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Sample GSM1127080 Query DataSets for GSM1127080
Status Public on Jun 22, 2013
Title H3K4me1 ChIP-Seq analysis of UCSF-4 embryonic stem cell line (A19296)
Sample type SRA
 
Source name A19296-1
Organism Homo sapiens
Characteristics submitted sample id: JOC170-4-DNA
biomaterial_type: cell line
line: UCSF-4
Sex: female
body site: Embryo ICM
histological type: Embryonic stem cell
is tumor: No
Extracted molecule genomic DNA
Extraction protocol library construction protocol: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2000
 
Description design description: H3K4me1 ChIP-Seq analysis of UCSF-4 embryonic stem cell line (A19296) using Illumina HiSeq 2000
library name: A19296
EXPERIMENT_TYPE: Histone H3K4me1
EXTRACTION_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Fisher 550 Sonic Dismembrator
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 10 min
CHIP_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
CHIP_PROTOCOL_CHROMATIN_AMOUNT: 5 ug
SIZE_FRACTION: 81-365 bp
CHIP_PROTOCOL_BEAD_TYPE: Sepharose A/G Bead Mix
CHIP_PROTOCOL_BEAD_AMOUNT: 20 ul
CHIP_PROTOCOL_ANTIBODY_AMOUNT: 5 ug
CHIP_ANTIBODY: H3K4me1
CHIP_ANTIBODY_PROVIDER: Diagenode
CHIP_ANTIBODY_CATALOG: pAb-037-050
CHIP_ANTIBODY_LOT: A399-002341P
****************
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: GSM1127080_UCSF-UBC.UCSF-4Star.H3K4me1.A19296.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A19296-1.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of UCSF-4* Cell Line H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K4me1 ChIP-Seq on the UCSF-4* Cell Line, Library A19296 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.17034
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: 51,385,031
FINDPEAKS_SCORE: 0.1149
FINDPEAKS_PERCENTILE: 23
HOTSPOT_SCORE: 0.2389
HOTSPOT_PERCENTILE: 25
IROC_SCORE: 0.8904
IROC_PERCENTILE: 16
POISSON_SCORE: 0.439
POISSON_PERCENTILE: 43
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

ANALYSIS FILE NAME: GSM1127080_UCSF-UBC.UCSF-4Star.H3K4me1.A19296.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A19296-1.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of UCSF-4Star Cell Line H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K4me1 ChIP-Seq read mappings from the UCSF-4Star Cell Line, Library A19296 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.17093
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: UCSF4* H3K4me1 96
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC UCSF-4* Cell Line Histone H3K4me1 Library A19296 EA Release 9


QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 51,385,031
FINDPEAKS_SCORE: 0.1149
FINDPEAKS_PERCENTILE: 23
HOTSPOT_SCORE: 0.2389
HOTSPOT_PERCENTILE: 25
IROC_SCORE: 0.8904
IROC_PERCENTILE: 16
POISSON_SCORE: 0.439
POISSON_PERCENTILE: 43
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

 
Submission date Apr 22, 2013
Last update date May 15, 2019
Contact name UCSF-UBC CENTER
Organization name UCSF-UBC
Street address UCSF-UBC
City San Francisco
State/province CA
ZIP/Postal code 94143
Country USA
 
Platform ID GPL11154
Series (1)
GSE16368 UCSF-UBC Human Reference Epigenome Mapping Project
Relations
Named Annotation GSM1127080_UCSF-UBC.UCSF-4Star.H3K4me1.A19296.wig.gz
SRA SRX1158117
BioSample SAMN03416736

Supplementary file Size Download File type/resource
GSM1127080_UCSF-UBC.UCSF-4Star.H3K4me1.A19296.bed.gz 779.8 Mb (ftp)(http) BED
GSM1127080_UCSF-UBC.UCSF-4Star.H3K4me1.A19296.wig.gz 57.1 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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