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Sample GSM469974 Query DataSets for GSM469974
Status Public on Jan 07, 2010
Title Reference Epigenome: ChIP-Seq Analysis of H3K9me3 in IMR90 Cells; renlab.H3K9me3.IMR90-01.01
Sample type SRA
 
Source name IMR90; renlab.H3K9me3.IMR90-01.01
Organism Homo sapiens
Characteristics cell_type: IMR90 cells
molecule: genomic DNA
disease: None
biomaterial_provider: ATCC
biomaterial_type: Cell Line
line: IMR90
lineage: NA
batch: 1
differentiation_stage: Fetal lung fibroblast
differentiation_method: NA
passage: 4
medium: Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)
Sex: Female
experiment_type: Histone H3K9me3
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: H3K9me3
chip_antibody_provider: Abcam
chip_antibody_catalog: ab8898
chip_antibody_lot: 484099
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_0001196
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Library name: LL224
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.1723
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.1121

****************
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: GSM469974_UCSD.IMR90.H3K9me3.UCSD_30WNVAAXX_2.bam
ANALYSIS ALIAS: UCSD.IMR90.H3K9me3.Level1.1
ANALYSIS TITLE: Mapping of IMR90 H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq for H3K9me3 in the IMR90 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.1800
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: GSM469974_UCSD.IMR90.H3K9me3.UCSD_42B3BAAXX_3.bam
ANALYSIS ALIAS: UCSD.IMR90.H3K9me3.Level1.2
ANALYSIS TITLE: Mapping of IMR90 H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq for H3K9me3 in the IMR90 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.1802
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: GSM469974_UCSD.IMR90.H3K9me3.UCSD_301FBAAXX_5.bam
ANALYSIS ALIAS: UCSD.IMR90.H3K9me3.Level1.3
ANALYSIS TITLE: Mapping of IMR90 H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq for H3K9me3 in the IMR90 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.1804
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: GSM469974_UCSD.IMR90.H3K9me3.UCSD_313BFAAXX_3.bam
ANALYSIS ALIAS: UCSD.IMR90.H3K9me3.Level1.4
ANALYSIS TITLE: Mapping of IMR90 H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq for H3K9me3 in the IMR90 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.1806
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: GSM469974_UCSD.IMR90.H3K9me3.wig
ANALYSIS ALIAS: UCSD.IMR90.H3K9me3.Level2.4
ANALYSIS TITLE: Raw Signal Density Graphs of IMR90 H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq read mappings for H3K9me3 in the IMR90 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.1807
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: GSM469974_UCSD.IMR90.H3K9me3.LL224.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K9me3.IMR90-01.01.hg19.level.1
ANALYSIS TITLE: Mapping of IMR90 Cell Line Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9me3 ChIP-Seq on the IMR90 Cell Line, Library LL224 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.4397
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: 0.4748
FINDPEAKS_PERCENTILE: 98
HOTSPOT_SCORE: 0.2682
HOTSPOT_PERCENTILE: 85
IROC_SCORE: 0.9446
IROC_PERCENTILE: 88
POISSON_SCORE: 0.5335
POISSON_PERCENTILE: 92

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

ANALYSIS FILE NAME: GSM469974_UCSD.IMR90.H3K9me3.LL224.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K9me3.IMR90-01.01.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of IMR90 Cell Line Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9me3 ChIP-Seq read mappings from the IMR90 Cell Line, Library LL224 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.4505
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: IMR90 H3K9me3 24
BROWSER_TRACK_DESCRIPTION: UCSD IMR90 Cell Line Histone H3K9me3 Library LL224 EA Release 2


QUALITY SCORES:
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED: 59
FINDPEAKS_SCORE: 0.4748
FINDPEAKS_PERCENTILE: 98
HOTSPOT_SCORE: 0.2682
HOTSPOT_PERCENTILE: 85
IROC_SCORE: 0.9446
IROC_PERCENTILE: 88
POISSON_SCORE: 0.5335
POISSON_PERCENTILE: 92

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

 
Submission date Nov 12, 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
SRA SRX012504
BioSample SAMN00004463
Named Annotation GSM469974_UCSD.IMR90.H3K9me3.wig.gz
Named Annotation GSM469974_UCSD.IMR90.H3K9me3.LL224.wig.gz

Supplementary file Size Download File type/resource
GSM469974_UCSD.IMR90.H3K9me3.LL224.bed.gz 279.4 Mb (ftp)(http) BED
GSM469974_UCSD.IMR90.H3K9me3.LL224.wig.gz 39.5 Mb (ftp)(http) WIG
GSM469974_UCSD.IMR90.H3K9me3.UCSD_301FBAAXX_5.bam 522.2 Mb (ftp)(http) BAM
GSM469974_UCSD.IMR90.H3K9me3.UCSD_30WNVAAXX_2.bam 555.3 Mb (ftp)(http) BAM
GSM469974_UCSD.IMR90.H3K9me3.UCSD_313BFAAXX_3.bam 740.5 Mb (ftp)(http) BAM
GSM469974_UCSD.IMR90.H3K9me3.UCSD_42B3BAAXX_3.bam 684.7 Mb (ftp)(http) BAM
GSM469974_UCSD.IMR90.H3K9me3.wig.gz 39.3 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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