|
| Status |
Public on Apr 05, 2012 |
| Title |
Digital Genomic Footprinting assay of Induced pluripotent stem cell; DGF.DS15153 |
| Sample type |
SRA |
| |
|
| Source name |
Human induced pluripotent stem cell line derived from foreskin fibroblasts, isolated as described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009).; DGF.DS15153
|
| Organism |
Homo sapiens |
| Characteristics |
sample alias: iPS-19.11-01
sample common name: iPS DF 19.11 Cell Line
molecule: genomic DNA
disease: None
biomaterial_provider: James Thompson Laboratory
biomaterial_type: Cell Line
line: iPS 19.11
lineage: Induced pluripotent stem cell line derived from foreskin fibroblasts
differentiation_stage: Induced pluripotent stem cell
differentiation_method: As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009).
passage: Between 30 and 40
medium: mTeSR
Sex: Male
batch: iPSC 19.11
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 HiSeq 2000 |
| |
|
| Description |
sample_term_id: NTR_0001173
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Digital Genomic Footprinting determination via DNase-seq
Library name: DGF.DS15153
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.11957
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.6813
****************
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: GSM909311_UW.iPS_DF_19.11.Digital_Genomic_Footprinting.DGF.DS15153.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DGF.DS15153.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of iPS DF 19.11 Cell Line Digital Genomic Footprinting Data
ANALYSIS DESCRIPTION: Illumina reads produced by Digital Genomic Footprinting on the iPS DF 19.11 Cell Line, Library DGF.DS15153 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.13113
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 8
QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 217,450,671
NUMBER_OF_DIGITAL_GENOMIC_FOOTPRINTING_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 5
FINDPEAKS_SCORE: 0.309
FINDPEAKS_PERCENTILE: 40
HOTSPOT_SCORE: 0.3498
HOTSPOT_PERCENTILE: 40
IROC_SCORE: 0.9916
IROC_PERCENTILE: 20
POISSON_SCORE: 0.4068
POISSON_PERCENTILE: 40
MAXIMUM_REPLICATE_CORRELATION: NA
**********************************************************************
ANALYSIS FILE NAME: GSM909311_UW.iPS_DF_19.11.Digital_Genomic_Footprinting.DGF.DS15153.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DGF.DS15153.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of iPS DF 19.11 Cell Line Digital Genomic Footprinting Data
ANALYSIS DESCRIPTION: Illumina Digital Genomic Footprinting read mappings from the iPS DF 19.11 Cell Line, Library DGF.DS15153 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.13118
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 8
BROWSER_TRACK_NAME: iD19.11 DGF 53
BROWSER_TRACK_DESCRIPTION: UW iPS DF 19.11 Cell Line Digital Genomic Footprinting Library DGF.DS15153 EA Release 8
QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 217,450,671
NUMBER_OF_DIGITAL_GENOMIC_FOOTPRINTING_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 5
FINDPEAKS_SCORE: 0.309
FINDPEAKS_PERCENTILE: 40
HOTSPOT_SCORE: 0.3498
HOTSPOT_PERCENTILE: 40
IROC_SCORE: 0.9916
IROC_PERCENTILE: 20
POISSON_SCORE: 0.4068
POISSON_PERCENTILE: 40
MAXIMUM_REPLICATE_CORRELATION: NA
**********************************************************************
|
| |
|
| Submission date |
Apr 04, 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 |
SRX135563 |
| BioSample |
SAMN00255375 |
| Named Annotation |
GSM909311_UW.iPS_DF_19.11.Digital_Genomic_Footprinting.DGF.DS15153.wig.gz |
