title: ChIP-Seq analysis of H3K4me3 in human Mobilized CD34 cells; 42LNLAAXX090804-7-S

description:
sample_term_id: CL_0000837
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Solexa-13497
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.2206
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.2205
****************
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: GSM537652_BI.Mobilized_CD34_Primary_Cells.H3K4me3.Mobilized_CD34_5_28_09.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 42LNLAAXX090804-7-S.hg19.level.1
ANALYSIS TITLE: Mapping of Mobilized CD34 Primary Cells Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me3 ChIP-Seq on Mobilized CD34 Primary Cells, Donor RO 01508 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.4678
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
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: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED: 62
FINDPEAKS_SCORE: 0.7113
FINDPEAKS_PERCENTILE: 90
HOTSPOT_SCORE: 0.6676
HOTSPOT_PERCENTILE: 90
IROC_SCORE: 0.9985
IROC_PERCENTILE: 42
POISSON_SCORE: 0.732
POISSON_PERCENTILE: 90

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

ANALYSIS FILE NAME: GSM537652_BI.Mobilized_CD34_Primary_Cells.H3K4me3.Mobilized_CD34_5_28_09.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 42LNLAAXX090804-7-S.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Mobilized CD34 Primary Cells Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me3 ChIP-Seq read mappings from Mobilized CD34 Primary Cells, Donor RO 01508 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.4952
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: MCD34 H3K4me3 28
BROWSER_TRACK_DESCRIPTION: BI Mobilized CD34 Primary Cells Histone H3K4me3 Donor RO 01508 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED: 62
FINDPEAKS_SCORE: 0.7113
FINDPEAKS_PERCENTILE: 90
HOTSPOT_SCORE: 0.6676
HOTSPOT_PERCENTILE: 90
IROC_SCORE: 0.9985
IROC_PERCENTILE: 42
POISSON_SCORE: 0.732
POISSON_PERCENTILE: 90

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

source_name: CD34 cells mobilized into peripheral blood; 42LNLAAXX090804-7-S

value: FHCRC

value: Primary Cell

value: Mobilized CD34 Primary Cells

value: Histone H3K4me3

value: Millipore


title: G529T

status: Public on Apr 28 2010

type: SRA

city: Piscataway

first: Sam

middle: Guoping

last: Gu

state: NJ

address: Nelson Labs A125, 604 Allison Road

department: Molecular Biology and Biochemistry

country: USA

institute: Rutgers University

description:
5' monophosphate dependent small RNA cloning
ggg

library_source: transcriptomic

data_processing: frequencies of  known and novel miRNAs expressed in human cervical cancer tissues and matched normal tissues calculated (see Series record)

molecule: total RNA

organism: Homo sapiens

source_name: cervical cancer

growth_protocol: not applicable

extract_protocol: Small RNA isolation was performed using mirVana miRNA isolation kit (Applied Biosystems/Ambion, Austin, TX). Purified small RNAs were ligated to the 3’-adaptor [“Linker-1”, IDT Inc., Coralville, IA] and 5’ adaptor [5’-ACGCTCTTCCGATCTv-3’ (uppercase, DNA; v=barcodes with triple RNA molecules: aaa, ggg, ccc or uuu; IDT Inc., Coralville, IA)] oligonucleotides. Products from the second ligation were gel-purified and reverse transcribed using the RT primer [5'-ATTGATGGTGCCTACAG-3’]. cDNA was amplified with 16-20 PCR cycles, using a forward primer 5'- GAT ACG GCG ACC ACC GAG ATC TAC ACT CTT TCC CTA CAC GAC GCT CTT CCG ATC T-3' and a reverse primer 5’-CAA GCA GAA GAC GGC ATA CGA GCT CTT CCG ATC TAT TGA TGG TGC CTA CAG-3', to produce sequencing libraries that were subjected to Solexa/Illumina sequencing platform.

treatment_protocol: not applicable

tag: diagnosis

value: squamous cell carcinoma

tag: tissue

value: tumor


title: G601N

description:
5' monophosphate dependent small RNA cloning
aaa

source_name: normal cervix

value: normal

value: normal cervix


title: ChIP-Seq analysis of H3K9me3 in human WA-7 cells; 30H88AAXX090617-1-S

city: Cambridge

first: BROAD

last: INSTITUTE

state: MA

institute: Broad Institute

description:
sample_term_id: NTR_0000837
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Solexa-12613
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.2197
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.2196
****************
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: GSM537639_BI.ES-WA7.H3K9me3.Solexa-12613.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 30H88AAXX090617-1-S.hg19.level.1
ANALYSIS TITLE: Mapping of ES-WA7 Cell Line Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9me3 ChIP-Seq on the ES-WA7 Cell Line, Library Solexa-12613 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.4823
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
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: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED: 59
FINDPEAKS_SCORE: 0.044
FINDPEAKS_PERCENTILE: 32
HOTSPOT_SCORE: 0.1543
HOTSPOT_PERCENTILE: 47
IROC_SCORE: 0.7132
IROC_PERCENTILE: 19
POISSON_SCORE: 0.3178
POISSON_PERCENTILE: 24

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

ANALYSIS FILE NAME: GSM537639_BI.ES-WA7.H3K9me3.Solexa-12613.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 30H88AAXX090617-1-S.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of ES-WA7 Cell Line Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9me3 ChIP-Seq read mappings from the ES-WA7 Cell Line, Library Solexa-12613 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.5097
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: ESWA7 H3K9me3 13
BROWSER_TRACK_DESCRIPTION: BI ES-WA7 Cell Line Histone H3K9me3 Library Solexa-12613 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED: 59
FINDPEAKS_SCORE: 0.044
FINDPEAKS_PERCENTILE: 32
HOTSPOT_SCORE: 0.1543
HOTSPOT_PERCENTILE: 47
IROC_SCORE: 0.7132
IROC_PERCENTILE: 19
POISSON_SCORE: 0.3178
POISSON_PERCENTILE: 24

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

molecule: genomic DNA

source_name: WA7 stem cells; 30H88AAXX090617-1-S

extract_protocol: Library construction protocol: Single read - Illumina

tag: molecule

value: genomic DNA

tag: disease

value: Harvard University

value: Cell Line

tag: line

tag: lineage

value: embrionic stem cell

value: undifferentiated

tag: passage

tag: medium

value: KSR

tag: sex

value: Female

tag: batch

value: Histone H3K9me3

value: SDS lysis

value: Bioruptor

value: 10 million cells

value: Protein A-Sepharose 4B

value: 70 ul bed volume

value: Abcam


title: ChIP-Seq analysis of H3K9me3 in human CD19 cells; 30EDEAAXX090127-2-S

description:
sample_term_id: CL_0000236
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Solexa-9770
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.2224
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.2223
****************
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: GSM537635_BI.CD19_Primary_Cells.H3K9me3.CD19_12_29_08.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 30EDEAAXX090127-2-S.hg19.level.1
ANALYSIS TITLE: Mapping of CD19 Primary Cells Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9me3 ChIP-Seq on CD19 Primary Cells, Donor CD19_12/29/08 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.4574
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
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: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED: 59
FINDPEAKS_SCORE: 0.162
FINDPEAKS_PERCENTILE: 76
HOTSPOT_SCORE: 0.2197
HOTSPOT_PERCENTILE: 76
IROC_SCORE: 0.8428
IROC_PERCENTILE: 56
POISSON_SCORE: 0.3913
POISSON_PERCENTILE: 56

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

ANALYSIS FILE NAME: GSM537635_BI.CD19_Primary_Cells.H3K9me3.CD19_12_29_08.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 30EDEAAXX090127-2-S.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of CD19 Primary Cells Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9me3 ChIP-Seq read mappings from CD19 Primary Cells, Donor CD19_12/29/08 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.4848
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: CD19 H3K9me3 29
BROWSER_TRACK_DESCRIPTION: BI CD19 Primary Cells Histone H3K9me3 Donor CD19_12/29/08 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED: 59
FINDPEAKS_SCORE: 0.162
FINDPEAKS_PERCENTILE: 76
HOTSPOT_SCORE: 0.2197
HOTSPOT_PERCENTILE: 76
IROC_SCORE: 0.8428
IROC_PERCENTILE: 56
POISSON_SCORE: 0.3913
POISSON_PERCENTILE: 56

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

source_name: flow sorted CD19+ cells from cord blood; 30EDEAAXX090127-2-S

value: FHCRC

value: Primary Cell

value: CD19 Primary Cells

tag: markers

value: Unknown

value: not passaged


title: ChIP-Seq analysis of H3K4me3 in human CD19 cells; 30EBYAAXX090127-3-S

description:
sample_term_id: CL_0000236
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Solexa-9763
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.2203
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.2202
****************
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: GSM537632_BI.CD19_Primary_Cells.H3K4me3.CD19_12_22_08.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 30EBYAAXX090127-3-S.hg19.level.1
ANALYSIS TITLE: Mapping of CD19 Primary Cells Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me3 ChIP-Seq on CD19 Primary Cells, Donor CD19_12/22/08 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.4740
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
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: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED: 62
FINDPEAKS_SCORE: 0.3554
FINDPEAKS_PERCENTILE: 47
HOTSPOT_SCORE: 0.3823
HOTSPOT_PERCENTILE: 52
IROC_SCORE: 0.9987
IROC_PERCENTILE: 47
POISSON_SCORE: 0.4278
POISSON_PERCENTILE: 39

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

ANALYSIS FILE NAME: GSM537632_BI.CD19_Primary_Cells.H3K4me3.CD19_12_22_08.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 30EBYAAXX090127-3-S.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of CD19 Primary Cells Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me3 ChIP-Seq read mappings from CD19 Primary Cells, Donor CD19_12/22/08 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.5014
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: CD19 H3K4me3 22
BROWSER_TRACK_DESCRIPTION: BI CD19 Primary Cells Histone H3K4me3 Donor CD19_12/22/08 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED: 62
FINDPEAKS_SCORE: 0.3554
FINDPEAKS_PERCENTILE: 47
HOTSPOT_SCORE: 0.3823
HOTSPOT_PERCENTILE: 52
IROC_SCORE: 0.9987
IROC_PERCENTILE: 47
POISSON_SCORE: 0.4278
POISSON_PERCENTILE: 39

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

source_name: flow sorted CD19+ cells from cord blood; 30EBYAAXX090127-3-S

value: genomic DNA

value: Histone H3K4me3


title: ChIP-Seq analysis of H3K36me3 in human CD19 cells; 30EBJAAXX090206-5-S

description:
sample_term_id: CL_0000236
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Solexa-9987
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.2161
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.2160
****************
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: GSM537630_BI.CD19_Primary_Cells.H3K36me3.CD19_12_29_08.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 30EBJAAXX090206-5-S.hg19.level.1
ANALYSIS TITLE: Mapping of CD19 Primary Cells Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K36me3 ChIP-Seq on CD19 Primary Cells, Donor CD19_12/29/08 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.4835
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
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: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED: 54
FINDPEAKS_SCORE: 0.5711
FINDPEAKS_PERCENTILE: 91
HOTSPOT_SCORE: 0.3741
HOTSPOT_PERCENTILE: 83
IROC_SCORE: 0.9862
IROC_PERCENTILE: 81
POISSON_SCORE: 0.7033
POISSON_PERCENTILE: 87

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

ANALYSIS FILE NAME: GSM537630_BI.CD19_Primary_Cells.H3K36me3.CD19_12_29_08.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 30EBJAAXX090206-5-S.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of CD19 Primary Cells Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K36me3 ChIP-Seq read mappings from CD19 Primary Cells, Donor CD19_12/29/08 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.5109
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: CD19 H3K36me3 29
BROWSER_TRACK_DESCRIPTION: BI CD19 Primary Cells Histone H3K36me3 Donor CD19_12/29/08 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED: 54
FINDPEAKS_SCORE: 0.5711
FINDPEAKS_PERCENTILE: 91
HOTSPOT_SCORE: 0.3741
HOTSPOT_PERCENTILE: 83
IROC_SCORE: 0.9862
IROC_PERCENTILE: 81
POISSON_SCORE: 0.7033
POISSON_PERCENTILE: 87

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

source_name: flow sorted CD19+ cells from cord blood; 30EBJAAXX090206-5-S

value: Histone H3K36me3


title: ChIP-Seq analysis of H3K4me1 in human cultured CD34 cells; 30E62AAXX090709-2-S

description:
sample_term_id: CL_0001059
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Solexa-12899
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.2269
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.2268
****************
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: GSM537628_BI.CD34_Cultured_Cells.H3K4me1.cultured_CD34_2_20_09.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 30E62AAXX090709-2-S.hg19.level.1
ANALYSIS TITLE: Mapping of CD34 Cultured Cells Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me1 ChIP-Seq on CD34 Cultured Cells, Donor cultured CD34_2/20/09 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.4704
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
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: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED: 43
FINDPEAKS_SCORE: 0.3802
FINDPEAKS_PERCENTILE: 58
HOTSPOT_SCORE: 0.4056
HOTSPOT_PERCENTILE: 63
IROC_SCORE: 0.9899
IROC_PERCENTILE: 60
POISSON_SCORE: 0.5086
POISSON_PERCENTILE: 35

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

ANALYSIS FILE NAME: GSM537628_BI.CD34_Cultured_Cells.H3K4me1.cultured_CD34_2_20_09.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 30E62AAXX090709-2-S.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of CD34 Cultured Cells Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me1 ChIP-Seq read mappings from CD34 Cultured Cells, Donor cultured CD34_2/20/09 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.4978
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: CD34 H3K4me1 20
BROWSER_TRACK_DESCRIPTION: BI CD34 Cultured Cells Histone H3K4me1 Donor cultured CD34_2/20/09 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED: 43
FINDPEAKS_SCORE: 0.3802
FINDPEAKS_PERCENTILE: 58
HOTSPOT_SCORE: 0.4056
HOTSPOT_PERCENTILE: 63
IROC_SCORE: 0.9899
IROC_PERCENTILE: 60
POISSON_SCORE: 0.5086
POISSON_PERCENTILE: 35

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

source_name: flow sorted CD34+ cells from cord blood expanded in short term culture; 30E62AAXX090709-2-S

value: CD34 Cultured Cells

value: cultured CD34_2/20/09

value: short term

value: Histone H3K4me1


title: ChIP-Seq analysis of H3K9ac in human hES I3 TESR cells; 30DRPAAXX090625-1-S

description:
sample_term_id: NTR_0000836
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Solexa-12682
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.2266
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.2265
****************
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: GSM537624_BI.ES-I3.H3K9ac.Solexa-12682.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 30DRPAAXX090625-1-S.hg19.level.1
ANALYSIS TITLE: Mapping of ES-I3 Cell Line Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9ac ChIP-Seq on the ES-I3 Cell Line, Library Solexa-12682 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.4598
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
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: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED: 35
FINDPEAKS_SCORE: 0.2092
FINDPEAKS_PERCENTILE: 57
HOTSPOT_SCORE: 0.2532
HOTSPOT_PERCENTILE: 54
IROC_SCORE: 0.9714
IROC_PERCENTILE: 37
POISSON_SCORE: 0.3415
POISSON_PERCENTILE: 34

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

ANALYSIS FILE NAME: GSM537624_BI.ES-I3.H3K9ac.Solexa-12682.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 30DRPAAXX090625-1-S.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of ES-I3 Cell Line Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9ac ChIP-Seq read mappings from the ES-I3 Cell Line, Library Solexa-12682 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.4872
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: ESI3 H3K9ac 82
BROWSER_TRACK_DESCRIPTION: BI ES-I3 Cell Line Histone H3K9ac Library Solexa-12682 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED: 35
FINDPEAKS_SCORE: 0.2092
FINDPEAKS_PERCENTILE: 57
HOTSPOT_SCORE: 0.2532
HOTSPOT_PERCENTILE: 54
IROC_SCORE: 0.9714
IROC_PERCENTILE: 37
POISSON_SCORE: 0.3415
POISSON_PERCENTILE: 34

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

source_name: I3(eye three) stem cells; 30DRPAAXX090625-1-S

value: Harvard University

value: Cell Line

value: hES I3 TESR

value: embrionic stem cell

value: undifferentiated

value: TESR

value: Female

value: Histone H3K9ac

value: SDS lysis

value: Bioruptor


title: ChIP-Seq analysis of H3K27me3 in human CD19 cells; 30EBYAAXX090127-7-S

description:
sample_term_id: CL_0000236
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Solexa-9764
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.2149
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.2148
****************
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: GSM537634_BI.CD19_Primary_Cells.H3K27me3.CD19_12_22_08.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 30EBYAAXX090127-7-S.hg19.level.1
ANALYSIS TITLE: Mapping of CD19 Primary Cells Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27me3 ChIP-Seq on CD19 Primary Cells, Donor CD19_12/22/08 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.4799
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
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: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED: 52
FINDPEAKS_SCORE: 0.1609
FINDPEAKS_PERCENTILE: 54
HOTSPOT_SCORE: 0.2421
HOTSPOT_PERCENTILE: 56
IROC_SCORE: 0.8683
IROC_PERCENTILE: 31
POISSON_SCORE: 0.4197
POISSON_PERCENTILE: 38

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

ANALYSIS FILE NAME: GSM537634_BI.CD19_Primary_Cells.H3K27me3.CD19_12_22_08.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 30EBYAAXX090127-7-S.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of CD19 Primary Cells Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27me3 ChIP-Seq read mappings from CD19 Primary Cells, Donor CD19_12/22/08 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.5073
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: CD19 H3K27me3 22
BROWSER_TRACK_DESCRIPTION: BI CD19 Primary Cells Histone H3K27me3 Donor CD19_12/22/08 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED: 52
FINDPEAKS_SCORE: 0.1609
FINDPEAKS_PERCENTILE: 54
HOTSPOT_SCORE: 0.2421
HOTSPOT_PERCENTILE: 56
IROC_SCORE: 0.8683
IROC_PERCENTILE: 31
POISSON_SCORE: 0.4197
POISSON_PERCENTILE: 38

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

source_name: flow sorted CD19+ cells from cord blood; 30EBYAAXX090127-7-S

value: genomic DNA

value: FHCRC

value: Primary Cell

value: CD19 Primary Cells

value: Unknown

value: not passaged

value: Histone H3K27me3

value: 10 million cells

value: Protein A-Sepharose 4B

value: 70 ul bed volume

value: Upstate


title: ChIP-Seq analysis of H3K4me3 in human WA-7 cells; 30DDNAAXX090707-8-S

description:
sample_term_id: NTR_0000837
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Solexa-13062
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.2191
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.2190
****************
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: GSM537623_BI.ES-WA7.H3K4me3.Solexa-13062.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 30DDNAAXX090707-8-S.hg19.level.1
ANALYSIS TITLE: Mapping of ES-WA7 Cell Line Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me3 ChIP-Seq on the ES-WA7 Cell Line, Library Solexa-13062 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.4672
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
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: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED: 62
FINDPEAKS_SCORE: 0.3467
FINDPEAKS_PERCENTILE: 44
HOTSPOT_SCORE: 0.4014
HOTSPOT_PERCENTILE: 54
IROC_SCORE: 0.9994
IROC_PERCENTILE: 56
POISSON_SCORE: 0.483
POISSON_PERCENTILE: 53

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

ANALYSIS FILE NAME: GSM537623_BI.ES-WA7.H3K4me3.Solexa-13062.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 30DDNAAXX090707-8-S.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of ES-WA7 Cell Line Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me3 ChIP-Seq read mappings from the ES-WA7 Cell Line, Library Solexa-13062 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.4946
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: ESWA7 H3K4me3 62
BROWSER_TRACK_DESCRIPTION: BI ES-WA7 Cell Line Histone H3K4me3 Library Solexa-13062 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED: 62
FINDPEAKS_SCORE: 0.3467
FINDPEAKS_PERCENTILE: 44
HOTSPOT_SCORE: 0.4014
HOTSPOT_PERCENTILE: 54
IROC_SCORE: 0.9994
IROC_PERCENTILE: 56
POISSON_SCORE: 0.483
POISSON_PERCENTILE: 53

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

source_name: WA7 stem cells; 30DDNAAXX090707-8-S

value: Harvard University

value: Cell Line

value: embrionic stem cell

value: undifferentiated

value: KSR

value: Histone H3K4me3

value: Millipore


title: ChIP-Seq analysis of H3K4me3 in human CD19 cells; 30CAVAAXX081115-7-S

description:
sample_term_id: CL_0000236
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Solexa-8319
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.2281
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.2280
****************
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: GSM537622_BI.CD19_Primary_Cells.H3K4me3.CD19_8_1_08.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 30CAVAAXX081115-7-S.hg19.level.1
ANALYSIS TITLE: Mapping of CD19 Primary Cells Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me3 ChIP-Seq on CD19 Primary Cells, Donor CD19_8/1/08 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.4604
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
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: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED: 62
FINDPEAKS_SCORE: 0.3627
FINDPEAKS_PERCENTILE: 50
HOTSPOT_SCORE: 0.3814
HOTSPOT_PERCENTILE: 51
IROC_SCORE: 0.9999
IROC_PERCENTILE: 74
POISSON_SCORE: 0.4432
POISSON_PERCENTILE: 44

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

ANALYSIS FILE NAME: GSM537622_BI.CD19_Primary_Cells.H3K4me3.CD19_8_1_08.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 30CAVAAXX081115-7-S.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of CD19 Primary Cells Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me3 ChIP-Seq read mappings from CD19 Primary Cells, Donor CD19_8/1/08 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.4878
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: CD19 H3K4me3 1
BROWSER_TRACK_DESCRIPTION: BI CD19 Primary Cells Histone H3K4me3 Donor CD19_8/1/08 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED: 62
FINDPEAKS_SCORE: 0.3627
FINDPEAKS_PERCENTILE: 50
HOTSPOT_SCORE: 0.3814
HOTSPOT_PERCENTILE: 51
IROC_SCORE: 0.9999
IROC_PERCENTILE: 74
POISSON_SCORE: 0.4432
POISSON_PERCENTILE: 44

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

source_name: flow sorted CD19+ cells from cord blood; 30CAVAAXX081115-7-S

value: genomic DNA

value: FHCRC

value: SDS lysis

value: Bioruptor

value: Abcam


title: Rice degradome

status: Public on May 04 2010

city: Stillwater

first: Ramanjulu

last: Sunkar

address: 246 Noble Research center

department: Biochemistry and Molecular biology

institute: Oklahoma State University

description:
sequencing the sliced transcripts containing 5'monophosphate
library_source: 20 nt tags from the 5' ends of uncapped, poly A RNA
library_selection: 5' phosphated end can be ligated to a RNA adaptor

data_processing: The data was processed using Cleavaland. All degradome sequences with exact sense matches to the structural RNAs are removed and the filtered dataset is mapped to the transcriptome. For each exact match to the sense strand of an mRNA and having the 5’ end of the degradome sequence coincident with the 10th nucleotide of complementarity to the small RNA are retained and then filtered.

molecule: polyA RNA

organism: Oryza sativa

source_name: seedlings

growth_protocol: Three week-old rice seedlings  grown on hydropic culture at  25°C with 16h/8h light/dark cycle.

extract_protocol: Poly A was isolated from 3 week-old rice seedlings. The sliced ends possessing 5’ monophosphate were ligated to an RNA adapter consisting MmeI recognition site in its 3’end. After ligation and RT-PCR, the PCR product was digested with MmeI. The digested PCR product was purified and ligated to a double-stranded DNA oligo. After PCR amplification, the final PCR product was purified and sequenced using sequencing-by-synthesis technology (Illumina).

tag: cultivar

value: spp japonica cv. Nipponbare


title: ChIP-Seq analysis of H3K36me3 in human CD19 cells; 30CAVAAXX081115-6-S

description:
sample_term_id: CL_0000236
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Solexa-8320
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.2278
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.2277
****************
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: GSM537621_BI.CD19_Primary_Cells.H3K36me3.CD19_8_1_08.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 30CAVAAXX081115-6-S.hg19.level.1
ANALYSIS TITLE: Mapping of CD19 Primary Cells Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K36me3 ChIP-Seq on CD19 Primary Cells, Donor CD19_8/1/08 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.4808
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
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: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED: 54
FINDPEAKS_SCORE: 0.225
FINDPEAKS_PERCENTILE: 46
HOTSPOT_SCORE: 0.3103
HOTSPOT_PERCENTILE: 66
IROC_SCORE: 0.8924
IROC_PERCENTILE: 24
POISSON_SCORE: 0.6474
POISSON_PERCENTILE: 81

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

ANALYSIS FILE NAME: GSM537621_BI.CD19_Primary_Cells.H3K36me3.CD19_8_1_08.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 30CAVAAXX081115-6-S.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of CD19 Primary Cells Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K36me3 ChIP-Seq read mappings from CD19 Primary Cells, Donor CD19_8/1/08 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.5082
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: CD19 H3K36me3 1
BROWSER_TRACK_DESCRIPTION: BI CD19 Primary Cells Histone H3K36me3 Donor CD19_8/1/08 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED: 54
FINDPEAKS_SCORE: 0.225
FINDPEAKS_PERCENTILE: 46
HOTSPOT_SCORE: 0.3103
HOTSPOT_PERCENTILE: 66
IROC_SCORE: 0.8924
IROC_PERCENTILE: 24
POISSON_SCORE: 0.6474
POISSON_PERCENTILE: 81

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

source_name: flow sorted CD19+ cells from cord blood; 30CAVAAXX081115-6-S

value: Primary Cell

value: CD19 Primary Cells

value: Unknown

value: not passaged

value: Histone H3K36me3

value: 10 million cells


title: Chromatin accessibility assay of human CD34 Primary Cells; DS13196

city: Seattle

first: Northwest

last: REMC

state: WA

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: DS13196
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.2423
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.2422
****************
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: GSM530663_UW.CD34.ChromatinAccessibility.CD34+-DS13196.wig
ANALYSIS ALIAS: UW.CD34.ChromatinAccessibility.DS13196
ANALYSIS TITLE: Raw Signal Density Graphs of CD34 Primary Cell Chromatin Accessibility 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%2FUniversity%20of%20Washington%2FANALYSIS%2FEDACC.2643
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: GSM530663_UW.Mobilized_CD34_Primary_Cells.ChromatinAccessibility.RO_01562.DS13196.bed
ANALYSIS ALIAS: DS13196.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 01562, Library DS13196 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.4120
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: 0.4735
FINDPEAKS_PERCENTILE: 22
HOTSPOT_SCORE: 0.3667
HOTSPOT_PERCENTILE: 22
IROC_SCORE: 0.9971
IROC_PERCENTILE: 55
POISSON_SCORE: 0.3874
POISSON_PERCENTILE: 12

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

ANALYSIS FILE NAME: GSM530663_UW.Mobilized_CD34_Primary_Cells.ChromatinAccessibility.RO_01562.DS13196.wig
ANALYSIS ALIAS: DS13196.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 01562, Library DS13196 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.4080
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 62 96
BROWSER_TRACK_DESCRIPTION: UW Mobilized CD34 Primary Cells DNase Hypersensitivity Donor RO 01562 Library DS13196 EA Release 2

QUALITY SCORES:
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED: 40
FINDPEAKS_SCORE: 0.4735
FINDPEAKS_PERCENTILE: 22
HOTSPOT_SCORE: 0.3667
HOTSPOT_PERCENTILE: 22
IROC_SCORE: 0.9971
IROC_PERCENTILE: 55
POISSON_SCORE: 0.3874
POISSON_PERCENTILE: 12

source_name: flow sorted CD34+ cells from cord blood; DS13196

value: FHCRC HEIMFELD

value: CD34 Primary Cells

value: 42 years

value: Male

value: Caucasian

value: Chromatin Accessibility

value: Qiagen minElut

value: Stamlab DNase Protocol


title: Chromatin accessibility assay of IMR90 Cell Line; DS13219

description:
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS13219
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.2432
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.1632
****************
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: GSM530665_IMR90-DS13219.uniques.36.hg18.bed
ANALYSIS ALIAS: DS13219-align
ANALYSIS TITLE: Alignments DS13219
ANALYSIS DESCRIPTION: Eland alignments of Chromatin Accessibility Illumina sequencing lane data to the human genome NCBI Build 36 (hg18)
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page:
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
SOFTWARE: Eland
SOFTWARE_VERSION: 1.5
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: GSM530665_UW.IMR90.ChromatinAccessibility.IMR90-DS13219.wig
ANALYSIS ALIAS: UW.IMR90.ChromatinAccessibility.DS13219
ANALYSIS TITLE: Raw Signal Density Graphs of IMR90 Cell Line Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from the IMR90 Cell Line 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%2FUniversity%20of%20Washington%2FANALYSIS%2FEDACC.2649
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: GSM530665_UW.IMR90.ChromatinAccessibility.DS13219.bed
ANALYSIS ALIAS: DS13219.hg19.level.1
ANALYSIS TITLE: Mapping of IMR90 Cell Line Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on the IMR90 Cell Line, Library DS13219 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.4101
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: 0.6099
FINDPEAKS_PERCENTILE: 62
HOTSPOT_SCORE: 0.4554
HOTSPOT_PERCENTILE: 57
IROC_SCORE: 0.9969
IROC_PERCENTILE: 52
POISSON_SCORE: 0.4667
POISSON_PERCENTILE: 30

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

ANALYSIS FILE NAME: GSM530665_UW.IMR90.ChromatinAccessibility.DS13219.wig
ANALYSIS ALIAS: DS13219.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of IMR90 Cell Line Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from the IMR90 Cell Line, Library DS13219 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.4061
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: IMR90 DNase 19 19
BROWSER_TRACK_DESCRIPTION: UW IMR90 Cell Line DNase Hypersensitivity Library DS13219 EA Release 2

QUALITY SCORES:
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED: 40
FINDPEAKS_SCORE: 0.6099
FINDPEAKS_PERCENTILE: 62
HOTSPOT_SCORE: 0.4554
HOTSPOT_PERCENTILE: 57
IROC_SCORE: 0.9969
IROC_PERCENTILE: 52
POISSON_SCORE: 0.4667
POISSON_PERCENTILE: 30

source_name: IMR90 Cell Line; DS13219

value: genomic DNA

value: ATCC

value: Cell Line

value: Fetal lung fibroblast

value: Eagle's Minimum Essential Medium, Catalog No. 30-2003.

tag: Sex

value: Female


title: Chromatin accessibility assay of human CD34 Primary Cells; DS13199

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: DS13199
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.2428
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.2427
****************
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: GSM530664_UW.CD34.ChromatinAccessibility.CD34+-DS13199.wig
ANALYSIS ALIAS: UW.CD34.ChromatinAccessibility.DS13199
ANALYSIS TITLE: Raw Signal Density Graphs of CD34 Primary Cell Chromatin Accessibility 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%2FUniversity%20of%20Washington%2FANALYSIS%2FEDACC.2644
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: GSM530664_UW.Mobilized_CD34_Primary_Cells.ChromatinAccessibility.RO_00738.DS13199.bed
ANALYSIS ALIAS: DS13199.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 00738, Library DS13199 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.4121
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: 0.4216
FINDPEAKS_PERCENTILE: 10
HOTSPOT_SCORE: 0.3195
HOTSPOT_PERCENTILE: 10
IROC_SCORE: 0.9974
IROC_PERCENTILE: 57
POISSON_SCORE: 0.3598
POISSON_PERCENTILE: 2

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

ANALYSIS FILE NAME: GSM530664_UW.Mobilized_CD34_Primary_Cells.ChromatinAccessibility.RO_00738.DS13199.wig
ANALYSIS ALIAS: DS13199.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 00738, Library DS13199 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.4081
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 38 99
BROWSER_TRACK_DESCRIPTION: UW Mobilized CD34 Primary Cells DNase Hypersensitivity Donor RO 00738 Library DS13199 EA Release 2

QUALITY SCORES:
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED: 40
FINDPEAKS_SCORE: 0.4216
FINDPEAKS_PERCENTILE: 10
HOTSPOT_SCORE: 0.3195
HOTSPOT_PERCENTILE: 10
IROC_SCORE: 0.9974
IROC_PERCENTILE: 57
POISSON_SCORE: 0.3598
POISSON_PERCENTILE: 2

source_name: flow sorted CD34+ cells from cord blood; DS13199

value: Primary Cell

value: 49 years


title: Chromatin accessibility assay of human CD34 Primary Cells; DS12785

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: DS12785
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.2418
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.2417
****************
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: GSM530660_UW.CD34.ChromatinAccessibility.CD34+-DS12785.wig
ANALYSIS ALIAS: UW.CD34.ChromatinAccessibility.DS12785
ANALYSIS TITLE: Raw Signal Density Graphs of CD34 Primary Cell Chromatin Accessibility 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%2FUniversity%20of%20Washington%2FANALYSIS%2FEDACC.2642
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: GSM530660_UW.Mobilized_CD34_Primary_Cells.ChromatinAccessibility.RO_01520.DS12785.bed
ANALYSIS ALIAS: DS12785.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 01520, Library DS12785 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.4116
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: 0.6232
FINDPEAKS_PERCENTILE: 72
HOTSPOT_SCORE: 0.5165
HOTSPOT_PERCENTILE: 70
IROC_SCORE: 0.9979
IROC_PERCENTILE: 75
POISSON_SCORE: 0.5003
POISSON_PERCENTILE: 45

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

ANALYSIS FILE NAME: GSM530660_UW.Mobilized_CD34_Primary_Cells.ChromatinAccessibility.RO_01520.DS12785.wig
ANALYSIS ALIAS: DS12785.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 01520, Library DS12785 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.4076
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 20 85
BROWSER_TRACK_DESCRIPTION: UW Mobilized CD34 Primary Cells DNase Hypersensitivity Donor RO 01520 Library DS12785 EA Release 2

QUALITY SCORES:
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED: 40
FINDPEAKS_SCORE: 0.6232
FINDPEAKS_PERCENTILE: 72
HOTSPOT_SCORE: 0.5165
HOTSPOT_PERCENTILE: 70
IROC_SCORE: 0.9979
IROC_PERCENTILE: 75
POISSON_SCORE: 0.5003
POISSON_PERCENTILE: 45

source_name: flow sorted CD34+ cells from cord blood; DS12785

value: 50 years


title: Chromatin accessibility assay of human CD34 Primary Cells; DS12771

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: DS12771
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.2408
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.2407
****************
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: GSM530658_UW.CD34.ChromatinAccessibility.CD34+-DS12771.wig
ANALYSIS ALIAS: UW.CD34.ChromatinAccessibility.DS12771
ANALYSIS TITLE: Raw Signal Density Graphs of CD34 Primary Cell Chromatin Accessibility 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%2FUniversity%20of%20Washington%2FANALYSIS%2FEDACC.2640
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: GSM530658_UW.Mobilized_CD34_Primary_Cells.ChromatinAccessibility.RO_01480.DS12771.bed
ANALYSIS ALIAS: DS12771.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 01480, Library DS12771 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.4112
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: 0.6529
FINDPEAKS_PERCENTILE: 75
HOTSPOT_SCORE: 0.5473
HOTSPOT_PERCENTILE: 82
IROC_SCORE: 0.9977
IROC_PERCENTILE: 70
POISSON_SCORE: 0.5362
POISSON_PERCENTILE: 60

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

ANALYSIS FILE NAME: GSM530658_UW.Mobilized_CD34_Primary_Cells.ChromatinAccessibility.RO_01480.DS12771.wig
ANALYSIS ALIAS: DS12771.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 01480, Library DS12771 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.4072
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 80 71
BROWSER_TRACK_DESCRIPTION: UW Mobilized CD34 Primary Cells DNase Hypersensitivity Donor RO 01480 Library DS12771 EA Release 2

QUALITY SCORES:
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED: 40
FINDPEAKS_SCORE: 0.6529
FINDPEAKS_PERCENTILE: 75
HOTSPOT_SCORE: 0.5473
HOTSPOT_PERCENTILE: 82
IROC_SCORE: 0.9977
IROC_PERCENTILE: 70
POISSON_SCORE: 0.5362
POISSON_PERCENTILE: 60

source_name: flow sorted CD34+ cells from cord blood; DS12771

value: FHCRC HEIMFELD

value: 27 years


title: Chromatin accessibility assay of Fetal Lung Primary Tissue; DS12817

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: DS12817
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.2471
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.2470
****************
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: GSM530662_UW.FetalLung.ChromatinAccessibility.fLung-DS12817.wig
ANALYSIS ALIAS: UW.FetalLung.ChromatinAccessibility.DS12817
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Lung Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from Fetal Lung 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%2FUniversity%20of%20Washington%2FANALYSIS%2FEDACC.2648
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: GSM530662_UW.Fetal_Lung.ChromatinAccessibility.H-22727.DS12817.bed
ANALYSIS ALIAS: DS12817.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-22727, Library DS12817 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.4138
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: 0.766
FINDPEAKS_PERCENTILE: 97
HOTSPOT_SCORE: 0.6099
HOTSPOT_PERCENTILE: 90
IROC_SCORE: 0.9978
IROC_PERCENTILE: 72
POISSON_SCORE: 0.6746
POISSON_PERCENTILE: 100

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

ANALYSIS FILE NAME: GSM530662_UW.Fetal_Lung.ChromatinAccessibility.H-22727.DS12817.wig
ANALYSIS ALIAS: DS12817.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-22727, Library DS12817 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.4098
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 27 17
BROWSER_TRACK_DESCRIPTION: UW Fetal Lung DNase Hypersensitivity Donor H-22727 Library DS12817 EA Release 2

QUALITY SCORES:
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED: 40
FINDPEAKS_SCORE: 0.766
FINDPEAKS_PERCENTILE: 97
HOTSPOT_SCORE: 0.6099
HOTSPOT_PERCENTILE: 90
IROC_SCORE: 0.9978
IROC_PERCENTILE: 72
POISSON_SCORE: 0.6746
POISSON_PERCENTILE: 100

source_name: Fetal Lung primary tissue, day 101; DS12817

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

value: Primary Tissue

value: fetal lung

value: UW

value: fetal

value: 101 days

value: Unknown


title: Chromatin accessibility assay of human CD34 Primary Cells; DS12734

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: DS12734
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.2402
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.2401
****************
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: GSM530657_UW.CD34.ChromatinAccessibility.CD34+-DS12734.wig
ANALYSIS ALIAS: UW.CD34.ChromatinAccessibility.DS12734
ANALYSIS TITLE: Raw Signal Density Graphs of CD34 Primary Cell Chromatin Accessibility 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%2FUniversity%20of%20Washington%2FANALYSIS%2FEDACC.2639
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: GSM530657_UW.Mobilized_CD34_Primary_Cells.ChromatinAccessibility.RO_01549.DS12734.bed
ANALYSIS ALIAS: DS12734.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 01549, Library DS12734 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.4108
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: 0.7758
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.6542
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9981
IROC_PERCENTILE: 80
POISSON_SCORE: 0.6468
POISSON_PERCENTILE: 95

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

ANALYSIS FILE NAME: GSM530657_UW.Mobilized_CD34_Primary_Cells.ChromatinAccessibility.RO_01549.DS12734.wig
ANALYSIS ALIAS: DS12734.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 01549, Library DS12734 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.4068
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 49 34
BROWSER_TRACK_DESCRIPTION: UW Mobilized CD34 Primary Cells DNase Hypersensitivity Donor RO 01549 Library DS12734 EA Release 2

QUALITY SCORES:
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED: 40
FINDPEAKS_SCORE: 0.7758
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.6542
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9981
IROC_PERCENTILE: 80
POISSON_SCORE: 0.6468
POISSON_PERCENTILE: 95

source_name: flow sorted CD34+ cells from cord blood; DS12734

value: genomic DNA

value: CD34 Primary Cells

value: 33 years

value: Caucasian

value: Chromatin Accessibility

value: Qiagen minElut

value: Stamlab DNase Protocol


title: Chromatin accessibility assay of human CD34 Primary Cells; DS12774

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: DS12774
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.2413
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
****************

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

ANALYSIS FILE NAME: GSM530659_UW.CD34.ChromatinAccessibility.CD34+-DS12774.wig
ANALYSIS ALIAS: UW.CD34.ChromatinAccessibility.DS12774
ANALYSIS TITLE: Raw Signal Density Graphs of CD34 Primary Cell Chromatin Accessibility 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%2FUniversity%20of%20Washington%2FANALYSIS%2FEDACC.2641
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: GSM530659_UW.Mobilized_CD34_Primary_Cells.ChromatinAccessibility.RO_01492.DS12774.bed
ANALYSIS ALIAS: DS12774.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 DS12774 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.4113
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: 0.6915
FINDPEAKS_PERCENTILE: 85
HOTSPOT_SCORE: 0.5938
HOTSPOT_PERCENTILE: 87
IROC_SCORE: 0.998
IROC_PERCENTILE: 77
POISSON_SCORE: 0.5724
POISSON_PERCENTILE: 75

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

ANALYSIS FILE NAME: GSM530659_UW.Mobilized_CD34_Primary_Cells.ChromatinAccessibility.RO_01492.DS12774.wig
ANALYSIS ALIAS: DS12774.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 DS12774 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.4073
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 74
BROWSER_TRACK_DESCRIPTION: UW Mobilized CD34 Primary Cells DNase Hypersensitivity Donor RO 01492 Library DS12774 EA Release 2

QUALITY SCORES:
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED: 40
FINDPEAKS_SCORE: 0.6915
FINDPEAKS_PERCENTILE: 85
HOTSPOT_SCORE: 0.5938
HOTSPOT_PERCENTILE: 87
IROC_SCORE: 0.998
IROC_PERCENTILE: 77
POISSON_SCORE: 0.5724
POISSON_PERCENTILE: 75

source_name: flow sorted CD34+ cells from cord blood; DS12774

value: Primary Cell

value: 39 years

value: Male


title: G601T

description:
5' monophosphate dependent small RNA cloning
ggg

data_processing: frequencies of  known and novel miRNAs expressed in human cervical cancer tissues and matched normal tissues calculated (see Series record)

source_name: cervical cancer

value: squamous cell carcinoma

value: tumor


title: Chromatin accessibility assay of Fetal Lung Primary Tissue; DS12646

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: DS12646
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.2467
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.2466
****************
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: GSM530656_UW.FetalLung.ChromatinAccessibility.fLung-DS12646.wig
ANALYSIS ALIAS: UW.FetalLung.ChromatinAccessibility.DS12646
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Lung Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from Fetal Lung 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%2FUniversity%20of%20Washington%2FANALYSIS%2FEDACC.2647
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: GSM530656_UW.Fetal_Lung.ChromatinAccessibility.H-22676.DS12646.bed
ANALYSIS ALIAS: DS12646.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-22676, Library DS12646 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.4115
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: 0.5543
FINDPEAKS_PERCENTILE: 47
HOTSPOT_SCORE: 0.4301
HOTSPOT_PERCENTILE: 52
IROC_SCORE: 0.9944
IROC_PERCENTILE: 20
POISSON_SCORE: 0.473
POISSON_PERCENTILE: 35

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

ANALYSIS FILE NAME: GSM530656_UW.Fetal_Lung.ChromatinAccessibility.H-22676.DS12646.wig
ANALYSIS ALIAS: DS12646.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-22676, Library DS12646 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.4075
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 76 46
BROWSER_TRACK_DESCRIPTION: UW Fetal Lung DNase Hypersensitivity Donor H-22676 Library DS12646 EA Release 2

QUALITY SCORES:
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED: 40
FINDPEAKS_SCORE: 0.5543
FINDPEAKS_PERCENTILE: 47
HOTSPOT_SCORE: 0.4301
HOTSPOT_PERCENTILE: 52
IROC_SCORE: 0.9944
IROC_PERCENTILE: 20
POISSON_SCORE: 0.473
POISSON_PERCENTILE: 35

source_name: Fetal Lung primary tissue, day 122; DS12646

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

value: Primary Tissue

value: fetal lung

value: 122 days


title: Chromatin accessibility assay of Fetal Adrenal Primary Tissue; DS12528

description:
sample_term_id: UBERON_0002369
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS12528
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.2444
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.2443
****************
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: GSM530653_UW.FetalAdrenalGland.ChromatinAccessibility.fAdrenal-DS12528.wig
ANALYSIS ALIAS: UW.FetalAdrenalGland.ChromatinAccessibility.DS12528
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Adrenal Gland Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from Fetal Adrenal Gland 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%2FUniversity%20of%20Washington%2FANALYSIS%2FEDACC.2634
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: GSM530653_UW.Fetal_Adrenal_Gland.ChromatinAccessibility.H-22662.DS12528.bed
ANALYSIS ALIAS: DS12528.hg19.level.1
ANALYSIS TITLE: Mapping of Fetal Adrenal Gland Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Adrenal Gland, Donor H-22662, Library DS12528 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.4117
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: 0.5861
FINDPEAKS_PERCENTILE: 57
HOTSPOT_SCORE: 0.4016
HOTSPOT_PERCENTILE: 42
IROC_SCORE: 0.9936
IROC_PERCENTILE: 10
POISSON_SCORE: 0.4944
POISSON_PERCENTILE: 37

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

ANALYSIS FILE NAME: GSM530653_UW.Fetal_Adrenal_Gland.ChromatinAccessibility.H-22662.DS12528.wig
ANALYSIS ALIAS: DS12528.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Adrenal Gland Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from Fetal Adrenal Gland, Donor H-22662, Library DS12528 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.4077
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: FAG DNase 62 28
BROWSER_TRACK_DESCRIPTION: UW Fetal Adrenal Gland DNase Hypersensitivity Donor H-22662 Library DS12528 EA Release 2

QUALITY SCORES:
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED: 40
FINDPEAKS_SCORE: 0.5861
FINDPEAKS_PERCENTILE: 57
HOTSPOT_SCORE: 0.4016
HOTSPOT_PERCENTILE: 42
IROC_SCORE: 0.9936
IROC_PERCENTILE: 10
POISSON_SCORE: 0.4944
POISSON_PERCENTILE: 37

source_name: Fetal Adrenal Gland primary tissue, day 96; DS12528

value: fetal adrenal

value: UW

value: fetal

value: 96 days

value: Unknown


title: Chromatin accessibility assay of Fetal Brain Primary Tissue; DS11872

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: DS11872
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.2449
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: GSM530651_UW.FetalBrain.ChromatinAccessibility.fBrain-DS11872.wig
ANALYSIS ALIAS: UW.FetalBrain.ChromatinAccessibility.DS11872
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Brain Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from Fetal Brain 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%2FUniversity%20of%20Washington%2FANALYSIS%2FEDACC.2635
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: GSM530651_UW.Fetal_Brain.ChromatinAccessibility.H-22510.DS11872.bed
ANALYSIS ALIAS: DS11872.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 DS11872 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.4123
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: 0.7566
FINDPEAKS_PERCENTILE: 95
HOTSPOT_SCORE: 0.6461
HOTSPOT_PERCENTILE: 97
IROC_SCORE: 0.9982
IROC_PERCENTILE: 82
POISSON_SCORE: 0.6396
POISSON_PERCENTILE: 92

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

ANALYSIS FILE NAME: GSM530651_UW.Fetal_Brain.ChromatinAccessibility.H-22510.DS11872.wig
ANALYSIS ALIAS: DS11872.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 DS11872 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.4083
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 72
BROWSER_TRACK_DESCRIPTION: UW Fetal Brain DNase Hypersensitivity Donor H-22510 Library DS11872 EA Release 2

QUALITY SCORES:
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED: 40
FINDPEAKS_SCORE: 0.7566
FINDPEAKS_PERCENTILE: 95
HOTSPOT_SCORE: 0.6461
HOTSPOT_PERCENTILE: 97
IROC_SCORE: 0.9982
IROC_PERCENTILE: 82
POISSON_SCORE: 0.6396
POISSON_PERCENTILE: 92

source_name: Fetal Brain primary tissue, day 122; DS11872

value: genomic DNA

value: fetal brain

value: Chromatin Accessibility