|
| Status |
Public on Feb 22, 2012 |
| Title |
Chromatin accessibility assay of H1 Cell Line; DS18873 |
| Sample type |
SRA |
| |
|
| Source name |
Human embryonic stem cells received from the James Thompson laboratory. Cells are from the H1 line.; DS18873
|
| Organism |
Homo sapiens |
| Characteristics |
sample alias: H1-13
sample common name: H1 Cell Line
molecule: genomic DNA
disease: None
biomaterial_provider: James Thompson Laboratory
biomaterial_type: Cell Line
line: H1
lineage: Embryonic Stem Cell
differentiation_stage: None
differentiation_method: None
passage: Between 20 and 40
medium: mTeSER
Sex: Male
batch: H1U
experiment_type: Chromatin Accessibility
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: EFO_0003042
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS18873
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.11262
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.3425
****************
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: GSM878616_UW.H1.ChromatinAccessibility.DS18873.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS18873.hg19.level.1.release.7
ANALYSIS TITLE: Mapping of H1 Cell Line Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on the H1 Cell Line, Library DS18873 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.12777
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 7
QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 48,286,828
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 58
FINDPEAKS_SCORE: 0.2768
FINDPEAKS_PERCENTILE: 12
HOTSPOT_SCORE: 0.277
HOTSPOT_PERCENTILE: 12
IROC_SCORE: 0.9942
IROC_PERCENTILE: 55
POISSON_SCORE: 0.3556
POISSON_PERCENTILE: 12
MAXIMUM_REPLICATE_CORRELATION: 1.0
**********************************************************************
ANALYSIS FILE NAME: GSM878616_UW.H1.ChromatinAccessibility.DS18873.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS18873.hg19.level.2.release.7
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Cell Line Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from the H1 Cell Line, Library DS18873 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.12835
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 7
BROWSER_TRACK_NAME: H1 DNase 73
BROWSER_TRACK_DESCRIPTION: UW H1 Cell Line DNase Hypersensitivity Library DS18873 EA Release 7
QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 48,286,828
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 58
FINDPEAKS_SCORE: 0.2768
FINDPEAKS_PERCENTILE: 12
HOTSPOT_SCORE: 0.277
HOTSPOT_PERCENTILE: 12
IROC_SCORE: 0.9942
IROC_PERCENTILE: 55
POISSON_SCORE: 0.3556
POISSON_PERCENTILE: 12
MAXIMUM_REPLICATE_CORRELATION: 1.0
**********************************************************************
|
| |
|
| Submission date |
Feb 21, 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 |
SRX121242 |
| BioSample |
SAMN00114950 |
| Named Annotation |
GSM878616_UW.H1.ChromatinAccessibility.DS18873.wig.gz |
