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Status |
Public on Feb 22, 2012 |
Title |
Chromatin accessibility assay of Fibroblasts, Fetal Skin, Quadriceps, Left; DS20046 |
Sample type |
SRA |
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Source name |
Fibroblasts, Fetal Skin, Quadriceps, Left, day 97 donor; DS20046
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Organism |
Homo sapiens |
Characteristics |
sample alias: fSkin_fibro_leg_L_quad.H-24259d97B2 sample common name: Fibroblasts, Fetal Skin, Quadriceps, Left molecule: genomic DNA disease: None biomaterial_provider: University of Washington, Congenital Defects Lab. Ian Glass biomaterial_type: Primary Cell Culture cell_type: Fibroblasts, Fetal Skin, Quadriceps, Left markers: NA culture_conditions: None donor_id: H-24259 donor_age: day 97 donor_health_status: NA donor_sex: Male donor_ethnicity: NA passage_if_expanded: short term experiment_type: Chromatin Accessibility extraction_protocol: Qiagen minElut dnase_protocol: http://www.roadmapepigenomics.org/protocols/type/experimental/
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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: CL_0002620 assay_term_id: OBI_0001853 nucleic_acid_term_id: SO_0000352 Design description: Chromatin accessibility determination via DNase-seq Library name: DS20046 EDACC Genboree Experiment Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.11414 EDACC Genboree Sample Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.11420 **************** 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: GSM878648_UW.Fibroblasts_Fetal_Skin_Quadriceps_Left.ChromatinAccessibility.H-24259.DS20046.bed ANALYSIS CENTER: EDACC ANALYSIS ALIAS: DS20046.hg19.level.1.release.7 ANALYSIS TITLE: Mapping of Fibroblasts Fetal Skin Quadriceps Left Chromatin Accessibility Data ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fibroblasts Fetal Skin Quadriceps Left, Donor H-24259, Library DS20046 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.12765 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: 48,421,425 NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 58 FINDPEAKS_SCORE: 0.5497 FINDPEAKS_PERCENTILE: 88 HOTSPOT_SCORE: 0.637 HOTSPOT_PERCENTILE: 91 IROC_SCORE: 0.997 IROC_PERCENTILE: 79 POISSON_SCORE: 0.6328 POISSON_PERCENTILE: 91 MAXIMUM_REPLICATE_CORRELATION: 1.0
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ANALYSIS FILE NAME: GSM878648_UW.Fibroblasts_Fetal_Skin_Quadriceps_Left.ChromatinAccessibility.H-24259.DS20046.wig ANALYSIS CENTER: EDACC ANALYSIS ALIAS: DS20046.hg19.level.2.release.7 ANALYSIS TITLE: Raw Signal Density Graphs of Fibroblasts Fetal Skin Quadriceps Left Chromatin Accessibility Data ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from Fibroblasts Fetal Skin Quadriceps Left, Donor H-24259, Library DS20046 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.12823 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: FFSQL DNase 59 46 BROWSER_TRACK_DESCRIPTION: UW Fibroblasts Fetal Skin Quadriceps Left DNase Hypersensitivity Donor H-24259 Library DS20046 EA Release 7
QUALITY SCORES: NUMBER_OF_MAPPED_READS: 48,421,425 NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 58 FINDPEAKS_SCORE: 0.5497 FINDPEAKS_PERCENTILE: 88 HOTSPOT_SCORE: 0.637 HOTSPOT_PERCENTILE: 91 IROC_SCORE: 0.997 IROC_PERCENTILE: 79 POISSON_SCORE: 0.6328 POISSON_PERCENTILE: 91 MAXIMUM_REPLICATE_CORRELATION: 1.0
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Submission date |
Feb 21, 2012 |
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 |
SRX121274 |
BioSample |
SAMN00791508 |
Named Annotation |
GSM878648_UW.Fibroblasts_Fetal_Skin_Quadriceps_Left.ChromatinAccessibility.H-24259.DS20046.wig.gz |
Supplementary file |
Size |
Download |
File type/resource |
GSM878648_UW.Fibroblasts_Fetal_Skin_Quadriceps_Left.ChromatinAccessibility.H-24259.DS20046.bed.gz |
637.4 Mb |
(ftp)(http) |
BED |
GSM878648_UW.Fibroblasts_Fetal_Skin_Quadriceps_Left.ChromatinAccessibility.H-24259.DS20046.wig.gz |
180.4 Mb |
(ftp)(http) |
WIG |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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