|
Status |
Public on Aug 03, 2009 |
Title |
Reference Epigenome: ChIP-Seq Analysis of H3K4me1 in hESC H1 (CDI-01) Cells; renlab.H3K4me1.CDI-01.01 |
Sample type |
SRA |
|
|
Source name |
CDI-01; renlab.H3K4me1.CDI-01.01
|
Organism |
Homo sapiens |
Characteristics |
molecule: genomic DNA disease: None biomaterial_provider: Cellular Dynamics International biomaterial_type: Cell Line line: H1 lineage: Embryonic Stem Cell differentiation_stage: None differentiation_method: None passage: Between 30 and 50 medium: mTeSER Sex: Male experiment_type: Histone H3K4me1 extraction_protocol: See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf extraction_protocol_type_of_sonicator: Branson Tip Sonicator extraction_protocol_sonication_cycles: 30 chip_protocol: See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf chip_protocol_chromatin_amount: 500 micrograms chip_protocol_bead_type: magnetic anti-rabbit chip_protocol_bead_amount: 33,500,000 chip_protocol_antibody_amount: 5 micrograms chip_antibody: H3K4me1 chip_antibody_provider: Abcam chip_antibody_catalog: ab8895 chip_antibody_lot: 535659
|
Extracted molecule |
genomic DNA |
Extraction protocol |
Library construction protocol: See http://bioinformatics-renlab.ucsd.edu/RenLabLibraryProtocolV1.pdf
|
|
|
Library strategy |
ChIP-Seq |
Library source |
genomic |
Library selection |
ChIP |
Instrument model |
Illumina Genome Analyzer II |
|
|
Description |
sample_term_id: EFO_0003042 assay_term_id: OBI_0000716 nucleic_acid_term_id: SO_0000352 Library name: LL228 EDACC Genboree Sample Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.890 EDACC Genboree Experiment Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.875
**************** For data usage terms and conditions, please refer to: http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies **************** BED and WIG files were replaced on April 29, 2014
|
Data processing |
**********************************************************************
ANALYSIS FILE NAME: GSM409307_UCSD.H3K4me1.bam ANALYSIS TITLE: Mapping of H1 H3K4me1 ChIP-Seq Data ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq for H3K4me1 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.1516 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: GSM409307_UCSD.H3K4me1.wig ANALYSIS TITLE: Raw Signal Density Graphs of H1 H3K4me1 ChIP-Seq Data ANALYSIS DESCRIPTION: Illumina ChIP-Seq read mappings for H3K4me1 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.1517 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: GSM409307_UCSD.H1.H3K4me1.LL228.bed ANALYSIS CENTER: EDACC ANALYSIS ALIAS: renlab.H3K4me1.CDI-01.01.hg19.level.1 ANALYSIS TITLE: Mapping of H1 Cell Line Histone H3K4me1 ChIP-Seq Data ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me1 ChIP-Seq on the H1 Cell Line, Library LL228 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.4415 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_H3K4me1_EXPERIMENTS_SCORED: 43 FINDPEAKS_SCORE: 0.0458 FINDPEAKS_PERCENTILE: 7 HOTSPOT_SCORE: 0.1997 HOTSPOT_PERCENTILE: 12 IROC_SCORE: 0.7639 IROC_PERCENTILE: 5 POISSON_SCORE: 0.4372 POISSON_PERCENTILE: 9
**********************************************************************
ANALYSIS FILE NAME: GSM409307_UCSD.H1.H3K4me1.LL228.wig ANALYSIS CENTER: EDACC ANALYSIS ALIAS: renlab.H3K4me1.CDI-01.01.hg19.level.2 ANALYSIS TITLE: Raw Signal Density Graphs of H1 Cell Line Histone H3K4me1 ChIP-Seq Data ANALYSIS DESCRIPTION: Illumina Histone H3K4me1 ChIP-Seq read mappings from the H1 Cell Line, Library LL228 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.4548 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 H3K4me1 28 BROWSER_TRACK_DESCRIPTION: UCSD H1 Cell Line Histone H3K4me1 Library LL228 EA Release 2
QUALITY SCORES: NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED: 43 FINDPEAKS_SCORE: 0.0458 FINDPEAKS_PERCENTILE: 7 HOTSPOT_SCORE: 0.1997 HOTSPOT_PERCENTILE: 12 IROC_SCORE: 0.7639 IROC_PERCENTILE: 5 POISSON_SCORE: 0.4372 POISSON_PERCENTILE: 9
**********************************************************************
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|
|
Submission date |
May 27, 2009 |
Last update date |
May 15, 2019 |
Contact name |
UCSD AND SALK |
Organization name |
University of California, San Diego
|
Street address |
Health Sciences Drive
|
City |
La Jolla |
State/province |
CA |
ZIP/Postal code |
92092 |
Country |
USA |
|
|
Platform ID |
GPL9115 |
Series (1) |
GSE16256 |
UCSD Human Reference Epigenome Mapping Project |
|
Relations |
Reanalyzed by |
GSE99453 |
SRA |
SRX006236 |
BioSample |
SAMN00004459 |
Named Annotation |
GSM409307_UCSD.H3K4me1.wig.gz |
Named Annotation |
GSM409307_UCSD.H1.H3K4me1.LL228.wig.gz |