title: Chromatin accessibility assay of Fetal brain tissue; DS14464

description:
sample_term_id: UBERON_0000955
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS14464
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.3144
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.3143
****************
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: GSM595920_fBrain-DS14464.hg19.bam
ANALYSIS ALIAS: DS14464-align
ANALYSIS TITLE: Alignments DS14464
ANALYSIS DESCRIPTION: Bowtie (v0.12.5) alignments of Chromatin Accessibility Illumina sequencing lane data to the human genome The Genome Reference Consortium GRCh37 (hg19)
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page:
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
SOFTWARE: Bowtie
SOFTWARE_VERSION: 0.12.5
MAXIMUM_ALIGNMENT_LENGTH: 36
MISMATCHES_ALLOWED: 2
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: not submitted
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: allowed
ALIGNMENT_POSTPROCESSING: none

**********************************************************************

ANALYSIS FILE NAME: GSM595920_fBrain-DS14464.75.20.filtered-density.36.hg19.wig
ANALYSIS ALIAS: DS14464-signal
ANALYSIS TITLE: Signal DS14464
ANALYSIS DESCRIPTION: Chromatin Accessibility data with a sliding window (+/-75bp) summation at 20 bp steps across the genome
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page:
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
SOFTWARE: signalmap
SOFTWARE_VERSION: 1.0
READ_EXTENSION: 150
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: NA

**********************************************************************

ANALYSIS FILE NAME: GSM595920_UW.Fetal_Brain.ChromatinAccessibility.H-22911.DS14464.bed
ANALYSIS ALIAS: DS14464.hg19.level.1
ANALYSIS TITLE: Mapping of Fetal Brain Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Brain, Donor H-22911, Library DS14464 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.4128
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: 0.6697
FINDPEAKS_PERCENTILE: 80
HOTSPOT_SCORE: 0.5464
HOTSPOT_PERCENTILE: 80
IROC_SCORE: 0.9969
IROC_PERCENTILE: 47
POISSON_SCORE: 0.5873
POISSON_PERCENTILE: 82

**********************************************************************

ANALYSIS FILE NAME: GSM595920_UW.Fetal_Brain.ChromatinAccessibility.H-22911.DS14464.wig
ANALYSIS ALIAS: DS14464.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Brain Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from Fetal Brain, Donor H-22911, Library DS14464 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.4088
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: FB DNase 11 64
BROWSER_TRACK_DESCRIPTION: UW Fetal Brain DNase Hypersensitivity Donor H-22911 Library DS14464 EA Release 2

QUALITY SCORES:
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED: 40
FINDPEAKS_SCORE: 0.6697
FINDPEAKS_PERCENTILE: 80
HOTSPOT_SCORE: 0.5464
HOTSPOT_PERCENTILE: 80
IROC_SCORE: 0.9969
IROC_PERCENTILE: 47
POISSON_SCORE: 0.5873
POISSON_PERCENTILE: 82

source_name: Fetal Brain primary tissue, day 117; DS14464

value: Primary Tissue

value: day 117


title: Chromatin accessibility assay of CD34+ Primary cells; DS14206

status: Public on Sep 21 2010

type: SRA

city: Seattle

first: Northwest

last: REMC

state: WA

country: USA

institute: University of Washington

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: DS14206
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.3106
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.2412
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

library_source: genomic

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM595919_CD34-DS14206.hg19.bam
ANALYSIS ALIAS: DS14206-align
ANALYSIS TITLE: Alignments DS14206
ANALYSIS DESCRIPTION: Bowtie (v0.12.5) alignments of Chromatin Accessibility Illumina sequencing lane data to the human genome The Genome Reference Consortium GRCh37 (hg19)
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page:
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
SOFTWARE: Bowtie
SOFTWARE_VERSION: 0.12.5
MAXIMUM_ALIGNMENT_LENGTH: 36
MISMATCHES_ALLOWED: 2
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: not submitted
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: allowed
ALIGNMENT_POSTPROCESSING: none

**********************************************************************

ANALYSIS FILE NAME: GSM595919_CD34-DS14206.75.20.filtered-density.36.hg19.wig
ANALYSIS ALIAS: DS14206-signal
ANALYSIS TITLE: Signal DS14206
ANALYSIS DESCRIPTION: Chromatin Accessibility data with a sliding window (+/-75bp) summation at 20 bp steps across the genome
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page:
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
SOFTWARE: signalmap
SOFTWARE_VERSION: 1.0
READ_EXTENSION: 150
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: NA

**********************************************************************

ANALYSIS FILE NAME: GSM595919_UW.Mobilized_CD34_Primary_Cells.ChromatinAccessibility.RO_01492.DS14206.bed
ANALYSIS ALIAS: DS14206.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 01492, Library DS14206 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.4130
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: 0.5009
FINDPEAKS_PERCENTILE: 30
HOTSPOT_SCORE: 0.4157
HOTSPOT_PERCENTILE: 47
IROC_SCORE: 0.9976
IROC_PERCENTILE: 65
POISSON_SCORE: 0.4719
POISSON_PERCENTILE: 32

**********************************************************************

ANALYSIS FILE NAME: GSM595919_UW.Mobilized_CD34_Primary_Cells.ChromatinAccessibility.RO_01492.DS14206.wig
ANALYSIS ALIAS: DS14206.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 01492, Library DS14206 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.4090
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 92 06
BROWSER_TRACK_DESCRIPTION: UW Mobilized CD34 Primary Cells DNase Hypersensitivity Donor RO 01492 Library DS14206 EA Release 2

QUALITY SCORES:
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED: 40
FINDPEAKS_SCORE: 0.5009
FINDPEAKS_PERCENTILE: 30
HOTSPOT_SCORE: 0.4157
HOTSPOT_PERCENTILE: 47
IROC_SCORE: 0.9976
IROC_PERCENTILE: 65
POISSON_SCORE: 0.4719
POISSON_PERCENTILE: 32

molecule: genomic DNA

organism: Homo sapiens

source_name: flow sorted CD34+ cells from cord blood; DS14206

extract_protocol: Library construction protocol: Single read - Illumina

tag: molecule

value: genomic DNA

tag: disease

value: FHCRC HEIMFELD

value: Primary Cell

value: CD34 Primary Cells

tag: markers

value: 39 years

value: Male

value: Caucasian

value: Chromatin Accessibility

value: Qiagen minElut

value: Stamlab DNase Protocol


title: Chromatin accessibility assay of Fetal lung tissue; DS14666

description:
sample_term_id: UBERON_0002048
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS14666
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.3128
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.3127
****************
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: GSM595921_fLung-DS14666.hg19.bam
ANALYSIS ALIAS: DS14666-align
ANALYSIS TITLE: Alignments DS14666
ANALYSIS DESCRIPTION: Bowtie (v0.12.5) alignments of Chromatin Accessibility Illumina sequencing lane data to the human genome The Genome Reference Consortium GRCh37 (hg19)
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page:
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
SOFTWARE: Bowtie
SOFTWARE_VERSION: 0.12.5
MAXIMUM_ALIGNMENT_LENGTH: 36
MISMATCHES_ALLOWED: 2
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: not submitted
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: allowed
ALIGNMENT_POSTPROCESSING: none

**********************************************************************

ANALYSIS FILE NAME: GSM595921_fLung-DS14666.75.20.filtered-density.36.hg19.wig
ANALYSIS ALIAS: DS14666-signal
ANALYSIS TITLE: Signal DS14666
ANALYSIS DESCRIPTION: Chromatin Accessibility data with a sliding window (+/-75bp) summation at 20 bp steps across the genome
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page:
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
SOFTWARE: signalmap
SOFTWARE_VERSION: 1.0
READ_EXTENSION: 150
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: NA

**********************************************************************

ANALYSIS FILE NAME: GSM595921_UW.Fetal_Lung.ChromatinAccessibility.H-23247.DS14666.bed
ANALYSIS ALIAS: DS14666.hg19.level.1
ANALYSIS TITLE: Mapping of Fetal Lung Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Lung, Donor H-23247, Library DS14666 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.4119
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: 0.5124
FINDPEAKS_PERCENTILE: 32
HOTSPOT_SCORE: 0.389
HOTSPOT_PERCENTILE: 30
IROC_SCORE: 0.994
IROC_PERCENTILE: 12
POISSON_SCORE: 0.5024
POISSON_PERCENTILE: 50

**********************************************************************

ANALYSIS FILE NAME: GSM595921_UW.Fetal_Lung.ChromatinAccessibility.H-23247.DS14666.wig
ANALYSIS ALIAS: DS14666.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Lung Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from Fetal Lung, Donor H-23247, Library DS14666 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.4079
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: FL DNase 47 66
BROWSER_TRACK_DESCRIPTION: UW Fetal Lung DNase Hypersensitivity Donor H-23247 Library DS14666 EA Release 2

QUALITY SCORES:
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED: 40
FINDPEAKS_SCORE: 0.5124
FINDPEAKS_PERCENTILE: 32
HOTSPOT_SCORE: 0.389
HOTSPOT_PERCENTILE: 30
IROC_SCORE: 0.994
IROC_PERCENTILE: 12
POISSON_SCORE: 0.5024
POISSON_PERCENTILE: 50

source_name: Fetal Lung primary tissue, day 67; DS14666

value: University of Washington, Congenital Defects Lab. Ian Glass

value: fetal lung

value: UW

value: fetal

value: day 67

value: Unknown


title: Chromatin accessibility assay of CD34+ Primary cells; DS14197

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: DS14197
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.3108
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.1659
****************
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: GSM595918_CD34-DS14197.hg19.bam
ANALYSIS ALIAS: DS14197-align
ANALYSIS TITLE: Alignments DS14197
ANALYSIS DESCRIPTION: Bowtie (v0.12.5) alignments of Chromatin Accessibility Illumina sequencing lane data to the human genome The Genome Reference Consortium GRCh37 (hg19)
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page:
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
SOFTWARE: Bowtie
SOFTWARE_VERSION: 0.12.5
MAXIMUM_ALIGNMENT_LENGTH: 36
MISMATCHES_ALLOWED: 2
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: not submitted
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: allowed
ALIGNMENT_POSTPROCESSING: none

**********************************************************************

ANALYSIS FILE NAME: GSM595918_CD34-DS14197.75.20.filtered-density.36.hg19.wig
ANALYSIS ALIAS: DS14197-signal
ANALYSIS TITLE: Signal DS14197
ANALYSIS DESCRIPTION: Chromatin Accessibility data with a sliding window (+/-75bp) summation at 20 bp steps across the genome
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page:
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
SOFTWARE: signalmap
SOFTWARE_VERSION: 1.0
READ_EXTENSION: 150
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: NA

**********************************************************************

ANALYSIS FILE NAME: GSM595918_UW.Mobilized_CD34_Primary_Cells.ChromatinAccessibility.RO_01535.DS14197.bed
ANALYSIS ALIAS: DS14197.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 DS14197 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.4109
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: 0.4722
FINDPEAKS_PERCENTILE: 20
HOTSPOT_SCORE: 0.3815
HOTSPOT_PERCENTILE: 27
IROC_SCORE: 0.9983
IROC_PERCENTILE: 90
POISSON_SCORE: 0.4302
POISSON_PERCENTILE: 20

**********************************************************************

ANALYSIS FILE NAME: GSM595918_UW.Mobilized_CD34_Primary_Cells.ChromatinAccessibility.RO_01535.DS14197.wig
ANALYSIS ALIAS: DS14197.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 DS14197 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.4069
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 97
BROWSER_TRACK_DESCRIPTION: UW Mobilized CD34 Primary Cells DNase Hypersensitivity Donor RO 01535 Library DS14197 EA Release 2

QUALITY SCORES:
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED: 40
FINDPEAKS_SCORE: 0.4722
FINDPEAKS_PERCENTILE: 20
HOTSPOT_SCORE: 0.3815
HOTSPOT_PERCENTILE: 27
IROC_SCORE: 0.9983
IROC_PERCENTILE: 90
POISSON_SCORE: 0.4302
POISSON_PERCENTILE: 20

source_name: flow sorted CD34+ cells from cord blood; DS14197


title: Chromatin accessibility assay of Fetal brain tissue; DS14718

description:
sample_term_id: UBERON_0000955
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS14718
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.3149
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.3146
****************
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: GSM595923_fBrain-DS14718.hg19.bam
ANALYSIS ALIAS: DS14718-align
ANALYSIS TITLE: Alignments DS14718
ANALYSIS DESCRIPTION: Bowtie (v0.12.5) alignments of Chromatin Accessibility Illumina sequencing lane data to the human genome The Genome Reference Consortium GRCh37 (hg19)
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page:
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
SOFTWARE: Bowtie
SOFTWARE_VERSION: 0.12.5
MAXIMUM_ALIGNMENT_LENGTH: 36
MISMATCHES_ALLOWED: 2
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: not submitted
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: allowed
ALIGNMENT_POSTPROCESSING: none

**********************************************************************

ANALYSIS FILE NAME: GSM595923_fBrain-DS14718.75.20.filtered-density.36.hg19.wig
ANALYSIS ALIAS: DS14718-signal
ANALYSIS TITLE: Signal DS14718
ANALYSIS DESCRIPTION: Chromatin Accessibility data with a sliding window (+/-75bp) summation at 20 bp steps across the genome
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page:
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
SOFTWARE: signalmap
SOFTWARE_VERSION: 1.0
READ_EXTENSION: 150
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: NA

**********************************************************************

ANALYSIS FILE NAME: GSM595923_UW.Fetal_Brain.ChromatinAccessibility.H-23266.DS14718.bed
ANALYSIS ALIAS: DS14718.hg19.level.1
ANALYSIS TITLE: Mapping of Fetal Brain Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Brain, Donor H-23266, Library DS14718 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.4106
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: 0.5215
FINDPEAKS_PERCENTILE: 35
HOTSPOT_SCORE: 0.4083
HOTSPOT_PERCENTILE: 45
IROC_SCORE: 0.9954
IROC_PERCENTILE: 25
POISSON_SCORE: 0.5003
POISSON_PERCENTILE: 47

**********************************************************************

ANALYSIS FILE NAME: GSM595923_UW.Fetal_Brain.ChromatinAccessibility.H-23266.DS14718.wig
ANALYSIS ALIAS: DS14718.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Brain Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from Fetal Brain, Donor H-23266, Library DS14718 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.4066
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: FB DNase 66 18
BROWSER_TRACK_DESCRIPTION: UW Fetal Brain DNase Hypersensitivity Donor H-23266 Library DS14718 EA Release 2

QUALITY SCORES:
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED: 40
FINDPEAKS_SCORE: 0.5215
FINDPEAKS_PERCENTILE: 35
HOTSPOT_SCORE: 0.4083
HOTSPOT_PERCENTILE: 45
IROC_SCORE: 0.9954
IROC_PERCENTILE: 25
POISSON_SCORE: 0.5003
POISSON_PERCENTILE: 47

source_name: Fetal Brain primary tissue, day 85; DS14718

value: Primary Tissue

value: fetal brain

value: day 85

value: Female


title: Brain - RNA-Seq

status: Public on Sep 23 2010

city: South San Francisco

first: Thomas

middle: D.

last: Wu

state: CA

address: 1 DNA Way

institute: Genentech, Inc.

description: Brain reference sample

library_source: transcriptomic

data_processing: Reads were analyzed in two ways to identify transcription-induced chimeras: (1) targeted alignment to a set of artificial exon-exon junctions between all exons of adjacent genes within 200,000 bp, and (2) spliced alignment to reference human genome build 36.1.  All alignments were performed with the program GSNAP. The most important alignments are not to a reference genome, but to a specialized database of artificial exon-exon junctions. Interested parties should refer to the 93-page Supplemental information document in related publication that contains the relevant alignment results (alignment data not submitted to GEO).

molecule: polyA RNA

source_name: Brain

extract_protocol: Qiagen AllPrep extraction kit was used according to the manufacturer's instructions.  RNA was random primed with polyA.

tag: sampleID

value: Ambion 6050

tag: organ

value: Brain

tag: subtype

value: Brain reference


title: Chromatin accessibility assay of Fetal lung tissue; DS13507

description:
sample_term_id: UBERON_0002048
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS13507
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.3119
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.3118
****************
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: GSM595915_fLung-DS13507.hg19.bam
ANALYSIS ALIAS: DS13507-align
ANALYSIS TITLE: Alignments DS13507
ANALYSIS DESCRIPTION: Bowtie (v0.12.5) alignments of Chromatin Accessibility Illumina sequencing lane data to the human genome The Genome Reference Consortium GRCh37 (hg19)
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page:
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
SOFTWARE: Bowtie
SOFTWARE_VERSION: 0.12.5
MAXIMUM_ALIGNMENT_LENGTH: 36
MISMATCHES_ALLOWED: 2
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: not submitted
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: allowed
ALIGNMENT_POSTPROCESSING: none

**********************************************************************

ANALYSIS FILE NAME: GSM595915_fLung-DS13507.75.20.filtered-density.36.hg19.wig
ANALYSIS ALIAS: DS13507-signal
ANALYSIS TITLE: Signal DS13507
ANALYSIS DESCRIPTION: Chromatin Accessibility data with a sliding window (+/-75bp) summation at 20 bp steps across the genome
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page:
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
SOFTWARE: signalmap
SOFTWARE_VERSION: 1.0
READ_EXTENSION: 150
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: NA

**********************************************************************

ANALYSIS FILE NAME: GSM595915_UW.Fetal_Lung.ChromatinAccessibility.H-22934B.DS13507.bed
ANALYSIS ALIAS: DS13507.hg19.level.1
ANALYSIS TITLE: Mapping of Fetal Lung Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Lung, Donor H-22934B, Library DS13507 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.4125
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: 0.6926
FINDPEAKS_PERCENTILE: 87
HOTSPOT_SCORE: 0.4924
HOTSPOT_PERCENTILE: 60
IROC_SCORE: 0.9943
IROC_PERCENTILE: 17
POISSON_SCORE: 0.5737
POISSON_PERCENTILE: 77

**********************************************************************

ANALYSIS FILE NAME: GSM595915_UW.Fetal_Lung.ChromatinAccessibility.H-22934B.DS13507.wig
ANALYSIS ALIAS: DS13507.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Lung Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from Fetal Lung, Donor H-22934B, Library DS13507 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.4085
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: FL DNase 4B 07
BROWSER_TRACK_DESCRIPTION: UW Fetal Lung DNase Hypersensitivity Donor H-22934B Library DS13507 EA Release 2

QUALITY SCORES:
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED: 40
FINDPEAKS_SCORE: 0.6926
FINDPEAKS_PERCENTILE: 87
HOTSPOT_SCORE: 0.4924
HOTSPOT_PERCENTILE: 60
IROC_SCORE: 0.9943
IROC_PERCENTILE: 17
POISSON_SCORE: 0.5737
POISSON_PERCENTILE: 77

source_name: Fetal Lung primary tissue, day 108; DS13507

value: genomic DNA

value: day 108


title: Chromatin accessibility assay of CD34+ Primary cells; DS14129

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: DS14129
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.3101
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.3100
****************
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: GSM595917_CD34-DS14129.hg19.bam
ANALYSIS ALIAS: DS14129-align
ANALYSIS TITLE: Alignments DS14129
ANALYSIS DESCRIPTION: Bowtie (v0.12.5) alignments of Chromatin Accessibility Illumina sequencing lane data to the human genome The Genome Reference Consortium GRCh37 (hg19)
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page:
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
SOFTWARE: Bowtie
SOFTWARE_VERSION: 0.12.5
MAXIMUM_ALIGNMENT_LENGTH: 36
MISMATCHES_ALLOWED: 2
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: not submitted
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: allowed
ALIGNMENT_POSTPROCESSING: none

**********************************************************************

ANALYSIS FILE NAME: GSM595917_CD34-DS14129.75.20.filtered-density.36.hg19.wig
ANALYSIS ALIAS: DS14129-signal
ANALYSIS TITLE: Signal DS14129
ANALYSIS DESCRIPTION: Chromatin Accessibility data with a sliding window (+/-75bp) summation at 20 bp steps across the genome
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page:
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
SOFTWARE: signalmap
SOFTWARE_VERSION: 1.0
READ_EXTENSION: 150
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: NA

**********************************************************************

ANALYSIS FILE NAME: GSM595917_UW.Mobilized_CD34_Primary_Cells.ChromatinAccessibility.RO_01517.DS14129.bed
ANALYSIS ALIAS: DS14129.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 01517, Library DS14129 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.4136
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: 0.5243
FINDPEAKS_PERCENTILE: 37
HOTSPOT_SCORE: 0.4378
HOTSPOT_PERCENTILE: 55
IROC_SCORE: 0.9984
IROC_PERCENTILE: 92
POISSON_SCORE: 0.457
POISSON_PERCENTILE: 27

**********************************************************************

ANALYSIS FILE NAME: GSM595917_UW.Mobilized_CD34_Primary_Cells.ChromatinAccessibility.RO_01517.DS14129.wig
ANALYSIS ALIAS: DS14129.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 01517, Library DS14129 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.4096
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 17 29
BROWSER_TRACK_DESCRIPTION: UW Mobilized CD34 Primary Cells DNase Hypersensitivity Donor RO 01517 Library DS14129 EA Release 2

QUALITY SCORES:
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED: 40
FINDPEAKS_SCORE: 0.5243
FINDPEAKS_PERCENTILE: 37
HOTSPOT_SCORE: 0.4378
HOTSPOT_PERCENTILE: 55
IROC_SCORE: 0.9984
IROC_PERCENTILE: 92
POISSON_SCORE: 0.457
POISSON_PERCENTILE: 27

source_name: flow sorted CD34+ cells, mobilized; DS14129

value: FHCRC HEIMFELD

value: Primary Cell

value: CD34 Primary Cells

value: year 43

value: Male

value: Caucasian

value: Chromatin Accessibility

value: Qiagen minElut


title: Chromatin accessibility assay of Fetal lung tissue; DS13985

description:
sample_term_id: UBERON_0002048
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS13985
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.3124
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.3123
****************
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: GSM595916_fLung-DS13985.hg19.bam
ANALYSIS ALIAS: DS13985-align
ANALYSIS TITLE: Alignments DS13985
ANALYSIS DESCRIPTION: Bowtie (v0.12.5) alignments of Chromatin Accessibility Illumina sequencing lane data to the human genome The Genome Reference Consortium GRCh37 (hg19)
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page:
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
SOFTWARE: Bowtie
SOFTWARE_VERSION: 0.12.5
MAXIMUM_ALIGNMENT_LENGTH: 36
MISMATCHES_ALLOWED: 2
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: not submitted
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: allowed
ALIGNMENT_POSTPROCESSING: none

**********************************************************************

ANALYSIS FILE NAME: GSM595916_fLung-DS13985.75.20.filtered-density.36.hg19.wig
ANALYSIS ALIAS: DS13985-signal
ANALYSIS TITLE: Signal DS13985
ANALYSIS DESCRIPTION: Chromatin Accessibility data with a sliding window (+/-75bp) summation at 20 bp steps across the genome
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page:
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
SOFTWARE: signalmap
SOFTWARE_VERSION: 1.0
READ_EXTENSION: 150
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: NA

**********************************************************************

ANALYSIS FILE NAME: GSM595916_UW.Fetal_Lung.ChromatinAccessibility.H-23090.DS13985.bed
ANALYSIS ALIAS: DS13985.hg19.level.1
ANALYSIS TITLE: Mapping of Fetal Lung Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Lung, Donor H-23090, Library DS13985 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.4114
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: 0.58
FINDPEAKS_PERCENTILE: 52
HOTSPOT_SCORE: 0.3625
HOTSPOT_PERCENTILE: 20
IROC_SCORE: 0.9923
IROC_PERCENTILE: 5
POISSON_SCORE: 0.5099
POISSON_PERCENTILE: 52

**********************************************************************

ANALYSIS FILE NAME: GSM595916_UW.Fetal_Lung.ChromatinAccessibility.H-23090.DS13985.wig
ANALYSIS ALIAS: DS13985.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Lung Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from Fetal Lung, Donor H-23090, Library DS13985 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.4074
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: FL DNase 90 85
BROWSER_TRACK_DESCRIPTION: UW Fetal Lung DNase Hypersensitivity Donor H-23090 Library DS13985 EA Release 2

QUALITY SCORES:
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED: 40
FINDPEAKS_SCORE: 0.58
FINDPEAKS_PERCENTILE: 52
HOTSPOT_SCORE: 0.3625
HOTSPOT_PERCENTILE: 20
IROC_SCORE: 0.9923
IROC_PERCENTILE: 5
POISSON_SCORE: 0.5099
POISSON_PERCENTILE: 52

source_name: Fetal Lung primary tissue, day 103; DS13985

value: University of Washington, Congenital Defects Lab. Ian Glass

value: Primary Tissue

value: fetal lung

value: UW

value: fetal

value: day 103

value: Stamlab DNase Protocol


title: Chromatin accessibility assay of Fetal brain tissue; DS14717

description:
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS14717
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.3147
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.3146
****************
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: GSM595922_fBrain-DS14717.hg19.bam
ANALYSIS ALIAS: DS14717-align
ANALYSIS TITLE: Alignments DS14717
ANALYSIS DESCRIPTION: Bowtie (v0.12.5) alignments of Chromatin Accessibility Illumina sequencing lane data to the human genome The Genome Reference Consortium GRCh37 (hg19)
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page:
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
SOFTWARE: Bowtie
SOFTWARE_VERSION: 0.12.5
MAXIMUM_ALIGNMENT_LENGTH: 36
MISMATCHES_ALLOWED: 2
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: not submitted
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: allowed
ALIGNMENT_POSTPROCESSING: none

**********************************************************************

ANALYSIS FILE NAME: GSM595922_fBrain-DS14717.75.20.filtered-density.36.hg19.wig
ANALYSIS ALIAS: DS14717-signal
ANALYSIS TITLE: Signal DS14717
ANALYSIS DESCRIPTION: Chromatin Accessibility data with a sliding window (+/-75bp) summation at 20 bp steps across the genome
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page:
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
SOFTWARE: signalmap
SOFTWARE_VERSION: 1.0
READ_EXTENSION: 150
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: NA

**********************************************************************

ANALYSIS FILE NAME: GSM595922_UW.Fetal_Brain.ChromatinAccessibility.H-23266.DS14717.bed
ANALYSIS ALIAS: DS14717.hg19.level.1
ANALYSIS TITLE: Mapping of Fetal Brain Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Brain, Donor H-23266, Library DS14717 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.4105
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: 0.5266
FINDPEAKS_PERCENTILE: 42
HOTSPOT_SCORE: 0.3922
HOTSPOT_PERCENTILE: 32
IROC_SCORE: 0.9954
IROC_PERCENTILE: 25
POISSON_SCORE: 0.5137
POISSON_PERCENTILE: 55

**********************************************************************

ANALYSIS FILE NAME: GSM595922_UW.Fetal_Brain.ChromatinAccessibility.H-23266.DS14717.wig
ANALYSIS ALIAS: DS14717.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Brain Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from Fetal Brain, Donor H-23266, Library DS14717 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.4065
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: FB DNase 66 17
BROWSER_TRACK_DESCRIPTION: UW Fetal Brain DNase Hypersensitivity Donor H-23266 Library DS14717 EA Release 2

QUALITY SCORES:
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED: 40
FINDPEAKS_SCORE: 0.5266
FINDPEAKS_PERCENTILE: 42
HOTSPOT_SCORE: 0.3922
HOTSPOT_PERCENTILE: 32
IROC_SCORE: 0.9954
IROC_PERCENTILE: 25
POISSON_SCORE: 0.5137
POISSON_PERCENTILE: 55

source_name: Fetal Brain primary tissue, day 85; DS14717

value: genomic DNA

value: fetal brain

value: day 85

value: Female


title: Chromatin accessibility assay of CD34+ Primary cells; DS12336

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: DS12336
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.3103
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.2397
****************
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: GSM595914_CD34-DS12336.hg19.bam
ANALYSIS ALIAS: DS12336-align
ANALYSIS TITLE: Alignments DS12336
ANALYSIS DESCRIPTION: Bowtie (v0.12.5) alignments of Chromatin Accessibility Illumina sequencing lane data to the human genome The Genome Reference Consortium GRCh37 (hg19)
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page:
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
SOFTWARE: Bowtie
SOFTWARE_VERSION: 0.12.5
MAXIMUM_ALIGNMENT_LENGTH: 36
MISMATCHES_ALLOWED: 2
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: not submitted
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: allowed
ALIGNMENT_POSTPROCESSING: none

**********************************************************************

ANALYSIS FILE NAME: GSM595914_CD34-DS12336.75.20.filtered-density.36.hg19.wig
ANALYSIS ALIAS: DS12336-signal
ANALYSIS TITLE: Signal DS12336
ANALYSIS DESCRIPTION: Chromatin Accessibility data with a sliding window (+/-75bp) summation at 20 bp steps across the genome
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page:
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
SOFTWARE: signalmap
SOFTWARE_VERSION: 1.0
READ_EXTENSION: 150
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: NA

**********************************************************************

ANALYSIS FILE NAME: GSM595914_UW.Mobilized_CD34_Primary_Cells.ChromatinAccessibility.RO_01536.DS12336.bed
ANALYSIS ALIAS: DS12336.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 01536, Library DS12336 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.4129
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: 0.3929
FINDPEAKS_PERCENTILE: 7
HOTSPOT_SCORE: 0.3003
HOTSPOT_PERCENTILE: 7
IROC_SCORE: 0.9969
IROC_PERCENTILE: 50
POISSON_SCORE: 0.3675
POISSON_PERCENTILE: 5

**********************************************************************

ANALYSIS FILE NAME: GSM595914_UW.Mobilized_CD34_Primary_Cells.ChromatinAccessibility.RO_01536.DS12336.wig
ANALYSIS ALIAS: DS12336.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 01536, Library DS12336 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.4089
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 36 36
BROWSER_TRACK_DESCRIPTION: UW Mobilized CD34 Primary Cells DNase Hypersensitivity Donor RO 01536 Library DS12336 EA Release 2

QUALITY SCORES:
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED: 40
FINDPEAKS_SCORE: 0.3929
FINDPEAKS_PERCENTILE: 7
HOTSPOT_SCORE: 0.3003
HOTSPOT_PERCENTILE: 7
IROC_SCORE: 0.9969
IROC_PERCENTILE: 50
POISSON_SCORE: 0.3675
POISSON_PERCENTILE: 5

source_name: flow sorted CD34+ cells from cord blood; DS12336

value: FHCRC HEIMFELD

value: Primary Cell

value: CD34 Primary Cells

value: 27 years

value: Hispanic


title: Chromatin accessibility assay of Fetal brain tissue; DS11877

description:
sample_term_id: UBERON_0000955
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS11877
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.3110
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.2448
****************
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: GSM595913_fBrain-DS11877.hg19.bam
ANALYSIS ALIAS: DS11877-align
ANALYSIS TITLE: Alignments DS11877
ANALYSIS DESCRIPTION: Bowtie (v0.12.5) alignments of Chromatin Accessibility Illumina sequencing lane data to the human genome The Genome Reference Consortium GRCh37 (hg19)
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page:
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
SOFTWARE: Bowtie
SOFTWARE_VERSION: 0.12.5
MAXIMUM_ALIGNMENT_LENGTH: 36
MISMATCHES_ALLOWED: 2
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: not submitted
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: allowed
ALIGNMENT_POSTPROCESSING: none

**********************************************************************

ANALYSIS FILE NAME: GSM595913_fBrain-DS11877.75.20.filtered-density.36.hg19.wig
ANALYSIS ALIAS: DS11877-signal
ANALYSIS TITLE: Signal DS11877
ANALYSIS DESCRIPTION: Chromatin Accessibility data with a sliding window (+/-75bp) summation at 20 bp steps across the genome
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page:
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
SOFTWARE: signalmap
SOFTWARE_VERSION: 1.0
READ_EXTENSION: 150
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: NA

**********************************************************************

ANALYSIS FILE NAME: GSM595913_UW.Fetal_Brain.ChromatinAccessibility.H-22510.DS11877.bed
ANALYSIS ALIAS: DS11877.hg19.level.1
ANALYSIS TITLE: Mapping of Fetal Brain Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Brain, Donor H-22510, Library DS11877 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.4124
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: 0.6764
FINDPEAKS_PERCENTILE: 82
HOTSPOT_SCORE: 0.559
HOTSPOT_PERCENTILE: 85
IROC_SCORE: 0.9975
IROC_PERCENTILE: 60
POISSON_SCORE: 0.5602
POISSON_PERCENTILE: 65

**********************************************************************

ANALYSIS FILE NAME: GSM595913_UW.Fetal_Brain.ChromatinAccessibility.H-22510.DS11877.wig
ANALYSIS ALIAS: DS11877.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Brain Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from Fetal Brain, Donor H-22510, Library DS11877 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.4084
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: FB DNase 10 77
BROWSER_TRACK_DESCRIPTION: UW Fetal Brain DNase Hypersensitivity Donor H-22510 Library DS11877 EA Release 2

QUALITY SCORES:
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED: 40
FINDPEAKS_SCORE: 0.6764
FINDPEAKS_PERCENTILE: 82
HOTSPOT_SCORE: 0.559
HOTSPOT_PERCENTILE: 85
IROC_SCORE: 0.9975
IROC_PERCENTILE: 60
POISSON_SCORE: 0.5602
POISSON_PERCENTILE: 65

source_name: Fetal Brain primary tissue, day 122; DS11877

value: 122 days

value: Male

value: Chromatin Accessibility

value: Qiagen minElut


title: Chromatin accessibility assay of human CD34 Primary Cells; DS12274

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

source_name: flow sorted CD34+ cells from cord blood; DS12274

value: Unknown


title: Chromatin accessibility assay of human CD34 Primary Cells; DS11202

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

source_name: flow sorted CD34+ cells from cord blood; DS11202


title: START (ES) L019

city: Stockholm

first: Sten

last: Linnarsson

address: Scheeles väg 2

department: MBB

country: Sweden

institute: Karolinska Institutet

description: Single-cell tagged reverse transcription (START) on 96 ES R1 cells

data_processing:
Matrix: Raw reads were sorted by barcode, trimmed to remove the barcode and any leading G or trailing A tracts, then mapped to the mouse genome using Bowtie with the default settings. Unmapped reads were discarded. Then, for each annotated feature in the NCBI 37.1 assembly, all mapping reads were counted to generate a raw count. Finally, the raw reads for each cell were normalized to transcripts per million (t.p.m.) . The output file is a tab-delimited matrix with one column per barcode (=single cell) and one row per annotated genome feature (gene, repeat, mitochondrial gene).
Wiggle: Aligned reads, regardless of barcode, were placed on the genome and the total coverage was calculated for each nucleotide position. One wiggle file was produced for each strand (_fw.wig.gz and _rev.wig.gz).

molecule: total RNA

organism: Mus musculus

source_name: ES R1

growth_protocol: ES R1 cells were cultured as previously described (Moliner, A., Enfors, P., Ibanez, C.F. & Andang, M. Mouse embryonic stem cell-derived spheres with distinct neurogenic potentials. Stem Cells Dev 17, 233-243 (2008)). MEFs and Neuro-2A cells were grown in DMEM with 10% FBS, 1x penicillin/streptomycin, 1x Glutamax and 0.05 mM 2-mercaptoethanol.

extract_protocol:
Cells were dissociated enzymatically using TrypLE Express (Invitrogen), washed and resuspended in phosphate-buffered saline (PBS). A single cell was collected into each well of a 96-well capture plate (AbGene Thermo-Fast 96 cat. No. 0600) by fluorescence-activated cell sorting (FACS), and the plate was immediately frozen on dry ice.
The cell capture plate contained a single cell per well in 5 µL of START buffer (20 mM Tris-HCl pH 8.0, 75 mM KCl, 6 mM MgCl2, 0.02% Tween-20) with 400 nM STRT-T30-BIO (5'-biotin-AAGCAGTGGTATCAACGCAGAGT30VN-3'; this and all other oligos were from Eurofins MWG Operon) and 400 nM STRT-FW-n (5'-AAGCAGTGGTATCAACGCAGAGTGGATGCTXXXXXrGrGrG-3', where “rG” denotes a riboguanine and “XXXXX” was a 5 bp barcode). Each well of the capture plate contained a different template-switching helper oligo (STRT-FW-n) with a distinct barcode.
To purify the cDNA and remove unreacted primers, 50 µL PB (Qiaquick PCR Purification Kit, Qiagen) was added to each well. All 96 reactions were pooled and purified over a single Qiaquick column. The cDNA was eluted in 30 µL EB in a 1.5 mL polyallomer tube (Beckman).
The whole 96-cell cDNA sample was amplified in a single tube in 100 µL of 200 µM dNTP, 200 µM STRT-PCR primer (5'-biotin-AAGCAGTGGTATCAACGCAGAGT-3’; Eurofins MWG Operon), 1x Advantage2 DNA Polymerase Mix (Clontech) in 1x Advantage2 PCR buffer (Clontech) with 1 min at 94°C followed by 25 cycles of 15 s at 95°C, 30 s at 65°C, 3 min at 68°C, with heated lid. An aliquot was visualized on a 1.2% agarose E-gel (Invitrogen) and the sample was amplified an additional 1-5 cycles if necessary.

tag: cell type

value: embryonic stem cell-derived spheres (ES R1)


title: START (Neuro2A) L023

description: Single-cell tagged reverse transcription (START) on 96 Neuro2A cells


title: START (ES) L006


title: START (MEF) L026

description: Single-cell tagged reverse transcription (START) on 96 mouse embryonic fibroblast cells (MEFs)

source_name: MEF

value: mouse embryonic fibroblasts (MEFs)


title: seq-AB46540_NIgG_N2_MXemb_2_A_EE1432

city: Chapel Hill

first: Everett

last: Zhou

state: NC

address: 1000 Manning Dr.

institute: UNC

description: input_experiment: seq-NA_N2_MXemb_3_A_EE1432

data_processing:
alignment: BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). See the link @ http://bio-bwa.sourceforge.net/.  The input is fastq and the output is sam file.
peak_calling: ChIP-Seq MACS Peak-calling:JL:1. Peak calls were determined by using Model-based Analysis of ChIP-Seq (MACS) software. MACS was supplied with the following parameters: tagSize = 25 mfold = 10,30 genomeSize = 90000000 bandwidth = 300 pvalue = 1e-5 Input = sam file Output = bed file
pipeline v.1.3, Data received between Feb 9 - May 30, 2009

organism: Caenorhabditis elegans

source_name: Caenorhabditis elegans_N2_MXemb

growth_protocol: Worm_embryo_growth_and_harvest_v5. Embryos were prepared by bleaching from gravid N2 adults grown in standard S-basal media liquid culture. Live embryos were cross-linked in M9 + 2% formaldehyde for 30 minutes at room temperature followed by quenching with 125mM glycine for 5 minutes. Embryos were then washed twice with M9 Buffer and once by FA buffer (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1 % sodium deoxycholate; 150 mM NaCl). Pellets were frozen at -80C. For a detailed protocol see http://www.modencode.org/.

extract_protocol: Worm_chromatin_immunoprecipitation_vKI2. Antibody was incubated with protein A/G beads at 4 oC for at least 1 hr to prepare antibody-beads complex. For each reaction, 0.5-2 mg of protein extract was taken and sarkosyl was added to 1% final concentration. The extract was precleared by incubating with protein A/G beads for 30 min at 4 oC. Before immunoprecipitation, 10% of extract was taken and treated with RNase. The extract was mixed with the antibody-beads complex and incubated overnight at 4C. After washing beads, immune complexes were eluted from beads twice with 150uL elution buffer (1% SDS in TE with 250 mM NaCl) for 15minutes at 65C. Samples were treated with proteinase K at 55C for 1-2hrs then transfer to 65C overnight to reverse crosslinks. DNA was cleaned up Qiagen PCR purification kit. For a detailed protocol see http://www.modencode.org/. || Solexa_Library_Prep_vKI1. DNA was incubated with End Repair Enzyme mix (Epicentre, Madison) to ensure blunt ends and then with Exo(-) Klenow fragment in the presence of dATP to add adenosine at the 3\` ends. The DNA fragments were ligated with single-end adaptor (Illumina) and then amplified by PCR with single end primers. The amplicon was loaded into an agarose gel, and size-selected DNA was recovered from the gel.

treatment_protocol: Worm_embryo_extraction_v3. Embryos were resuspended in FA buffer (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1 % sodium deoxycholate; 150 mM NaCl) + protease inhibitors (Calbiochem Cat# 539131). Using a Branson sonifier microtip, samples were sonicated on ice at the following settings: 35% amplitude, 0.9 sec on, 0.1 sec off, 12 pulses, 10 times. Cell debris was removed by centrifuging at 13,000 g for 15 minutes at 4?C and taking the supernatant. Protein concentration was determined by Bradford Assay and extracts were aliquoted at stored at -80C. For a detailed protocol see http://www.modencode.org/.

tag: strain

tag: Stage

value: MXemb

tag: chip antibody

value: NIgG

tag: antibody manufacturer

value: Abcam

tag: antibody catalog #


title: Chromatin accessibility assay of human CD34 Primary Cells; DS11666

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: DS11666
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.1654
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.1655
****************
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: GSM493387_DS11666.UWStam_090817_SOLEXA-1GA-2_0014_FC42APL_5.bam
ANALYSIS ALIAS: UW.CD34.ChromatinAccessibility.Level1.11
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.1838
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: GSM493387_DS11666.UWStam_090827_SOLEXA-1GA-1_0019_FC42L5P_3.bam
ANALYSIS ALIAS: UW.CD34.ChromatinAccessibility.Level1.12
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.1840
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: GSM493387_DS11666.UWStam_090827_SOLEXA-1GA-1_0019_FC42L5P_4.bam
ANALYSIS ALIAS: UW.CD34.ChromatinAccessibility.Level1.13
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.1842
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: GSM493387_UW.CD34.rep3.ChromatinAccessibility.CD34+-DS11666.wig
ANALYSIS ALIAS: UW.CD34.ChromatinAccessibility.Level2.combined.3
ANALYSIS TITLE: Raw Signal Density Graphs of CD34 Chromatin Accessibility Replicate 3 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.1856
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: GSM493387_UW.Mobilized_CD34_Primary_Cells.ChromatinAccessibility.RO_01527.DS11666.bed
ANALYSIS ALIAS: DS11666.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 01527, Library DS11666 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.4132
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: 0.4495
FINDPEAKS_PERCENTILE: 12
HOTSPOT_SCORE: 0.3399
HOTSPOT_PERCENTILE: 12
IROC_SCORE: 0.9976
IROC_PERCENTILE: 67
POISSON_SCORE: 0.3734
POISSON_PERCENTILE: 7

**********************************************************************

ANALYSIS FILE NAME: GSM493387_UW.Mobilized_CD34_Primary_Cells.ChromatinAccessibility.RO_01527.DS11666.wig
ANALYSIS ALIAS: DS11666.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 01527, Library DS11666 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.4092
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 27 66
BROWSER_TRACK_DESCRIPTION: UW Mobilized CD34 Primary Cells DNase Hypersensitivity Donor RO 01527 Library DS11666 EA Release 2

QUALITY SCORES:
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED: 40
FINDPEAKS_SCORE: 0.4495
FINDPEAKS_PERCENTILE: 12
HOTSPOT_SCORE: 0.3399
HOTSPOT_PERCENTILE: 12
IROC_SCORE: 0.9976
IROC_PERCENTILE: 67
POISSON_SCORE: 0.3734
POISSON_PERCENTILE: 7

source_name: flow sorted CD34+ cells from cord blood; DS11666

value: genomic DNA

value: Stamlab DNase Protocol


title: START (ES) L013


title: GM12056_RNAseq

status: Public on Sep 20 2010

city: Philadelphia

first: Michael

middle: Patrick

last: Morley

state: PA

address: 3400 Civic Center Blvd, Bldg 421

department: Penn Cardiovascular Institute

institute: Perelman School of Medicine at the University of Pennsylvania

description: polyA RNA_RNAseq

data_processing: For alignment of the short reads sequences to the human reference sequence (HG18) and identification of SNPs, we used the program MAQ (version 0.6.8)26.  To minimize sequence errors, we used the first 40 of the 50 nucleotides in each sequence read for our analysis.  For the alignment, we used the default settings of MAQ: allowing up to 2 mismatches per read and requiring that the mismatch base qualities to be less than 70.  From the aligned reads with map quality scores of 30 or higher, we identified SNPs.  For this analysis, we used only known SNPs in (dbSNP 129).  To call a sample to be heterozygous at a SNP for our DAE analysis, we required that each allele to be represented in at least 5% of the total reads covering that locus.  To determine the expression level of a gene, we calculated RPKM as per Mortazavi et al17.

source_name: lymphoblastoid cell line

growth_protocol: Immortalized B cells were grown at a density of 5 x 105 cells/mL in RPMI 1640 with 15 % fetal bovine serum, 2 mM L-glutamine, and 100 U/mL penicillin-streptomycin.

extract_protocol: mRNA-Seq was performed as recommended by the manufacturer (Illumina). Briefly, poly(A) mRNA was fragmented and first strand cDNA generated using random hexamers.  Following second strand cDNA synthesis, end repair, addition of a single A base, adaptor ligation, agarose gel isolation of ~200 bp cDNA and PCR amplification of the ~200 bp cDNA, the samples were sequenced using the Illumina Genome Analyzer.

tag: coriell cell line repository identifier


title: GM12815_RNAseq

description: polyA RNA_RNAseq


title: GM12057_RNAseq

description: polyA RNA_RNAseq


title: GM12145_RNAseq

description: polyA RNA_RNAseq


title: GM12874_RNAseq

description: polyA RNA_RNAseq


title: GM12813_RNAseq

description: polyA RNA_RNAseq


title: GM12891_RNAseq

description: polyA RNA_RNAseq


title: GM12872_RNAseq

description: polyA RNA_RNAseq


title: GM12043_RNAseq

description: polyA RNA_RNAseq


title: GM12044_RNAseq

description: polyA RNA_RNAseq


title: GM12762_RNAseq

description: polyA RNA_RNAseq


title: GM12144_RNAseq

description: polyA RNA_RNAseq


title: GM12750_RNAseq

description: polyA RNA_RNAseq


title: GM12006_RNAseq

description: polyA RNA_RNAseq


title: GM12717_RNAseq

description: polyA RNA_RNAseq


title: GM12003_RNAseq

description: polyA RNA_RNAseq


title: GM12814_RNAseq

description: polyA RNA_RNAseq


title: GM11992_RNAseq

description: polyA RNA_RNAseq


title: GM11994_RNAseq

description: polyA RNA_RNAseq


title: GM11993_RNAseq

description: polyA RNA_RNAseq


title: GM12716_RNAseq

description: polyA RNA_RNAseq


title: GM12264_RNAseq

description: polyA RNA_RNAseq


title: GM11882_RNAseq

description: polyA RNA_RNAseq


title: GM12155_RNAseq

description: polyA RNA_RNAseq


title: GM11881_RNAseq

description: polyA RNA_RNAseq


title: GM11839_RNAseq

description: polyA RNA_RNAseq


title: GM11832_RNAseq

description: polyA RNA_RNAseq


title: GM12005_RNAseq

description: polyA RNA_RNAseq


title: GM11830_RNAseq

description: polyA RNA_RNAseq


title: GM07056_RNAseq

description: polyA RNA_RNAseq


title: GM07345_RNAseq

description: polyA RNA_RNAseq


title: GM11829_RNAseq

description: polyA RNA_RNAseq


title: GM12004_RNAseq

description: polyA RNA_RNAseq


title: GM07022_RNAseq

description: polyA RNA_RNAseq


title: GM07034_RNAseq

description: polyA RNA_RNAseq


title: GM07000_RNAseq

description: polyA RNA_RNAseq


title: GM06993_RNAseq

description: polyA RNA_RNAseq


title: GM06985_RNAseq

description: polyA RNA_RNAseq


title: GM06994_RNAseq

description: polyA RNA_RNAseq


title: CY3003 (tra1-L3733A)

city: London

first: Christopher

last: Brandl

state: Ontario

address: 1151 Richmond St.

department: Biochemistry

country: Canada

institute: University of Western Ontario

library_source: synthetic

data_processing: Alignment: The sequencing reads were mapped onto the Saccharomyces cerevisiae genomic sequence (May, 1, 2009) using the novoindex and novoalign programs with the default parameters, except that reads mapping to two or more places in the genome were placed at one position at random. With this option novoalign marks a read as uniquely or repetitively mapping in the genome; only uniquely mapping reads were used for the subsequent analysis and 83% and 84% of the CY2706 and CY3003 reads were mapped uniquely. Uniquely mapped reads were placed into bins composed of protein-coding genes, tRNA and rRNA genes as defined by the gff file. Only reads that did not overlap the start or end position of the gene were counted and reads mapping to the top and bottom strands were tabulated separately.

organism: Saccharomyces cerevisiae

source_name: whole cell lysate

growth_protocol: Yeast cells, CY2706 and CY3003, were grown at 30˚ in YP media containing 2% glucose to an A600 = 2.0.

extract_protocol: RNA was purified from 108 cells after glass bead disruption as described previously (MUTIU and BRANDL 2005; MUTIU et al. 2007b). RNA integrity numbers of greater than 8.9 were determined for each RNA sample using an Agilent 2100 Bioanalyzer at the The London Regional Genomics Centre Microarray Facility. mRNA-Seq libraries were constructed and sequencing were performed on the Illumina/Solexa Genome Analyzer II platform  at the DNA Facility at Iowa State University. The CY2706 and CY3003 samples were each run on a single Illumina GAII lane, producing 13014880 reads for CY2706 and 11156078 reads for CY3003 that were 35 nucleotides long.


title: CY2706 (TRA1-wt)


title: GM07055_RNAseq

description: polyA RNA_RNAseq


title: H3K9/14Ac_HeLa

status: Public on Sep 17 2010

city: Nijmegen

first: Hendrik

last: Marks

address: Geert Grooteplein 26/28

department: Molecular Biology

country: Netherlands

institute: Radboud University Nijmegen, RIMLS

description: Chromatin IP against H3K9/14Ac

data_processing: Reads (36 bp) were aligned to the human (Homo Sapiens) reference genome. Sequences were aligned to the human HG18 reference genome using the Illumina Analysis Pipeline allowing one mismatch. Unless specified otherwise, only the tags uniquely aligning to the genome were considered for further analysis. The 36 bp sequence reads were directionally extended to 300 bp, corresponding to the length of the original fragments used for sequencing. The output data were converted to Browser Extensible Data (BED) files for downstream analysis and Wiggle (WIG) files for viewing the data in the UCSC Genome Browser. All ChIP-Seq sequence analyses were conducted based on the Human NCBI Built 36.1 genome assembly (HG18) accessed from the Ensembl (release 54; May 2009) or the UCSC (assembly March 2006) Genome Browsers.

source_name: Human cervical carcinoma cell line

growth_protocol: Transfected HeLa Kyoto cells were FACS sorted (Epics Altra flowcytometer, Beckman Coulter) for GFP positive cells, and cultured for 3-4 passages in DMEM with 10% FCS under 500 µg/ml G418 selection at 37˚C before usage for the ChIP and ChIP-Seq experiments. Generation of the BACs with GFP-fusion constructs within the endogenous genomic context of the target gene, and transfections of HeLa cells, were performed according to Poser et al (2008).

extract_protocol:
Stable Transfections with GFP-fusion constructs within the endogenous genomic context of the target gene
ChIP experiments were performed using 3.3x10^6 cells per ChIP according to standard protocols (Denissov et al, 2007), with two minor modifications. Crosslinking of the cells was performed on the culture plates for 20 minutes, while ChIP’ed DNA was purified by Qiaquick PCR purification Kit (Qiagen cat. no. 28106).

tag: cell line

value: HeLa Kyoto cell line

tag: sample type

value: Antibody H3K9/14Ac from Diagenode (pAb-ACHBHS-044)

tag: antibody

value: Diagenode


title: H3K79me3_HeLa

description: Chromatin IP against H3K79me3

value: Antibody H3K79me3 from Abcam (ab2621)