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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Oct 15, 2011 |
| Title |
Chromatin accessibility assay of Fetal Renal Pelvis; DS18431 |
| Sample type |
SRA |
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| Source name |
Fetal Kidney, renal, pelvis primary tissue, day 127; DS18431
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| Organism |
Homo sapiens |
| Characteristics |
sample alias: fKidney_renal_pelvis.H-24078d127
sample common name: Fetal Renal Pelvis
molecule: genomic DNA
disease: None
biomaterial_provider: University of Washington, Congenital Defects Lab. Ian Glass
biomaterial_type: Primary Tissue
tissue_type: Fetal Renal Pelvis
tissue_depot: UW
collection_method: fetal
donor_id: H-24078
donor_age: day 127
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_0001224
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS18431
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.9991
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.9990
****************
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: GSM817177_UW.Fetal_Renal_Pelvis.ChromatinAccessibility.H-24078.DS18431.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS18431.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of Fetal Renal Pelvis Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Renal Pelvis, Donor H-24078, Library DS18431 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.12597
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: 31,273,429
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.2728
FINDPEAKS_PERCENTILE: 11
HOTSPOT_SCORE: 0.277
HOTSPOT_PERCENTILE: 11
IROC_SCORE: 0.9871
IROC_PERCENTILE: 6
POISSON_SCORE: 0.3688
POISSON_PERCENTILE: 17
MAXIMUM_REPLICATE_CORRELATION: 0.96
**********************************************************************
ANALYSIS FILE NAME: GSM817177_UW.Fetal_Renal_Pelvis.ChromatinAccessibility.H-24078.DS18431.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS18431.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Renal Pelvis Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from Fetal Renal Pelvis, Donor H-24078, Library DS18431 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.12660
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: FRP DNase 78 31
BROWSER_TRACK_DESCRIPTION: UW Fetal Renal Pelvis DNase Hypersensitivity Donor H-24078 Library DS18431 EA Release 6
QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 31,273,429
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.2728
FINDPEAKS_PERCENTILE: 11
HOTSPOT_SCORE: 0.277
HOTSPOT_PERCENTILE: 11
IROC_SCORE: 0.9871
IROC_PERCENTILE: 6
POISSON_SCORE: 0.3688
POISSON_PERCENTILE: 17
MAXIMUM_REPLICATE_CORRELATION: 0.96
**********************************************************************
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| Submission date |
Oct 14, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Northwest REMC |
| E-mail(s) |
[email protected]
|
| 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 (2) |
| GSE18927 |
University of Washington Human Reference Epigenome Mapping Project |
| GSE51336 |
Mouse regulatory DNA landscapes reveal global principles of cis-regulatory evolution |
|
| Relations |
| SRA |
SRX100973 |
| BioSample |
SAMN00739184 |
| Named Annotation |
GSM817177_UW.Fetal_Renal_Pelvis.ChromatinAccessibility.H-24078.DS18431.wig.gz |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM817177_UW.Fetal_Renal_Pelvis.ChromatinAccessibility.H-24078.DS18431.bed.gz |
466.7 Mb |
(ftp)(http) |
BED |
| GSM817177_UW.Fetal_Renal_Pelvis.ChromatinAccessibility.H-24078.DS18431.wig.gz |
223.5 Mb |
(ftp)(http) |
WIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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