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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jun 22, 2013 |
| Title |
H3K27ac ChIP-Seq analysis of peripheral mononuclear cell from TC016 (A21638) |
| Sample type |
SRA |
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| Source name |
A21638-1
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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 |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
design description: H3K27ac ChIP-Seq analysis of peripheral mononuclear cell from TC016 (A21638) using Illumina HiSeq 2000
library name: A21638
EXPERIMENT_TYPE: Histone H3K27ac
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: 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: 94-294 bp
CHIP_PROTOCOL_BEAD_TYPE: Sepharose A/G Bead Mix
CHIP_PROTOCOL_BEAD_AMOUNT: 20 ul
CHIP_PROTOCOL_ANTIBODY_AMOUNT: 2.5 ug
CHIP_ANTIBODY: H3K27ac
CHIP_ANTIBODY_PROVIDER: Abcam
CHIP_ANTIBODY_CATALOG: ab4729
CHIP_ANTIBODY_LOT: GR28147-1
****************
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: GSM1127137_UCSF-UBC.Peripheral_Blood_Mononuclear_Primary_Cells.H3K27ac.TC016.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A21638-1.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Peripheral Blood Mononuclear Primary Cells H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27ac ChIP-Seq on Peripheral Blood Mononuclear Primary Cells, Donor TC016, Library A21638 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.17031
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: 24,518,890
FINDPEAKS_SCORE: 0.0609
FINDPEAKS_PERCENTILE: 4
HOTSPOT_SCORE: 0.112
HOTSPOT_PERCENTILE: 8
IROC_SCORE: 0.9724
IROC_PERCENTILE: 13
POISSON_SCORE: 0.1732
POISSON_PERCENTILE: 1
MAXIMUM_REPLICATE_CORRELATION: 0.96
**********************************************************************
ANALYSIS FILE NAME: GSM1127137_UCSF-UBC.Peripheral_Blood_Mononuclear_Primary_Cells.H3K27ac.TC016.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A21638-1.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Peripheral Blood Mononuclear Primary Cells H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27ac ChIP-Seq read mappings from Peripheral Blood Mononuclear Primary Cells, Donor TC016, Library A21638 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.17090
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 H3K27ac 16 38
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Peripheral Blood Mononuclear Primary Cells Histone H3K27ac Donor TC016 Library A21638 EA Release 9
QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 24,518,890
FINDPEAKS_SCORE: 0.0609
FINDPEAKS_PERCENTILE: 4
HOTSPOT_SCORE: 0.112
HOTSPOT_PERCENTILE: 8
IROC_SCORE: 0.9724
IROC_PERCENTILE: 13
POISSON_SCORE: 0.1732
POISSON_PERCENTILE: 1
MAXIMUM_REPLICATE_CORRELATION: 0.96
**********************************************************************
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| Submission date |
Apr 22, 2013 |
| 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 |
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| Relations |
| Named Annotation |
GSM1127137_UCSF-UBC.Peripheral_Blood_Mononuclear_Primary_Cells.H3K27ac.TC016.wig.gz |
| SRA |
SRX1157723 |
| BioSample |
SAMN03416836 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1127137_UCSF-UBC.Peripheral_Blood_Mononuclear_Primary_Cells.H3K27ac.TC016.bed.gz |
364.6 Mb |
(ftp)(http) |
BED |
| GSM1127137_UCSF-UBC.Peripheral_Blood_Mononuclear_Primary_Cells.H3K27ac.TC016.wig.gz |
44.9 Mb |
(ftp)(http) |
WIG |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
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