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Status |
Public on Apr 17, 2012 |
Title |
ChIP-Seq input analysis of foreskin keratinocyte from skin01 (A05019) |
Sample type |
SRA |
|
|
Source name |
A05019-1
|
Organism |
Homo sapiens |
Characteristics |
submitted sample id: PF133-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 '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 |
RANDOM |
Instrument model |
Illumina Genome Analyzer IIx |
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Description |
design description: ChIP-Seq input analysis of foreskin keratinocyte from skin01 (A05019) using Illumina Genome Analyzer IIx library name: A05019 EXPERIMENT_TYPE: ChIP-Seq Input 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: 20 min CHIP_PROTOCOL: Input CHIP_PROTOCOL_CHROMATIN_AMOUNT: 5 ug SIZE_FRACTION: 135-499 bp **************** 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: GSM817242_UCSF-UBC.Penis_Foreskin_Keratinocyte_Primary_Cells.Input.skin01.bed ANALYSIS CENTER: EDACC ANALYSIS ALIAS: A05019-1.hg19.level.1.release.6 ANALYSIS TITLE: Mapping of Penis Foreskin Keratinocyte Primary Cells ChIP-Seq Input Data ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input 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.12539 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: 25,266,774 NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 15 FINDPEAKS_SCORE: 0.0875 FINDPEAKS_PERCENTILE: 100 HOTSPOT_SCORE: 0.2823 HOTSPOT_PERCENTILE: 100 IROC_SCORE: 0.9121 IROC_PERCENTILE: 33 POISSON_SCORE: 0.5554 POISSON_PERCENTILE: 100 MAXIMUM_REPLICATE_CORRELATION: NA
**********************************************************************
ANALYSIS FILE NAME: GSM817242_UCSF-UBC.Penis_Foreskin_Keratinocyte_Primary_Cells.Input.skin01.wig ANALYSIS CENTER: EDACC ANALYSIS ALIAS: A05019-1.hg19.level.2.release.6 ANALYSIS TITLE: Raw Signal Density Graphs of Penis Foreskin Keratinocyte Primary Cells ChIP-Seq Input Data ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input 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.12562 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 Input 01 19 BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells ChIP-Seq Input Donor skin01 Library A05019 EA Release 6
QUALITY SCORES: NUMBER_OF_MAPPED_READS: 25,266,774 NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 15 FINDPEAKS_SCORE: 0.0875 FINDPEAKS_PERCENTILE: 100 HOTSPOT_SCORE: 0.2823 HOTSPOT_PERCENTILE: 100 IROC_SCORE: 0.9121 IROC_PERCENTILE: 33 POISSON_SCORE: 0.5554 POISSON_PERCENTILE: 100 MAXIMUM_REPLICATE_CORRELATION: NA
**********************************************************************
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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 |
|
|
Platform ID |
GPL10999 |
Series (1) |
GSE16368 |
UCSF-UBC Human Reference Epigenome Mapping Project |
|
Relations |
Named Annotation |
GSM817242_UCSF-UBC.Penis_Foreskin_Keratinocyte_Primary_Cells.Input.skin01.wig.gz |
SRA |
SRX1157640 |
BioSample |
SAMN03416826 |