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| Status |
Public on Aug 06, 2011 |
| Title |
Chromatin accessibility assay of Penis Foreskin Melanocytes Primary Cells; DS18601 |
| Sample type |
SRA |
| |
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| Source name |
Penis, Foreskin, Melanocyte Primary Cells skin01; DS18601
|
| Organism |
Homo sapiens |
| Characteristics |
sample alias: Penis, Foreskin, Melanocyte skin01
sample common name: Penis, Foreskin, Melanocyte Primary Cells
molecule: genomic DNA
disease: None
biomaterial_provider: SFVAMC Dermatology
biomaterial_type: Primary Cell Culture
cell_type: Melanocyte
markers: NA
culture_conditions: Invitrogen 154CF + HKGS + .07mM Ca
donor_id: skin01
donor_age: Neonate
donor_health_status: Disease Free
donor_sex: Male
donor_ethnicity: NA
passage_if_expanded: 2
karyotype: 46, XY
parity: 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 |
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS18601
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.8463
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSF-UBC%2FSAMPLE%2FEDACC.7321
****************
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: GSM774244_UW.Penis_Foreskin_Melanocyte_Primary_Cells.ChromatinAccessibility.skin01.DS18601.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS18601.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Penis Foreskin Melanocyte Primary Cells Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Penis Foreskin Melanocyte Primary Cells, Donor skin01, Library DS18601 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.10393
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 5
QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 45,263,473
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 47
FINDPEAKS_SCORE: 0.4665
FINDPEAKS_PERCENTILE: 60
HOTSPOT_SCORE: 0.4705
HOTSPOT_PERCENTILE: 62
IROC_SCORE: 0.9945
IROC_PERCENTILE: 62
POISSON_SCORE: 0.5365
POISSON_PERCENTILE: 72
MAXIMUM_REPLICATE_CORRELATION: 1.0
**********************************************************************
ANALYSIS FILE NAME: GSM774244_UW.Penis_Foreskin_Melanocyte_Primary_Cells.ChromatinAccessibility.skin01.DS18601.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS18601.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Penis Foreskin Melanocyte Primary Cells Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from Penis Foreskin Melanocyte Primary Cells, Donor skin01, Library DS18601 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.10346
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 5
BROWSER_TRACK_NAME: PFM DNase 01 01
BROWSER_TRACK_DESCRIPTION: UW Penis Foreskin Melanocyte Primary Cells DNase Hypersensitivity Donor skin01 Library DS18601 EA Release 5
QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 45,263,473
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 47
FINDPEAKS_SCORE: 0.4665
FINDPEAKS_PERCENTILE: 60
HOTSPOT_SCORE: 0.4705
HOTSPOT_PERCENTILE: 62
IROC_SCORE: 0.9945
IROC_PERCENTILE: 62
POISSON_SCORE: 0.5365
POISSON_PERCENTILE: 72
MAXIMUM_REPLICATE_CORRELATION: 1.0
**********************************************************************
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| Submission date |
Aug 05, 2011 |
| 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 |
| |
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| Platform ID |
GPL11154 |
| Series (1) |
| GSE18927 |
University of Washington Human Reference Epigenome Mapping Project |
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| Relations |
| SRA |
SRX089283 |
| BioSample |
SAMN00259543 |
| Named Annotation |
GSM774244_UW.Penis_Foreskin_Melanocyte_Primary_Cells.ChromatinAccessibility.skin01.DS18601.wig.gz |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM774244_UW.Penis_Foreskin_Melanocyte_Primary_Cells.ChromatinAccessibility.skin01.DS18601.bed.gz |
635.9 Mb |
(ftp)(http) |
BED |
| GSM774244_UW.Penis_Foreskin_Melanocyte_Primary_Cells.ChromatinAccessibility.skin01.DS18601.wig.gz |
222.9 Mb |
(ftp)(http) |
WIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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