|
| Status |
Public on Sep 21, 2010 |
| Title |
Chromatin accessibility assay of human CD34 Primary Cells; DS12274 |
| Sample type |
SRA |
| |
|
| Source name |
flow sorted CD34+ cells from cord blood; DS12274
|
| 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 01535
donor_age: NA
donor_health_status: NA
donor_sex: Unknown
donor_ethnicity: NA
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: DS12274
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.1659
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.1660
****************
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: GSM493384_DS12274.UWStam_091005_SOLEXA-1GA-1_0033_FC42Y24_7.bam
ANALYSIS ALIAS: UW.CD34.ChromatinAccessibility.Level1.1
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.1832
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: GSM493384_DS12274.UWStam_091022_SOLEXA-1GA-1_0040_FC42N46_6.bam
ANALYSIS ALIAS: UW.CD34.ChromatinAccessibility.Level1.2
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.1834
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: GSM493384_DS12274.UWStam_091022_SOLEXA-1GA-1_0040_FC42N46_7.bam
ANALYSIS ALIAS: UW.CD34.ChromatinAccessibility.Level1.3
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.1836
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: GSM493384_UW.CD34.rep1.ChromatinAccessibility.CD34+-DS12274.wig
ANALYSIS ALIAS: UW.CD34.ChromatinAccessibility.Level2.combined.1
ANALYSIS TITLE: Raw Signal Density Graphs of CD34 Chromatin Accessibility Replicate 1 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.1855
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: GSM493384_UW.Mobilized_CD34_Primary_Cells.ChromatinAccessibility.RO_01535.DS12274.bed
ANALYSIS ALIAS: DS12274.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 01535, Library DS12274 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.4100
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: 0.7443
FINDPEAKS_PERCENTILE: 92
HOTSPOT_SCORE: 0.6446
HOTSPOT_PERCENTILE: 95
IROC_SCORE: 0.9984
IROC_PERCENTILE: 95
POISSON_SCORE: 0.6126
POISSON_PERCENTILE: 90
**********************************************************************
ANALYSIS FILE NAME: GSM493384_UW.Mobilized_CD34_Primary_Cells.ChromatinAccessibility.RO_01535.DS12274.wig
ANALYSIS ALIAS: DS12274.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 01535, Library DS12274 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.4060
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 35 74
BROWSER_TRACK_DESCRIPTION: UW Mobilized CD34 Primary Cells DNase Hypersensitivity Donor RO 01535 Library DS12274 EA Release 2
QUALITY SCORES:
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED: 40
FINDPEAKS_SCORE: 0.7443
FINDPEAKS_PERCENTILE: 92
HOTSPOT_SCORE: 0.6446
HOTSPOT_PERCENTILE: 95
IROC_SCORE: 0.9984
IROC_PERCENTILE: 95
POISSON_SCORE: 0.6126
POISSON_PERCENTILE: 90
|
| |
|
| Submission date |
Jan 05, 2010 |
| 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 |
GPL9115 |
| Series (1) |
| GSE18927 |
University of Washington Human Reference Epigenome Mapping Project |
|
| Relations |
| SRA |
SRX015228 |
| BioSample |
SAMN00007322 |
| Named Annotation |
GSM493384_UW.Mobilized_CD34_Primary_Cells.ChromatinAccessibility.RO_01535.DS12274.wig.gz |
| Named Annotation |
GSM493384_UW.CD34.rep1.ChromatinAccessibility.CD34+-DS12274.wig.gz |
