|
| Status |
Public on May 12, 2011 |
| Title |
Digital Genomic Footprinting assay of Moblized CD34 Primary Cells; DGF.DS12274 |
| Sample type |
SRA |
| |
|
| Source name |
flow sorted CD34+ cells from cord blood; DGF.DS12274
|
| Organism |
Homo sapiens |
| Characteristics |
sample alias: RO 01535
sample common name: CD34 Primary Cells
molecule: genomic DNA
disease: None
biomaterial_provider: FHCRC HEIMFELD
biomaterial_type: Primary Cell
cell_type: CD34 Primary Cells
markers: CD34+
donor_id: RO 01535
donor_age: NA
donor_health_status: NA
donor_sex: Unknown
donor_ethnicity: NA
passage_if_expanded: 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)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Library construction protocol: Single read - Illumina
|
| |
|
| Library strategy |
DNase-Hypersensitivity |
| Library source |
genomic |
| Library selection |
DNAse |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
sample_term_id: CL_0000837
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Digital Genomic Footprinting determination via DNase-seq
Library name: DGF.DS12274
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.7422
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.1659
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************
|
| Data processing |
**********************************************************************
ANALYSIS FILE NAME: GSM723022_UW.Mobilized_CD34_Primary_Cells.Digital_Genomic_Footprinting.RO_01535.DGF.DS12274.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DGF.DS12274.hg19.level.1.release.4
ANALYSIS TITLE: Mapping of Mobilized CD34 Primary Cells Digital Genomic Footprinting Data
ANALYSIS DESCRIPTION: Illumina reads produced by Digital Genomic Footprinting on Mobilized CD34 Primary Cells, Donor RO 01535, Library DGF.DS12274 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.7630
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 4
QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 242,028,273
NUMBER_OF_DIGITAL_GENOMIC_FOOTPRINTING_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 5
FINDPEAKS_SCORE: 0.6629
FINDPEAKS_PERCENTILE: 80
HOTSPOT_SCORE: 0.6652
HOTSPOT_PERCENTILE: 80
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.6301
POISSON_PERCENTILE: 60
**********************************************************************
ANALYSIS FILE NAME: GSM723022_UW.Mobilized_CD34_Primary_Cells.Digital_Genomic_Footprinting.RO_01535.DGF.DS12274.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DGF.DS12274.hg19.level.2.release.4
ANALYSIS TITLE: Raw Signal Density Graphs of Mobilized CD34 Primary Cells Digital Genomic Footprinting Data
ANALYSIS DESCRIPTION: Illumina Digital Genomic Footprinting read mappings from Mobilized CD34 Primary Cells, Donor RO 01535, Library DGF.DS12274 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.7635
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 4
BROWSER_TRACK_NAME: MCD34 DGF 35 74
BROWSER_TRACK_DESCRIPTION: UW CD34 Primary Cells Digital Genomic Footprinting Donor RO 01535 Library DGF.DS12274 EA Release 4
QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 242,028,273
NUMBER_OF_DIGITAL_GENOMIC_FOOTPRINTING_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 5
FINDPEAKS_SCORE: 0.6629
FINDPEAKS_PERCENTILE: 80
HOTSPOT_SCORE: 0.6652
HOTSPOT_PERCENTILE: 80
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.6301
POISSON_PERCENTILE: 60
**********************************************************************
|
| |
|
| Submission date |
May 11, 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 |
| |
|
| Platform ID |
GPL10999 |
| Series (2) |
| GSE18927 |
University of Washington Human Reference Epigenome Mapping Project |
| GSE51341 |
Conservation of mouse-human trans-regulatory circuitry despite high cis-regulatory divergence |
|
| Relations |
| SRA |
SRX062365 |
| BioSample |
SAMN00007322 |
| Named Annotation |
GSM723022_UW.Mobilized_CD34_Primary_Cells.Digital_Genomic_Footprinting.RO_01535.DGF.DS12274.wig.gz |
