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Status |
Public on Apr 17, 2012 |
Title |
H3K27me3 ChIP-Seq analysis of foreskin keratinocyte from skin01 (A05937) |
Sample type |
SRA |
|
|
Source name |
A05937-1
|
Organism |
Homo sapiens |
Characteristics |
submitted sample id: PF177-DNA donor_id: skin01 Sex: male body site: Penis histological type: Keratinocyte is tumor: No biomaterial_type: primary cell culture cell type: foreskin keratinocyte
|
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/)
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Library strategy |
ChIP-Seq |
Library source |
genomic |
Library selection |
ChIP |
Instrument model |
Illumina HiSeq 2000 |
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|
Description |
design description: H3K27me3 ChIP-Seq analysis of foreskin keratinocyte from skin01 (A05937) using Illumina HiSeq 2000 library name: A05937 EXPERIMENT_TYPE: Histone H3K27me3 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: Bioruptor EXTRACTION_PROTOCOL_SONICATION_CYCLES: 20 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: 88-338 bp CHIP_PROTOCOL_BEAD_TYPE: Protein A/G Beads CHIP_PROTOCOL_BEAD_AMOUNT: 15 ul CHIP_PROTOCOL_ANTIBODY_AMOUNT: 10 ul CHIP_ANTIBODY: H3K27me3 CHIP_ANTIBODY_PROVIDER: Cell Signaling Technology CHIP_ANTIBODY_CATALOG: 9733S CHIP_ANTIBODY_LOT: GR16377-1 **************** 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: GSM817229_UCSF-UBC.Penis_Foreskin_Keratinocyte_Primary_Cells.H3K27me3.skin01.A05937.bed ANALYSIS CENTER: EDACC ANALYSIS ALIAS: A02886-1-A05937-1.hg19.level.1.release.6 ANALYSIS TITLE: Mapping of Penis Foreskin Keratinocyte Primary Cells Histone H3K27me3 ChIP-Seq Data ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27me3 ChIP-Seq on Penis Foreskin Keratinocyte Primary Cells, Donor skin01 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.12530 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 6
QUALITY SCORES: NUMBER_OF_MAPPED_READS: 22,957,162 NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 10 FINDPEAKS_SCORE: 0.0079 FINDPEAKS_PERCENTILE: 20 HOTSPOT_SCORE: 0.089 HOTSPOT_PERCENTILE: 40 IROC_SCORE: 0.6779 IROC_PERCENTILE: 20 POISSON_SCORE: 0.2195 POISSON_PERCENTILE: 30 MAXIMUM_REPLICATE_CORRELATION: 0.76
**********************************************************************
ANALYSIS FILE NAME: GSM817229_UCSF-UBC.Penis_Foreskin_Keratinocyte_Primary_Cells.H3K27me3.skin01.A05937.wig ANALYSIS CENTER: EDACC ANALYSIS ALIAS: A02886-1-A05937-1.hg19.level.2.release.6 ANALYSIS TITLE: Raw Signal Density Graphs of Penis Foreskin Keratinocyte Primary Cells Histone H3K27me3 ChIP-Seq Data ANALYSIS DESCRIPTION: Illumina Histone H3K27me3 ChIP-Seq read mappings from Penis Foreskin Keratinocyte Primary Cells, Donor skin01 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.12553 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 6 BROWSER_TRACK_NAME: PFK H3K27me3 01 37 BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells Histone H3K27me3 Donor skin01 Library A02886 EA Release 6
QUALITY SCORES: NUMBER_OF_MAPPED_READS: 22,957,162 NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 10 FINDPEAKS_SCORE: 0.0079 FINDPEAKS_PERCENTILE: 20 HOTSPOT_SCORE: 0.089 HOTSPOT_PERCENTILE: 40 IROC_SCORE: 0.6779 IROC_PERCENTILE: 20 POISSON_SCORE: 0.2195 POISSON_PERCENTILE: 30 MAXIMUM_REPLICATE_CORRELATION: 0.76
**********************************************************************
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Submission date |
Oct 14, 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 |
|
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Platform ID |
GPL11154 |
Series (1) |
GSE16368 |
UCSF-UBC Human Reference Epigenome Mapping Project |
|
Relations |
Named Annotation |
GSM817229_UCSF-UBC.Penis_Foreskin_Keratinocyte_Primary_Cells.H3K27me3.skin01.A05937.wig.gz |
SRA |
SRX1157645 |
BioSample |
SAMN03416701 |