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Status |
Public on Oct 15, 2011 |
Title |
Chromatin accessibility assay of Fetal Renal Cortex, Left; DS18931 |
Sample type |
SRA |
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Source name |
Fetal Kidney, renal, cortex, Left primary tissue, day 120; DS18931
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Organism |
Homo sapiens |
Characteristics |
sample alias: fKidney_renal_cortex_Left.H-24169d120 sample common name: Fetal Renal Cortex, Left molecule: genomic DNA disease: None biomaterial_provider: University of Washington, Congenital Defects Lab. Ian Glass biomaterial_type: Primary Tissue tissue_type: Fetal Renal Cortex, Left tissue_depot: UW collection_method: fetal donor_id: H-24169 donor_age: day 120 donor_health_status: NA donor_sex: Male 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 HiSeq 2000 |
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Description |
sample_term_id: UBERON_0001225 assay_term_id: OBI_0001853 nucleic_acid_term_id: SO_0000352 Design description: Chromatin accessibility determination via DNase-seq Library name: DS18931 EDACC Genboree Experiment Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.10018 EDACC Genboree Sample Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.10017 **************** 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: GSM817203_UW.Fetal_Renal_Cortex_Left.ChromatinAccessibility.H-24169.DS18931.bed ANALYSIS CENTER: EDACC ANALYSIS ALIAS: DS18931.hg19.level.1.release.6 ANALYSIS TITLE: Mapping of Fetal Renal Cortex Left Chromatin Accessibility Data ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Renal Cortex Left, Donor H-24169, Library DS18931 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.12623 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 6
QUALITY SCORES: NUMBER_OF_MAPPED_READS: 23,113,025 NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63 FINDPEAKS_SCORE: 0.3662 FINDPEAKS_PERCENTILE: 48 HOTSPOT_SCORE: 0.3653 HOTSPOT_PERCENTILE: 49 IROC_SCORE: 0.993 IROC_PERCENTILE: 46 POISSON_SCORE: 0.44 POISSON_PERCENTILE: 46 MAXIMUM_REPLICATE_CORRELATION: 0.97
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ANALYSIS FILE NAME: GSM817203_UW.Fetal_Renal_Cortex_Left.ChromatinAccessibility.H-24169.DS18931.wig ANALYSIS CENTER: EDACC ANALYSIS ALIAS: DS18931.hg19.level.2.release.6 ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Renal Cortex Left Chromatin Accessibility Data ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from Fetal Renal Cortex Left, Donor H-24169, Library DS18931 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.12686 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 6 BROWSER_TRACK_NAME: FRCL DNase 69 31 BROWSER_TRACK_DESCRIPTION: UW Fetal Renal Cortex Left DNase Hypersensitivity Donor H-24169 Library DS18931 EA Release 6
QUALITY SCORES: NUMBER_OF_MAPPED_READS: 23,113,025 NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63 FINDPEAKS_SCORE: 0.3662 FINDPEAKS_PERCENTILE: 48 HOTSPOT_SCORE: 0.3653 HOTSPOT_PERCENTILE: 49 IROC_SCORE: 0.993 IROC_PERCENTILE: 46 POISSON_SCORE: 0.44 POISSON_PERCENTILE: 46 MAXIMUM_REPLICATE_CORRELATION: 0.97
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Submission date |
Oct 14, 2011 |
Last update date |
May 15, 2019 |
Contact name |
Northwest REMC |
E-mail(s) |
[email protected]
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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 |
GPL11154 |
Series (1) |
GSE18927 |
University of Washington Human Reference Epigenome Mapping Project |
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Relations |
SRA |
SRX100999 |
BioSample |
SAMN00739180 |
Named Annotation |
GSM817203_UW.Fetal_Renal_Cortex_Left.ChromatinAccessibility.H-24169.DS18931.wig.gz |
Supplementary file |
Size |
Download |
File type/resource |
GSM817203_UW.Fetal_Renal_Cortex_Left.ChromatinAccessibility.H-24169.DS18931.bed.gz |
345.3 Mb |
(ftp)(http) |
BED |
GSM817203_UW.Fetal_Renal_Cortex_Left.ChromatinAccessibility.H-24169.DS18931.wig.gz |
178.6 Mb |
(ftp)(http) |
WIG |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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