|
Status |
Public on Sep 02, 2011 |
Title |
H3K36me3 ChIP-Seq analysis of breast variant human mammary epithelial cell from RM035 (HS1993) |
Sample type |
SRA |
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|
Source name |
HS1993-1
|
Organism |
Homo sapiens |
Characteristics |
submitted sample id: PF068-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/)
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Library strategy |
ChIP-Seq |
Library source |
genomic |
Library selection |
ChIP |
Instrument model |
Illumina Genome Analyzer IIx |
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Description |
design description: H3K36me3 ChIP-Seq analysis of breast variant human mammary epithelial cell from RM035 (HS1993) using Illumina Genome Analyzer IIx library name: HS1993 EXPERIMENT_TYPE: Histone H3K36me3 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: 25 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: 1 ug SIZE_FRACTION: 232-462 bp CHIP_PROTOCOL_BEAD_TYPE: Protein G Mag Beads CHIP_PROTOCOL_BEAD_AMOUNT: 15 ul CHIP_PROTOCOL_ANTIBODY_AMOUNT: 2 ug CHIP_ANTIBODY: H3K36me3 CHIP_ANTIBODY_PROVIDER: Diagenode CHIP_ANTIBODY_CATALOG: pAb-058-050 CHIP_ANTIBODY_LOT: A241-0011 **************** For data usage terms and conditions, please refer to: http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies ****************
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Data processing |
**********************************************************************
ANALYSIS FILE NAME: GSM693275_UCSF-UBC.Breast_vHMEC.H3K36me3.RM035.bed ANALYSIS CENTER: EDACC ANALYSIS ALIAS: HS1993-1.hg19.level.1.release.4 ANALYSIS TITLE: Mapping of Breast vHMEC Histone H3K36me3 ChIP-Seq Data ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K36me3 ChIP-Seq on Breast vHMEC, Donor RM035, Library HS1993 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.8194 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: 64,049,542 NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 7 FINDPEAKS_SCORE: 0.1142 FINDPEAKS_PERCENTILE: 57 HOTSPOT_SCORE: 0.1787 HOTSPOT_PERCENTILE: 57 IROC_SCORE: 0.9178 IROC_PERCENTILE: 57 POISSON_SCORE: 0.4814 POISSON_PERCENTILE: 57 MAXIMUM_REPLICATE_CORRELATION: NA
**********************************************************************
ANALYSIS FILE NAME: GSM693275_UCSF-UBC.Breast_vHMEC.H3K36me3.RM035.wig ANALYSIS CENTER: EDACC ANALYSIS ALIAS: HS1993-1.hg19.level.2.release.4 ANALYSIS TITLE: Raw Signal Density Graphs of Breast vHMEC Histone H3K36me3 ChIP-Seq Data ANALYSIS DESCRIPTION: Illumina Histone H3K36me3 ChIP-Seq read mappings from Breast vHMEC, Donor RM035, Library HS1993 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.8214 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: Bv H3K36me3 35 BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Breast vHMEC Histone H3K36me3 Donor RM035 Library HS1993-1 EA Release 4
QUALITY SCORES: NUMBER_OF_MAPPED_READS: 64,049,542 NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 7 FINDPEAKS_SCORE: 0.1142 FINDPEAKS_PERCENTILE: 57 HOTSPOT_SCORE: 0.1787 HOTSPOT_PERCENTILE: 57 IROC_SCORE: 0.9178 IROC_PERCENTILE: 57 POISSON_SCORE: 0.4814 POISSON_PERCENTILE: 57 MAXIMUM_REPLICATE_CORRELATION: NA
**********************************************************************
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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 |
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Relations |
Named Annotation |
GSM693275_UCSF-UBC.Breast_vHMEC.H3K36me3.RM035.wig.gz |
SRA |
SRX1157839 |
BioSample |
SAMN03416810 |