|
| Status |
Public on Oct 15, 2011 |
| Title |
Chromatin accessibility assay of H1 BMP4 Derived Mesendoderm Cultured Cells; DS18732 |
| Sample type |
SRA |
| |
|
| Source name |
Human embryonic stem cells received from the James Thomson laboratory. Cells are from the H1 line and are differentiated into mesendoderm by treatment with BMP4.; DS18732
|
| Organism |
Homo sapiens |
| Characteristics |
sample alias: BMP4-03
sample common name: H1 BMP4 Derived Mesendoderm Cultured Cells
molecule: genomic DNA
disease: None
biomaterial_provider: James Thomson Laboratory
biomaterial_type: Cell Line
line: H1
lineage: Embryonic Stem Cell
differentiation_stage: Embryonic stem cell differentiated into mesendoderm by treatment with BMP4
differentiation_method: H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days
passage: Between 20 and 30
medium: E8
Sex: Male
batch: BMP4-3
experiment_type: Chromatin Accessibility
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: NTR_0000856
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS18732
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.10113
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.7805
****************
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: GSM817198_UW.H1_BMP4_Derived_Mesendoderm_Cultured_Cells.ChromatinAccessibility.DS18732.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS18732.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of H1 BMP4 Derived Mesendoderm Cultured Cells Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on the H1 BMP4 Derived Mesendoderm Cultured Cells, Library DS18732 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.12618
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 6
QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 25,261,865
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.2847
FINDPEAKS_PERCENTILE: 19
HOTSPOT_SCORE: 0.3046
HOTSPOT_PERCENTILE: 24
IROC_SCORE: 0.9885
IROC_PERCENTILE: 14
POISSON_SCORE: 0.3994
POISSON_PERCENTILE: 27
MAXIMUM_REPLICATE_CORRELATION: 1.0
**********************************************************************
ANALYSIS FILE NAME: GSM817198_UW.H1_BMP4_Derived_Mesendoderm_Cultured_Cells.ChromatinAccessibility.DS18732.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS18732.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of H1 BMP4 Derived Mesendoderm Cultured Cells Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from the H1 BMP4 Derived Mesendoderm Cultured Cells, Library DS18732 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.12681
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 6
BROWSER_TRACK_NAME: HBDM DNase 32
BROWSER_TRACK_DESCRIPTION: UW H1 BMP4 Derived Mesendoderm Cultured Cells DNase Hypersensitivity Donor Library DS18732 EA Release 6
QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 25,261,865
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.2847
FINDPEAKS_PERCENTILE: 19
HOTSPOT_SCORE: 0.3046
HOTSPOT_PERCENTILE: 24
IROC_SCORE: 0.9885
IROC_PERCENTILE: 14
POISSON_SCORE: 0.3994
POISSON_PERCENTILE: 27
MAXIMUM_REPLICATE_CORRELATION: 1.0
**********************************************************************
|
| |
|
| Submission date |
Oct 14, 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 (1) |
| GSE18927 |
University of Washington Human Reference Epigenome Mapping Project |
|
| Relations |
| SRA |
SRX100994 |
| BioSample |
SAMN00631730 |
| Named Annotation |
GSM817198_UW.H1_BMP4_Derived_Mesendoderm_Cultured_Cells.ChromatinAccessibility.DS18732.wig.gz |
