|
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
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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
**********************************************************************
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|
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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 |