|
Status |
Public on May 12, 2011 |
Title |
Digital Genomic Footprinting assay of Fetal Lung; DGF.DS14724 |
Sample type |
SRA |
|
|
Source name |
Fetal Lung primary tissue, day 85; DGF.DS14724
|
Organism |
Homo sapiens |
Characteristics |
sample alias: fLung.H-23266d85 sample common name: Fetal Lung molecule: genomic DNA disease: None biomaterial_provider: University of Washington, Congenital Defects Lab. Ian Glass biomaterial_type: Primary Tissue tissue_type: fetal lung tissue_depot: UW collection_method: fetal donor_id: H-23266 donor_age: day 85 donor_health_status: NA donor_sex: Female donor_ethnicity: NA experiment_type: Digital Genomic Footprinting extraction_protocol: Qiagen minElut dnase_protocol: Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)
|
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 IIx |
|
|
Description |
sample_term_id: UBERON_0002048 assay_term_id: OBI_0001853 nucleic_acid_term_id: SO_0000352 Design description: Digital Genomic Footprinting determination via DNase-seq Library name: DGF.DS14724 EDACC Genboree Experiment Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.7409 EDACC Genboree Sample Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.3130 **************** 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: GSM723025_UW.Fetal_Lung.Digital_Genomic_Footprinting.H-23266.DGF.DS14724.bed ANALYSIS CENTER: EDACC ANALYSIS ALIAS: DGF.DS14724.hg19.level.1.release.4 ANALYSIS TITLE: Mapping of Fetal Lung Digital Genomic Footprinting Data ANALYSIS DESCRIPTION: Illumina reads produced by Digital Genomic Footprinting on Fetal Lung, Donor H-23266, Library DGF.DS14724 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.7631 DATA_ANALYSIS_LEVEL: 1 EXPERIMENT_TYPE: Digital Genomic Footprinting 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 4
QUALITY SCORES: NUMBER_OF_MAPPED_READS: 288,539,741 NUMBER_OF_DIGITAL_GENOMIC_FOOTPRINTING_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 5 FINDPEAKS_SCORE: 0.6616 FINDPEAKS_PERCENTILE: 60 HOTSPOT_SCORE: 0.6416 HOTSPOT_PERCENTILE: 60 IROC_SCORE: 0.9961 IROC_PERCENTILE: 20 POISSON_SCORE: 0.6651 POISSON_PERCENTILE: 100
**********************************************************************
ANALYSIS FILE NAME: GSM723025_UW.Fetal_Lung.Digital_Genomic_Footprinting.H-23266.DGF.DS14724.wig ANALYSIS CENTER: EDACC ANALYSIS ALIAS: DGF.DS14724.hg19.level.2.release.4 ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Lung Digital Genomic Footprinting Data ANALYSIS DESCRIPTION: Illumina Digital Genomic Footprinting read mappings from Fetal Lung, Donor H-23266, Library DGF.DS14724 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.7636 DATA_ANALYSIS_LEVEL: 2 EXPERIMENT_TYPE: Digital Genomic Footprinting 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 4 BROWSER_TRACK_NAME: FL DGF 66 24 BROWSER_TRACK_DESCRIPTION: UW Fetal Lung Digital Genomic Footprinting Donor H-23266 Library DGF.DS14724 EA Release 4
QUALITY SCORES: NUMBER_OF_MAPPED_READS: 288,539,741 NUMBER_OF_DIGITAL_GENOMIC_FOOTPRINTING_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 5 FINDPEAKS_SCORE: 0.6616 FINDPEAKS_PERCENTILE: 60 HOTSPOT_SCORE: 0.6416 HOTSPOT_PERCENTILE: 60 IROC_SCORE: 0.9961 IROC_PERCENTILE: 20 POISSON_SCORE: 0.6651 POISSON_PERCENTILE: 100
**********************************************************************
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|
|
Submission date |
May 11, 2011 |
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 |
GPL10999 |
Series (1) |
GSE18927 |
University of Washington Human Reference Epigenome Mapping Project |
|
Relations |
SRA |
SRX062368 |
BioSample |
SAMN00113498 |
Named Annotation |
GSM723025_UW.Fetal_Lung.Digital_Genomic_Footprinting.H-23266.DGF.DS14724.wig.gz |