|
| Status |
Public on Jan 07, 2010 |
| Title |
Reference Epigenome: ChIP-Seq Analysis of H3K4me3 in IMR90 Cells; renlab.H3K4me3.IMR90-01.01 |
| Sample type |
SRA |
| |
|
| Source name |
IMR90; renlab.H3K4me3.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 H3K4me3
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: H3K4me3
chip_antibody_provider: Abcam
chip_antibody_catalog: ab8580
chip_antibody_lot: unknown
|
| 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: LL221
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.1731
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: GSM469970_UCSD.IMR90.H3K4me3.UCSD_30WPBAAXX_6.bam
ANALYSIS ALIAS: UCSD.IMR90.H3K4me3.Level1.1
ANALYSIS TITLE: Mapping of IMR90 H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq for H3K4me3 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.1794
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: GSM469970_UCSD.IMR90.H3K4me3.UCSD_301FBAAXX_2.bam
ANALYSIS ALIAS: UCSD.IMR90.H3K4me3.Level1.2
ANALYSIS TITLE: Mapping of IMR90 H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq for H3K4me3 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.1796
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: GSM469970_UCSD.IMR90.H3K4me3.wig
ANALYSIS ALIAS: UCSD.IMR90.H3K4me3.Level2.1
ANALYSIS TITLE: Raw Signal Density Graphs of IMR90 H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq read mappings for H3K4me3 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.1797
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: GSM469970_UCSD.IMR90.H3K4me3.LL221.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4me3.IMR90-01.01.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 LL221 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.4408
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: 0.909
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.8482
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9994
IROC_PERCENTILE: 56
POISSON_SCORE: 0.9124
POISSON_PERCENTILE: 100
**********************************************************************
ANALYSIS FILE NAME: GSM469970_UCSD.IMR90.H3K4me3.LL221.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4me3.IMR90-01.01.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 LL221 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.4457
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 21
BROWSER_TRACK_DESCRIPTION: UCSD IMR90 Cell Line Histone H3K4me3 Library LL221 EA Release 2
QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED: 62
FINDPEAKS_SCORE: 0.909
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.8482
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9994
IROC_PERCENTILE: 56
POISSON_SCORE: 0.9124
POISSON_PERCENTILE: 100
**********************************************************************
|
| |
|
| 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 |
| Reanalyzed by |
GSE99453 |
| SRA |
SRX012500 |
| BioSample |
SAMN00004463 |
| Named Annotation |
GSM469970_UCSD.IMR90.H3K4me3.wig.gz |
| Named Annotation |
GSM469970_UCSD.IMR90.H3K4me3.LL221.wig.gz |
