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Sample GSM521901 Query DataSets for GSM521901
Status Public on Mar 22, 2010
Title Reference Epigenome: ChIP-Seq Analysis of H3K4me3 in IMR90 Cells; renlab.H3K4me3.IMR90-02.01
Sample type SRA
 
Source name IMR90 Cell Line, biological replicate 2; renlab.H3K4me3.IMR90-02.01
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: 4
differentiation_stage: Fetal lung fibroblast
differentiation_method: NA
passage: NA
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 H3K4me3
extraction_protocol: See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf
extraction_protocol_type_of_sonicator: Bioruptor
extraction_protocol_sonication_cycles: 120
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: H3K4me3
chip_antibody_provider: Active Motif
chip_antibody_catalog: AM39159
chip_antibody_lot: 15808002
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
Design description: ChIP-Seq Analysis of H3K4me3 in IMR90 cells. Sequencing was done on the Illumina GAII platform.
Library name: SK03
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.1990
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.1957
****************
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: GSM521901_UCSD.IMR90.H3K4me3.SK03.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4me3.IMR90-02.01.hg19.level.1
ANALYSIS TITLE: Mapping of IMR90 Cell Line Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me3 ChIP-Seq on the IMR90 Cell Line, Library SK03 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.4405
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_H3K4me3_EXPERIMENTS_SCORED: 62
FINDPEAKS_SCORE: 0.8457
FINDPEAKS_PERCENTILE: 98
HOTSPOT_SCORE: 0.7673
HOTSPOT_PERCENTILE: 98
IROC_SCORE: 0.9967
IROC_PERCENTILE: 23
POISSON_SCORE: 0.838
POISSON_PERCENTILE: 98

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

ANALYSIS FILE NAME: GSM521901_UCSD.IMR90.H3K4me3.SK03.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4me3.IMR90-02.01.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of IMR90 Cell Line Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me3 ChIP-Seq read mappings from the IMR90 Cell Line, Library SK03 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.4531
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 H3K4me3 03
BROWSER_TRACK_DESCRIPTION: UCSD IMR90 Cell Line Histone H3K4me3 Library SK03 EA Release 2


QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED: 62
FINDPEAKS_SCORE: 0.8457
FINDPEAKS_PERCENTILE: 98
HOTSPOT_SCORE: 0.7673
HOTSPOT_PERCENTILE: 98
IROC_SCORE: 0.9967
IROC_PERCENTILE: 23
POISSON_SCORE: 0.838
POISSON_PERCENTILE: 98

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

 
Submission date Mar 12, 2010
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 SRX017520
BioSample SAMN00009762
Named Annotation GSM521901_UCSD.IMR90.H3K4me3.SK03.wig.gz

Supplementary file Size Download File type/resource
GSM521901_UCSD.IMR90.H3K4me3.SK03.bed.gz 235.0 Mb (ftp)(http) BED
GSM521901_UCSD.IMR90.H3K4me3.SK03.wig.gz 18.8 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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