|
Status |
Public on Mar 22, 2010 |
Title |
Chromatin accessibility assay of Fetal Kidney Primary Tissue; DS10986 |
Sample type |
SRA |
|
|
Source name |
Fetal Kidney primary tissue, day 82; DS10986
|
Organism |
Homo sapiens |
Characteristics |
molecule: genomic DNA disease: None biomaterial_provider: University of Washington, Congenital Defects Lab. Ian Glass biomaterial_type: Primary Tissue tissue_type: fetal kidney tissue_depot: UW collection_method: fetal donor_id: H-22337 donor_age: 82 days donor_health_status: NA donor_sex: Female donor_ethnicity: Caucasian experiment_type: Chromatin Accessibility extraction_protocol: Qiagen minElut dnase_protocol: Stamlab DNase Protocol
|
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 Genome Analyzer II |
|
|
Description |
sample_term_id: UBERON_0002113 assay_term_id: OBI_0001853 nucleic_acid_term_id: SO_0000352 Design description: Chromatin accessibility determination via DNase-seq Library name: DS10986 EDACC Genboree Sample Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.1675 EDACC Genboree Experiment Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.1676 **************** 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: GSM493385_DS10986.UWStam_090616_SOLEXA-1GA-1_0007_FC427K6_4.bam ANALYSIS ALIAS: UW.FetalKidney.ChromatinAccessibility.Level1.1 ANALYSIS TITLE: Mapping of Fetal Kidney Chromatin Accessibility Data ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Kidney primary tissue were mapped to the human genome (NCBI Build 36.1) using Pash. ANALYSIS TYPE: REFERENCE_ALIGNMENT EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.1864 DATA_ANALYSIS_LEVEL: 1 EXPERIMENT_TYPE: Chromatin Accessibility 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
**********************************************************************
ANALYSIS FILE NAME: GSM493385_DS10986.UWStam_090629_SOLEXA-1GA-1_0011_FC42AT0_7.bam ANALYSIS ALIAS: UW.FetalKidney.ChromatinAccessibility.Level1.2 ANALYSIS TITLE: Mapping of Fetal Kidney Chromatin Accessibility Data ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Kidney primary tissue were mapped to the human genome (NCBI Build 36.1) using Pash. ANALYSIS TYPE: REFERENCE_ALIGNMENT EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.1865 DATA_ANALYSIS_LEVEL: 1 EXPERIMENT_TYPE: Chromatin Accessibility 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
**********************************************************************
ANALYSIS FILE NAME: GSM493385_DS10986.UWStam_090804_SOLEXA-1GA-2_0009_FC42ALL_3.bam ANALYSIS ALIAS: UW.FetalKidney.ChromatinAccessibility.Level1.3 ANALYSIS TITLE: Mapping of Fetal Kidney Chromatin Accessibility Data ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Kidney primary tissue were mapped to the human genome (NCBI Build 36.1) using Pash. ANALYSIS TYPE: REFERENCE_ALIGNMENT EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.1866 DATA_ANALYSIS_LEVEL: 1 EXPERIMENT_TYPE: Chromatin Accessibility 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
**********************************************************************
ANALYSIS FILE NAME: GSM493385_UW.FetalKidney.ChromatinAccessibility.fKidney-DS10986.wig ANALYSIS ALIAS: UW.FetalKidney.ChromatinAccessibility.DS10986 ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Kidney Chromatin Accessibility Data ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from Fetal Kidney 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%2FUniversity%20of%20Washington%2FANALYSIS%2FEDACC.2645 DATA_ANALYSIS_LEVEL: 2 EXPERIMENT_TYPE: Chromatin Accessibility SOFTWARE: In house programs and scripts SOFTWARE_VERSION: NA READ_EXTENSION: 200bp GENOMIC_WINDOW: 20bp TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
**********************************************************************
ANALYSIS FILE NAME: GSM493385_UW.Fetal_Kidney.ChromatinAccessibility.H-22337.DS10986.bed ANALYSIS ALIAS: DS10986.hg19.level.1 ANALYSIS TITLE: Mapping of Fetal Kidney Chromatin Accessibility Data ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Kidney, Donor H-22337, Library DS10986 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.4104 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 2
QUALITY SCORES: NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED: 40 FINDPEAKS_SCORE: 0.526 FINDPEAKS_PERCENTILE: 40 HOTSPOT_SCORE: 0.397 HOTSPOT_PERCENTILE: 40 IROC_SCORE: 0.9941 IROC_PERCENTILE: 15 POISSON_SCORE: 0.5375 POISSON_PERCENTILE: 62
**********************************************************************
ANALYSIS FILE NAME: GSM493385_UW.Fetal_Kidney.ChromatinAccessibility.H-22337.DS10986.wig ANALYSIS ALIAS: DS10986.hg19.level.2 ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Kidney Chromatin Accessibility Data ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from Fetal Kidney, Donor H-22337, Library DS10986 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.4064 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 2 BROWSER_TRACK_NAME: FK DNase 37 86 BROWSER_TRACK_DESCRIPTION: UW Fetal Kidney DNase Hypersensitivity Donor H-22337 Library DS10986 EA Release 2
QUALITY SCORES: NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED: 40 FINDPEAKS_SCORE: 0.526 FINDPEAKS_PERCENTILE: 40 HOTSPOT_SCORE: 0.397 HOTSPOT_PERCENTILE: 40 IROC_SCORE: 0.9941 IROC_PERCENTILE: 15 POISSON_SCORE: 0.5375 POISSON_PERCENTILE: 62
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|
|
Submission date |
Jan 05, 2010 |
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 |
GPL9115 |
Series (1) |
GSE18927 |
University of Washington Human Reference Epigenome Mapping Project |
|
Relations |
SRA |
SRX015225 |
BioSample |
SAMN00007323 |
Named Annotation |
GSM493385_UW.FetalKidney.ChromatinAccessibility.fKidney-DS10986.wig.gz |
Named Annotation |
GSM493385_UW.Fetal_Kidney.ChromatinAccessibility.H-22337.DS10986.wig.gz |