title: BCL6

city: San Francisco

first: Huimin

last: Geng

address: 513 Parnassus Ave., MSB HSW 1201

department: Department of Laboratory Medicine

institute: UCSF

description: Sample 2

data_processing:
Counts: Raw image data were converted into base calls via the Illumina pipeline CASAVA version 1.7 with default parameters. All 36-bp-long reads were mapped to the reference human genome sequence, hg18, using Illumina’s ELAND aligner with the default parameters. Only reads mapping uniquely to the genome with not more than 2 mismatches were retained for downstream analysis.
Peaks: Peak detection was performed with the ChIPseeqer program (Giannopoulou and Elemento, BMC Bioinformatics 2011, 12:277) and annotated to genes and/or promoters based on hg18 refseq genes downloaded from the UCSC Genome Browser
Genome_build: hg18
Supplementary_files_format_and_content: wiggle track raw reads counts (bigWig files) and peak files (*wgl.bed files)

growth_protocol: OCI-Ly7 were grown in medium containing 90% Iscove’s (Cellgro, Manassas, VA), 10% fetal bovine serum (Gemini, Irvine,CA), and 1% penicillin/streptomycin (Invitrogen, Carlsbad, CA)

extract_protocol: Genomic DNA-fragment libraries were prepared using the Illumina ChIP-seq Library preparation Kit following the manufacture’s instructions (Illumina, CA). Briefly 10ng of purified ChIP DNA was end repaired by conversion of overhangs into phosphorylated blunt ends with the use of T4 DNA polymerase and E. coli DNA polymerase I Klenow fragment. Illumina single-end adapters were ligated to the ends of the DNA fragments. Ligation products were purified on a 2% agarose gel with a size selection of 200-300bp. Fifteen PCR cycles were performed with Illumina genomic DNA primers that anneal to the ends of the adapters. The purified PCR-amplified fragment libraries were quantified with the use of the PicoGreen dsDNA Quantitation Assay with the Qubit Fluorometer (Invitrogen, CA). The size range of libraries was validated on the Agilent Technologies 2100 Bioanalyzer with the High Sensitivity DNA Kit (Agilent, CA).

treatment_protocol: ChIP: OCI-Ly7 cells were fixed with 1% formaldehyde, lysed and sonicated to generate fragments less than 500bp. Sonicated lysates were incubated with antibodies overnight and after increasing stringency washes immunocomplexes were recovered and DNA was isolated.

value: OCI-Ly7 lymphoma cells

value: Bcl-6 Antibody (N-3)

tag: chip antibody host/amount

value: Rabbit poly/5ug

tag: chip antibody vendor

value: Santa Cruz

tag: chip antibody cat. #


title: input

status: Public on Jun 27 2013

type: SRA

state: CA

country: USA

description: Sample 3

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

tag: cell type


title: BACH2

description: Sample 1

tag: chip antibody

tag: chip antibody provider

value: developed by Melnick Lab


title: DG75-eGFP B

city: Würzburg

first: Florian

last: Erhard

address: Versbacher Str. 7

department: Institut für Virologie und Immunbiologie

country: Germany

institute: Julius-Maximilians-Universität Würzburg

description: crosslinked ribonucleoprotein complexes

library_source: transcriptomic

data_processing:
The 3' sequencing adapter sequence are trimmed from each sequencing read using a specially tailored sequence alignment variant that alignes a prefix of the adapter sequence to a suffix of each sequencing read.
Equal sequences are collapsed and mapped to the human genome (hg19), the KSHV genome (NC_009333.1) and the human transcriptome (Ensembl v60) using Bowtie version 0.12.7
Mapped reads are then submitted to PARma for cluster identification and microRNA assignment
Genome_build: hg19
Supplementary_files_format_and_content: BED files containing cluster positions

molecule: total RNA

source_name: B-cell line

extract_protocol:
A total of 3*10^8 cells per replicate were grown and treated with 4-thiouridine (Sigma) for 14 hours (final concentration 100 uM). Cells were pelleted and washed in cold PBS. Aliquotes of 5*10^7 cells were resuspended in 5 ml of cold PBS, placed in a 15 cm petri dish and irradiated at 365 nm with 100 mJ twice on ice, with 30 s break in between. Crosslinked cells were collected, pelleted and snap-frozen. PAR-CLIP was performed using 11A9 anti-Ago2 monoclonal antibody
PAR-CLIP

tag: cell line


title: Dscam isoforms Profiling for S2

city: Gießen

first: Andreas

last: Gogol-Döring

address: Wiesenstraße 14

department: MNI

institute: Technische Hochschule MIttelhessen

data_processing:
Library strategy: Circularization-Assisted Multi-Segment Sequencing
The bases were called from the raw images using the offline base caller OLB-1.9.0. Note that due to our special multiple-segment sequencing protocol, the control lane produced output only for the first segment which contained the barcodes. Therefore the quality values of the produced fastq files are not reliable.
The read files were demultiplexed according to the barcodes. The barcodes consist of two parts which are ligated during the circularization step and then sequenced as one segment. A read was only retained if both parts of the barcode matched to the same reference sequence with at most one mismatch.
The three exonic segments of each read were aligned separately to the drosophila melanogaster dscam exon sequences using bowtie2 (parameters: --very-sensitive-local -5 3). Only the reads for which all three segments could uniquely be mapped to exons from the respective cluster were retained.
Genome_build: dm3
Supplementary_files_format_and_content: The processed data files contain the number of reads for each combination of exon 4 (1..12), exon 6 (1..48) and exon 9 (1..33).

organism: Drosophila melanogaster

source_name: S2 cell line

extract_protocol:
total RNAs were extracted using Trizol reagent following manufacturer's protocol.
Libraries were prepared using customized pipeline for our Circularization-Assisted Multi-Segment Sequencing. In brief, first, using RT-PCR with the barcode-indexed primers targeting constitutive exon 3 and exon 10, Dscam mRNA was reverse-transcribed and amplified. After circularization of the 2kb RT-PCR products and another round of PCR with the primers targeting constitutive exon 7 and exon 8, the amplification product of approximately 1kb in length was then sequenced.

tag: sample type

value: cell line derived from embryonic hemocytes

tag: gene

value: Dscam


title: Cyst_24h_1

status: Public on Jun 28 2013

city: Stanford

first: Gretchen

middle: Marie

last: Ehrenkaufer

address: Grant S-143, 300 Pasteur Dr.

department: Microbiology and Immunology

institute: Stanford Uninversity

data_processing:
Primary analysis by SOLiD Instrument Control Software
Colorspace reads were trimmed to 35 bp to remove 3' end
Alignments were performed with Bowtie (version 0.12.7) with the parameters: -v 3 -m 1
FPKM values were calculated with Cufflinks (version 2.0.0)
Genome_build: Entamoeba invadens version 1.3 (http://amoebadb.org)
Supplementary_files_format_and_content: FPKM (Fragments Per Kilobase of transcript per Million mapped reads) data for all genes in each sample are listed in a single file

organism: Entamoeba invadens

source_name: E. invadens 24h cysts

growth_protocol: E. invadens was grown in LYI under standard axenic culture conditions

extract_protocol:
At each time point, parasites were harvested by chilling on ice, spun down, and washed 1x in cold PBS.  All samples were lysed using a French press at 400psi. Following lysis, RNA was isolated using Trizol (Invitrogen) following the manufacturer's protocol.
5µg total RNA was treated with Terminator enzyme (Epicentre) to degrade uncapped RNAs (60min at 30°C in 20µl total reaction), followed by heat inactivation for 10min at 65°C. Samples were diluted to 100µl in 1x DNAse buffer, and treated with DNAseI (Life Technologies) for 20min at room temperature. Samples were then purified using the Ribominus cleanup protocol (Life Technologies) and reanalyzed by the BioAnalyzer to determine the level of enrichment of mRNA. First-strand cDNA synthesis was performed using a modified version of the SMART porticol and 30ng of mRNA-enriched RNA as a template. Adaptors containing restriction sites for SfiI were incorporated into the cDNA using a template switching mechanism at the 5’ end of the RNA transcript. For SMART PCR amplification of first-strand cDNA, a SMART PCR primer was used to anneal to identical sequence regions on both the 3’ and 5’ adaptors. Following 20-24 cycles of PCR amplification using Advantage Taq (Clontech) according to manufacturer’s instructions samples were digested with SfiI (New England Biolabs) to remove the majority of adaptor sequences. Samples were purified using a nucelospin column (Macherey Nagel) to remove digested adaptors. Amplified, double stranded cDNA was used to prepare SOLiD fragment libraries according to the manufacturer's protocols (Life Technologies). Briefly, cDNA was fragmented by sonication on a Covaris S2 sonicator (Covaris ) and end-repaired in preparation for P1 and P2 adaptor ligation. Adaptors were ligated and the samples size selected and amplified by standard PCR. DNA was bound to SOLiD P1 beads and amplified by emulsion PCR, followed by enrichment for templated beads.
All libraries were sequenced on a SOLiD 4 sequencer (Life Technologies), to produce 50bp reads.

treatment_protocol: Encystation was induced by transfer of trophzoites to 47% LG (low glucose) media, and incubating for specified time (8, 24, 48 or 72 hours) at 25°C. Excystation was induced by harvesting mature (72 hour) cysts and incubating overnight in distilled water at 4°C. Cysts were then transferred to excysatation media (Mitra, B.N, et al.  (2010). Int J Parasitol 40, 751-760) for 2 or 8h at 25°C.

tag: isolation method

value: Lysis by French Press; RNA isolated using Trizol (Invitrogen)

tag: strain

tag: mrna enrichment

value: Terminator treatment (Epicentre), followed by cleanup on RiboMinus column (Invitrogen)

tag: Stage

value: 24 hour encysting parasites


title: Dscam isoforms Profiling for L1

source_name: whole fruit fly from 1st larval stage

value: whole fruit fly

tag: age

value: 24-36 h after egg laying


title: DG75-eGFP A

description: crosslinked ribonucleoprotein complexes


title: Dscam isoforms Profiling for Pupa

source_name: whole fruit fly from pupal stage

value: 0-48 h after puparium formation


title: Dscam isoforms Profiling for L3

source_name: whole fruit fly from 3rd larval stage

value: 96-108 h after egg laying


title: ARmo_100nM

city: Tampere

first: Janne

last: Seppälä

address: Biokatu 8

country: Finland

institute: Institute of Biomedical Technology

data_processing:
Illumina Genome Analyzer II base calling software
The raw reads alignment was carried out with Bowtie and the reads were mapped on the human genome version 19 (hg19). Two mismatches were allowed in the seed region of the read (-n 2), with the default seed length of 28 bp. Only the best alignment was chosen.
The peak detection (i.e., binding site detection) step of the ChIP-seq analysis was performed with the tool MACS 1.3.7. using the default p-value threshold (p=0.00001), high-confidence fold-enrichment of 10 (--mfold 10) for model building and approximately half of the maximum sonication size (--bw 175) for the cell line samples and p-value threshold of 0.0001 and --mfold 5 for the xenograft samples.
Genome_build: hg19
Supplementary_files_format_and_content: "pcDNA3.1/Armo/Arhi_pool_IgG_control" and "LuCaP_pool_IgG_control" were used as controls in peak detection in for cell line and xenograft samples, respectively. The file "high_confidence_ARBSs.bed" was created by using the peaks of ARmo_1nM, ARhi_1nM and pcDNA3.1_100nM

source_name: ARmo cell line

growth_protocol: The establishment of LNCaP cells overexpressing AR has been described previously (Waltering et al., 2009). Two PC xenografts, LuCaP69 and LuCaP73, grown in intact male mice, were provided by one of the investigators (RLV).

extract_protocol:
The chromatin was sonicated to reach a fragment size of 150-300 bp with Bioruptor UCD-200TM-EX instrument (Diagenode Inc., Liège, Belgium), diluted 1:10 in 1% Triton-X100, 2 mM EDTA, 20 mM Tris-HCl, 150 mM NaCl containing 2X protease inhibitor and precleared for 1 hour with 100 μg of yeast tRNA (Invitrogen Inc., Carlsbad, California, USA) and 20 μl of preimmune rabbit serum (Santa Cruz Inc., Santa Cruz, California, USA) followed by 1 hour incubation with 40 μl of 50% slurry of Gammabind Sepharose beads (GE Healthcare Bio-Sciences, Piscataway, New Jersey, USA) at 4°C. The beads were precipitated and 10 μg of normal rabbit IgG (Santa Cruz Inc., Santa Cruz, California, USA) or 10 μg of anti-AR (clone N20; Santa Cruz Inc., Santa Cruz, California, USA) or 10 μl of anti-AR polyclonal antibody (AR3) (provided by one of the authors: O. A. J.) (Karvonen et al., 1997, Thompson et al., 2006) were added to the supernatant for overnight incubation. The complexes were then incubated with 70 μl of Gammabind Sepharose beads (GE Healthcare Bio-Sciences, Piscataway, New Jersey, USA) 50% slurry for 4 hours and precipitated. The beads were washed sequentially for 10 min ach in TSE I (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl, and 150 mM NaCl), TSE II (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl, and 500 mM NaCl), and buffer III (0.25 M LiCl, 1% NP-40, 1% deoxycholate, 1 mM EDTA, and 10 mM Tris-HCl). Beads were then washed two times with TE buffer. The complexes were then eluted from the beads incubating for 15 minutes at 37°C twice with 1% SDS, 0.1 M NaHCO3. The eluates were pooled and treated for 1 hour at 37°C with RNAase A (Qiagen Inc., California, USA) and 1 hour with proteinase K (Finnzymes Oy, Espoo, Finland), then heated at 65°C for 6 3 hours to reverse the formaldehyde cross-linking. The DNA fragments were purified with a DNA purification kit (QIAquick PCR purification Kit, Qiagen Inc., California, USA) and eluted in 100μl of elution buffer. The libraries of ChIP DNA were prepared and sequenced with Genome analyzer II (Illumina Inc., San Diego, California, USA) according to the manufacturer’s protocol. Each sample was sequenced in one lane. The raw reads were obtained using Illumina analysis pipeline.
Standard illumina protocol
one sample per illumina lane

treatment_protocol: The cells were maintained under geneticin 250 μg/ml (Invitrogen Inc., Carlsbad, CA, USA). Four million cells were plated and hormone-deprived for 4 days and treated with DHT at different concentrations for 2 h. Cells were fixed by adding formaldehyde (Merck KGaA, Darmstadt, Germany) in 1% final concentration for 10 min at room temperature and lysed in 1% sodium dodecyl sulfate, 10 mM EDTA, 50 mM Tris–HCl containing 2X protease inhibitor (Roche Inc., Mannheim, Germany). To perform tissue ChIP, 3 ml of phosphate-buffered saline containing 2X protease inhibitor (Roche Inc.) were added to 40 × 20 μm sections of freshly frozen xenograft specimens. They were first vigorously mixed three times with syringe and 14G needle, then four times with 25G needle. The cells were fixed for 10 min in room temperature by adding 1/10 volume of fixation solution (11% formaldehyde, 0.1 M NaCl, 1 mM EDTA, 0.5 mM EGTA, 50 mM HEPES). Fixation was stopped by adding 1/20 volume of 2.5 M glycine for 5 min at room temperature. The cells were pelleted, washed twice in phosphate-buffered saline containing 2X protease inhibitor (Roche Inc.) and lysed as above. The chromatin was immunoprecipitated with 10 μg of normal rabbit immunoglobulin G (Santa Cruz Inc., Santa Cruz, CA, USA) or 10 μl of anti-AR polyclonal antibody (AR3) (provided by one of the investigators: OAJ).

value: LNCaP-ARmo

tag: ar overexpression

value: 2 - 4 fold

tag: dht treatment

value: AR


title: Dscam isoforms Profiling for L2

source_name: whole fruit fly from 2nd larval stage

value: 60-72 h after egg laying


title: Dscam isoforms Profiling for Adult Brain

source_name: Adult Brain

value: dissected adult brain

value: 1-3 days old female after eclosion


title: Dscam isoforms Profiling for Embryo

source_name: whole fruit fly from embryonic stage

value: 13-18 h after egg laying


title: input lysate Bach2 WT

city: Bethesda

first: Golnaz

last: Vahedi

state: MD

address: 9000 Rockville Pike Bldg 10 Rm 13C101A

department: NIAMS

institute: National Institutes of Health

description:
input lysate for reference control
RUN DATE: 7/6/2010

data_processing:
Sequence reads were obtained and mapped to the mouse mm9 genomes using bowtie allowing 2 mismatches and only uniquely mappable reads were reported.ChIP-seq were processed by MACS with  pvalue cutoff = 1.00e-05
Genome_build: mm9
Supplementary_files_format_and_content: ChIP-seq:  MACS-generated bed files

organism: Mus musculus

source_name: primary CD4+ T cells from spleen and lymph nodes

growth_protocol: Control and Bach2-deficient naïve CD4+CD44-CD25-CD62L+ T cells were isolated and sorted on the flow cytometer. Cells were cultured with plate-bound anti-CD3 and anti-CD28 (10 ug/ml each)either under: Th1conditions (IL-12 (20 ng ml) and anti-IL-4 neutralizing antibodies (10 μgml-1); Th2 conditions (IL-4 (20 ng ml-1) and anti-IFN-γneutralizing antibodies (10 μg ml-1); Th17 conditions (IL-6 (20 ng ml-1) plus human TGF-β1 (2 ng ml-1) and anti-IFN-γ neutralizing antibodies (10 μg ml-1) and anti-IL-4 neutralizing antibodies (10 μg ml-1)) or iTreg conditions(IL-2 (100 IU ml-1) plus human TGF-β1 (5 ng ml-1) for 3 days.

extract_protocol: Cells were chemically cross linked by 1% formaldehyde. Cell lysates were made by appropriate sonication and protein-DNA complexes were isolated with antibody.  Libraries were prepared according to Illumina's instructions. Briefly, DNA was end-repaired and the blunt, phosphorylated ends were treated with Taq polymerase 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 celland sequenced on HiSeq 2000.

tag: genotype/variation

value: wild type

value: in vitro polarized inducible regulatory cells for 3 days

tag: passages

value: FACS sorted naive CD4+T cells cultured in vitro for 3 days under iTreg condition

value: none (input lysate)


title: ChIP Bach2 WT

description:
Chromatin IP against Bach2
RUN DATE: 7/6/2010

value: anti-Bach2 - rabbit antibody (generated in-house, Tohoku University)


title: FANCD2_IP_UV treated

city: BOSTON

first: eunmi

last: Park

state: MA

address: 44 Binney street

institute: Dana-Farber Cancer Institute

data_processing:
Briefly, we mapped the reads with Bowtie version 0.12.7 to hg19 using the parameters -n 1 (which restricts the number of missmatches allowed in the alignment seed region to 1)  and -m 1 (which suppresses all alignments for a read if more than 1 alignment exists for that read in the genome).
For each report we generated we first use a program called "makeTagDirectory.pl" to prepare the read data for analysis by HOMER (e.g., it normalizes and provides basic QC).
Then we use a program called 'analyzeChIP-Seq.pl' in HOMER that automates the analysis by stringing the following functions (programs) together into a pipeline: Peak finding / Transcript detection / Feature identification (findPeaks)
Genome_build: mm9
Supplementary_files_format_and_content: HOMER Peaks Text files

source_name: FANCD2_IP_UV treated

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303).

treatment_protocol: UV treatment (30J), harvest post 3hour after UV treatment

value: human cell lines (kidney, embryonic)

tag: antibody


title: mRNA-iTreg Bach2KO3

description:
mRNA_seq
RUN DATE: 7/6/2010

data_processing:
RNA-seq:  Tophat and cufflinks. Sequence reads from each cDNA library were mapped onto the mouse genome build mm9 using tophat and the mappable data were then processed by Cufflinks (Trapnell et al.). The obtained data were normalized based on RPKM (reads per kilobase exon model per million mapped reads).
Genome_build: mm9
Supplementary_files_format_and_content: RNA-seq:  normalized rpkm files

extract_protocol: Total RNA was prepared from approximately 1 million cells by using mirVana miRNA Isolation Kit(AM1560, ABI). 200 ng of total RNA was subsequently used to prepare RNA-seq library byusing TruSeq SRRNA sample prep kit (FC-122-1001, Illumina) by following manufacturer’s protocol.The resulted libraries are sequenced using the Illumina HiSeq 2000. Only unique reads of 50 bp were mapped to the mouse genome (mm9) using Tophat and Cufflinks.


title: FANCD2_IP_UV untreated

source_name: FANCD2_IP_UV untreated


title: PU.1Ad-PU.1

city: Philadelphia

first: Joanna

middle: R

last: DiSpirito

state: PA

address: Smilow Center for Translational Research, 3400 Civic Center Boulevard

department: IDOM

institute: University of Pennsylvania

data_processing:
Solexa analysis pipeline.
For ChIP and input samples, reads were aligned to mm9 using Bowtie (version 0.12.8). Mapped reads had no more than two mismatches in their first 27 bp and redundant reads mapping to the same 5' position were removed.
Reads from both replicates were pooled prior to peak calling.
Peak calling was performed using the HOMER (v3.15) FindPeaks algorithm (default -factor settings, 0.1% FDR).
Genome_build: MGSCv37
Supplementary_files_format_and_content: BED files containing genomic locations and unique names of all peaks called in each ChIP experiment.

source_name: 3T3-L1 adipocyte, day 10, adeno-PU1 72hrs, PU.1 ChIP

growth_protocol: 3T3-L1 pre-adipocytes were maintained in DMEM (Hi glucose) + 10% FBS + 1% PennStrep. For differentiation, cells were grown to confluence and media was changed (day -2). Two days later (day 0), a DMI cocktail was added consisting of 1uM dexamethasone, 0.5mM 3-isobutyl-1-methylxanthine and 10ug/mL insulin. On day 2, media was changed to maintenance media + 10ug/mL insulin. On day 4, media was changed to maintenance media. By day 7, differentiation to mature adipocytes was considered complete and cells were infected with adenovirus.

extract_protocol:
Cells were cross-linked in 1% formaldehyde for 10 min, followed by quenching with 1/20 volume of 2.5 M glycine solution, and two washes with 1× PBS. Nuclei were extracted by brief probe sonication in hypotonic lysis buffer (20mM Hepes, 3mM MgCl2, 250mM sucrose, 0.2% NP-40, 3mM beta-mercaptoethanol) followed by three washes of nuclei in this buffer. Nuclei were lysed in ChIP SDS lysis buffer (50 mM HEPES, 1% SDS, 10 mM EDTA), followed by sonication with a Bioruptor (Diagenode) - 2x cycles of 30" ON, 30" OFF x 7.5'. 5% of the extract was removed for input DNA and the remainder was used for ChIP. Extracts were diluted in ChIP dilution buffer (50 mM Hepes/NaOH at ph 7.5, 155 mM NaCl, 1.1% Triton X-100, 0.11% Na-deoxycholate, 1 mM PMSF, Complete protease inhibitor tablet) and incubated with 10ug of Ab for 16h at 4°C. Antibody-antigen complexes were captured on ProteinA-sepharose beads (GE, CL-4B) for four hours followed by a series of bead washing steps : 1x 1' with ChIP dilution buffer, 1x 5' with ChIP dilution buffer, 1x 5' with ChIP dilution buffer +500mM NaCl, 1x 5' with ChIP wash buffer (10mM Tris-HCl pH 8, 1mM EDTA, 250mM LiCl, 0.5% NP-40, 0.5% NaDOC). Elution from beads and cross-link reversal of ChIPs and inputs was performed overnight at 65°C in ChIP elution buffer (50mM Tris-HCl pH 8, 10mM EDTA, 1% SDS). Proteins were digested with Proteinase K and DNA was isolated using phenol/chloroform/isoamyl alcohol.
Libraries for each ChIP-Seq experiment were prepared as per Illumina's instructions (http://www.illumina.com). Briefly, DNA fragments were blunted, phosphorylated, and ligated to Illumina library adapters. Size selection was performed using gel electrophoresis by excising DNA fragments at 200 ± 50 base pairs. Following gel purification, PCR amplification was performed (30 s at 98°C; [10 s at 98°C, 30 s at 65°C, 30 s at 72°C] × 18 cycles; 5 min at 72°C). Amplified material was evaluated on an Agilent 2100 Bioanalyzer to ensure proper size selection.

treatment_protocol: For adipocyte infections, purified adenoviruses were incubated in low-serum media (maintenance media with 0.5% FBS) containing 0.5μg/mL poly-L-lysine for two hours at 25C. Adipocytes were washed once with PBS then incubated with adenovirus (5mL of diluted virus per 10cm dish). After four hours, additional low-serum media was added (5mL per 10cm dish). After 16 hours, low serum media was replaced with growth media and cells were incubated under standard conditions until harvest (24-72 hours post-infection).

value: adipocytes

tag: treatment group

value: PU.1 T-21 (Santa Cruz, sc-352x)


title: PU.1Ad-PPARg

source_name: 3T3-L1 adipocyte, day 10, adeno-PU1 72hrs, PPARg ChIP

tag: cell type

value: PPARg H-100 (Santa Cruz, sc-7196x)


title: mRNA-iTreg Bach2KO2

description:
mRNA_seq
RUN DATE: 7/6/2010


title: LACZAd-input

source_name: 3T3-L1 adipocyte, day 10, adeno-LACZ 72hrs, input

value: adeno-LACZ

tag: chip antibody


title: PU.1Ad-input

source_name: 3T3-L1 adipocyte, day 10, adeno-PU1 72hrs, input


title: EXP_6_Pool_RNA_K2_10.14.09

status: Public on Jun 29 2013

city: St Louis

first: Federico

middle: E

last: Rey

state: MO

address: 4444 Forest Park Blvd

department: Pathology

institute: Washington University

description: Fecal pellet from a mouse (NMRI) colonized with 9-gut bacteria. Mouse was fed a polysaccharide rich diet (BK chow)

data_processing:
Splitting barcodes - Sequence runs were split into their respective experiments using the 4-bp/8bp barcode at the beginning of each sequencing read.
Mapping reads - After dividing sequence runs by barcode, we mapped the reads to the relevant genomes using the ssaha2 algorithm
Handling ties - Reads that map non-uniquely were added to each gene in proportion to each gene’s fraction of unique-match counts (e.g., a non-unique read that maps equally well to gene A with 18 unique reads and gene B with 2 unique reads will be scored as 0.9 count to gene A and 0.1 count to gene B). We added a pseudocount (i.e. added 1) to each gene count prior to normalization to account for differences in sampling depth.

organism:
[Clostridium] symbiosum
Bacteroides thetaiotaomicron VPI-5482
Bacteroides ovatus ATCC 8483
Bacteroides caccae ATCC 43185
Collinsella aerofaciens ATCC 25986
Marvinbryantia formatexigens DSM 14469
Escherichia coli str. K-12 substr. MG1655
Agathobacter rectalis ATCC 33656
Desulfovibrio piger GOR1

source_name: Fecal

extract_protocol:
Each frozen sample was suspended in a solution containing 500 mL of acid-washed glass beads (Sigma-Aldrich), 500 mL of extraction buffer A (200 mM NaCl, 20 mM EDTA), 210 mL of 20% SDS, and 500 mL of a mixture of phenol:chloroform:isoamyl alcohol (125:24:1, pH 4.5; Ambion), and then lysed by using a bead beater (BioSpec Products; maximal setting; 4 min at room temperature). Cellular debris was removed by centrifugation (8,000 × g; 3 min at 4°C). The extraction was repeated, and nucleic acids were precipitated with isopropanol and sodium acetate (pH 5.5).
DNA libraries were prepared for sequencing using a modified version of Illumina's sample preparation protocol (see  PMID:22030749 for protocol details)

treatment_protocol: Fecal samples obtained from mice  were immediately frozen at -80C and maintained at this temperature prior to processing.

tag: rna subtype

value: rRNA depleted total RNA

tag: source

tag: processed data filename


title: granulocytes

city: Camperdown

first: william

last: ritchie

state: NSW

address: Building 93

country: Australia

institute: centenary institute

data_processing:
Illumina Pipeline 1.5 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, then mapped to mm8 whole genome using bowtie v0.12.7
Alternative transcription start sites and gene expression were determined using Cufflinks Version 0.92.
Genome_build: mm9 & hg19
Supplementary_files_format_and_content: GTF file of transcripts

source_name: granulocytes

extract_protocol:
Promyelocytes, myelocytes and granulocytes were purified using fluorescence activated cell sorting. RNA was extracted using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit 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: bone marrow

value: 8-10 weeks


title: myelocytes

source_name: myelocytes


title: promyelocytes

source_name: promyelocytes


title: mRNA-iTreg WT2

description:
mRNA_seq
RUN DATE: 7/6/2010


title: 2i P12 (1) RNA-Seq

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

country: United Kingdom

institute: Altos Labs

data_processing:
Libraries were sequenced on either an Illumina GAIIx or an Illumina HiSeq using the default RTA (v1.9) analysis software.
Raw Bisulfite-Seq reads were trimmed to remove both poor quality calls and adapters using Trim Galore (v0.2.2, default parameters; www.bioinformatics.babraham.ac.uk/projects/trim_galore/)
Remaining Bisulfite-Seq reads were mapped to the mouse genome (NCBIM37) using Bismark (v0.7.4, default parameters), and CpG methylation calls were extracted using the Bismark methylation extractor (v0.7.4).
RNA-Seq data was mapped to the mouse genome (NCBIM37) assembly using TopHat (v1.4.1, options -g 1) in conjunction with gene models from Ensembl release 61.
Reads were mapped to overlapping transcripts using SeqMonk (www.bioinformatics.babraham.ac.uk/projects/seqmonk/) and log2 read counts per million reads were calculated for all transcripts. Counts were adjusted by matching distributions between samples.
Genome_build: NCBI37
Supplementary_files_format_and_content: Bismark CpG methylation call files are tab delimited and contain 5 colums: (1) read ID; (2) methylation state, whereby '+' = methylated, and '-' = unmethylated; (3) chromosome; (4) position; (5) context call, whereby 'Z' = methylated CpG, and 'z' = unmethylated CpG
Supplementary_files_format_and_content: Quantitated RNA-Seq data files are delimted and contain the following 7 columns: (1) mRNA name (Ensembl); (2) Chromosome; (3) Start; (4) End; (5) Strand; (6) Description (Ensembl); (7) log2 Expression Value

source_name: ES cells

growth_protocol: ESCs were cultured without feeders either in standard serum-containing media (DMEM 4500 mg/L glucose, 4 mM L-glutamine and 110 mg/L sodium pyruvate, 15% fetal bovine serum, 1 U/ml penicillin, 1 μg/ml streptomycin, 0.1mM nonessential amino acids, 50 uM beta-mercaptoethanol, 103 U/ml LIF ESGRO) or under 2i culturing conditions (serum-free N2B27 supplemented with 1000 U/ml LIF and Mek inhibitor PD0325901 (1 uM) and Gsk3 inhibitor CH99021 (3 uM)).

extract_protocol:
Genomic DNA was prepared using QIAamp DNA Micro Kit or AllPrep DNA/RNA mini kit (QIAGEN). RNA was extracted using either the AllPrep DNA/RNA mini kit or RNeasy® mini kit (QIAGEN) and subjected to DNAase treatment using the Ambion DNA-free™ kit according to the manufacturers’ instructions.
mRNA library preparation for RNA-seq was done as previously described (Ficz et al., 2011). For BS-seq library preparation DNA samples were fragmented by sonication (Covaris) and adaptor ligated (using Illumina supplied methylated adaptors and NEBnext library preparation kit). Subsequently, DNA was bisulfite-treated using the Sigma Imprint kit, according to the manufacturer’s instructions (one step protocol). Final library amplification (16 cycles) was done using Pfu Turbo Cx (Agilent), after which the libraries were gel-purified using QIAGEN Minelute kit.

tag: cell line

value: E14 ES


title: 2i P12 (2) RNA-Seq

tag: strain


title: mRNA-iTreg WT3

description:
mRNA_seq
RUN DATE: 7/6/2010


title: mRNA-iTreg WT1

description:
mRNA_seq
RUN DATE: 7/6/2010


title: mRNA-Th17

description:
mRNA_seq
RUN DATE: 7/6/2010

value: in vitro polarized T helper17 cells for 3 days

value: FACS sorted naive CD4+T cells cultured in vitro for 3 days under Th17 condition


title: mRNA-Th2

description:
mRNA_seq
RUN DATE: 7/6/2010

value: in vitro polarized T helper2 cells for 3 days

value: FACS sorted naive CD4+T cells cultured in vitro for 3 days under Th2 condition


title: Serum P12 (1) RNA-Seq


title: mRNA-Th1

description:
mRNA_seq
RUN DATE: 7/6/2010

value: wild type

value: in vitro polarized T helper1 cells for 3 days

value: FACS sorted naive CD4+T cells cultured in vitro for 3 days under Th1 condition


title: LACZAd-PPARg

source_name: 3T3-L1 adipocyte, day 10, adeno-LACZ 72hrs, PPARg ChIP


title: mRNA-naïve

description:
mRNA_seq
RUN DATE: 7/6/2010

value: freshly isolated naive CD4+ T cells

value: FACS sorted naive CD4+T cells


title: P0 RNA-Seq


title: Wnt5a 1 RNA-Seq

status: Public on Jun 26 2013

city: Birmingham

first: Rosa

last: Serra

state: AL

address: 1918 University Blvd. 660 MCLM

department: Cell Biology

institute: University of Alabama at Birmingham

data_processing:
CASAVA version 1.8.0 was used to convert the *.bcl files to *.fastq files.
TopHat version 2.0.0 was used to align the *.fastq files to the UCSC mm9 reference genome using the default settings and parameter -r 150.
Cufflinks version 1.3.0 was used with default settings to calculate transcript abundances from the TopHat alignment files (*.bam) and also calculate differential expression.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited *.txt file of the isoform transcript list containing columns for nearest reference ID, gene name, locus, status and FPKM value which were derived from the Cufflinks suite of tools, Cuffdiff.

source_name: 4T1 Wnt5a transduced

growth_protocol: Vector control and Wnt5a expressing 4T1 cells were grown to 70% confluency under conditions recommended by ATCC.

extract_protocol:
RNA was isolated using Trizol. 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.


title: Vector 1 RNA-Seq

source_name: 4T1 vector transduced

value: Control


title: HeLa siMBNL1+2

city: Barcelona

first: Manuel

last: Irimia

state: Barcelona

address: 88 Dr. Aiguader

department: MELIS

country: Spain

institute: Universitat Pompeu Fabra - Centre for Genomic Regulation

data_processing:
Full genomic sequences for the analyzed species were downloaded from the Ensembl database. Full transcriptomic sequences for all species were downloaded from Ensembl. For each gene, the canonical transcript was selected for gene expression analysis based on BioMart.
For each species, we assembled all canonical transcript (as defined above) sequences. In order to calculate the effective number of unique mappable positions in each transcript (i.e. the effective length) we performed the following steps. For each read length k, we extracted the L-k+1 (L being the transcript length) k-mer sequences from each canonical transcript and then aligned the full set of k-mers against the respective genome using Bowtie, allowing for a maximum of two mismatches. k-mers with no or one unique genomic alignment were then likewise aligned back to the canonical transcriptome. For each transcript, the number of such k-mers having a unique transcriptomic alignment was determined. This corresponds to the transcript’s effective number of unique mappable positions for k-mer mRNA-Seq reads. For each sample, the corresponding mRNA-Seq data were aligned against the respective genome using Bowtie, allowing for a maximum of two mismatches. Reads with one unique genomic alignment were then aligned against the canonical transcriptome and, for each transcript, the number of reads with one unique transcriptomic alignment were counted. Gene expression levels were determined as reads per thousand mappable positions of target transcript sequence per million of reads, where the reads uniquely align to the analyzed transcriptome. This procedure for estimating gene expression levels is a corrected version of the widely used RPKM (reads per kilobase of target transcript sequence per million of total reads) metric, and is referred to as “cRPKM” [Labbe RM et al. Stem Cells (2012)].
Genome_build: hg19, mm9
Supplementary_files_format_and_content: Tab-delimited text files include cRPKM values (as defined above), as well as the total read count for each gene's canonical transcript

molecule: polyA RNA

source_name: HeLa cell line

growth_protocol: HeLa and 293T cell lines were maintained in Dulbecco's Modified Eagle Medium (DMEM) supplemented with 10% Fetal Bovine Serum (FBS) and antibiotics (penicillin/streptomycin). Neuro2A (N2A) cells were grown in DMEM supplemented with 10% FBS, sodium pyruvate, MEM, non-essential amino acids, and penicillin/streptomycin.

extract_protocol:
Total RNA was extracted using Tri Reagent (Sigma) or RNeasy columns (Qiagen)
Standard Illumina library preparation according to manufacturer

treatment_protocol: Cells were transfected with SMART-pool siRNAs (Dharmacon) using DharmaFECT1 reagent (Dharmacon), as recommended by the manufacturer. A non-targeting siRNA pool was used as a control. Cells were harvested 48 or 72 hours post transfection.

tag: treatment

value: MBNL1 and MBNL2 SMART-pool siRNAs

value: HeLa


title: HeLa nt_control

value: non-targeting siRNA pool


title: 293T siMBNL1+2

source_name: 293T cell line


title: 293T nt_control


title: mRNA-iTreg Bach2KO1

description:
mRNA_seq
RUN DATE: 7/6/2010

source_name: primary CD4+ T cells from spleen and lymph nodes

value: in vitro polarized inducible regulatory cells for 3 days

value: FACS sorted naive CD4+T cells cultured in vitro for 3 days under iTreg condition


title: SI clone e day 21

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

source_name: secondary reprogramming cells

growth_protocol: Secondary MEFs were isolated and treated with doxycycline to induce reprogramming

extract_protocol:
mRNA was purified using Qiagen RNAeasy kit with on-column DNAse treatment
RNA libraries were prepared for sequencing using standard Illumina Truseq kit protocols

treatment_protocol: Secondary MEFs were treated with doxycycline for 21 days

tag: time

value: dox

value: secondary reprogramming cells


title: PtrpC:GLS1

status: Public on Jun 25 2013

city: Halle (Saale)

first: Ely

middle: Oliveira

last: -Garcia

state: Sachen-Anhalt

address: Betty Heimann Straße 3

department: Institut für Agrar- und Ernährungswissenschaften (IAEW)

data_processing:
Image analysis, basecalling, and quality check was performed with the Illumina data analysis pipeline RTA v.13.48 and/or OLB v1.9 and CASAVA v1.8.2.
Illumina NG mRNA sequencing was performed with samples from non-infected maize leaves and from leaves infected by the WT and the PtrpC:GLS1 strains. Identical amounts of mRNA from three independent samples of each treatment were mixed, and Illumina sequencing was performed by ServiceXS B.V. (Leiden, The Netherlands), using the paired-end sequencing protocol. Datasets of 100 bp reads yielding 4.5 Gb of Illumina-filtered sequence data per sample were obtained. For further analyses reads ≥ 70 bp with a phred score ≥ Q20 were selected. The filtering was performed by FastqFilter version 2.05 (ServiceXS). The obtained reads were aligned to the Zea mays B73 reference genome (ftp.maizegdb.org), using BWA version 0.5.9 (Li and Durbin, 2009) and TopHat version 1.4.0 (Trapnell et al., 2009), and corresponded to a minimum of 36,020 unique transcripts. The counts obtained were normalized according to Mortazavi et al. (2008).
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Mortazavi et al., Nat. Methods 5, 621-628, 2008. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: ZmB73_5a.59
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

organism: Zea mays

source_name: 3rd and 2nd leaves

extract_protocol:
Samples from non-infected maize leaves and from leaves infected by the WT and the PtrpC:GLS1 strains were colected, flash frozen in nitrogen, and RNA was extracted using a peqGOLD Total RNA Kit (PEQLAB, Erlangen, Germany ) and pretreated with RQ1 RNase-free DNase (Promega, Madison, WI, USA) .Illumina NG mRNA sequencing was performed with 1 µg of total RNA.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: infection

value: PtrpC:GLS1 strain (PtrpC:GLS1)

value: leaves

tag: age

value: 21 days old maize plants


title: Control_WT_ChIP-seq

city: Beijing

first: Junling

last: Pang

address: No.12 Zhongguancun South St.,Haidian District

country: China

institute: Chinese Academy of Agricultural Sciences

data_processing:
ChIP-seq analysis: Alignment of the ChIP-seq data to the reference genome was carried out using BWA software (Li and Durbin 2009) allowing at most 3 mismatches. Reads that are mapped to a unique genomic location were chosen, and only a random one was picked for copy-duplicates (reads mapped to the same location). To make it comparable between different samples, RPM values were calculated with 10 kb windows along the genome.
ChIP-bisulfite-seq analysis: Bisulfate sequencing reads were mapped to the reference genome using BRAT software (Harris et al. 2010). Cytosines covered by at least two reads were chosen for further analysis. The mean DNA methylation level of selected regions was calculated separately for “CG”, “CHG” and “CHH”.
Genome_build: Zea mays B73 RefGen_v2
Supplementary_files_format_and_content: BED files contain the uniquely and non-redundently mapped reads of the ChIP-seq; TEXT files contain the ChIP-BS results for the DNA methylation level in each C site.

source_name: maize

extract_protocol:
Extracted nuclei were digested with micrococcal nuclease (Sigma-Al drich). The digested chromatin was used for ChIP experiments using the maize CENH3 antibody.
The maize CENH3 antibody is a rabbit polyclonal antiserum and was raised against the peptides: C-RPGTVALREIRKYQKS; STSATPERAAGTGGR-C. Keyhole limpet hemocyanin (KLH)-conjugated peptide was used to immunize rabbits. Anti-CENH3 polyclonal antibodies were affinity-purified using the peptides conjugated to Sulfo-link coupling Gel (Pierce) performed by GL Biochem (Shanghai) Ltd.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303).180-400 bp fragments (contained the joint) were selected by gel extraction.

tag: developmental stage

value: trefoil stage

value: seedling

tag: molecule subtype

value: ChIPed DNA


title: Mock

value: non-inoculated control (Mock)


title: WT

value: wild-type strain - M2 (WT)


title: sDic-15_ChIP-seq

tag: genotype/variation


title: sDic-15_ChIP-bisulfite-seq

description: The ChIPed DNA was treated with sodium bisulfite and prepared for Illumina sequencing


title: T3-5_ChIP-seq

value: T3-5 (20+0):progenitor of sDic15


title: Control_ChIP-seq


title: Dp3a_ChIP-seq


title: C40

city: Frederiksberg

first: Kirstine

last: Klitgaard

address: Bulowsvej 27

country: Denmark

institute: National Veterinary Laboratory

description: 16S rRNA

data_processing:
The 454 pyrosequencing reads were processed using the Ribosomal Database Project’s (RDP) Pyrosequencing Pipeline (Cole et al. 2005; Cole et al. 2009).
The raw sequences were parsed by barcodes using the Pipeline Initial Process.
The amplicons were screened for the presence of both forward and reverse primers, allowing 2 or fewer mismatches to the primer sequences, no ambiguous base calls and a 200-base minimum sequence length.
Supplementary_files_format_and_content: tab-delimited text files listing phylotype abundance for each sample

organism: Bos taurus

source_name: Treponema spp.

extract_protocol:
Skin biopsies of 6 mm were taken from the centre of the lesion using a sterile biopsy punch. The biopsies were cut in small pieces, suspended in 0.5 ml of sterile PBS and frozen at -20 ºC. Bacterial DNA was extracted from tissue samples (approximately 2mm2) using the DNeasy Tissue Kit (Qiagen, Hilden, Germany). First, the biopsy samples were incubated for 1.5 h at 55°C in 180 µl lysis buffer with 20 µl proteinase K provided in the kit. All subsequent steps were performed according to the instructions provided by the manufacturer. For each sample, 2 µl of template DNA was applied for the construction of sequencing libraries.
DNA was amplified by PCR using the Treponema specific primers designed for this study. Each sample was amplified with a unique primer with an added hexamer barcode at the 5’ end of the forward and reverse primer. Amplification of the target region was carried out in a 50 µl reaction mix which contained 1 × AmpliTaq buffer (Applied Biosystems, Carlsbad, CA), 100 µM of each deoxynucleoside triphophate (Amersham Biosciences, Piscataway, NJ), 0.2 pmol of each primer, 2.5 U of AmpliTaq DNA polymerase (Applied biosystems), and 2 µl of template DNA. Thermal cycling using a T3 Thermocycler (Biometram Göttingen, Germany) was performed as follows: denaturation at 94°C for 3 min and 30 s, followed by 30 cycles of denaturation at 94°C for 45 s, annealing at 59°C for 45 s, and extension at 72°C for 1 min, followed by a final elongation step of 5 min. Equal amounts of all 40 amplicons were pooled (final concentration of 5 µg) and purified with the Qiagen Mini Elute kit (Qiagen), according to the protocol provided by the manufacturer. Next generation sequencing was performed by LCG Genomics (Teddington, Middlesex, UK) using Roche / 454 Genome Sequencer FLX + Titanium according to their standard procedure (1/4 PLP).

value: Digital dermatitis lesion

tag: breed

value: holstein

tag: sampling date

tag: herd no.


title: C38

description: 16S rRNA


title: C39

description: 16S rRNA


title: Serum P12 (2) RNA-Seq

value: E14 ES

tag: passages


title: C37

description: 16S rRNA


title: C36

description: 16S rRNA


title: C33

description: 16S rRNA


title: C35

description: 16S rRNA


title: C34

description: 16S rRNA


title: C31

description: 16S rRNA


title: C32

description: 16S rRNA


title: ESC_CGR8

source_name: CGR8 embryonic stem cell line

value: untreated


title: C29

description: 16S rRNA


title: C28

description: 16S rRNA


title: C26

description: 16S rRNA


title: C30

description: 16S rRNA


title: C23

description: 16S rRNA


title: C25

description: 16S rRNA


title: C24

description: 16S rRNA


title: Dp3a_ChIP-bisulfite-seq

tag: chip antibody


title: C22

description: 16S rRNA


title: C18

description: 16S rRNA


title: C19

description: 16S rRNA


title: C20

description: 16S rRNA


title: C21

description: 16S rRNA


title: C16

description: 16S rRNA


title: C15

description: 16S rRNA


title: C14

description: 16S rRNA


title: C17

description: 16S rRNA


title: C10

description: 16S rRNA


title: C12

description: 16S rRNA


title: C13

description: 16S rRNA


title: C9

description: 16S rRNA


title: C8

description: 16S rRNA


title: C6

description: 16S rRNA


title: E14Tg2a_Input_DNA

city: La Jolla

first: Yuliang

last: Tan

state: California

address: Room 345, CMM West, 9500 Gilman Drive, Mail Code 0648

department: School of Medicine

institute: University of California, San Diego

data_processing:
The raw ChIP-Seq data mapped uniquely to the mouse genome NCBI Build 37 (UCSC, mm9) by Bowtie.
We then employed the algorithm described in previous paper (Ferrari R, et al. Genome Res. 2012) to evaluate the significantly accumulated peaks of these reads in the genome.
The distribution of these peaks around other protein’s peak centers was determined by sitepro. The Pearson’s correlation was calculated with Cistrome. Functional annotation of ChIP regions was obtained with GREAT, using the basal plus extension association rules and the mouse genome (mm9) as background.
Genome_build: mm9
Supplementary_files_format_and_content: Wig files and Bed files are generated with algorithm described in previous paper (Ferrari R, et al. Genome Res. 2012).

source_name: Mouse embryonic stem cells (E14)

growth_protocol: Mouse embryonic stem cell line E14Tg2a (CRL-1820) was obtained from ATCC and cultured in Knockout™ Dulbecco’s Modified Eagle’s Medium (Invitrogen, Cat # 10829-018) supplemented with 15% ES-qualified FBS (Omega Sci, Cat # FB-05, Lot # 104100), 2mM GlutaMAX™-I Supplement I (Invitrogen, Cat # 35050-061), 0.1 mM MEM Non-Essential Amino Acids Solution (Invitrogen, Cat # 11140-050), 55 nM 2-mercaptoethanol (Invitrogen, Cat # 21985-023) and 1,000 units/ml LIF (Millipore, ESG1107). Mouse ESCs were maintained at 37 °C, 5% carbon dioxide, fed with fresh media daily, and passaged onto new plates at an average ratio of 1:5 after trypsin dissociation.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with H3K56ac antibody.
Chromatin immunoprecipitation (ChIP) was performed using about 20 milloin cells with the following protocol described earlier. Briefly, E14Tg2a cells were cross linked with formaldehyde for 10 minutes, lysed in 10mM Tris-EDTA pH 8.0 with 1% SDS, and sonicated (Fisher Scientific #550 Sonic Dismembrator) on ice 4 times at 15 second pulses interrupted by 45 second pauses on power 4 followed by 2 times at 20 seconds pulses interrupted by 40 seconds pauses on power 2. Clarified sheared chromatin was immunoprecipitated with antibodies to histone H3K56ac (generated by Michael Grunstein's lab) overnight at 4°C. Immunoprecipitated DNA was collected with protein A dynabeads for 3 hours, washed twice for 5 minutes at 4°C with wash buffers and eluted with 1% SDS. Eluates were heated at 65°C to reverse crosslinks, treated with RNase and proteinase K, and DNA was purified with the Qiagen PCR purification kit. 10ng DNA was amplified using the ChIPSeq DNA Sample Prep. Kit (Illumina, P/N # 1003473), and sequenced with Illumina Genome Analyzer Hiseq2000 at the UCLA Broad Stem Cell Research Center high throughput sequencing facility.

tag: cell type

value: embryonic stem cells


title: C7

description: 16S rRNA


title: C27

description: 16S rRNA


title: E14Tg2a_H3K56ac_ChIPSeq


title: LIN28B_PARCLIP

city: Berlin

first: Robin

last: Graf

address: Robert Rössle Str. 10

department: Immune Regulation and Cancer

institute: Max Delbrueck Center for Molecular Medicine

description:
PARCLIP RNA
binding sites
HEK293 cells stably express FLAG-tagged LIN28B, that may be induced by Tamoxifen.

data_processing:
Note: due to special 5p adapter, 2nts need to be removed at 5p of each read in libraries 4SU_1 and 4SU_2 prior to any processing
Adapters were removed by customized script; clipped reads were aligned using BWA (version 0.5.8c) to spliced mature mRNAs (hg18); alignments were processed using samtools (version 0.1.8); clusters were generated based on pileup files and ranked based on G:A transitions and G deletions; overlapping clusters of 6SG and 4SU libraries were fused.
4SU barcodes: TCTCTGCTCGTATGCCGTCTTCTGCTTG for 4SU_1, TCTCGTATCGTATGCCGTCTTCTGCTTG for 4SU_2.
6SG barcode: TCTGGGATCGTATGCCGTCTTCTGCTTG.
4SU_CSD barcode: TCTCCATTCGTATGCCGTCTTCTGCTTG.
4SU_ZND: TCTTTTATCGTATGCCGTCTTCTGCTTG.
Genome_build: hg18
Supplementary_files_format_and_content: The .bed file reports binding sites.  Columns:  chromosome, start_position, end_position, cluster_id, score, strand, crosslink_start, crosslink_end, nan, nan.

source_name: HEK293 cell culture

extract_protocol: PAR-CLIP and small RNA cloning (Hafner et al. 2010 Cell 141, 129–141)

tag: cell line stably expresses

tag: par-clip antibody

value: FLAG

tag: culture medium

value: DMEM


title: Input_32D

city: Boston

first: Marc

middle: A.

last: Kerenyi

state: Massachusetts

address: 1 Blackfan Street - Karp Research Building

department: Hematology / Oncology

institute: Boston Children's Hospital and Dana Farber Cancer Institute

description: 32D granuolocytic progenitor cells

data_processing:
Basecalls performed using Solexa pipeline for data generated by HiSeq 2000 or Helicos pipeline for data generated by Helicos Heliscope.
Sequencing reads were aligned to mouse genome assembly mm9 using Illumina software pipeline (data generated by HiSeq 2000) or Helisphere (data generated by Helicos).
Only ChIP-seq reads that aligned to exactly one location in the reference mouse genome (mm9) were retained for downstream data analysis.
Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/).
The wig files were generated by a moving window of size 200bp. The tag count in the windown was further normalized in unit RPKM (# read per kb per million total reads) for ChIP-seq data generated by HiSeq 2000.
Genome_build: mm9
Supplementary_files_format_and_content: Mapped read bed file, wig file, and peak bed file

source_name: 32D granuolocytic progenitor cells (bone marrow)

growth_protocol: 32D cells were cultured in RPMI 1640 medium with 2 mM L-glutamine adjusted to contain 1.5 g/L sodium bicarbonate, 4.5 g/L glucose, 10 mM HEPES, and 1.0 mM sodium pyruvate supplemented with:10% heat-inactivated fetal bovine serum and 5ng/mL IL-3 (R&D Systems). Cultures were maintained at a cell density between 2 X 10 exp5 and 1 X 10 exp6 viable cells/mL.

extract_protocol: Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody or no antibody for Input samples.  ChIP DNA was quantified by Qubit assay HS kit. ChIP DNA was quantified by Qubit assay HS kit. Libraries were prepared from 10-20 ng of ChIP DNA according to Illumina's instructions accompanying the ChIP-Seq DNA Sample Prep Kit (IP-102-1001). Briefly, DNA was end-repaired with 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. Products of ~200±25 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel, purified using Gel Extraction kit (Qiagen) and PCR amplified using Phusion Polymerase with Illumina primers for 18 cycles. Amplified fragments were then purified using QIAquick PCR purification Kit (Qiagen). The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries generated from Lsd1-ChIP (from 32D cells + matching input control), H3K4me1-ChIP and H3K27ac-ChIP (from wild type and Lsd1 knockout Gr1dim Mac1+ cells + matching input control) were sequenced on a HiSeq2000 sequencing system of the Center for Cancer Computational Biology at the Dana-Farber Cancer Institute following the manufacturer's protocols. Raw ChIP-Seq data were processed using the Illumina software pipeline. ChIP-Seq reads were aligned to the reference mouse genome (mm9, NCBI Build 37).

treatment_protocol: For the Lsd1 ChIP, 5-10x107 32D cells were 1.5mM EGS in PBS (ethylene glycolbis [succinimidyl succinate], Sigma) for 20 min at room temperature before continuing to 1% formaldehyde fixation for 10 minutes at room temperature. Crosslinking was stopped with 125mM glycine for 5 minutes and cells were rinsed twice with 1X PBS. Cells were resuspended, lysed in lysis buffer, and sonicated to solubilize and shear cross-linked DNA. The samples were sonicated using a Heat Systems Ultrasonic Processor with a micro tip (settings: duty cycle 60%, output 4.5, 1 sec pulse, 30 sec. 6-10 times with at least 60 second pause between pulse sets) while suspended in a sonication buffer containing 10mM Tris-HCl pH7.4, 300mM NaCl, 1mM EDTA, 0.1% SDS, 1% Triton X-100, 0.1% NaDOC.  Samples were kept on an ethanol ice bath at all times. The resulting whole cell extract was split into chromatin aliquots equivalent to 10x106 of input cells and incubated overnight at 4°C with approximately 5 µg of the appropriate antibody. Protein A Dynabeads (Invitrogen) were used for collection of chromatin. Beads were washed 2X with 10mM Tris-HCl pH 7.4, 1mM EDTA, 0.1% SDS, 1% Triton X-100, 0.1% NaDOC; 2X with 10mM Tris-HCl pH 7.4, 300mM NaCl, 1mM EDTA, 0.1% SDS, 1% Triton X-100, 0.1% NaDOC; 2x with 10mM Tris-HCl pH 8.0, 250mM LiCl, 2mM EDTA, 0.5% NP40, 0.5% NaDOC and 2X with TE. Bound complexes were eluted from the beads (50 mM Tris-Hcl, pH 8.0, 10 mM EDTA and 1% SDS) by heating at 65°C for 1 hour with occasional vortexing. Crosslinking was reversed by overnight incubation at 65°C. Ten percent of input DNA was also treated for crosslink reversal.


title: Input_Gr1dim_WT_Illumina

description: FACS-purified primary Gr1dim Mac1+ bone marrow granulocyte progenitor cells

growth_protocol: Freshly isolated primary bone marrow cells, the cells have NOT been cultured in vitro.

treatment_protocol: Both, Lsd1fl/fl and Lsd1fl/fl Mx1Cre mice were injected with three doses of high molecular weight p(I:C) (Invivogen, San Diego, USA) at a concentration of 12.5µg/g body weight. Forty million Gr1dim Mac1+ were cross-linked with 1% formaldehyde for 10 min at room temperature. Crosslinking was stopped with 125mM glycine for 5 minutes and cells were rinsed twice with 1X PBS. Cells were resuspended, lysed in lysis buffer, and sonicated to solubilize and shear cross-linked DNA. The samples were sonicated using a Heat Systems Ultrasonic Processor with a micro tip (settings: duty cycle 60%, output 4.5, 1 sec pulse, 30 sec. 6-10 times with at least 60 second pause between pulse sets) while suspended in a sonication buffer containing 10mM Tris-HCl pH7.4, 300mM NaCl, 1mM EDTA, 0.1% SDS, 1% Triton X-100, 0.1% NaDOC.  Samples were kept on an ethanol ice bath at all times. The resulting whole cell extract was split into chromatin aliquots equivalent to 10x106 of input cells and incubated overnight at 4°C with approximately 5 µg of the appropriate antibody. Protein A Dynabeads (Invitrogen) were used for collection of chromatin. Beads were washed 2X with 10mM Tris-HCl pH 7.4, 1mM EDTA, 0.1% SDS, 1% Triton X-100, 0.1% NaDOC; 2X with 10mM Tris-HCl pH 7.4, 300mM NaCl, 1mM EDTA, 0.1% SDS, 1% Triton X-100, 0.1% NaDOC; 2x with 10mM Tris-HCl pH 8.0, 250mM LiCl, 2mM EDTA, 0.5% NP40, 0.5% NaDOC and 2X with TE. Bound complexes were eluted from the beads (50 mM Tris-Hcl, pH 8.0, 10 mM EDTA and 1% SDS) by heating at 65°C for 1 hour with occasional vortexing. Crosslinking was reversed by overnight incubation at 65°C. Ten percent of input DNA was also treated for crosslink reversal.

value: Bone marrow derived Gr1dim Mac1+ granulocytic progenitor cells

tag: strain

value: Lsd1fl/fl (wild type)


title: H3K27ac_Gr1dim_WT

source_name: Gr1dim Mac1+ granulocytic progenitor cells

tag: antibody vendor/catalog/lot#


title: Lsd1_32D

description: 32D granuolocytic progenitor cells

value: 32D granuolocytic progenitor cells (bone marrow)

value: Abcam, ab17721


title: H3K27ac_Gr1dim_Lsd1_KO

value: Lsd1fl/fl Mx1Cre (knockout)


title: Input_Gr1dim_Lsd1_KO_Illumina


title: H3K4me1_Gr1dim_WT


title: H3K4me1_Gr1dim_Lsd1_KO


title: C11

description: 16S rRNA

tag: tissue


title: mock-DM+BMP2

city: Milan

first: Gabriele

last: Bucci

address: Via Olgettina 60

department: Center of Translational Genomics and Bioinformatics

country: Italy

institute: Università vita e Salute Ospedale San Raffaele

data_processing:
basecalling Illumina RTA 1.13
CASAVA 1.8
aligner Bowtie 0.12.7
alternative splicing and differential expression: TopHat 1.4.1, CuffLinks 1.3.0
Genome_build: mm9
Supplementary_files_format_and_content: cufflink's FPKM 'transcript.gtf' file

source_name: BMP2-treated mock-transfected C2C12 cells

growth_protocol: Murine mesenchimal C2C12 cells (obtained from ATCC, no. CRL-1772, Lot no. 58236521) were cultured in DMEM plus 20% FBS (Growth Medium, GM).

extract_protocol:
The RNA-Seq library was generated from total RNA prepared using miRNeasy (Qiagen, Milan, I) and purified twice with Sera-mag Magnetic Oligo(dT) Beads (Thermo Fisher, Waltham, MA) according to Illumina’s sample preparation instruction at LC-Sciences (Houston, TX). ). Purified mRNA samples were treated with a divalent cation solution followed by ethanol precipitation. Fragmented mRNAs were preceded for cDNA synthesis.
The double-stranded cDNA fragments were end-repaired and 5’ and 3’ Ligation of Illumina’s paired-end oligo adapters was performed. The library was purified on a 2% agarose gel (250±25 bps). The cDNA library was enriched by 18 cycles of PCR, gel purified, and used for cluster generation on Illumina’s Cluster Station and then sequenced on Illumina HiSeqTM 2000 following vendor’s instruction.

treatment_protocol: Myogenic differentiation of C2C12 cells was induced by incubation in DMEM plus 2% horse serum (Differentiation Medium, DM). Osteoblastic differentiation of C2C12 cells was induced by the addition of 100-300 ng/ml of recombinant BMP2 (R&D Systems, Minneapolis, MN).

tag: cell line

value: C2C12 mesenchymal precursor cell line

value: control

tag: agent


title: shKSRP-GM

source_name: untreated shKSRP-transfected C2C12 cells

value: KSRP knockdown


title: mock-GM

source_name: untreated mock-transfected C2C12 cells


title: ChIP-Seq analysis of H3K4me3 in human CD56+ ectoderm cells; DNA_Lib 1810

status: Public on Jun 24 2013

first: BROAD

last: INSTITUTE

institute: Broad Institute

description:
sample_term_id: CL_0000221
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 1810
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.15783
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.13314
****************
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: GSM1112843_BI.hESC_Derived_CD56+_Ectoderm_Cultured_Cells.H3K4me3.DNA_Lib_1810.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 1810.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of hESC Derived CD56+ Ectoderm Cultured Cells H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K4me3 ChIP-Seq on the hESC Derived CD56+ Ectoderm Cultured Cells, Library DNA_Lib 1810, 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.17242
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 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 5,600,784
FINDPEAKS_SCORE: 0.48
FINDPEAKS_PERCENTILE: 71
HOTSPOT_SCORE: 0.53
HOTSPOT_PERCENTILE: 84
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.54
POISSON_PERCENTILE: 86
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

ANALYSIS FILE NAME: GSM1112843_BI.hESC_Derived_CD56+_Ectoderm_Cultured_Cells.H3K4me3.DNA_Lib_1810.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 1810.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of hESC Derived CD56+ Ectoderm Cultured Cells H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K4me3 ChIP-Seq read mappings from the hESC Derived CD56+ Ectoderm Cultured Cells, Library DNA_Lib 1810, 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.17425
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 9
BROWSER_TRACK_NAME: hDCEcto H3K4me3 10
BROWSER_TRACK_DESCRIPTION: BI hESC Derived CD56+ Ectoderm Cultured Cells Histone H3K4me3 Library DNA_Lib 1810 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 5,600,784
FINDPEAKS_SCORE: 0.48
FINDPEAKS_PERCENTILE: 71
HOTSPOT_SCORE: 0.53
HOTSPOT_PERCENTILE: 84
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.54
POISSON_PERCENTILE: 86
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

source_name: CD56+ ectodermal germ layer cells derived in vitro from embrionic stem cells by culture in the presence of inhibitors of the BMP, TGFbeta, and WNT signaling pathways.; DNA_Lib 1810

extract_protocol: Library construction protocol: Single read - Illumina

tag: sample common name

tag: sra sample accession

tag: lineage

value: ectoderm

tag: medium

value: Days 0-5:DMEM F12, 15% KSR, Dorsomorphin (2um), A83-01 (2um), PNU 74654 (2um)

tag: disease

value: presumed normal

tag: passage

tag: line

value: CD56+ ectoderm

value: adherence

tag: batch

value: BioSAli 877

value: Cell Line

tag: Sex

value: Male

value: Harvard

value: Protein A-Sepharose 4B

value: 0.5 to 3 million cells

value: cell/nuclei lysis

value: ~1 ug

value: 10 ul bed volume

value: Millipore

value: Histone H3K4me3

value: Branson


title: Bisulfite-Seq analysis of WGBS_Lib 19 derived from human HUES64 derived CD184+ cells; WGBS_Lib 19

description:
sample_term_id: CL_0000223
assay_term_id: OBI_0001863
nucleic_acid_term_id: SO_0000352
Design description: WGBS REMC Sequencing on Illumina
Library name: WGBS_Lib 19
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.15802
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.15805
****************
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: GSM1112848_BI.hESC_Derived_CD184+_Endoderm_Cultured_Cells.Bisulfite-Seq.WGBS_Lib_19.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: WGBS_Lib 19.hg19.level.2.release.9
ANALYSIS TITLE: Methylation Proportion Graphs of hESC Derived CD184+ Endoderm Cultured Cells Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from hESC Derived CD184+ Endoderm Cultured Cells, Donor WGBS_Lib 19 were processed into graphs of methylation proportions. Methylation proportions were calculated as (methylated calls / (methylated calls + unmethylated calls)) for all CpGs covered by at least 4 reads. Reads from the + and - strands were combined for methylation proportion calculations.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.18742
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
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: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: hDCE BS 19
BROWSER_TRACK_DESCRIPTION: BI hESC Derived CD184+ Endoderm Cultured Cells Bisulfite-Seq Library WGBS_Lib 19 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 616,625,520
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 99.25
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE: 67
MAXIMUM_REPLICATE_CORRELATION: 1.0

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

source_name: CD184+ endoderm differentiated in vitro from stem cells; WGBS_Lib 19

extract_protocol: Library construction protocol: Genomic DNA (1.5~5µg) was fragmented to 100-500 bp using a Covaris S2. Purified DNA fragments were end-repaired. After A-tailing, the DNA fragments were ligated with methylated paired-end adapters. Adapter-attached DNA fragments of 300-400 bp, which contain 150-250 bp genomic DNA inserts, were gel-purified. The purified DNA fragments were subjected to two cycles of sodium bisulfite conversion using the EpiTect Bisulfite kit (Qiagen). Adapter-attached, bisulfite-converted DNA molecules were enriched by PCR using PfuTurboCx Hotstart DNA polymerase (Stratagene). The PCR amplified DNA fragments were subjected to a second gel size selection to remove PCR primers and adapter dimers. The enriched library was quantified using a Qubit fluorometer and Quant-iT dsDNA HS Assay Kit. Library sequencing was performed using 101 BP PE Illumina technology.

value: CD184+ endoderm cultured cells

tag: sample alias

value: BioSam 705

value: endoderm

value: RPMI 100ng/mL Activin A 50ng/mL Wnt3a

value: HUES64 derived CD184+

value: in vitro culture

value: BioSAli 875

value: differentiated

value: 2x5hrs Epitect Kit

value: 5 ug

value: Covaris shearing, duty cycle 5%, intensity 5, cycles / burst 200, duration 9 minutes

value: T4 Ligase (2,000U/ul) 16C o/n

value: Illumina paired end adapter

value: Standard Protocol (Smith et al., Methods 48, 226-232)

value: DNA Methylation

value: Smith et al., Methods 48, 226-232

value: SPRI Beads

value: Pfu Turbo Cx hot start

value: Covaris S2 (TM)


title: C5

description: 16S rRNA

value: Digital dermatitis lesion

tag: breed

value: holstein

tag: sampling date

tag: herd no.


title: Bisulfite-Seq analysis of WGBS_Lib 26 derived from human HUES64 cells; WGBS_Lib 26

description:
sample_term_id: NTR_0000853
assay_term_id: OBI_0001863
nucleic_acid_term_id: SO_0000352
Design description: WGBS REMC Sequencing on Illumina
Library name: WGBS_Lib 26
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.15546
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.15550
****************
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: GSM1112840_BI.HUES64.Bisulfite-Seq.WGBS_Lib_26.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: WGBS_Lib 26.hg19.level.2.release.9
ANALYSIS TITLE: Methylation Proportion Graphs of HUES64 Cell Line Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from the HUES64 Cell Line, Library WGBS_Lib 26 were processed into graphs of methylation proportions. Methylation proportions were calculated as (methylated calls / (methylated calls + unmethylated calls)) for all CpGs covered by at least 4 reads. Reads from the + and - strands were combined for methylation proportion calculations.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.18734
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
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: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: HUES64 BS 26
BROWSER_TRACK_DESCRIPTION: BI HUES64 Cell Line Bisulfite-Seq Library WGBS_Lib 26 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 760,414,347
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 98.84
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE: 16
MAXIMUM_REPLICATE_CORRELATION: 1.0

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

source_name: Harvard University ES Cell 64 AKA HUES 64; WGBS_Lib 26

value: BioSam 806

value: HUES64 Cell Line

value: HUES general media - KO DMEM, 20% KSR, bFGF (10ng/mL)

value: presumed normal

value: BioSAli 1012

value: Cell Line

value: undifferentiated

value: Male

value: Harvard


title: Bisulfite-Seq analysis of WGBS_Lib 39 derived from human HUES64 cells; WGBS_Lib 39

description:
sample_term_id: NTR_0000853
assay_term_id: OBI_0001863
nucleic_acid_term_id: SO_0000352
Design description: WGBS REMC Sequencing on Illumina
Library name: WGBS_Lib 39
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.15547
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.15549
****************
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: GSM1112841_BI.HUES64.Bisulfite-Seq.WGBS_Lib_39.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: WGBS_Lib 39.hg19.level.2.release.9
ANALYSIS TITLE: Methylation Proportion Graphs of HUES64 Cell Line Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from the HUES64 Cell Line, Library WGBS_Lib 39 were processed into graphs of methylation proportions. Methylation proportions were calculated as (methylated calls / (methylated calls + unmethylated calls)) for all CpGs covered by at least 4 reads. Reads from the + and - strands were combined for methylation proportion calculations.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.18735
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
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: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: HUES64 BS 39
BROWSER_TRACK_DESCRIPTION: BI HUES64 Cell Line Bisulfite-Seq Library WGBS_Lib 39 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 535,710,536
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 98.89
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE: 19
MAXIMUM_REPLICATE_CORRELATION: 1.0

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

source_name: Harvard University ES Cell 64 AKA HUES 64; WGBS_Lib 39

value: BioSam 1122

value: BioSAli 1345

value: 2x5hrs Epitect Kit

value: 5 ug

value: Covaris shearing, duty cycle 5%, intensity 5, cycles / burst 200, duration 9 minutes

value: T4 Ligase (2,000U/ul) 16C o/n

value: Illumina paired end adapter

value: Standard Protocol (Smith et al., Methods 48, 226-232)


title: ChIP-Seq analysis of H3K27ac in human HUES64 derived CD184+ cells; DNA_Lib 3189

description:
sample_term_id: CL_0000223
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 3189
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.15387
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.15413
****************
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: GSM1112830_BI.hESC_Derived_CD184+_Endoderm_Cultured_Cells.H3K27ac.DNA_Lib_3189.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 3189.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of hESC Derived CD184+ Endoderm Cultured Cells H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27ac ChIP-Seq on the hESC Derived CD184+ Endoderm Cultured Cells, Library DNA_Lib 3189, 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.17245
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 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 17,628,829
FINDPEAKS_SCORE: 0.1242
FINDPEAKS_PERCENTILE: 9
HOTSPOT_SCORE: 0.0
HOTSPOT_PERCENTILE: 6
IROC_SCORE: 0.973
IROC_PERCENTILE: 15
POISSON_SCORE: 0.3342
POISSON_PERCENTILE: 19
MAXIMUM_REPLICATE_CORRELATION: 0.33

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

ANALYSIS FILE NAME: GSM1112830_BI.hESC_Derived_CD184+_Endoderm_Cultured_Cells.H3K27ac.DNA_Lib_3189.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 3189.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of hESC Derived CD184+ Endoderm Cultured Cells H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27ac ChIP-Seq read mappings from the hESC Derived CD184+ Endoderm Cultured Cells, Library DNA_Lib 3189, 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.17428
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 9
BROWSER_TRACK_NAME: hDCE H3K27ac 89
BROWSER_TRACK_DESCRIPTION: BI hESC Derived CD184+ Endoderm Cultured Cells Histone H3K27ac Library DNA_Lib 3189 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 17,628,829
FINDPEAKS_SCORE: 0.1242
FINDPEAKS_PERCENTILE: 9
HOTSPOT_SCORE: 0.0
HOTSPOT_PERCENTILE: 6
IROC_SCORE: 0.973
IROC_PERCENTILE: 15
POISSON_SCORE: 0.3342
POISSON_PERCENTILE: 19
MAXIMUM_REPLICATE_CORRELATION: 0.33

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

source_name: CD184+ endoderm differentiated in vitro from stem cells; DNA_Lib 3189

value: CD184+ endoderm cultured cells

value: BioSam 1246

value: endoderm

value: RPMI 100ng/mL Activin A 50ng/mL Wnt3a

value: HUES64 derived CD184+

value: in vitro culture

value: BioSAli 1888

value: differentiated

value: Protein A-Sepharose 4B

value: 0.5 to 3 million cells

value: cell/nuclei lysis

value: ~1 ug

value: 10 ul bed volume

value: Active Motif

value: Histone H3K27ac

value: Branson


title: Bisulfite-Seq analysis of WGBS_Lib 25 derived from human CD56+ mesoderm cells; WGBS_Lib 25

description:
sample_term_id: CL_0000222
assay_term_id: OBI_0001863
nucleic_acid_term_id: SO_0000352
Design description: WGBS REMC Sequencing on Illumina
Library name: WGBS_Lib 25
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.15548
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.11768
****************
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: GSM1112842_BI.hESC_Derived_CD56+_Mesoderm_Cultured_Cells.Bisulfite-Seq.WGBS_Lib_25.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: WGBS_Lib 25.hg19.level.2.release.9
ANALYSIS TITLE: Methylation Proportion Graphs of hESC Derived CD56+ Mesoderm Cultured Cells Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from hESC Derived CD56+ Mesoderm Cultured Cells, Donor WGBS_Lib 25 were processed into graphs of methylation proportions. Methylation proportions were calculated as (methylated calls / (methylated calls + unmethylated calls)) for all CpGs covered by at least 4 reads. Reads from the + and - strands were combined for methylation proportion calculations.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.18733
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
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: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: hDCM BS 25
BROWSER_TRACK_DESCRIPTION: BI hESC Derived CD56+ Mesoderm Cultured Cells Bisulfite-Seq Library WGBS_Lib 25 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 576,334,807
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 99.56
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE: 86
MAXIMUM_REPLICATE_CORRELATION: 1.0

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

source_name: HUES64 differentiated with Activin A, BMP4, VEGF and bFGF for 24 hours, then with BMP4, VEGF and bFGF for an additional 4 days. ; WGBS_Lib 25

value: mesoderm

value: Day 0-1:DMEM F12, 0.5% FBS, Activin A (100ng/mL) BMP4 (100ng/mL), VEGF (100ng/mL), and bFGF (20ng/mL). Days 1-5:DMEM F12, 0.5% FBS, BMP4 (100ng/mL), VEGF (100ng/mL), and bFGF (20ng/mL)

value: presumed normal

value: CD56+ mesoderm

value: adherence

value: BioSAli 713

value: Cell Line

value: intermediate

value: Male

value: Harvard

value: 2x5hrs Epitect Kit

value: 5 ug

value: Covaris shearing, duty cycle 5%, intensity 5, cycles / burst 200, duration 9 minutes

value: T4 Ligase (2,000U/ul) 16C o/n

value: Illumina paired end adapter

value: Standard Protocol (Smith et al., Methods 48, 226-232)

value: DNA Methylation

value: Smith et al., Methods 48, 226-232

value: SPRI Beads

value: Pfu Turbo Cx hot start

value: Covaris S2 (TM)


title: Bisulfite-Seq analysis of WGBS_Lib 24 derived from human CD56+ mesoderm cells; WGBS_Lib 24

description:
sample_term_id: CL_0000222
assay_term_id: OBI_0001863
nucleic_acid_term_id: SO_0000352
Design description: WGBS REMC Sequencing on Illumina
Library name: WGBS_Lib 24
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.15545
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.11767
****************
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: GSM1112839_BI.hESC_Derived_CD56+_Mesoderm_Cultured_Cells.Bisulfite-Seq.WGBS_Lib_24.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: WGBS_Lib 24.hg19.level.2.release.9
ANALYSIS TITLE: Methylation Proportion Graphs of hESC Derived CD56+ Mesoderm Cultured Cells Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from hESC Derived CD56+ Mesoderm Cultured Cells, Donor WGBS_Lib 24 were processed into graphs of methylation proportions. Methylation proportions were calculated as (methylated calls / (methylated calls + unmethylated calls)) for all CpGs covered by at least 4 reads. Reads from the + and - strands were combined for methylation proportion calculations.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.18732
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
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: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: hDCM BS 24
BROWSER_TRACK_DESCRIPTION: BI hESC Derived CD56+ Mesoderm Cultured Cells Bisulfite-Seq Library WGBS_Lib 24 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 706,093,995
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 99.55
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE: 84
MAXIMUM_REPLICATE_CORRELATION: 1.0

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

source_name: HUES64 differentiated with Activin A, BMP4, VEGF and bFGF for 24 hours, then with BMP4, VEGF and bFGF for an additional 4 days. ; WGBS_Lib 24

value: mesoderm

value: Day 0-1:DMEM F12, 0.5% FBS, Activin A (100ng/mL) BMP4 (100ng/mL), VEGF (100ng/mL), and bFGF (20ng/mL). Days 1-5:DMEM F12, 0.5% FBS, BMP4 (100ng/mL), VEGF (100ng/mL), and bFGF (20ng/mL)

value: presumed normal

value: CD56+ mesoderm

value: adherence

value: BioSAli 712


title: ChIP-Seq analysis of H3K27ac in human CD56+ mesoderm cells; DNA_Lib 3198

description:
sample_term_id: CL_0000222
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 3198
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.15389
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.15415
****************
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: GSM1112832_BI.hESC_Derived_CD56+_Mesoderm_Cultured_Cells.H3K27ac.DNA_Lib_3198.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 3198.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of hESC Derived CD56+ Mesoderm Cultured Cells H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27ac ChIP-Seq on the hESC Derived CD56+ Mesoderm Cultured Cells, Library DNA_Lib 3198, 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.17237
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 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 15,099,524
FINDPEAKS_SCORE: 0.2028
FINDPEAKS_PERCENTILE: 22
HOTSPOT_SCORE: 0.0
HOTSPOT_PERCENTILE: 6
IROC_SCORE: 0.9724
IROC_PERCENTILE: 13
POISSON_SCORE: 0.3933
POISSON_PERCENTILE: 29
MAXIMUM_REPLICATE_CORRELATION: 0.54

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

ANALYSIS FILE NAME: GSM1112832_BI.hESC_Derived_CD56+_Mesoderm_Cultured_Cells.H3K27ac.DNA_Lib_3198.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 3198.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of hESC Derived CD56+ Mesoderm Cultured Cells H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27ac ChIP-Seq read mappings from the hESC Derived CD56+ Mesoderm Cultured Cells, Library DNA_Lib 3198, 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.17420
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 9
BROWSER_TRACK_NAME: hDCM H3K27ac 98
BROWSER_TRACK_DESCRIPTION: BI hESC Derived CD56+ Mesoderm Cultured Cells Histone H3K27ac Library DNA_Lib 3198 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 15,099,524
FINDPEAKS_SCORE: 0.2028
FINDPEAKS_PERCENTILE: 22
HOTSPOT_SCORE: 0.0
HOTSPOT_PERCENTILE: 6
IROC_SCORE: 0.9724
IROC_PERCENTILE: 13
POISSON_SCORE: 0.3933
POISSON_PERCENTILE: 29
MAXIMUM_REPLICATE_CORRELATION: 0.54

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

source_name: HUES64 differentiated with Activin A, BMP4, VEGF and bFGF for 24 hours, then with BMP4, VEGF and bFGF for an additional 4 days. ; DNA_Lib 3198

value: BioSam 1250

value: CD56 mesoderm - Day 0-1:DMEM F12, 0.5% FBS, Activin A (100ng/mL) BMP4 (100ng/mL), VEGF (100ng/mL), and bFGF (20ng/mL). Days 1-5:DMEM F12, 0.5% FBS, BMP4 (100ng/mL), VEGF (100ng/mL), and bFGF (20ng/mL)

value: BioSAli 1893

value: Cell Line

value: intermediate

value: Male

value: Harvard

value: Protein A-Sepharose 4B

value: 0.5 to 3 million cells

value: cell/nuclei lysis

value: ~1 ug

value: 10 ul bed volume

value: Active Motif

value: Histone H3K27ac

value: Branson


title: ChIP-Seq analysis of H3K27ac in human HUES64 derived CD184+ cells; DNA_Lib 3188

description:
sample_term_id: CL_0000223
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 3188
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.15388
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.15414
****************
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: GSM1112831_BI.hESC_Derived_CD184+_Endoderm_Cultured_Cells.H3K27ac.DNA_Lib_3188.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 3188.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of hESC Derived CD184+ Endoderm Cultured Cells H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27ac ChIP-Seq on the hESC Derived CD184+ Endoderm Cultured Cells, Library DNA_Lib 3188, 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.17244
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 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 15,969,682
FINDPEAKS_SCORE: 0.2233
FINDPEAKS_PERCENTILE: 25
HOTSPOT_SCORE: 0.3235
HOTSPOT_PERCENTILE: 34
IROC_SCORE: 0.9657
IROC_PERCENTILE: 11
POISSON_SCORE: 0.4326
POISSON_PERCENTILE: 40
MAXIMUM_REPLICATE_CORRELATION: 0.33

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

ANALYSIS FILE NAME: GSM1112831_BI.hESC_Derived_CD184+_Endoderm_Cultured_Cells.H3K27ac.DNA_Lib_3188.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 3188.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of hESC Derived CD184+ Endoderm Cultured Cells H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27ac ChIP-Seq read mappings from the hESC Derived CD184+ Endoderm Cultured Cells, Library DNA_Lib 3188, 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.17427
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 9
BROWSER_TRACK_NAME: hDCE H3K27ac 88
BROWSER_TRACK_DESCRIPTION: BI hESC Derived CD184+ Endoderm Cultured Cells Histone H3K27ac Library DNA_Lib 3188 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 15,969,682
FINDPEAKS_SCORE: 0.2233
FINDPEAKS_PERCENTILE: 25
HOTSPOT_SCORE: 0.3235
HOTSPOT_PERCENTILE: 34
IROC_SCORE: 0.9657
IROC_PERCENTILE: 11
POISSON_SCORE: 0.4326
POISSON_PERCENTILE: 40
MAXIMUM_REPLICATE_CORRELATION: 0.33

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

source_name: CD184+ endoderm differentiated in vitro from stem cells; DNA_Lib 3188

value: CD184+ endoderm cultured cells

value: BioSam 1245

value: endoderm

value: RPMI 100ng/mL Activin A 50ng/mL Wnt3a

value: presumed normal

value: HUES64 derived CD184+

value: in vitro culture

value: BioSAli 1887

value: differentiated