|
Status |
Public on Jun 04, 2012 |
Title |
ChIP-Seq input analysis of foreskin melanocyte from skin02 (A08748) |
Sample type |
SRA |
|
|
Source name |
A08748-1
|
Organism |
Homo sapiens |
Characteristics |
submitted sample id: JOC130-DNA donor_id: skin02 Sex: male body site: Penis histological type: Melanocyte is tumor: No biomaterial_type: primary cell culture cell type: foreskin melanocyte
|
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 |
RANDOM |
Instrument model |
Illumina HiSeq 2000 |
|
|
Description |
design description: ChIP-Seq input analysis of foreskin melanocyte from skin02 (A08748) using Illumina HiSeq 2000 library name: A08748 EXPERIMENT_TYPE: ChIP-Seq Input 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: Input CHIP_PROTOCOL_CHROMATIN_AMOUNT: N/A SIZE_FRACTION: 87-297 bp **************** 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: GSM941741_UCSF-UBC.Penis_Foreskin_Melanocyte_Primary_Cells.Input.skin02.bed ANALYSIS CENTER: EDACC ANALYSIS ALIAS: A08748-1.hg19.level.1.release.7 ANALYSIS TITLE: Mapping of Penis Foreskin Melanocyte Primary Cells ChIP-Seq Input Data ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on Penis Foreskin Melanocyte Primary Cells, Donor skin02 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.12870 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 7
QUALITY SCORES: NUMBER_OF_MAPPED_READS: 22,644,201 NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 6 FINDPEAKS_SCORE: 0.002 FINDPEAKS_PERCENTILE: 33 HOTSPOT_SCORE: 0.0107 HOTSPOT_PERCENTILE: 17 IROC_SCORE: 0.0 IROC_PERCENTILE: 33 POISSON_SCORE: 0.0339 POISSON_PERCENTILE: 17 MAXIMUM_REPLICATE_CORRELATION: 0.91
**********************************************************************
ANALYSIS FILE NAME: GSM941741_UCSF-UBC.Penis_Foreskin_Melanocyte_Primary_Cells.Input.skin02.wig ANALYSIS CENTER: EDACC ANALYSIS ALIAS: A08748-1.hg19.level.2.release.7 ANALYSIS TITLE: Raw Signal Density Graphs of Penis Foreskin Melanocyte Primary Cells ChIP-Seq Input Data ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from Penis Foreskin Melanocyte Primary Cells, Donor skin02 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.12894 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 7 BROWSER_TRACK_NAME: PFM Input 02 48 BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells ChIP-Seq Input Donor skin02 Library A08748 EA Release 7
QUALITY SCORES: NUMBER_OF_MAPPED_READS: 22,644,201 NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 6 FINDPEAKS_SCORE: 0.002 FINDPEAKS_PERCENTILE: 33 HOTSPOT_SCORE: 0.0107 HOTSPOT_PERCENTILE: 17 IROC_SCORE: 0.0 IROC_PERCENTILE: 33 POISSON_SCORE: 0.0339 POISSON_PERCENTILE: 17 MAXIMUM_REPLICATE_CORRELATION: 0.91
**********************************************************************
|
|
|
Submission date |
Jun 01, 2012 |
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 |
GPL11154 |
Series (1) |
GSE16368 |
UCSF-UBC Human Reference Epigenome Mapping Project |
|
Relations |
Named Annotation |
GSM941741_UCSF-UBC.Penis_Foreskin_Melanocyte_Primary_Cells.Input.skin02.wig.gz |
SRA |
SRX1157668 |
BioSample |
SAMN03416781 |