|
Status |
Public on Dec 28, 2011 |
Title |
ChIP-Seq analysis of H3K4me3 in human stomach mucosa cells; DNA_Lib 317 |
Sample type |
SRA |
|
|
Source name |
Primary stomach mucosal tissue; DNA_Lib 317
|
Organism |
Homo sapiens |
Characteristics |
sample alias: 235 sample common name: Stomach Mucosa collection_method: Surgery donor_health_status: NK stomach mucosa, stomach rmvd as part of pancr. CA molecule: genomic DNA disease: NK stomach mucosa, stomach rmvd as part of pancr. CA tissue_type: Stomach Mucosa donor_ethnicity: Caucasian donor_sex: Male biomaterial_type: Primary Tissue tissue_depot: Stomach donor_id: 157 biomaterial_provider: MGH donor_age: 59.0 Years chip_protocol_bead_type: Protein A-Sepharose 4B chip_antibody: H3K4me3 chip_protocol_chromatin_amount: 0.5 to 3 million cells extraction_protocol: cell/nuclei lysis chip_protocol_antibody_amount: ~1 ug chip_protocol_bead_amount: 10 ul bed volume chip_protocol: Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles: 1 chip_antibody_catalog: 07-473 chip_antibody_provider: Millipore chip_antibody_lot: DAM1623866 experiment_type: Histone H3K4me3 extraction_protocol_type_of_sonicator: Branson
|
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 HiSeq 2000 |
|
|
Description |
sample_term_id: UBERON_0001199 assay_term_id: OBI_0000716 nucleic_acid_term_id: SO_0000352 Design description: Human Chromatin IP REMC Sequencing on Illumina Library name: DNA_Lib 317 EDACC Genboree Experiment Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8632 EDACC Genboree Sample Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9453 **************** 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: GSM772942_BI.Stomach_Mucosa.H3K4me3.157.bed ANALYSIS CENTER: EDACC ANALYSIS ALIAS: DNA_Lib 317-DNA_Lib 317-DNA_Lib 317-DNA_Lib 317.hg19.level.1.release.5 ANALYSIS TITLE: Mapping of Stomach Mucosa Histone H3K4me3 ChIP-Seq Data ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me3 ChIP-Seq on Stomach Mucosa, Donor 157, 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.10630 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 5
QUALITY SCORES: NUMBER_OF_MAPPED_READS: 23,997,237 NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54 FINDPEAKS_SCORE: 0.0722 FINDPEAKS_PERCENTILE: 7 HOTSPOT_SCORE: 0.1282 HOTSPOT_PERCENTILE: 7 IROC_SCORE: 0.984 IROC_PERCENTILE: 20 POISSON_SCORE: 0.176 POISSON_PERCENTILE: 6 MAXIMUM_REPLICATE_CORRELATION: 0.75
**********************************************************************
ANALYSIS FILE NAME: GSM772942_BI.Stomach_Mucosa.H3K4me3.157.wig ANALYSIS CENTER: EDACC ANALYSIS ALIAS: DNA_Lib 317-DNA_Lib 317-DNA_Lib 317-DNA_Lib 317.hg19.level.2.release.5 ANALYSIS TITLE: Raw Signal Density Graphs of Stomach Mucosa Histone H3K4me3 ChIP-Seq Data ANALYSIS DESCRIPTION: Illumina Histone H3K4me3 ChIP-Seq read mappings from Stomach Mucosa, Donor 157, 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.10894 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 5 BROWSER_TRACK_NAME: SM H3K4me3 57 17 BROWSER_TRACK_DESCRIPTION: BI Stomach Mucosa Histone H3K4me3 Donor 157 Library DNA_Lib 317 EA Release 5
QUALITY SCORES: NUMBER_OF_MAPPED_READS: 23,997,237 NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54 FINDPEAKS_SCORE: 0.0722 FINDPEAKS_PERCENTILE: 7 HOTSPOT_SCORE: 0.1282 HOTSPOT_PERCENTILE: 7 IROC_SCORE: 0.984 IROC_PERCENTILE: 20 POISSON_SCORE: 0.176 POISSON_PERCENTILE: 6 MAXIMUM_REPLICATE_CORRELATION: 0.75
**********************************************************************
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|
|
Submission date |
Aug 03, 2011 |
Last update date |
Jan 29, 2015 |
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 |
GPL11154 |
Series (1) |
GSE17312 |
BI Human Reference Epigenome Mapping Project |
|
Relations |
BioSample |
SAMN00691466 |
Named Annotation |
GSM772942_BI.Stomach_Mucosa.H3K4me3.157.wig.gz |