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Sample GSM613875 Query DataSets for GSM613875
Status Public on Nov 11, 2010
Title H3K9me3 ChIP-Seq analysis of breast variant human mammary epithelial cell from RM035 (HS2617)
Sample type SRA
 
Source name HS2617-1
Organism Homo sapiens
Characteristics submitted sample id: PF085A-DNA
donor_id: RM035
Sex: female
body site: Breast
histological type: Variant human mammary epithelial cell culture
is tumor: No
biomaterial_type: primary cell culture
cell type: breast variant human mammary epithelial cell
Extracted molecule genomic DNA
Extraction protocol library construction protocol: Refer to document 'REMC ChIP and Library Construction Protocol' from the Farnham Lab 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 Genome Analyzer IIx
 
Description design description: H3K9me3 ChIP-Seq analysis of breast variant human mammary epithelial cell from RM035 (HS2617) using Illumina Genome Analyzer IIx
library name: HS2617
EXPERIMENT_TYPE: Histone H3K9me3
EXTRACTION_PROTOCOL: Refer to document 'REMC ChIP and Library Construction Protocol' from the Farnham Lab at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Bioruptor
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 30 min
CHIP_PROTOCOL: Refer to document 'REMC ChIP and Library Construction Protocol' from the Farnham Lab 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: 259-571 bp
CHIP_PROTOCOL_BEAD_TYPE: Protein G Mag Beads
CHIP_PROTOCOL_BEAD_AMOUNT: 15 ul
CHIP_PROTOCOL_ANTIBODY_AMOUNT: 20 ul
CHIP_ANTIBODY: H3K9me3
CHIP_ANTIBODY_PROVIDER: Cell Signaling Technology
CHIP_ANTIBODY_CATALOG: 9754S
CHIP_ANTIBODY_LOT: 1
****************
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: GSM613875_UCSF-UBC.Breast_vHMEC.H3K9me3.RM035.HS2617.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: HS2617-1_623YCAAXX.hg19.level.1
ANALYSIS TITLE: Mapping of Breast vHMEC Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9me3 ChIP-Seq on Breast vHMEC, Donor RM035, Library HS2617 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.4316
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_H3K9me3_EXPERIMENTS_SCORED: 59
FINDPEAKS_SCORE: 0.0725
FINDPEAKS_PERCENTILE: 47
HOTSPOT_SCORE: 0.1198
HOTSPOT_PERCENTILE: 37
IROC_SCORE: 0.8135
IROC_PERCENTILE: 47
POISSON_SCORE: 0.4678
POISSON_PERCENTILE: 76

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

ANALYSIS FILE NAME: GSM613875_UCSF-UBC.Breast_vHMEC.H3K9me3.RM035.HS2617.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: HS2617-1_623YCAAXX.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Breast vHMEC Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9me3 ChIP-Seq read mappings from Breast vHMEC, Donor RM035, Library HS2617 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.4365
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: Bv H3K9me3 35 17
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-UCD Breast vHMEC Histone H3K9me3 Donor RM035 Library HS2617 EA Release 2


QUALITY SCORES:
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED: 59
FINDPEAKS_SCORE: 0.0725
FINDPEAKS_PERCENTILE: 47
HOTSPOT_SCORE: 0.1198
HOTSPOT_PERCENTILE: 37
IROC_SCORE: 0.8135
IROC_PERCENTILE: 47
POISSON_SCORE: 0.4678
POISSON_PERCENTILE: 76

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

 
Submission date Oct 28, 2010
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 GPL10999
Series (1)
GSE16368 UCSF-UBC Human Reference Epigenome Mapping Project
Relations
Named Annotation GSM613875_UCSF-UBC.Breast_vHMEC.H3K9me3.RM035.HS2617.wig.gz
SRA SRX1157858
BioSample SAMN03416800

Supplementary file Size Download File type/resource
GSM613875_UCSF-UBC.Breast_vHMEC.H3K9me3.RM035.HS2617.bed.gz 272.4 Mb (ftp)(http) BED
GSM613875_UCSF-UBC.Breast_vHMEC.H3K9me3.RM035.HS2617.wig.gz 37.8 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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