|
Status |
Public on Jan 06, 2010 |
Title |
Chromatin accessibility assay of IMR90 Cell Line; DS11759 |
Sample type |
SRA |
|
|
Source name |
IMR90 Cell Line; DS11759
|
Organism |
Homo sapiens |
Characteristics |
molecule: genomic DNA disease: None biomaterial_provider: ATCC biomaterial_type: Cell Line line: IMR90 lineage: NA differentiation_stage: Fetal lung fibroblast differentiation_method: NA passage: 4 medium: Eagle's Minimum Essential Medium, Catalog No. 30-2003. Sex: Female batch: CCL-186 experiment_type: Chromatin Accessibility extraction_protocol: Qiagen minElut dnase_protocol: Stamlab DNase Protocol
|
Extracted molecule |
genomic DNA |
Extraction protocol |
Library construction protocol: Single read - Illumina
|
|
|
Library strategy |
DNase-Hypersensitivity |
Library source |
genomic |
Library selection |
DNAse |
Instrument model |
Illumina Genome Analyzer II |
|
|
Description |
Design description: Chromatin accessibility determination via DNase-seq Library name: DS11759 EDACC Genboree Sample Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.1632 EDACC Genboree Experiment Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.1633 **************** 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: GSM468792_IMR90-DS11759.UWStam_090902_SOLEXA-1GA-1_0021_FC42KVW_2.bam ANALYSIS ALIAS: UW.IMR90.ChromatinAccessibility.Level1.1 ANALYSIS TITLE: Mapping of IMR90 Chromatin Accessibility Data ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on 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.1844 DATA_ANALYSIS_LEVEL: 1 EXPERIMENT_TYPE: Chromatin Accessibility 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: GSM468792_IMR90-DS11759.UWStam_090921_SOLEXA-1GA-1_0028_FC42YD0_4.bam ANALYSIS ALIAS: UW.IMR90.ChromatinAccessibility.Level1.2 ANALYSIS TITLE: Mapping of IMR90 Chromatin Accessibility Data ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on 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.1846 DATA_ANALYSIS_LEVEL: 1 EXPERIMENT_TYPE: Chromatin Accessibility 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: GSM468792_UW.IMR90.rep1.ChromatinAccessibility.IMR90-DS11759.wig ANALYSIS ALIAS: UW.IMR90.ChromatinAccessibility.Level2.combined.1 ANALYSIS TITLE: Raw Signal Density Graphs of IMR90 Chromatin Accessibility Replicate 1 Data ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from 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.1857 DATA_ANALYSIS_LEVEL: 2 EXPERIMENT_TYPE: Chromatin Accessibility 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: GSM468792_UW.IMR90.ChromatinAccessibility.DS11759.bed ANALYSIS ALIAS: DS11759.hg19.level.1 ANALYSIS TITLE: Mapping of IMR90 Cell Line Chromatin Accessibility Data ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on the IMR90 Cell Line, Library DS11759 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.4126 DATA_ANALYSIS_LEVEL: 1 EXPERIMENT_TYPE: Chromatin Accessibility 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: None ALIGNMENT_POSTPROCESSING: None RELEASE_NUMBER: Human Epigenome Atlas 2
QUALITY SCORES: NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED: 40 FINDPEAKS_SCORE: 0.3846 FINDPEAKS_PERCENTILE: 5 HOTSPOT_SCORE: 0.2914 HOTSPOT_PERCENTILE: 5 IROC_SCORE: 0.9966 IROC_PERCENTILE: 37 POISSON_SCORE: 0.3873 POISSON_PERCENTILE: 10
**********************************************************************
ANALYSIS FILE NAME: GSM468792_UW.IMR90.ChromatinAccessibility.DS11759.wig ANALYSIS ALIAS: DS11759.hg19.level.2 ANALYSIS TITLE: Raw Signal Density Graphs of IMR90 Cell Line Chromatin Accessibility Data ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from the IMR90 Cell Line, Library DS11759 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.4086 DATA_ANALYSIS_LEVEL: 2 EXPERIMENT_TYPE: Chromatin Accessibility GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19 SOFTWARE: In house programs and scripts SOFTWARE_VERSION: NA READ_EXTENSION: 0bp GENOMIC_WINDOW: 150bp TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None RELEASE_NUMBER: Human Epigenome Atlas 2 BROWSER_TRACK_NAME: IMR90 DNase 59 59 BROWSER_TRACK_DESCRIPTION: UW IMR90 Cell Line DNase Hypersensitivity Library DS11759 EA Release 2
QUALITY SCORES: NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED: 40 FINDPEAKS_SCORE: 0.3846 FINDPEAKS_PERCENTILE: 5 HOTSPOT_SCORE: 0.2914 HOTSPOT_PERCENTILE: 5 IROC_SCORE: 0.9966 IROC_PERCENTILE: 37 POISSON_SCORE: 0.3873 POISSON_PERCENTILE: 10
|
|
|
Submission date |
Nov 06, 2009 |
Last update date |
May 15, 2019 |
Contact name |
Northwest REMC |
E-mail(s) |
rharris1@bcm.tmc.edu
|
Organization name |
University of Washington
|
Street address |
-
|
City |
Seattle |
State/province |
WA |
ZIP/Postal code |
98195 |
Country |
USA |
|
|
Platform ID |
GPL9115 |
Series (1) |
GSE18927 |
University of Washington Human Reference Epigenome Mapping Project |
|
Relations |
SRA |
SRX012425 |
BioSample |
SAMN00004755 |
Named Annotation |
GSM468792_UW.IMR90.rep1.ChromatinAccessibility.IMR90-DS11759.wig.gz |
Named Annotation |
GSM468792_UW.IMR90.ChromatinAccessibility.DS11759.wig.gz |