|
Status |
Public on Sep 21, 2010 |
Title |
Chromatin accessibility assay of human CD34 Primary Cells; DS11202 |
Sample type |
SRA |
|
|
Source name |
flow sorted CD34+ cells from cord blood; DS11202
|
Organism |
Homo sapiens |
Characteristics |
molecule: genomic DNA disease: None biomaterial_provider: FHCRC HEIMFELD biomaterial_type: Primary Cell cell_type: CD34 Primary Cells markers: CD34+ donor_id: RO 01508 donor_age: 36 donor_health_status: NA donor_sex: Male donor_ethnicity: Hispanic passage_if_expanded: NA experiment_type: Chromatin Accessibility extraction_protocol: Qiagen minElut dnase_protocol: Stamlab DNase Protocol
|
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 II |
|
|
Description |
sample_term_id: CL_0000837 assay_term_id: OBI_0001853 nucleic_acid_term_id: SO_0000352 Design description: Chromatin accessibility determination via DNase-seq Library name: DS11202 EDACC Genboree Sample Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.1645 EDACC Genboree Experiment Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.1646 **************** 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: GSM493386_DS11202.UWStam_090710_SOLEXA-1GA-1_0016_FC42ANR_2.bam ANALYSIS ALIAS: UW.CD34.ChromatinAccessibility.Level1.5 ANALYSIS TITLE: Mapping of CD34 Chromatin Accessibility Data ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on CD34 primary cells were mapped to the human genome (NCBI Build 36.1) using Pash. ANALYSIS TYPE: REFERENCE_ALIGNMENT EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.1868 DATA_ANALYSIS_LEVEL: 1 EXPERIMENT_TYPE: Chromatin Accessibility 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
**********************************************************************
ANALYSIS FILE NAME: GSM493386_DS11202.UWStam_090721_SOLEXA-1GA-2_0005_FC42AT8_7.bam ANALYSIS ALIAS: UW.CD34.ChromatinAccessibility.Level1.6 ANALYSIS TITLE: Mapping of CD34 Chromatin Accessibility Data ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on CD34 primary cells were mapped to the human genome (NCBI Build 36.1) using Pash. ANALYSIS TYPE: REFERENCE_ALIGNMENT EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.1869 DATA_ANALYSIS_LEVEL: 1 EXPERIMENT_TYPE: Chromatin Accessibility 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
**********************************************************************
ANALYSIS FILE NAME: GSM493386_DS11202.UWStam_090817_SOLEXA-1GA-2_0014_FC42APL_2.bam ANALYSIS ALIAS: UW.CD34.ChromatinAccessibility.Level1.7 ANALYSIS TITLE: Mapping of CD34 Chromatin Accessibility Data ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on CD34 primary cells were mapped to the human genome (NCBI Build 36.1) using Pash. ANALYSIS TYPE: REFERENCE_ALIGNMENT EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.1870 DATA_ANALYSIS_LEVEL: 1 EXPERIMENT_TYPE: Chromatin Accessibility 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
**********************************************************************
ANALYSIS FILE NAME: GSM493386_DS11202.UWStam_090817_SOLEXA-1GA-2_0014_FC42APL_3.bam ANALYSIS ALIAS: UW.CD34.ChromatinAccessibility.Level1.8 ANALYSIS TITLE: Mapping of CD34 Chromatin Accessibility Data ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on CD34 primary cells were mapped to the human genome (NCBI Build 36.1) using Pash. ANALYSIS TYPE: REFERENCE_ALIGNMENT EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.1871 DATA_ANALYSIS_LEVEL: 1 EXPERIMENT_TYPE: Chromatin Accessibility 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
**********************************************************************
ANALYSIS FILE NAME: GSM493386_DS11202.UWStam_090817_SOLEXA-1GA-2_0014_FC42APL_4.bam ANALYSIS ALIAS: UW.CD34.ChromatinAccessibility.Level1.9 ANALYSIS TITLE: Mapping of CD34 Chromatin Accessibility Data ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on CD34 primary cells were mapped to the human genome (NCBI Build 36.1) using Pash. ANALYSIS TYPE: REFERENCE_ALIGNMENT EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.1872 DATA_ANALYSIS_LEVEL: 1 EXPERIMENT_TYPE: Chromatin Accessibility 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
**********************************************************************
ANALYSIS FILE NAME: GSM493386_DS11202.UWStam_090827_SOLEXA-1GA-1_0019_FC42L5P_1.bam ANALYSIS ALIAS: UW.CD34.ChromatinAccessibility.Level1.10 ANALYSIS TITLE: Mapping of CD34 Chromatin Accessibility Data ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on CD34 primary cells were mapped to the human genome (NCBI Build 36.1) using Pash. ANALYSIS TYPE: REFERENCE_ALIGNMENT EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.1873 DATA_ANALYSIS_LEVEL: 1 EXPERIMENT_TYPE: Chromatin Accessibility 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
**********************************************************************
ANALYSIS FILE NAME: GSM493386_DS11202.UWStam_090827_SOLEXA-1GA-1_0019_FC42L5P_2.bam ANALYSIS ALIAS: UW.CD34.ChromatinAccessibility.Level1.14 ANALYSIS TITLE: Mapping of CD34 Chromatin Accessibility Data ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on CD34 primary cells were mapped to the human genome (NCBI Build 36.1) using Pash. ANALYSIS TYPE: REFERENCE_ALIGNMENT EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.1874 DATA_ANALYSIS_LEVEL: 1 EXPERIMENT_TYPE: Chromatin Accessibility 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
**********************************************************************
ANALYSIS FILE NAME: GSM493386_UW.CD34.rep2.ChromatinAccessibility.CD34+-DS11202.wig ANALYSIS ALIAS: UW.CD34.ChromatinAccessibility.Level2.combined.2 ANALYSIS TITLE: Raw Signal Density Graphs of CD34 Chromatin Accessibility Replicate 2 Data ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from CD34 primary cells 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.1875 DATA_ANALYSIS_LEVEL: 2 EXPERIMENT_TYPE: Chromatin Accessibility SOFTWARE: In house programs and scripts SOFTWARE_VERSION: NA READ_EXTENSION: 200bp GENOMIC_WINDOW: 20bp TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
**********************************************************************
ANALYSIS FILE NAME: GSM493386_UW.Mobilized_CD34_Primary_Cells.ChromatinAccessibility.RO_01508.DS11202.bed ANALYSIS ALIAS: DS11202.hg19.level.1 ANALYSIS TITLE: Mapping of Mobilized CD34 Primary Cells Chromatin Accessibility Data ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Mobilized CD34 Primary Cells, Donor RO 01508, Library DS11202 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.4102 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 2
QUALITY SCORES: NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED: 40 FINDPEAKS_SCORE: 0.4658 FINDPEAKS_PERCENTILE: 17 HOTSPOT_SCORE: 0.3758 HOTSPOT_PERCENTILE: 25 IROC_SCORE: 0.9976 IROC_PERCENTILE: 62 POISSON_SCORE: 0.4133 POISSON_PERCENTILE: 17
**********************************************************************
ANALYSIS FILE NAME: GSM493386_UW.Mobilized_CD34_Primary_Cells.ChromatinAccessibility.RO_01508.DS11202.wig ANALYSIS ALIAS: DS11202.hg19.level.2 ANALYSIS TITLE: Raw Signal Density Graphs of Mobilized CD34 Primary Cells Chromatin Accessibility Data ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from Mobilized CD34 Primary Cells, Donor RO 01508, Library DS11202 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.4062 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 2 BROWSER_TRACK_NAME: MCD34 DNase 08 02 BROWSER_TRACK_DESCRIPTION: UW Mobilized CD34 Primary Cells DNase Hypersensitivity Donor RO 01508 Library DS11202 EA Release 2
QUALITY SCORES: NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED: 40 FINDPEAKS_SCORE: 0.4658 FINDPEAKS_PERCENTILE: 17 HOTSPOT_SCORE: 0.3758 HOTSPOT_PERCENTILE: 25 IROC_SCORE: 0.9976 IROC_PERCENTILE: 62 POISSON_SCORE: 0.4133 POISSON_PERCENTILE: 17
|
|
|
Submission date |
Jan 05, 2010 |
Last update date |
May 15, 2019 |
Contact name |
Northwest REMC |
E-mail(s) |
[email protected]
|
Organization name |
University of Washington
|
Street address |
-
|
City |
Seattle |
State/province |
WA |
ZIP/Postal code |
98195 |
Country |
USA |
|
|
Platform ID |
GPL9115 |
Series (1) |
GSE18927 |
University of Washington Human Reference Epigenome Mapping Project |
|
Relations |
SRA |
SRX015226 |
BioSample |
SAMN00007320 |
Named Annotation |
GSM493386_UW.Mobilized_CD34_Primary_Cells.ChromatinAccessibility.RO_01508.DS11202.wig.gz |
Named Annotation |
GSM493386_UW.CD34.rep2.ChromatinAccessibility.CD34+-DS11202.wig.gz |
Supplementary file |
Size |
Download |
File type/resource |
GSM493386_DS11202.UWStam_090710_SOLEXA-1GA-1_0016_FC42ANR_2.bam |
590.4 Mb |
(ftp)(http) |
BAM |
GSM493386_DS11202.UWStam_090721_SOLEXA-1GA-2_0005_FC42AT8_7.bam |
585.5 Mb |
(ftp)(http) |
BAM |
GSM493386_DS11202.UWStam_090817_SOLEXA-1GA-2_0014_FC42APL_2.bam |
535.2 Mb |
(ftp)(http) |
BAM |
GSM493386_DS11202.UWStam_090817_SOLEXA-1GA-2_0014_FC42APL_3.bam |
545.2 Mb |
(ftp)(http) |
BAM |
GSM493386_DS11202.UWStam_090817_SOLEXA-1GA-2_0014_FC42APL_4.bam |
561.8 Mb |
(ftp)(http) |
BAM |
GSM493386_DS11202.UWStam_090827_SOLEXA-1GA-1_0019_FC42L5P_1.bam |
820.1 Mb |
(ftp)(http) |
BAM |
GSM493386_DS11202.UWStam_090827_SOLEXA-1GA-1_0019_FC42L5P_2.bam |
836.0 Mb |
(ftp)(http) |
BAM |
GSM493386_UW.CD34.rep2.ChromatinAccessibility.CD34+-DS11202.wig.gz |
40.7 Mb |
(ftp)(http) |
WIG |
GSM493386_UW.Mobilized_CD34_Primary_Cells.ChromatinAccessibility.RO_01508.DS11202.bed.gz |
437.1 Mb |
(ftp)(http) |
BED |
GSM493386_UW.Mobilized_CD34_Primary_Cells.ChromatinAccessibility.RO_01508.DS11202.wig.gz |
205.3 Mb |
(ftp)(http) |
WIG |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |