|
Status |
Public on Nov 01, 2012 |
Title |
Chromatin accessibility assay of Fetal Brain; DNase.DS20780 |
Sample type |
SRA |
|
|
Source name |
Fetal Brain primary tissue, day 105; DNase.DS20780
|
Organism |
Homo sapiens |
Characteristics |
sample alias: fBrain.H-24510d105 sample common name: Fetal Brain molecule: genomic DNA disease: None biomaterial_provider: University of Washington, Congenital Defects Lab. Ian Glass biomaterial_type: Primary Tissue tissue_type: Fetal Brain tissue_depot: UW collection_method: fetal donor_id: H-24510 donor_age: day 105 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_0000955 assay_term_id: OBI_0001853 nucleic_acid_term_id: SO_0000352 Design description: Chromatin accessibility determination via DNase-seq Library name: DNase.DS20780 EDACC Genboree Experiment Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.14467 EDACC Genboree Sample Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.14466 **************** 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: GSM1027328_UW.Fetal_Brain.ChromatinAccessibility.H-24510.DNase.DS20780.bed ANALYSIS CENTER: EDACC ANALYSIS ALIAS: DNase.DS20780.hg19.level.1.release.9 ANALYSIS TITLE: Mapping of Fetal Brain Chromatin Accessibility Data ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Brain, Donor H-24510, Library DNase.DS20780 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.17623 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 9
QUALITY SCORES: NUMBER_OF_MAPPED_READS: 42,789,897 FINDPEAKS_SCORE: 0.4921 FINDPEAKS_PERCENTILE: 85 HOTSPOT_SCORE: 0.4807 HOTSPOT_PERCENTILE: 83 IROC_SCORE: 0.9945 IROC_PERCENTILE: 76 POISSON_SCORE: 0.5285 POISSON_PERCENTILE: 76 MAXIMUM_REPLICATE_CORRELATION: 0.98
**********************************************************************
ANALYSIS FILE NAME: GSM1027328_UW.Fetal_Brain.ChromatinAccessibility.H-24510.DNase.DS20780.wig ANALYSIS CENTER: EDACC ANALYSIS ALIAS: DNase.DS20780.hg19.level.2.release.9 ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Brain Chromatin Accessibility Data ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from Fetal Brain, Donor H-24510, Library DNase.DS20780 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.17577 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 9 BROWSER_TRACK_NAME: FB DNase 10 80 BROWSER_TRACK_DESCRIPTION: UW Fetal Brain DNase Hypersensitivity Donor H-24510 Library DNase.DS20780 EA Release 9
QUALITY SCORES: NUMBER_OF_MAPPED_READS: 42,789,897 FINDPEAKS_SCORE: 0.4921 FINDPEAKS_PERCENTILE: 85 HOTSPOT_SCORE: 0.4807 HOTSPOT_PERCENTILE: 83 IROC_SCORE: 0.9945 IROC_PERCENTILE: 76 POISSON_SCORE: 0.5285 POISSON_PERCENTILE: 76 MAXIMUM_REPLICATE_CORRELATION: 0.98
**********************************************************************
|
|
|
Submission date |
Oct 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 (2) |
GSE18927 |
University of Washington Human Reference Epigenome Mapping Project |
GSE51336 |
Mouse regulatory DNA landscapes reveal global principles of cis-regulatory evolution |
|
Relations |
SRA |
SRX201815 |
BioSample |
SAMN01797251 |
Named Annotation |
GSM1027328_UW.Fetal_Brain.ChromatinAccessibility.H-24510.DNase.DS20780.wig.gz |