|
| Status |
Public on Mar 22, 2010 |
| Title |
Reference Epigenome: ChIP-Seq Analysis of H3K4ac in IMR90 Cells; renlab.H3K4ac.IMR90-02.01 |
| Sample type |
SRA |
| |
|
| Source name |
IMR90 Cell Line, biological replicate 2; renlab.H3K4ac.IMR90-02.01
|
| Organism |
Homo sapiens |
| Characteristics |
molecule: genomic DNA
disease: None
biomaterial_provider: ATCC
biomaterial_type: Cell Line
line: IMR90
lineage: NA
batch: 3
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 H3K4ac
extraction_protocol: See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf
extraction_protocol_type_of_sonicator: Biorupter
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: H3K4ac
chip_antibody_provider: Upstate
chip_antibody_catalog: 07-539
chip_antibody_lot: 26747
|
| 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 H3K4ac in IMR90 cells. Sequencing was done on the Illumina GAII platform.
Library name: SK16
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.2026
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.2019
****************
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: GSM521894_UCSD.IMR90.H3K4ac.SK16.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4ac.IMR90-02.01.hg19.level.1
ANALYSIS TITLE: Mapping of IMR90 Cell Line Histone H3K4ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4ac ChIP-Seq on the IMR90 Cell Line, Library SK16 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.5167
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_H3K4ac_EXPERIMENTS_SCORED: 3
FINDPEAKS_SCORE: 0.7559
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.4939
HOTSPOT_PERCENTILE: 67
IROC_SCORE: 0.9967
IROC_PERCENTILE: 67
POISSON_SCORE: 0.7229
POISSON_PERCENTILE: 100
**********************************************************************
ANALYSIS FILE NAME: GSM521894_UCSD.IMR90.H3K4ac.SK16.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4ac.IMR90-02.01.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of IMR90 Cell Line Histone H3K4ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4ac ChIP-Seq read mappings from the IMR90 Cell Line, Library SK16 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.4529
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 H3K4ac 16
BROWSER_TRACK_DESCRIPTION: UCSD IMR90 Cell Line Histone H3K4ac Library SK16 EA Release 2
QUALITY SCORES:
NUMBER_OF_H3K4ac_EXPERIMENTS_SCORED: 3
FINDPEAKS_SCORE: 0.7559
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.4939
HOTSPOT_PERCENTILE: 67
IROC_SCORE: 0.9967
IROC_PERCENTILE: 67
POISSON_SCORE: 0.7229
POISSON_PERCENTILE: 100
**********************************************************************
|
| |
|
| 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 |
| SRA |
SRX017513 |
| BioSample |
SAMN00009761 |
| Named Annotation |
GSM521894_UCSD.IMR90.H3K4ac.SK16.wig.gz |
