determined using Agilent High Sensitivity DNA Kit and a 2100 Bioanalyzer Instrument system (Agilent).  Libraries were constructed using the NEBNext DNA Sample Prep Kit (NEB) with the following modifications: End Repair was performed with 1µl of Enzyme mix and adapters were ligated using 4µl of Ligase. We used 10µl of a 1 in 100 dilution of Illumina Adapters (Multiplexing Sample Preparation Oliogonucleotide Kit) for 10ng of DNA and amplified with 25 µM each of the following custom primers:  PCR primer 1.0  5’-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT-3’  Index primer  5’-CAAGCAGAAGACGGCATACGAGAT[INDEX]CAGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT-3’  *Indexes were according to the six bases tags developed by Illumina.  The amplified libraries were purified using Ampure beads and size selected using 2% E-Gel® EX (Invitrogen), the distribution of fragments in the purified fraction was determined using a High Sensitivity Bioanalyzer kit and a 2100 Bioanalyzer Instrument system (Agilent). For equimolar pooling of the libraries, the relative concentration of the libraries was determined by realtime using Agilent QPCR Library Quantification Kit and a MX3005P instrument (Agilent). Finally, in order to determine the volume to use for sequencing, a second realtime was performed to measure the relative concentration of the pool compared to a previously sequenced ChIP library. Sequencing was performed as 50bp paired end on a GAIIx according to Illumina specifications using Cluster Generation Kit v4 and Sequencing Kit v4 in combination with illumina SCS 2.6/ RTA 1.6 software.

treatment_protocol: WT and ATRX KO ES cells in culture

value: ATRX KO

tag: cell type

value: ES Cell


title: D551 day 3

description:
PMA RNA-seq at reprogramming day3
FPKM_table_PMA_RNA-seq.txt


title: C4

source_name: control rep 4 liver


title: H3.3 input in  Wild type Mouse ES Cells

description: Chip-seq Input

source_name: mES Cells

value: wt


title: D551 Fib rep1


title: C3

source_name: control rep 3 liver


title: H3.3ChIP in  ATRX Knockout Mouse ES Cells

description: Chip-seq

tag: chip antibody

value: Millipore 09-838


title: C2

source_name: control rep 2 liver


title: 3xFNLDD

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

country: Japan

institute: Osaka univ.

description: The chromatin complexes derived from Ba/F3 cells expressing control 3xFNLDD are immunoprecipitated with anti-FLAG M2 Ab (Sigma-Aldrich).

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence using Cutadapt, and mapped to GRCm38/mm10 genes from Ensembl using blast with default parameters.
The genes for mapping contains both cDNA and ncRNA.
Reads per million mapped reads (RPM) were calculated against each gene. The number of reads falling in the genes were counted and normalized by total reads of the samples. The total reads were adjusted to a million.
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: tab-delimited text files include read count and RPM values for 3xFNLDD and 3xFN-Tel-TAL samples.

source_name: Immunoprecipitants prepared from Ba/F3 expressing 3xFNLDD

extract_protocol:
enChIP-RNA was harvested using Isogen II (Nippon Gene). Illumina TruSeq RNA Sample Prep Kit v2 was used with 60 ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina TruSeq RNA Preparation V2 Guide Rev. C.

value: Ba/F3-derived cells

value: control 3xFNLDD

value: anti-FLAG M2 Ab (Sigma-Aldrich)


title: H3.3ChIP in  Wild type Mouse ES Cells

description: Chip-seq


title: 3xFN-Tel-TAL

description: The chromatin complexes derived from Ba/F3 cells expressing 3xFN-Tel-TAL are immunoprecipitated with anti-FLAG Ab.

source_name: Immunoprecipitants prepared from Ba/F3 expressing 3xFN-Tel-TAL


title: C1

source_name: control rep 1 liver


title: C8

source_name: control rep 8 liver


title: mm8-CD8-Naive-H3K27me3

status: Public on Apr 15 2015

city: Bethesda

first: Nicholas

last: Restifo

state: MD

address: 9000 Rockville pike

institute: NIH

data_processing:
ChIP-seq reads of largely 25 base pairs (bp) corresponding to H3K4me3 or H3K27me3 modification levels were obtained with the Solexa Analysis Pipeline. All reads were mapped to the mouse genome (mm8)
We then filtered these genome-mapped reads by retaining only reads that fell in “islands” of enriched ChIP signals found by the SICER tool. Note that SICER relies on a clustering approach and Poisson statistics in fixed-size windows along the genome to find gapped windows or islands of enriched signals.
We used settings recommended in SICER v1.1 documentation for using SICER without a control library–specifically, we used counts of unique reads falling in 200bp windows, gapsize of 1 window for H3K4me3 and 3 windows for H3K27me3, fragment size of 150bp (which corresponds to shifting mapped reads by 75bp to center them on the fragment), effective fraction of mm8 genome uniquely mappable by 25bp reads to 0.778, and finally expected false positives or E-value of 500 islands.
The SICER-filtered, mapped reads are called modification tags or simply tags in the text.
Genome_build: mm8
Supplementary_files_format_and_content: wig files were generated with ChIP peaks read counts

source_name: T cells

growth_protocol: Naïve CD8+ T cells isolated directly from spleen of C57BL/6J mice using MACS purification.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
ChIP-seq libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Central memory (TCM) and effector memory (TEM) T cells were generated in vitro with functional anti-CD3 (1µg/ml) and anti-CD28 (1µg/ml) antibody with IL-2-containing (100 IU/ml) complete media. T cells were cultured for 5 days and subsequently FACS-sorted based on CD62L and CD44 expression. Stem-cell memory (TSCM) T cells were cultured in the same conditions as TCM and TEM with the addition of an inhibitor of GSK-3β (5µM TWS119 Tocris Bioscience).

value: spleen

value: CD8+ T cells

tag: t cell subset

value: naïve

tag: chip antibody vendor

value: Upstate

tag: chip antibody cat. #


title: mm8-CD8-Naive-H3K4me3

tag: strain

value: Abcam


title: mm8-CD8-EM-H3K27me3

value: effector memory (EM)


title: mm8-CD8-TSCM-H3K27me3

value: Stem-cell memory (TSCM)


title: mm8-CD8-EM-H3K4me3


title: mm8-CD8-TSCM-H3K4me3


title: mm8-CD8-CM-H3K27me3

value: central memory (CM)


title: mm8-CD8-CM-H3K4me3


title: HS_Rad21_ChIPSeq WCE

city: Onna-son

first: Norihiko

last: Nakazawa

state: Okinawa

address: 1919-1 Tancha

department: G0 Cell Unit

institute: Okinawa Institute of Science and Technology Graduate University

description: processed data file: HS_Rad21-3FLAG.w500.b10.pseuduvalue10.Ratio.wig

data_processing:
After each completed sequencing run, raw image files from the illumina sequencer were computationally processed to obtain nucleotide-base calls.  The standard analytical pipeline provided by illumina (CASAVA 1.8.2) was used for base-calling and demultiplexing of samples with an index sequence that was attached to the template during sample preparation.
Subsequent to base-calling and demultiplexing, sequencing reads were aligned to the S. pombe genome sequence (downloaded from Ensemble genomes [ftp://ftp.ensemblgenomes.org/pub/fungi/current/fasta/schizosaccharomyces_pombe/dna/], Schizosaccharomyces_pombe.ASM294v1.16.dna.chromosome I, II, III & MT FASTA format) using Bowtie alignment software (bowtie-bio.sourceforge.net) with default parameters. To avoid artifacts associated with spuriously high read numbers, the 10x average read number was set as maximum at each location.
To compare precipitated DNA (IP) and input DNA (WCE) data, the total read number of each sample was normalized to 10 million.  The whole genome was then scanned using a sliding window to smooth the data (window = 500 bp, step = 10 bp).
Before calculating a ratio, to avoid dividing by a small number caused by low WCE coverage, we added a pseudocount of 10 to all windows of each sample.  ChIP enrichment was calculated as the ratio of IP to WCE for each window.
This ratio was used for visualization of the ChIP-seq profile along three chromosomes using an Integrated Genome Browser (IGB, ver. 7.0.3).
Genome_build: S. pombe genome sequence (downloaded from Ensemble genomes [ftp://ftp.ensemblgenomes.org/pub/fungi/current/fasta/schizosaccharomyces_pombe/dna/], Schizosaccharomyces_pombe.ASM294v1.16.dna.chromosome I, II, III & MT FASTA format)
Supplementary_files_format_and_content: wig files for ChIP enrichment calculated as the ratio of IP to WCE

source_name: Cells cultivated in rich media

growth_protocol: Temperature-shift experiments were performed as previously reported (Nakazawa et al. 2011), using nda3-KM311 mutant.  Cs mutant cells were grown in YPD at 30°C (a permissive temperature).  When cell concentrations reached 4×10^6 cells/mL, cultures were transferred to 20°C and incubated for 8 hr to (reversibly) block spindle formation and to arrest cells at a prometaphase-like stage (Hiraoka et al. 1984). Asynchronously cultured cells were also harvested at 20°C for 8 hr in the absence of nda3-KM311.

extract_protocol:
Sonicated and cross-linked chromatin were prepared from S. pombe cell extracts (Nakazawa et al., 2008). DNA samples co-precipitated with anti-FLAG antibody were prepared along with input DNA (whole cell extract [WCE] DNA).
Prepared DNA libraries were processed by single-end sequencing (36 bp) on the iIlumina Genome Analyzer GA IIx, according to the manufacturer’s instructions.
ReferenceHiraoka et al., 1984 Cell 39, 349-358. Nakazawa et al., 2008 J Cell Biol 180, 1115-1131. Nakazawa et al., 2011 J Cell Sci 124, 1795-1807.

treatment_protocol: For temperature-shift (T-shift) conditions in asynchronously cultured cells, cells incubated at 20°C for 8 h were shifted to 36°C for 9 min.

value: Rad21-FLAG strain after temperature-shift from 20C to 36C

tag: passages

value: Treated by 36°C for 9min

tag: molecule subtype

value: WCE (Whole Cell Extract) Input DNA


title: HS_Rad21_ChIPSeq IP

value: anti-Flag M2 antibody

value: Sigma-Aldrich

tag: chip antibody lot #

value: Immunoprecipitated genomic DNA


title: HS_Cut14_ChIPSeq WCE

description: processed data file: HS_Cut14-3FLAG.w500.b10.pseuduvalue10.Ratio.wig

value: Cut14-FLAG strain after temperature-shift from 20C to 36C


title: HS_Top2_ChIPSeq WCE

description: processed data file: HS_Top2-3FLAG.w500.b10.pseuduvalue10.Ratio.wig

value: Top2-FLAG strain after temperature-shift from 20C to 36C


title: AS_Cut14_ChIPSeq WCE

description: processed data file: AS_Cut14-3FLAG.w500.b10.pseuduvalue10.Ratio.wig

value: Asynchronously dividing cells derived from Cut14-3FLAG strain

value: Cultivated at 20°C for 8hr


title: AS_Rad21_ChIPSeq WCE

description: processed data file: AS_Rad21-3FLAG.w500.b10.pseuduvalue10.Ratio.wig

value: Asynchronously dividing cells derived from Rad21-3FLAG strain


title: AS_Top2_ChIPSeq WCE

description: processed data file: AS_Top2-3FLAG.w500.b10.pseuduvalue10.Ratio.wig

value: Asynchronously dividing cells derived from Top2-3FLAG strain


title: HS_Cut14_ChIPSeq IP


title: HS_Top2_ChIPSeq IP


title: AS_Top2_ChIPSeq IP


title: AS_Rad21_ChIPSeq IP


title: nda3_Top2_ChIPSeq IP

description: processed data file: nda3_Top2-3FLAG.w500.b10.pseuduvalue10.Ratio.wig

value: nda3-KM311 Top2-3FLAG

value: Mitotically arrested cells derived from Top2-3FLAG strain in nda3-KM311 cold-sensitive mutant


title: nda3_Top2_ChIPSeq WCE


title: AS_Cut14_ChIPSeq IP


title: nda3_Rad21_ChIPSeq IP

description: processed data file: nda3_Rad21-3FLAG.w500.b10.pseuduvalue10.Ratio.wig

value: nda3-KM311 Rad21-3FLAG

value: Mitotically arrested cells derived from Rad21-3FLAG strain in nda3-KM311 cold-sensitive mutant


title: nda3_Cut14_ChIPSeq WCE

description: processed data file: nda3_Cut14-3FLAG.w500.b10.pseuduvalue10.Ratio.wig

value: nda3-KM311 Cut14-3FLAG

value: Mitotically arrested cells derived from Cut14-3FLAG strain in nda3-KM311 cold-sensitive mutant


title: nda3_Rad21_ChIPSeq WCE


title: nda3_Cut14_ChIPSeq IP


title: ChIPseq_GS_WT_ubH2A_2

city: Cincinnati

first: Satoshi

last: Namekawa

state: Ohio

address: 3333 Burnet Ave

institute: Cincinnati Children's Hospital Medical Center

description:
genomic DNA, Cross link
wardrobe number: 1152

data_processing:
Data analysis was performed in Wardrobe Experiment Management System (https://code.google.com/p/genome-tools/).
Reads were aligned to the mouse genome (mm10) with bowtie (version 1.0.0(8)) and displayed on a local mirror of UCSC genome browser as coverage.
Genome_build: mm10
Supplementary_files_format_and_content: For RNA-seq data, reads were mapped to the mm10 genome using tophat (version 2.0.9 (10)) and assigned to the refseq genes using Wardrobe algorithm. For-ChIP-seq, Islands enrichment were identified using MACS2

source_name: Cultured germline stem cells

growth_protocol: GS cells were cultured in normal condition.PS and RS were isolated from adult wild-type or Scml2-KO mice with BSA gradient methods

extract_protocol:
For ChIP-seq of crosslink samples, lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibodies. For ChIP-seq of MNase samples, lysate was digested with Mnase and Histone-DNA complexes were isolated with antibodies. For RNA-seq, RNA was purified using RNeasy mini kit.
DNA library for ChIP-seq (both crosslink and MNase samples) was prepared with NEBNext® ChIP-Seq Library Prep Master Mix Set for Illumina® (NEB) and Agencourt AMPure XP (Beckman Coulter). For RNA-seq, TruSeq™ RNA Sample Prep Kit v2 -Set A was used for library construction.

tag: genotype/variation

value: Wild-type

value: CD1 x C57BL/6

value: Rabbit anti-ubH2A (Cell Signaling, #8240 )


title: MNase-seq_PS_WT_ubH2A_2

description:
genomic DNA, Mnase
wardrobe number: 497

source_name: Isolated pachytene spermatocytes


title: MNase-seq_PS_KO_ubH2A_2

description:
genomic DNA, Mnase
wardrobe number: 498


title: RNAseq_THY1+_WT_1

description: wardrobe number: 1136

source_name: Isolated THY1+ undifferentiated spermatogonia


title: RNAseq_THY1+_KO_2

description: wardrobe number: 1107


title: ChIPseq_PS_WT_Input_CL

description:
genomic DNA, Cross link
wardrobe number: 273

value: none (input)


title: RNAseq_THY1+_KO_1

description: wardrobe number: 1105


title: RNAseq_THY1+_WT_2

description: wardrobe number: 1137


title: si-cMyc_MEF_RNASEQ_1

city: Smithville

first: Sharon

last: Dent

state: Texas

address: 1800 Park Road 1C Unit Number: 0116 Smithville, TX 78957  Room Number: SRC1.104

department: Dept. of Molecular Carcinogenesis

institute: The University of Texas MD Anderson Cancer Center

data_processing:
The raw reads in ChIP-Seq datasets were mapped to the NCBI build 37 (UCSC mm9) using Bowtie (version 0.12.8) (Langmead et al. 2009).
Data were filtered using the following specifications…
RNA-Seq reads were aligned to NCBI build 37 (UCSC mm9), using TopHat 2.0.9 (Trapnell et al. 2009). For RNA-Seq data in mESCs, three steps of normalization were performed. The first step of normalization was performed using the ERCC synthetic spike-in RNA sequences (http://tools.invitrogen.com/downloads/ERCC92.fa) and aligning them along with all other RNA-Seq reads. Second, expression values were computed as fragments per kilobase of exon per million fragments mapped (FPKM) for each gene and spike-in sequence using NGSUtils (Breese and Liu 2013). Lastly, FPKM values for each gene were normalized to spike-in values using loess normalization through loess.normalize function in affy package of R (Gautier et al. 2004). The log2 fold change of normalized FPKM values were used to detect differentially expressed genes. For reprogramming RNA-Seq data, the number of reads aligning to the exons of each gene was computed using HTSeq (Anders and Huber 2010).
EdgeR was applied to determine differentially expressed genes at a false discovery rate (FDR) adjusted P value (q-value) of 1 % (Robinson et al. 2010). Integrative Genomics Browser (IGV) (Robinson et al. 2011; Thorvaldsdottir et al. 2013) was used to visualize RNA-Seq reads along Gcn5 gene, using the NCBI build 37 (UCSC mm9).
Supplementary_files_format_and_content: rpkm files were generated.

source_name: 2o 1B MEFs

growth_protocol: All mESCs were maintained in DMEM with high glucose (Gibco) supplemented with 15% FBS (Wisent), 2 mM L-glutamine (Gibco), 0.1 mM non-essential amino acids (Gibco), 1% penicillin/streptomycin (Gibco), 0.1 mM b-mercaptoethanol (Sigma) and 1000 U/mL of LIF / ESGRO (Chemicon). AB1 mESCs were cultured on 0.1% gelatin coated plates. R1 mESCs and Gcn5flox/flox mESCs were cultured on dishes with Mitomycin-C treated MEFs. Embryoid bodies were seeded as hanging drops of 400 mESCs in mES media lacking LIF. After 3 days the EBs were transferred to non-adherent bacterial grade dishes and cultured for a maximum of 6 addition days. 2o 1B MEFs were maintained in DMEM with high glucose, 10% FBS, 2mM L-glutamine and 1% penicillin/streptomycin.

extract_protocol:
2o 1B MEFs (p5) were seeded as 1.2 x 106 cells on 0.1 % gelatin coated 15 cm plates and treated 24 hrs later with 1.5 μg/mL of Doxycycline (Dox) in mES media, while control cells were kept in mES media in the absence of Dox. The cells were collected after 2 days of Dox exposure and processed as previously described (Beyer et al. 2013), with the exception of chromatin sonication, where 10 x 20 pulses (25 % amplitude) of the Sonicator 4000 (QSonica) were used, and 15 μg of chromatin was precipitated with 1 μg of c-Myc antibody (sc-764, Santa Cruz).
RNASeq Libraries were prepared according to the Illumina TruSeq Strandard Total RNA Sample Preparation Kit (with Ribo-Zero Gold, RS-122-2301), 10 pM of each library was sequenced according to standard Illumina protocols on an Illumina HiSeq 2000.

treatment_protocol: Gene knockdown experiments were performed in 2o 1B MEFs. Cells were transfected with siRNA using Lipofectamine RNAiMAX (Invitrogen) upon seeding 2.25 x 104 cells / well of a 12 well plate. All siRNA pools (siGenome, Dharmacon) were used at 40 nM and individual siRNAs (siGenome, Dharmacon) were used at 10 nM concentrations. After 24 hrs, Doxycycline was added to the cells in mES media. 2 days later cells were lysed for RNA isolation to assess knockdown efficiency, or remained in Dox mES media for a total of 5 days after which cells were fixed with 4% PFA and stained for alkaline phosphatase activity (Vector Red, Alkaline Phosphatase substrate kit; Vector Labs). Image analysis and quantification of AP positive area was determined using a Celigo Imaging Cell Cytometer (Cyntellect). For the rescue experiments, siRNA transfections were performed in an identical manner, but were transfected 4 hrs later with 0.5 μg of pCMV6, pCMVSport2 Flag-Gcn5 or pCMVSport2 Flag-Gcn5 E568A using Fugene HD (Roche) at a ratio of 2.8 μL to 1 μg of DNA.

value: MEFs

value: 2o 1B MEFs

tag: sirna

value: sic-Myc


title: si-Gcn5_MEF_RNASEQ_1


title: si-cMyc_D2_RNASEQ_2

value: Doxycycline


title: Control_D2_RNASEQ_2

value: siControl


title: Control_MEF_RNASEQ_2


title: si-cMyc_MEF_RNASEQ_2


title: si-Gcn5_MEF_RNASEQ_2


title: si-Gcn5_D2_RNASEQ_2


title: Biotin_input_2_ChIPSeq

data_processing:
The raw reads in ChIP-Seq datasets were mapped to the NCBI build 37 (UCSC mm9) using Bowtie (version 0.12.8) (Langmead et al. 2009).
Data were filtered using the following specifications…
Peaks were called using using MACS (version 2.0.10)(Zhang et al. 2008) at a q-value threshold of 0.05 using input as a control. The enriched regions from each biological replicate of samples were intersected with BEDTools (version 2.13.3)(Quinlan and Hall 2010) to form the final peak set for Gcn5 bioChIPs.
Alignment files were processed to obtain normalized density files in bedgraph format using the makeUCSCfile program in Homer (Hypergeometric Optimization of Motif Enrichment) software (Heinz et al. 2010). First, each tag was extended to 200 bp. Then, ChIP-fragment density was defined by the total number of overlapping ChIP-fragments at each genomic position and reported at each 25 bp bins (normalized to the total number of 10 million tags). For visualization, normalized density files in bedgraph format were uploaded to the UCSC genome browser (http://genome.ucsc.edu) and IGV (Integrative Genomics Browser) (Robinson et al. 2011; Thorvaldsdottir et al. 2013).
Genome_build: mm9
Supplementary_files_format_and_content: bedgraph files were generated.

source_name: AB1 ES cells

extract_protocol:
Approximately 2.0 x 107 BirAV5-FLBioGcn5 and BirAV5-FLBio mESCs were crosslinked with 1% formaldehyde in the culture media for 10 min at room temperature, quenched with 125 mM glycine and washed three times with PBS containing protease inhibitors. The cells were lysed in SDS Lysis Buffer (1 % SDS, 10 mM EDTA and 50 mM Tris-HCl, pH 8.1) for 30 min on ice and sonicated with a Branson Sonifier 450 sonicator (output 1.5, duty 60 %) for 2 cycles, followed by 10 min in the Bioruptor (Diagenode) for 30 sec on/off at the high setting for 5 cycles. Sonicated samples were centrifuged to remove the insoluable debris, diluted 1:10 with ChIP Dilution Buffer (0.01 % SDS, 1.1 % Triton X-100, 1.2 mM EDTA, 16.7 mM Tris-HCl, pH 8.1 and 167 mM NaCl) and were precleared with Dynabeads Protein A (Invitrogen) for 1.5 hrs. Subsequently, the pre-cleared lysates were incubated with Dynabeads MyOne Streptavidin T1 (Invitrogen) overnight at 4oC. The subsequent bioChIP steps were carried out as previously described (Kim et al. 2009).
Libraries were prepared using a modified version of the Illumina TruSeq ChIP Sample Prep protocol. Briefly, ChIP DNA was end repaired (End-It DNA End-Repair Kit - Epicenter), 3’ adenylated with Klenow 3’-5’ exo (New England Biolabs) and ligated to Illumina Tru-Seq adapters (diluted 1:7) with DNA ligase (New England Biolabs). 5 x PCR amplification cycles were performed on the adapter ligated ChIP DNA, 250-300 bp products were purified from a 2 % agarose gel and amplified for 10 additional PCR cycles. Libraries concentrations were determined with a Library Quantification Kit (Kapa Biosystems). 10 pM of each library was sequenced on an Illumina HiSeq 2000 as outlined by Illumina.

treatment_protocol: Mouse Gcn5 cDNA was sub-cloned into the XbaI site of pEF1αFLBio vector to generate the pEF1αFLBioGcn5 plasmid. AB1 mESCs stably expressing in vivo biotinylated Gcn5 (BirAV5-FLBioGcn5) were generated as previously described (Kim et al. 2009). A control cell line (BirAV5-FLBio) that stably expressed BirA and FLBio alone was established in a similar manner. Stable expression of in vivo biotinylated Gcn5 was confirmed by anti-Gcn5 (Cell Signaling Technology), anti-Streptavidin (ThermoScientific), and anti-V5 (Invitrogen) immunoblots.

value: ES cells

tag: antibody


title: Control_MEF_RNASEQ_1


title: Biotin_2_ChIPSeq


title: si-cMyc_D2_RNASEQ_1


title: ChIPseq_PS_WT_Scml2

description:
genomic DNA, Cross link
wardrobe number: 276

value: Rabbit anti-Scml2 (produced in-house; Hasegawa et al.)


title: Gcn5_2_ChIPSeq


title: Gcn5_input_1_ChIPSeq


title: Biotin_input_1_ChIPSeq


title: D2_Input_ChIPSeq

growth_protocol: 2o 1B MEFs were maintained in DMEM with high glucose, 10% FBS, 2mM L-glutamine and 1% penicillin/streptomycin.

extract_protocol:
2o 1B MEFs (p5) were seeded as 1.2 x 106 cells on 0.1 % gelatin coated 15 cm plates and treated 24 hrs later with 1.5 μg/mL of Doxycycline (Dox) in mES media, while control cells were kept in mES media in the absence of Dox. The cells were collected after 2 days of Dox exposure and processed as previously described (Beyer et al. 2013), with the exception of chromatin sonication, where 10 x 20 pulses (25 % amplitude) of the Sonicator 4000 (QSonica) were used, and 15 μg of chromatin was precipitated with 1 μg of c-Myc antibody (sc-764, Santa Cruz).
Libraries were prepared using a modified version of the Illumina TruSeq ChIP Sample Prep protocol. Briefly, ChIP DNA was end repaired (End-It DNA End-Repair Kit - Epicenter), 3’ adenylated with Klenow 3’-5’ exo (New England Biolabs) and ligated to Illumina Tru-Seq adapters (diluted 1:7) with DNA ligase (New England Biolabs). 5 x PCR amplification cycles were performed on the adapter ligated ChIP DNA, 250-300 bp products were purified from a 2 % agarose gel and amplified for 10 additional PCR cycles. Libraries concentrations were determined with a Library Quantification Kit (Kapa Biosystems). 10 pM of each library was sequenced on an Illumina HiSeq 2000 as outlined by Illumina.


title: Gcn5_1_ChIPSeq


title: Myc_D2_ChIPSeq

value: c-Myc antibody (sc-764, Santa Cruz)


title: Gcn5_input_2_ChIPSeq


title: D0_Input_ChIPSeq


title: si-Gcn5_D2_RNASEQ_1


title: Gcn5_KO_2_RNASEQ

data_processing:
The raw reads in ChIP-Seq datasets were mapped to the NCBI build 37 (UCSC mm9) using Bowtie (version 0.12.8) (Langmead et al. 2009).
Data were filtered using the following specifications…
RNA-Seq reads were aligned to NCBI build 37 (UCSC mm9), using TopHat 2.0.9 (Trapnell et al. 2009). For RNA-Seq data in mESCs, three steps of normalization were performed. The first step of normalization was performed using the ERCC synthetic spike-in RNA sequences (http://tools.invitrogen.com/downloads/ERCC92.fa) and aligning them along with all other RNA-Seq reads. Second, expression values were computed as fragments per kilobase of exon per million fragments mapped (FPKM) for each gene and spike-in sequence using NGSUtils (Breese and Liu 2013). Lastly, FPKM values for each gene were normalized to spike-in values using loess normalization through loess.normalize function in affy package of R (Gautier et al. 2004). The log2 fold change of normalized FPKM values were used to detect differentially expressed genes. For reprogramming RNA-Seq data, the number of reads aligning to the exons of each gene was computed using HTSeq (Anders and Huber 2010).
EdgeR was applied to determine differentially expressed genes at a false discovery rate (FDR) adjusted P value (q-value) of 1 % (Robinson et al. 2010). Integrative Genomics Browser (IGV) (Robinson et al. 2011; Thorvaldsdottir et al. 2013) was used to visualize RNA-Seq reads along Gcn5 gene, using the NCBI build 37 (UCSC mm9).
Supplementary_files_format_and_content: fpkm files were generated.

source_name: 6-C4 ES cells

extract_protocol:
Total cellular RNA and genomic DNA were isolated from 1.0 x 106 cells of the 4-1, 4C2, 6-1 and 6C4 lines using the AllPrep DNA/RNA Mini Kit (Qiagen). The concentration of genomic DNA was monitored to ensure that the samples were nearly equivalent (within 7.5 % of each other). 1 μg of RNA was subsequently spiked with 2 μL of 1:100 ERCC Spike-In Mix #1 or #2 prior to RNA-Seq library preparation.
RNASeq Libraries were prepared according to the Illumina TruSeq Strandard Total RNA Sample Preparation Kit (with Ribo-Zero Gold, RS-122-2301), 10 pM of each library was sequenced according to standard Illumina protocols on an Illumina HiSeq 2000.

treatment_protocol: Male and female Gcn5flox/flox mice were bred and checked for plugs daily. At E3.5, uteri were removed and flushed with mES medium containing 0.02 mM HEPES. Blastocysts were cultured with mES medium in 60 mm culture dishes plated with gamma-irradiated STO feeders for 3 days. When blastocysts had adhered to the feeder layer, inner cell mass outgrowths were aspirated and plated individually in single wells of a 24-well plate. The next day, each well was split 1:1 in mES media using 0.25 % trypsin-EDTA. The cells were fed with mES cells medium daily and split 1:1 every 3 days until the ES cells colonies were visible. When several well-formed colonies were visible, the cells were spilt and plated on 60 mm culture dishes and expanded. For genotyping, feeders were removed by re-plating two or three times on non-gelatin coated dishes for 40-50 minutes, to remove the majority of feeder cells. The Gcn5flox/flox genotype was verified by PCR with the primers WL20 5’-CACAGAGCTTCTTGGAGACC-3’ and WL21-3 5’-GGCTTGATTCCTGTACCTCC-3’. To generate Gcn5Δ3-18Δ3-18 mESCs, Gcn5 flox/flox cells were transiently transfected with the pBS598 EF1α-EGFPcre vector (Addgene) using Effectene Transfection Reagent (Qiagen). GFP positive and negative ES cells were sorted 72 hours after the transfection by FACS and subsequently re-seeded and expanded with mES media for nearly one week until individual colonies were picked from the GFP+ (4C2, 6C4) and GFP- (4-1 and 6-1) populations. Cell were collected for genotyping from each line to confirm that exons 3-18 of Gcn5 had been excised by Cre recombinase in 4C2 and 6C4, but not 4-1 and 6-1 mESCs. All cells were genotyped by PCR with the primers WL20 and WL23 5’-ATAGTAGCGACTGCGCAACC-3’. qRT-PCR along with immunoblots verified that Gcn5 expression was not detectable in either 4C2 or 6C4 cells. G-banding cytogenetic analysis (Texas Children’s Hospital and Cell Line Genetics) identified that all newly derived ES cell lines had a normal male karyotype.

value: 6-C4 ES cells


title: PITX2KO_RNASeq_rep1

city: Cleveland

first: Jeff

last: Hsu

state: OH

address: 9500 Euclid Ave

department: Cellular and Molecular Medicine

institute: Cleveland Clinic Lerner Research Institute

data_processing:
Basecalls and deplexing performed using CASAVA version 1.4
mRNAseq reads aligned using tophat version 2.0.4 to hg19 using the options: read mismatches (3)
htseq counts was used to obtain gene level counts against the ensembl transcript annotation version 71
miRNAseq reads were aligned using STAR aligner version 2.3.0e to hg19 using the default parameters
FeatureCounts was used to count reads that fell within the ensembl transcript annotation version 71
miRNA counts were collapsed to the highest expressed family member as annotated by miRBase using a custom script
Genome_build: hg19
Supplementary_files_format_and_content: abundance measurements

source_name: H9 Cardiomyocyte_PITX2KO_RNASeq

growth_protocol: Atrial like cardiomyocytes were generated by differentiation of H9 cells by plating cells into growth factor reduced matrigel and cultred in MEF fibroblast media (R&D systems) for 3 days before growth factors (Noggin and retinoic acid).

extract_protocol:
RNA was harvested using Qiagen total RNA kits
RNA libraries for RNASeq were prepared for sequencing using standard Illumina protocols at University of Chicago Genomics Facility

treatment_protocol: 100 pmol of a custom PANCR siRNA, 100 pmol of a custom PANCR siRNA (siRNA (Ambion silencer select cat#4392420, ids: S10557, S10558, and S10559), , or 100 pmol of a control scramble siRNA (Ambion silencer select cat # 4390843) were transfected in differentiated H9 induced cardiomyocytes using the RNAiMax (Invitrogen) transfection reagent according to manufactures specifications

value: ES-derived cardiomyocytes

tag: sirna knockdown

value: poly-A mRNA


title: PITX2KO_RNASeq_rep3


title: PITX2KO_RNASeq_rep2


title: Control_D2_RNASEQ_1


title: Biotin_1_ChIPSeq


title: PANCRKO_RNASeq_rep3

source_name: H9 Cardiomyocyte_PANCRKO_RNASeq

value: PANCR


title: Gcn5_KO_1_RNASEQ

source_name: 4-C2 ES cells

value: 4-C2 ES cells


title: PANCRKO_RNASeq_rep1


title: Gcn5_WT_2_RNASEQ

source_name: 6-1 ES cells

value: 6-1 ES cells


title: Scramble_RNASeq_rep3

source_name: H9 Cardiomyocyte_Scramble_RNASeq

value: Scrambled


title: Gcn5_WT_1_RNASEQ

source_name: 4-1 ES cells

value: 4-1 ES cells


title: Scramble_RNASeq_rep2


title: GDNF_N-02

city: Nan Jing

first: wang

last: Min

state: Jiang Su

address: Hanzhong Road 140,

department: State key laboratory of reproductive medicine

country: China

institute: Nan Jing Medical Univerity

description: lncRNA

data_processing:
Illumina OLB1.9.4 software used for basecalling.
Primary sequencing data that produced by Illumina HiSeqTM 2000, , is subjected to quality control (QC) that determine if a resequencing step is needed. raw reads are filtered into clean reads which will be aligned to the reference sequences with SOAPaligner/SOAP2. The alignment data is utilized to calculate distribution of reads on reference genes and perform coverage analysis. If alignment result passes QC, we will proceed with downstream analysis including gene expression, gene structure refinement, alternative splicing, novel transcript prediction and annotation and SNP detection.
Per Kilobase of exon per Megabase of library size (RPKM) were calculated.
Genome_build: NONCODE V3.0 (http://noncode.org/download.php)
Supplementary_files_format_and_content: tab-delimited text files include reads numbers、Length、 RPKM values for each Sample

source_name: Testis

growth_protocol: germ cells were isolated from five 6-8 day old C57BL/6 and Thy1 positive cells were enriched through magnetic-activated cell sorting. Cells were plated at a density of 1.5 to 2*105/well on a 12-well plate with mitotically inactivated STO feeder layer. The long-term propagation of SSCs were supported by a defined serum free medium containing minimal essential medium, 2% Bovine serum albumin, 20 ng/ml of GDNF, 150 ng/ml of GFRA1, and 1 ng/ml of basic fibroblast growth factor FGF2. Cultures were maintained at 37°C in an incubator with humidified 5% CO2 and 95% air atmosphere. Medium was replaced every 2-3 days and cells were subcultured at a ratio of 1:2 or 1:3 every 5 to 6 days.

extract_protocol:
After all GDNF treatment, cultured germ cell clumps were gently blowed with a 200μl pipette, and followed by Total RNA isolationusing Trizol reagent and sequencing by Illumina HiSeqTM 2000
RNA libraries were prepared for sequencing using standard Illumina protocols

value: spermatogonial stem cells

value: normal culture


title: GDNF_8hr-01

description: lncRNA

value: GDNF 8 hr refreshed


title: GDNF_8hr-02

description: lncRNA


title: GDNF_0hr-02

description: lncRNA

value: GDNF 18hr withdrawal


title: iBAT_D8_ISO_plus_JMJD1A

city: meguro-ku

first: Takeshi

last: Inagaki

state: Tokyo

address: 4-6-1 Komaba

institute: Univ of Tokyo

data_processing:
All DNA-fragments binding were mapped onto build mm9 (NCBI Build 37) by a mapping program ELAND (http://support.illumina.com/sequencing/sequencing_software/casava.html) based on the 5’-side 36 bp sequences.
Genome_build: mm9
Supplementary_files_format_and_content: bar. formatted file

growth_protocol: iBATs were established by infecting retrovirus expressing SV40 Large T antigen to brown adipocytes isolated from C57BL/6 mouse at P3. iBATs were mainteined in 0.1% BSA containing DMEM and differentiated by the treatment of subconfluent cell for 2 days with insulin (5 μg/ml) and indomethacin (125 μM) in basal medium. The cells were then treated with medium containing insulin (5 μg/ml) which was replenished every other day.

extract_protocol:
Cells were crosslinked with 1.5 mM ethylene glycol bis(succinimidylsuccinate) (EGS) (Thermo Scientific) for 30 min at RT and subsequent fixation by adding 1% formaldehyde. After 10 min, fixation was terminated by adding 0.2 M glycine. Nuclear pellets were prepared for ChIP.
Libraries were prepared according to Illumina's instructions.

treatment_protocol: iBATs at day 8 of differentiation were treated with 1 μM isporoterenol (ISO) or vehicle for 2 hr

tag: ChIP

tag: cell

value: immortalized brown adipocytes (iBATs)

value: isoproterenol (1 μM, 2 hr)


title: iBAT_D8_ISO_plus_PPARg

value: Ppar-g

tag: treatment


title: GDNF_0hr-01

description: lncRNA


title: iBAT_D8_ISO_minus_JMJD1A

value: vehicle


title: Myc_D0_ChIPSeq

value: 2o 1B MEFs

value: c-Myc antibody (sc-764, Santa Cruz)


title: tg4tg.rep2

city: Houston

first: kaifu

last: chen

address: 1 Baylor plaza, suite 450A

institute: Baylor College of Medicine

data_processing:
Reads were aligned by Tophat with parameters --mate-std-dev 100 and -r 100, aligned reads were assigned to UCSC known Genes by the htseq-count function in HTSeq with parameters  -q -m intersection-strict -s no
Genome_build: mm9
Supplementary_files_format_and_content: text files with gene and counts for each sample

molecule: polyA RNA

source_name: hypothalamus

growth_protocol: All animals were housed and supplied with water and normal chow according to the standard procesures at Baylor College of Medicine.

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

treatment_protocol: Mice were sacrificed under anesthesia and the hypothalamus tissues were quickly dissected over ice. Tissue samples were homogenized in PureZOL Reagent (Bio-Rad) through a Polytron disruption method and purified using an Aurum Total RNA Fatty and Fibrous Tissue Kit (Bio-Rad) following the manufacturer’s instructions. RNAs were polyA-selected, amplified and sequenced using an Illumina Solexa HiSeq system following the manufacturer’s instructions.

tag: genotype

value: MeCP2 transgenic

tag: age

value: 7 weeks

tag: tissue type

value: hypothalamus


title: iBAT_D8_ISO_minus_PPARg


title: tg4tg.rep3


title: iBAT_D8_ISO_plus_ARID1A


title: tg4tg.rep1


title: iBAT_D8_ISO_plus_BRG1


title: wt4tg.rep3

value: Wild type for MeCP2 transgenic


title: PANCRKO_RNASeq_rep2

tag: cell type

value: ES-derived cardiomyocytes

value: PANCR

value: poly-A mRNA


title: wt4tg.rep2


title: iBAT_D8_ISO_minus_ARID1A


title: GDNF_N-01

description: lncRNA

value: spermatogonial stem cells


title: iBAT_D8_ISO_minus_BRG1


title: iBAT_D8_ISO_minus_FAIRE

value: FAIRE


title: iBAT_D8_ISO_plus_H3K27Ac


title: ko4ko.rep2

value: MeCP2 knockout


title: Scramble_RNASeq_rep1

value: Scrambled


title: wt4ko.rep1

value: Wild type for MeCP2 knockout


title: wt4tg.rep1


title: iBAT_D8_ISO_minus_H3K27Ac

value: immortalized brown adipocytes (iBATs)


title: iBAT_D8_ISO_plus_H3K4me3

value: isoproterenol (1 μM, 2 hr)


title: ko4ko.rep1


title: ko4ko.rep3


title: ko4ko

data_processing:
Reads were aligned by Bowtie, with parameters -v 3 -a -m 1 --best --strata -X 1000
Reads density were calculated by the dpos function in DANPOS 2.2.0 with parameters --count 100000000 --frsz 140 --extend 80 --fdr 0
Genome_build: mm9
Supplementary_files_format_and_content: Bowtie default wig output format

extract_protocol:
Tissue samples were washed in cold PBS and re-suspended in RSB buffer (10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl2, 0.2% NP-40, protease inhibitors). Nuclei pellets were digested with Micrococcal Nuclease in the presence of 1 mM CaCl2. Reactions were terminated by adding 10 mM EDTA. The chromatin preparations were then purified using a QIAGEN PCR Purification Kit. Mononucleosome was used for downstream library preparation.
Libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mice were sacrificed under anesthesia and the hypothalamus tissues were quickly dissected over ice.


title: Rps6 Inoc

city: West Lafayette

first: Meixia

last: Zhao

state: IN

address: 915 W State Steet

department: Agronomy

institute: Purdue University

data_processing:
base-calling
The small RNA raw sequencing data was trimmed with filtrations of low quality reads, adapter sequences, reads shorter than 17 nt, and then mapped to the soybean reference genome (Glycine max v1.1; Schmuta et al. 2010) and P. sojae genome (Tyler et al. 2006) respectively using Bowtie (Langmead et al. 2009) allowing only perfect matches.
The soybean genome mapped reads matching P. sojae genome and structural noncoding RNAs (t/r/sn/snoRNAs) from Rfam (http://rfam.sanger.ac.uk) and GtRNAdb (Chan and Lowe, 2008) were removed for further analysis.
The small RNAs were normalized as transcripts per million genome matched reads (TPM).
Novel miRNAs were predicted by modified miREAP with the parameters of -A 18 -B 26 -a 18 -b 25 -d 400 -f 25.
Genome_build: Gmax_v1.1_189.fa
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample

organism: Glycine max

source_name: Soybean hypocotyl - P. sojae inoculated

growth_protocol: greenhouse

extract_protocol:
Qiagen miRNeasy Mini Kit, Cat. No. 217004
Small RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation Kit, Cat. No. RS-200-0012 with standard Illumina protocols

treatment_protocol: Standard hypototyl inoculation

tag: tissue

value: stem hypocotyl

tag: line


title: MeCP2 ChIP

data_processing:
Reads were aligned by Bowtie, with parameters  -p 8 -v 3 -a -m 1 --best --strata -X 1000, then density of aligned reads was calculated by the dtriple function in danpos 2.2.0, with command line: python danpos.py dtriple aligned_reads_dir/  -a 10 -r 0 -k 0 -j 0 --frsz 140 -c 75000000
Genome_build: mm9
Supplementary_files_format_and_content: Wig files with read density

extract_protocol:
Mouse hypothalamus tissues were fixed in in 1% formaldehyde in PBS for 10 minutes at room temperature. After quenching the fixation with 125 mM glycine in PBS, the samples were homogenized in hypotonic solutions to release the cytoplasmic fractions. Nuclei were collected at 11,000 rpm in a table-top centrifuge. Chromatin was prepared using a method of sonication followed by a brief Micrococcal Nuclease (Worthington) digestion for 5 minutes at 37°C.  Reactions were stopped by addition of EGTA. The chromatin was then collected by spinning at 13,000 rpm in a table-top centrifuge for 10 minutes. All ChIP experiments were performed using anti-GFP antibody.Precipitated chromatin and input samples were then reverse crosslinked and treated with proteinase K. DNA was recovered and eluted in water using a QIAGEN PCR Purification Kit.
libraries were prepared for sequencing using standard Illumina protocols

value: Mecp2-/y; MECP2-EGFP


title: wt4ko


title: Rps3-c Inoc


title: Rps3-a Inoc


title: Rps5 Inoc


title: Rps3-b Inoc


title: Rps1-c Inoc


title: Rps1-a Inoc


title: Rps1-k Inoc


title: Williams Inoc

value: Williams


title: wt4ko.rep3


title: Rps5 mock

source_name: Soybean hypocotyl - mock-inoculated


title: Rps3-c mock


title: Rps4 mock


title: Rps3-a mock


title: Rps1-a mock


title: Rps1-k mock


title: Rps3-b mock


title: wt4ko.rep2


title: IgG_ChIP-seq

city: Pretoria

first: Steven

middle: Grant

last: Hussey

state: Gauteng

address: Lynnwood Road, Hatfield

department: Genetics

country: South Africa

institute: University of Pretoria

data_processing:
Reads were filtered, retaining those with quality value >=20 for >50% of read length, and <10% of "N" bases
Trimming of reads from 5' end to reduce primer contamination
Aligning of reads to E. grandis reference genome v.1.1. (www.phytozome.net) using Bowtie2
Peak calling (MACS2)
Irreproducible Discovery Rate analysis
Genome_build: Eucalyptus grandis v.1.1

organism: Eucalyptus grandis

source_name: Developing secondary xylem

growth_protocol: Developing xylem was sampled from seven-year-old ramets growing in clonal trial in KwaMbonambi, KwaZulu-Natal Province, South Africa in September 2012 (early spring).

extract_protocol:
Developing secondary xylem was ground to a powder in liquid nitrogen and fixed in 1% formaldehyde for 30 min on ice. Chromatin isolation and sonication was performed using standard protocols (Kaufman et al. 2010. Nature Prot. 5:457–472). ChIP-seq was performed as described (Adli & Bernstein. 2011. Nature Prot. 6:1656-1668)
ChIP and input DNA was amplified (Adli & Bernstein. 2011. Nature Prot. 6:1656-1668), digested with BciVI to yield 3' A overhangs and ligated to standard Illumina HiSeq 2500 adapters (library construction and sequencing service provided by Beijing Genome Institute)

tag: clone

value: Developing secondary xylem

tag: chip antibody

value: Naïve mouse IgG2a (sc-3878, Santa Cruz Biotechnology, CA)


title: Williams mock


title: Rps4 Inoc


title: Input_rep2


title: H3K4me3_ChIP-seq_rep2

value: Anti-H3K4me3 (Millipore #07-473)


title: Input_rep1


title: MeCP2 input

value: 7 weeks

value: hypothalamus


title: H3K4me3_ChIP-seq_rep1


title: PITX2KO_smallRNASeq_rep2

description: processed data file: miRNA.counts.txt

source_name: H9 Cardiomyocyte_PITX2KO_smallRNASeq

value: ES-derived cardiomyocytes

tag: molecule subtype

value: miRNA


title: PANCRKO_smallRNASeq_rep1

description: processed data file: miRNA.counts.txt

source_name: H9 Cardiomyocyte_PANCRKO_smallRNASeq

value: PANCR


title: PITX2KO_smallRNASeq_rep1

description: processed data file: miRNA.counts.txt


title: PANCRKO_smallRNASeq_rep2

description: processed data file: miRNA.counts.txt


title: Scramble_smallRNASeq_rep3

description: processed data file: miRNA.counts.txt

source_name: H9 Cardiomyocyte_Scramble_smallRNASeq


title: PITX2KO_smallRNASeq_rep3

description: processed data file: miRNA.counts.txt


title: PANCRKO_smallRNASeq_rep3

description: processed data file: miRNA.counts.txt


title: Rps6 mock


title: Scramble_smallRNASeq_rep2

description: processed data file: miRNA.counts.txt


title: Day 14 Fgf2-treated Neural Progenitor Cells, Replicate3

city: Chuo-ku

first: Keiko

last: Muguruma

state: Kobe

address: 2-2-3 Minatojima-minamimachi

institute: RIKEN:Center for Developmental Biology

data_processing:
Basecalls were performed using illumina RTA  software (version 1.17.21.3) and reads were de-multiplexed using bcl2fastq ( version 1.8.4).
Quality check of the reads was performes using FastQC(version 0.11.2). High quality reads were mapped to hg19 human genome assembly using Tophat (version 2.0.8b) with default parameter settings.
Number of reads originating from genes were quantified by cuffdiff program in Cufflinks package (version 2.1.1). These count values were subsequently used to test for differential expression using edgeR(version 3.2.4)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files including normalized expression values for each sample

source_name: Neural progenitor cells

growth_protocol: hESCs were differentiated in three-dimenstional condition with SFEBq culture.

extract_protocol:
hESC-derived neural progenitors were collected, and RNA was extracted with buffer RLT in Rneasy kit (Quiagen cat#74104).
Libraries were prepared using 1μg of total RNA, according to the protocol of TruSeq Stranded mRNA Sample Prep Kit

value: ES-derived neural progenitor cells

tag: passage number


title: Day 14 Fgf2-treated Neural Progenitor Cells, Replicate2


title: Day 14 Fgf2-treated Neural Progenitor Cells, Replicate1


title: Scramble_smallRNASeq_rep1

description: processed data file: miRNA.counts.txt


title: Rps1-c mock


title: Day 14 Control Neural Progenitior Cells, Replicate 2

value: control


title: Day 14 Control Neural Progenitior Cells, Replicate 1


title: RRP6 deletion prep 4

status: Public on Apr 14 2015

city: Indianapolis

first: Yunlong

last: Liu

address: 410 West 10th Street

department: Medical and Molecular Genetics

institute: Indiana University School of Medicine

data_processing:
Sequence reads were aligned with BFAST (v.0.7.0a) towards reference genome and junction library. Details refers to Breese and Liu, Bioinformatics, 2013, PMID: 23314324
Aligned reads were fitered with NGSUtils (Breese and Liu, Bioinformatics 2013), only unique mapped reads with no more than 2 mismatchs were kept.
Read counts were calculated with NGSUtils.
Differential expression analysis was performed using edgeR.
Genome_build: sacCer3
Supplementary_files_format_and_content: tab-delimited text file includes raw counts, log2 fold change values, p-values and FDR for all samples.

organism: Saccharomyces cerevisiae

source_name: RRP6 deletion prep 4

growth_protocol: All cells were grown to an OD600 of 0.8

extract_protocol:
Hot acid phenol extraction
SOLiD Total RNA-seq Kit

tag: genotype/variation

value: rrp6 deletion


title: RRP6 deletion prep 1

source_name: RRP6 deletion prep 1


title: WT prep 4

source_name: WT prep 4

value: wild type


title: WT prep 1

source_name: WT prep 1


title: RRP6 deletion prep 3

source_name: RRP6 deletion prep 3


title: ChIP-seq, Liver_Input_WT_pred_6am, replicate 1

first: Hee-Woong

last: Lim

address: 3333 Burnet Ave. MLC 7024

department: Division of Biomedical Informatics

data_processing:
1) ChIP-seq: ChIP-seq reads were aligned to the mouse genome mm9 using Bowtie with options ‘-k 1 -m 1 --best -strata’. After the alignment, down-sampling was performed to avoid read saturation in highly enriched regions. Specifically, after randomly selecting 15 million reads from each ChIP-seq run, redundant reads were removed, and peak calling was performed using Homer with a previously published input sample [GSM1044696] (You et al., 2013). Peaks were re-sized to 200 bp, and those meeting a threshold of 2 RPM were chosen for further study. Peaks located in the ENCODE blacklist regions were discarded. Based on the initial peak calling results, reproducibility was confirmed using Spearman’s rank correlation coefficient. Replicate pairs were then pooled into a single data set for each condition, followed by final peak-calling.
2) ChIP-exo: ChIP-exo reads were aligned to the mouse genome mm9 like ChIP-seq samples. To define a preliminary set of ChIP-exo elementary peaks on the forward and reverse strands, initial peak calling was performed separately for each biological replicate by examining the 5‘ ends of reads using GeneTrack (Albert et al., 2008) with options, ‘-s 3 -e 10’. Peak calling was also performed after pooling replicates for each condition. Reproducible and strong elementary peaks were selected from pooled replicates if they overlapped peaks from each replicate by at least by 5 bp (out of 10 bp). Elementary peaks located within the ENCODE blacklist regions were discarded.
Genome_build: mm9
Supplementary_files_format_and_content: 1) ChIP-seq peak files in BED format 2) ChIP-exo peak files in txt format contaning elementary peaks from each strand

source_name: Liver tissue

growth_protocol: Mice were back-crossed for at least four generations to the BALB/c background. Twelve-week-old male GRdim and GR+/+ litter-mate controls were maintained in a 12 hour dark /light cycle, and 6 am and 6 pm tissues were collected at the beginning of the light and dark phases, respectively.

extract_protocol:
Liver tissue isolated from sacrificed mice was immediately frozen in liquid nitrogen. To process for ChIP, the tissue was thawed, minced and crosslinked in 1 % formaldehyde/PBS. Cells were disrupted and nuclei purified by dounce homogenization in a hypotonic buffer (20 mM HEPES/NaOH pH 7.5, 0.25 M sucrose, 3 mM MgCl2, 0.2% NP-40, 3 mM 2-mercaptoethanol, Complete protease inhibitor cocktail). To prepare ChIP extracts, nuclei were suspended SDS lysis buffer (50 mM HEPES/NaOH pH 7.5, 1% SDS, 10 mM EDTA, Complete protease inhibitor), incubated at 4 C for 10 min, and subjected to microtip probe sonication under conditions optimized for IP efficiency.
ChIP-Seq libraries were produced and sequenced according to Illumina protocols. ChIP-exo libraries were produced for Illumina sequencing. Libraries were multiplexed for sequencing.

treatment_protocol: Mice were treated for 24 hours with s.c. applied prednisolone pellets (12mg/kg; Innovative Research of America)

tag: strain

value: back-crossed to the BALB/c

value: None (Input)


title: WT prep 2

source_name: WT prep 2


title: ChIP-seq, Liver_Input_WT_6pm, replicate 2


title: ChIP-seq, Liver_Input_WT_6am, replicate 1


title: Methylated DNA-Seq Pemt KO

city: Okayama

first: Jun

last: Wada

address: 2-5-1 Shikata-cho, Kita-ku

department: Department of Nephrology, Rheumatology, Endocrinology and Metabolism

institute: Okayama University

data_processing:
Base-calling performed using HiSeq Control Software (HCS) v1.5.15.1, Real Time Analysis (RTA) v1.13.48, CASAVA v1.8.2
Mapping to Mus musculus genome sequence, July 2007 (NCBI37/mm9) assebly, by Bowtie[1] (version 0.12.7)
Enrich regions were detected using MACS[2] (version 1.4.2) in Methylated DNA-Seq Pemt KO (PG0042_A01_annotation) and in Methylated DNA-Seq Pemt WT (PG0042_A02_annotation)
Enrich regions were detected using MACS[2] (version 1.4.2) in Methylated DNA-Seq Pemt KO (PG0042_A03_annotation) comparing with Methylated DNA-Seq Pemt WT as control.
Enrich regions were detected using MACS[2] (version 1.4.2) in Methylated DNA-Seq Pemt WT (PG0042_A04_annotation) comparing with Methylated DNA-Seq Pemt KO as control.
Genome_build: mm9
Supplementary_files_format_and_content: PG0042_A01_annotation.txt [Methylated DNA-Seq Pemt KO]
Supplementary_files_format_and_content: PG0042_A02_annotation.txt [Methylated DNA-Seq Pemt WT]
Supplementary_files_format_and_content: PG0042_A03_annotation.txt [Methylated DNA-Seq Pemt WT is set as control]
Supplementary_files_format_and_content: PG0042_A04_annotation.txt [Methylated DNA-Seq Pemt KO is set as control]

source_name: Pemt-/- under HFHS diet #128

extract_protocol:
genomic DNA was extracted and purified from mouse liver samples using Qiagen DNeasy Kit according to standard instructions
Bisulphite converted DNAs were enriched with EpiXplore Methylation DNA Enrichment Kit (Clontech). Genomic DNA libraries was prepared by TruSeq ChIP Sample Preparation Kit (Illumina).

value: Pemt KO

value: Liver

tag: diet

value: HFHS diet


title: ChIP-seq, Liver_Input_WT_pred_6am, replicate 2


title: ChIP-seq, Liver_Input_GRdim_pred_6am, replicate 2


title: ChIP-seq, Liver_Input_WT_6am, replicate 2


title: ChIP-seq, Liver_Input_GRdim_6pm, replicate 2


title: ChIP-seq, Liver_Input_GRdim_6pm, replicate 1


title: ChIP-seq, Liver_Input_GRdim_pred_6am, replicate 1


title: ChIP-seq, Liver_Input_GRdim_6am, replicate 2


title: ChIP-seq, Liver_Input_WT_6pm, replicate 1


title: ChIP-seq, Liver_CEBPb_WT_pred_6am

description: replicate 1 & 2

value: CEBPb, sc-150, Santa Cruz

tag: collection time

value: prednisolone


title: ChIP-seq, Liver_CEBPb_WT_6am

description: replicate 1 & 2


title: ChIP-seq, Liver_Input_GRdim_6am, replicate 1


title: RRP6 deletion prep 2

source_name: RRP6 deletion prep 2


title: Day 14 Control Neural Progenitior Cells, Replicate 3


title: N10

city: Stanford

first: Cheryl

middle: L

last: Smith

address: 300 Pasteur Dr.

department: Pathology

institute: Stanford University

description: library strategy: 3'-biased RNAseq (3SEQ)

data_processing:
Trimming: The first 18 bases and the last 7 bases of the HiSeq F1 reads were trimmed to make them the same length as the GAIIx reads; for all data, Prior to read mapping, 3' poly(A) sequences likely to be derived from the mRNA poly(A) tail were trimmed.
A Mus musculus castaneus genome was created in silico by applying the high-quality Cast SNPs [Keane, T. M. et al. Mouse genomic variation and its effect on phenotypes and gene regulation. Nature 477, 289-294, (2011).] to the reference C57BL/6 genome mm9. For B6, we used the mm9 genome. For each of these two reference genomes, a transcriptome was computed using RefSeq annotations, including spliced transcripts of all genes separated by 200 nucleotides, and each spliced transcriptome was added to its reference genome sequence.
Bowtie2 was used to align reads to composite genomes (Cast or B6 including spliced transcripts) with bowtie2 settings "“-k 200 --score-min L,0,-0.10 --rdg 2,2 --rfg 2,2 --mp 1,1"
Reads derived from repetitive regions of the genome were filtered as follows: If the difference in edit distance (1 for each mismatch and 2 for each indel) between a read’s best alignment and its second-best alignment was within 3, the read was discarded. Reads were also filtered out unless all best alignments in the composite genome corresponded to the same genomic position.
Each aligned read was then consolidated into a single genomic alignment, including intronic splice gaps.
Gene expression was quantified using only reads mapping to exons. Read counts were normalized by the total number of sequenced reads per library, multiplied by 1x106, resulting in reads per million.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files include Total Reads: per sample measure of expression as number of reads mapped to any exon of a given gene; Cast Votes: per sample number of reads mapping to a given gene and containing Cast-specific snp(s); B6 Votes: per sample number of reads mapping to a given gene and containing B6-specific snp(s); N2 Genotypes: per sample inferred genotypes of homozygous (1) or heterozygous (0.5) at each gene locus
Supplementary_files_format_and_content: samp-expr_F1.tsv: Total Reads_F1
Supplementary_files_format_and_content: samp-allele-gene-c-votes_F1.tsv: Cast Votes_F1
Supplementary_files_format_and_content: samp-allele-gene-b-votes_F1.tsv: B6 Votes_F1
Supplementary_files_format_and_content: samp-expr_N2.tsv: Total Reads_N2
Supplementary_files_format_and_content: samp-allele-gene-c-votes_N2.tsv: Cast Votes_N2
Supplementary_files_format_and_content: samp-allele-gene-b-votes_N2.tsv: B6 Votes_N2
Supplementary_files_format_and_content: genotypes.tsv: N2 Genotypes

source_name: whole embryo

extract_protocol:
Whole embryos were separated from all extra-embryonic material and homogenized in Trizol; total RNA was extracted and mRNA subsequently purified using Qiagen Oligotex.
Libraries were prepared according to Beck, A. H. et al. 3'-end sequencing for expression quantification (3SEQ) from archival tumor samples. PloS one 5, e8768, (2010).

tag: generation

tag: maternal strain

tag: paternal strain

tag: developmental stage

value: Embryonic day 11.5

tag: litter

tag: embryo id

tag: somite number

tag: sequencing run

tag: sequencing lane

value: N


title: N12


title: N11


title: N09


title: WT prep 3

source_name: WT prep 3


title: Methylated DNA-Seq Pemt WT

source_name: Pemt+/+ under HFHS diet #75

value: Pemt WT

tag: tissue


title: N04


title: N08


title: N05


title: N06


title: N02


title: N03


title: input_ChIPSeq_abl

city: San Antonio

first: Kexin

last: Xu

state: TX

address: 7703 Floyd Curl, MC 8257

department: Molecular Medicine

institute: UT Health Science Center at San Antonio

data_processing:
Basecalls performed using CASAVA 1.6.0
ChIP-Seq reads are aligned to hg19 using Bowtie with default configurations, only uniqly mapped reads are kept
Redundant reads (reads mapped to exactly the same location) are removed
Peaks are called using MACS2 2.0.9
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files are generated using MACS2+bedGraphToBigWig

source_name: prostate cancer cells

growth_protocol: LNCaP-abl (abl) cells were routinely maintained in phenol-red-free RPMI with 10% charcoal-stripped FBS plus 1% antibiotics.

extract_protocol: Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with specific antibodies. Libraries were prepared using ThruPLEX-FD Prep Kit (Rubicon Genomics). The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina NextSeq 500 system following the manufacturer's protocols.

treatment_protocol: For the purpose of ChIP experiments, the cells were kept in androgen-depleted medium for 3 days before the cells were collected.

tag: cell line

value: LNCaP-abl

tag: cell type

value: androgen-independent prostate cancer cells

tag: passages

tag: chip antibodies


title: N07


title: M11

value: M


title: N01


title: M12


title: M09


title: E2F1_ChIPSeq_abl

value: Santa Cruz Biotechnology (sc-193) and BD Pharmingen (554213)


title: brat1-1_BS_Seq

city: Beijing

first: huanwei

last: huang

address: 7 Science Park Rd., ZGC life science park

institute: NIBS

data_processing:
Illumina Casava1.8 software used for basecalling.
For data analysis, reads were mapped to the TAIR10 genome by Bismark (v0.10.0) allowing up to two mismatches.
DNA methylation was calculated when cytosine sites had at least three-fold coverage. DNA methylation levels in every 50-base-pair window were compared between wild-type and mutant plants using Fisher’s exact test.
The differentially methylated windows were combined to generate differently methylated regions when their gap size was ≤50 base pairs.
Genome_build: tair10
Supplementary_files_format_and_content: For each genotype, three bigwig files were generated. Where each file represents data of methylation levels in three sequence contexts (CpG, CHG, CHH)

organism: Arabidopsis thaliana

source_name: Seedlings

growth_protocol: Arabidopsis seeds were surface-sterilized and placed on MS (Murashige and Skoog) agar medium. Then the MS plates were incubated at 23ºC with 16-h-light and 8-h-dark for 10 days.

extract_protocol:
Seeding materials was ground into powder in liquid nitrogen; Genomic DNA was extracted from 10-day-old Arabidopsis seedlings with the DNeasy Plant Mini Kit (QIAGEN, 69104).
5ug of genomic DNA was sonicated and end-repaired. Cytosine-methylated adaptors from Illumina were ligated according to manufacturer’s instructions. Unmethylated cytosine residues were converted to uracils using the EpiTect bisulfite Kit (Qiagen, Valencia, CA). libraries were prepared for sequencing  according to the manufacturer's (Illumina, Inc) instructions.

tag: ecotype

value: Columbia

tag: genotype/variation


title: brp1-1_BS_Seq


title: brat1nrpe1_mRNA_rep3

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced clean reads were mapped to Arabidopsis thaliana (tair10) whole genome using tophat v2.0.12 with parameters --bowtie1 --no-coverage-search --segment-length 20 -g 10 -p 10
Gene annotation and calculation of FPKM values was carried out using Cufflinks (v2.0.1) with the provision of a GTF annotation file (tair10).
Gene expression differences were assessed by Cuffdiff use upper-quartile normalization, with false discovery rate correction for multiple testing.
Genome_build: tair10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

extract_protocol:
Seeding materials was ground into powder in liquid nitrogen; Total RNA was extracted from 0.2 g of 10-day-old Arabidopsis seedlings with Trizol reagent (Invitrogen) ; then total RNA samples were treated with DNase I and the mRNA is enriched by using the oligo(dT) magnetic beads.
RNA libraries were prepared for sequencing using standard Illumina protocols


title: M07


title: ros1-4_BS_Seq


title: M08


title: M06


title: WT_BS_Seq

value: WT


title: brat1nrpe1_mRNA_rep2


title: brat1nrpe1_mRNA_rep1


title: M05


title: M04


title: M03


title: nrpe1_mRNA_rep2


title: M10


title: L12

value: L


title: M02


title: nrpe1_mRNA_rep1


title: brat1_mRNA_rep2


title: brat1_mRNA_rep1


title: WT_mRNA_rep3


title: L11


title: L10


title: L08


title: L09


title: nrpe1_mRNA_rep3


title: L02


title: K11

value: K


title: L07


title: WT_mRNA_rep1


title: L03


title: L04


title: K10


title: K12


title: L06


title: L01


title: L05


title: K09


title: K07


title: K08


title: M01


title: brat1_mRNA_rep3


title: K06


title: K03


title: K05


title: WT_mRNA_rep2


title: K04


title: K02


title: J11

value: J


title: K01


title: J09


title: J06


title: J07


title: J08


title: I12

value: I


title: J01


title: J03


title: I10


title: I09


title: I11


title: I08


title: J04


title: I07


title: J02


title: I06


title: I05


title: I03


title: I04


title: I02


title: I01


title: J12


title: J10


title: H12

value: H


title: H10


title: H11


title: H09


title: J05


title: H07


title: H06


title: H05


title: H01


title: H03


title: G11

value: G


title: G12


title: H02


title: G10


title: G09


title: G08


title: G04


title: G05


title: G07


title: G06


title: G03


title: G02


title: F10

value: F


title: F09


title: F08


title: G01


title: F12


title: F06


title: F07


title: H08


title: F04


title: F05


title: F03


title: F02


title: F01


title: E06

value: E


title: E08

value: Embryonic day 11.5


title: E11


title: E10


title: E07


title: E09


title: F11


title: E05


title: E02


title: D12

value: D


title: E03


title: E01


title: D11


title: D09


title: D05


title: D08


title: Control hippocampus E18.5 dpc replicate 1 run 2

city: Barcelona

first: Manuel

last: Irimia

state: Barcelona

address: 88 Dr. Aiguader

department: MELIS

country: Spain

institute: Universitat Pompeu Fabra - Centre for Genomic Regulation

description: MmumRNA-50-Embr_E18_Brain_HP_Cont_a_exprRPKM.txt

data_processing:
Full genomic sequences for the analyzed species were downloaded from the UCSC Genome Browser database. Full transcriptomic sequences for all species were downloaded from Ensembl. For each gene, the canonical transcript was selected for gene expression analysis based on BioMart.
For each species, we assembled all canonical transcript (as defined above) sequences. In order to calculate the effective number of unique mappable positions in each transcript (i.e. the effective length) we performed the following steps. For each read length k, we extracted the L-k+1 (L being the transcript length) k-mer sequences from each canonical transcript and then aligned the full set of k-mers against the respective genome using Bowtie, allowing for a maximum of two mismatches. k-mers with no or one unique genomic alignment were then likewise aligned back to the canonical transcriptome. For each transcript, the number of such k-mers having a unique transcriptomic alignment was determined. This corresponds to the transcript’s effective number of unique mappable positions for k-mer mRNA-Seq reads. For each sample, the corresponding mRNA-Seq data were aligned against the respective genome using Bowtie, allowing for a maximum of two mismatches. Reads with one unique genomic alignment were then aligned against the canonical transcriptome and, for each transcript, the number of reads with one unique transcriptomic alignment were counted. Gene expression levels were determined as reads per thousand mappable positions of target transcript sequence per million of reads, where the reads uniquely align to the analyzed transcriptome. This procedure for estimating gene expression levels is a corrected version of the widely used RPKM (reads per kilobase of target transcript sequence per million of total reads) metric, and is referred to as “cRPKM” [Labbe RM et al. Stem Cells (2012)].
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files include cRPKM values (as defined above), as well as the total read count for each gene's canonical transcript

source_name: E18.5 dpc hippocampus

extract_protocol:
mRNA was purified using Sigma Tri Reagent
RNA libraries were prepared for sequencing using standard Illumina Truseq kit protocols

treatment_protocol: Stem cells containing the conditional nSR100lox allele were ordered from EUCOMM (project # 71507, clones EPD0538_3_A08 AND EPD0538_3_A09) (Friedel et al. 2007) and aggregated with outbred ICR morula. Following confirmation of germline transmission, mice bearing the nSR100lox allele were maintained on a C57Bl/6N background and crossed with the B6.C-Tg(CMV-cre)1Cgn/J line from the Jackson Laboratory. Excision of exons 7 and 8 in resulting nSR100+/Δ7-8 mice is confirmed by PCR and sequencing.

value: Wild type

tag: embryonic stage

value: E18.5 dpc


title: nSR100/Srrm4 KO hippocampus E18.5 dpc replicate 1 run 1

description: MmumRNA-50-Embr_E18_Brain_HP_KO_a_exprRPKM.txt

value: nSR100/Srmm4 KO


title: E04

tag: generation


title: D04

tag: maternal strain


title: D07

tag: paternal strain


title: D10

tag: developmental stage


title: Control hippocampus E18.5 dpc replicate 2

description: MmumRNA-50-Embr_E18_Brain_HP_Cont_b_exprRPKM.txt


title: nSR100/Srrm4 KO hippocampus E18.5 dpc replicate 1 run 2


title: E12

tag: litter


title: D06

tag: embryo id


title: nSR100/Srrm4 KO hippocampus E18.5 dpc replicate 2

description: MmumRNA-50-Embr_E18_Brain_HP_KO_b_exprRPKM.txt


title: nSR100/Srrm4 KO cortex E18.5 dpc replicate 2

description: MmumRNA-50-Embr_E18_Brain_CX_KO_b_exprRPKM.txt

source_name: E18.5 dpc cortex


title: D03

tag: somite number


title: nSR100/Srrm4 KO cortex E18.5 dpc replicate 1 run 2

description: MmumRNA-50-Embr_E18_Brain_CX_KO_a_exprRPKM.txt


title: D02

tag: sequencing run


title: D01

tag: sequencing lane


title: C12

value: C


title: Control cortex E18.5 dpc replicate 2

description: MmumRNA-50-Embr_E18_Brain_CX_Cont_b_exprRPKM.txt


title: Control cortex E18.5 dpc replicate 1 run 2

description: MmumRNA-50-Embr_E18_Brain_CX_Cont_a_exprRPKM.txt


title: C11


title: C10


title: Control cortex E18.5 dpc replicate 1 run 1


title: C09


title: H8

city: Seongnam-si

first: Nayoung

last: Kim

state: Gyeonggi-do

address: 173-82, Gumi-ro, Bundang-gu

department: Internal Medicine

country: South Korea

description: This preliminary study suggests that long-term administration of PPI may cause changes of microbiota in the terminal ileum and weight loss.

data_processing:
The basic analysis was conducted as described previously (Chun et al., 2010; Hur et al., 2011; Kim et al., 2012a).
Reads obtained from different samples were sorted by unique barcodes of each PCR product. The barcode, linker, and primer sequences were removed from the original sequencing reads. Reads containing two or more ambiguous nucleotides, reads with a low quality score (average score < 25), or reads shorter than 300 bp, were discarded.
Potential chimeric sequences were detected by the Bellerophon method, which compares the BLASTN search results between the forward half and reverse half sequences (Huber et al., 2004). After removing the chimeric sequences, the taxonomic classification of each read was assigned against the EzTaxon-e database, which contains the 16S rRNA gene sequence of type strains that have valid published names and representative species level phylotypes of either cultured or uncultured entries in the GenBank database with complete hierarchical taxonomic classification from the phylum to the species.
The richness and diversity of samples were determined by ACE, Chao1 and Jackknife estimation. In addition, Simpson diversity index and Shannon diversity index at 3% distance was calculated in the CL community program (Chunlab Inc., Seoul, Korea). Good’s method was used to calculate sequencing coverage (Li et al., 2009).
Random subsampling was conducted to equalize the read size of samples for comparing different read sizes among samples. To compare the operational taxonomic units (OTUs) between samples, shared OTUs were obtained with the XOR analysis of the CL community program (Chunlab Inc.). UniFrac-based principal coordinates analysis was used to compare the microbial communities of sub-groups.
Genome_build: EzTaxon-e database (http://eztaxon-e.ezbiocloud.net)
Supplementary_files_format_and_content: tab-delimited text files include ‘microbial phylotypes classification’ for each sample

organism: rat gut metagenome

source_name: rat gut metagenome_with_lansoprazole (PPI)_50weeks

growth_protocol: Specific pathogen-free, 344, male Fischer (F344) rats were used (Orient, Seoul, Korea). The animals were housed in a cage maintained at 23°C, with 12-h: 12-h light/dark cycles under specific pathogen-free conditions.

extract_protocol:
The flushed material was centrifuged at 20,000 × g for 30 min to pellet bacteria. The pellet was processed to extract total microbial DNA by using a commercial kit (iNtRON Biotechnology, Gyeonggi, Korea). This study was approved by the Institutional Animal Care and Use Committee (IACUC) of Seoul National University Bundang Hospital (IACUC No.: BA0903-040/013-01).
The DNA samples from eleven 74-week-old F344 rats were subjected to pyrosequencing. PCR amplification was performed using primers targeting the V1 to V3 regions of the 16S rRNA gene with extracted DNA. For bacterial amplification, barcoded primer of 9F and 541R (http://oklbb.ezbiocloud.net/content/1001). The amplifications was carried out under the following conditions: initial denaturation at 95oC for 5 min, followed by 30 cycles of denaturation at 94oC for 30 sec, primer annealing at 55oC for 45 sec, and extension at 72oC for 1min 30 sec, with a final elongation at 72oC for 5 min.  The pyrosequencing was carried out at Chunlab, Inc. (Seoul, Korea) with GS FLX Sequencing system, the modified laboratory benchtop form of 454 sequencing systems (Roche, Branford, CT, USA) according to the manufacturer’s instructions.

treatment_protocol: Twenty-four week old F344 rats were fed with (n = 5) or without (n = 6) lansoprazole for 50 weeks. The control (vehicle) group was fed with ad libitum only Purina rat chow and lansoprazole group were fed with rat chow containing lansoprazole (5 mg/kg) until sacrifice. The rats were fasted but allowed water for 12 h before the experiments. The animals were anesthetized by zoletil and rompun mixture and killed by decapitation. A 1-cm length of the terminal ileum per rat was obtained and phosphate-buffered saline was flushed through the lumens.

tag: host organism

value: Rattus norvegicus

tag: host organism strain

value: Fischer (F344) rat

tag: host tissue

value: ileum

tag: treatment to host

value: fed with lansoprazole for 50 weeks


title: H04


title: C07


title: C08


title: H4

institute: Seoul National University Bundang Hospital


title: C05


title: ga.cb.1-3

value: Castaneus (Cast)

value: gaIIx


title: C06


title: ga.cb.1-1


title: H2


title: C17

source_name: rat gut metagenome_without_lansoprazole (PPI)_50weeks

value: fed without lansoprazole for 50 weeks


title: C04


title: C03


title: C02


title: ga.bc.5-6


title: B11

value: B


title: B10


title: ga.bc.5-5


title: C15


title: B08


title: ga.bc.5-4


title: Control hippocampus E18.5 dpc replicate 1 run 1


title: B07


title: B12


title: C13


title: B06


title: ga.bc.5-3


title: B5


title: C01


title: ga.bc.5-7


title: C16


title: ga.cb.1-4


title: B04


title: ga.bc.3-4


title: nSR100/Srrm4 KO cortex E18.5 dpc replicate 1 run 1


title: B02


title: B3


title: ga.cb.1-2


title: ga.bc.3-3


title: C14


title: B09


title: B03


title: B1


title: A12

value: A


title: ga.bc.3-1


title: A11


title: A10


title: B05


title: KC

city: ILLKIRCH

first: nicolas

last: charlet

address: 1 Rue laurent Fries

country: France

institute: IGBMC

data_processing:
FASTQ files were generated with CASAVA v1.8.2. (Illumina)
Reads were trimmed for adaptor,  low-quality sequences were removed and reads were mapped to hg19
Reads were counted using htseq-count
reads were calculated using DEXseq
Alternative splicing was analyzed using DEXSEQ and  KISSPLICE (http://kissplice.prabi.fr/)
Genome_build: hg19
Supplementary_files_format_and_content: txt

source_name: Myotonic Dystrophy type 1

extract_protocol:
Total RNA from heart samples was extracted by Trizol
mRNA libraries were created using TruSeq RNA Sample Preparation v2 Kit (Illumina). Briefly, mRNA was purified from 1 µg total RNA using poly-T oligo-attached magnetic beads and fragmented using divalent cations at 94°C for 8 minutes. The cleaved mRNA fragments were reverse transcribed to cDNA using random primers then the second strand of the cDNA was synthesized using DNA Polymerase I and RNase H. The double stranded cDNA fragments were blunted using T4 DNA polymerase, Klenow DNA polymerase and T4 PNK. A single 'A' nucleotide was added to the 3' ends of the blunt DNA fragments using a Klenow fragment (3' to 5'exo minus) enzyme. The cDNA fragments were ligated to double stranded adapters using T4 DNA Ligase. The ligated products were enriched by PCR amplification (30 sec at 98°C; [10 sec at 98°C, 30 sec at 60°C, 30 sec at 72°C] x 12 cycles; 5 min at 72°C). Then surplus PCR primers were removed by purification using AMPure XP beads (Agencourt Biosciences Corporation). DNA libraries were checked for quality and quantified using 2100 Bioanalyzer (Agilent), then sequenced at 7pM concentration using Hiseq 2000 (Illumina) as paired-end 2x100 base reads.

tag: tissue

value: left ventricle

tag: disease state

value: myotonic dystrophy


title: A09

value: Embryonic day 11.5


title: A08


title: A07


title: A05


title: DM17


title: A06


title: A03


title: A04


title: A02


title: hs2.cb.2-6


title: ALS13

source_name: Control

value: control


title: ALS14


title: hs1.cb.2-6


title: B01


title: hs1.cb.2-5


title: A01


title: hs2.cb.2-5


title: hs2.cb.2-2


title: hs2.cb.2-3


title: hs1.cb.2-2


title: AML-15746

city: New York

first: Yanwen

last: Jiang

state: NY

institute: Weill Cornell Medical College

description: disease: acute myeloid leukemia

data_processing:
FASTQ files were generated by using the Illumina CASAVA 1.8.2 pipeline.
Raw reads alignment and CpG methylation call were formed by using an in-house pipeline described in Akalin et al., PLoSGenetics, 2012.
Genome_build: mm9
Supplementary_files_format_and_content: methycall files are in .txt format

source_name: Hematopoietic stem cells

growth_protocol: Primary, uncultured cells.

extract_protocol:
DNA was extracted using the Allprep DNA/RNA purification Kit (Qiagen) and analyzed using a Bioanalyzer (Agilent Technologies).
ERRBS libraries were prepared according to a previously published protocol (Akalin et al., PLoSGenetics, 2012).

treatment_protocol: The hematopoietic stem cells, characterized by lin-, Sca+, and cKit+, were sorted from mice and lin-cd34+cd38-cd90+ cells sorted from human AML samples

tag: cell type

value: hematopoietic stem cells

tag: cell markers

tag: genotype

value: Tet2 mutant; Flt3-ITD

tag: strain


title: AML-16320

description: disease: acute myeloid leukemia