|
Status |
Public on Sep 02, 2011 |
Title |
H3K9ac ChIP-Seq analysis of breast myoepithelial cell from RM066 (HS2444) |
Sample type |
SRA |
|
|
Source name |
HS2444-1
|
Organism |
Homo sapiens |
Characteristics |
submitted sample id: JOC54-DNA donor_id: RM066 Sex: female body site: Breast histological type: Myoepithelial cell is tumor: No biomaterial_type: primary cell cell_type: breast myoepithelial cell
|
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 Genome Analyzer IIx |
|
|
Description |
design description: H3K9ac ChIP-Seq analysis of breast myoepithelial cell from RM066 (HS2444) using Illumina Genome Analyzer IIx library name: HS2444 EXPERIMENT_TYPE: Histone H3K9ac 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: 1 ug SIZE_FRACTION: 55-280 bp CHIP_PROTOCOL_BEAD_TYPE: Sepharose A/G Bead Mix CHIP_PROTOCOL_BEAD_AMOUNT: 20 ul CHIP_PROTOCOL_ANTIBODY_AMOUNT: 10 ul CHIP_ANTIBODY: H3K9ac CHIP_ANTIBODY_PROVIDER: Cell Signaling Technology CHIP_ANTIBODY_CATALOG: 9649S 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: GSM693276_UCSF-UBC.Breast_Myoepithelial_Cells.H3K9ac.RM066.bed ANALYSIS CENTER: EDACC ANALYSIS ALIAS: HS2444-1.hg19.level.1.release.4 ANALYSIS TITLE: Mapping of Breast Myoepithelial Cells Histone H3K9ac ChIP-Seq Data ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9ac ChIP-Seq on Breast Myoepithelial Cells, Donor RM066 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.8188 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 4
QUALITY SCORES: NUMBER_OF_MAPPED_READS: 10,416,409 NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 3 FINDPEAKS_SCORE: 0.1319 FINDPEAKS_PERCENTILE: 33 HOTSPOT_SCORE: 0.2469 HOTSPOT_PERCENTILE: 67 IROC_SCORE: 0.9055 IROC_PERCENTILE: 33 POISSON_SCORE: 0.3166 POISSON_PERCENTILE: 67 MAXIMUM_REPLICATE_CORRELATION: 0.87
**********************************************************************
ANALYSIS FILE NAME: GSM693276_UCSF-UBC.Breast_Myoepithelial_Cells.H3K9ac.RM066.wig ANALYSIS CENTER: EDACC ANALYSIS ALIAS: HS2444-1.hg19.level.2.release.4 ANALYSIS TITLE: Raw Signal Density Graphs of Breast Myoepithelial Cells Histone H3K9ac ChIP-Seq Data ANALYSIS DESCRIPTION: Illumina Histone H3K9ac ChIP-Seq read mappings from Breast Myoepithelial Cells, Donor RM066 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.8208 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 4 BROWSER_TRACK_NAME: BMC H3K9ac 66 BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Breast Myoepithelial Cells Histone H3K9ac Donor RM066 Library HS2444-1 EA Release 4
QUALITY SCORES: NUMBER_OF_MAPPED_READS: 10,416,409 NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 3 FINDPEAKS_SCORE: 0.1319 FINDPEAKS_PERCENTILE: 33 HOTSPOT_SCORE: 0.2469 HOTSPOT_PERCENTILE: 67 IROC_SCORE: 0.9055 IROC_PERCENTILE: 33 POISSON_SCORE: 0.3166 POISSON_PERCENTILE: 67 MAXIMUM_REPLICATE_CORRELATION: 0.87
**********************************************************************
|
|
|
Submission date |
Mar 17, 2011 |
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 |
GSM693276_UCSF-UBC.Breast_Myoepithelial_Cells.H3K9ac.RM066.wig.gz |
SRA |
SRX1157854 |
BioSample |
SAMN03416816 |