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Status |
Public on Aug 06, 2011 |
Title |
Chromatin accessibility assay of Fetal Kidney, Left; DS17140 |
Sample type |
SRA |
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Source name |
Fetal Kidney, Left primary tissue, day 107; DS17140
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Organism |
Homo sapiens |
Characteristics |
sample alias: fKidney_Left.H-23758d107 sample common name: Fetal Kidney, Left molecule: genomic DNA disease: None biomaterial_provider: University of Washington, Congenital Defects Lab. Ian Glass biomaterial_type: Primary Tissue tissue_type: Fetal Kidney, Left tissue_depot: UW collection_method: fetal donor_id: H-23758 donor_age: day 107 donor_health_status: NA donor_sex: Female donor_ethnicity: NA experiment_type: Chromatin Accessibility extraction_protocol: Qiagen minElut dnase_protocol: Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)
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Extracted molecule |
genomic DNA |
Extraction protocol |
Library construction protocol: Single read - Illumina
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Library strategy |
DNase-Hypersensitivity |
Library source |
genomic |
Library selection |
DNAse |
Instrument model |
Illumina Genome Analyzer IIx |
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Description |
sample_term_id: UBERON_0004538 assay_term_id: OBI_0001853 nucleic_acid_term_id: SO_0000352 Design description: Chromatin accessibility determination via DNase-seq Library name: DS17140 EDACC Genboree Experiment Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.8357 EDACC Genboree Sample Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.8356 **************** For data usage terms and conditions, please refer to: http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies ****************
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Data processing |
**********************************************************************
ANALYSIS FILE NAME: GSM774209_UW.Fetal_Kidney_Left.ChromatinAccessibility.H-23758.DS17140.bed ANALYSIS CENTER: EDACC ANALYSIS ALIAS: DS17140.hg19.level.1.release.5 ANALYSIS TITLE: Mapping of Fetal Kidney Left Chromatin Accessibility Data ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Kidney Left, Donor H-23758, Library DS17140 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.10388 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 5
QUALITY SCORES: NUMBER_OF_MAPPED_READS: 30,395,163 NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 47 FINDPEAKS_SCORE: 0.3944 FINDPEAKS_PERCENTILE: 36 HOTSPOT_SCORE: 0.3909 HOTSPOT_PERCENTILE: 36 IROC_SCORE: 0.9866 IROC_PERCENTILE: 2 POISSON_SCORE: 0.4417 POISSON_PERCENTILE: 40 MAXIMUM_REPLICATE_CORRELATION: 0.92
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ANALYSIS FILE NAME: GSM774209_UW.Fetal_Kidney_Left.ChromatinAccessibility.H-23758.DS17140.wig ANALYSIS CENTER: EDACC ANALYSIS ALIAS: DS17140.hg19.level.2.release.5 ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Kidney Left Chromatin Accessibility Data ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from Fetal Kidney Left, Donor H-23758, Library DS17140 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.10341 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 5 BROWSER_TRACK_NAME: FKL DNase 58 40 BROWSER_TRACK_DESCRIPTION: UW Fetal Kidney Left DNase Hypersensitivity Donor H-23758 Library DS17140 EA Release 5
QUALITY SCORES: NUMBER_OF_MAPPED_READS: 30,395,163 NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 47 FINDPEAKS_SCORE: 0.3944 FINDPEAKS_PERCENTILE: 36 HOTSPOT_SCORE: 0.3909 HOTSPOT_PERCENTILE: 36 IROC_SCORE: 0.9866 IROC_PERCENTILE: 2 POISSON_SCORE: 0.4417 POISSON_PERCENTILE: 40 MAXIMUM_REPLICATE_CORRELATION: 0.92
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Submission date |
Aug 05, 2011 |
Last update date |
May 15, 2019 |
Contact name |
Northwest REMC |
E-mail(s) |
rharris1@bcm.tmc.edu
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Organization name |
University of Washington
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Street address |
-
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City |
Seattle |
State/province |
WA |
ZIP/Postal code |
98195 |
Country |
USA |
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Platform ID |
GPL10999 |
Series (1) |
GSE18927 |
University of Washington Human Reference Epigenome Mapping Project |
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Relations |
SRA |
SRX089248 |
BioSample |
SAMN00696697 |
Named Annotation |
GSM774209_UW.Fetal_Kidney_Left.ChromatinAccessibility.H-23758.DS17140.wig.gz |
Supplementary file |
Size |
Download |
File type/resource |
GSM774209_UW.Fetal_Kidney_Left.ChromatinAccessibility.H-23758.DS17140.bed.gz |
367.9 Mb |
(ftp)(http) |
BED |
GSM774209_UW.Fetal_Kidney_Left.ChromatinAccessibility.H-23758.DS17140.wig.gz |
170.6 Mb |
(ftp)(http) |
WIG |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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