|
| Status |
Public on Nov 01, 2012 |
| Title |
Digital Genomic Footprinting assay of Fetal Thymus; DGF.DS20341 |
| Sample type |
SRA |
| |
|
| Source name |
Fetal Thymus primary tissue, day 113; DGF.DS20341
|
| Organism |
Homo sapiens |
| Characteristics |
sample alias: fThymus.H-24409d113
sample common name: Fetal Thymus
molecule: genomic DNA
disease: None
biomaterial_provider: University of Washington, Congenital Defects Lab. Ian Glass
biomaterial_type: Primary Tissue
tissue_type: Fetal Thymus
tissue_depot: UW
collection_method: fetal
donor_id: H-24409
donor_age: day 113
donor_health_status: NA
donor_sex: Female
donor_ethnicity: 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: UBERON_0002370
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Digital Genomic Footprinting determination via DNase-seq
Library name: DGF.DS20341
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.14546
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.11269
****************
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: GSM1027351_UW.Fetal_Thymus.Digital_Genomic_Footprinting.H-24409.DGF.DS20341.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DGF.DS20341.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Fetal Thymus Digital Genomic Footprinting Data
ANALYSIS DESCRIPTION: Illumina reads produced by Digital Genomic Footprinting on Fetal Thymus, Donor H-24409, Library DGF.DS20341 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.15151
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: 329,108,296
NUMBER_OF_DIGITAL_GENOMIC_FOOTPRINTING_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 11
FINDPEAKS_SCORE: 0.3576
FINDPEAKS_PERCENTILE: 9
HOTSPOT_SCORE: 0.3393
HOTSPOT_PERCENTILE: 9
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.3707
POISSON_PERCENTILE: 9
MAXIMUM_REPLICATE_CORRELATION: NA
**********************************************************************
ANALYSIS FILE NAME: GSM1027351_UW.Fetal_Thymus.Digital_Genomic_Footprinting.H-24409.DGF.DS20341.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DGF.DS20341.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Thymus Digital Genomic Footprinting Data
ANALYSIS DESCRIPTION: Illumina Digital Genomic Footprinting read mappings from Fetal Thymus, Donor H-24409, Library DGF.DS20341 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.15162
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: FT DGF 09 41
BROWSER_TRACK_DESCRIPTION: UW Fetal Thymus Digital Genomic Footprinting Donor H-24409 Library DGF.DS20341 EA Release 9
QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 329,108,296
NUMBER_OF_DIGITAL_GENOMIC_FOOTPRINTING_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 11
FINDPEAKS_SCORE: 0.3576
FINDPEAKS_PERCENTILE: 9
HOTSPOT_SCORE: 0.3393
HOTSPOT_PERCENTILE: 9
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.3707
POISSON_PERCENTILE: 9
MAXIMUM_REPLICATE_CORRELATION: NA
**********************************************************************
|
| |
|
| Submission date |
Oct 29, 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 (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 |
SRX201838 |
| BioSample |
SAMN00791549 |
| Named Annotation |
GSM1027351_UW.Fetal_Thymus.Digital_Genomic_Footprinting.H-24409.DGF.DS20341.wig.gz |
