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Sample GSM493386 Query DataSets for GSM493386
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
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Raw data are available in SRA
Processed data provided as supplementary file

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