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Status |
Public on Jun 22, 2013 |
Title |
ChIP-Seq input analysis of peripheral mononuclear cell from TC016 (A21639) |
Sample type |
SRA |
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Source name |
A21639-1
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Organism |
Homo sapiens |
Characteristics |
submitted sample id: JOC200-2-DNA donor_id: TC016 Sex: female body site: Blood histological type: Peripheral blood mononuclear cell is tumor: No biomaterial_type: primary cell cell_type: Peripheral blood mononuclear cell
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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 |
RANDOM |
Instrument model |
Illumina HiSeq 2000 |
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Description |
design description: ChIP-Seq input analysis of peripheral mononuclear cell from TC016 (A21639) using Illumina HiSeq 2000 library name: A21639 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: 0.1 ug SIZE_FRACTION: 94-294 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: GSM1127149_UCSF-UBC.Peripheral_Blood_Mononuclear_Primary_Cells.Input.TC016.bed ANALYSIS CENTER: EDACC ANALYSIS ALIAS: A21639-1.hg19.level.1.release.9 ANALYSIS TITLE: Mapping of Peripheral Blood Mononuclear Primary Cells Input ChIP-Seq Data ANALYSIS DESCRIPTION: Illumina reads produced by Input ChIP-Seq on Peripheral Blood Mononuclear Primary Cells, Donor TC016, Library A21639 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.17058 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 9
QUALITY SCORES: NUMBER_OF_MAPPED_READS: 38,037,164 FINDPEAKS_SCORE: 0.0053 FINDPEAKS_PERCENTILE: 34 HOTSPOT_SCORE: 0.0039 HOTSPOT_PERCENTILE: 22 IROC_SCORE: 0.0 IROC_PERCENTILE: 25 POISSON_SCORE: 0.017 POISSON_PERCENTILE: 5 MAXIMUM_REPLICATE_CORRELATION: 0.99
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ANALYSIS FILE NAME: GSM1127149_UCSF-UBC.Peripheral_Blood_Mononuclear_Primary_Cells.Input.TC016.wig ANALYSIS CENTER: EDACC ANALYSIS ALIAS: A21639-1.hg19.level.2.release.9 ANALYSIS TITLE: Raw Signal Density Graphs of Peripheral Blood Mononuclear Primary Cells Input ChIP-Seq Data ANALYSIS DESCRIPTION: Illumina Input ChIP-Seq read mappings from Peripheral Blood Mononuclear Primary Cells, Donor TC016, Library A21639 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.17117 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 9 BROWSER_TRACK_NAME: PBM Input 16 39 BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Peripheral Blood Mononuclear Primary Cells ChIP-Seq Input Donor TC016 Library A21639 EA Release 9
QUALITY SCORES: NUMBER_OF_MAPPED_READS: 38,037,164 FINDPEAKS_SCORE: 0.0053 FINDPEAKS_PERCENTILE: 34 HOTSPOT_SCORE: 0.0039 HOTSPOT_PERCENTILE: 22 IROC_SCORE: 0.0 IROC_PERCENTILE: 25 POISSON_SCORE: 0.017 POISSON_PERCENTILE: 5 MAXIMUM_REPLICATE_CORRELATION: 0.99
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Submission date |
Apr 22, 2013 |
Last update date |
May 15, 2019 |
Contact name |
UCSF-UBC CENTER |
Organization name |
UCSF-UBC
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Street address |
UCSF-UBC
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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 |
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Relations |
Named Annotation |
GSM1127149_UCSF-UBC.Peripheral_Blood_Mononuclear_Primary_Cells.Input.TC016.wig.gz |
SRA |
SRX1157724 |
BioSample |
SAMN03416836 |
Supplementary file |
Size |
Download |
File type/resource |
GSM1127149_UCSF-UBC.Peripheral_Blood_Mononuclear_Primary_Cells.Input.TC016.bed.gz |
562.0 Mb |
(ftp)(http) |
BED |
GSM1127149_UCSF-UBC.Peripheral_Blood_Mononuclear_Primary_Cells.Input.TC016.wig.gz |
54.9 Mb |
(ftp)(http) |
WIG |
SRA Run Selector |
Processed data provided as supplementary file |
Raw data are available in SRA |
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