|
Status |
Public on Mar 30, 2012 |
Title |
Chromatin accessibility assay of H1 Derived Mesenchymal Stem Cells; DS21042 |
Sample type |
SRA |
|
|
Source name |
Human embryonic stem cells received from the James Thomson laboratory. Cells are from the H1 line and are differentiated into mesenchymal stem cells.; DS21042
|
Organism |
Homo sapiens |
Characteristics |
sample alias: MSC-02 sample common name: H1 Derived Mesenchymal Stem Cells molecule: genomic DNA disease: None biomaterial_provider: James Thomson Laboratory biomaterial_type: Cell Line line: H1 lineage: Embryonic Stem Cell differentiation_stage: Embryonic stem cell differentiated into mesenchymal stem cells differentiation_method: Publication in progress passage: 6 medium: Publication in progress Sex: Male batch: MSC-2 experiment_type: Chromatin Accessibility extraction_protocol: Qiagen minElut dnase_protocol: http://www.roadmapepigenomics.org/protocols/type/experimental/
|
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 HiSeq 2000 |
|
|
Description |
Design description: Chromatin accessibility determination via DNase-seq Library name: DS21042 EDACC Genboree Experiment Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.11905 EDACC Genboree Sample Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.7914 **************** 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: GSM906381_UW.H1_Derived_Mesenchymal_Stem_Cells.ChromatinAccessibility.DS21042.bed ANALYSIS CENTER: EDACC ANALYSIS ALIAS: DS21042.hg19.level.1.release.8 ANALYSIS TITLE: Mapping of H1 Derived Mesenchymal Stem Cells ChromatinAccessibility Data ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on the H1 Derived Mesenchymal Stem Cells, Library DS21042 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.13375 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 8
QUALITY SCORES: NUMBER_OF_MAPPED_READS: 54,319,010 NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 3 FINDPEAKS_SCORE: 0.5177 FINDPEAKS_PERCENTILE: 100 HOTSPOT_SCORE: 0.5563 HOTSPOT_PERCENTILE: 100 IROC_SCORE: 0.9941 IROC_PERCENTILE: 33 POISSON_SCORE: 0.5809 POISSON_PERCENTILE: 100 MAXIMUM_REPLICATE_CORRELATION: 0.98
**********************************************************************
ANALYSIS FILE NAME: GSM906381_UW.H1_Derived_Mesenchymal_Stem_Cells.ChromatinAccessibility.DS21042.wig ANALYSIS CENTER: EDACC ANALYSIS ALIAS: DS21042.hg19.level.2.release.8 ANALYSIS TITLE: Raw Signal Density Graphs of H1 Derived Mesenchymal Stem Cells ChromatinAccessibility Data ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from the H1 Derived Mesenchymal Stem Cells, Library DS21042 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.13378 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 8 BROWSER_TRACK_NAME: HDMSC DNase 42 BROWSER_TRACK_DESCRIPTION: UW H1 Derived Mesenchymal Stem Cells DNase Hypersensitivity Library DS21042 EA Release 8
QUALITY SCORES: NUMBER_OF_MAPPED_READS: 54,319,010 NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 3 FINDPEAKS_SCORE: 0.5177 FINDPEAKS_PERCENTILE: 100 HOTSPOT_SCORE: 0.5563 HOTSPOT_PERCENTILE: 100 IROC_SCORE: 0.9941 IROC_PERCENTILE: 33 POISSON_SCORE: 0.5809 POISSON_PERCENTILE: 100 MAXIMUM_REPLICATE_CORRELATION: 0.98
**********************************************************************
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|
|
Submission date |
Mar 29, 2012 |
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 |
GPL11154 |
Series (1) |
GSE18927 |
University of Washington Human Reference Epigenome Mapping Project |
|
Relations |
SRA |
SRX134723 |
BioSample |
SAMN00678167 |
Named Annotation |
GSM906381_UW.H1_Derived_Mesenchymal_Stem_Cells.ChromatinAccessibility.DS21042.wig.gz |