|
|
GEO help: Mouse over screen elements for information. |
|
Status |
Public on Feb 22, 2012 |
Title |
Chromatin accessibility assay of Fetal Muscle, Arm; DS19270 |
Sample type |
SRA |
|
|
Source name |
Fetal Muscle, Arm primary tissue, day 96; DS19270
|
Organism |
Homo sapiens |
Characteristics |
sample alias: fMuscle_Arm.H-24244d96 sample common name: Fetal Muscle, Arm molecule: genomic DNA disease: None biomaterial_provider: University of Washington, Congenital Defects Lab. Ian Glass biomaterial_type: Primary Tissue tissue_type: Fetal Muscle, Arm tissue_depot: UW collection_method: fetal donor_id: H-24244 donor_age: day 96 donor_health_status: NA donor_sex: Male donor_ethnicity: NA 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 |
sample_term_id: UBERON_0001499 assay_term_id: OBI_0001853 nucleic_acid_term_id: SO_0000352 Design description: Chromatin accessibility determination via DNase-seq Library name: DS19270 EDACC Genboree Experiment Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.11532 EDACC Genboree Sample Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.11531 **************** 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: GSM878625_UW.Fetal_Muscle_Arm.ChromatinAccessibility.H-24244.DS19270.bed ANALYSIS CENTER: EDACC ANALYSIS ALIAS: DS19270.hg19.level.1.release.7 ANALYSIS TITLE: Mapping of Fetal Muscle Arm Chromatin Accessibility Data ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Muscle Arm, Donor H-24244, Library DS19270 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.12757 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 7
QUALITY SCORES: NUMBER_OF_MAPPED_READS: 33,987,181 NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 58 FINDPEAKS_SCORE: 0.4402 FINDPEAKS_PERCENTILE: 52 HOTSPOT_SCORE: 0.4265 HOTSPOT_PERCENTILE: 52 IROC_SCORE: 0.9928 IROC_PERCENTILE: 29 POISSON_SCORE: 0.4874 POISSON_PERCENTILE: 52 MAXIMUM_REPLICATE_CORRELATION: 0.98
**********************************************************************
ANALYSIS FILE NAME: GSM878625_UW.Fetal_Muscle_Arm.ChromatinAccessibility.H-24244.DS19270.wig ANALYSIS CENTER: EDACC ANALYSIS ALIAS: DS19270.hg19.level.2.release.7 ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Muscle Arm Chromatin Accessibility Data ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from Fetal Muscle Arm, Donor H-24244, Library DS19270 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.12815 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 7 BROWSER_TRACK_NAME: FMA DNase 44 70 BROWSER_TRACK_DESCRIPTION: UW Fetal Muscle Arm DNase Hypersensitivity Donor H-24244 Library DS19270 EA Release 7
QUALITY SCORES: NUMBER_OF_MAPPED_READS: 33,987,181 NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 58 FINDPEAKS_SCORE: 0.4402 FINDPEAKS_PERCENTILE: 52 HOTSPOT_SCORE: 0.4265 HOTSPOT_PERCENTILE: 52 IROC_SCORE: 0.9928 IROC_PERCENTILE: 29 POISSON_SCORE: 0.4874 POISSON_PERCENTILE: 52 MAXIMUM_REPLICATE_CORRELATION: 0.98
**********************************************************************
|
|
|
Submission date |
Feb 21, 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 |
SRX121251 |
BioSample |
SAMN00791528 |
Named Annotation |
GSM878625_UW.Fetal_Muscle_Arm.ChromatinAccessibility.H-24244.DS19270.wig.gz |
Supplementary file |
Size |
Download |
File type/resource |
GSM878625_UW.Fetal_Muscle_Arm.ChromatinAccessibility.H-24244.DS19270.bed.gz |
504.0 Mb |
(ftp)(http) |
BED |
GSM878625_UW.Fetal_Muscle_Arm.ChromatinAccessibility.H-24244.DS19270.wig.gz |
206.0 Mb |
(ftp)(http) |
WIG |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
|
|
|
|
|