title: ChIP-Seq analysis of H3K4me3 in human HUES64 derived CD184+ cells; DNA_Lib 241

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 241
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.11688
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9460
****************
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: GSM916060_BI.hESC_Derived_CD184+_Endoderm_Cultured_Cells.H3K4me3.DNA_Lib_241.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 241-DNA_Lib 241-DNA_Lib 241-DNA_Lib 241-DNA_Lib 241.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of hESC Derived CD184+ Endoderm Cultured Cells H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K4me3 ChIP-Seq on the hESC Derived CD184+ Endoderm Cultured Cells, Library DNA_Lib 241, 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.13385
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 28,393,686
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 14
FINDPEAKS_SCORE: 0.2501
FINDPEAKS_PERCENTILE: 43
HOTSPOT_SCORE: 0.3037
HOTSPOT_PERCENTILE: 43
IROC_SCORE: 0.9895
IROC_PERCENTILE: 17
POISSON_SCORE: 0.4118
POISSON_PERCENTILE: 50
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM916060_BI.hESC_Derived_CD184+_Endoderm_Cultured_Cells.H3K4me3.DNA_Lib_241.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 241-DNA_Lib 241-DNA_Lib 241-DNA_Lib 241-DNA_Lib 241.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of hESC Derived CD184+ Endoderm Cultured Cells H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K4me3 ChIP-Seq read mappings from the hESC Derived CD184+ Endoderm Cultured Cells, Library DNA_Lib 241, 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.13405
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 8
BROWSER_TRACK_NAME: hDCE H3K4me3 41
BROWSER_TRACK_DESCRIPTION: BI hESC Derived CD184+ Endoderm Cultured Cells Histone H3K4me3 Library DNA_Lib 241 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 28,393,686
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 14
FINDPEAKS_SCORE: 0.2501
FINDPEAKS_PERCENTILE: 43
HOTSPOT_SCORE: 0.3037
HOTSPOT_PERCENTILE: 43
IROC_SCORE: 0.9895
IROC_PERCENTILE: 17
POISSON_SCORE: 0.4118
POISSON_PERCENTILE: 50
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

source_name: CD184+ endoderm differentiated in vitro from stem cells; DNA_Lib 241

value: genomic DNA

value: presumed normal

value: Protein A-Sepharose 4B

value: 0.5 to 3 million cells

value: Millipore

value: Histone H3K4me3


title: Eri1_wildtype

status: Public on Jul 11 2012

type: SRA

city: San Francisco

first: Molly

middle: Fisher

last: Thomas

state: CA

address: 513 Parnassus Ave

department: Microbiology and Immunology

country: USA

institute: University of California San Francisco

description:
15 - 30 nt RNA
small RNA-seq

library_source: transcriptomic

data_processing: Processed BED and .txt File Generation: For all reads, the 5' end of the read was treated as the small RNA 5' nucleotide, and the 3' end of the small RNA was determined by the 3'-most perfect match to the first 6 nt of the 3' adaptor. Reads without a perfect 6-nt adapter match were discarded. All adapter-extrated reads 15-30 nt in length were mapped the the University of California at Santa Cruz mm8 assembly of the mouse genome by searching for exact matches over the entire sequence. .txt files contain sequences 15-30 nt long that have been trimmed of adapter sequences. .BED files contain a subset of sequences from the .txt files that map uniquely to the mouse genome (mm8) with no more than two mismatches.

molecule: total RNA

organism: Mus musculus

growth_protocol: CD4+ T cells from spleen and lymph nodes (superficial cervical, facial, axillary, brachial, and inguinal) were purified and stimulated in vitro for 44 hours with anti-CD3 (2C11) and anti-CD28 (37.51) antibodies in Th2 conditions (1000 U/ml IL-4 and 5Âµg/ml anti-IFN-gamma)

extract_protocol: Total RNA was isolated using the miRNeasy kit (Qiagen) and small (18-30 nt) RNA was size fractionated by gel extraction. 3' linkers (5'P-TCGTATGCCGTCTTCTGCTTGidT) were ligated to small RNAs by the Rnl2 (1-249) enzyme (NEB) followed by 5' linker ligation (GUUCAGAGUUCUACAGUCCGACGAUC) by Rnl1 (NEB). RNA was then reverse transcribed using SS III and amplified by PCR for 15 cycles. Amplified cDNA was purified by gel-extraction. The purified cDNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

tag: cell type

value: CD4+ T cell

tag: strain


title: PolyA RNA_A. queenslandica precompetent larvae_library2_b

status: Public on Jul 10 2012

city: Santa Barbara

first: Cecilia

last: Conaco

state: California

address: BioII

department: Neuroscience Research Institute

institute: University of California at Santa Barbara

description:
PRE2
Precompetent larvae (<3 hours after emergence from brood chambers)

data_processing: 50nt reads obtained from sequencing runs were analyzed in color space using the SOLiD RNA Analysis Pipeline Tool (http://solidsoftwaretools.com/gf/project/transcriptome).  Reads were aligned to sponge contigs using the âanchor-extendâ method as previously described (Tang, Barbacioru et al. (2010) Nature Protocols 5(3)). Assembled sponge contigs and gene models (processed data file build: Aqu1) are publicly available at http://spongezome.metazome.net/ (Srivastava, Simakov et al. (2010) Nature 466(7307)). Peak files were generated by plotting read coverage across all contigs for each run.

molecule: polyA RNA

organism: Amphimedon queenslandica

source_name: Precompetent larvae

growth_protocol: Amphimedon tissues were collected at different developmental stages: precompetent (<3 hours after emergence from brood chambers); competent (>6 hours after emergence); postlarva (>4 hours after settlement); adult (no brood chambers)

extract_protocol: RNA from larvae and postlarvae was extracted directly with Trizol [Invitrogen]. Adult tissues without brood chambers were cleaned of macroscopic debris then ground in liquid nitrogen before RNA extraction with Trizol. Contaminating DNA was removed using the DNAfree kit [Ambion]. The poly(A) RNA fraction was enriched using the MicroPoly(A)Purist kit [Ambion] and ribosomal RNA was depleted using the RiboMinus Eukaryote kit [Invitrogen]. RNA quality was monitored using the Agilent Bioanalyzer RNA 6000 Pico Assay. Fragment libraries were prepared as described in Cloonan et al. (2008) Nat. Methods 5(7). Briefly, approximately 250ng of purified poly(A) RNA was subjected to 95Â°C until most of the RNA formed 50-200nt fragments. First-strand cDNA synthesis was primed with a 3â adapter-tagged random hexamer primer using SuperScript II reverse transcriptase. Second strand cDNA was synthesized using a 5â template switching adapter-tagged oligonucleotide. cDNA libraries were amplified using limited PCR cycles and fragments averaging 150bp in length were purified. Libraries were quantified by PCR and fragment size was verified using the Agilent Bioanalyzer DNA 1000 Assay. Fragment libraries were sequenced at 50 base pair reads using the Applied Biosystems SOLiD sequencer (version 3.0).

tag: developmental stage

value: Precompetent larvae

tag: tissue

value: Amphimedon tissues


title: PolyA RNA_A. queenslandica competent larvae_library2_a

description:
COMP2
Competent larvae (>6 hours after emergence from brood chambers)

source_name: Competent larvae

value: Competent larvae


title: PolyA RNA_A. queenslandica adult_library1_b

description:
ADULT
Adult tissue (no brood chambers)

source_name: Adult

value: Adult


title: PolyA RNA_A. queenslandica competent larvae_library1_a

description:
COMP1
Competent larvae (>6 hours after emergence from brood chambers)


title: PolyA RNA_A. queenslandica competent larvae_library2_b


title: PolyA RNA_A. queenslandica competent larvae_library1_b


title: PolyA RNA_A. queenslandica post-larvae_library1_a

description:
POST
Postlarvae (>4 hours after settlement)

source_name: Postlarvae

value: Postlarvae


title: PolyA RNA_A. queenslandica adult_library1_a

description:
ADULT
Adult tissue (no brood chambers)


title: PolyA RNA_A. queenslandica precompetent larvae_library2_a


title: PolyA RNA_A. queenslandica precompetent larvae_library1_a

description:
PRE1
Precompetent larvae (<3 hours after emergence from brood chambers)


title: Nipponbare [BS-Seq]

city: St. Louis

first: Blake

middle: C.

last: Meyers

state: MO

address: 975 N Warson Road

institute: Donald Danforth Plant Science Center

description:
Oryza sativa spp japonica (NPB)
Using leaf tissue from the sample, BS-seq was performed using premethylated adaptors.  The processed file indicates the chromosome, position, and the frequency of As, Cs, Gs, Ts, Ns, on the forward and reverse strand.  Note that BS converted cytosines are shown as Ts and not as Cs.

library_source: genomic

data_processing:
Bisulfite sequenced reads from all libraries (NPB, 93-11, and hybrids) were mapped to the Oryza sativa japonica (cv Nipponbare) v6.1 reference genome using BS-seeker allowing for up to three mismatches.  Reads that mapped with equal efficiency to multiple sites were discarded.  Using these reads as a scaffold, custom NPB and 93-11 genomes specific to our samples were built.  Genotypes were called only when coverage consisted of at least three reads per strand and over 90% of the reads were in agreement.  These custom genomes were used to call SNPs.   DNA methylation was calculated as the percent of cytosines that failed to undergo bisulfite conversion.  DNA methylation context was determined based on the sequence in NPB.  For most analyses, the sites which were considered was limited to those that had comparable coverage levels in all libraries which was defined to be at least 5, and not more than 25 reads.   Epimutations were determined by finding sites where the implied methylation level of each sample was outside of the 5% confidence intervals of the other sample based on a binomial distribution.   The difference in implied methylation levels also needed to be greater than a threshold based on the mean context specific methylation.  Transcripts enriched for differential methylation were identified by using a binomial test [To be provided as a supplementary table to the manuscript].  The inputs for this test were the number of epimutations present, the number of cytosines in the gene with sufficient coverage in the respective libraries, and the overall epimutation rate for the genome. Transcripts with P values below .01 were considered to be enriched for epimutations.
Genome_build: MSU Osativa V6.1
Supplementary_files_format_and_content: The processed file indicates the chromosome, position, and the frequency of As, Cs, Gs, Ts, Ns, on the forward and reverse strand.  Note that BS converted cytosines are shown as Ts and not as Cs.

molecule: genomic DNA

organism: Oryza sativa Japonica Group

source_name: leaf tissue

growth_protocol: Rice seeds were surface sterilized with 40% (V/V) sodium hypochlorite solution and transferred on 1/2 Murashige and Skoog medium. After germination, rice seedlings were transplanted into soil and grown at 26℃/20℃ under a 10h light/14h dark cycle in growth chamber. Fully expanded leaves from 6-week-old plants were collected for library construction.

extract_protocol: BS-seq libraries were made from genomic DNA isolated from leaf tissues of Oryza sativa japonica (Nipponbare, NPB) , Oryza sativa indica (93-11) and their two reciprocal hybrid offspring, 93-11 X NPB and NPB X 93-11 by a previously published method using pre-methylated Illumina adapters.

value: leaf


title: PolyA RNA_A. queenslandica precompetent larvae_library1_b


title: Nipponbare [RNA-Seq]

description: Oryza sativa spp japonica (NPB)

data_processing:
RNA-seq: the adapter sequences were removed from the reads using a Perl script, generating mRNA sequence tags. The resulting tags were matched to the Rice MSU reference genome annotation version 6.1 using the default parameters of TopHat. Differential expression was determined using a Poisson test. Starting with the number of reads per kilobase per million reads (RPKM) of one sample, we use the Poisson test to compute the probability of the observing the RPKM values in the other sample and vice versa.  If either yielded a P value below 10-5 and there was at least a 2 fold change and an absolute difference of at least 100 RPKM, the gene was called differentially expressed.
sRNA-seq: the adapter sequences were removed from the sequence reas using a Perl script, generating small RNA sequences plus abundances. The sRNA signatures were matched to the Rice MSU reference genome annotation version 6.1 using Bowtie. We allowed up to three mismatches and required the sRNA sinatures to map uniquely to the genome. The matches were filtered based on size and only 24 nt sinature reads were kept.
Genome_build: Rice MSU reference genome annotation version 6.1
Supplementary_files_format_and_content: The RNA-seq raw files NPB-904a.fastq, 93-11a-777.fastq, NPBX93-11a-906.fastq, and 93-11XNPBa-905.fastq
Supplementary_files_format_and_content: The RNA-seq raw files NPB-904b.fastq, 93-11b-777.fastq, NPBX93-11b-906.fastq, and 93-11XNPBb-905.fastq are Casava 1.8 FASTQ format
Supplementary_files_format_and_content: The sRNA raw files 93-11-787.fastq  and  NPBX93-11-788.fastq are Casava 1.7 FASTQ format and NPB-370,93-11XNPB-369 are Illumina Scarf Format
Supplementary_files_format_and_content: The sRNA and RNA-seq processed files are text containing distinct smallRNAs and mRNAs with their raw abundances respectively after removing the adapter sequences

growth_protocol: Rice plants (NPB, 93-11 and hybrids) were  grown in growth chamber at 26℃/20℃ under a 10h light/14h dark cycle

extract_protocol:
RNA-seq libraries were made from total RNA isolated from leaf tissues of Oryza sativa japonica (Nipponbare, NPB) , Oryza sativa indica (93-11) and their two reciprocal hybrid offspring, 93-11 X NPB and NPB X 93-11, using TRIzol reagent (Invitrogen, Life Technologies, USA). Total RNA (10 ug) for each sample were used for purifying the poly-A containing mRNA molecules, RNA amplification and synthesis of double stranded cDNAs that were ligated to adapters, thus preparing the libraries for sequencing on the Illumina GAII. The RNA-Seq library preparation protocol was followed as described in Illumina’s standard protocol for RNA-seq libraries (Illumina, San Diego, CA). Libraries were sequenced on an Illumina GAII at the Delaware Biotechnology Institute (Newark, DE). This generated 74,171,650 total reads from NPB, 71, 535, 918 total reads from Oryza sativa indica (93-11), 74,999,214 total reads from the reciprocal hybrid offspring 93-11 X NPB and 78,592,119 total reads from the reciprocal hybrid offspring NPB X 93-11.
Small RNA libraries were constructed from total RNA isolated from leaf tissues of Oryza sativa japonica (Nipponbare) , Oryza sativa indica (93-11) and their two reciprocal hybrid offspring, 93-11 X NPB and NPB X 93-11using TRIzol reagent (Invitrogen, Life Technologies, USA). The sRNA library preparation protocol is based on Illumina’s sRNA Sequencing Sample Preparation Guide (Illumina, San Diego, CA). The libraries were sequenced on an Illumina GAII at the Delaware Biotechnology Institute (Newark, DE).


title: 93-11 X NPB [BS-Seq]

description:
Oryza sativa spp indica (93-11) X Oryza sativa spp japonica (NPB)
Using leaf tissue from the sample, BS-seq was performed using premethylated adaptors.  The processed file indicates the chromosome, position, and the frequency of As, Cs, Gs, Ts, Ns, on the forward and reverse strand.  Note that BS converted cytosines are shown as Ts and not as Cs.  Two separate files are included for those that were better remapped to the 9311 chromosome, and the NPB chromosome respectively.

organism: Oryza sativa Indica Group x Oryza sativa Japonica Group


title: Nipponbare [sRNA-Seq]

description: Oryza sativa spp japonica (NPB)


title: 93-11 X NPB [sRNA-Seq]

description: Oryza sativa spp indica (93-11) X Oryza sativa spp japonica (NPB)


title: 93-11 X NPB [RNA-Seq]


title: 93-11 [BS-Seq]

description:
Oryza sativa spp indica (93-11)
Using leaf tissue from the sample, BS-seq was performed using premethylated adaptors.  The processed file indicates the chromosome, position, and the frequency of As, Cs, Gs, Ts, Ns, on the forward and reverse strand.  Note that BS converted cytosines are shown as Ts and not as Cs.

organism: Oryza sativa Indica Group


title: NPB X 93-11 [sRNA-Seq]

description: Oryza sativa spp japonica (NPB) X Oryza sativa spp indica (93-11)

organism: Oryza sativa Japonica Group x Oryza sativa Indica Group


title: NPB X 93-11 [BS-Seq]

description:
Oryza sativa spp japonica (NPB) X Oryza sativa spp indica (93-11)
Using leaf tissue from the sample, BS-seq was performed using premethylated adaptors.  The processed file indicates the chromosome, position, and the frequency of As, Cs, Gs, Ts, Ns, on the forward and reverse strand.  Note that BS converted cytosines are shown as Ts and not as Cs.  Two separate files are included for those that were better remapped to the 9311 chromosome, and the NPB chromosome respectively.


title: 93-11 [RNA-Seq]

description: Oryza sativa spp indica (93-11)


title: 93-11 [sRNA-Seq]

description: Oryza sativa spp indica (93-11)


title: miApoB (small RNA)

city: Amsterdam

first: Piotr

last: Maczuga

state: Nord Holland

address: Meibergdreef 61

country: Netherlands

institute: UniQure

data_processing:
Illumina Casava1.8.2 software used for basecalling.
The raw sequencing data produced was processed removing the sequence reads which were of too low quality (only "passing filter" reads were selected), and discarding reads that aligned against the PhiX control. In total, we generated 16016701 reads for sample miApoB, and 15843150 reads for sample shApoB.
The obtained reads were adaptor-trimmed, which decreased the average read size from ~36bp to ~25bp. The custom adapter sequenced used for trimming all the bases extending 5’ was: GTGACTGGAGTTCC-TTGGCACCCGAGAATTCCA.
Next, both data sets from shApoB and miApoB samples were grouped based on the match to the reference sequence and the obtained unique small RNAs were aligned to the sequence of pre-miApoB: GATCCTGGAGGCTTGC-TGAAGGCTGTATGCTGATGGACAGGTCAATCAATCTTGTTTTGGCCACTGACTGACAAGATTGAGACCTGTCCATCAGGACACAAGGCCTGTTACTAGCACTCACATGGAACAAATGGCCCAGATCTGGCCGCAG or shApoB: GATCCCCGATTGATTGACCTGTCCATTTCAAGAGAATGGACAGGTCAATCAATC-TTTTTCAGCTT sequence, respectively.
Supplementary_files_format_and_content: Spreadsheet including reads abundancy. Figure 1 and showing alliingment with references miApoB and shApoB sequences
Genome_build: miRBase Release 18: November 2011

organism: Homo sapiens

source_name: miApoB

extract_protocol: HEK293T cells were transfected with 4 µg shApoB- or miApoB-expression plasmids using Lipofectamine 2000 reagent using manufacturers protocol and total RNA was isolated from cells 48 hr post-transfection using Trizol. Small RNA sequencing libraries were generated using high-quality total RNA as input and the NEXTflex Small RNA Sequencing kit (Bioo Scientific, USA). Briefly, the small RNA species were subjected to ligation with 3' and 5' RNA adapters, first strand reverse transcription, and PCR amplification. Sample-specific barcodes were introduced in the PCR step. The PCR products were separated on TBE-PAGE electrophoresis and the expected band around 140-160bp was recovered for each sample.  The libraries were multiplexed, clustered, and sequenced on an Illumina HiSeq 2000.

tag: cell source

value: ATCC  CRL-11268™

value: Kidney

tag: genotype

value: wild type


title: PBS

description: processed data file = Expression.txt

data_processing:
Illumina Casava1.8.2 software used for basecalling.
The raw sequencing data produced was processed removing the sequence reads which were of too low quality (only "passing filter" reads were selected). Each read file (sample), in the FASTQ format, was individually aligned against the mouse reference genome (15 May 2012 NCBI build 38.1) using CLC Bio-Genomic Workbench and the expression abundance for each gene (RPKM) was calculated according to Montazavi et al.
Genome_build: mouse reference genome (15 May 2012 NCBI build 38.1)
Supplementary_files_format_and_content: Spreadsheet including annotation of reads to the reference genome

source_name: PBS

extract_protocol: Liver were removed, flash frozen on liquid nitrogen, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used

value: liver

tag: age

value: 9 wk post injection


title: miApoB

description: processed data file = Expression.txt

value: 8 wk post injection


title: Input_DNA

city: Seattle

first: Lucas

middle: T

last: Gray

state: WA

address: 615 Westlake Ave N

department: Molecular Genetics

institute: Allen Institute for Brain Science

data_processing:
Base calls were made using Illumina RTA 1.5
Raw reads were aligned to the hg18 human genome using Bowtie v0.12.7 with settings -n 0 -m 1 --chumkmbs=256 -S to SAM format
A fragment map was generated using a PERL script that treated paired end reads as the boundaries of IPed fragments. Only regions of at least 5 overlapping fragments were mapped to a WIG file.
Peaks were called using MACS v1.4 with a p-value < 1e-12, ERANGE v3.2.1 with the setting -minimum 2 and QuEST v2.4 with settings for transcription factor ChIP and custom peak calling parameters (20, 10, 3)
Summits were located for peaks identified by all 3 peak callers using a PERL script that searched for the highest point of fragment overlap in each common peak
Genome_build: hg18
Supplementary_files_format_and_content: WIG file was generated using a PERL script that treated paired end reads as the boundaries of IPed fragments. Only regions of at least 5 overlapping fragments were mapped. Scores represent the number of fragments overlapping each genomic position.

source_name: UVSS1KO Cells

growth_protocol: UVSS1KO cells expressing CSB-PGBD3 were cultured in Dulbecco's Modified Eagle Medium (DMEM) supplemented with 10% FBS, penicillin, and streptomycin with 200 µg/mL hygromycin.

extract_protocol: Nuclei crosslinked with 0.5% formaldehyde were sonicated and precleared with crosslinked Staph A cells. ChIPs were performed with a 1:200 dilution of mouse monoclonal 1B1 directed against the N-terminus of CSB (Hua-Ying Fan, University of Pennsylvania) precipitated using Protein G Dynabeads (Invitrogen). The input sample was digested with RNase, protease, and decrosslinked without enrichment by ChIP. The input sample was digested with RNase, protease, and decrosslinked without enrichment by ChIP. The ends of the ChIP and input samples were repaired using End-It (Epicentre), A-tailed using Taq polymerase (Invitrogen), and Illumina paired-end sequencing adapters were ligated using Quick T4 DNA Ligase (NEB). DNA fragments ranging from 400 to 700 bp were selected and purified by PAGE, then preamplified for 9 (input) or 12 cycles (ChIP) using Illumina paired-end preamplification primers and BioRad iTaq supermix. The preamplified samples were purified using a Qiagen PCR Cleanup kit and sequenced on the Genome Analyzer.

value: SV40 Immortalized Fibroblast

tag: chip antibody


title: miScr

description: processed data file = Expression.txt

source_name: miScr


title: CSB-PGBD3_ChIP-Seq

value: Mouse monoclonal anti-CSB N Terminus (1B1)


title: shScr

description: processed data file = Expression.txt

source_name: shScr


title: shApoB

description: processed data file = Expression.txt

source_name: shApoB


title: Chip Seq H3K36me3 in ER:Ras expressing IMR90 with no treatment SLX3168

status: Public on Jul 09 2012

city: Cambridge

first: Rafik

last: Salama

address: Li Ka Shing Centre, Robinson Way

country: United Kingdom

institute: Cancer Research UK

data_processing:
Basecalls performed using CASAVA version 1.7
ChIP-seq reads were aligned to the hg18 genome assembly using bwa 0.6.1 with the default parameters
BAM files were filtered and all reads with quality score below 15 are skipped, then the resulting BAM is filtered using the UCSC Duke excluded regions for hg18
Rseg differential was used to identify significant domains in the data using mode 2 versus input
Genome_build: NCBI Build 36.1 (HG18)
Supplementary_files_format_and_content: UCSC bed format of significant regions identified by Rseg

source_name: IMR90 Human Diploid Fibroblasts

growth_protocol: DMEM supplemented with 10% FBS and antibiotics in 5% oxygen for IMR90 cells

extract_protocol: Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody. After end-repair and addition of an ‘A’ base to the 3’ ends, the adapters were ligated to the ends of the DNA Fragments using 2 µl of fourtyfold diluted ‘Adapter oligo mix’ in a total reaction volume of 25 µl. Between these steps, the DNA was purified using the DNA Clean-and-Concentrator-5 kit (Zymo Research). Subsequently, the DNA was amplified by 18 cycles of PCR, purified with MinElute PCR Purification Kit, and eluted with 32 µl of 10 mM tris buffer at pH8.5. The PCR-product was sized fractionated on 2% agarose gel and a gel slice containing the 200-300 bp fragments was excised. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: 100 nM 4OHT for 6 days in ER:Ras-expressing IMR90 cells to induced ER:Ras

tag: chip antibody catalog #

tag: chip antibody manufacturer

value: Wako

tag: treatment

value: no treatment

tag: transgene

tag: gender

value: female

tag: cell line

value: H3K4me3 CMA333


title: Chip Seq H3K4me3 in ER:Ras expressing IMR90 d6 4OHT SLX3208

value: d6 4OHT

value: H3K4me3 CMA304


title: Chip Seq H3K27me3 in male human liver with unknown age H3K27me3_liver_hsaHH1294

source_name: Human Liver

value: male

value: H3K4me3 CMA323


title: Chip Seq H3K9me3 in male human liver with unknown age H3K9me3_liver_hsaCRI1

value: H3K4me3 CMA318


title: NPB X 93-11 [RNA-Seq]

value: leaf


title: Chip Seq H3K36me3 in ER:Ras expressing IMR90 d6 4OHT SLX3169


title: Chip Seq H3K9me2 in ER:Ras expressing IMR90 d6 4OHT SLX3209

value: H3K4me3 CMA317


title: Chip Seq H3K27me3 in ER:Ras expressing IMR90 d6 4OHT SLX3351


title: Chip Seq H3K9me2 in ER:Ras expressing IMR90 with no treatment SLX3212


title: Chip Seq H3K9me2 in ER:Ras expressing IMR90 d6 4OHT SLX2981


title: Chip Seq H3K9me2 in ER:Ras expressing IMR90 with no treatment SLX2975


title: Chip Seq H3K27me3 in ER:Ras expressing IMR90 with no treatment SLX2978


title: Chip Seq H3K9me3 in ER:Ras expressing IMR90 d6 4OHT SLX2980


title: Chip Seq H3K9me3 in ER:Ras expressing IMR90 with no treatment SLX2976


title: H4ac_HDAC3_KO_UT

city: Vienna

first: Iros

last: Barozzi

address: Borschkegasse 8a

country: Austria

institute: Medical University Vienna

description: Chromatin IP against H4ac

data_processing: Alignment: sequence reads were mapped to the mouse mm9 genome using Bowtie (PMID: 19261174). All reads with a unique match to the genome with two or fewer mismatches were retained.

growth_protocol: Bone marrow cells isolated from C57BL/6 mice were plated in 10 cm plates in 5ml of BM-medium (high glucose DMEM supplemented with 20% low endotoxin fetal bovine serum, 30% L929-conditioned medium, 1% glutamine, 1%, Pen/Strep, 0.5% Sodium Pyruvate, 0.1% β-mercaptoethanol). Cultures were fed with 2.5 ml of fresh medium every two days.

extract_protocol: ChIP lysates were generated from 2x10^8 cells. Cells were fixed in 1% formaldehyde for 10min.  Lysate was immunoprecipitated with 10ug of antibody. Antibodies were pre-bound overnight to 100ul of G protein-coupled paramagnetic beads in PBS/BSA 0.5%. Beads were then added to lysates (the preclearing step was omitted) and incubation was let to proceed overnight. Beads were washed 6 times in a modified RIPA buffer (50mM Hepes pH 7.6, 500mM LiCl, 1mM EDTA, 1% NP-40, 0.7% Na-deoxycholate) and once in TE containing 50mM NaCl. DNA was eluted in TE containing 2% SDS and crosslinks reversed by incubation overnight at 65ºC. DNA was then purified by Qiaquick columns (Qiagen) and quantified using PicoGreen (Invitrogen). ChIP DNA was prepared for Solexa 2G sequencing using a standard protocol consisting in blunting, addition of dA overhangs, ligation of Illumina adapters, selection on gel and PCR. A mixture of T4 DNA polymerase, DNA polymerase I and T4 kinase was used according to manufacturer's instruction.

treatment_protocol: Macrophages were stimulated with lipopolysaccharide (LPS, 100 ng/ml)

tag: genotype/variation

value: knockout (HDAC3 -/-)

value: Primary bone marrow-derived macrophages (BMDM) cells (7th day of differentiation)

tag: antibody

value: Anti-acetyl-Histone H4

tag: antibody vendor

value: Upstate/Millipore

tag: antibody catalog number

value: No treatment


title: H4ac_HDAC3_KO_LPS_4h

description: Chromatin IP against H4ac

tag: strain

tag: cell type

value: LPS (100 ng/ml) for 4hrs


title: H4ac_wt_LPS_4h

description: Chromatin IP against H4ac

value: wild type (HDAC3 +/-)


title: ER:Ras expressing IMR90 with no treatment Input Input_No_4OHT

value: no treatment Input


title: Chip Seq H3K4me3 in ER:Ras expressing IMR90 with no treatment SLX3162

value: Wako

value: no treatment

value: female


title: Chip Seq H3K4me3 in ER:Ras expressing IMR90 with no treatment SLX640

value: H3K4me3 CMA304


title: CB RNA_seq

city: Shanghai

first: Chengshu

last: Wang

address: 300 Fenglin Road

department: Institute of Plant Physiology and Ecology

country: China

institute: Shanghai Institutes for Biological Sciences, CAS

description: Processed data (tag copy number file: CB_TagCopyNumber.txt) represented in Data table below.

data_processing: After base calling by transforming the raw image data into sequence data, the 3' adaptor was cleaned and the tags with “N” or the tags with only one copy were removed to generate clean tags. All clean tags were mapped onto the Beauveria bassiana predicted genes (representing reference genome with GenBank accession number ADAH00000000 (PID: 38719)) by allowing no more than 1nt mismatch. Clean tags mapped to different genes were filtered. The remaining clean tags were designed as unambiguous clean tags. The number of unambiguous clean tags mapped to each gene was calculated and then normalized to TPM (number of transcripts per million clean tags).

organism: Beauveria bassiana

source_name: Fungal cells isolated from the fifith instar larvae of cotton bollworm 48 hours post injection with conidia

growth_protocol: Conidia of B. bassiana ARSEF 2860 strain from day 14 potato dextrose agar were used for different assays. For analysis of transcriptional adaptation to insect hemocoel, the 5th instar larvae of cotton bollworm was injected with spore suspension (10 microlitter each of 108 spores/ml) for 48 hours. Hemolymph from infected insects was collected on ice and immediately applied on top of a step gradient of 25 and 50% Centricoll (Sigma). The fungal cells were purified by centrifugation at 10,000g for 10 min at 4 degree C. For induction on insect cuticles, the hind wings from locusts (Locusta migratoria) were collected, air-dried for a month and surface sterilized in 10% H2O2 (10 min). The wings were washed in sterile water twice and dipped in the conidial suspensions (2 * 107 spores per ml) of B. bassiana for 20 seconds. The inoculated wings were placed on 1% water agar and incubated at 25 degree C for 24 hrs. For analysis of transcriptional adaptation to plant root exudates, the mycelia harvested from 36 hour Sabouraud dextrose broth were incubated in corn seed exudates for another 24 hours. Root exudates were prepared as we described before, in brief, the corn seeds were surface sterilized in 10% H2O2 (10 min), washed twice with sterile water and germinated on mesh with seeds immerged in half in water in a container for one week after the formation of roots. The exudates were collected and sterilized before inoculation of fungal mycelia.

extract_protocol:
RNA was extracted with a Qiagen RNeasy kit plus on-column treatment with RNase-free DNase I.
Messenger RNA was purified from 6 µg of the total RNA from each sample using Oligo (dT) magnetic beads and reversely transcribed into cDNA. The generation of 5' CATG ends of tags was conducted using the endonuclease NlaIII and the Illumina adapter 1 was added to the 5' ends. The combination of the Illumina adapter 1 and CATG site is the recognition site of MmeI, which cuts the cDNA at 17bp downstream of the CATG site, producing tags with adapter 1. After removing 3' fragments with magnetic beads precipitation, the Illumina adapter 2 was introduced at the 3' ends of each tag to generate the tag libraries. After 15 cycles of linear PCR amplification, 85 base strips were purified by 6% TBE PAGE Gel electrophoresis and the single-chain molecules fixed onto the Solexa Sequencing Chip (flowcell) for sequencing with the method of sequencing by synthesis (SBS). Each tunnel will generate millions of raw reads with sequencing length of 35bp.

value: ARSEF 2860

tag: niche

value: insect hemocoel


title: Chip Seq H3K36me3 in ER:Ras expressing IMR90 d6 4OHT SLX936

value: d6 4OHT

value: H3K4me3 CMA333


title: Chip Seq H3K4me3 in ER:Ras expressing IMR90 d6 4OHT SLX643


title: Chip Seq H3K36me3 in ER:Ras expressing IMR90 with no treatment SLX934


title: FOXK1 H140 ChIP-seq

city: Hanover

first: Gavin

middle: D

last: Grant

state: NH

address: 7400 Remsen

department: Genetics

institute: Geisel School of Medicine

data_processing:
Fastqfiles were mapped using Bowtie software (v 0.12.5) using "best" flag
Enriched peaks were identified independently in each dataset using MACS (v. 1.3.7, mfold 15, p<0.001)
Genome_build: HG19

source_name: HeLa

growth_protocol: HeLa cells were passaged in a 37C, humidity controlled, CO2 equilibrated incubator in DMEM (Life Technologies) media containing 10% FBS (Life Technologies), and 1% Penn-Strep (Life Technologies)

extract_protocol: HeLa cells were fixed with 1% formaldehyde before the DNA was sonicated to a fragment length of 200-600bp with a Bioruptor® (Diagenode, Sparta, NJ).  Antibodies were bound to a mix of Protein A and Protein G Dynabeads® (Life Technologies, Grand Island, NY) before an 18 hour incubation at 4°C with the fragmented DNA. DNA was washed and crosslinks reversed before purification with a QIAquick™ PCR purification kit (QIAGEN, Valencia, CA).  DNA concentrations were measured using Quant-iT™ PicoGreen® (Life Technologies, Grand Island, NY).  A library was constructed from the bound fragments per manufacturer’s protocols and the DNA fragments from each independent ChIP were sequenced independently at the UNC High Throughput Sequencing Facility using an Illumina Genome Analyzer II.

value: HeLa

value: epithelial

tag: vendor

value: Santa Cruz

tag: catalog/lot#


title: Chip Seq H3K27me3 in ER:Ras expressing IMR90 with no treatment SLX642

value: H3K4me3 CMA323


title: FOXK1 G22 ChIP-seq


title: RE RNA_seq

description: Processed data (tag copy number file: RE_TagCopyNumber.txt) represented in Data table below.

source_name: Mycelia grown in corn root exudates for 24 hours

value: plant root exudate


title: Chip Seq H3K9me2 in ER:Ras expressing IMR90 with no treatment SLX926

value: H3K4me3 CMA317


title: Chip Seq H3K9me2 in ER:Ras expressing IMR90 d6 4OHT SLX927


title: Chip Seq H3K9me3 in ER:Ras expressing IMR90 d6 4OHT SLX644

value: H3K4me3 CMA318


title: Chip Seq H3K9me3 in ER:Ras expressing IMR90 with no treatment SLX641


title: shApoB (small RNA)

tag: cell source

value: ATCC  CRL-11268™

tag: tissue

value: Kidney

tag: genotype

value: wild type


title: GATA3 RPMI-8402_ChipSeq, rep2

first: Richard

middle: A

last: Young

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

description:
Chromatin IP against GATA3 RPMI-8402.
09162011_C0082ABXX_4.CGATGT
Barcode (already removed): CGATGT

data_processing:
Images analysis and base calling were done using the Solexa pipeline.
Reads were aligned to human genome build hg18 using Bowtie with parameters -e 70 -k 2 -m 2 -n 2 --best --concise. Seed length (-l) was set to read length for each dataset.
Genome_build: hg18
Supplementary_files_format_and_content: WIG files: Aligned sequences were extended 150bp upstream and 0bp downstream (with respect to read strand) and allocated into 25bp bins. Counts were normalized to reads per million, and bins with at least 1 read per million are shown.

source_name: T-ALL cell line, GATA3 ChIP

growth_protocol: Human RPMI-8402 cells were purchased from the German Collection of Microorganisms and Cell Culture (DSMZ), Leibniz, Germany. Cells were maintained under typical conditions in RPMI media with 10% bovine calf serum. For location analysis, cells were grown to a density of 1 million per ml and 99% viability prior to cross-linking with formaldehyde for 20 min.

extract_protocol: Whole cell extracts (WCEs) were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 4500 bp were immunoprecipitated using different antibodies. Purified immunoprecipitated DNA were prepared for sequencing using the Beckman SPRIworks fragment library system with adapters from the Illumina TruSeq DNA kit. DNA fragments were end repaired, ligated and size selected using SPRIworks. DNA was then subjected to 18 cycles of PCR using oligos provided by Illumina.

value: T-cell acute lymphoblastic leukemia (T-ALL) cells

tag: chip antibody

tag: antibody catalog number (lot#)


title: TAL1 RPMI-8402_ChipSeq, rep2

description:
Chromatin IP against TAL1 RPMI-8402.
07192011_D0E2HABXX_4.ACAGTG
Barcode (already removed): ACAGTG

source_name: T-ALL cell line, TAL1 ChIP


title: HEB RPMI-8402_ChipSeq, rep1

description:
Chromatin IP against HEB RPMI-8402.
07192011_D0E2HABXX_4.GCCAAT
Barcode (already removed): GCCAAT

source_name: T-ALL cell line, HEB ChIP


title: TAL1 RPMI-8402_ChipSeq, rep1

description:
Chromatin IP against TAL1 RPMI-8402.
09162011_C0082ABXX_4.GGCTAC
Barcode (already removed): GGCTAC


title: HEB RPMI-8402_ChipSeq, rep2

description:
Chromatin IP against HEB RPMI-8402.
09162011_C0082ABXX_4.CTTGTA
Barcode (already removed): CTTGTA


title: ER:Ras expressing IMR90 d6 4OHT Input Input_d6_4OHT

tag: treatment

value: d6 4OHT Input

tag: transgene

value: female


title: Chip Seq H3K4me3 in ER:Ras-induced senescent IMR90 with Lenti-sh-HMGA1 SLX3613

tag: chip antibody catalog #

tag: chip antibody manufacturer

value: Wako

tag: gender

tag: cell line

value: H3K4me3 CMA304


title: GATA3 RPMI-8402_ChipSeq, rep1

description:
Chromatin IP against GATA3 RPMI-8402.
07192011_D0E2HABXX_4.ACTTGA
Barcode (already removed): ACTTGA

tag: antibody vendor


title: Chip Seq H3K4me3 in ER:Ras expressing IMR90 with no 4OHT with sh-HMGA1/MSCV SLX3597

value: no 4OHT with sh-HMGA1/MSCV


title: H4ac_wt_UT

description: Chromatin IP against H4ac

tag: strain

tag: genotype/variation

value: wild type (HDAC3 +/-)

value: Primary bone marrow-derived macrophages (BMDM) cells (7th day of differentiation)

tag: antibody

value: Anti-acetyl-Histone H4

value: Upstate/Millipore

tag: antibody catalog number

value: No treatment


title: E2A RPMI-8402_ChipSeq, rep2

description:
Chromatin IP against E2A RPMI-8402.
09162011_C0082ABXX_4.ATCACG
Barcode (already removed): ATCACG

source_name: T-ALL cell line, E2A ChIP

tag: cell type

value: Santa Cruz


title: E2A RPMI-8402_ChipSeq, rep1

description:
Chromatin IP against E2A RPMI-8402.
07192011_D0E2HABXX_4.CAGATC
Barcode (already removed): CAGATC


title: Chip Seq H3K36me3 in ER:Ras expressing IMR90 with no 4OHT with sh-HMGA1/MSCV SLX3598

value: H3K4me3 CMA333


title: Chip Seq H3K4me3 in ER:Ras expressing IMR90 with no 4OHT with shRb SLX3605

value: no 4OHT with shRb


title: Chip Seq H3K4me3 in ER:Ras expressing IMR90 d6 4OHT with sh-HMGA1/MSCV SLX3601

value: d6 4OHT with sh-HMGA1/MSCV


title: Chip Seq H3K36me3 in ER:Ras expressing IMR90 with no 4OHT with sh-Rb SLX3606

value: no 4OHT with sh-Rb


title: LW RNA_seq

description: Processed data (tag copy number file: LW_TagCopyNumber.txt) represented in Data table below.

source_name: Fungal cells differentiated on locust hind wings 24 hours post inoculation

value: ARSEF 2860

tag: niche

value: insect cuticle


title: Chip Seq H3K36me3 in ER:Ras expressing IMR90 d6 4OHT with sh-HMGA1/MSCV SLX3602


title: Chip Seq H3K36me3 in ER:Ras expressing IMR90 d6 4OHT with sh-Rb SLX3610

value: d6 4OHT with sh-Rb


title: Chip Seq H3K27me3 in ER:Ras expressing IMR90 d6 4OHT with sh-HMGA1/MSCV SLX3600

value: female

value: H3K4me3 CMA323


title: Chip Seq H3K27me3 in ER:Ras expressing IMR90 with no 4OHT with shRb SLX3604

value: Wako


title: Chip Seq H3K27me3 in ER:Ras expressing IMR90 with no 4OHT with sh-HMGA1/SIN SLX3592

value: no 4OHT with sh-HMGA1/SIN


title: Chip Seq H3K27me3 in ER:Ras expressing IMR90 d6 4OHT with sh-Rb SLX3608


title: Chip Seq H3K27me3 in ER:Ras expressing IMR90 with no 4OHT with sh-HMGA1/MSCV SLX3596

value: no 4OHT with sh-HMGA1/MSCV


title: Chip Seq H3K27me3 in ER:Ras expressing IMR90 d6 4OHT with sh-HMGA1/SIN SLX3594

value: d6 4OHT with sh-HMGA1/SIN


title: Chip Seq H3K27me3 in ER:Ras expressing IMR90 d6 4OHT SLX645

value: d6 4OHT


title: WCE Input RPMI-8402_ChipSeq

description:
Chromatin IP against WCE Input RPMI-8402.
07192011_D0E2HABXX_2.CTTGTA
Barcode (already removed): CTTGTA

source_name: T-ALL cell line, WCE input

value: T-cell acute lymphoblastic leukemia (T-ALL) cells


title: Chip Seq H3K9me3 in ER:Ras expressing IMR90 with no 4OHT with shRb SLX3603

value: H3K4me3 CMA318


title: Chip Seq H3K27me3 in ER:Ras expressing IMR90 d6 4OHT SLX3340


title: Chip Seq H3K9me3 in ER:Ras-induced senescent IMR90 with Lenti-sh-HMGA1 SLX3611


title: Chip Seq H3K9me3 in ER:Ras-induced senescent IMR90 with Lenti-sh-Rb SLX3615

value: Lenti-sh-Rb


title: Chip Seq H3K27me3 in ER:Ras-induced senescent IMR90 with Lenti-sh-Rb SLX3616


title: Chip Seq H3K9me3 in ER:Ras expressing IMR90 with no 4OHT with sh-HMGA1/SIN SLX3591


title: Chip Seq H3K9me3 in ER:Ras expressing IMR90 with no 4OHT with sh-HMGA1/MSCV SLX3595


title: Chip Seq H3K9me3 in ER:Ras expressing IMR90 d6 4OHT with sh-HMGA1/MSCV SLX3599


title: Chip Seq H3K36me3 in ER:Ras-induced senescent IMR90 with Lenti-sh-HMGA1 SLX3614

value: H3K4me3 CMA333


title: WT_hminus_IP_1

status: Public on Jul 07 2012

city: Beijing

first: Zhi-Xiong

last: Zhou

address: No.7, ZGC Life Science Park

institute: National Institute of Biological Sciences, Beijing

data_processing:
Basecalling by Illumina Casava software
Sequencing reads were trimmed for index sequence, and mapped to S. pombe reference genome using SOAP2 software, allowing only perfectly and uniquely-matched reads
Genome_build: S. pombe 972 strain
Supplementary_files_format_and_content: bed file. The values indicate the number of sequencing reads mapped to certain location.

organism: Schizosaccharomyces pombe

source_name: Haploid cells

growth_protocol: Cells used for ChIP assay were cultured in EMM (Edinburgh Minimal Medium) with necessary supplements at 30°C unless otherwise noted.

extract_protocol: ChIP DNA or input DNA was pre-denatured at 95°C and quenched on ice. The DNA was mixed with two pre-annealed adaptors added at final concentrations of 1.5 uM each. Adaptor 1 was composed of oligo A (5'-GCTCTTCCGATCXXXXCNNNNNN-3') and oligo B (5'-p-GXXXXGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT-NH2-3'). XXXX in the oligo sequence denotes 4-nucleotide multiplex indexes. Adaptor 2 was composed of oligo C (5'-NNNNNNGTTCAGAGTTCTGCGACAGGAGAG-NH2-3') and oligo D (5'-CAAGCAGAAGACGGCATACGACCTCTCCTGTCGCAGAACTCTGAAC-3'). The ligation reaction was conducted using the Quick Ligation Kit (New England Biolabs) at 16°C overnight. The ligation product was then separated on a Low Range Ultra agarose gel (Bio-Rad). DNA in the 250-500-bp range was retrieved with the GFX PCR DNA and Gel Band Purification Kit (GE Healthcare). The gel-purified DNA was amplified by PCR using primers P1 (5'-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGA-3') and P2 (5'-CAAGCAGAAGACGGCATACGA-3') for 25 cycles. The PCR product was processed by gel-based size selection, again retaining DNA in the 250-500-bp range. Equal amounts of DNA tagged with different multiplex indexes were mixed together and sequenced on an Illumina GA-II instrument using the sequence primer 5'-ACACTCTTTCCCTACACGACGCTCTTCCGATC-3'.

value: h- leu1-32 rad22-CFP-TAP-natMX

value: IgG Sepharose 6 Fast Flow

tag: antibody vendor/catalog#

value: GE Healthcare, 17-0969-02


title: WT_hminus_IP_2

tag: genotype


title: WT_hplus_input

value: h+ ura4-D18 leu1-32 his3-D1 rad22-CFP-TAP-natMX


title: WT_hplus_IP

tag: chip antibody


title: pifq RNA-Seq replicate 2

status: Public on Jul 08 2012

city: Stanford

first: Eunkyoo

last: Oh

address: 260 Panama Street

department: Plant Biology

institute: Carnegie Institution

description: RNA-Seq of pifq replicate 2

data_processing:
Total reads were mapped to the Arabidopsis thaliana genome (TAIR9, www.arabidopsis.org) using TopHat software. Read counts corresponding genes were generated using HTSeq with union mode.
Genome Build:
Q_L2.count.txt: Arabidopsis TAIR9

organism: Arabidopsis thaliana

source_name: pifq RNA-Seq

growth_protocol: Seedlings were grown on MS medium containing BRZ (brassinosteroid biosynthesis inhibitor) in the dark  for 5 days before harvesting.

extract_protocol: Total RNA was extracted from 5-day-old seedlings using the Spectrum Plant Total RNA kit (Sigma, USA). Libraries were constructed using TruSeqTM RNA Sample Preparation Kit (Illumina) according to the manufacturer’s procedure.

tag: ecotype

value: pifq (a quadruple mutant lacking PIF1, 3, 4, and 5)

tag: tissue

value: etiolated 5d-old seedlings


title: Col-0 RNA-Seq replicate 2

description: RNA-Seq of Col-0 replicate 2

data_processing:
Total reads were mapped to the Arabidopsis thaliana genome (TAIR9, www.arabidopsis.org) using TopHat software. Read counts corresponding genes were generated using HTSeq with union mode.
Genome Build:
C_L2.count.txt: Arabidopsis TAIR9

source_name: Col-0 RNA-Seq

value: wild type


title: bzr1-1D RNA-Seq replicate 2

description: RNA-Seq of bzr1-1D replicate 2

data_processing:
Total reads were mapped to the Arabidopsis thaliana genome (TAIR9, www.arabidopsis.org) using TopHat software. Read counts corresponding genes were generated using HTSeq with union mode.
Genome Build:
B_L2.count.txt: Arabidopsis TAIR9

source_name: bzr1-1D RNA-Seq

value: bzr1-1D mutant


title: WT_hminus_input_2


title: bzr1-1D RNA-Seq replicate 1

description: RNA-Seq of bzr1-1D replicate 1

data_processing:
Total reads were mapped to the Arabidopsis thaliana genome (TAIR9, www.arabidopsis.org) using TopHat software. Read counts corresponding genes were generated using HTSeq with union mode.
Genome Build:
B_L1.count.txt: Arabidopsis TAIR9


title: Col-0 RNA-Seq replicate 1

description: RNA-Seq of Col-0 replicate 1

data_processing:
Total reads were mapped to the Arabidopsis thaliana genome (TAIR9, www.arabidopsis.org) using TopHat software. Read counts corresponding genes were generated using HTSeq with union mode.
Genome Build:
C_L1.count.txt: Arabidopsis TAIR9


title: pifq;bzr1-1D RNA-Seq replicate 1

description: RNA-Seq of pifq;bzr1-1D replicate 1

data_processing:
Total reads were mapped to the Arabidopsis thaliana genome (TAIR9, www.arabidopsis.org) using TopHat software. Read counts corresponding genes were generated using HTSeq with union mode.
Genome Build:
QB_L1.count.txt: Arabidopsis TAIR9

source_name: pifq;bzr1-1D RNA-Seq

value: pifq;bzr1-1D mutant


title: pifq RNA-Seq replicate 1

description: RNA-Seq of pifq replicate 1

data_processing:
Total reads were mapped to the Arabidopsis thaliana genome (TAIR9, www.arabidopsis.org) using TopHat software. Read counts corresponding genes were generated using HTSeq with union mode.
Genome Build:
Q_L1.count.txt: Arabidopsis TAIR9


title: WT_hminus_input_1


title: pifq;bzr1-1D RNA-Seq replicate 2

description: RNA-Seq of pifq;bzr1-1D replicate 2

data_processing:
Total reads were mapped to the Arabidopsis thaliana genome (TAIR9, www.arabidopsis.org) using TopHat software. Read counts corresponding genes were generated using HTSeq with union mode.
Genome Build:
QB_L2.count.txt: Arabidopsis TAIR9


title: Col-0 ChIP-Seq

description: Chromatin IP against PIF4 transcription factor

data_processing:
Alignment : The raw sequence data were processed using Illumina sequence data analysis pipeline GAPipeline1.3.2. Sequences in Solexa FASTQ format were mapped to the Arabidopsis genome, TAIR9. Only unique mapping reads were used to determine PIF4 binding peaks.
Peaks: Peak detection was performed with Plant Research International ChIP-seq Analysis Tool (PRI-CAT) (http://www.ab.wur.nl/pricat/)
Genome Build:
Col.aln: Arabidopsis genome (TAIR9)

source_name: Etiolated seedlings

growth_protocol: Transgenic plants expressiong PIF4-myc driven by native PIF4 promoter (pPIF4::PIF4-myc) are grown in the dark for 5 days.

extract_protocol: Lysates were clarified from sonicated nuclei and PIF4-myc-DNA complexes were isolated with anti-myc antibody.  Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 18 cycles and library fragments of ~300 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina Genome Analyzer IIx following the manufacturer's protocols.

value: Etiolated seedlings

value: anti-myc antibody

tag: vendor/catalog#

value: Cell Signaling #2276


title: swi3_IP

value: h- leu1-32 his3-D1swi3D::kanMX rad22-CFP-TAP-natMX


title: Chip Seq H3K27me3 in ER:Ras-induced senescent IMR90 with Lenti-sh-HMGA1 SLX3612

source_name: IMR90 Human Diploid Fibroblasts

tag: chip antibody catalog #

value: Wako

tag: treatment

tag: transgene

value: female

value: H3K4me3 CMA323


title: swi3_input


title: Chip Seq H3K9me3 in ER:Ras expressing IMR90 d6 4OHT with sh-Rb SLX3607

value: d6 4OHT with sh-Rb

tag: gender

tag: cell line

value: H3K4me3 CMA318


title: swi1_input

value: h- leu1-32 swi1D::kanMX rad22-CFP-TAP-natMX


title: smt0_IP

value: h- smt0 leu1-32 ura4-D18 rad22-CFP-TAP-natMX

value: IgG Sepharose 6 Fast Flow

value: GE Healthcare, 17-0969-02


title: smt0_wce


title: rtt109_IP

value: h+ leu1-32 ura4-D18 rtt109D::kanMX rad22-CFP-TAP-natMX


title: rtt109_wce


title: rtt109_hst4_input

value: h-leu1-32 rtt109D::kanMX hst4D::kanMX rad22-CFP-TAP-natMX


title: PIF4 ChIP-Seq

data_processing:
Alignment : The raw sequence data were processed using Illumina sequence data analysis pipeline GAPipeline1.3.2. Sequences in Solexa FASTQ format were mapped to the Arabidopsis genome, TAIR9. Only unique mapping reads were used to determine PIF4 binding peaks.
Peaks: Peak detection was performed with Plant Research International ChIP-seq Analysis Tool (PRI-CAT) (http://www.ab.wur.nl/pricat/)
Genome Build:
PIF4.aln: Arabidopsis genome (TAIR9)
PIF4_peaks.wig: Arabidopsis genome (TAIR9)


title: pfh1_R23_permissive_IP

value: h- leu1-32 pfh1-R23 rad22-CFP-TAP-natMX


title: pfh1_R23_non.permissive_IP


title: hst4_Rad52_YFP_IP_2

value: h+ leu1-32 ura4-D18 hst4D::kanMX rad22-YFP-kanMX

value: GFP-Trap

value: ChromoTek, 101022001A


title: hst4_Rad52_YFP_input


title: pfh1_R20_non.permissive_IP

value: h- leu1-32 pfh1-R20 rad22-CFP-TAP-natMX


title: hst4_IP_2

value: h- leu1-32 hst4D::kanMX rad22-CFP-TAP-natMX


title: swi1_IP


title: hst4_input_2


title: hst4_Rpa1_input

value: h- leu1-32 ura4-D18 hst4D::kanMX rad11-TAP::kanR


title: pfh1_R20_SPATRNAVAL.01D_non.permissive_IP

value: h+ leu1-32 ura4-D18 pfh1-R20 SPATRNAVAL.01::ura4 rad22-CFP-TAP-natMX


title: pfh1_R20_non.permissive_IP_2

value: h+ leu1-32 ura4-D18 pfh1-R20 rad22-CFP-TAP-natMX  ura4 marker replacing a potential origin between SPBTRNAGLN.01 and  SPBTRNAGLN.03


title: hst4_mus7_IP

value: h- leu1-32 hst4D::kanMX mms22D::hphMX rad22-CFP-TAP-natMX


title: hst4_mus7_input


title: slm9_IP_1


title: hst4_IP_3


title: hst4_histoneD1D3_input

value: h+ leu1-32 ura4-D18 his3-D1 arg3-D4 (hht1-hhf1)::his3 (hht1-hhf3)::arg3 hhf2::ura4 hst4::kanMX rad22-CFP-TAP-natMX


title: pfh1_R20_permissive_IP


title: rtt109_hst4_IP


title: hst4_H3K56Q_IP

value: h- ura4-D18 leu1-32 his3-D1 arg3-D4 ade6-M210 (hht1-hhf1)D::his3 (hht3-hhf3)D::arg3 hhf2K56Q hst4::kanMX rad22-CFP-TAP-natMX


title: hst4_H3K56A_IP

value: h- ura4-D18 leu1-32 his3-D1 arg3-D4 ade6-M210(hht1-hhf1)D::his3 (hht3-hhf3)D::arg3 hhf2K56A hst4D::kanMX rad22-CFP-TAP-natMX


title: hst4_histoneD1D3_IP

value: IgG Sepharose 6 Fast Flow


title: hst4_Rad52_YFP_IP_1


title: hst4_H3K56R_input

value: h- ura4-D18 leu1-32 his3-D1 arg3-D4 ade6-M210 (hht1-hhf1)D::his3 (hht3-hhf3)D::arg3 hhf2K56R hst4D::kanMX rad22-CFP-TAP-natMX


title: hst4_H3K56R_IP

value: GE Healthcare, 17-0969-02


title: hst4_H3K56A_input


title: hst4_cdc25_Asyn._IP


title: hst4_Rpa1_IP


title: hst4_cdc25_90min_IP


title: hst4_IP_1


title: hst4_input_1


title: hst4_cdc25_80min_IP

value: h- leu1-32 hst4D::kanMX cdc25-22 rad22-CFP-TAP-natMX


title: hst4_cdc25_40min_IP


title: hst4_cdc25_70min_IP


title: hst4_cdc25_100min_IP


title: hst4_cdc25_110min_IP


title: hst4_cdc25_130min_IP


title: hst4_cdc25_120min_IP


title: HO_IP

value: h+ leu1-32 his3-D1 arg3::HOsite-natMX nmt1terminator::[pJR-41XH+HO]  rad22-2xFLAG-kanMX

value: Anti-FLAG M2 Affinity Gel

value: Sigma, A2220


title: HO_input


title: Reference Epigenome: ChIP-Seq Analysis of H3K4me1 in BMP4 Trophoblast Cells; renlab.H3K4me1.BMP4T.04.01

city: La Jolla

first: UCSD AND

last: SALK

address: Health Sciences Drive

institute: University of California, San Diego

description:
sample_term_id: UBERON_0000088
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K4me1 in BMP4 Trophoblast Cells. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AY258
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.13336
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.12116
****************
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: GSM956018_UCSD.H1_BMP4_Derived_Trophoblast_Cultured_Cells.H3K4me1.AY258.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4me1.BMP4T.04.01.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of H1 BMP4 Derived Trophoblast Cultured Cells H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K4me1 ChIP-Seq on H1 BMP4 Derived Trophoblast Cultured Cells, Library AY258, 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.16458
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: 25,986,913
FINDPEAKS_SCORE: 0.3934
FINDPEAKS_PERCENTILE: 75
HOTSPOT_SCORE: 0.4595
HOTSPOT_PERCENTILE: 79
IROC_SCORE: 0.9892
IROC_PERCENTILE: 67
POISSON_SCORE: 0.5538
POISSON_PERCENTILE: 75
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM956018_UCSD.H1_BMP4_Derived_Trophoblast_Cultured_Cells.H3K4me1.AY258.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4me1.BMP4T.04.01.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of H1 BMP4 Derived Trophoblast Cultured Cells H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K4me1 ChIP-Seq read mappings from the H1 BMP4 Derived Trophoblast Cultured Cells, Library AY258, 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.16612
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: HBDT H3K4me1 58
BROWSER_TRACK_DESCRIPTION: UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K4me1 Library AY258 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 25,986,913
FINDPEAKS_SCORE: 0.3934
FINDPEAKS_PERCENTILE: 75
HOTSPOT_SCORE: 0.4595
HOTSPOT_PERCENTILE: 79
IROC_SCORE: 0.9892
IROC_PERCENTILE: 67
POISSON_SCORE: 0.5538
POISSON_PERCENTILE: 75
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

source_name: Human embryonic stem cells received from the James Thomson laboratory.  Cells are from the H1 line and are differentiated into trophoblast by treatment with BMP4.; renlab.H3K4me1.BMP4T.04.01

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

tag: sample alias

tag: sample common name

tag: molecule

value: genomic DNA

tag: disease

value: James Thomson Laboratory

value: Cell Line

tag: line

tag: lineage

value: Embryonic Stem Cell

value: Embryonic stem cell differentiated into trophoblast by treatment with BMP4

value: H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days

tag: passage

tag: medium

tag: Sex

value: Male

tag: batch

value: Histone H3K4me1

value: Biorupter

value: 500 micrograms

value: magnetic anti-rabbit

value: 5 micrograms

value: Abcam


title: histone.D3_IP

tag: genotype

value: h- ura4-D18 leu1-32 his3-D1 arg3-D4 (hht3-hhf3)D::arg3 hhf2::ura4 Otr1:ade6 rad22-CFP-TAP-natMX

tag: chip antibody

value: IgG Sepharose 6 Fast Flow

tag: antibody vendor/catalog#

value: GE Healthcare, 17-0969-02


title: histone.D1.D3_IP_3

value: h- leu1-32 ura4-D18 his3-D1 arg3-D4 (hht1-hhf1)D::his3 (hht3-hhf3)D::arg3 Tf2-12-neoAI::ura4 rad22-CFP-TAP-natMX


title: histone.D1.D3_IP_1

value: h- leu1-32 ura4-D18 his3-D1 arg3-D4 (hht1-hhf1)::his3 (hht1-hhf3)::arg3 hhf2::ura4 rad22-CFP-TAP-natMX Otr1R::ade6


title: histone.D1.D3_input_1


title: Reference Epigenome: ChIP-Seq Analysis of H3K36me3 in BMP4 Trophoblast Cells; renlab.H3K36me3.BMP4T.04.01

description:
sample_term_id: UBERON_0000088
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K36me3 in BMP4 Trophoblast Cells. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AY259
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.13324
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.12116
****************
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: GSM956012_UCSD.H1_BMP4_Derived_Trophoblast_Cultured_Cells.H3K36me3.AY259.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K36me3.BMP4T.04.01.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of H1 BMP4 Derived Trophoblast Cultured Cells H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K36me3 ChIP-Seq on H1 BMP4 Derived Trophoblast Cultured Cells, Library AY259, 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.16452
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: 22,656,735
FINDPEAKS_SCORE: 0.5022
FINDPEAKS_PERCENTILE: 94
HOTSPOT_SCORE: 0.4847
HOTSPOT_PERCENTILE: 98
IROC_SCORE: 0.9984
IROC_PERCENTILE: 98
POISSON_SCORE: 0.5953
POISSON_PERCENTILE: 82
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM956012_UCSD.H1_BMP4_Derived_Trophoblast_Cultured_Cells.H3K36me3.AY259.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K36me3.BMP4T.04.01.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of H1 BMP4 Derived Trophoblast Cultured Cells H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K36me3 ChIP-Seq read mappings from the H1 BMP4 Derived Trophoblast Cultured Cells, Library AY259, 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.16606
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: HBDT H3K36me3 59
BROWSER_TRACK_DESCRIPTION: UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K36me3 Library AY259 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 22,656,735
FINDPEAKS_SCORE: 0.5022
FINDPEAKS_PERCENTILE: 94
HOTSPOT_SCORE: 0.4847
HOTSPOT_PERCENTILE: 98
IROC_SCORE: 0.9984
IROC_PERCENTILE: 98
POISSON_SCORE: 0.5953
POISSON_PERCENTILE: 82
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

source_name: Human embryonic stem cells received from the James Thomson laboratory.  Cells are from the H1 line and are differentiated into trophoblast by treatment with BMP4.; renlab.H3K36me3.BMP4T.04.01

value: genomic DNA

value: James Thomson Laboratory

value: Histone H3K36me3


title: histone.D1.D3_IP_2


title: Reference Epigenome: ChIP-Seq Analysis of H3K4ac in BMP4 Mesendoderm Cells; renlab.H3K4ac.BMP4M.01.01

description:
sample_term_id: NTR_0000856
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K4ac in BMP4 Mesendoderm Cells. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AK413
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.13095
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.11177
****************
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: GSM956017_UCSD.H1_BMP4_Derived_Mesendoderm_Cultured_Cells.H3K4ac.AK413.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4ac.BMP4M.01.01.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of H1 BMP4 Derived Mesendoderm Cultured Cells H3K4ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K4ac ChIP-Seq on H1 BMP4 Derived Mesendoderm Cultured Cells, Library AK413, 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.16347
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: 14,084,851
FINDPEAKS_SCORE: 0.2025
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.3404
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9359
IROC_PERCENTILE: 100
POISSON_SCORE: 0.4508
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM956017_UCSD.H1_BMP4_Derived_Mesendoderm_Cultured_Cells.H3K4ac.AK413.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4ac.BMP4M.01.01.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of H1 BMP4 Derived Mesendoderm Cultured Cells H3K4ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K4ac ChIP-Seq read mappings from the H1 BMP4 Derived Mesendoderm Cultured Cells, Library AK413, 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.16501
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: HBDM H3K4ac 13
BROWSER_TRACK_DESCRIPTION: UCSD H1 BMP4 Derived Mesendoderm Cultured Cells Histone H3K4ac Library AK413 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 14,084,851
FINDPEAKS_SCORE: 0.2025
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.3404
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9359
IROC_PERCENTILE: 100
POISSON_SCORE: 0.4508
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: Human embryonic stem cells received from the James Thomson laboratory.  Cells are from the H1 line and are differentiated into mesendoderm by treatment with BMP4.; renlab.H3K4ac.BMP4M.01.01

value: Cell Line

value: Embryonic Stem Cell

value: Embryonic stem cell differentiated into mesendoderm by treatment with BMP4

value: H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days

value: Between 25 and 35

value: Histone H3K4ac

value: Upstate


title: Reference Epigenome: ChIP-Seq Analysis of H4K8ac in BMP4 Mesendoderm Cells; renlab.H4K8ac.BMP4M.01.01

description:
sample_term_id: NTR_0000856
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H4K8ac in BMP4 Mesendoderm Cells. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AK417
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.13097
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.11184
****************
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: GSM956028_UCSD.H1_BMP4_Derived_Mesendoderm_Cultured_Cells.H4K8ac.AK417.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H4K8ac.BMP4M.01.01.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of H1 BMP4 Derived Mesendoderm Cultured Cells H4K8ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H4K8ac ChIP-Seq on H1 BMP4 Derived Mesendoderm Cultured Cells, Library AK417, 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.16427
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: 14,296,780
FINDPEAKS_SCORE: 0.062
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.2099
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.812
IROC_PERCENTILE: 100
POISSON_SCORE: 0.3081
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM956028_UCSD.H1_BMP4_Derived_Mesendoderm_Cultured_Cells.H4K8ac.AK417.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H4K8ac.BMP4M.01.01.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of H1 BMP4 Derived Mesendoderm Cultured Cells H4K8ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H4K8ac ChIP-Seq read mappings from the H1 BMP4 Derived Mesendoderm Cultured Cells, Library AK417, 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.16581
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: HBDM H4K8ac 17
BROWSER_TRACK_DESCRIPTION: UCSD H1 BMP4 Derived Mesendoderm Cultured Cells Histone H4K8ac Library AK417 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 14,296,780
FINDPEAKS_SCORE: 0.062
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.2099
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.812
IROC_PERCENTILE: 100
POISSON_SCORE: 0.3081
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: Human embryonic stem cells received from the James Thomson laboratory.  Cells are from the H1 line and are differentiated into mesendoderm by treatment with BMP4.; renlab.H4K8ac.BMP4M.01.01

value: Male

value: Histone H4K8ac

value: Biorupter

value: 500 micrograms

value: magnetic anti-rabbit

value: 5 micrograms

value: Millipore


title: cbp1_IP_2

value: h- leu1-32 cbp1D::kanMX rad22-CFP-TAP-natMX

value: IgG Sepharose 6 Fast Flow

value: GE Healthcare, 17-0969-02


title: Reference Epigenome: ChIP-Seq Analysis of H3K27me3 in Neural Progenitor Cells; renlab.H3K27me3.NPC.04.01

description:
sample_term_id: CL_0000047
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K27me3 in Neural Progenitor Cells. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AK409
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.13091
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.13084
****************
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: GSM956010_UCSD.H1_Derived_Neuronal_Progenitor_Cultured_Cells.H3K27me3.AK409.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27me3.NPC.04.01.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of H1 Derived Neuronal Progenitor Cultured Cells H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27me3 ChIP-Seq on H1 Derived Neuronal Progenitor Cultured Cells, Library AK409, 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.16472
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: 18,279,165
FINDPEAKS_SCORE: 0.0385
FINDPEAKS_PERCENTILE: 32
HOTSPOT_SCORE: 0.1164
HOTSPOT_PERCENTILE: 20
IROC_SCORE: 0.9734
IROC_PERCENTILE: 90
POISSON_SCORE: 0.1866
POISSON_PERCENTILE: 5
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

ANALYSIS FILE NAME: GSM956010_UCSD.H1_Derived_Neuronal_Progenitor_Cultured_Cells.H3K27me3.AK409.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27me3.NPC.04.01.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Derived Neuronal Progenitor Cultured Cells H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27me3 ChIP-Seq read mappings from the H1 Derived Neuronal Progenitor Cultured Cells, Library AK409, 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.16626
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: HDNP H3K27me3 09
BROWSER_TRACK_DESCRIPTION: UCSD H1 Derived Neuronal Progenitor Cultured Cells Histone H3K27me3 Library AK409 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 18,279,165
FINDPEAKS_SCORE: 0.0385
FINDPEAKS_PERCENTILE: 32
HOTSPOT_SCORE: 0.1164
HOTSPOT_PERCENTILE: 20
IROC_SCORE: 0.9734
IROC_PERCENTILE: 90
POISSON_SCORE: 0.1866
POISSON_PERCENTILE: 5
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

source_name: Human embryonic stem cells received from the James Thomson laboratory.  Cells are from the H1 line and are differentiated into neural progenitor cells.; renlab.H3K27me3.NPC.04.01

value: genomic DNA

value: James Thomson Laboratory

value: Cell Line

value: Embryonic stem cell differentiated into neural progenitor cells

value: Publication in progress

value: Histone H3K27me3

value: Active Motif


title: Reference Epigenome: ChIP-Seq Analysis of H3K27ac in Neural Progenitor Cells; renlab.H3K27ac.NPC.05.01

description:
sample_term_id: CL_0000047
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K27ac in Neural Progenitor Cells. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AK408
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.13087
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.13084
****************
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: GSM956008_UCSD.H1_Derived_Neuronal_Progenitor_Cultured_Cells.H3K27ac.AK408.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27ac.NPC.05.01.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of H1 Derived Neuronal Progenitor Cultured Cells H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27ac ChIP-Seq on H1 Derived Neuronal Progenitor Cultured Cells, Library AK408, 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.16360
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: 16,634,551
FINDPEAKS_SCORE: 0.1335
FINDPEAKS_PERCENTILE: 6
HOTSPOT_SCORE: 0.2288
HOTSPOT_PERCENTILE: 13
IROC_SCORE: 0.9912
IROC_PERCENTILE: 31
POISSON_SCORE: 0.275
POISSON_PERCENTILE: 6
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM956008_UCSD.H1_Derived_Neuronal_Progenitor_Cultured_Cells.H3K27ac.AK408.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27ac.NPC.05.01.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Derived Neuronal Progenitor Cultured Cells H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27ac ChIP-Seq read mappings from the H1 Derived Neuronal Progenitor Cultured Cells, Library AK408, 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.16514
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: HDNP H3K27ac 08
BROWSER_TRACK_DESCRIPTION: UCSD H1 Derived Neuronal Progenitor Cultured Cells Histone H3K27ac Library AK408 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 16,634,551
FINDPEAKS_SCORE: 0.1335
FINDPEAKS_PERCENTILE: 6
HOTSPOT_SCORE: 0.2288
HOTSPOT_PERCENTILE: 13
IROC_SCORE: 0.9912
IROC_PERCENTILE: 31
POISSON_SCORE: 0.275
POISSON_PERCENTILE: 6
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

source_name: Human embryonic stem cells received from the James Thomson laboratory.  Cells are from the H1 line and are differentiated into neural progenitor cells.; renlab.H3K27ac.NPC.05.01

value: Embryonic Stem Cell

value: Male

value: Histone H3K27ac


title: cbp1_IP_1

data_processing:
Basecalling by Illumina Casava software
Sequencing reads were trimmed for index sequence, and mapped to S. pombe reference genome using SOAP2 software, allowing only perfectly and uniquely-matched reads
Genome_build: S. pombe 972 strain
Supplementary_files_format_and_content: bed file. The values indicate the number of sequencing reads mapped to certain location.


title: ams2_IP_2

value: h- leu1-32 ams2D::kanMX rad22-CFP-TAP-natMX


title: Reference Epigenome: ChIP-Seq Analysis of H3K18ac in Neural Progenitor Cells; renlab.H3K18ac.NPC.02.01

description:
sample_term_id: CL_0000047
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K18ac in Neural Progenitor Cells. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: CY11
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.13363
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.13084
****************
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: GSM956007_UCSD.H1_Derived_Neuronal_Progenitor_Cultured_Cells.H3K18ac.CY11.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K18ac.NPC.02.01.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of H1 Derived Neuronal Progenitor Cultured Cells H3K18ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K18ac ChIP-Seq on H1 Derived Neuronal Progenitor Cultured Cells, Library CY11, 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.16449
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: 38,846,564
FINDPEAKS_SCORE: 0.1294
FINDPEAKS_PERCENTILE: 50
HOTSPOT_SCORE: 0.2516
HOTSPOT_PERCENTILE: 50
IROC_SCORE: 0.9077
IROC_PERCENTILE: 50
POISSON_SCORE: 0.4611
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM956007_UCSD.H1_Derived_Neuronal_Progenitor_Cultured_Cells.H3K18ac.CY11.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K18ac.NPC.02.01.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Derived Neuronal Progenitor Cultured Cells H3K18ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K18ac ChIP-Seq read mappings from the H1 Derived Neuronal Progenitor Cultured Cells, Library CY11, 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.16603
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: HDNP H3K18ac 11
BROWSER_TRACK_DESCRIPTION: UCSD H1 Derived Neuronal Progenitor Cultured Cells Histone H3K18ac Library CY11 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 38,846,564
FINDPEAKS_SCORE: 0.1294
FINDPEAKS_PERCENTILE: 50
HOTSPOT_SCORE: 0.2516
HOTSPOT_PERCENTILE: 50
IROC_SCORE: 0.9077
IROC_PERCENTILE: 50
POISSON_SCORE: 0.4611
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

source_name: Human embryonic stem cells received from the James Thomson laboratory.  Cells are from the H1 line and are differentiated into neural progenitor cells.; renlab.H3K18ac.NPC.02.01

value: Histone H3K18ac

value: Biorupter

value: 500 micrograms

value: magnetic anti-rabbit

value: Abcam


title: ams2_IP_1

value: IgG Sepharose 6 Fast Flow

value: GE Healthcare, 17-0969-02


title: hst4_cdc25_50min_IP

value: h- leu1-32 hst4D::kanMX cdc25-22 rad22-CFP-TAP-natMX


title: Reference Epigenome: ChIP-Seq Analysis of H2BK5ac in Neural Progenitor Cells; renlab.H2BK5ac.NPC.01.01

description:
sample_term_id: CL_0000047
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H2BK5ac in Neural Progenitor Cells. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: CY10
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.13358
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.13084
****************
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: GSM956005_UCSD.H1_Derived_Neuronal_Progenitor_Cultured_Cells.H2BK5ac.CY10.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H2BK5ac.NPC.01.01.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of H1 Derived Neuronal Progenitor Cultured Cells H2BK5ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H2BK5ac ChIP-Seq on H1 Derived Neuronal Progenitor Cultured Cells, Library CY10, 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.16349
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: 26,139,143
FINDPEAKS_SCORE: 0.0289
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.1847
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.8032
IROC_PERCENTILE: 100
POISSON_SCORE: 0.3994
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM956005_UCSD.H1_Derived_Neuronal_Progenitor_Cultured_Cells.H2BK5ac.CY10.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H2BK5ac.NPC.01.01.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Derived Neuronal Progenitor Cultured Cells H2BK5ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H2BK5ac ChIP-Seq read mappings from the H1 Derived Neuronal Progenitor Cultured Cells, Library CY10, 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.16503
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: HDNP H2BK5ac 10
BROWSER_TRACK_DESCRIPTION: UCSD H1 Derived Neuronal Progenitor Cultured Cells Histone H2BK5ac Library CY10 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 26,139,143
FINDPEAKS_SCORE: 0.0289
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.1847
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.8032
IROC_PERCENTILE: 100
POISSON_SCORE: 0.3994
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: Human embryonic stem cells received from the James Thomson laboratory.  Cells are from the H1 line and are differentiated into neural progenitor cells.; renlab.H2BK5ac.NPC.01.01

value: genomic DNA

value: James Thomson Laboratory

value: Cell Line

value: Histone H2BK5ac

value: 5 micrograms


title: Reference Epigenome: ChIP-Seq Analysis of H2BK15ac in Neural Progenitor Cells; renlab.H2BK15ac.NPC.01.01

description:
sample_term_id: CL_0000047
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H2BK15ac in Neural Progenitor Cells. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AK422
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.13105
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.10100
****************
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: GSM956003_UCSD.H1_Derived_Neuronal_Progenitor_Cultured_Cells.H2BK15ac.AK422.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H2BK15ac.NPC.01.01.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of H1 Derived Neuronal Progenitor Cultured Cells H2BK15ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H2BK15ac ChIP-Seq on H1 Derived Neuronal Progenitor Cultured Cells, Library AK422, 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.16470
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: 27,188,196
FINDPEAKS_SCORE: 0.003
FINDPEAKS_PERCENTILE: 25
HOTSPOT_SCORE: 0.0547
HOTSPOT_PERCENTILE: 25
IROC_SCORE: 0.4912
IROC_PERCENTILE: 25
POISSON_SCORE: 0.1686
POISSON_PERCENTILE: 25
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM956003_UCSD.H1_Derived_Neuronal_Progenitor_Cultured_Cells.H2BK15ac.AK422.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H2BK15ac.NPC.01.01.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Derived Neuronal Progenitor Cultured Cells H2BK15ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H2BK15ac ChIP-Seq read mappings from the H1 Derived Neuronal Progenitor Cultured Cells, Library AK422, 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.16624
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: HDNP H2BK15ac 22
BROWSER_TRACK_DESCRIPTION: UCSD H1 Derived Neuronal Progenitor Cultured Cells Histone H2BK15ac Library AK422 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 27,188,196
FINDPEAKS_SCORE: 0.003
FINDPEAKS_PERCENTILE: 25
HOTSPOT_SCORE: 0.0547
HOTSPOT_PERCENTILE: 25
IROC_SCORE: 0.4912
IROC_PERCENTILE: 25
POISSON_SCORE: 0.1686
POISSON_PERCENTILE: 25
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

source_name: Human embryonic stem cells received from the James Thomson laboratory.  Cells are from the H1 line and are differentiated into neural progenitor cells.; renlab.H2BK15ac.NPC.01.01

value: Embryonic Stem Cell

value: Embryonic stem cell differentiated into neural progenitor cells

value: Publication in progress

value: Histone H2BK15ac