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| Status |
Public on Oct 25, 2012 |
| Title |
Digital Genomic Footprinting assay of Breast vHMEC; DGF.DS18406 |
| Sample type |
SRA |
| |
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| Source name |
Breast, vHMEC, RM035; DGF.DS18406
|
| Organism |
Homo sapiens |
| Characteristics |
sample alias: Breast vHMEC RM035
sample common name: Breast, vHMEC
molecule: genomic DNA
disease: None
biomaterial_provider: Tlsty Lab, University of California, San Francisco
biomaterial_type: Primary Cell Culture
cell_type: Variant Human Mammary Epithelial Cells
markers: NA
culture_conditions: spilt 1:5 in MEGM medium (Lonza Inc.)
donor_id: RM035
donor_age: 18
donor_health_status: Disease Free
donor_sex: Female
donor_ethnicity: Caucasian
passage_if_expanded: 8
karyotype: 46,XX,1dmin
parity: N/A
experiment_type: Digital Genomic Footprinting
extraction_protocol: Qiagen minElut
dnase_protocol: http://www.roadmapepigenomics.org/protocols/type/experimental/
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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_0002327
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Digital Genomic Footprinting determination via DNase-seq
Library name: DGF.DS18406
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.14170
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSF-UBC%2FSAMPLE%2FEDACC.2872
****************
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: GSM1024609_UW.Breast_vHMEC.Digital_Genomic_Footprinting.RM035.DGF.DS18406.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DGF.DS18406.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Breast vHMEC Digital Genomic Footprinting Data
ANALYSIS DESCRIPTION: Illumina reads produced by Digital Genomic Footprinting on Breast vHMEC, Donor RM035, Library DGF.DS18406 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.15145
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 9
QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 346,018,292
NUMBER_OF_DIGITAL_GENOMIC_FOOTPRINTING_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 11
FINDPEAKS_SCORE: 0.4046
FINDPEAKS_PERCENTILE: 27
HOTSPOT_SCORE: 0.4816
HOTSPOT_PERCENTILE: 55
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.5142
POISSON_PERCENTILE: 55
MAXIMUM_REPLICATE_CORRELATION: NA
**********************************************************************
ANALYSIS FILE NAME: GSM1024609_UW.Breast_vHMEC.Digital_Genomic_Footprinting.RM035.DGF.DS18406.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DGF.DS18406.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Breast vHMEC Digital Genomic Footprinting Data
ANALYSIS DESCRIPTION: Illumina Digital Genomic Footprinting read mappings from Breast vHMEC, Donor RM035, Library DGF.DS18406 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.15156
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 9
BROWSER_TRACK_NAME: Bv DGF 35 06
BROWSER_TRACK_DESCRIPTION: UW Breast vHMEC Digital Genomic Footprinting Donor RM035 Library DGF.DS18406 EA Release 9
QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 346,018,292
NUMBER_OF_DIGITAL_GENOMIC_FOOTPRINTING_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 11
FINDPEAKS_SCORE: 0.4046
FINDPEAKS_PERCENTILE: 27
HOTSPOT_SCORE: 0.4816
HOTSPOT_PERCENTILE: 55
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.5142
POISSON_PERCENTILE: 55
MAXIMUM_REPLICATE_CORRELATION: NA
**********************************************************************
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| Submission date |
Oct 24, 2012 |
| 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 |
|
| Relations |
| SRA |
SRX201197 |
| BioSample |
SAMN00117167 |
| Named Annotation |
GSM1024609_UW.Breast_vHMEC.Digital_Genomic_Footprinting.RM035.DGF.DS18406.wig.gz |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1024609_UW.Breast_vHMEC.Digital_Genomic_Footprinting.RM035.DGF.DS18406.bed.gz |
3.8 Gb |
(ftp)(http) |
BED |
| GSM1024609_UW.Breast_vHMEC.Digital_Genomic_Footprinting.RM035.DGF.DS18406.wig.gz |
377.3 Mb |
(ftp)(http) |
WIG |
SRA Run Selector |
| Raw data are available in SRA |
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