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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Apr 05, 2012 |
| Title |
Digital Genomic Footprinting assay of Penis Foreskin Fibroblast Primary Cells; DGF.DS18224 |
| Sample type |
SRA |
| |
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| Source name |
Penis, Foreskin, Fibroblast Primary Cells skin01; DGF.DS18224
|
| Organism |
Homo sapiens |
| Characteristics |
sample alias: Penis, Foreskin, Fibroblast skin01
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 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: Digital Genomic Footprinting
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: CL_1001608
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Digital Genomic Footprinting determination via DNase-seq
Library name: DGF.DS18224
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.12000
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSF-UBC%2FSAMPLE%2FEDACC.7320
****************
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: GSM909312_UW.Penis_Foreskin_Fibroblast_Primary_Cells.Digital_Genomic_Footprinting.skin01.DGF.DS18224.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DGF.DS18224.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of Penis Foreskin Fibroblast Primary Cells Digital Genomic Footprinting Data
ANALYSIS DESCRIPTION: Illumina reads produced by Digital Genomic Footprinting on Penis Foreskin Fibroblast Primary Cells, Donor skin01, Library DGF.DS18224 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.13112
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Digital Genomic Footprinting
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 8
QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 433,775,987
NUMBER_OF_DIGITAL_GENOMIC_FOOTPRINTING_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 5
FINDPEAKS_SCORE: 0.6769
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.6776
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9983
IROC_PERCENTILE: 40
POISSON_SCORE: 0.7024
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: NA
**********************************************************************
ANALYSIS FILE NAME: GSM909312_UW.Penis_Foreskin_Fibroblast_Primary_Cells.Digital_Genomic_Footprinting.skin01.DGF.DS18224.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DGF.DS18224.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of Penis Foreskin Fibroblast Primary Cells Digital Genomic Footprinting Data
ANALYSIS DESCRIPTION: Illumina Digital Genomic Footprinting read mappings from Penis Foreskin Fibroblast Primary Cells, Donor skin01, Library DGF.DS18224 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.13117
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Digital Genomic Footprinting
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 8
BROWSER_TRACK_NAME: PFF DGF 01 24
BROWSER_TRACK_DESCRIPTION: UW Penis Foreskin Fibroblast Primary Cells Digital Genomic Footprinting Donor skin01 Library DGF.DS18224 EA Release 8
QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 433,775,987
NUMBER_OF_DIGITAL_GENOMIC_FOOTPRINTING_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 5
FINDPEAKS_SCORE: 0.6769
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.6776
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9983
IROC_PERCENTILE: 40
POISSON_SCORE: 0.7024
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: NA
**********************************************************************
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| Submission date |
Apr 04, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Northwest REMC |
| E-mail(s) |
[email protected]
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| 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 (1) |
| GSE18927 |
University of Washington Human Reference Epigenome Mapping Project |
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| Relations |
| SRA |
SRX135564 |
| BioSample |
SAMN00259542 |
| Named Annotation |
GSM909312_UW.Penis_Foreskin_Fibroblast_Primary_Cells.Digital_Genomic_Footprinting.skin01.DGF.DS18224.wig.gz |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM909312_UW.Penis_Foreskin_Fibroblast_Primary_Cells.Digital_Genomic_Footprinting.skin01.DGF.DS18224.bed.gz |
5.2 Gb |
(ftp)(http) |
BED |
| GSM909312_UW.Penis_Foreskin_Fibroblast_Primary_Cells.Digital_Genomic_Footprinting.skin01.DGF.DS18224.wig.gz |
361.6 Mb |
(ftp)(http) |
WIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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