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Sample GSM466734 Query DataSets for GSM466734
Status Public on Jan 07, 2010
Title Reference Epigenome: ChIP-Seq Analysis of H3K27me3 in hESC H1 (hESC-01) Cells; renlab.H3K27me3.hESC-01.01
Sample type SRA
 
Source name hESC-01; renlab.H3K27me3.hESC-01.01
Organism Homo sapiens
Characteristics molecule: genomic DNA
disease: None
biomaterial_provider: James Thompson Laboratory
biomaterial_type: Cell Line
line: H1
lineage: Embryonic Stem Cell
differentiation_stage: None
differentiation_method: None
passage: Between 25 and 45
medium: mTeSER
Sex: Male
batch: 1
experiment_type: Histone H3K27me3
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: H3K27me3
chip_antibody_provider: Upstate
chip_antibody_catalog: 07-449
chip_antibody_lot: DAM1514011
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
 
Description sample_term_id: EFO_0003042
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Library name: LL314
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.1600
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.1595

****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************
Data processing **********************************************************************

ANALYSIS FILE NAME: GSM466734_UCSD.H1.H3K27me3.UCSD_2008_09_25_5.bam
ANALYSIS ALIAS: UCSD.H3K27me3.Level1.2.4
ANALYSIS TITLE: Mapping of H1 H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq for H3K27me3 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.1782
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: GSM466734_UCSD.H1.H3K27me3.UCSD_30RNPAAXX_4.bam
ANALYSIS ALIAS: UCSD.H3K27me3.Level1.2.1
ANALYSIS TITLE: Mapping of H1 H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq for H3K27me3 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.1776
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: GSM466734_UCSD.H1.H3K27me3.UCSD_42B3BAAXX_7.bam
ANALYSIS ALIAS: UCSD.H3K27me3.Level1.2.2
ANALYSIS TITLE: Mapping of H1 H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq for H3K27me3 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.1778
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: GSM466734_UCSD.H1.H3K27me3.UCSD_313BFAAXX_7.bam
ANALYSIS ALIAS: UCSD.H3K27me3.Level1.2.3
ANALYSIS TITLE: Mapping of H1 H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq for H3K27me3 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.1780
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: GSM466734_UCSD.H1.H3K27me3.wig
ANALYSIS ALIAS: UCSD.H3K27me3.Level2.2.4
ANALYSIS TITLE: Raw Signal Density Graphs of H1 H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq read mappings for H3K27me3 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.1783
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: GSM466734_UCSD.H1.H3K27me3.LL314.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27me3.hESC-01.01-renlab.H3K27me3.hESC-01.02-renlab.H3K27me3.hESC-01.03.hg19.level.1
ANALYSIS TITLE: Mapping of H1 Cell Line Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27me3 ChIP-Seq on the H1 Cell Line, Library LL314 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.4401
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_H3K27me3_EXPERIMENTS_SCORED: 52
FINDPEAKS_SCORE: 0.4568
FINDPEAKS_PERCENTILE: 96
HOTSPOT_SCORE: 0.497
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9672
IROC_PERCENTILE: 81
POISSON_SCORE: 0.5322
POISSON_PERCENTILE: 77

**********************************************************************

ANALYSIS FILE NAME: GSM466734_UCSD.H1.H3K27me3.LL314.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27me3.hESC-01.01-renlab.H3K27me3.hESC-01.02-renlab.H3K27me3.hESC-01.03.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Cell Line Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27me3 ChIP-Seq read mappings from the H1 Cell Line, Library LL314 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.4494
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 H3K27me3 14
BROWSER_TRACK_DESCRIPTION: UCSD H1 Cell Line Histone H3K27me3 Library LL314 EA Release 2


QUALITY SCORES:
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED: 52
FINDPEAKS_SCORE: 0.4568
FINDPEAKS_PERCENTILE: 96
HOTSPOT_SCORE: 0.497
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9672
IROC_PERCENTILE: 81
POISSON_SCORE: 0.5322
POISSON_PERCENTILE: 77

**********************************************************************

 
Submission date Oct 30, 2009
Last update date Nov 05, 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 GPL9052
Series (1)
GSE16256 UCSD Human Reference Epigenome Mapping Project
Relations
SRA SRX012368
BioSample SAMN00004698
Named Annotation GSM466734_UCSD.H1.H3K27me3.wig.gz
Named Annotation GSM466734_UCSD.H1.H3K27me3.LL314.wig.gz

Supplementary file Size Download File type/resource
GSM466734_UCSD.H1.H3K27me3.LL314.bed.gz 117.4 Mb (ftp)(http) BED
GSM466734_UCSD.H1.H3K27me3.LL314.wig.gz 21.3 Mb (ftp)(http) WIG
GSM466734_UCSD.H1.H3K27me3.UCSD_2008_09_25_5.bam 725.1 Mb (ftp)(http) BAM
GSM466734_UCSD.H1.H3K27me3.UCSD_30RNPAAXX_4.bam 942.4 Mb (ftp)(http) BAM
GSM466734_UCSD.H1.H3K27me3.UCSD_313BFAAXX_7.bam 558.9 Mb (ftp)(http) BAM
GSM466734_UCSD.H1.H3K27me3.UCSD_42B3BAAXX_7.bam 723.7 Mb (ftp)(http) BAM
GSM466734_UCSD.H1.H3K27me3.wig.gz 25.2 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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