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Status |
Public on Mar 31, 2011 |
Title |
ChIP-Seq analysis of H3K9me3 in HUES64 cells; Lib:MC:20101025:06--ChIP:MC:20101020:06:ES cell HUES_64:H3K9Me3 |
Sample type |
SRA |
|
|
Source name |
Harvard University Embryonic Stem Cells; Lib:MC:20101025:06--ChIP:MC:20101020:06:ES cell HUES_64:H3K9Me3
|
Organism |
Homo sapiens |
Characteristics |
sample alias: 196 sample common name: HUES64 Cell Line lineage: embrionic stem cell medium: KSR molecule: genomic DNA disease: none passage: NA line: HUES64 differentiation_method: NA batch: ES cell HUES_64-1 biomaterial_type: Cell Line differentiation_stage: undifferentiated Sex: Unknown biomaterial_provider: Harvard University chip_protocol_bead_type: Protein A-Sepharose 4B chip_antibody: H3K9Me3 chip_protocol_chromatin_amount: 10 million cells extraction_protocol: SDS lysis chip_protocol_antibody_amount: 2-15 ug chip_protocol_bead_amount: 70 ul bed volume chip_protocol: Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles: 1 chip_antibody_catalog: ab8898 chip_antibody_provider: Abcam chip_antibody_lot: 484088 experiment_type: Histone H3K9me3 extraction_protocol_type_of_sonicator: Bioruptor
|
Extracted molecule |
genomic DNA |
Extraction protocol |
Library construction protocol: Single read - Illumina
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|
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Library strategy |
ChIP-Seq |
Library source |
genomic |
Library selection |
ChIP |
Instrument model |
Illumina Genome Analyzer IIx |
|
|
Description |
sample_term_id: NTR_0000853 assay_term_id: OBI_0000716 nucleic_acid_term_id: SO_0000352 Design description: Human Chromatin IP REMC Sequencing on Illumina Library name: Lib:MC:20101025:06--ChIP:MC:20101020:06:ES cell HUES_64:H3K9Me3 EDACC Genboree Experiment Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5669 EDACC Genboree Sample Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5931 **************** 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: GSM669928_BI.HUES64.H3K9me3.Lib_MC_20101025_06--ChIP_MC_20101020_06_ES_cell_HUES_64_H3K9Me3.bed ANALYSIS CENTER: EDACC ANALYSIS ALIAS: Lib:MC:20101025:06--ChIP:MC:20101020:06:ES cell HUES_64:H3K9Me3.hg19.level.1.release.3 ANALYSIS TITLE: Mapping of HUES64 Cell Line Histone H3K9me3 ChIP-Seq Data ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9me3 ChIP-Seq on the HUES64 Cell Line, Library Lib:MC:20101025:06--ChIP:MC:20101020:06:ES cell HUES_64:H3K9Me3 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.6582 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 3
QUALITY SCORES: NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 60 FINDPEAKS_SCORE: 0.2897 FINDPEAKS_PERCENTILE: 96 HOTSPOT_SCORE: 0.241 HOTSPOT_PERCENTILE: 92 IROC_SCORE: 0.969 IROC_PERCENTILE: 100 POISSON_SCORE: 0.4338 POISSON_PERCENTILE: 96
**********************************************************************
ANALYSIS FILE NAME: GSM669928_BI.HUES64.H3K9me3.Lib_MC_20101025_06--ChIP_MC_20101020_06_ES_cell_HUES_64_H3K9Me3.wig ANALYSIS CENTER: EDACC ANALYSIS ALIAS: Lib:MC:20101025:06--ChIP:MC:20101020:06:ES cell HUES_64:H3K9Me3.hg19.level.2.release.3 ANALYSIS TITLE: Raw Signal Density Graphs of HUES64 Cell Line Histone H3K9me3 ChIP-Seq Data ANALYSIS DESCRIPTION: Illumina Histone H3K9me3 ChIP-Seq read mappings from the HUES64 Cell Line, Library Lib:MC:20101025:06--ChIP:MC:20101020:06:ES cell HUES_64:H3K9Me3 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.6792 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 3 BROWSER_TRACK_NAME: HUES64 H3K9me3 e3 BROWSER_TRACK_DESCRIPTION: BI HUES64 Cell Line Histone H3K9me3 Library Lib:MC:20101025:06--ChIP:MC:20101020:06:ES cell HUES_64:H3K9Me3 EA Release 3
QUALITY SCORES: NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 60 FINDPEAKS_SCORE: 0.2897 FINDPEAKS_PERCENTILE: 96 HOTSPOT_SCORE: 0.241 HOTSPOT_PERCENTILE: 92 IROC_SCORE: 0.969 IROC_PERCENTILE: 100 POISSON_SCORE: 0.4338 POISSON_PERCENTILE: 96
**********************************************************************
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Submission date |
Feb 07, 2011 |
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 |
GPL10999 |
Series (1) |
GSE19465 |
BI Human Reference Epigenome Mapping Project: ChIP-Seq in human subject |
|
Relations |
SRA |
SRX040975 |
BioSample |
SAMN00205667 |
Named Annotation |
GSM669928_BI.HUES64.H3K9me3.Lib_MC_20101025_06--ChIP_MC_20101020_06_ES_cell_HUES_64_H3K9Me3.wig.gz |