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Sample GSM1027336 Query DataSets for GSM1027336
Status Public on Nov 01, 2012
Title Chromatin accessibility assay of Fetal Kidney, Left; DNase.DS20920
Sample type SRA
 
Source name Fetal Kidney, Left primary tissue, day 98; DNase.DS20920
Organism Homo sapiens
Characteristics sample alias: fKidney_Left.H-24568d98
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-24568
donor_age: day 98
donor_health_status: NA
donor_sex: Female
donor_ethnicity: NA
experiment_type: Chromatin Accessibility
extraction_protocol: Qiagen minElut
dnase_protocol: http://www.roadmapepigenomics.org/protocols/type/experimental/
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 HiSeq 2000
 
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: DNase.DS20920
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.14455
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.14454
****************
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: GSM1027336_UW.Fetal_Kidney_Left.ChromatinAccessibility.H-24568.DNase.DS20920.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNase.DS20920.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Fetal Kidney Left Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Kidney Left, Donor H-24568, Library DNase.DS20920 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.17589
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 9


QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 60,393,843
FINDPEAKS_SCORE: 0.44
FINDPEAKS_PERCENTILE: 65
HOTSPOT_SCORE: 0.423
HOTSPOT_PERCENTILE: 61
IROC_SCORE: 0.9906
IROC_PERCENTILE: 28
POISSON_SCORE: 0.4954
POISSON_PERCENTILE: 65
MAXIMUM_REPLICATE_CORRELATION: 0.97

**********************************************************************

ANALYSIS FILE NAME: GSM1027336_UW.Fetal_Kidney_Left.ChromatinAccessibility.H-24568.DNase.DS20920.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNase.DS20920.hg19.level.2.release.9
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-24568, Library DNase.DS20920 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.17543
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 9
BROWSER_TRACK_NAME: FKL DNase 68 20
BROWSER_TRACK_DESCRIPTION: UW Fetal Kidney Left DNase Hypersensitivity Donor H-24568 Library DNase.DS20920 EA Release 9


QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 60,393,843
FINDPEAKS_SCORE: 0.44
FINDPEAKS_PERCENTILE: 65
HOTSPOT_SCORE: 0.423
HOTSPOT_PERCENTILE: 61
IROC_SCORE: 0.9906
IROC_PERCENTILE: 28
POISSON_SCORE: 0.4954
POISSON_PERCENTILE: 65
MAXIMUM_REPLICATE_CORRELATION: 0.97

**********************************************************************

 
Submission date Oct 29, 2012
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 GPL11154
Series (2)
GSE18927 University of Washington Human Reference Epigenome Mapping Project
GSE51336 Mouse regulatory DNA landscapes reveal global principles of cis-regulatory evolution
Relations
SRA SRX201823
BioSample SAMN01797254
Named Annotation GSM1027336_UW.Fetal_Kidney_Left.ChromatinAccessibility.H-24568.DNase.DS20920.wig.gz

Supplementary file Size Download File type/resource
GSM1027336_UW.Fetal_Kidney_Left.ChromatinAccessibility.H-24568.DNase.DS20920.bed.gz 879.1 Mb (ftp)(http) BED
GSM1027336_UW.Fetal_Kidney_Left.ChromatinAccessibility.H-24568.DNase.DS20920.wig.gz 268.4 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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