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Status |
Public on Jun 22, 2013 |
Title |
H3K4me3 ChIP-Seq analysis of UCSF-4 embryonic stem cell line (A19297) |
Sample type |
SRA |
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Source name |
A19297-1
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Organism |
Homo sapiens |
Characteristics |
submitted sample id: JOC170-4-DNA biomaterial_type: cell line line: UCSF-4 Sex: female body site: Embryo ICM histological type: Embryonic stem cell is tumor: No
|
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: H3K4me3 ChIP-Seq analysis of UCSF-4 embryonic stem cell line (A19297) using Illumina HiSeq 2000 library name: A19297 EXPERIMENT_TYPE: Histone H3K4me3 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: 10 ug SIZE_FRACTION: 73-366 bp CHIP_PROTOCOL_BEAD_TYPE: Sepharose A/G Bead Mix CHIP_PROTOCOL_BEAD_AMOUNT: 20 ul CHIP_PROTOCOL_ANTIBODY_AMOUNT: 5 ug CHIP_ANTIBODY: H3K4me3 CHIP_ANTIBODY_PROVIDER: Cell Signaling Technology CHIP_ANTIBODY_CATALOG: 9751S CHIP_ANTIBODY_LOT: 4 **************** 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: GSM1127063_UCSF-UBC.UCSF-4Star.H3K4me3.A19297.bed ANALYSIS CENTER: EDACC ANALYSIS ALIAS: A19297-1.hg19.level.1.release.9 ANALYSIS TITLE: Mapping of UCSF-4* Cell Line H3K4me3 ChIP-Seq Data ANALYSIS DESCRIPTION: Illumina reads produced by H3K4me3 ChIP-Seq on the UCSF-4* Cell Line, Library A19297 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.17017 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: 40,450,743 FINDPEAKS_SCORE: 0.2094 FINDPEAKS_PERCENTILE: 18 HOTSPOT_SCORE: 0.2157 HOTSPOT_PERCENTILE: 11 IROC_SCORE: 1.0 IROC_PERCENTILE: 100 POISSON_SCORE: 0.2286 POISSON_PERCENTILE: 9 MAXIMUM_REPLICATE_CORRELATION: 0.96
**********************************************************************
ANALYSIS FILE NAME: GSM1127063_UCSF-UBC.UCSF-4Star.H3K4me3.A19297.wig ANALYSIS CENTER: EDACC ANALYSIS ALIAS: A19297-1.hg19.level.2.release.9 ANALYSIS TITLE: Raw Signal Density Graphs of UCSF-4Star Cell Line H3K4me3 ChIP-Seq Data ANALYSIS DESCRIPTION: Illumina H3K4me3 ChIP-Seq read mappings from the UCSF-4Star Cell Line, Library A19297 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.17076 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: UCSF4* H3K4me3 97 BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC UCSF-4* Cell Line Histone H3K4me3 Library A19297 EA Release 9
QUALITY SCORES: NUMBER_OF_MAPPED_READS: 40,450,743 FINDPEAKS_SCORE: 0.2094 FINDPEAKS_PERCENTILE: 18 HOTSPOT_SCORE: 0.2157 HOTSPOT_PERCENTILE: 11 IROC_SCORE: 1.0 IROC_PERCENTILE: 100 POISSON_SCORE: 0.2286 POISSON_PERCENTILE: 9 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 |
GSM1127063_UCSF-UBC.UCSF-4Star.H3K4me3.A19297.wig.gz |
SRA |
SRX1158118 |
BioSample |
SAMN03416736 |