|
Status |
Public on Nov 14, 2012 |
Title |
Digital Genomic Footprinting assay of flow sorted CD4+ Cells; DGF.DS17881 |
Sample type |
SRA |
|
|
Source name |
flow sorted CD4+ Cells, year 37; DGF.DS17881
|
Organism |
Homo sapiens |
Characteristics |
sample alias: CD4.RO_01736 sample common name: CD4 Primary Cells molecule: genomic DNA disease: None biomaterial_provider: FHCRC HEIMFELD biomaterial_type: Primary Cell cell_type: CD4 Primary Cells markers: CD4+ donor_id: RO 01701 donor_age: year 37 donor_health_status: NA donor_sex: Male donor_ethnicity: Hispanic passage_if_expanded: NA experiment_type: Digital Genomic Footprinting extraction_protocol: Qiagen minElut dnase_protocol: http://www.roadmapepigenomics.org/protocols/type/experimental/
|
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 HiSeq 2000 |
|
|
Description |
sample_term_id: CL_0000492 assay_term_id: OBI_0001853 nucleic_acid_term_id: SO_0000352 Design description: Digital Genomic Footprinting determination via DNase-seq Library name: DGF.DS17881 EDACC Genboree Experiment Page:
EDACC Genboree Sample Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.7018 **************** 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: GSM1036374_UW.CD4_Primary_Cells.Digital_Genomic_Footprinting.RO_01701.DGF.DS17881.bed ANALYSIS CENTER: EDACC ANALYSIS ALIAS: DGF.DS17881.hg19.level.1.release.9 ANALYSIS TITLE: Mapping of CD4 Primary Cells Digital Genomic Footprinting Data ANALYSIS DESCRIPTION: Illumina reads produced by Digital Genomic Footprinting on CD4 Primary Cells, Donor RO 01701, Library DGF.DS17881 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.15144 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: 118,253,141 NUMBER_OF_DIGITAL_GENOMIC_FOOTPRINTING_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 11 FINDPEAKS_SCORE: 0.481 FINDPEAKS_PERCENTILE: 55 HOTSPOT_SCORE: 0.4805 HOTSPOT_PERCENTILE: 45 IROC_SCORE: 1.0 IROC_PERCENTILE: 100 POISSON_SCORE: 0.4583 POISSON_PERCENTILE: 36 MAXIMUM_REPLICATE_CORRELATION: NA
**********************************************************************
ANALYSIS FILE NAME: GSM1036374_UW.CD4_Primary_Cells.Digital_Genomic_Footprinting.RO_01701.DGF.DS17881.wig ANALYSIS CENTER: EDACC ANALYSIS ALIAS: DGF.DS17881.hg19.level.2.release.9 ANALYSIS TITLE: Raw Signal Density Graphs of CD4 Primary Cells Digital Genomic Footprinting Data ANALYSIS DESCRIPTION: Illumina Digital Genomic Footprinting read mappings from CD4 Primary Cells, Donor RO 01701, Library DGF.DS17881 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.15155 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: CD4 DGF 01 81 BROWSER_TRACK_DESCRIPTION: UW CD4 Primary Cells Digital Genomic Footprinting Donor RO 01701 Library DGF.DS17881 EA Release 9
QUALITY SCORES: NUMBER_OF_MAPPED_READS: 118,253,141 NUMBER_OF_DIGITAL_GENOMIC_FOOTPRINTING_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 11 FINDPEAKS_SCORE: 0.481 FINDPEAKS_PERCENTILE: 55 HOTSPOT_SCORE: 0.4805 HOTSPOT_PERCENTILE: 45 IROC_SCORE: 1.0 IROC_PERCENTILE: 100 POISSON_SCORE: 0.4583 POISSON_PERCENTILE: 36 MAXIMUM_REPLICATE_CORRELATION: NA
**********************************************************************
|
|
|
Submission date |
Nov 13, 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 |
|
|
Platform ID |
GPL11154 |
Series (1) |
GSE18927 |
University of Washington Human Reference Epigenome Mapping Project |
|
Relations |
SRA |
SRX204404 |
BioSample |
SAMN00254256 |
Named Annotation |
GSM1036374_UW.CD4_Primary_Cells.Digital_Genomic_Footprinting.RO_01701.DGF.DS17881.wig.gz |