title: 12hr Input

value: Rpb1 (Millipore 05-623-Z)


title: K562 GMUCT A

status: Public on Mar 08 2014

type: SRA

city: Philadelphia,

first: Nathan

middle: Daniel

last: Berkowitz

state: Pennsylvania

address: 433 S University Ave.

department: Biology

country: USA

institute: University of Pennsylvania

description: GMUCT

library_source: transcriptomic

data_processing:
Basecalls performed with most up-to-date version of Illumina base calling software
3' adapter sequences were trimmed using cutadapt (version 0.9.5 with parameters -e 0.06 -O 6 -m 14), and reads were subsequently aligned to the genome using bowtie (human) or tophat (Arabidopsis)
read counts per transcript were found using HTSeq
Genome_build: hg19 (Arabidopsis) or TAIR9 (human cell line)

molecule: total RNA

organism: Homo sapiens

source_name: K562 cells

extract_protocol:
miRNeasy Mini Kit
TruSeq Small RNA Sample Prep Kit
GMUCT 2.0

tag: cell type

value: K562 cells

tag: method

value: GMUCT

tag: molecule

value: uncapped/cleaved RNA


title: K562 GMUCT B

description: GMUCT


title: HeLa GMUCT B

description: GMUCT

source_name: HeLa cells

value: HeLa cells


title: HeLa GMUCT A

description: GMUCT


title: HEK293 GMUCT A

description: GMUCT

source_name: HEK293 cells

value: HEK293 cells


title: HEK293 GMUCT B

description: GMUCT


title: Chlamydomonas reinhardtii CC-4349 48h minus N, 8h + acetate

status: Public on Mar 09 2014

city: Los Angeles

first: Sabeeha

last: Merchant

state: California

address: 607 Charles E. Young Drive East

department: Department of Chemistry and Biochemistry

institute: University of California Los Angeles

description:
UGTWcwnA8HS1
Illumina's RNA-Seq whole transcriptome analysis.
mRNA

data_processing:
Illumina's proprietary software was used for basecalling.
The reads were aligned using bowtie in single-end mode and with a maximum tolerance of 3 mismatches to the Au10.2 transcripts sequences (http://www.phytozome.net/chlamy), corresponding to the version 4.0 assembly of the Chlamydomonas genome.
Expression estimates were obtained for each individual run in units of RPKMs (reads per kilobase of mappable transcript length per million mapped reads) after normalization by the number of aligned reads and transcript mappable length.
Genome_build: Version 4.0 assembly of the Chlamydomonas genome (http://genome.jgi-psf.org/Chlre4/Chlre4.home.html)
Supplementary_files_format_and_content: Processed data file corresponds to expression estimates per sample, in units of RPKMs.

organism: Chlamydomonas reinhardtii

source_name: Chlamydomonas cultured cells, CC-4349, 48 h minus nitrogen, 8h after acetate boost

growth_protocol: Cultures used for the experiments to generate RNA for RNA-sequencing were grown in 1000 ml HSM-medium in 2.8 l flasks in the light (25 µmol photons per m2 per s) under the same conditions until they had reached a cell density of 4x10^6 cells per mL. They were then processed as indicated in the treatment protocol.

extract_protocol:
Total RNA was isolated at time-points indicated in the text according to a method described in Boyle et al. 2012.
For quantitative transcriptomes, RNAs were sequenced at LANL.

treatment_protocol: Once the cultures had reached 4x10^6 cells per mL they were washed in HSM - ammonium chloride and resuspended in 2.8 l flasks to a final cell density of 2x10^6 cells per ml, final volume of 1 l. Cells for RNA preparation were sampled at the indicated timepoints.

tag: strain/background

tag: treatment

value: 48 h minus nitrogen, then acetate boost

tag: time point

value: 8h after acetate boost


title: 7weeks_infected

city: Edinburgh

first: Amy

last: Buck

address: West Mains Road

country: United Kingdom

institute: The University of Edinburgh

description: Illumina small RNA Sample Preparation Kit version 1.5/ GAIIX

data_processing:
Raw reads  were obtained in fastq format and 3' adapters trimmed using cutadapt, requiring at least a 6 bp match to the adapter sequence and a quality threshold of 20
Only reads that contained the adapter were retained; reads were subsequently collapsed on primary fasta sequence and those present in only one copy within a sample were discarded
Trimmed, collapsed reads ≥17 bp were then aligned to mouse (MM9) or S. mansoni genomes (V5.0) using BOWTIE version 0.12.5, requiring a perfect match to the full length of the sequence.
Reads that mapped to either genome were then BLASTN aligned against the RFAM database [BLASTN parameters: -max_target_seqs 1 -outfmt '6 std qseq sseq' -task blastn -word_size 6 -dust no] and categorized according to matches to Rfam class (e.g. tRNA, etc.).  Mouse reads without RFAM similarities (other than miRNAs) were aligned to mature miRNAs in miRBase version 19
Genome_build: MM9 and V5.0

organism: Mus musculus

source_name: Serum

extract_protocol:
Blood was collected via cardiac bleed, RNA was extracted from serum according to miRVANA PARIS protocol
RNA libraries were prepared for sequencing using Illumina small RNA Sample Preparation Kit version 1.5 and TruSeq Small RNA protocol

treatment_protocol: Sample2 - S.mansoni infection dose: ceracrie 180, 7 weeks infection, Sample 3: S.mansoni infection dose: cercariae 80, 8 weeks infection

tag: Sex

value: female

tag: strain

tag: infection dose and wk p.i.

value: S.mansoni Cercarie 180, Wk7

tag: serum volume

value: Pool of 8 samples:400ul total volume


title: Col-0 GMUCT B

description: GMUCT

organism: Arabidopsis thaliana

source_name: flower bud

value: flower bud

tag: ecotype/cultivar


title: 7weeks_naive


title: Col-0 mRNA-Seq B

description: poly-T capture

value: poly-T capture

value: mRNA


title: Col-0 mRNA-Seq A

description: poly-T capture


title: Col-0 GMUCT A

description: GMUCT


title: 8weeks_infected

description: TruSeq Small RNA protocol/HiSeq2

value: S.mansoni Cercarie 80, Wk8

value: Pool of 3 samples:300ul total volume


title: 8weeks_naive

description: TruSeq Small RNA protocol/HiSeq2


title: M101909L20

status: Public on Mar 07 2014

city: Minneapolis

first: Charles

middle: Edward

last: Determan Jr

state: MN

address: PWB B150 516 Delware St.

department: Department of Surgery

institute: University of Minnesota

data_processing:
Illumina Casava v1.8.2 software used for basecalling.
TopHat v1.5.0 using default settings
BAM files sorted using SAMtools
Raw counts estimated by the Python script HTSeq count
Identified contigs converted to human orthologs with BiomaRt Bioconductor package.  HUGO names were used for subsequent analysis
EdgeR v3.2.4 was used with Trimmed mean of M values normalization to calculate differentially expressed genes with respect to time and fed state
Genome_build: Sscrofa10.2.69
Supplementary_files_format_and_content: Supplementary file on Series record with htseq estimated counts of each ensemble gene id, contains all samples by column

organism: Sus scrofa

source_name: Liver

extract_protocol:
Liver biopsies were flash frozen with liquid nitrogen and stored until further processing.  RNA was extracted using the QIAGEN RNeasy Kit.  Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: liver

value: Yorkshire-Landrace

tag: fed status

value: Fasted

tag: survival

value: Lived

value: 20 hours after resuscitation began

value: liver biopsy


title: M111510L2

value: 2 hours after resuscitation began


title: M111510L8

value: 8 hours after resuscitation began


title: M101909LB

value: Baseline


title: M111510LB


title: M111510L20


title: M101909L2


title: M101111L2


title: M101111L8


title: M092110D20

value: Died


title: M092110DB


title: M092109L2


title: M092109L8


title: M091409LB

value: Carbohydrate Prefed


title: M092109L20


title: M092109LB


title: M091409L20


title: M091409L8


title: M101111LB


title: M082410L8


title: M101909L8


title: M092110D8


title: M092110D2


title: M062711DB


title: M091409L2


title: M082410LB


title: M062711D8


title: M062209L20


title: M062209LB


title: M082410L20


title: M062711D2


title: M062209L8


title: M062011LB


title: M062011L20


title: M062011L8


title: M062011L2


title: M062209L2


title: M082410L2


title: M061410L8


title: M061410L2


title: M060512LB


title: M101111L20


title: M060512L20


title: M062711D20


title: M060512L2


title: M060512L8


title: M061410L20


title: M052112LB


title: M052112L8


title: M052112L20


title: M051010LB


title: M051010L20


title: M051010L2


title: M051010L8


title: M040212LB


title: M040212L8


title: M040212L20


title: M031912DB


title: M031912D2


title: M061410LB


title: M031510D8


title: M031912D8


title: M031510D20


title: M030810L8


title: M030810L2


title: M022012LB


title: M030810L20


title: M031510D2


title: M030810LB


title: M022012L8


title: M022012L20


title: M022012L2


title: M021510L8


title: M021510L2


title: M052112L2


title: M040212L2


title: M021510LB


title: M031510DB


title: M012510DB


title: M020612L2


title: M020612L8


title: M020612L20


title: M020612LB


title: M012510D20


title: M012412L20


title: M012412LB


title: M012510D8


title: M012412L2


title: M031912D20


title: M012412L8


title: M021510L20


title: MNase-H3K4me1 Rag

city: MARSEILLE CEDEX 09

first: Aurelie

last: Bergon

address: parc scientifique de Luminy, case 928

country: France

institute: TAGC INSERM U1090

library_source: genomic

data_processing:
Sequencing of Pol II ChIP and MNase-ChIP DNA samples was performed on an AB SOLiD V4.0 (Life Technologies) according to the manufacturer’s protocol and mapped onto the NCBI37/mm9 reference genome using the SOLiD pre-processing pipeline (bioscope). Only uniquely mapped sequence tags were used for further analysis. To reduce the risk of potential bias, we discarded all tags with exactly the same coordinates using samtools rmdup. Finally, using custom script, reads from BAM file were then elongated to 245 bp (Pol II) or 146 bp (Mnase-ChIP). Then, the values were summed up in non-overlapping 100 bp bins along each chromosome. The summed values were finally normalized by dividing them by the overall mean values per bin, in order to obtain wig file.
Genome_build: Mouse samples : MM9
Supplementary_files_format_and_content: wig

molecule: genomic DNA

source_name: thymocyte

growth_protocol: Rag2-/- (DRag)  male mice bred on a C57BL/6J background were used in this study. Mice were housed under specific pathogen-free conditions and handled in keeping with European directives.

extract_protocol: Chromatin Preparation (ChIP): Pol II ChIP was carried out as described elsewhere (Boyer et al, 2005) using N20 Abs (sc-899X, Santa Cruz Biotechnology), with minor modifications. Briefly, 1 ml of chromatin extract corresponding to 10E6 cells was pre-washed with 40 ml of magnetic beads (Invitrogen) for 1 h at 41C in a rotating wheel. The ChIP procedure was then carried out using Abs/bead complexes (4 mg of Ab/40 ml beads). After reverse crosslinking, enriched DNA fragments were extracted with phenol/chloroform and recovered using the Qiaquick PCR-purification kit (Qiagen, Germany). Mononucleosome preparation of native chromatin (MNase-ChIP) was carried out as described (Umlauf et al, 2004), with minor modifications. Briefly, the nuclei from 20E6 of either DRag or DRagCD3 thymocytes were digested with 10 U Mnase (Roche, Switzerland) for 10 min and the soluble chromatin fraction (mononucleosomes) from the equivalent of 5E6 of cells was used for ChIP using Abs against H3K4me1 (Abcam, Cambridge, UK; Cat. No: 8895, 4 mg) and H3K4me3 (Abcam; Cat. No: 8580, 3 mg). The quality of individual ChIP samples was checked at known target sites by qPCR and DNA size was verified on a 2100 Bioanalyzer (Agilent Technologies).     Sequencing  10 ng of ChIP were used for high throughput sequencing. Standard Applied Biosystems Life Technologies protocols were followed for the creation of short-insert bar-coded libraries (insert length ~150 bp) according to the ChIP-seq Kit Guide from the manufacturer (cms_079323.pdf) and library preparation guide (cms_081748.pdf). The library was PCR amplified with 15 cycles. The amplified fragments were verified on a 2100 Bioanalyzer (Agilent, USA) before sequencing on an AB SOLiDTM (Life Technologies) according to the manufacturer’s protocol.

treatment_protocol: To obtain DRagCD3 thymocytes, 4-week-old mice were injected intraperitoneally with 75 mg of monoclonal antibodies (Abs) against CD3e (Cat. No: 553058, BD Bioscience, San Diego, CA); and thymi were collected 7 days after the injection.

value: thymus

tag: passages

tag: developmental stage

value: DRag thymocytes

tag: antibody

value: H3K4me1 (Abcam, Cambridge, UK; Cat. No:8895, 4 mg)


title: PolII N20 Rag

value: N20 Abs (sc-899X, Santa Cruz Biotechnology)


title: PolII N20 RagCD3

value: DRagCD3 thymocytes


title: MNase-H3K4me1 RagCD3


title: Nr10 +GlcN

city: Jena

first: Marco

last: Groth

address: Beutenbergstraße 11

department: Core Facility - Next Generation Sequencing

country: Germany

institute: Leibniz Institute on Aging - FLI

data_processing:
Illumina Casava software used for extraction of FASTQ files
FASTQ files were mapped using Tophat (v1.4.1); C. elegans samples were mapped vs. the C. elegans genome (ce10); M. musculus samples were mapped vs. the M. musculus genome (mm10)
For counting the reads per gene (raw counts) the Python package HTSeq was used in mode ‘union’ together with the Ensembl gene annotation. Only uniquely mapable reads were regarded.
Genome_build: ce10
Genome_build: mm10
Supplementary_files_format_and_content: Nr01-12_25-36_counts_ce_mm.xls

organism: Caenorhabditis elegans

source_name: total RNA from whole animals

extract_protocol:
Total RNA was isolated using QIAzol (Qiagen, Hilden, Germany) based on the phenol/chloroform extraction method.  Afterwards the RNA was quantified photometrically with a NanoDrop 1000 (PeqLab, Erlangen, Germany) and stored at -80 °C until use.
For library preparation an amount of 2 μg of total RNA per sample was processed using Illumina’s TruSeqTM RNA Sample Prep Kit (Illumina; San Diego; CA, USA) following the manufacturer’s instruction.

value: Bristol N2

value: Adult (48 hours after L4)

tag: agent

value: 100 µM GlcN


title: Nr12 +GlcN


title: Nr11 +GlcN


title: MNase-H3K4me3 Rag

value: H3K4me3 (Abcam; Cat. No:8580, 3 mg)


title: Nr09 +GlcN


title: Nr08 +GlcN


title: Nr06 -GlcN

value: control


title: Nr05 -GlcN


title: M012510D2

value: liver

value: Yorkshire-Landrace

value: Fasted


title: Nr04 -GlcN


title: 2276_8_KEP_3

city: Amsterdam

first: Karin

middle: E

last: de Visser

address: Plesmanlaan 121

department: Immunology

country: Netherlands

institute: Netherlands Cancer Institute

data_processing:
Sequence reads were mapped to Mus Musculus NCBI build 37 using Tophat version 2.0.6 with parameters --library-type fr-unstranded, --no-coverage-search -M --transcriptome-index, Ensembl GTF version 66
Readcounts were obtained by counting the number of reads per gene using HTSeq-count.
In order to determine the genes that are differentially expressed, the R package Limma is used. Within this package the Voom method was used to transform the count data to log2 counts per million
Genome_build: Mus Musculus NCBI build 37
Supplementary_files_format_and_content: tab-delimited text file containing the output of the differential expression analysis. This file includes the absolute gene expressions, the normalized gene expressions, the fold change and the p-value.

source_name: neutrophils

extract_protocol:
Ly6G+ neutrophils were isolated by magnetic column from blood of mice. RNA was isolated using Trizol and then treated with DNase I. Samples were put over a Qiagen RNeasy column for cleanup. RNA quality was confirmed with a 2100 Bioanalyzer from Agilent.
RNA-Seq libraries were prepared using the reagents provided in the Illumina TruSeq™ RNA Sample Preparation Kit, following the manufacturer’s protocol. Libraries were PCR amplified for 12 cycles and sequenced on an Illumina HiSeq 2000 System with TruSeq re

value: FVB/N

value: blood

tag: genotype


title: 2276_9_KEP_4


title: Nr02 -GlcN


title: 2276_7_KEP_2


title: 2276_5_WT_5

value: wild-type


title: Nr03 -GlcN


title: MNase-H3K4me3 RagCD3


title: 2276_4_KEP_4


title: 2276_3_WT_3


title: 2276_2_WT_2


title: Nr36 +GlcN

source_name: total RNA from liver

value: 108 weeks of age

value: 10 g / kg GlcN in Diet


title: Nr35 +GlcN


title: 2276_1_WT_1


title: Nr34 +GlcN


title: Nr28 -GlcN


title: Nr27 -GlcN


title: Nr32 +GlcN


title: Nr33 +GlcN


title: Nr30 -GlcN


title: Nr07 +GlcN


title: Nr31 +GlcN


title: Nr25 -GlcN


title: Nr26 -GlcN


title: Nr29 -GlcN


title: Nr01 -GlcN


title: 2276_6_KEP_1


title: control kidney 2

city: Pittsburgh

first: Jacqueline

last: Ho

state: PA

address: 4401 Penn Avenue

department: Pediatrics

institute: Children's Hospital of Pittsburgh

data_processing:
read alignment: tophat-2.0.9; parameters: --transcriptome-only --mate-inner-dist 15 --mate-std-dev 75 --microexon-search --splice-mismatches 2 --min-anchor 5
duplicates removal: picard-toos-1.94;  MarkDuplicates.jar; paramters: REMOVE_DUPLICATES=TRUE
filtering: samtools -f0x0003 -b -o (only mapped pairs)
fragment counting: dexseq_count.py -p yes -s no
gene-level aggregation: R; read.HTSeqCounts() ; geneCountTable() ; add the two lanes
Genome_build: NCBIM37
Supplementary_files_format_and_content: expression_cpm.txt; tab-delimited values; rows correspond to genes, columns to samples; values are counts per million fragments mapped

source_name: Embryonic kidney day 16

extract_protocol:
Embryonic kidneys were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. The Illumina TruSeq RNA Library Preparation Kit (generated by Tufts University Genomics Core; http://tucf-genomics.tufts.edu/) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: kidney

value: embryonic day 16


title: mutant kidney 2

value: Six2-TGC, miR-17~92 flx/flx


title: mutant kidney 3


title: control kidney 1


title: control kidney 3


title: mutant kidney 1


title: follicular thyroid carcinoma_FTC6

city: Warsaw

first: Michal

last: Swierniak

address: Banacha 2C

department: Centre of New Technologies

country: Poland

institute: University of Warsaw

description: snap-frozen tissue

data_processing:
Pipeline A: direct mapping - adapter cutting (cutadapt), human mature miRBase v18 alignment (bowtie2), sam to bam format compression (samtools), reads counting (R/Bioconductor ShortRead library), RPM normalization
Pipeline B: individual counting - adapter cutting (cutadapt), reads counting, median counts per sequence > 0  filtering,  isoform grouping (sequence sorting), RPM normalization
Pipeline C: summarized counting -  adapter cutting (cutadapt), reads counting, median counts per sequence > 0  filtering,  isoform grouping (sequence sorting), summary of sequences with the same seeds (first 8 bases), RPM normalization
Supplementary_files_format_and_content: Pipeline A: direct mapping - tab separated text file with normalized abundance measurements (RPM) of sequences aligned to hsa mature miRBase v18
Supplementary_files_format_and_content: Pipeline B: individual counting - tab separated text file with RPM normalized miRNA isoform counts in 20 samples
Supplementary_files_format_and_content: Pipeline C: summarized counting - tab separated text file with RPM normalized miRNA counts per seed in 20 samples

source_name: follicular thyroid carcinoma cells

extract_protocol:
500 ng of total RNA prepared from the tumor samples was used in the small RNA  protocol with the TruSeq™ Small RNA sample prepkit v2 (Illumina) according to the instructions of the manufacturer.  The barcoded libraries were size restricted between 140 and 165bp, purified and quantified using the Library  Quantification Kit - Illumina/Universal (KAPABiosystems) according to the instructions of the manufacturer.
A pool of ten libraries was used for cluster generation at a concentration of 10nM using an Illumina cBot. Sequencing of 50 bp was performed with an Illumina HighScan-SQ sequencer using version 3 chemistry and flowcell according to the instructions of the manufacturer.

tag: thyroid tissue type

value: follicular thyroid carcinoma

tag: place of origin

value: Germany


title: follicular thyroid carcinoma_FTC16

description: snap-frozen tissue

value: Poland


title: follicular thyroid carcinoma_FTC5

description: snap-frozen tissue


title: follicular thyroid carcinoma_FTC7

description: snap-frozen tissue


title: follicular thyroid carcinoma_FTC9

description: snap-frozen tissue


title: follicular thyroid carcinoma_FTC2

description: snap-frozen tissue


title: follicular thyroid carcinoma_FTC3

description: snap-frozen tissue


title: follicular thyroid carcinoma_FTC15

description: snap-frozen tissue


title: follicular adenoma_FA11

description: snap-frozen tissue

source_name: follicular thyroid adenoma cells

value: follicular thyroid adenoma


title: follicular thyroid carcinoma_FTC12

description: snap-frozen tissue


title: follicular adenoma_FA10

description: snap-frozen tissue


title: follicular adenoma_FA7

description: snap-frozen tissue


title: follicular adenoma_FA8

description: snap-frozen tissue


title: follicular adenoma_FA4

description: snap-frozen tissue


title: follicular adenoma_FA9

description: snap-frozen tissue


title: follicular adenoma_FA5

description: snap-frozen tissue


title: Ras-expressing Replicate 1

city: Stockholm

first: Ulrich

last: Theopold

address: Svante Arrhenius Laboratories 20c

department: Molecular Biology and Functional Genomics

country: Sweden

institute: Stockholm University

description: Sample 4

data_processing:
Base conversion was done using Illumina’s OLB v1.9.
Reads were mapped to Drosophila_melanogaster.BDGP5.25.64.gtf using Tophat v1.0.14 (Trapnell et al, 2009)
Cufflinks v0.0.5 was used to calculate FPKM values
Cuffcompare and Cuffdiff were used to calculate the differential gene expression between the samples
Cufflinks, Cuffcompare and Cuffdiff were run using Galaxy (https://main.g2.bx.psu.edu/root)
Genome_build: Drosophila_melanogaster.BDGP5.25.64.gtf (Release 5 http://www.ncbi.nlm.nih.gov/assembly/GCF_000001215.2/)
Supplementary_files_format_and_content: The .txt files report gene expression data [output files of Cufflinks].
Supplementary_files_format_and_content: The .xls files report differential gene expression [output files of Cuffdiff].  The .xls files are linked to the Series record as supplementary files.

organism: Drosophila melanogaster

source_name: Fat body

growth_protocol: yeast-potato meal

extract_protocol: RNA extraction: fat body tissues collected in Trizol (Invitrogen Cat. no.:10296-028), wortex and and freeze at -80C. After thawing the Qiagen RNeasy Mini Kit (Cat. no.: 74104) was used to prepare RNA. Qiagen DNase for DNA degradation and subsequent purification was applied. Multiplex library was constructed for mRNA sequencing using Illumina adaptors and subjected to HiSeq2000 sequencing.

treatment_protocol: no treatment

value: offsprings of Bx Gal4 x UAS-RAS V12

value: wandering larvae

tag: genotype/variation

value: Ras-expressing

value: fat body


title: Control Repl3A

description: Sample 3A

data_processing:
Base conversion was done using Illumina’s OLB v1.9.
Reads were mapped to Drosophila_melanogaster.BDGP5.25.64.gtf using Tophat v1.0.14 (Trapnell et al, 2009)
Cufflinks v0.0.5 was used to calculate FPKM values
Cuffcompare and Cuffdiff were used to calculate the differential gene expression between the samples
Cufflinks, Cuffcompare and Cuffdiff were run using Galaxy (https://main.g2.bx.psu.edu/root)
Genome_build: Drosophila_melanogaster.BDGP5.25.64.gtf (Release 5 http://www.ncbi.nlm.nih.gov/assembly/GCF_000001215.2/)
Supplementary_files_format_and_content: The .txt files report gene expression data [output files of Cufflinks]. The merged .txt file is identical to that linked to Sample 'Control Repl3B (re-sequenced)'.
Supplementary_files_format_and_content: The .xls files report differential gene expression [output files of Cuffdiff].  The .xls files are linked to the Series record as supplementary files.

value: offsprings of Bx Gal4 x W1118

value: Control


title: Ras-expressing Replicate 2

description: Sample 5


title: Control Repl3B (re-sequenced)

description: Sample 3B [i.e., re-sequenced sample]

data_processing:
Base conversion was done using Illumina’s OLB v1.9.
Reads were mapped to Drosophila_melanogaster.BDGP5.25.64.gtf using Tophat v1.0.14 (Trapnell et al, 2009)
Cufflinks v0.0.5 was used to calculate FPKM values
Cuffcompare and Cuffdiff were used to calculate the differential gene expression between the samples
Cufflinks, Cuffcompare and Cuffdiff were run using Galaxy (https://main.g2.bx.psu.edu/root)
Genome_build: Drosophila_melanogaster.BDGP5.25.64.gtf (Release 5 http://www.ncbi.nlm.nih.gov/assembly/GCF_000001215.2/)
Supplementary_files_format_and_content: The .txt files report gene expression data [output files of Cufflinks]. The merged .txt file is identical to that linked to Sample 'Control Repl3A'.
Supplementary_files_format_and_content: The .xls files report differential gene expression [output files of Cuffdiff].  The .xls files are linked to the Series record as supplementary files.


title: Ras-expressing Replicate 3

description: Sample 6


title: follicular adenoma_FA2

description: snap-frozen tissue


title: follicular adenoma_FA1

description: snap-frozen tissue


title: follicular thyroid carcinoma_FTC14

description: snap-frozen tissue


title: Control Repl2

description: Sample 2


title: Control Repl1

description: Sample 1


title: TFIIS_RNAi_3NT_AB_(20120921_12_4_4)

status: Public on Mar 06 2014

city: Seattle

first: Jorja

last: Henikoff

state: WA

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

description: 3' position of nascent transcript (3'NT) from cells treated with dsRNA targeting TFIIS. Replicates A and B.

data_processing: 1. We obtained  Drosophila_melanogaster.BDGP5.68.ncrna.fasta from BDGP and trimmed each entry to the last 35nt. 2. We used Bowtie (0.12.7 - Sep 7 2010) to align 25bp single-end reads against the last 35bp of the ncRNA file. 3. We used Bowtie to align unmapped reads from 2. to release r5.30 (Jul 2010) of the D.melanogaster genomic sequence obtained from FlyBase. If a read was mapped to multiple locations, one location was picked at random.  4. We extracted properly aligned reads (Supplementary files .bed) 5. We separated reads mapped to the forward and reverse strands and combined aligned reads from replicates A and B (Supplementary file AB.wig).

source_name: Other

extract_protocol: Drosophila S2-DRSC cells were obtained from the Drosophila Genomics Resource Center (Stock #181) and only passages 10-20 were used for experiments.  Cells were cultured in Schneider's media supplemented with 10% heat inactivated FBS at 25 degrees C, with an ~30hr doubling time.  dsRNA was synthesized using NEB reagents and protocols from PCR templates containing the T7 promoter sequence.  PCR primers were as follows: H2Av Forward (5'- TAATACGACTCACTATAGGGCGAAACCGAATTCCGTAGAA - 3') H2Av Reverse (5- TAATACGACTCACTATAGGGAGTAGGCCTGCGACAGA -3'), YL-1 (DRSC02765) and TFIIS control (PMID: 15629721). To administer dsRNA, 2.5 x 10^6  log phase cells / cm^2  surface area were brought up in Schneider's without FBS (0.1mL/cm^2) and seeded in 150cm^2 flasks.  30 microg dsRNA/1x10^6  cells was incubated with cells for 1 hour with intermittent mixing.  After incubation with dsRNA, an equal volume of Schneider's with 20% FBS was added and cells were grown for 96 hours before harvesting.  We modified protocols from  (PMID: 20007866; PMID: 22343941, 2012; PMID: 11340173) to fractionate cells and isolate nascent RNA.  dsRNA treated cells were harvested and pelleted by centrifugation for 1' at 1,000 x g at 4 degrees C.  Cells were quickly washed with 2mL ice cold PBS supplemented with 10 microg/mL alpha-Amanitin to inhibit transcription, split into two separate 2ml tubes, and then pelleted by centrifugation 3' at 3,000 x g.  The cells were then lysed in 0.9mL ice cold Buffer A (1microl/mL SUPERase*In, protease inhibitor (Roche), 10mM Hepes 7.9, 10mM KCl, 3mM MgCl2, 0.34M sucrose, 10% glycerol, 1mM DTT, 0.1% Triton X-100) supplemented with 10microg/mL alpha-Amanitin, 8' on wet ice with intermittent mixing.  Nuclei were then pelleted as before and brought up in 0.9mL buffer B (1microl/mL SUPERase*In 9mM EDTA, 0.2mM EGTA, 1mM DTT, protease inhibitor (Roche), 0.1% Triton X-100) 15' on wet ice, and repeated 2x or until nuclei lyse.  The chromatin pellet was then brought up in 0.9mL buffer B+ (1microl/mL SUPERase*In, 20mM EDTA, 0.2mM EGTA, 2mM spermine, 5mM spermidine, 1mM DTT, protease inhibitor (Roche)) and washed 3x.  The final insoluble pellet was brought up in 1mL Buffer B+.  The two pellets from the same original flask were pooled and dissolved in 10mL Trizol and RNA was isolated according to manufacturer's instructions. Nascent RNA was treated with DNase (RQ1, Roche) and extracted with acid phenol and ethanol precipitated with GlycoBlue and 0.3M NaOAc.  We selected for the presence of a 5' cap using Terminator 5'-Phosphate-Dependent Exonuclease (Epicentre), as described (PMID: 20007866). Nascent, capped RNA was purified with acid phenol as before. Libraries were constructed as described for NET-seq (Churchman and Weissman, 2012) with the following modifications.  Ligated RNA was digested with pH 10.3 alkaline fragmentation buffer for 30'.  Reverse transcriptase primer concentration was reduced to 1.09 microM in RT reaction mix.  Libraries were amplified with KAPA HiFi under limiting cycles.  Following amplification, PCR reactions were purified with AMPure XP beads at a 1:1 ratio before PAGE purification to aid in the elimination of empty products.  Biological replicates were sequenced for each condition.

tag: cell line


title: GFP_RNAi_MNase_AB_(20120606_77_12_5)

description: Chromatin digested to mostly mononucleosomes (~80%) from cells treated with dsRNA targeting GFP. Replicates A and B.

data_processing: 1. We used Bowtie (0.12.7 - Sep 7 2010) to map paired-end 25bp reads to release r5.30 (Jul 2010) of the D.melanogaster genomic sequence obtained from FlyBase. If a read was mapped to multiple locations, one location was picked at random 2. We extracted properly paired reads (Supplementary files .bed) 3. For each base pair in the genome, we counted the number of paired-end fragments aligned over it. 4. We normalized base pair counts by dividing by the total number of counts for all base pairs and then multiplying by the total number of base pairs in the genome.  5. We selected insert fragments 76-150 base pairs in length, repeated steps 3. and 4. and made a combined file of two replicates (Supplementary file AB.wig).

source_name: MNased chromatin

extract_protocol: Drosophila S2-DRSC cells were obtained from the Drosophila Genomics Resource Center (Stock #181) and only passages 10-20 were used for experiments.  Cells were cultured in Schneider's media supplemented with 10% heat inactivated FBS at 25 degrees C, with an ~30hr doubling time.  dsRNA was synthesized using NEB reagents and protocols from PCR templates containing the T7 promoter sequence.  PCR primers were as follows: H2Av Forward (5'- TAATACGACTCACTATAGGGCGAAACCGAATTCCGTAGAA - 3') H2Av Reverse (5- TAATACGACTCACTATAGGGAGTAGGCCTGCGACAGA -3'), and GFP control (PMID: 16204180). To administer dsRNA, 2.5 x 10^6  log phase cells / cm^2  surface area were brought up in Schneider's without FBS (0.1mL/cm^2) and seeded in 25cm^2 flasks.  30microg dsRNA/1x10^6 cells was incubated with cells for 1 hour with intermittent mixing.  After incubation with dsRNA, an equal volume of Schneider's with 20% FBS was added and cells were grown for 96 hours before harvesting.  Cells were pelleted 2' at 600 x g, washed with 5mL RT PBS, and centrifuged 2' at 600 x g.  Cells were resuspended in 1.9mL ice cold HM2 (10mM Hepes pH 7.4, 2mM MgCl2, 0.5mM PMSF), incubated 2' on ice, and lysed with 0.6% NP-40 with intermittent pipetting for 5' on ice.  Nuclei were centrifuged 10' at 100 x g at 4°C and washed with 1mL HM2 and centrifuged 5' at 100 x g at 4 degrees C.  Nuclei were brought up in 150microl HM2, warmed to 37 degrees C for 2', CaCl2 was added to 1mM, and digested with 0.066U MNase.  50 microl aliquots were taken out and terminated with 5mM EDTA on ice after 5', 10', and 15'.  Time-points that were similarly digested to mostly mononucleosomes (~80%) were sequenced using a protocol similar to PMID: 22025700 with modifications. We used the TruSeq oligo design to enable barcoding of libraries and modified AMPure XP to sample ratio to 1:1 to accommodate longer adapter sequences.  Biological replicates were sequenced for each condition.


title: H3K27ac_chambers_ChIP-seq

first: Vincent

middle: M.

last: Christoffels

state: N/A (NA)

address: Meibergdreef 15  K2-159

department: Medical Biology

institute: Amsterdam UMC

description: Sample run through SOLiD wildfire

data_processing:
Reads were then processed and aligned to the mouse reference genome (NCBI Build 37, mm9) using bowtie for SOLiD (1.1.2), allowing a maximum of two mismatches. The resulting BAM files were converted to SAM files using the SAMTools package. To generate the bed files, peaks were called on the SAM file using the OccuPeak method (submitted for publication). The Wig files were created using the MACS application (1.0.1) in Galaxy and subsequently converted to bigWigs using the Wig-to-bigWig application(1.1.0) in Galaxy.
Genome_build: mm9
Supplementary_files_format_and_content: H3K27ac_chambers_e10.5_mouse.bigWig and H3K27ac_avc_e10.5_mouse.bigWig are bigWig files visualizing the H3K27ac chromatin mark in chamber myocardium and atrioventricular canal myocardium respectively. H3K27ac_chambers_e10.5_mouse.bed and H3K27ac_avc_e10.5_mouse.bed are bed files containing peaks called with the OccuPeak method (submitted for publication).

extract_protocol:
ChIP
Material was used for library preparation with standard SOLiD library construction kit for SOLiD sequencing (Applied Biosystems, #4443713, #4400413).

tag: strain background

value: FVB/N

value: Katushka+ EGFP+

tag: Stage

value: chambers

tag: chip antibody

tag: chip antibody vendor

value: Abcam

tag: chip antibody catalog #


title: H2Av_RNAi_3NT_AB_(20120921_34_5_5)

description: 3' position of nascent transcript (3'NT) from cells treated with dsRNA targeting H2Av. Replicates A and B.

extract_protocol: Drosophila S2-DRSC cells were obtained from the Drosophila Genomics Resource Center (Stock #181) and only passages 10-20 were used for experiments.  Cells were cultured in Schneider's media supplemented with 10% heat inactivated FBS at 25 degrees C, with an ~30hr doubling time.  dsRNA was synthesized using NEB reagents and protocols from PCR templates containing the T7 promoter sequence.  PCR primers were as follows: H2Av Forward (5'- TAATACGACTCACTATAGGGCGAAACCGAATTCCGTAGAA - 3') H2Av Reverse (5- TAATACGACTCACTATAGGGAGTAGGCCTGCGACAGA -3'), YL-1 (DRSC02765) and GFP control (PMID: 16204180). To administer dsRNA, 2.5 x 10^6  log phase cells / cm^2  surface area were brought up in Schneider's without FBS (0.1mL/cm^2) and seeded in 150cm^2 flasks.  30 microg dsRNA/1x10^6  cells was incubated with cells for 1 hour with intermittent mixing.  After incubation with dsRNA, an equal volume of Schneider's with 20% FBS was added and cells were grown for 96 hours before harvesting.  We modified protocols from  (PMID: 20007866; PMID: 22343941, 2012; PMID: 11340173) to fractionate cells and isolate nascent RNA.  dsRNA treated cells were harvested and pelleted by centrifugation for 1' at 1,000 x g at 4 degrees C.  Cells were quickly washed with 2mL ice cold PBS supplemented with 10 microg/mL alpha-Amanitin to inhibit transcription, split into two separate 2ml tubes, and then pelleted by centrifugation 3' at 3,000 x g.  The cells were then lysed in 0.9mL ice cold Buffer A (1microl/mL SUPERase*In, protease inhibitor (Roche), 10mM Hepes 7.9, 10mM KCl, 3mM MgCl2, 0.34M sucrose, 10% glycerol, 1mM DTT, 0.1% Triton X-100) supplemented with 10microg/mL alpha-Amanitin, 8' on wet ice with intermittent mixing.  Nuclei were then pelleted as before and brought up in 0.9mL buffer B (1microl/mL SUPERase*In 9mM EDTA, 0.2mM EGTA, 1mM DTT, protease inhibitor (Roche), 0.1% Triton X-100) 15' on wet ice, and repeated 2x or until nuclei lyse.  The chromatin pellet was then brought up in 0.9mL buffer B+ (1microl/mL SUPERase*In, 20mM EDTA, 0.2mM EGTA, 2mM spermine, 5mM spermidine, 1mM DTT, protease inhibitor (Roche)) and washed 3x.  The final insoluble pellet was brought up in 1mL Buffer B+.  The two pellets from the same original flask were pooled and dissolved in 10mL Trizol and RNA was isolated according to manufacturer's instructions. Nascent RNA was treated with DNase (RQ1, Roche) and extracted with acid phenol and ethanol precipitated with GlycoBlue and 0.3M NaOAc.  We selected for the presence of a 5' cap using Terminator 5'-Phosphate-Dependent Exonuclease (Epicentre), as described (PMID: 20007866). Nascent, capped RNA was purified with acid phenol as before. Libraries were constructed as described for NET-seq (Churchman and Weissman, 2012) with the following modifications.  Ligated RNA was digested with pH 10.3 alkaline fragmentation buffer for 30'.  Reverse transcriptase primer concentration was reduced to 1.09 microM in RT reaction mix.  Libraries were amplified with KAPA HiFi under limiting cycles.  Following amplification, PCR reactions were purified with AMPure XP beads at a 1:1 ratio before PAGE purification to aid in the elimination of empty products.  Biological replicates were sequenced for each condition.


title: H3K27ac_avc_ChIP-seq

description: Sample run through SOLiD wildfire

tag: tissue

value: atrioventricular canal


title: CSB∆N1 input DNA

city: Philadelphia

first: Jieun

last: Jeong

address: 3400 Civic Center Blvd

institute: The University of Pennsylvania

data_processing:
ChIP-seq reads were aligned to the hg19 genome assembly using bowtie 0.12.7 using option of -k 1 –m 1 --best --strata
Peaks were called using Homer with a default option
Genome_build: hg19
Supplementary_files_format_and_content: bed files were generated after peak calling

source_name: CSB∆N1 input DNA

extract_protocol:
Cells were collected in Buffer B (150 mM NaCl, 0.5 mM MgCl2, 20 mM HEPES pH7.8, 10% Glycerol, 0.5% Triton X-100) and soluble CSB was removed from nuclei by centrifugation at 1500 RPM for 5 min at 4°C.  The resulting cell pellets were subsequently fixed with 1% formaldehyde for 10 min at room temperature. Crossed-linked cells were sonicated at 40% amplitude (30 sec on, 90sec off, for 24 min total) using The Branson 101-135-126 Sonifier.  Chromatin IP (ChIP) was performed using monoclonal anti-CSB antibody against the N-terminal 507 amino acids (1B1),
To generate the library from ChIP experiments, ChIP-Seq Library Protocol with multiplexing was used. This protocol was developed before Illumina released its multiplex truSeq ChIP-seq kit, and the details can be found on http://ngsc.med.upenn.edu/. According to the protocol, 10 ng of ChIP DNA product was used to start the library construction.

tag: cell type

value: fibroblast


title: CSB input DNA

source_name: CSB input DNA


title: follicular adenoma_FA3

description: snap-frozen tissue


title: CSB∆N1 CHIP

source_name: CSB∆N1 CHIP


title: H2Av_RNAi_MNase_AB_(20120606_77_6_4)

description: Chromatin digested to mostly mononucleosomes (~80%) from cells treated with dsRNA targeting H2Av. Replicates A and B.


title: CSB CHIP

source_name: CSB CHIP


title: YL1_RNAi_3NT_AB_(20120921_56_6_6)

description: 3' position of nascent transcript (3'NT) from cells treated with dsRNA targeting YL-1. Replicates A and B.


title: M106A Input

city: Bethesda

first: Yuelin

middle: Jack

last: Zhu

state: MD

address: 9000 Rockville Pike

department: Genetics Branch, Center for Cancer Research

institute: NCI

description: lymphoblast

data_processing:
Basecalls performed using CASAVA version 1.9
ChIP-seq reads were aligned to the mm9 genome assembly using BWA 0.5.9-r26-dev
Data were filtered using the following specifications…
Peaks were called using in-house developed software Peakfinder (Sven Bilke).
Genome_build: mm9

source_name: 106A cell line

growth_protocol: Cell lines grown in IMDM/15% FBS/%1 L-Glut/%1 PenStrep. Cytokine independent.

extract_protocol:
ChIP was performed using a ChIP-IT kit from Active Motif (Carlsbad, CA), following the manufacturer’s recommended protocol with minor modifications as described in supplementary methods. Antibodies used were:  anti-H3K4me3 (17-614, Millipore), anti-H3K27me3 (07-449, Millipore), anti-V5 (R960-25, Life Technologies), anti-FLAG (M2. Sigma Aldrich) and anti RNA Polymerase II (CTD4H8, Santa Cruz).
ChIP DNA (10 ng) was end-repaired and phosphorylated using T4 polymerase, Klenow, and T4 Polynucleotide Kinase. An A-overhang was introduced using exo-Klenow and then ligated to Illumina paired-end adapters with DNA ligase. Ligated products were size selected on a Caliper LabChip XT to a mean size of 240bp +/- 20%. The libraries were amplified with Illumina PCR Primer InPE1.0, PCR Primer InPE2.0 and PCR Primer Indexes and sequenced on Illumina GAIIx or MiSeq sequencers under a single-end run protocol.

treatment_protocol: Cells were crosslinked with 1% formaldehyde at room temperature for 15 minutes. The cells were then sheared with a VirSonic 100 sonicator (VirTis) for 40 cycles of 10x 1-second pulses.

value: 106A cell line

value: Input

tag: sample type

value: Cytokine independent

tag: strain

value: NUP98-PHF23 pre-T LBL derived cell line

tag: source

value: NUP98-PHF23 pre-T LBL derived cell line, mouse 106


title: YFP-

city: New Haven

first: Taehyuk

last: Kang

state: CT

address: 300 George

department: Neurology

institute: Yale University

data_processing:
Validated libraries were applied to the 75 bp, paired end sequencing process of HiSeq 2500 (Illumina) to generate raw sequencing FASTQ data files.
The quality control check of FASTQ files was carried out by FastQC:ReadQC (version 0.52) analysis in Galaxy web-based platform.
The sequences passed on ‘per base sequence quality’ were mapped on the UCSC mm10 mouse genome (Dec. 2011 Mus musculus assembly (Genome Reference Consortium Mouse Build 38)) using Tophat-2.0.9 including Bowtie-2-2.1.0 and Samtools-0.1.18. As the option of library type in Tophat, ‘fr-unstranded’ for Illumina TruSeq protocol was set as the default and the option of ‘no-novel-juncs’ was chosen to quantify the reference annotation only.
Cuffdiff, a separate program of Cufflinks-2.1.1, analyzed the differentially regulated transcriptional level among the reference transcriptoms of our samples and the results were visualized and further manipulated by CummeRbund-2.12.
Genome_build: mm10
Supplementary_files_format_and_content: A xlsx file contains two spreadsheets containing FPKM value and normalized_count for all samples, respectively.

source_name: neurons

growth_protocol: Vegfr3YFP and Vegfr3YFP-negative cells were FACS-sorted from two separated groups of Vegfr3::YFP mice (16 mice/ each group; 12-30.105 Vegfr3YFP cells/group).

extract_protocol:
After an 18h-culture period, the cells were collected in eppendorf tubes, washed in PBS, and the total RNAs were extracted by Qiagen RNA Micro kit (QIAGEN, Valencia, CA).
The mRNA library construction were performed by SMARTer Ultra Low RNA Kit for Illumina Sequencing pherchased from Clontech Laboratory (Mountain View, CA) using manufacturer's protocol.

treatment_protocol: Vegfr3YFP  and Vegfr3YFP-negative cells were suspended in CCM were seeded in 24-well plates with or without VEGF-C (50ng/ml).

tag: cell population

value: Vegfr3 YFP negative

value: SGZ-originated Neurons

tag: culture period

value: 18 hrs


title: YFP+/Vegfc

source_name: Neural stem cells

value: Vegfr3 YFP positive

value: SGZ-originated Neural stem cells

tag: treated with

value: VEGF-C (50ng/ml)


title: YFP-/Vegfc


title: M106A H3K4me3

description: lymphoblast


title: M106A H3K27me3

description: lymphoblast


title: GFP_RNAi_3NT_AB_(20120921_12_4_4)

description: 3' position of nascent transcript (3'NT) from cells treated with dsRNA targeting GFP. Replicates A and B.


title: 961C H3K4me3

description: myeloblast

source_name: 961C cell line

value: 961C cell line

value: NUP98-PHF23 AML derived cell line

value: NUP98-PHF23 AML derived cell line, mouse 961


title: YFP+


title: 961C-V5 NP23

description: myeloblast


title: 961C Input

description: myeloblast


title: 748T Input

description: lymphoblast

source_name: 748T cell line

value: 748T cell line

value: NUP98-PHF23 pre-T LBL derived cell line, mouse 748


title: 961C H3K27me3

description: myeloblast


title: 748T H3K4me3

description: lymphoblast


title: YL1_RNAi_IN_AB_(20130308_55_5_4)

description: Chromatin digested to mostly mononucleosomes (~80%), extracted for ChIP with 80mM salt and needle, from cells treated with dsRNA targeting YL-1. Replicates A and B.

data_processing: 1. We used Novoalign (2.08.03 - Oct 17 2012) to map paired-end 50bp reads to release r5.30 (Jul 2010) of the D.melanogaster genomic sequence obtained from FlyBase. If a read was mapped to multiple locations, one location was picked at random 2. We extracted properly paired reads (Supplementary files .bed) 3. For each base pair in the genome, we counted the number of paired-end fragments aligned over it. 4. We normalized base pair counts by dividing by the total number of counts for all base pairs and then multiplying by the total number of base pairs in the genome.  5. We selected mapped insert fragments between 76 and 160 bps in length from two replicates A and B and repeated steps 3. and 4. (Supplementary file AB.wig).

source_name: Input

extract_protocol: Drosophila S2-DRSC cells were obtained from the Drosophila Genomics Resource Center (Stock #181) and only passages 10-20 were used for experiments.  Cells were cultured in Schneider's media supplemented with 10% heat inactivated FBS at 25°C, with an ~30hr doubling time.  dsRNA was synthesized using NEB reagents and protocols from PCR templates containing the T7 promoter sequence.  PCR primers were as follows: H2Av Forward (5'- TAATACGACTCACTATAGGGCGAAACCGAATTCCGTAGAA - 3') H2Av Reverse (5- TAATACGACTCACTATAGGGAGTAGGCCTGCGACAGA -3'), YL-1 (DRSC02765) and GFP control (PMID: 16204180). To administer dsRNA, 2.5 x 10^6  log phase cells / cm^2  surface area were brought up in Schneider's without FBS (0.1mL/cm^2) and seeded in 75cm^2 flasks.  30#g dsRNA/1x10^6  cells was incubated with cells for 1 hour with intermittent mixing.  After incubation with dsRNA, an equal volume of Schneider's with 20% FBS was added and cells were grown for 96 hours before harvesting.  Cells were pelleted 2' at 600 x g, washed with 10mL RT PBS, and centrifuged 2' at 600 x g.  Cells were resuspended in 4mL ice cold HM2 (10mM Hepes pH 7.4, 2mM MgCl2, 0.5mM PMSF), incubated 2' on ice, and lysed with 0.6% NP-40 with intermittent pipetting for 5' on ice.  Nuclei were centrifuged 10' at 100 x g at 4 degrees C and washed with 2mL HM2 and centrifuged 5' at 100 x g at 4 degrees C.  Nuclei were brought up in 450 microliters HM2, warmed to 37 degrees C for 2', CaCl2 was added to 1mM, and digested with 0.5U MNase for 10'. Following MNase digestion and termination with 5mM EDTA, nuclei were incubated for 30' on ice and then pelleted 5' at 400 x g at 4 degrees C and supernatant was saved on ice (S1).  Nuclei pellets were brought up in 600ul HE80 (10mM Hepes 7.4, 0.25mM EDTA, 80mM NaCl, 0.5mM PMSF) 15' on ice, and passed 4x through a 20ga needle and 4x through a 26ga needle to solubilize nucleosomes.  The soluble fraction was combined with S1 and clarified 2' at max speed.  An aliquot was set aside as input and 10 microliters H2Av antibody (Active Motif #39715) was incubated overnight on nutator.  Equlibrated Protein G Dynabeads were added for 3 hours to recover antibody and bound nucleosomes.  The beads were then washed at least 3x5' each with HE80.  DNA libraries were prepared using a protocol similar to PMID: 22025700 with modifications. We used the TruSeq oligo design to enable barcoding of samples and modified AMPure XP to sample ratio to 1:1 to accommodate longer adapter sequences.  Biological replicates were sequenced for each condition.


title: BRCA1_mono

city: Miami

first: Alessandro

last: Gardini

state: FL

address: 1501 NW 10 Avenue

department: Sylvester Comprehensive Cancer Center

institute: University of Miami

data_processing:
Image analysis: Firecrest (Illumina pipeline 1.9, default parameters)
base calling: Bustard (Illumina pipeline 1.9, default parameters)
alignment BOWTIE v 0.12.7 (default parameters)
tag density files bam2wig (from Biotoolbox)
Genome_build: hg 18
Supplementary_files_format_and_content: bigwig

extract_protocol: ChIP-Seq DNA Sample Prep Kit (Illumina, inc.)

value: anti-BRCA1 mouse monoclonal D-9


title: HUVEC_Pol II DMSO 24hr hypoxia replicate 1

city: 4-6-1, Komaba, Meguroku

first: Takahide

last: Kohro

state: Tokyo

country: Japan

institute: LSBM, RCAST

description: Chromatin IP against Pol II

data_processing:
Basecalls performed using CASAVA version 1.7
ChIP-seq reads were aligned to the hg18 genome assembly using bowtie version 1.0.0 with the default parameters.
Peaks were called using QuEST version with the following paramaters.
Positive region size (300), KDE bandwidth (30) for PPARd, Positive region size (600), KDE bandwidth (60) for PolII, Positive region size (1000), KDE bandwidth (100) for H3K27Ac. ChIP extension fold enrichment (3), ChIP to background fold enrichment (3) were commonly used for all conditions.
Genome_build: hg18
Supplementary_files_format_and_content: wig files were generated by QuEST which represent kernel density smoothed p values.

source_name: HUVECs

growth_protocol: Human umbilical vein endothelial cells (HUVECs) (Lonza, Basel, Switzerland) were cultured in EGM2MV medium (Lonza).  HUVECs were used within the first 6 passages.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: 3x10^6 HUVEC cells were plated in 15cm2 culture plate, and cultivated for 3 days.  HUVECs were treated with PPARβ/δ agonist (GW501516 100nM) and/or hypoxia (1%O2) for 24hours, then H3K27ac binding regions were identified.  Normoxia and DMSO was used as a control condition.

value: Human umbilical vein cells

tag: passage

value: within 6 passage

value: Pol II


title: HUVEC_Pol II PPARβ/δagonist 24hr hypoxia replicate 1

description: Chromatin IP against Pol II


title: 748T H3K27me3

description: lymphoblast

value: Cytokine independent

value: NUP98-PHF23 pre-T LBL derived cell line


title: YL1_RNAi_H2AvPD_AB_(20130308_55_11_12)

description: Native H2Av ChIP from cells treated with dsRNA targeting YL-1. Replicates A and B.

source_name: ChIPed chromatin, Active Motif H2Av pAb #39715

tag: antibody

value: Active Motif H2Av pAb #39715


title: 7298-2 Input

description: lymphoblast

source_name: 7298/2 cell line

value: 7298/2 cell line

value: Input

value: C57BL/6+C3H hybrid

value: SCL-LMO1 pre-T LBL derived cell line

value: SCL-LMO1 pre-T LBL derived cell line  Control cell line


title: HUVEC_Pol II PPARβ/δagonist 24hr normoxia replicate 1

description: Chromatin IP against Pol II


title: HUVEC_Pol II DMSO 24hr normoxia replicate 1

description: Chromatin IP against Pol II


title: GFP_RNAi_IN_AB_(20130308_55_1_7)

description: Chromatin digested to mostly mononucleosomes (~80%), extracted for ChIP with 80mM salt and needle, from cells treated with dsRNA targeting GFP. Replicates A and B.


title: 7298-2 H3K4me3

description: lymphoblast


title: H2Av_RNAi_H2AvPD_AB_(20130308_55_8_10)

description: Native H2Av ChIP from cells treated with dsRNA targeting H2Av. Replicates A and B.


title: HUVEC PPARβ/δ DMSO 24hr hypoxia replicate 1

description: Chromatin IP against PPARβ/δ

value: PPARβ/δ


title: H2Av_RNAi_IN_AB_(20130308_55_3_9)

description: Chromatin digested to mostly mononucleosomes (~80%), extracted for ChIP with 80mM salt and needle, from cells treated with dsRNA targeting H2Av. Replicates A and B.


title: HUVEC PPARβ/δ PPARβ/δagonist 24hr hypoxia replicate 1

description: Chromatin IP against PPARβ/δ


title: fibrospheresDerivedFromTAF4-/-_rep2

city: Illkirch

first: Igor

last: Martianov

address: 1 rue Laurent Fries

institute: IGBMC

data_processing:
Illumina Casava1.8 software was used for image analysis and basecalling.
Sequence reads mapped to reference genome mm9/NCBI37 using Tophat (Trapnell et al., 2009) v1.2.0 with bowtie v0.12.7.
Genome_build: mm9
Supplementary_files_format_and_content: The ReadCountPerGene.tsv file is a tab separated text file containing the raw read count and the normalized number of reads for each Ensembl Gene (Ensembl v61).

molecule: polyA RNA

source_name: TAF4-/- immortalized mouse embryonic fibroblasts.

extract_protocol: Libraries for high throughput DNA sequencing were created using “TruSeq™ RNA Sample Preparation v2 Kit” (Illumina). Briefly, mRNA was purified from 2 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). The libraries were loaded in the flow cell at 8pM concentration and clusters were generated in the Cbot and sequenced in the Illumina Hiseq 2500 as single-end 50 base reads. FASTQ files were generated with CASAVA v1.8.2.

tag: genotype

value: fibrosphere

tag: treatment

tag: genetic background


title: HUVEC PPARβ/δ DMSO 24hr normoxia replicate 1

description: Chromatin IP against PPARβ/δ


title: HUVEC PPARβ/δ PPARβ/δagonist 24hr normoxia replicate 1

description: Chromatin IP against PPARβ/δ


title: GFP_RNAi_H2AvPD_AB_(20130308_55_2_8)

description: Native H2Av ChIP from cells treated with dsRNA targeting GFP. Replicates A and B.

tag: cell line


title: fibrospheresDerivedFromTAF4-/-_rep1

value: immortalized mouse embryonic fibroblasts


title: HUVEC_H3K27Ac PPARβ/δagonist 24hr hypoxia replicate 1

description: Chromatin IP against H3K27Ac

tag: chip antibody


title: TAF4-/-_Confluent_rep1

value: confluent cells


title: TAF4-/-_Confluent_rep2


title: TAF4-/-_nonConfluent_rep2

value: non-confluent cells


title: HUVEC_Pol II PPARβ/δagonist 24hr hypoxia replicate 2

description: Chromatin IP against Pol II


title: HUVEC_H3K27Ac PPARβ/δagonist 24hr normoxia replicate 1

description: Chromatin IP against H3K27Ac


title: HUVEC_Pol II DMSO 24hr hypoxia replicate 2

description: Chromatin IP against Pol II


title: TAF4-/-_nonConfluent_rep1


title: HUVEC_Pol II PPARβ/δagonist 24hr normoxia replicate 2

description: Chromatin IP against Pol II


title: ARN_cl1_RA_72h_rep1

data_processing:
Illumina Pipeline v1.4 software was used for image analysis and basecalling.
The 16-base long reads (excluding the 4-base DpnII recognition site) were aligned to DpnII tag tables generated by Stowers Institute http://research.stowers-institute.org/microarray/tag_tables/index.html using Eland.
Genome_build: mm9
Supplementary_files_format_and_content: The NormalizedTagCountPerGenes.tsv file is a tab separated text file containing the normalized number of reads for each Ensembl Gene (Annotations from Ensembl Core v53_37f) .

extract_protocol: Sequencing libraries were prepared from 1 µg of total RNA using reagents from the DpnII Digital Gene Expression Tag Profiling kit (Part # 1003803 Rev. B protocol, Illumina). mRNA was captured on magnetic oligo(dT) beads and reverse transcribed into single-strand cDNA and double-stranded cDNA was then synthesized. The cDNA attached to the beads was digested using the restriction enzyme DpnII. A DpnII adapter was ligated to the DpnII cleavage sites. The adapter-ligated cDNA was then digested with MmeI to release 17bp fragments of cDNA from the magnetic bead. The fragments were dephosphorylated and purified by phenol-chloroform. A second adapter was ligated at the MmeI cleavage sites. The adapter-ligated cDNA fragments were amplified by PCR (30 sec at 98°C; [10 sec at 98°C, 30 sec at 60°C, 15 sec at 72°C] x 15 cycles; 10 min at 72°C) and the PCR products were purified on a 6% TBE PAGE gel. The 85 bp PCR products were excised from the gel and eluted overnight, followed by ethanol precipitation. DNA libraries were checked for quality and quantified using 2100 Bioanalyzer (Agilent).The libraries were loaded in the flowcell at 8pM concentration and clusters were generated following Illumina’s instructions. Libraries were sequenced on the Illumina Genome Analyzer II as single read 18 bases reads, following the manufacturer's protocols.

value: retinoic acid

tag: time


title: ARN_cl1_RA_72h_rep2


title: HUVEC_Pol II DMSO 24hr normoxia replicate 2

description: Chromatin IP against Pol II

value: Human umbilical vein cells


title: ARN_cl1_RA_12h_rep3


title: ARN_cl1_RA_12h_rep2


title: 7298-2 H3K27me3

description: lymphoblast


title: HUVEC PPARβ/δ PPARβ/δagonist 24hr hypoxia replicate 2

description: Chromatin IP against PPARβ/δ

value: within 6 passage


title: ARN_cl1_RA_12h_rep1


title: HUVEC PPARβ/δ DMSO 24hr hypoxia replicate 2

description: Chromatin IP against PPARβ/δ


title: HUVEC PPARβ/δ PPARβ/δagonist 24hr normoxia replicate 2

description: Chromatin IP against PPARβ/δ


title: ARN_cl1_12h_rep2


title: ARN_cl1_12h_rep1


title: HUVEC_H3K27Ac DMSO 24hr hypoxia replicate 2

description: Chromatin IP against H3K27Ac


title: HUVEC_H3K27Ac PPARβ/δagonist 24hr normoxia replicate 2

description: Chromatin IP against H3K27Ac


title: MuscleT_RNASeq

city: xiamen

first: zeng

last: zhen

address: daxue road

country: China

institute: xiamen university

description: T RNA library

data_processing:
Cleanning raw reads use perl script to produce clean reads
Mapping clean reads onto reference use tophat
Calculatint gene RPKM use perl script
Screenning diff genes use perl script
Put on GO and KEGG annotation use perl script
Genome_build: oyster.gene.cds.reference.fasta
Supplementary_files_format_and_content: tab-delimited excel of RPKM;

organism: Magallana angulata

source_name: muscles

growth_protocol: The diploid oysters were obtained on diploid×diploid crosses while the triploid oysters were obtained by chemically-induced retention of polar body II  on the same genitors. All of these oysters were maintained for one year, using the same temperature and food availability conditions

extract_protocol:
Use oligo dt to extract samples mRNA
The DGE libraries were prepared using Illumina Gene Expression Sample Prep Kit. Single-chain molecules were fixed onto a Solexa Sequencing and sequenced by Illumina HiSeq™ 2000 System

value: Adductor muscles

tag: tissue type

value: Triploid oyster


title: STLOHI

first: Joe

last: Craft

address: 300 Cedar St.

department: Immunobiology

data_processing:
Bustard was used for basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using bowtie v0.12.8 with parameters  -q -n 2 -m 1 -p 8 -t
Gerald was used for sequence analysis, and ELAND was used to sequence alignment
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: spleen

extract_protocol:
Spleens were removed at 8 days post-LCMV infection. Cells were sorted based on CD4+CD44+ Ly6c and PSGL-1 expression (LO LO ,LO HI, and HI HI, respectively). RNA was isolated using Qiazol reagent and miRNeasy kit. Sample preparation and Illumina HiSeq 2000 sequencing was conducted at the Yale Center for Genomic Analysis.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: 8 days post-infection

value: CD4+CD44+Ly6cLO PSGL-1HI


title: MuscleDM_RNASeq

description: DM RNA library

tag: tissue

value: Diploid oyster


title: STLOLO

description:
alldiff_nonovel.txt
LOLOdiff_nonovel.txt

tag: cell type

value: CD4+CD44+Ly6cLO PSGL-1LO


title: WTLOLO

value: WT


title: WTHIHI

value: CD4+CD44+Ly6cHI PSGL-1HI


title: WTLOHI


title: MuscleDF_RNASeq

description: DF RNA library


title: H3K9ac 14-16 hr OR embryo D.melanogaster ChIP Rep2

status: Public on Mar 05 2014

city: Boston

first: Peter

middle: J

last: Park

state: MA

address: 10 Shattuck St

department: Center for Biomedical Informatics

institute: Harvard Medical School

data_processing: SPP Peak calling protocol. The aligned reads were called using SPP R package (ver.1.10, Kharchenko et al., Nat.Biotech 2008). The binding characteristics and tag shift were estimated using SPP get.binding.characteristics() function. The reads showing abnormality were removed using SPP remove.local.tag.anomalies() function. The regions of enrichment were identified as continuous blocks of positions that exhibit significant enrichment of IP over input reads. The significance of enrichment was assessed within a 1Kb window around each point using a Poisson model. A position was considered significantly enriched if the number of IP read counts was significantly higher (Z-score > 3) than the number of input read counts, after adjusting for the total number of reads sequenced in IP and input measurements.

source_name: H3K9ac 14-16 hr OR Emb ChIP expt.2488

extract_protocol:
Flies are grown in population cages. After the larvae mature into flies in the inoculated tubs, the flies are transferred to the population cages. The adult flies are raised over a 22-day cycle, with cycles overlapping so that when one adult population has become less productive, another is ready to take its place.
Embryos not older than 16h were collected, bleached in 2.5-3.0% Na-hypochlorite solution, washed two times in cold EWB. Incubated with freshly made 1.8% formaldehyde in X-linking buffer in the presence of of n-heptane.After incubation, embryos were re-suspended in Stop solution Washed at +40C in ChIP wash A solution and then at +40C in ChIP wash B. After sedimentation of the embryos ChIP wash B solution was removed and the embryos were used in an experiment or frozen in liquid N2.
1. Add 30ml of PAS (50% suspension in RIPA (-PMSF)) to 500ml of crosslinked chromatin. Incubate 1h at +40C. 2. Spin suspensions for 2min at top speed +40C. Transfer supernatants to new tubes. Add 5ml of 100mM PMSF solution in isopropanol to each 500ml aliquot of precleared chromatin. 3. Add appropriate amount of antibody to each reaction. Do not forget to set up no Ab control. Incubate for 15 hours at +40C on rotating weel. 4. Add 40ml of PAS (50% suspension in RIPA (-PMSF)), incubate 3h at +40C on rotating weel. 5. Wash the beads 5 times 10min each with 1ml of RIPA, then one time with 1ml of LiCl ChIP buffer and finally twice with 1ml of TE. To pellet the beads between washes spin samples for 20sec +40C at top speed. Do all the washes at +40C. 6. Resuspend the beads in 100ml TE add 1ml (final 50mg/ml) of RNAse A (10mg/ml) incubate 30min at +370C. 7. Add 7.5ml (final 0.5%) of 10% SDS and 3.8ml (final 0.5mg/ml) of Proteinase K (20mg/ml). Incubate overnight at +370C. 8. Transfer samples at +650C, incubate 6h. 9. Add 4.5ml of 5M NaCl (140mM final). Extract samples with 150ml of phenol-chloroform by vortexing for 30 sec, centrifuge for 10 min at RT, take 120ml of aqueous phase, back-extract organic phase with 150ml of TEN 140 (10mM Tris-HCl pH8.0; 1mM EDTA; 140mM NaCl). Take 150ml of aqueous phase. Combine aqueous phases (you will get 120ml + 150ml=270ml of solution). 10. Extract samples with 300ml of chloroform by vortexing for 30 sec, centrifuge for 5 min at RT. Transfer the upper aqueous phase into the new tube. Add 30ml of 3M NaAc pH 5.0 and 2ml of glycogen (5mg/ml) to aqueous phase. Precipitate DNA with 900ml of EtOH at -700C for 1h. 11. Spin for 10min, top speed at +40C. Wash the pellet in 300ml of 70%EtOH 12. Spin for 10min, top speed at +40C. If you plan to do qPCR analysis only dissolve the pellet in 150ml of pure H2O. If you plan to do both qPCR and microarray hybridization then first dilute DNA pellets in 12ml of pure H2O transfer 4ml of DNA solution to a new eppendorf tube and add 46ml of pure H2O. Use the latter for qPCR and the former for subsequent amplification and labeling. Store DNA solutions at -200C. 13. Prepare dilutions of DNA isolated from the original crosslinked chromatin (also called ?Input DNA? or simply ?Input?) following the chart below. Use the stock with concentration of 0.5% of input DNA per ml of solution (see: ?Isolation of ChIP Input DNA? protocol).
Protocol for making libraries for ChIP-seq with Illumina platform, using the TruSeq DNA Sample Prep Kit. http://www.illumina.com/products/truseq_dna_sample_prep_kit.ilmn

tag: developmental stage

value: Embryo 14-16hr OR

value: wild type


title: H3K9ac 14-16 hr OR embryo D.melanogaster ChIP Rep1

source_name: H3K9ac 14-16 hr OR Emb ChIP expt.1911

tag: strain


title: H3K9ac 14-16 hr OR embryo D.melanogaster Input Rep1

description: Served as Input for: 1911.enrichment.clusters.gff3

source_name: H3K9ac 14-16 hr OR Emb Input expt.1912


title: H3K4me2-Abcam 14-16 hr OR embryo D.melanogaster ChIP Rep2

source_name: H3K4me2-Abcam 14-16 hr OR Emb ChIP expt.1959

value: Oregon-R (official name :Oregon-R-modENCODE)


title: H3K4me2-Abcam 14-16 hr OR embryo D.melanogaster Input Rep2

description: Served as Input for: 1959.enrichment.clusters.gff3

source_name: H3K4me2-Abcam 14-16 hr OR Emb Input expt.1962


title: H3K4me2-Abcam 14-16 hr OR embryo D.melanogaster ChIP Rep1

source_name: H3K4me2-Abcam 14-16 hr OR Emb ChIP expt.1976


title: H3K4me2-Abcam 14-16 hr OR embryo D.melanogaster Input Rep1

description: Served as Input for: 1976.enrichment.clusters.gff3

source_name: H3K4me2-Abcam 14-16 hr OR Emb Input expt.1815


title: ARN_cl1_12h_rep3

value: immortalized mouse embryonic fibroblasts


title: HUVEC PPARβ/δ DMSO 24hr normoxia replicate 2

description: Chromatin IP against PPARβ/δ

value: PPARβ/δ


title: HUVEC_H3K27Ac PPARβ/δagonist 24hr hypoxia replicate 2

description: Chromatin IP against H3K27Ac


title: Input DNA, empty vector infected cells (hev)

city: Milan

first: Francesco

last: Blasi

address: Via Adamello 16

country: Italy

institute: IFOM

data_processing:
FastQ files were filtered using fastX toolkit (version 0.0.13.2). The following filters were applied: trimming of nucleotides from the most right position if median quality score across reads smaller than 20 (Phred 33 code); clipping on both side if adapters were identified by fastqc; elimination of reads with more than 20% of nucleotide presenting a quality score below 20
ChIP-sequencing were aligned to the mm9 genome using bowtie 0.12.8. Configuration:maximum number of mismatches = 2; reports max 1 alignment; discard reads with more than 1 alignment
Duplicated reads were removed using samtools rmdup (version 0.1.18)
Peaks were called using MACS (version 1.4.0), with default parameters for Meis1 and Prep1. Only peaks with a p-val below 10e-06 were retained.
Genome_build: mm9
Supplementary_files_format_and_content: wig and bed files generated with bowtie and macs

source_name: Embryonic fibroblast

growth_protocol: Mouse embronic fibroblasts (MEFs) were taken from E14.5 Prep1 hypomorphic embros and cultured in DMEM supplemented with 10% FBS and 2mM L-glutamin. Mefs were passed every 2-3 days.

extract_protocol:
Lysates were clarified from sonicated nuclei and  Meis1-DNA  or Prep1-DNA complexes were isolated with specific antibodies.
Libraries were prepared according to Illumina's instructions accompanying the TruSeq ChIP Sample Prep Kit, 48 Samples-Set A Box, (part # 15034288).  Briefly, Input DNA (5-10 ng) was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 14 cycles. The resultant library fragments were ~300 bp. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the HiSeq 2000 following the manufacturer's protocols.

value: empty vector infected cells (hev)

tag: passages

value: Prep1 hypomorphic


title: Input DNA, Meis1-Prep1 overexpressing cells (hMP)

value: Meis1-Prep1 overexpressing cells (hMP)


title: Prep1_ChIPSeq, Meis1-Prep1 overexpressing cells (hMP)

value: Prep1(N-15X) (Santa Cruz Biotechnology, sc-6245X, lot# F2003)


title: Meis1/2_ChIPSeq, Meis1-Prep1 overexpressing cells (hMP)

value: Meis1/2 (Santa Cruz Biotechnology, sc-10599X, lot# C2912)


title: STHIHI


title: HUVEC_H3K27Ac DMSO 24hr normoxia replicate 2

description: Chromatin IP against H3K27Ac

value: Human umbilical vein cells

value: within 6 passage


title: Meis1/2_ChIPSeq, Meis1 overexpressing cells (hM)

value: Meis1 overexpressing cells (hM)


title: Meis1/2_ChIPSeq, empty vector infected cells (heV)

value: empty vector infected cells (heV)


title: Col #1

city: Columbus

first: Kengo

last: Morohashi

state: OH

address: 1060 Carmack Rd

department: Molecular Genetics

institute: The Ohio State University

description: Sample 9

data_processing:
CASAVA version 1.8.2 was used to generate fastq files and demultiplexing.
RNA-seq reads were aligned to the Arabidopsis thaliana genome assembly version TAIR10 using TopHat version 1.4.1 using the gff file version for TAIR10
Alignment files were compared for differential gene expression using the Cuffdiff option of the Cufflink program (version 1.0.3)
Genome_build: Arabidopsis thaliana genome assembly version TAIR10
Supplementary_files_format_and_content: gene_exp.diff are tabulator delimiter files generated with Cuffdiff. genes.fpkm_tracking tracks the summed FPKM of transcripts sharing each gene_id and gene_exp.dif tracks the results of tests

source_name: Col

growth_protocol: Arabidopsis thaliana plants (ecotype Col-0) were grown at 22°C and a 16-h photoperiod (65 μE m−2 s−1) on half-strength MS medium and 0.7 % plant tissue culture agar. Entire seedlings were collected at 10 days after sawing.

extract_protocol:
Three independent biological replicates were done. Total RNA was extracted using the RNeasy plant mini kit followed by DNaseI treatment (Qiagen). The RNA was subjected to DNaseI (Promega) treatment and tested by PCR to ensure no genomic DNA contamination. The preparation of mRNA-Seq libraries with bilogical duplicates was performed according to instructions from the Illumina mRNA-Seq sample preparation kit (15008136 Illumina).
According to manufactor's instruction (Illumina TruSeq RNA kit Part # 15008136 Rev. A)

tag: ecotype

tag: genotype/variation

value: 10d-old seedling


title: ibl1 mutant #1

description: Sample 7

source_name: ibl1 mutant


title: IBL1 overexpression #2

description: Sample 6

source_name: IBL1 overexpression


title: H3K9ac 14-16 hr OR embryo D.melanogaster Input Rep2

description: Served as Input for: 2488.enrichment.clusters.gff3

source_name: H3K9ac 14-16 hr OR Emb Input expt.1733


title: ibl1 mutant #2

description: Sample 8


title: Col #2

description: Sample 10


title: Reference Epigenome: ChIP-Seq Analysis of H3K27me3 in Human Small Bowel Tissue; renlab.H3K27me3.STL001SB.01.01

city: La Jolla

first: UCSD AND

last: SALK

state: CA

address: Health Sciences Drive

institute: University of California, San Diego

description:
sample_term_id: UBERON_0002108
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K27me3 in Human Small Bowel Tissue. Sequencing was done on the Illumina Genome Analyzer IIx platform.
Library name: AK224
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.12259
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.12250
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM915332_UCSD.Small_Intestine.H3K27me3.STL001.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27me3.STL001SB.01.01.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of Small Intestine H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27me3 ChIP-Seq on Small Intestine, Donor STL001, were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.13495
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 29,713,661
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 19
FINDPEAKS_SCORE: 0.0393
FINDPEAKS_PERCENTILE: 47
HOTSPOT_SCORE: 0.1736
HOTSPOT_PERCENTILE: 58
IROC_SCORE: 0.8051
IROC_PERCENTILE: 33
POISSON_SCORE: 0.3794
POISSON_PERCENTILE: 74
MAXIMUM_REPLICATE_CORRELATION: NA

**********************************************************************

ANALYSIS FILE NAME: GSM915332_UCSD.Small_Intestine.H3K27me3.STL001.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27me3.STL001SB.01.01.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of Small Intestine H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27me3 ChIP-Seq read mappings from Small Intestine, Donor STL001, were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.13615
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 8
BROWSER_TRACK_NAME: SI H3K27me3 01 24
BROWSER_TRACK_DESCRIPTION: UCSD Small Intestine Histone H3K27me3 Donor STL001 Library AK224 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 29,713,661
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 19
FINDPEAKS_SCORE: 0.0393
FINDPEAKS_PERCENTILE: 47
HOTSPOT_SCORE: 0.1736
HOTSPOT_PERCENTILE: 58
IROC_SCORE: 0.8051
IROC_PERCENTILE: 33
POISSON_SCORE: 0.3794
POISSON_PERCENTILE: 74
MAXIMUM_REPLICATE_CORRELATION: NA

**********************************************************************

source_name: Small Intestine tissue; renlab.H3K27me3.STL001SB.01.01

extract_protocol: Library construction protocol: See http://bioinformatics-renlab.ucsd.edu/RenLabLibraryProtocolV1.pdf

tag: sample alias

tag: sample common name

value: Small Intestine

tag: molecule

value: genomic DNA

tag: disease

value: Shin Lin, Stanford University

value: Primary Tissue

value: Autopsy

value: healthy, no prior medical history (NO diabetes, hypertension, coronary artery disease, cancer)

value: Male

value: Caucasian and African American

value: Histone H3K27me3

value: Biorupter

value: 500 micrograms

value: magnetic anti-rabbit

value: 5 micrograms

value: Active Motif


title: IBL1 overexpression #1

description: Sample 5


title: Reference Epigenome: ChIP-Seq Analysis of H3K27me3 in Human Sigmoid Colon Tissue; renlab.H3K27me3.STL001SG.01.01

description:
sample_term_id: UBERON_0001159
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K27me3 in Human Sigmoid Colon Tissue. Sequencing was done on the Illumina Genome Analyzer IIx platform.
Library name: AK230
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.12268
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.12265
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM915333_UCSD.Sigmoid_Colon.H3K27me3.STL001.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27me3.STL001SG.01.01.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of Sigmoid Colon H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27me3 ChIP-Seq on Sigmoid Colon, Donor STL001, were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.13508
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 28,105,704
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 19
FINDPEAKS_SCORE: 0.0208
FINDPEAKS_PERCENTILE: 37
HOTSPOT_SCORE: 0.1442
HOTSPOT_PERCENTILE: 37
IROC_SCORE: 0.7158
IROC_PERCENTILE: 13
POISSON_SCORE: 0.3256
POISSON_PERCENTILE: 53
MAXIMUM_REPLICATE_CORRELATION: 0.97

**********************************************************************

ANALYSIS FILE NAME: GSM915333_UCSD.Sigmoid_Colon.H3K27me3.STL001.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27me3.STL001SG.01.01.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of Sigmoid Colon H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27me3 ChIP-Seq read mappings from Sigmoid Colon, Donor STL001, were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.13628
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 8
BROWSER_TRACK_NAME: SC H3K27me3 01 30
BROWSER_TRACK_DESCRIPTION: UCSD Sigmoid Colon Histone H3K27me3 Donor STL001 Library AK230 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 28,105,704
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 19
FINDPEAKS_SCORE: 0.0208
FINDPEAKS_PERCENTILE: 37
HOTSPOT_SCORE: 0.1442
HOTSPOT_PERCENTILE: 37
IROC_SCORE: 0.7158
IROC_PERCENTILE: 13
POISSON_SCORE: 0.3256
POISSON_PERCENTILE: 53
MAXIMUM_REPLICATE_CORRELATION: 0.97

**********************************************************************

source_name: Sigmoid Colon tissue; renlab.H3K27me3.STL001SG.01.01

value: Sigmoid Colon


title: ibh1 mutant #2

description: Sample 4

source_name: ibh1 mutant


title: IBH1 overexpression #1

description: Sample 1

source_name: IBH1 overexpression


title: IBH1 overexpression #2

description: Sample 2


title: Input DNA, Meis1 overexpressing cells (hM)

value: Meis1 overexpressing cells (hM)

value: Prep1 hypomorphic


title: BioMock_ChIPSeq

city: Torino

last: Neri

state: Italy

address: Via Nizza 52

institute: University of Torino

description: chromatin

data_processing:
Basecalls performed using CASAVA version 1.8
ChIP-seq reads were aligned to the mm9 genome assembly using Bowtie v0.12.7 using the following parameters : -q --max /dev/null -v 1  -S --sam-nohead -m 1
Data were filtered using the following specifications: duplicate reads were filtered out
Peaks were called using MACS v1.4.1 with the following setting: --gsize=mm --nolambda --bw=300 -p 1e-8
Genome_build: mm9
Supplementary_files_format_and_content: BED files of bound regions were calculated using MACS with respective control (biomock for bioMyc and IgG for Max) at pvalue 1E-8

source_name: ESC E14

extract_protocol:
Chromatin was extracted from crosslinked cells using SDS lysis buffer.
Chromatin was immunoprecipiate with specific beads and DNA was eluted and de-crosslinked.

tag: cell line background

value: embryonic stem cells (ESCs)

value: parental wild type

value: Dynabeads  MyOneTM Streptavidin T1

tag: chip antibody vendor

value: Invitrogen

tag: chip antibody cat. #


title: Max_ChIPSeq

description: chromatin

tag: chip antibody

value: anti-Max

value: santa cruz biotechnology


title: BioMyc_ChIPSeq

description: chromatin

value: a stable clone (of E14 mESCs) expressing Biotin-tagged Myc


title: Control-ChIP-Seq

data_processing:
CASAVA version 1.8.2 was used to generate fastq files and demultiplexing.
ChIP-seq reads were aligned to the TAIR9 genome assembly using Bowtie with a default parameters except three mismatch allowed.
The uniquely aligned data was subjected to perform the Model-based Analysis of ChIP-Seq (MACS) (version 1.4.0beta) for finding peaks (P<10-5, no duplicated fragments allowed).
Genome_build: TAIR9
Supplementary_files_format_and_content: MACS (version 1.4.0beta) generated BED files, 110328_c4_peaks.bed and 110328_c4_summits.bed, by comparison of IBL1-ChIP-Seq and Control-ChIP-Seq and WIG files,110328_c4_treat_afterfiting_all.wig.gz and 110328_c4_control_afterfiting_all.wig.gz for peak distributions of IBL1-ChIP-Seq and Control-ChIP-Seq, respectively.

source_name: Seedlings

growth_protocol: Arabidopsis thaliana plants (ecotype Col-0) were grown at 22°C and a 16-h photoperiod (65 μE m−2 s−1) on half-strength MS medium and 0.7 % plant tissue culture agar. Entire seedlings were collected at 10 days after sowing.

extract_protocol: ChIP DNA pooled from three independent ChIP experiments were subjected to end repair and A-base addition, followed by ligation with adapters, Mltplx_Short and Mltplx_Long (Dataset S7). Gel purified ligated libraries were amplified by Phusion Taq (New England Biolabs) with 18 cycles by using MltplxPCR1.0 and two different primers, PCR2.0_indx2 for IBH1OE or PCR2.0_indx6 for Col-0, respectively.

treatment_protocol: No treatment

tag: line

value: p35S::GFP (GFP OE)

value: 10d-old seedling

value: GFP

value: abcam


title: JAG-GFP replicate 2

city: NORWICH

first: Robert

last: Sablowski

state: Norfolk

address: The John Innes Centre

department: CDB

institute: JIC

data_processing:
Basecalls performed using CASAVA version 1.8
Sequenced reads were mapped to TAIR10 whole genome using SOAPv2 -r 0
CSAR (default parameter except backg=20) was used for the peak calling step
Genome_build: TAIR10
Supplementary_files_format_and_content: csv; significant binding sites

source_name: JAG-GFP

growth_protocol: Plants were grown under long day conditions (16 h light and 8 h dark) at 18° C day temperature and at 20° C night temperature at 80% humidity.

extract_protocol:
pJAG:JAG-GFP jag-2 and wild-type L-er control plants were used. 1300-1500 mg  (fresh weight) of inflorescence apices per sample were fixed in 35 ml fixation buffer (0.4 M sucrose, 10mM Tris pH 8, 1 mM EDTA pH 8.5, 1% formaldehyde, 100 µM PMSF) under vacuum for 20 min on ice. Cross-linking was stopped with 100 µM  glycine for 10 min on ice. After two washes with sterile water, the tissue was blotted dry and frozen in liquid nitrogen. Nuclei were purified as described [Gomez-Mena et al., 2005, Development 132: 429-438] and resupended in 1 ml of sonication buffer containing 500 mM Hepes, 150 mM NaCl, 5 mM MgCl2, 10% TRITON X-100 and ½ a tablet of protease inhibitor cocktail complete Mini, EDTA-free (Roche). Sonication was performed in a Bioruptor waterbath sonicator at 4°C (2 x 5 min high power level with 30 sec on/30sec off cycles) resulting in an average fragment size of 500 bp.  After centrifugation, the supernatant was mixed with 500 ul of immunoprecipitation buffer containing 0.5M Hepes, 150 mM NaCl, 5 mM MgCl2 , 10% TRITON X-100, 1 mg/ml BSA and 25 µl of anti-GFP µMACS Microbeads (Milteyi Biotec), incubated on ice for 30 min and loaded on a µ Column (Milteyi Biotec) that had been equilibrated with 200 µl immunoprecipitation buffer and placed into a magnetic µMACS separator (Milteyi Biotec). After washing twice with 400 µl and twice with 200 µl of immunoprecipitation buffer, then twice with 200 µl TE buffer (100 mM Tris pH 8, 10 mM EDTA pH 8), DNA was eluted once with 20 µl and twice with 50 µl of preheated (96° C) elution buffer containing 50 mM Tris pH8, 10 mM EDTA, 50 mM DTT and 1% SDS. 100 µl of TE-buffer and 9 µl of 25 mg/ml Proteinase K (Sigma) were added to the eluted samples and to the input control samples. Crosslinking was reverted in eluted and input samples at 37°C overnight, followed by addition of 9 µl of 25 mg/ml Proteinase K and 8 h incubation at 65° C, phenol-chloroform extraction and precipitation with ethanol overnight at -20° C. After washing in 70% EtOH, the air-dried DNA was resuspended in 100 µl PCR-grade water (Roche), purified using a PCR purification Kit (18104, Qiagen) and stored at -80° C.
Illumina TruSeq ChIP-Seq libraries (three pJAG: JAG-GFP replicates and three wild-type controls) were produced as described [Kaufmann et al, 2009, PLoS Biology 7: e90.]

value: jag-2, JAG:JAG-GFP

value: inflorescence tips (only unopened buds)


title: IBL1-ChIP-Seq

value: p35S::IBH1-GFP (IBH1OE)


title: JAG-GFP replicate 3


title: JAG wild-type replicate 2

source_name: JAG wild-type

value: wt


title: IgG-ChIPSeq

city: Nutley

first: Hai-Hui

last: Xue

state: NJ

address: 111 Ideation Way

department: Center for Discovery and Innovation

institute: Hackensack University Medical Center

data_processing:
Basecalls performed using Illumina Casava version 1.8
ChIP-Seq reads were mapped to mouse genome (mm9) using Bowtie v.0.12.5. Bowtie parameters allowed up to two mismatches per read.
Peak calling by MACS v.1.4.1. Peaks were called using bandwidth 300 bp;  P-value of 1.00e-10.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include positions (chr, start, end) and fold enrichment values for each identified peaks

source_name: mouse splenic CD8 T cells

extract_protocol:
CD8 T cells were then crosslinked, sonicated with Covaris instrument, and ChIP was done with either Tcf1 antibody or control IgG.  For control IgG, pre-immune rabbit serum that we obtained from a different antibody production project was used to match the anti-Tcf1 (which is unfractionated rabbit antiserum rather than IgG).The immunoprecipitated fragments were reverse-crosslinked and purified.
chromatin DNA fragments were end-repaired, and ligated with Illumina adaptors. The DNA was then PCR amplified with for 18 cycles and library fragments of 220-400 bp were purified from gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: CD8 T cells were isolated from wild-type C57BL/6 mice by negative selection (the target cells are thus untouched).

value: spleen

value: splenic CD8 T cells

value: rabbit IgG (pre-immune rabbit serum)


title: Tcf1-ChIPSeq

value: custom made antiserum for Tcf1


title: ibh1 mutant #1

description: Sample 3


title: FLER-DS13290

city: SEATTLE

first: John

middle: A

last: Stamatoyannopoulos

address: 2211 Elliott Avenue, 6th Floor

department: Genome Sciences

institute: Altius Institute / University of Washington

description: cultured erythroid cells derived from human fetal liver, replicate 2

data_processing:
Basecalls performed with Illumina RTA version 1.12.4.2
Illumina chastity filtered reads were aligned to the Human GRCh37/hg19 reference with bowtie version 0.12.7 with the following parameter equivalents: bowtie -p <nodes> -n 2 -m 1 --best --phred33-quals
Nucleotide cleavage signal was generated across the genome by summing the 5' read positions at each location where reads mapped , using the bedmap utility from the BEDOPS suite: https://github.com/bedops/bedops
per base bigWig files were generated with bedGraphToBigWig (UCSC)
FDR 1% Peaks were called with the Hotspot program: http://www.uwencode.org/proj/hotspot/ with the default configuration for 36mer mappability
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: Signal, bigWig; Peaks, bed

source_name: fetal livers cells

growth_protocol: FL cells (50–100-day gestation) were obtained from the fetal tissue repository (University of Washington Birth Defects Research Laboratory). MPB CD34+ cells and dissociated FL cells were cultured in an erythroid induction medium to generate adult- and fetal-type erythroid cells composed of Stemline hematopoietic stem cell growth and expansion medium (Sigma-Aldrich) supplemented with 2 mM L-glutamine, 1× penicillin/streptomycin, 0.1 mM MEM nonessential amino acids (all from Mediatech), 0.1 mM β-mercaptoethanol, 200 μg/mL iron-saturated transferrin,10 μM ethanolamine, 10 μg/mL insulin (all from Sigma-Aldrich), 6 U/mL erythropoietin, 50 ng/mL stem cell factor (both from Amgen, Thousand Oakes, CA), 20 ng/mL interleukin-3, 20 ng/mL interleukin-6, 40 ng/mL insulin-like growth factor-1, 10 ng/mL vascular endothelial growth factor (all from Peprotech, Rocky Hill, NJ), 5% protein-free hybridoma medium, 1 × insulin-transferrin–selenium (both from Invitrogen), and 1 × EX-CYTE (Millipore, Billerica, MA). At the end of the culture, cell composition was determined by flow cytometry. Fourteen days after culture, staining with anti-glycophorin-A antibody (DAKO, Glostrup, Denmark) revealed that ~50% of cells where erythroid cells, expressing glycophorin-A, FLERs were enriched to over 95% purity using MACS system as per the manufacturer's instruction (Miltenyi Biotec, Auburn, CA). The surface expression of CD71 or CD36 by glycophorin-A+ erythroblasts was also analyzed by flow cytometry using Fluorescein isothiocyanate-conjugated anti-CD71 or Allophycocyanin-conjugated anti-CD36 antibodies (both from BD Biosciences, San Jose, CA). Cells were acquired using FACScalibur (BD Biosciences), and the results were analyzed with Flowjo X (Tree Star Inc., Ashland, OR). Gatings were set according to isotype controls.

extract_protocol:
Refer to the Nuclei isolation section of John et.al. Current Protocols in Molecular Biology PMID: 23821440
Illumina TruSeq v2

value: Fetal (50–100-day gestation)

value: fetal liver derived erythroid cells

tag: replicate


title: IgG_ChIPSeq

description: chromatin

value: embryonic stem cells (ESCs)

value: parental wild type

value: anti-IgG


title: 9wk: 211

status: Public on Mar 04 2014

first: Matt

last: Cannon

address: 700 Children's Dr.

department: Center for Childhood Cancer

institute: Nationwide Children's Hospital

data_processing:
library strategy: Sequence of PCR amplification of bisulfite converted genomic DNA of numerous loci
We aligned all reads to the mouse genome and determined the methylation status of each CpG for every read covering this position using Bismark
We then error corrected the overlapping portion of the read using a custom perl script, keeping the base call with the highest base quality
We summarized methylation data using the bismark methylation_extractor and a custom perl script
We summarized data for each CpG using custom scripts in R
Genome_build: mm9
Supplementary_files_format_and_content: SerreLocusSpecificCountsNov2013.txt contains data from all samples. The first and second columns are the chromosome and base location. The following columns are data, with two consecutive columns per sample. The first is the total number of methylated reads at that position, and the second is the total number of reads at that position.
Supplementary_files_format_and_content: SerreLocusSpecificPercentsNov2013.txt contains data from all samples. The first and second columns are the chromosome and base location. The following columns are the percent methylation at each locus for each sample, with one column per sample.

source_name: maternal-Low fat_adult-Low fat

extract_protocol:
We extracted DNA from the liver of all 9-week-old males using the DNeasy Blood and Tissue kit (Qiagen Inc., Valencia, CA, USA).
We bisulfite treated 2 µg of DNA from each of the 40 liver tissues using the MethylCode Bisulfite Conversion kit (Invitrogen, Carslbad, CA, USA) and PCR amplified 22 loci. We pooled all PCR products generated from a single individual to prepare a sequencing library incorporating a unique barcode.

tag: age

value: nine weeks

tag: gender

value: male

tag: maternal diet

value: Low fat

tag: adult diet

tag: tissue

value: liver


title: 9wk: 208

source_name: maternal-Low fat_adult-High fat

tag: strain

value: High fat


title: 9wk: 207


title: 9wk: 209


title: 9wk: 210