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| Status |
Public on Jul 06, 2011 |
| Title |
Chromatin accessibility assay of Breast_vHMEC; DS18406 |
| Sample type |
SRA |
| |
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| Source name |
Breast, vHMEC, RM035; DS18406
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| 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: 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: CL_0002327
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS18406
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.7555
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: GSM753973_UW.Breast_vHMEC.ChromatinAccessibility.RM035.DS18406.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS18406.hg19.level.1.release.4
ANALYSIS TITLE: Mapping of Breast vHMEC Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Breast vHMEC, Donor RM035, Library 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.7687
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 4
QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 31,386,613
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.3982
FINDPEAKS_PERCENTILE: 61
HOTSPOT_SCORE: 0.4808
HOTSPOT_PERCENTILE: 80
IROC_SCORE: 0.9973
IROC_PERCENTILE: 93
POISSON_SCORE: 0.5033
POISSON_PERCENTILE: 69
MAXIMUM_REPLICATE_CORRELATION: 1.0
**********************************************************************
ANALYSIS FILE NAME: GSM753973_UW.Breast_vHMEC.ChromatinAccessibility.RM035.DS18406.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS18406.hg19.level.2.release.4
ANALYSIS TITLE: Raw Signal Density Graphs of Breast vHMEC Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from Breast vHMEC, Donor RM035, Library 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.7741
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 4
BROWSER_TRACK_NAME: Bv DNase 35 06
BROWSER_TRACK_DESCRIPTION: UW Breast vHMEC DNase Hypersensitivity Donor RM035 Library DS18406 EA Release 4
QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 31,386,613
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 52
FINDPEAKS_SCORE: 0.3982
FINDPEAKS_PERCENTILE: 61
HOTSPOT_SCORE: 0.4808
HOTSPOT_PERCENTILE: 80
IROC_SCORE: 0.9973
IROC_PERCENTILE: 93
POISSON_SCORE: 0.5033
POISSON_PERCENTILE: 69
MAXIMUM_REPLICATE_CORRELATION: 1.0
**********************************************************************
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| Submission date |
Jul 03, 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 |
SRX081373 |
| BioSample |
SAMN00117167 |
| Named Annotation |
GSM753973_UW.Breast_vHMEC.ChromatinAccessibility.RM035.DS18406.wig.gz |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM753973_UW.Breast_vHMEC.ChromatinAccessibility.RM035.DS18406.bed.gz |
429.1 Mb |
(ftp)(http) |
BED |
| GSM753973_UW.Breast_vHMEC.ChromatinAccessibility.RM035.DS18406.wig.gz |
169.4 Mb |
(ftp)(http) |
WIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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