|
Status |
Public on Oct 15, 2011 |
Title |
Chromatin accessibility assay of H1 BMP4 Derived Mesendoderm Cultured Cells; DS19310 |
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.; DS19310
|
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
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|
Library strategy |
DNase-Hypersensitivity |
Library source |
genomic |
Library selection |
DNAse |
Instrument model |
Illumina HiSeq 2000 |
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|
Description |
Design description: Chromatin accessibility determination via DNase-seq Library name: DS19310 EDACC Genboree Experiment Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.10108 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: GSM817215_UW.H1_BMP4_Derived_Mesendoderm_Cultured_Cells.ChromatinAccessibility.DS19310.bed ANALYSIS CENTER: EDACC ANALYSIS ALIAS: DS19310.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 DS19310 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.12635 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: 30,822,811 NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63 FINDPEAKS_SCORE: 0.399 FINDPEAKS_PERCENTILE: 59 HOTSPOT_SCORE: 0.4537 HOTSPOT_PERCENTILE: 75 IROC_SCORE: 0.9946 IROC_PERCENTILE: 73 POISSON_SCORE: 0.4899 POISSON_PERCENTILE: 63 MAXIMUM_REPLICATE_CORRELATION: 1.0
**********************************************************************
ANALYSIS FILE NAME: GSM817215_UW.H1_BMP4_Derived_Mesendoderm_Cultured_Cells.ChromatinAccessibility.DS19310.wig ANALYSIS CENTER: EDACC ANALYSIS ALIAS: DS19310.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 DS19310 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.12698 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 10 BROWSER_TRACK_DESCRIPTION: UW H1 BMP4 Derived Mesendoderm Cultured Cells DNase Hypersensitivity Donor Library DS19310 EA Release 6
QUALITY SCORES: NUMBER_OF_MAPPED_READS: 30,822,811 NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63 FINDPEAKS_SCORE: 0.399 FINDPEAKS_PERCENTILE: 59 HOTSPOT_SCORE: 0.4537 HOTSPOT_PERCENTILE: 75 IROC_SCORE: 0.9946 IROC_PERCENTILE: 73 POISSON_SCORE: 0.4899 POISSON_PERCENTILE: 63 MAXIMUM_REPLICATE_CORRELATION: 1.0
**********************************************************************
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|
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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 |
GPL11154 |
Series (1) |
GSE18927 |
University of Washington Human Reference Epigenome Mapping Project |
|
Relations |
SRA |
SRX101011 |
BioSample |
SAMN00631730 |
Named Annotation |
GSM817215_UW.H1_BMP4_Derived_Mesendoderm_Cultured_Cells.ChromatinAccessibility.DS19310.wig.gz |