|
Status |
Public on Nov 12, 2010 |
Title |
ChIP-Seq analysis of WCE in human colonic mucosa cells; Lib:XZ:20100513:07--ChIP:XZ:20100503:07:colonic mucosa:WCE |
Sample type |
SRA |
|
|
Source name |
Primary colonic mucosal tissue; Lib:XZ:20100513:07--ChIP:XZ:20100503:07:colonic mucosa:WCE
|
Organism |
Homo sapiens |
Characteristics |
collection_method: surgery donor_health_status: "normal mucosa, adeno. CA of Cecum" molecule: genomic DNA disease: none tissue_type: mucosa passage_if_expanded: NA donor_ethnicity: white donor_sex: Female biomaterial_type: Primary Tissue tissue_depot: colon donor_id: 32 biomaterial_provider: MGH Pathology donor_age: 73 extraction_protocol_sonication_cycles: 1 chip_protocol_chromatin_amount: standard extraction_protocol: SDS lysis experiment_type: ChIP-Seq Input chip_protocol: Input extraction_protocol_type_of_sonicator: Bioruptor
|
Extracted molecule |
genomic DNA |
Extraction protocol |
Library construction protocol: Single read - Illumina
|
|
|
Library strategy |
ChIP-Seq |
Library source |
genomic |
Library selection |
RANDOM |
Instrument model |
Illumina Genome Analyzer II |
|
|
Description |
sample_term_id: UBERON_0000317 assay_term_id: OBI_0000716 nucleic_acid_term_id: SO_0000352 Design description: Human Chromatin IP REMC Sequencing on Illumina Library name: Lib:XZ:20100513:07--ChIP:XZ:20100503:07:colonic mucosa:WCE EDACC Genboree Experiment Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3253 EDACC Genboree Sample Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3354 **************** 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: GSM621669_BI.Colonic_Mucosa.Input.32.bed ANALYSIS CENTER: EDACC ANALYSIS ALIAS: Lib:XZ:20100513:07--ChIP:XZ:20100503:07:colonic mucosa:WCE.hg19.level.1 ANALYSIS TITLE: Mapping of Colonic Mucosa ChIP-Seq Input Data ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on Colonic Mucosa, Donor 32 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.4762 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_Input_EXPERIMENTS_SCORED: 67 FINDPEAKS_SCORE: 0.0059 FINDPEAKS_PERCENTILE: 19 HOTSPOT_SCORE: 0.0221 HOTSPOT_PERCENTILE: 36 IROC_SCORE: 0.9671 IROC_PERCENTILE: 79 POISSON_SCORE: 0.1808 POISSON_PERCENTILE: 15
**********************************************************************
ANALYSIS FILE NAME: GSM621669_BI.Colonic_Mucosa.Input.32.wig ANALYSIS CENTER: EDACC ANALYSIS ALIAS: Lib:XZ:20100513:07--ChIP:XZ:20100503:07:colonic mucosa:WCE.hg19.level.2 ANALYSIS TITLE: Raw Signal Density Graphs of Colonic Mucosa ChIP-Seq Input Data ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from Colonic Mucosa, Donor 32 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.5036 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: CM Input 32 BROWSER_TRACK_DESCRIPTION: BI Colonic Mucosa ChIP-Seq Input Donor 32 EA Release 2
QUALITY SCORES: NUMBER_OF_Input_EXPERIMENTS_SCORED: 67 FINDPEAKS_SCORE: 0.0059 FINDPEAKS_PERCENTILE: 19 HOTSPOT_SCORE: 0.0221 HOTSPOT_PERCENTILE: 36 IROC_SCORE: 0.9671 IROC_PERCENTILE: 79 POISSON_SCORE: 0.1808 POISSON_PERCENTILE: 15
**********************************************************************
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|
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Submission date |
Nov 10, 2010 |
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 |
GPL9115 |
Series (1) |
GSE19465 |
BI Human Reference Epigenome Mapping Project: ChIP-Seq in human subject |
|
Relations |
BioSample |
SAMN00119942 |
Named Annotation |
GSM621669_BI.Colonic_Mucosa.Input.32.wig.gz |