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Status |
Public on Aug 03, 2009 |
Title |
H3K9me3 ChIP-Seq analysis of H1 embryonic stem cell line (HS0998) |
Sample type |
SRA |
|
|
Source name |
HS0998-1
|
Organism |
Homo sapiens |
Characteristics |
submitted sample id: PF004-DNA biomaterial_type: cell line line: H1 Sex: male body site: Embryo ICM histological type: Embryonic stem cell is tumor: No
|
Extracted molecule |
genomic DNA |
Extraction protocol |
library construction protocol: Refer to document 'REMC ChIP and Library Construction Protocol' from the Farnham Lab 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 Genome Analyzer II |
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|
Description |
design description: H3K9me3 ChIP-Seq analysis of H1 embryonic stem cell line (HS0998) using Illumina Genome Analyzer II library name: HS0998 EXPERIMENT_TYPE: Histone H3K9me3 EXTRACTION_PROTOCOL: Refer to document 'REMC ChIP and Library Construction Protocol' from the Farnham Lab at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/) EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Bioruptor EXTRACTION_PROTOCOL_SONICATION_CYCLES: 15 min CHIP_PROTOCOL: Refer to document 'REMC ChIP and Library Construction Protocol' from the Farnham Lab at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/) CHIP_PROTOCOL_CHROMATIN_AMOUNT: 44 ug SIZE_FRACTION: 60-280 bp CHIP_PROTOCOL_BEAD_TYPE: Protein G Mag Beads CHIP_PROTOCOL_BEAD_AMOUNT: 30 ul CHIP_PROTOCOL_ANTIBODY_AMOUNT: N/A CHIP_ANTIBODY: H3K9me3 CHIP_ANTIBODY_PROVIDER: Abcam CHIP_ANTIBODY_CATALOG: ab8898 CHIP_ANTIBODY_LOT: 492774 **************** 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: GSM428291_UCSF-UBC.H3K9me3.1.bam ANALYSIS TITLE: Mapping of H1 H3K9me3 ChIP-Seq Data ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq for H3K9me3 in the H1 cell line were mapped to the human genome (NCBI Build 36.1) using Pash. ANALYSIS TYPE: REFERENCE ALIGNMENT EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.1534 DATA_ANALYSIS_LEVEL: 1 EXPERIMENT_TYPE: ChIP-Seq 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: None ALIGNMENT_POSTPROCESSING: None
**********************************************************************
ANALYSIS FILE NAME: GSM428291_UCSF-UBC.H3K9me3.2.bam ANALYSIS TITLE: Mapping of H1 H3K9me3 ChIP-Seq Data ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq for H3K9me3 in the H1 cell line were mapped to the human genome (NCBI Build 36.1) using Pash. ANALYSIS TYPE: REFERENCE ALIGNMENT EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.1535 DATA_ANALYSIS_LEVEL: 1 EXPERIMENT_TYPE: ChIP-Seq 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: None ALIGNMENT_POSTPROCESSING: None
**********************************************************************
ANALYSIS FILE NAME: GSM428291_UCSF-UBC.H3K9me3.3.bam ANALYSIS TITLE: Mapping of H1 H3K9me3 ChIP-Seq Data ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq for H3K9me3 in the H1 cell line were mapped to the human genome (NCBI Build 36.1) using Pash. ANALYSIS TYPE: REFERENCE ALIGNMENT EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.1536 DATA_ANALYSIS_LEVEL: 1 EXPERIMENT_TYPE: ChIP-Seq 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: None ALIGNMENT_POSTPROCESSING: None
**********************************************************************
ANALYSIS FILE NAME: GSM428291_UCSF-UBC.H3K9me3.4.bam ANALYSIS TITLE: Mapping of H1 H3K9me3 ChIP-Seq Data ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq for H3K9me3 in the H1 cell line were mapped to the human genome (NCBI Build 36.1) using Pash. ANALYSIS TYPE: REFERENCE ALIGNMENT EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.1537 DATA_ANALYSIS_LEVEL: 1 EXPERIMENT_TYPE: ChIP-Seq 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: None ALIGNMENT_POSTPROCESSING: None
**********************************************************************
ANALYSIS FILE NAME: GSM428291_UCSF-UBC.H3K9me3.wig ANALYSIS TITLE: Raw Signal Density Graphs of H1 H3K9me3 ChIP-Seq Data ANALYSIS DESCRIPTION: Illumina ChIP-Seq read mappings for H3K9me3 in the H1 cell line 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.1538 DATA_ANALYSIS_LEVEL: 2 EXPERIMENT_TYPE: ChIP-Seq SOFTWARE: In house programs and scripts SOFTWARE_VERSION: NA READ_EXTENSION: 200bp GENOMIC_WINDOW: 20bp TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
**********************************************************************
ANALYSIS FILE NAME: GSM428291_UCSF-UBC.H1.H3K9me3.H1EScd1-me3K9-A.bed ANALYSIS CENTER: EDACC ANALYSIS ALIAS: HS0998-1_30WLLAAXX-HS0998-1_305Y8AAXX-HS0998-1_313MWAAXX-HS0998-1_3061PAAXX.hg19.level.1 ANALYSIS TITLE: Mapping of H1 Cell Line Histone H3K9me3 ChIP-Seq Data ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9me3 ChIP-Seq on the H1 Cell Line, Library H1EScd1-me3K9-A 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.4307 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 2
QUALITY SCORES: NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED: 59 FINDPEAKS_SCORE: 0.2638 FINDPEAKS_PERCENTILE: 88 HOTSPOT_SCORE: 0.2167 HOTSPOT_PERCENTILE: 73 IROC_SCORE: 0.9721 IROC_PERCENTILE: 92 POISSON_SCORE: 0.4156 POISSON_PERCENTILE: 61
**********************************************************************
ANALYSIS FILE NAME: GSM428291_UCSF-UBC.H1.H3K9me3.H1EScd1-me3K9-A.wig ANALYSIS CENTER: EDACC ANALYSIS ALIAS: HS0998-1_30WLLAAXX-HS0998-1_305Y8AAXX-HS0998-1_313MWAAXX-HS0998-1_3061PAAXX.hg19.level.2 ANALYSIS TITLE: Raw Signal Density Graphs of H1 Cell Line Histone H3K9me3 ChIP-Seq Data ANALYSIS DESCRIPTION: Illumina Histone H3K9me3 ChIP-Seq read mappings from the H1 Cell Line, Library H1EScd1-me3K9-A 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.4356 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 2 BROWSER_TRACK_NAME: H1 H3K9me3 A BROWSER_TRACK_DESCRIPTION: UCSF-UBC-UCD H1 Cell Line Histone H3K9me3 Library H1EScd1-me3K9-A EA Release 2
QUALITY SCORES: NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED: 59 FINDPEAKS_SCORE: 0.2638 FINDPEAKS_PERCENTILE: 88 HOTSPOT_SCORE: 0.2167 HOTSPOT_PERCENTILE: 73 IROC_SCORE: 0.9721 IROC_PERCENTILE: 92 POISSON_SCORE: 0.4156 POISSON_PERCENTILE: 61
**********************************************************************
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Submission date |
Jul 15, 2009 |
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 |
GPL9115 |
Series (1) |
GSE16368 |
UCSF-UBC Human Reference Epigenome Mapping Project |
|
Relations |
Named Annotation |
GSM428291_UCSF-UBC.H3K9me3.wig.gz |
Named Annotation |
GSM428291_UCSF-UBC.H1.H3K9me3.H1EScd1-me3K9-A.wig.gz |
SRA |
SRX006263 |
BioSample |
SAMN03416720 |