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GEO help: Mouse over screen elements for information. |
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Status |
Public on Nov 01, 2012 |
Title |
Digital Genomic Footprinting assay of Fetal Muscle, Arm; DGF.DS17765 |
Sample type |
SRA |
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Source name |
Fetal Muscle, Arm primary tissue, day 91; DGF.DS17765
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Organism |
Homo sapiens |
Characteristics |
sample alias: fMuscle_Arm.H-23914d91 sample common name: Fetal Muscle, Arm molecule: genomic DNA disease: None biomaterial_provider: University of Washington, Congenital Defects Lab. Ian Glass biomaterial_type: Primary Tissue tissue_type: Fetal Muscle, Arm tissue_depot: UW collection_method: fetal donor_id: H-23914 donor_age: day 91 donor_health_status: NA donor_sex: Male donor_ethnicity: NA experiment_type: Digital Genomic Footprinting 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 HiSeq 2000 |
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Description |
sample_term_id: UBERON_0001499 assay_term_id: OBI_0001853 nucleic_acid_term_id: SO_0000352 Design description: Digital Genomic Footprinting determination via DNase-seq Library name: DGF.DS17765 EDACC Genboree Experiment Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.14550 EDACC Genboree Sample Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.8512 **************** 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: GSM1027349_UW.Fetal_Muscle_Arm.Digital_Genomic_Footprinting.H-23914.DGF.DS17765.bed ANALYSIS CENTER: EDACC ANALYSIS ALIAS: DGF.DS17765.hg19.level.1.release.9 ANALYSIS TITLE: Mapping of Fetal Muscle Arm Digital Genomic Footprinting Data ANALYSIS DESCRIPTION: Illumina reads produced by Digital Genomic Footprinting on Fetal Muscle Arm, Donor H-23914, Library DGF.DS17765 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.15153 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 9
QUALITY SCORES: NUMBER_OF_MAPPED_READS: 207,283,076 NUMBER_OF_DIGITAL_GENOMIC_FOOTPRINTING_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 11 FINDPEAKS_SCORE: 0.5236 FINDPEAKS_PERCENTILE: 82 HOTSPOT_SCORE: 0.5407 HOTSPOT_PERCENTILE: 82 IROC_SCORE: 0.9884 IROC_PERCENTILE: 18 POISSON_SCORE: 0.5557 POISSON_PERCENTILE: 82 MAXIMUM_REPLICATE_CORRELATION: NA
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ANALYSIS FILE NAME: GSM1027349_UW.Fetal_Muscle_Arm.Digital_Genomic_Footprinting.H-23914.DGF.DS17765.wig ANALYSIS CENTER: EDACC ANALYSIS ALIAS: DGF.DS17765.hg19.level.2.release.9 ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Muscle Arm Digital Genomic Footprinting Data ANALYSIS DESCRIPTION: Illumina Digital Genomic Footprinting read mappings from Fetal Muscle Arm, Donor H-23914, Library DGF.DS17765 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.15164 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 9 BROWSER_TRACK_NAME: FMA DGF 14 65 BROWSER_TRACK_DESCRIPTION: UW Fetal Muscle Arm Digital Genomic Footprinting Donor H-23914 Library DGF.DS17765 EA Release 9
QUALITY SCORES: NUMBER_OF_MAPPED_READS: 207,283,076 NUMBER_OF_DIGITAL_GENOMIC_FOOTPRINTING_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 11 FINDPEAKS_SCORE: 0.5236 FINDPEAKS_PERCENTILE: 82 HOTSPOT_SCORE: 0.5407 HOTSPOT_PERCENTILE: 82 IROC_SCORE: 0.9884 IROC_PERCENTILE: 18 POISSON_SCORE: 0.5557 POISSON_PERCENTILE: 82 MAXIMUM_REPLICATE_CORRELATION: NA
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Submission date |
Oct 29, 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 |
GPL11154 |
Series (1) |
GSE18927 |
University of Washington Human Reference Epigenome Mapping Project |
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Relations |
SRA |
SRX201836 |
BioSample |
SAMN00696706 |
Named Annotation |
GSM1027349_UW.Fetal_Muscle_Arm.Digital_Genomic_Footprinting.H-23914.DGF.DS17765.wig.gz |
Supplementary file |
Size |
Download |
File type/resource |
GSM1027349_UW.Fetal_Muscle_Arm.Digital_Genomic_Footprinting.H-23914.DGF.DS17765.bed.gz |
2.5 Gb |
(ftp)(http) |
BED |
GSM1027349_UW.Fetal_Muscle_Arm.Digital_Genomic_Footprinting.H-23914.DGF.DS17765.wig.gz |
315.7 Mb |
(ftp)(http) |
WIG |
SRA Run Selector |
Raw data are available in SRA |
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