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| Status |
Public on Oct 15, 2011 |
| Title |
Chromatin accessibility assay of Penis Foreskin Fibroblast Primary Cells; DS18252 |
| Sample type |
SRA |
| |
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| Source name |
Penis, Foreskin, Fibroblast Primary Cells skin02; DS18252
|
| Organism |
Homo sapiens |
| Characteristics |
sample alias: Penis, Foreskin, Fibroblast skin02
sample common name: Penis, Foreskin, Fibroblast Primary Cells
molecule: genomic DNA
disease: None
biomaterial_provider: SFVAMC Dermatology
biomaterial_type: Primary Cell Culture
cell_type: Fibroblast
markers: NA
culture_conditions: Invitrogen 106 + LSGS
donor_id: skin02
donor_age: Neonate
donor_health_status: Disease Free
donor_sex: Male
donor_ethnicity: NA
passage_if_expanded: 4
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 Genome Analyzer IIx |
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| Description |
sample_term_id: CL_1001608
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS18252
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.10119
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSF-UBC%2FSAMPLE%2FEDACC.9574
****************
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: GSM817169_UW.Penis_Foreskin_Fibroblast_Primary_Cells.ChromatinAccessibility.skin02.DS18252.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS18252.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of Penis Foreskin Fibroblast Primary Cells Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Penis Foreskin Fibroblast Primary Cells, Donor skin02, Library DS18252 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.12589
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: 32,169,657
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.6688
FINDPEAKS_PERCENTILE: 98
HOTSPOT_SCORE: 0.7011
HOTSPOT_PERCENTILE: 98
IROC_SCORE: 0.999
IROC_PERCENTILE: 98
POISSON_SCORE: 0.6977
POISSON_PERCENTILE: 98
MAXIMUM_REPLICATE_CORRELATION: 1.0
**********************************************************************
ANALYSIS FILE NAME: GSM817169_UW.Penis_Foreskin_Fibroblast_Primary_Cells.ChromatinAccessibility.skin02.DS18252.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS18252.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of Penis Foreskin Fibroblast Primary Cells Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from Penis Foreskin Fibroblast Primary Cells, Donor skin02, Library DS18252 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.12652
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: PFF DNase 02 52
BROWSER_TRACK_DESCRIPTION: UW Penis Foreskin Fibroblast Primary Cells DNase Hypersensitivity Donor skin02 Library DS18252 EA Release 6
QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 32,169,657
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.6688
FINDPEAKS_PERCENTILE: 98
HOTSPOT_SCORE: 0.7011
HOTSPOT_PERCENTILE: 98
IROC_SCORE: 0.999
IROC_PERCENTILE: 98
POISSON_SCORE: 0.6977
POISSON_PERCENTILE: 98
MAXIMUM_REPLICATE_CORRELATION: 1.0
**********************************************************************
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| Submission date |
Oct 14, 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 |
GPL10999 |
| Series (1) |
| GSE18927 |
University of Washington Human Reference Epigenome Mapping Project |
|
| Relations |
| SRA |
SRX100965 |
| BioSample |
SAMN00727776 |
| Named Annotation |
GSM817169_UW.Penis_Foreskin_Fibroblast_Primary_Cells.ChromatinAccessibility.skin02.DS18252.wig.gz |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM817169_UW.Penis_Foreskin_Fibroblast_Primary_Cells.ChromatinAccessibility.skin02.DS18252.bed.gz |
413.3 Mb |
(ftp)(http) |
BED |
| GSM817169_UW.Penis_Foreskin_Fibroblast_Primary_Cells.ChromatinAccessibility.skin02.DS18252.wig.gz |
125.3 Mb |
(ftp)(http) |
WIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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