|
| Status |
Public on Apr 28, 2010 |
| Title |
ChIP-Seq analysis of H3K4me3 in human hLiver cells; 61GKJAAXX100226-4-S |
| Sample type |
SRA |
| |
|
| Source name |
normal adult liver; 61GKJAAXX100226-4-S
|
| Organism |
Homo sapiens |
| Characteristics |
molecule: genomic DNA
disease: none
biomaterial_provider: MGH Pathology
biomaterial_type: Primary Tissue
tissue_type: liver
tissue_depot: liver
collection_method: surgery
donor_id: 5.0
donor_age: NA
donor_health_status: none
donor_sex: Male
donor_ethnicity: NA
experiment_type: Histone H3K4me3
extraction_protocol: SDS lysis
extraction_protocol_type_of_sonicator: Bioruptor
extraction_protocol_sonication_cycles: 1
chip_protocol: Bernstein_BROAD_ENCODE_protocol
chip_protocol_chromatin_amount: 10 million cells
chip_protocol_bead_type: Protein A-Sepharose 4B
chip_protocol_bead_amount: 70 ul bed volume
chip_protocol_antibody_amount: 2-15 ug
chip_antibody: H3K4Me3
chip_antibody_provider: Millipore
chip_antibody_catalog: 07-473
chip_antibody_lot: DAM1623866
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Library construction protocol: Single read - Illumina
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
sample_term_id: UBERON_0002107
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Solexa-20738
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.2533
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.2563
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************
BED and WIG files were replaced on April 29, 2014
|
| Data processing |
**********************************************************************
ANALYSIS FILE NAME: GSM537709_BI.Adult_Liver.H3K4me3.5.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 61GKJAAXX100226-4-S.hg19.level.1
ANALYSIS TITLE: Mapping of Adult Liver Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me3 ChIP-Seq on Adult Liver, Donor 5.0 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.4811
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: 0.3716
FINDPEAKS_PERCENTILE: 52
HOTSPOT_SCORE: 0.0
HOTSPOT_PERCENTILE: NA
IROC_SCORE: 0.9961
IROC_PERCENTILE: 19
POISSON_SCORE: 0.5711
POISSON_PERCENTILE: 71
**********************************************************************
ANALYSIS FILE NAME: GSM537709_BI.Adult_Liver.H3K4me3.5.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 61GKJAAXX100226-4-S.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Adult Liver Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me3 ChIP-Seq read mappings from Adult Liver, Donor 5.0 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.5085
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: AL H3K4me3 5.0
BROWSER_TRACK_DESCRIPTION: BI Adult Liver Histone H3K4me3 Donor 5.0 EA Release 2
QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED: 62
FINDPEAKS_SCORE: 0.3716
FINDPEAKS_PERCENTILE: 52
HOTSPOT_SCORE: 0.0
HOTSPOT_PERCENTILE: NA
IROC_SCORE: 0.9961
IROC_PERCENTILE: 19
POISSON_SCORE: 0.5711
POISSON_PERCENTILE: 71
**********************************************************************
|
| |
|
| Submission date |
Apr 26, 2010 |
| Last update date |
May 30, 2017 |
| Contact name |
BROAD INSTITUTE |
| E-mail(s) |
rharris1@bcm.tmc.edu
|
| Organization name |
Broad Institute
|
| Street address |
-
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02142 |
| Country |
USA |
| |
|
| Platform ID |
GPL9115 |
| Series (1) |
| GSE19465 |
BI Human Reference Epigenome Mapping Project: ChIP-Seq in human subject |
|
| Relations |
| Reanalyzed by |
GSE99453 |
| BioSample |
SAMN00012133 |
| Named Annotation |
GSM537709_BI.Adult_Liver.H3K4me3.5.wig.gz |
