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Sample GSM773003 Query DataSets for GSM773003
Status Public on Dec 28, 2011
Title ChIP-Seq analysis of H3K9ac in human HUES64 derived CD184+ cells; DNA_Lib 238
Sample type SRA
 
Source name CD184+ endoderm differentiated in vitro from stem cells; DNA_Lib 238
Organism Homo sapiens
Characteristics cell_type: CD184+ endoderm cultured cells
sample alias: 263
sample common name: hESC Derived CD184+ Endoderm Cultured Cells
lineage: NA
medium: RPMI 100ng/mL Activin A 50ng/mL Wnt3a
molecule: genomic DNA
disease: presumed normal
passage: 1
line: HUES64 derived CD184+
differentiation_method: in vitro culture
batch: BioSAli 137
biomaterial_type: Cell Line
differentiation_stage: differentiated
Sex: Male
biomaterial_provider: Harvard University
chip_protocol_bead_type: Protein A-Sepharose 4B
chip_antibody: H3K9ac
chip_protocol_chromatin_amount: 0.5 to 3 million cells
extraction_protocol: cell/nuclei lysis
chip_protocol_antibody_amount: ~1 ug
chip_protocol_bead_amount: 10 ul bed volume
chip_protocol: Bernstein_BROAD_ENCODE_protocol
extraction_protocol_sonication_cycles: 1
chip_antibody_catalog: ab4441
chip_antibody_provider: Abcam
chip_antibody_lot: 550799
experiment_type: Histone H3K9ac
extraction_protocol_type_of_sonicator: Branson
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 HiSeq 2000
 
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 238
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8693
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: GSM773003_BI.hESC_Derived_CD184+_Endoderm_Cultured_Cells.H3K9ac.DNA_Lib_238.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 238-DNA_Lib 238-DNA_Lib 238-DNA_Lib 238-DNA_Lib 238.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of hESC Derived CD184+ Endoderm Cultured Cells Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9ac ChIP-Seq on hESC Derived CD184+ Endoderm Cultured Cells, Donor DNA_Lib 238, 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.10825
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 5


QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 26,879,749
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 19
FINDPEAKS_SCORE: 0.1142
FINDPEAKS_PERCENTILE: 32
HOTSPOT_SCORE: 0.1597
HOTSPOT_PERCENTILE: 26
IROC_SCORE: 0.9982
IROC_PERCENTILE: 95
POISSON_SCORE: 0.1982
POISSON_PERCENTILE: 26
MAXIMUM_REPLICATE_CORRELATION: 0.92

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

ANALYSIS FILE NAME: GSM773003_BI.hESC_Derived_CD184+_Endoderm_Cultured_Cells.H3K9ac.DNA_Lib_238.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 238-DNA_Lib 238-DNA_Lib 238-DNA_Lib 238-DNA_Lib 238.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of hESC Derived CD184+ Endoderm Cultured Cells Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9ac ChIP-Seq read mappings from hESC Derived CD184+ Endoderm Cultured Cells, Donor DNA_Lib 238, 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.11089
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 5
BROWSER_TRACK_NAME: hDCE H3K9ac 38
BROWSER_TRACK_DESCRIPTION: BI hESC Derived CD184+ Endoderm Cultured Cells Histone H3K9ac Library DNA_Lib 238 EA Release 5


QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 26,879,749
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 19
FINDPEAKS_SCORE: 0.1142
FINDPEAKS_PERCENTILE: 32
HOTSPOT_SCORE: 0.1597
HOTSPOT_PERCENTILE: 26
IROC_SCORE: 0.9982
IROC_PERCENTILE: 95
POISSON_SCORE: 0.1982
POISSON_PERCENTILE: 26
MAXIMUM_REPLICATE_CORRELATION: 0.92

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

 
Submission date Aug 03, 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 GPL11154
Series (1)
GSE17312 BI Human Reference Epigenome Mapping Project
Relations
SRA SRX088918
BioSample SAMN00691473
Named Annotation GSM773003_BI.hESC_Derived_CD184+_Endoderm_Cultured_Cells.H3K9ac.DNA_Lib_238.wig.gz

Supplementary file Size Download File type/resource
GSM773003_BI.hESC_Derived_CD184+_Endoderm_Cultured_Cells.H3K9ac.DNA_Lib_238.bed.gz 420.0 Mb (ftp)(http) BED
GSM773003_BI.hESC_Derived_CD184+_Endoderm_Cultured_Cells.H3K9ac.DNA_Lib_238.wig.gz 46.3 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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