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Sample GSM537623 Query DataSets for GSM537623
Status Public on Apr 28, 2010
Title ChIP-Seq analysis of H3K4me3 in human WA-7 cells; 30DDNAAXX090707-8-S
Sample type SRA
 
Source name WA7 stem cells; 30DDNAAXX090707-8-S
Organism Homo sapiens
Characteristics molecule: genomic DNA
disease: none
biomaterial_provider: Harvard University
biomaterial_type: Cell Line
line: WA-7
lineage: embrionic stem cell
differentiation_stage: undifferentiated
differentiation_method: none
passage: 46
medium: KSR
sex: Female
batch: 12/25/08
experiment_type: Histone H3K4me3
extraction_protocol: SDS lysis
extraction_protocol_type_of_sonicator: Bioruptor
extraction_protocol_sonication_cycles: 1
chip_protocol: Bernstein_BROAD_ENCODE_protocol
chip_protocol_chromatin_amount: 10 million cells
chip_protocol_bead_type: Protein A-Sepharose 4B
chip_protocol_bead_amount: 70 ul bed volume
chip_protocol_antibody_amount: 2-15 ug
chip_antibody: H3K4Me3
chip_antibody_provider: Millipore
chip_antibody_catalog: 07-473
chip_antibody_lot: R0903B0054
Extracted molecule genomic DNA
Extraction protocol Library construction protocol: Single read - Illumina
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer II
 
Description sample_term_id: NTR_0000837
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Solexa-13062
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.2191
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.2190
****************
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: GSM537623_BI.ES-WA7.H3K4me3.Solexa-13062.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 30DDNAAXX090707-8-S.hg19.level.1
ANALYSIS TITLE: Mapping of ES-WA7 Cell Line Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me3 ChIP-Seq on the ES-WA7 Cell Line, Library Solexa-13062 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.4672
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 2


QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED: 62
FINDPEAKS_SCORE: 0.3467
FINDPEAKS_PERCENTILE: 44
HOTSPOT_SCORE: 0.4014
HOTSPOT_PERCENTILE: 54
IROC_SCORE: 0.9994
IROC_PERCENTILE: 56
POISSON_SCORE: 0.483
POISSON_PERCENTILE: 53

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

ANALYSIS FILE NAME: GSM537623_BI.ES-WA7.H3K4me3.Solexa-13062.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 30DDNAAXX090707-8-S.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of ES-WA7 Cell Line Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me3 ChIP-Seq read mappings from the ES-WA7 Cell Line, Library Solexa-13062 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.4946
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 2
BROWSER_TRACK_NAME: ESWA7 H3K4me3 62
BROWSER_TRACK_DESCRIPTION: BI ES-WA7 Cell Line Histone H3K4me3 Library Solexa-13062 EA Release 2


QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED: 62
FINDPEAKS_SCORE: 0.3467
FINDPEAKS_PERCENTILE: 44
HOTSPOT_SCORE: 0.4014
HOTSPOT_PERCENTILE: 54
IROC_SCORE: 0.9994
IROC_PERCENTILE: 56
POISSON_SCORE: 0.483
POISSON_PERCENTILE: 53

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

 
Submission date Apr 26, 2010
Last update date May 15, 2019
Contact name BROAD INSTITUTE
E-mail(s) rharris1@bcm.tmc.edu
Organization name Broad Institute
Street address -
City Cambridge
State/province MA
ZIP/Postal code 02142
Country USA
 
Platform ID GPL9115
Series (1)
GSE17312 BI Human Reference Epigenome Mapping Project
Relations
BioSample SAMN00012251
SRA SRX019883
Named Annotation GSM537623_BI.ES-WA7.H3K4me3.Solexa-13062.wig.gz

Supplementary file Size Download File type/resource
GSM537623_BI.ES-WA7.H3K4me3.Solexa-13062.bed.gz 82.1 Mb (ftp)(http) BED
GSM537623_BI.ES-WA7.H3K4me3.Solexa-13062.wig.gz 19.3 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data not provided for this record
Raw data are available in SRA

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