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Status |
Public on Jun 22, 2013 |
Title |
H3K27ac ChIP-Seq analysis of placenta (amniotic membrane) tissue from CTL02 (A21722) |
Sample type |
SRA |
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Source name |
A21722-1
|
Organism |
Homo sapiens |
Characteristics |
submitted sample id: JOC217-DNA donor_id: CTL02 Sex: male body site: Placenta histological type: Amnion tissue is tumor: No biomaterial_type: primary tissue tissue_type: placenta (amniotic membrane) tissue
|
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 placenta (amniotic membrane) tissue from CTL02 (A21722) using Illumina HiSeq 2000 library name: A21722 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: 15 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: 4.5 ug SIZE_FRACTION: 151-463 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: GR55451-1 **************** 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: GSM1127132_UCSF-UBC.Placenta_Amnion.H3K27ac.CTL02.bed ANALYSIS CENTER: EDACC ANALYSIS ALIAS: A21722-1.hg19.level.1.release.9 ANALYSIS TITLE: Mapping of Placenta Amnion H3K27ac ChIP-Seq Data ANALYSIS DESCRIPTION: Illumina reads produced by H3K27ac ChIP-Seq on Placenta Amnion, Donor CTL02 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.17055 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: 28,256,387 FINDPEAKS_SCORE: 0.0041 FINDPEAKS_PERCENTILE: 1 HOTSPOT_SCORE: 0.0754 HOTSPOT_PERCENTILE: 7 IROC_SCORE: 0.658 IROC_PERCENTILE: 1 POISSON_SCORE: 0.1914 POISSON_PERCENTILE: 4 MAXIMUM_REPLICATE_CORRELATION: NA
**********************************************************************
ANALYSIS FILE NAME: GSM1127132_UCSF-UBC.Placenta_Amnion.H3K27ac.CTL02.wig ANALYSIS CENTER: EDACC ANALYSIS ALIAS: A21722-1.hg19.level.2.release.9 ANALYSIS TITLE: Raw Signal Density Graphs of Placenta Amnion H3K27ac ChIP-Seq Data ANALYSIS DESCRIPTION: Illumina H3K27ac ChIP-Seq read mappings from Placenta Amnion, Donor CTL02 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.17114 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: PA H3K27ac 02 22 BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Placenta Amnion Histone H3K27ac Donor CTL02 Library A21722 EA Release 9
QUALITY SCORES: NUMBER_OF_MAPPED_READS: 28,256,387 FINDPEAKS_SCORE: 0.0041 FINDPEAKS_PERCENTILE: 1 HOTSPOT_SCORE: 0.0754 HOTSPOT_PERCENTILE: 7 IROC_SCORE: 0.658 IROC_PERCENTILE: 1 POISSON_SCORE: 0.1914 POISSON_PERCENTILE: 4 MAXIMUM_REPLICATE_CORRELATION: NA
**********************************************************************
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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 |
GSM1127132_UCSF-UBC.Placenta_Amnion.H3K27ac.CTL02.wig.gz |
SRA |
SRX1157777 |
BioSample |
SAMN03416769 |