title: ChIP-Seq analysis of WCE in Cultured CD34 cells; Lib:RI:20101012:06--ChIP:MA:20100927:06:CD34 expanded:WCE

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: Lib:RI:20101012:06--ChIP:MA:20100927:06:CD34 expanded:WCE
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5670
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3896
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************
BED and WIG files were replaced on April 29, 2014

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

ANALYSIS FILE NAME: GSM669929_BI.CD34_Cultured_Cells.Input.123_rel2.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20090601:04--ChIP:MC:20090601:04:Cultured CD34:WCE.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of CD34 Cultured Cells ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from CD34 Cultured Cells, Donor 123 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.4868
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 Input 23
BROWSER_TRACK_DESCRIPTION: BI CD34 Cultured Cells ChIP-Seq Input Donor 123 EA Release 2

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED: 67
FINDPEAKS_SCORE: 0.0067
FINDPEAKS_PERCENTILE: 30
HOTSPOT_SCORE: 0.0062
HOTSPOT_PERCENTILE: 20
IROC_SCORE: 0.9815
IROC_PERCENTILE: 87
POISSON_SCORE: 0.1906
POISSON_PERCENTILE: 21

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

ANALYSIS FILE NAME: GSM669929_BI.CD34_Cultured_Cells.Input.123.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:RI:20101012:06--ChIP:MA:20100927:06:CD34 expanded:WCE-Lib:MC:20090601:04--ChIP:MC:20090601:04:Cultured CD34:WCE.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of CD34 Cultured Cells ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on CD34 Cultured Cells, Donor 123 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.6472
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 3

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 61
FINDPEAKS_SCORE: 0.0069
FINDPEAKS_PERCENTILE: 60
HOTSPOT_SCORE: 0.0273
HOTSPOT_PERCENTILE: 80
IROC_SCORE: 0.9752
IROC_PERCENTILE: 52
POISSON_SCORE: 0.0705
POISSON_PERCENTILE: 73

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

ANALYSIS FILE NAME: GSM669929_BI.CD34_Cultured_Cells.Input.123.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:RI:20101012:06--ChIP:MA:20100927:06:CD34 expanded:WCE-Lib:MC:20090601:04--ChIP:MC:20090601:04:Cultured CD34:WCE.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of CD34 Cultured Cells ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from CD34 Cultured Cells, Donor 123 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.6682
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 3
BROWSER_TRACK_NAME: CD34 Input 23
BROWSER_TRACK_DESCRIPTION: BI CD34 Cultured Cells ChIP-Seq Input Donor 123 Library Lib:RI:20101012:06--ChIP:MA:20100927:06:CD34 expanded:WCE EA Release 3

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 61
FINDPEAKS_SCORE: 0.0069
FINDPEAKS_PERCENTILE: 60
HOTSPOT_SCORE: 0.0273
HOTSPOT_PERCENTILE: 80
IROC_SCORE: 0.9752
IROC_PERCENTILE: 52
POISSON_SCORE: 0.0705
POISSON_PERCENTILE: 73

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

source_name: flow sorted CD34+ cells from cord blood expanded in short term culture; Lib:RI:20101012:06--ChIP:MA:20100927:06:CD34 expanded:WCE

value: standard

value: SDS lysis

value: ChIP-Seq Input

value: Input


title: ChIP-Seq analysis of H3K9ac; ant. caudate cls; Lib:XZ:20100921:19--ChIP:XZ:20100914:19:anterior caudate :H3K9Ac

status: Public on Mar 31 2011

type: SRA

city: Cambridge

first: BROAD

last: INSTITUTE

state: MA

country: USA

institute: Broad Institute

description:
sample_term_id: UBERON_0001873
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:XZ:20100921:19--ChIP:XZ:20100914:19:anterior caudate :H3K9Ac
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5691
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5936
****************
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: GSM669950_BI.Brain_Anterior_Caudate.H3K9ac.112.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100921:19--ChIP:XZ:20100914:19:anterior caudate :H3K9Ac.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Brain Anterior Caudate Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9ac ChIP-Seq on Brain Anterior Caudate, Donor 112 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.6455
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 3

QUALITY SCORES:
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 40
FINDPEAKS_SCORE: 0.144
FINDPEAKS_PERCENTILE: 40
HOTSPOT_SCORE: 0.2092
HOTSPOT_PERCENTILE: 40
IROC_SCORE: 0.9885
IROC_PERCENTILE: 16
POISSON_SCORE: 0.2972
POISSON_PERCENTILE: 40

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

ANALYSIS FILE NAME: GSM669950_BI.Brain_Anterior_Caudate.H3K9ac.112.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100921:19--ChIP:XZ:20100914:19:anterior caudate :H3K9Ac.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of Brain Anterior Caudate Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9ac ChIP-Seq read mappings from Brain Anterior Caudate, Donor 112 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.6665
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 3
BROWSER_TRACK_NAME: BAC H3K9ac 12
BROWSER_TRACK_DESCRIPTION: BI Brain Anterior Caudate Histone H3K9ac Donor 112 Library Lib:XZ:20100921:19--ChIP:XZ:20100914:19:anterior caudate :H3K9Ac EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 40
FINDPEAKS_SCORE: 0.144
FINDPEAKS_PERCENTILE: 40
HOTSPOT_SCORE: 0.2092
HOTSPOT_PERCENTILE: 40
IROC_SCORE: 0.9885
IROC_PERCENTILE: 16
POISSON_SCORE: 0.2972
POISSON_PERCENTILE: 40

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

molecule: genomic DNA

organism: Homo sapiens

source_name: human post mortem brain region from a non Alzheimer's donor; Lib:XZ:20100921:19--ChIP:XZ:20100914:19:anterior caudate :H3K9Ac

extract_protocol: Library construction protocol: Single read - Illumina

tag: sample alias

tag: sample common name

value: Brain, Anterior Caudate

value: post-mortem

tag: molecule

value: genomic DNA

tag: disease

value: Anterior Caudate

value: Female

value: Primary Tissue

value: brain

value: Rush University Medical Center

value: Protein A-Sepharose 4B

value: 10 million cells

value: 70 ul bed volume

value: Abcam

value: Histone H3K9ac

value: Bioruptor


title: ChIP-Seq analysis of H3K4me1; substantia nigra cells; Lib:XZ:20100921:01--ChIP:XZ:20100914:01:substantia nigra:H3K4Me1

description:
sample_term_id: UBERON_0002038
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:XZ:20100921:01--ChIP:XZ:20100914:01:substantia nigra:H3K4Me1
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5682
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5938
****************
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: GSM669941_BI.Brain_Substantia_Nigra.H3K4me1.112.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100921:01--ChIP:XZ:20100914:01:substantia nigra:H3K4Me1.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Brain Substantia Nigra Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me1 ChIP-Seq on Brain Substantia Nigra, Donor 112 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.6553
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 3

QUALITY SCORES:
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 50
FINDPEAKS_SCORE: 0.1215
FINDPEAKS_PERCENTILE: 25
HOTSPOT_SCORE: 0.2177
HOTSPOT_PERCENTILE: 25
IROC_SCORE: 0.9255
IROC_PERCENTILE: 21
POISSON_SCORE: 0.3937
POISSON_PERCENTILE: 25

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

ANALYSIS FILE NAME: GSM669941_BI.Brain_Substantia_Nigra.H3K4me1.112.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100921:01--ChIP:XZ:20100914:01:substantia nigra:H3K4Me1.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of Brain Substantia Nigra Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me1 ChIP-Seq read mappings from Brain Substantia Nigra, Donor 112 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.6763
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 3
BROWSER_TRACK_NAME: BSN H3K4me1 12
BROWSER_TRACK_DESCRIPTION: BI Brain Substantia Nigra Histone H3K4me1 Donor 112 Library Lib:XZ:20100921:01--ChIP:XZ:20100914:01:substantia nigra:H3K4Me1 EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 50
FINDPEAKS_SCORE: 0.1215
FINDPEAKS_PERCENTILE: 25
HOTSPOT_SCORE: 0.2177
HOTSPOT_PERCENTILE: 25
IROC_SCORE: 0.9255
IROC_PERCENTILE: 21
POISSON_SCORE: 0.3937
POISSON_PERCENTILE: 25

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

source_name: human post mortem brain region from a non Alzheimer's donor; Lib:XZ:20100921:01--ChIP:XZ:20100914:01:substantia nigra:H3K4Me1

value: Brain, Substantia Nigra

value: Substantia Nigra

value: SDS lysis

value: Histone H3K4me1


title: ChIP-Seq analysis of H3K9me3 in HUES64 cells; Lib:MC:20101025:06--ChIP:MC:20101020:06:ES cell HUES_64:H3K9Me3

description:
sample_term_id: NTR_0000853
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:MC:20101025:06--ChIP:MC:20101020:06:ES cell HUES_64:H3K9Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5669
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5931
****************
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: GSM669928_BI.HUES64.H3K9me3.Lib_MC_20101025_06--ChIP_MC_20101020_06_ES_cell_HUES_64_H3K9Me3.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20101025:06--ChIP:MC:20101020:06:ES cell HUES_64:H3K9Me3.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of HUES64 Cell Line Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9me3 ChIP-Seq on the HUES64 Cell Line, Library Lib:MC:20101025:06--ChIP:MC:20101020:06:ES cell HUES_64:H3K9Me3 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.6582
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 3

QUALITY SCORES:
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 60
FINDPEAKS_SCORE: 0.2897
FINDPEAKS_PERCENTILE: 96
HOTSPOT_SCORE: 0.241
HOTSPOT_PERCENTILE: 92
IROC_SCORE: 0.969
IROC_PERCENTILE: 100
POISSON_SCORE: 0.4338
POISSON_PERCENTILE: 96

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

ANALYSIS FILE NAME: GSM669928_BI.HUES64.H3K9me3.Lib_MC_20101025_06--ChIP_MC_20101020_06_ES_cell_HUES_64_H3K9Me3.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20101025:06--ChIP:MC:20101020:06:ES cell HUES_64:H3K9Me3.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of HUES64 Cell Line Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9me3 ChIP-Seq read mappings from the HUES64 Cell Line, Library Lib:MC:20101025:06--ChIP:MC:20101020:06:ES cell HUES_64:H3K9Me3 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.6792
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 3
BROWSER_TRACK_NAME: HUES64 H3K9me3 e3
BROWSER_TRACK_DESCRIPTION: BI HUES64 Cell Line Histone H3K9me3 Library Lib:MC:20101025:06--ChIP:MC:20101020:06:ES cell HUES_64:H3K9Me3 EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 60
FINDPEAKS_SCORE: 0.2897
FINDPEAKS_PERCENTILE: 96
HOTSPOT_SCORE: 0.241
HOTSPOT_PERCENTILE: 92
IROC_SCORE: 0.969
IROC_PERCENTILE: 100
POISSON_SCORE: 0.4338
POISSON_PERCENTILE: 96

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

source_name: Harvard University Embryonic Stem Cells; Lib:MC:20101025:06--ChIP:MC:20101020:06:ES cell HUES_64:H3K9Me3

value: HUES64 Cell Line

tag: lineage

value: embrionic stem cell

tag: medium

value: KSR

tag: passage

tag: line

tag: batch

value: ES cell HUES_64-1

value: Cell Line

value: undifferentiated

tag: Sex

value: Unknown

value: Harvard University

value: Histone H3K9me3


title: ChIP-Seq analysis of WCE in WA-7 cells; Lib:MC:20100211:05--ChIP:MC:20100208:05:WA07:WCE

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: Lib:MC:20100211:05--ChIP:MC:20100208:05:WA07:WCE
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5667
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5952
****************
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: GSM669926_BI.ES-WA7.Input.Lib_MC_20100211_05--ChIP_MC_20100208_05_WA07_WCE.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100211:05--ChIP:MC:20100208:05:WA07:WCE.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of ES-WA7 Cell Line ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on the ES-WA7 Cell Line, Library Lib:MC:20100211:05--ChIP:MC:20100208:05:WA07:WCE 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.6460
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 3

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 61
FINDPEAKS_SCORE: 0.1603
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.2775
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.918
IROC_PERCENTILE: 48
POISSON_SCORE: 0.3349
POISSON_PERCENTILE: 100

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

ANALYSIS FILE NAME: GSM669926_BI.ES-WA7.Input.Lib_MC_20100211_05--ChIP_MC_20100208_05_WA07_WCE.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100211:05--ChIP:MC:20100208:05:WA07:WCE.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of ES-WA7 Cell Line ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from the ES-WA7 Cell Line, Library Lib:MC:20100211:05--ChIP:MC:20100208:05:WA07:WCE 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.6670
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 3
BROWSER_TRACK_NAME: ESWA7 Input CE
BROWSER_TRACK_DESCRIPTION: BI ES-WA7 Cell Line ChIP-Seq Input Library Lib:MC:20100211:05--ChIP:MC:20100208:05:WA07:WCE EA Release 3

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 61
FINDPEAKS_SCORE: 0.1603
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.2775
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.918
IROC_PERCENTILE: 48
POISSON_SCORE: 0.3349
POISSON_PERCENTILE: 100

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

source_name: H7 (WA07) embryonic stem cells; NIH Approval # NIHhESC-10-0061; Lib:MC:20100211:05--ChIP:MC:20100208:05:WA07:WCE

value: ES-WA7 Cell Line

value: genomic DNA

value: standard

value: ChIP-Seq Input

value: Input


title: ChIP-Seq analysis of H3K9me3 in cingulate gyrus cells; Lib:XZ:20100924:13--ChIP:XZ:20100914:13:cingulate gyrus:H3K9Me3

description:
sample_term_id: UBERON_0002967
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:XZ:20100924:13--ChIP:XZ:20100914:13:cingulate gyrus:H3K9Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5664
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5934
****************
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: GSM669923_BI.Brain_Cingulate_Gyrus.H3K9me3.112.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100924:13--ChIP:XZ:20100914:13:cingulate gyrus:H3K9Me3.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Brain Cingulate Gyrus Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9me3 ChIP-Seq on Brain Cingulate Gyrus, Donor 112 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.6558
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 3

QUALITY SCORES:
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 60
FINDPEAKS_SCORE: 0.0197
FINDPEAKS_PERCENTILE: 15
HOTSPOT_SCORE: 0.0627
HOTSPOT_PERCENTILE: 19
IROC_SCORE: 0.8419
IROC_PERCENTILE: 42
POISSON_SCORE: 0.1598
POISSON_PERCENTILE: 15

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

ANALYSIS FILE NAME: GSM669923_BI.Brain_Cingulate_Gyrus.H3K9me3.112.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100924:13--ChIP:XZ:20100914:13:cingulate gyrus:H3K9Me3.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of Brain Cingulate Gyrus Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9me3 ChIP-Seq read mappings from Brain Cingulate Gyrus, Donor 112 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.6768
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 3
BROWSER_TRACK_NAME: BCG H3K9me3 12
BROWSER_TRACK_DESCRIPTION: BI Brain Cingulate Gyrus Histone H3K9me3 Donor 112 Library Lib:XZ:20100924:13--ChIP:XZ:20100914:13:cingulate gyrus:H3K9Me3 EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 60
FINDPEAKS_SCORE: 0.0197
FINDPEAKS_PERCENTILE: 15
HOTSPOT_SCORE: 0.0627
HOTSPOT_PERCENTILE: 19
IROC_SCORE: 0.8419
IROC_PERCENTILE: 42
POISSON_SCORE: 0.1598
POISSON_PERCENTILE: 15

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

source_name: human post mortem brain region from a non Alzheimer's donor; Lib:XZ:20100924:13--ChIP:XZ:20100914:13:cingulate gyrus:H3K9Me3

value: Brain, Cingulate Gyrus

value: post-mortem

value: Cingulate Gyrus

value: Female

value: Primary Tissue

value: brain

value: Rush University Medical Center

value: Protein A-Sepharose 4B

value: 10 million cells

value: 70 ul bed volume

value: Abcam

value: Bioruptor


title: ChIP-Seq analysis of H3K27me3; ant. caudate cls; Lib:XZ:20100921:17--ChIP:XZ:20100914:17:anterior caudate

description:
sample_term_id: UBERON_0001873
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:XZ:20100921:17--ChIP:XZ:20100914:17:anterior caudate
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5656
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5936
****************
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: GSM669915_BI.Brain_Anterior_Caudate.H3K27me3.112.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100921:17--ChIP:XZ:20100914:17:anterior caudate.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Brain Anterior Caudate Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27me3 ChIP-Seq on Brain Anterior Caudate, Donor 112 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.6458
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 3

QUALITY SCORES:
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 52
FINDPEAKS_SCORE: 0.0085
FINDPEAKS_PERCENTILE: 10
HOTSPOT_SCORE: 0.0409
HOTSPOT_PERCENTILE: 5
IROC_SCORE: 0.8331
IROC_PERCENTILE: 25
POISSON_SCORE: 0.1575
POISSON_PERCENTILE: 10

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

ANALYSIS FILE NAME: GSM669915_BI.Brain_Anterior_Caudate.H3K27me3.112.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100921:17--ChIP:XZ:20100914:17:anterior caudate.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of Brain Anterior Caudate Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27me3 ChIP-Seq read mappings from Brain Anterior Caudate, Donor 112 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.6668
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 3
BROWSER_TRACK_NAME: BAC H3K27me3 12
BROWSER_TRACK_DESCRIPTION: BI Brain Anterior Caudate Histone H3K27me3 Donor 112 Library Lib:XZ:20100921:17--ChIP:XZ:20100914:17:anterior caudate. EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 52
FINDPEAKS_SCORE: 0.0085
FINDPEAKS_PERCENTILE: 10
HOTSPOT_SCORE: 0.0409
HOTSPOT_PERCENTILE: 5
IROC_SCORE: 0.8331
IROC_PERCENTILE: 25
POISSON_SCORE: 0.1575
POISSON_PERCENTILE: 10

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

source_name: human post mortem brain region from a non Alzheimer's donor; Lib:XZ:20100921:17--ChIP:XZ:20100914:17:anterior caudate

value: Brain, Anterior Caudate

value: Anterior Caudate

value: SDS lysis

value: Millipore

value: Histone H3K27me3


title: ChIP-Seq analysis of H3K9ac; inf. temp. lobe cls; Lib:XZ:20100924:19--ChIP:XZ:20100914:19:inferior temporal lobe:H3K9Ac

description:
sample_term_id: UBERON_0001871
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:XZ:20100924:19--ChIP:XZ:20100914:19:inferior temporal lobe:H3K9Ac
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5659
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5933
****************
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: GSM669918_BI.Brain_Inferior_Temporal_Lobe.H3K9ac.112.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100924:19--ChIP:XZ:20100914:19:inferior temporal lobe:H3K9Ac.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Brain Inferior Temporal Lobe Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9ac ChIP-Seq on Brain Inferior Temporal Lobe, Donor 112 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.6510
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 3

QUALITY SCORES:
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 40
FINDPEAKS_SCORE: 0.1726
FINDPEAKS_PERCENTILE: 68
HOTSPOT_SCORE: 0.232
HOTSPOT_PERCENTILE: 64
IROC_SCORE: 0.9891
IROC_PERCENTILE: 28
POISSON_SCORE: 0.3156
POISSON_PERCENTILE: 56

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

ANALYSIS FILE NAME: GSM669918_BI.Brain_Inferior_Temporal_Lobe.H3K9ac.112.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100924:19--ChIP:XZ:20100914:19:inferior temporal lobe:H3K9Ac.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of Brain Inferior Temporal Lobe Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9ac ChIP-Seq read mappings from Brain Inferior Temporal Lobe, Donor 112 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.6720
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 3
BROWSER_TRACK_NAME: BITL H3K9ac 12
BROWSER_TRACK_DESCRIPTION: BI Brain Inferior Temporal Lobe Histone H3K9ac Donor 112 Library Lib:XZ:20100924:19--ChIP:XZ:20100914:19:inferior temporal lobe:H3K9Ac EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 40
FINDPEAKS_SCORE: 0.1726
FINDPEAKS_PERCENTILE: 68
HOTSPOT_SCORE: 0.232
HOTSPOT_PERCENTILE: 64
IROC_SCORE: 0.9891
IROC_PERCENTILE: 28
POISSON_SCORE: 0.3156
POISSON_PERCENTILE: 56

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

source_name: human post mortem brain region from a non Alzheimer's donor; Lib:XZ:20100924:19--ChIP:XZ:20100914:19:inferior temporal lobe:H3K9Ac

value: Brain, Inferior Temporal Lobe

value: genomic DNA

value: Inferior Temporal Lobe

value: Histone H3K9ac


title: ChIP-Seq analysis of H3K4me1 in HUES48 cells; Lib:MC:20101025:07--ChIP:MC:20101020:07:ES cell HUES_48:H3K4Me1

description:
sample_term_id: NTR_0000848
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:MC:20101025:07--ChIP:MC:20101020:07:ES cell HUES_48:H3K4Me1
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5695
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5930
****************
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: GSM669954_BI.HUES48.H3K4me1.Lib_MC_20101025_07--ChIP_MC_20101020_07_ES_cell_HUES_48_H3K4Me1.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20101025:07--ChIP:MC:20101020:07:ES cell HUES_48:H3K4Me1.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of HUES48 Cell Line Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me1 ChIP-Seq on the HUES48 Cell Line, Library Lib:MC:20101025:07--ChIP:MC:20101020:07:ES cell HUES_48:H3K4Me1 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.6475
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 3

QUALITY SCORES:
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 50
FINDPEAKS_SCORE: 0.2547
FINDPEAKS_PERCENTILE: 36
HOTSPOT_SCORE: 0.3364
HOTSPOT_PERCENTILE: 39
IROC_SCORE: 0.9612
IROC_PERCENTILE: 39
POISSON_SCORE: 0.4983
POISSON_PERCENTILE: 43

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

ANALYSIS FILE NAME: GSM669954_BI.HUES48.H3K4me1.Lib_MC_20101025_07--ChIP_MC_20101020_07_ES_cell_HUES_48_H3K4Me1.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20101025:07--ChIP:MC:20101020:07:ES cell HUES_48:H3K4Me1.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of HUES48 Cell Line Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me1 ChIP-Seq read mappings from the HUES48 Cell Line, Library Lib:MC:20101025:07--ChIP:MC:20101020:07:ES cell HUES_48:H3K4Me1 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.6685
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 3
BROWSER_TRACK_NAME: HUES48 H3K4me1 e1
BROWSER_TRACK_DESCRIPTION: BI HUES48 Cell Line Histone H3K4me1 Library Lib:MC:20101025:07--ChIP:MC:20101020:07:ES cell HUES_48:H3K4Me1 EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 50
FINDPEAKS_SCORE: 0.2547
FINDPEAKS_PERCENTILE: 36
HOTSPOT_SCORE: 0.3364
HOTSPOT_PERCENTILE: 39
IROC_SCORE: 0.9612
IROC_PERCENTILE: 39
POISSON_SCORE: 0.4983
POISSON_PERCENTILE: 43

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

source_name: Harvard University Embryonic Stem Cells; Lib:MC:20101025:07--ChIP:MC:20101020:07:ES cell HUES_48:H3K4Me1

value: HUES48 stem cells

value: HUES48 Cell Line

value: embrionic stem cell

value: KSR

value: ES cell HUES_48-1

value: Cell Line

value: undifferentiated

value: Unknown

value: Harvard University

value: Histone H3K4me1


title: ChIP-Seq analysis of H3K36me3 in HUES64 cells; Lib:MC:20101025:03--ChIP:MC:20101020:03:ES cell HUES_64:H3K36Me3

description:
sample_term_id: NTR_0000853
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:MC:20101025:03--ChIP:MC:20101020:03:ES cell HUES_64:H3K36Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5673
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5931
****************
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: GSM669932_BI.HUES64.H3K36me3.Lib_MC_20101025_03--ChIP_MC_20101020_03_ES_cell_HUES_64_H3K36Me3.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20101025:03--ChIP:MC:20101020:03:ES cell HUES_64:H3K36Me3.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of HUES64 Cell Line Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K36me3 ChIP-Seq on the HUES64 Cell Line, Library Lib:MC:20101025:03--ChIP:MC:20101020:03:ES cell HUES_64:H3K36Me3 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.6496
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 3

QUALITY SCORES:
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 59
FINDPEAKS_SCORE: 0.3832
FINDPEAKS_PERCENTILE: 77
HOTSPOT_SCORE: 0.3406
HOTSPOT_PERCENTILE: 73
IROC_SCORE: 0.9952
IROC_PERCENTILE: 88
POISSON_SCORE: 0.5288
POISSON_PERCENTILE: 77

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

ANALYSIS FILE NAME: GSM669932_BI.HUES64.H3K36me3.Lib_MC_20101025_03--ChIP_MC_20101020_03_ES_cell_HUES_64_H3K36Me3.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20101025:03--ChIP:MC:20101020:03:ES cell HUES_64:H3K36Me3.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of HUES64 Cell Line Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K36me3 ChIP-Seq read mappings from the HUES64 Cell Line, Library Lib:MC:20101025:03--ChIP:MC:20101020:03:ES cell HUES_64:H3K36Me3 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.6706
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 3
BROWSER_TRACK_NAME: HUES64 H3K36me3 e3
BROWSER_TRACK_DESCRIPTION: BI HUES64 Cell Line Histone H3K36me3 Library Lib:MC:20101025:03--ChIP:MC:20101020:03:ES cell HUES_64:H3K36Me3 EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 59
FINDPEAKS_SCORE: 0.3832
FINDPEAKS_PERCENTILE: 77
HOTSPOT_SCORE: 0.3406
HOTSPOT_PERCENTILE: 73
IROC_SCORE: 0.9952
IROC_PERCENTILE: 88
POISSON_SCORE: 0.5288
POISSON_PERCENTILE: 77

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

source_name: Harvard University Embryonic Stem Cells; Lib:MC:20101025:03--ChIP:MC:20101020:03:ES cell HUES_64:H3K36Me3

value: HUES64 Cell Line

value: ES cell HUES_64-1

value: Protein A-Sepharose 4B

value: 10 million cells

value: SDS lysis

value: 70 ul bed volume

value: Abcam

value: Histone H3K36me3

value: Bioruptor


title: ChIP-Seq analysis of H3K27me3; hippocampus mid cls; Lib:XZ:20100921:11--ChIP:XZ:20100914:11:hippocampus middle:H3K27Me3

description:
sample_term_id: EFO_0000530
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:XZ:20100921:11--ChIP:XZ:20100914:11:hippocampus middle:H3K27Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5654
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5937
****************
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: GSM669913_BI.Brain_Hippocampus_Middle.H3K27me3.112.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100921:11--ChIP:XZ:20100914:11:hippocampus middle:H3K27Me3.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Brain Hippocampus Middle Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27me3 ChIP-Seq on Brain Hippocampus Middle, Donor 112 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.6476
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 3

QUALITY SCORES:
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 52
FINDPEAKS_SCORE: 0.0101
FINDPEAKS_PERCENTILE: 15
HOTSPOT_SCORE: 0.0628
HOTSPOT_PERCENTILE: 15
IROC_SCORE: 0.7857
IROC_PERCENTILE: 15
POISSON_SCORE: 0.1723
POISSON_PERCENTILE: 25

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

ANALYSIS FILE NAME: GSM669913_BI.Brain_Hippocampus_Middle.H3K27me3.112.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100921:11--ChIP:XZ:20100914:11:hippocampus middle:H3K27Me3.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of Brain Hippocampus Middle Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27me3 ChIP-Seq read mappings from Brain Hippocampus Middle, Donor 112 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.6686
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 3
BROWSER_TRACK_NAME: BHM H3K27me3 12
BROWSER_TRACK_DESCRIPTION: BI Brain Hippocampus Middle Histone H3K27me3 Donor 112 Library Lib:XZ:20100921:11--ChIP:XZ:20100914:11:hippocampus middle:H3K27Me3 EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 52
FINDPEAKS_SCORE: 0.0101
FINDPEAKS_PERCENTILE: 15
HOTSPOT_SCORE: 0.0628
HOTSPOT_PERCENTILE: 15
IROC_SCORE: 0.7857
IROC_PERCENTILE: 15
POISSON_SCORE: 0.1723
POISSON_PERCENTILE: 25

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

source_name: human post mortem brain region from a non Alzheimer's donor; Lib:XZ:20100921:11--ChIP:XZ:20100914:11:hippocampus middle:H3K27Me3

value: Brain, Hippocampus Middle

value: post-mortem

value: genomic DNA

value: Hippocampus Middle

value: Female

value: Primary Tissue

value: brain

value: Rush University Medical Center

value: Millipore

value: Histone H3K27me3


title: ChIP-Seq analysis of H3K36me3 in fetal lung cells; Lib:XZ:20100731:02--ChIP:XZ:20100726:02:fetal lung:H3K36Me3

description:
sample_term_id: UBERON_0002048
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:XZ:20100731:02--ChIP:XZ:20100726:02:fetal lung:H3K36Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5653
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5943
****************
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: GSM669912_BI.Fetal_Lung.H3K36me3.UW_H23284.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100731:02--ChIP:XZ:20100726:02:fetal lung:H3K36Me3.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Fetal Lung Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K36me3 ChIP-Seq on Fetal Lung, Donor UW H23284 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.6507
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 3

QUALITY SCORES:
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 59
FINDPEAKS_SCORE: 0.0876
FINDPEAKS_PERCENTILE: 23
HOTSPOT_SCORE: 0.1892
HOTSPOT_PERCENTILE: 27
IROC_SCORE: 0.9015
IROC_PERCENTILE: 19
POISSON_SCORE: 0.4148
POISSON_PERCENTILE: 42

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

ANALYSIS FILE NAME: GSM669912_BI.Fetal_Lung.H3K36me3.UW_H23284.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100731:02--ChIP:XZ:20100726:02:fetal lung:H3K36Me3.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Lung Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K36me3 ChIP-Seq read mappings from Fetal Lung, Donor UW H23284 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.6717
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 3
BROWSER_TRACK_NAME: FL H3K36me3 84
BROWSER_TRACK_DESCRIPTION: BI Fetal Lung Histone H3K36me3 Donor UW H23284 Library Lib:XZ:20100731:02--ChIP:XZ:20100726:02:fetal lung:H3K36Me3 EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 59
FINDPEAKS_SCORE: 0.0876
FINDPEAKS_PERCENTILE: 23
HOTSPOT_SCORE: 0.1892
HOTSPOT_PERCENTILE: 27
IROC_SCORE: 0.9015
IROC_PERCENTILE: 19
POISSON_SCORE: 0.4148
POISSON_PERCENTILE: 42

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

source_name: Primary fetal lung tissue; Lib:XZ:20100731:02--ChIP:XZ:20100726:02:fetal lung:H3K36Me3

value: Fetal Lung

value: surgery

value: Fetal lung

value: lung

value: UW

value: 96 days

value: Protein A-Sepharose 4B


title: ChIP-Seq analysis of H3K9ac; hippocampus mid cls; Lib:XZ:20100921:12--ChIP:XZ:20100914:12:hippocampus middle:H3K9Ac

description:
sample_term_id: EFO_0000530
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:XZ:20100921:12--ChIP:XZ:20100914:12:hippocampus middle:H3K9Ac
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5647
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5937
****************
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: GSM669906_BI.Brain_Hippocampus_Middle.H3K9ac.112.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100921:12--ChIP:XZ:20100914:12:hippocampus middle:H3K9Ac.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Brain Hippocampus Middle Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9ac ChIP-Seq on Brain Hippocampus Middle, Donor 112 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.6556
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 3

QUALITY SCORES:
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 40
FINDPEAKS_SCORE: 0.1722
FINDPEAKS_PERCENTILE: 64
HOTSPOT_SCORE: 0.2257
HOTSPOT_PERCENTILE: 48
IROC_SCORE: 0.9912
IROC_PERCENTILE: 40
POISSON_SCORE: 0.3179
POISSON_PERCENTILE: 60

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

ANALYSIS FILE NAME: GSM669906_BI.Brain_Hippocampus_Middle.H3K9ac.112.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100921:12--ChIP:XZ:20100914:12:hippocampus middle:H3K9Ac.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of Brain Hippocampus Middle Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9ac ChIP-Seq read mappings from Brain Hippocampus Middle, Donor 112 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.6766
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 3
BROWSER_TRACK_NAME: BHM H3K9ac 12
BROWSER_TRACK_DESCRIPTION: BI Brain Hippocampus Middle Histone H3K9ac Donor 112 Library Lib:XZ:20100921:12--ChIP:XZ:20100914:12:hippocampus middle:H3K9Ac EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 40
FINDPEAKS_SCORE: 0.1722
FINDPEAKS_PERCENTILE: 64
HOTSPOT_SCORE: 0.2257
HOTSPOT_PERCENTILE: 48
IROC_SCORE: 0.9912
IROC_PERCENTILE: 40
POISSON_SCORE: 0.3179
POISSON_PERCENTILE: 60

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

source_name: human post mortem brain region from a non Alzheimer's donor; Lib:XZ:20100921:12--ChIP:XZ:20100914:12:hippocampus middle:H3K9Ac

value: Brain, Hippocampus Middle

value: 10 million cells

value: SDS lysis

value: 70 ul bed volume

value: Abcam

value: Histone H3K9ac

value: Bioruptor


title: ChIP-Seq analysis of H3K4me1 in Cultured CD34 cells; Lib:RI:20101012:01--ChIP:MA:20100927:01:CD34 expanded:H3K4Me1

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: Lib:RI:20101012:01--ChIP:MA:20100927:01:CD34 expanded:H3K4Me1
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5648
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3896
****************
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: GSM669907_BI.CD34_Cultured_Cells.H3K4me1.123.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:RI:20101012:01--ChIP:MA:20100927:01:CD34 expanded:H3K4Me1.hg19.level.1.release.3
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 123 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.6577
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 3

QUALITY SCORES:
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 50
FINDPEAKS_SCORE: 0.3943
FINDPEAKS_PERCENTILE: 61
HOTSPOT_SCORE: 0.421
HOTSPOT_PERCENTILE: 57
IROC_SCORE: 0.9955
IROC_PERCENTILE: 71
POISSON_SCORE: 0.5144
POISSON_PERCENTILE: 54

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

ANALYSIS FILE NAME: GSM669907_BI.CD34_Cultured_Cells.H3K4me1.123.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:RI:20101012:01--ChIP:MA:20100927:01:CD34 expanded:H3K4Me1.hg19.level.2.release.3
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 123 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.6787
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 3
BROWSER_TRACK_NAME: CD34 H3K4me1 23
BROWSER_TRACK_DESCRIPTION: BI CD34 Cultured Cells Histone H3K4me1 Donor 123 Library Lib:RI:20101012:01--ChIP:MA:20100927:01:CD34 expanded:H3K4Me1 EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 50
FINDPEAKS_SCORE: 0.3943
FINDPEAKS_PERCENTILE: 61
HOTSPOT_SCORE: 0.421
HOTSPOT_PERCENTILE: 57
IROC_SCORE: 0.9955
IROC_PERCENTILE: 71
POISSON_SCORE: 0.5144
POISSON_PERCENTILE: 54

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

source_name: flow sorted CD34+ cells from cord blood expanded in short term culture; Lib:RI:20101012:01--ChIP:MA:20100927:01:CD34 expanded:H3K4Me1

value: CD34 Cultured Cells

value: genomic DNA

tag: markers

value: short term

value: cultured CD34

value: Unknown

value: Primary Cell

value: FHCRC

value: Histone H3K4me1


title: ChIP-Seq analysis of H3K4me3 in cingulate gyrus cells; Lib:XZ:20100924:09--ChIP:XZ:20100914:09:cingulate gyrus:H3K4Me3

description:
sample_term_id: UBERON_0002967
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:XZ:20100924:09--ChIP:XZ:20100914:09:cingulate gyrus:H3K4Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5646
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5934
****************
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: GSM669905_BI.Brain_Cingulate_Gyrus.H3K4me3.112.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100924:09--ChIP:XZ:20100914:09:cingulate gyrus:H3K4Me3.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Brain Cingulate Gyrus Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me3 ChIP-Seq on Brain Cingulate Gyrus, Donor 112 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.6481
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 3

QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.1888
FINDPEAKS_PERCENTILE: 20
HOTSPOT_SCORE: 0.2161
HOTSPOT_PERCENTILE: 20
IROC_SCORE: 0.9998
IROC_PERCENTILE: 88
POISSON_SCORE: 0.2513
POISSON_PERCENTILE: 16

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

ANALYSIS FILE NAME: GSM669905_BI.Brain_Cingulate_Gyrus.H3K4me3.112.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100924:09--ChIP:XZ:20100914:09:cingulate gyrus:H3K4Me3.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of Brain Cingulate Gyrus Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me3 ChIP-Seq read mappings from Brain Cingulate Gyrus, Donor 112 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.6691
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 3
BROWSER_TRACK_NAME: BCG H3K4me3 12
BROWSER_TRACK_DESCRIPTION: BI Brain Cingulate Gyrus Histone H3K4me3 Donor 112 Library Lib:XZ:20100924:09--ChIP:XZ:20100914:09:cingulate gyrus:H3K4Me3 EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.1888
FINDPEAKS_PERCENTILE: 20
HOTSPOT_SCORE: 0.2161
HOTSPOT_PERCENTILE: 20
IROC_SCORE: 0.9998
IROC_PERCENTILE: 88
POISSON_SCORE: 0.2513
POISSON_PERCENTILE: 16

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

source_name: human post mortem brain region from a non Alzheimer's donor; Lib:XZ:20100924:09--ChIP:XZ:20100914:09:cingulate gyrus:H3K4Me3

value: Brain, Cingulate Gyrus

value: post-mortem

value: Cingulate Gyrus

value: Female

value: Primary Tissue

value: brain

value: Rush University Medical Center

value: Millipore

value: Histone H3K4me3


title: ChIP-Seq analysis of H3K36me3 in HUES 6 cells; Lib:XZ:20101004:03--ChIP:XZ:20100930:03:ES cell HUES_6:H3K36Me3

description:
sample_term_id: NTR_0000841
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:XZ:20101004:03--ChIP:XZ:20100930:03:ES cell HUES_6:H3K36Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5627
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5642
****************
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: GSM669898_BI.HUES6.H3K36me3.Lib_XZ_20101004_03--ChIP_XZ_20100930_03_ES_cell_HUES_6_H3K36Me3.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20101004:03--ChIP:XZ:20100930:03:ES cell HUES_6:H3K36Me3.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of HUES6 Cell Line Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K36me3 ChIP-Seq on the HUES6 Cell Line, Library Lib:XZ:20101004:03--ChIP:XZ:20100930:03:ES cell HUES_6:H3K36Me3 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.6557
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 3

QUALITY SCORES:
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 59
FINDPEAKS_SCORE: 0.3749
FINDPEAKS_PERCENTILE: 73
HOTSPOT_SCORE: 0.3505
HOTSPOT_PERCENTILE: 81
IROC_SCORE: 0.9936
IROC_PERCENTILE: 81
POISSON_SCORE: 0.5284
POISSON_PERCENTILE: 73

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

ANALYSIS FILE NAME: GSM669898_BI.HUES6.H3K36me3.Lib_XZ_20101004_03--ChIP_XZ_20100930_03_ES_cell_HUES_6_H3K36Me3.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20101004:03--ChIP:XZ:20100930:03:ES cell HUES_6:H3K36Me3.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of HUES6 Cell Line Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K36me3 ChIP-Seq read mappings from the HUES6 Cell Line, Library Lib:XZ:20101004:03--ChIP:XZ:20100930:03:ES cell HUES_6:H3K36Me3 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.6767
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 3
BROWSER_TRACK_NAME: HUES6 H3K36me3 e3.1
BROWSER_TRACK_DESCRIPTION: BI HUES6 Cell Line Histone H3K36me3 Library Lib:XZ:20101004:03--ChIP:XZ:20100930:03:ES cell HUES_6:H3K36Me3 EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 59
FINDPEAKS_SCORE: 0.3749
FINDPEAKS_PERCENTILE: 73
HOTSPOT_SCORE: 0.3505
HOTSPOT_PERCENTILE: 81
IROC_SCORE: 0.9936
IROC_PERCENTILE: 81
POISSON_SCORE: 0.5284
POISSON_PERCENTILE: 73

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

source_name: Harvard University Embryonic Stem Cells; Lib:XZ:20101004:03--ChIP:XZ:20100930:03:ES cell HUES_6:H3K36Me3

value: HUES6 Cell Line

value: embrionic stem cell

value: KSR

value: HUES 6

value: ES cell HUES_6-1

value: Cell Line

value: undifferentiated

value: Harvard University

value: Protein A-Sepharose 4B

value: 10 million cells

value: SDS lysis

value: 70 ul bed volume

value: Abcam

value: Histone H3K36me3

value: Bioruptor


title: Bisulfite-Seq analysis of RRBS747 derived from human H9 cells; RRBS747

description:
sample_term_id: NTR_0000838
assay_term_id: OBI_0001862
nucleic_acid_term_id: SO_0000352
Design description: RRBS REMC Sequencing on Illumina
Library name: RRBS747
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.6032
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.6042
****************
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: GSM669901_BI.H9.RRBS.RRBS747-748.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RRBS747-RRBS748.hg19.level.2
ANALYSIS TITLE: Methylation Proportion Graphs of H9 Cell Line RRBS Data
ANALYSIS DESCRIPTION: Illumina RRBS read mappings from the H9 Cell Line, Libraries RRBS747-748 were processed into graphs of methylation proportions. Methylation proportions were calculated as (methylated calls / (methylated calls + unmethylated calls)) for all CpGs covered by at least 4 reads.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6841
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Reduced Representation Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19 MspI restriction fragments 40-220bp
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
GENOMIC_WINDOW: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 3
BROWSER_TRACK_NAME: H9 RRBS 47
BROWSER_TRACK_DESCRIPTION: BI H9 Cell Line RRBS Libraries RRBS747-748 EA Release 3
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 98.9

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

source_name: H9 (WA09) embryonic stem cells; NIH Approval # NIHhESC-10-0062; RRBS747

extract_protocol: Library construction protocol: Smith et al., Methods 48, 226-232

value: H9 Cell Line

value: 10% KOSR (Invitrogen)

value: genomic DNA

value: Female

value: 2x5hrs Epitect Kit

value: 20 ng

value: T4 Ligase (2,000U/ul) 16C o/n

value: 5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT

value: 5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT

value: Standard Protocol (Smith et al., Methods 48, 226-232)

value: DNA Methylation

value: Smith et al., Methods 48, 226-232

value: Gel size selection

value: Pfu Turbo Cx hot start


title: ChIP-Seq analysis of H3K9ac in WA-7 cells; Lib:MC:20100818:06--ChIP:MC:20100816:01:WA07:H3K9Ac

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: Lib:MC:20100818:06--ChIP:MC:20100816:01:WA07:H3K9Ac
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5625
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5643
****************
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: GSM669896_BI.ES-WA7.H3K9ac.Lib_MC_20100818_06--ChIP_MC_20100816_01_WA07_H3K9Ac.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100818:06--ChIP:MC:20100816:01:WA07:H3K9Ac.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of ES-WA7 Cell Line Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9ac ChIP-Seq on the ES-WA7 Cell Line, Library Lib:MC:20100818:06--ChIP:MC:20100816:01:WA07:H3K9Ac 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.6541
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 3

QUALITY SCORES:
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 40
FINDPEAKS_SCORE: 0.1709
FINDPEAKS_PERCENTILE: 56
HOTSPOT_SCORE: 0.2291
HOTSPOT_PERCENTILE: 60
IROC_SCORE: 0.9931
IROC_PERCENTILE: 56
POISSON_SCORE: 0.304
POISSON_PERCENTILE: 52

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

ANALYSIS FILE NAME: GSM669896_BI.ES-WA7.H3K9ac.Lib_MC_20100818_06--ChIP_MC_20100816_01_WA07_H3K9Ac.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100818:06--ChIP:MC:20100816:01:WA07:H3K9Ac.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of ES-WA7 Cell Line Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9ac ChIP-Seq read mappings from the ES-WA7 Cell Line, Library Lib:MC:20100818:06--ChIP:MC:20100816:01:WA07:H3K9Ac 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.6751
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 3
BROWSER_TRACK_NAME: ESWA7 H3K9ac Ac
BROWSER_TRACK_DESCRIPTION: BI ES-WA7 Cell Line Histone H3K9ac Library Lib:MC:20100818:06--ChIP:MC:20100816:01:WA07:H3K9Ac EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 40
FINDPEAKS_SCORE: 0.1709
FINDPEAKS_PERCENTILE: 56
HOTSPOT_SCORE: 0.2291
HOTSPOT_PERCENTILE: 60
IROC_SCORE: 0.9931
IROC_PERCENTILE: 56
POISSON_SCORE: 0.304
POISSON_PERCENTILE: 52

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

source_name: H7 (WA07) embryonic stem cells; NIH Approval # NIHhESC-10-0061; Lib:MC:20100818:06--ChIP:MC:20100816:01:WA07:H3K9Ac

value: ES-WA7 Cell Line

value: embrionic stem cell

value: KSR

value: Cell Line

value: undifferentiated

value: Unknown

value: Harvard University

value: Protein A-Sepharose 4B

value: 10 million cells

value: SDS lysis

value: 70 ul bed volume

value: Abcam

value: Histone H3K9ac


title: ChIP-Seq analysis of H3K9ac in HUES 6 cells; Lib:XZ:20101004:12--ChIP:XZ:20100930:12:ES cell HUES_6:H3K9Ac

description:
sample_term_id: NTR_0000841
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:XZ:20101004:12--ChIP:XZ:20100930:12:ES cell HUES_6:H3K9Ac
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5619
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5644
****************
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: GSM669890_BI.HUES6.H3K9ac.Lib_XZ_20101004_12--ChIP_XZ_20100930_12_ES_cell_HUES_6_H3K9Ac.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20101004:12--ChIP:XZ:20100930:12:ES cell HUES_6:H3K9Ac.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of HUES6 Cell Line Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9ac ChIP-Seq on the HUES6 Cell Line, Library Lib:XZ:20101004:12--ChIP:XZ:20100930:12:ES cell HUES_6:H3K9Ac 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.6598
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 3

QUALITY SCORES:
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 40
FINDPEAKS_SCORE: 0.361
FINDPEAKS_PERCENTILE: 80
HOTSPOT_SCORE: 0.4163
HOTSPOT_PERCENTILE: 92
IROC_SCORE: 0.9924
IROC_PERCENTILE: 48
POISSON_SCORE: 0.4477
POISSON_PERCENTILE: 88

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

ANALYSIS FILE NAME: GSM669890_BI.HUES6.H3K9ac.Lib_XZ_20101004_12--ChIP_XZ_20100930_12_ES_cell_HUES_6_H3K9Ac.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20101004:12--ChIP:XZ:20100930:12:ES cell HUES_6:H3K9Ac.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of HUES6 Cell Line Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9ac ChIP-Seq read mappings from the HUES6 Cell Line, Library Lib:XZ:20101004:12--ChIP:XZ:20100930:12:ES cell HUES_6:H3K9Ac 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.6808
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 3
BROWSER_TRACK_NAME: HUES6 H3K9ac Ac.2
BROWSER_TRACK_DESCRIPTION: BI HUES6 Cell Line Histone H3K9ac Library Lib:XZ:20101004:12--ChIP:XZ:20100930:12:ES cell HUES_6:H3K9Ac EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 40
FINDPEAKS_SCORE: 0.361
FINDPEAKS_PERCENTILE: 80
HOTSPOT_SCORE: 0.4163
HOTSPOT_PERCENTILE: 92
IROC_SCORE: 0.9924
IROC_PERCENTILE: 48
POISSON_SCORE: 0.4477
POISSON_PERCENTILE: 88

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

source_name: Harvard University Embryonic Stem Cells; Lib:XZ:20101004:12--ChIP:XZ:20100930:12:ES cell HUES_6:H3K9Ac

value: HUES6 Cell Line

value: genomic DNA

value: HUES 6

value: ES cell HUES_6-2

value: Bioruptor


title: ChIP-Seq analysis of H3K4me1 in HUES 6 cells; Lib:XZ:20101004:08--ChIP:XZ:20100930:08:ES cell HUES_6:H3K4Me1

description:
sample_term_id: NTR_0000841
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:XZ:20101004:08--ChIP:XZ:20100930:08:ES cell HUES_6:H3K4Me1
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5620
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5644
****************
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: GSM669891_BI.HUES6.H3K4me1.Lib_XZ_20101004_08--ChIP_XZ_20100930_08_ES_cell_HUES_6_H3K4Me1.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20101004:08--ChIP:XZ:20100930:08:ES cell HUES_6:H3K4Me1.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of HUES6 Cell Line Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me1 ChIP-Seq on the HUES6 Cell Line, Library Lib:XZ:20101004:08--ChIP:XZ:20100930:08:ES cell HUES_6:H3K4Me1 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.6477
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 3

QUALITY SCORES:
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 50
FINDPEAKS_SCORE: 0.36
FINDPEAKS_PERCENTILE: 57
HOTSPOT_SCORE: 0.4317
HOTSPOT_PERCENTILE: 61
IROC_SCORE: 0.9817
IROC_PERCENTILE: 57
POISSON_SCORE: 0.5852
POISSON_PERCENTILE: 71

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

ANALYSIS FILE NAME: GSM669891_BI.HUES6.H3K4me1.Lib_XZ_20101004_08--ChIP_XZ_20100930_08_ES_cell_HUES_6_H3K4Me1.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20101004:08--ChIP:XZ:20100930:08:ES cell HUES_6:H3K4Me1.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of HUES6 Cell Line Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me1 ChIP-Seq read mappings from the HUES6 Cell Line, Library Lib:XZ:20101004:08--ChIP:XZ:20100930:08:ES cell HUES_6:H3K4Me1 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.6687
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 3
BROWSER_TRACK_NAME: HUES6 H3K4me1 e1.2
BROWSER_TRACK_DESCRIPTION: BI HUES6 Cell Line Histone H3K4me1 Library Lib:XZ:20101004:08--ChIP:XZ:20100930:08:ES cell HUES_6:H3K4Me1 EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 50
FINDPEAKS_SCORE: 0.36
FINDPEAKS_PERCENTILE: 57
HOTSPOT_SCORE: 0.4317
HOTSPOT_PERCENTILE: 61
IROC_SCORE: 0.9817
IROC_PERCENTILE: 57
POISSON_SCORE: 0.5852
POISSON_PERCENTILE: 71

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

source_name: Harvard University Embryonic Stem Cells; Lib:XZ:20101004:08--ChIP:XZ:20100930:08:ES cell HUES_6:H3K4Me1

value: embrionic stem cell

value: Histone H3K4me1


title: ChIP-Seq analysis of H3K36me3 in HUES 6 cells; Lib:XZ:20101004:10--ChIP:XZ:20100930:10:ES cell HUES_6:H3K36Me3

description:
sample_term_id: NTR_0000841
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:XZ:20101004:10--ChIP:XZ:20100930:10:ES cell HUES_6:H3K36Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5621
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5644
****************
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: GSM669892_BI.HUES6.H3K36me3.Lib_XZ_20101004_10--ChIP_XZ_20100930_10_ES_cell_HUES_6_H3K36Me3.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20101004:10--ChIP:XZ:20100930:10:ES cell HUES_6:H3K36Me3.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of HUES6 Cell Line Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K36me3 ChIP-Seq on the HUES6 Cell Line, Library Lib:XZ:20101004:10--ChIP:XZ:20100930:10:ES cell HUES_6:H3K36Me3 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.6559
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 3

QUALITY SCORES:
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 59
FINDPEAKS_SCORE: 0.3411
FINDPEAKS_PERCENTILE: 69
HOTSPOT_SCORE: 0.3184
HOTSPOT_PERCENTILE: 62
IROC_SCORE: 0.9897
IROC_PERCENTILE: 58
POISSON_SCORE: 0.5132
POISSON_PERCENTILE: 69

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

ANALYSIS FILE NAME: GSM669892_BI.HUES6.H3K36me3.Lib_XZ_20101004_10--ChIP_XZ_20100930_10_ES_cell_HUES_6_H3K36Me3.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20101004:10--ChIP:XZ:20100930:10:ES cell HUES_6:H3K36Me3.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of HUES6 Cell Line Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K36me3 ChIP-Seq read mappings from the HUES6 Cell Line, Library Lib:XZ:20101004:10--ChIP:XZ:20100930:10:ES cell HUES_6:H3K36Me3 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.6769
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 3
BROWSER_TRACK_NAME: HUES6 H3K36me3 e3.2
BROWSER_TRACK_DESCRIPTION: BI HUES6 Cell Line Histone H3K36me3 Library Lib:XZ:20101004:10--ChIP:XZ:20100930:10:ES cell HUES_6:H3K36Me3 EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 59
FINDPEAKS_SCORE: 0.3411
FINDPEAKS_PERCENTILE: 69
HOTSPOT_SCORE: 0.3184
HOTSPOT_PERCENTILE: 62
IROC_SCORE: 0.9897
IROC_PERCENTILE: 58
POISSON_SCORE: 0.5132
POISSON_PERCENTILE: 69

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

source_name: Harvard University Embryonic Stem Cells; Lib:XZ:20101004:10--ChIP:XZ:20100930:10:ES cell HUES_6:H3K36Me3

value: KSR

value: Cell Line

value: Histone H3K36me3


city: San Francisco

first: UCSF-UBC

last: CENTER

state: CA

address: UCSF-UBC

institute: UCSF-UBC

description:
design description: RNA-Seq analysis of breast progenitor enriched cell from RM080 (A01031) using Illumina Genome Analyzer IIx
library name: A01031
EXPERIMENT_TYPE: mRNA-Seq
EXTRACTION_PROTOCOL: Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instructions.
LIBRARY_GENERATION_PCR_POLYMERASE_TYPE: Phusion
LIBRARY_GENERATION_PCR_THERMOCYCLING_PROGRAM: 98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold
LIBRARY_GENERATION_PCR_NUMBER_CYCLES: 15
LIBRARY_GENERATION_PCR_F_PRIMER_SEQUENCE: AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT
LIBRARY_GENERATION_PCR_R_PRIMER_SEQUENCE: CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT
LIBRARY_GENERATION_PCR_PRIMER_CONC: 0.5 uM
LIBRARY_GENERATION_PCR_PRODUCT_ISOLATION_PROTOCOL: 8% Novex TBE PAGE gel purification
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PRIMER_SEQUENCE: NNNNNN
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PROTOCOL: Invitrogen Superscript II RT
LIBRARY_GENERATION_PCR_TEMPLATE: cDNA
EXTRACTION_PROTOCOL_MRNA_ENRICHMENT: Purification of polyA+ mRNA using MultiMACS 96 Separation Unit
RNA_PREPARATION_INITIAL_RNA_QLTY: RIN 7.3
RNA_PREPARATION_INITIAL_RNA_QNTY: N/A
LIBRARY_FRAGMENTATION: COVARIS E210
LIBRARY_FRAGMENT_SIZE_RANGE: 233-440 bp
****************
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: transcriptomic

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

ANALYSIS FILE NAME: GSM669622_UCSF-UBC.Breast_Stem_Cells.mRNA-Seq.RM080.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A01031-1.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Breast Stem Cells mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by mRNA-Seq on Breast Stem Cells, Donor RM080 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.6318
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: mRNA-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: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 3

QUALITY SCORES:
NUMBER_OF_MRNA-SEQ_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 7
PERCENT_READS_MAPPING_TO_UCSC_GENES: 88.4
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 14

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

ANALYSIS FILE NAME: GSM669622_UCSF-UBC.Breast_Stem_Cells.mRNA-Seq.RM080.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A01031-1.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of Breast Stem Cells mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina mRNA-Seq read mappings from Breast Stem Cells, Donor RM080 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.6325
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 3
BROWSER_TRACK_NAME: BSC mRNA 80
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Breast Stem Cells mRNA-Seq Donor RM080 Library A01031-1 EA Release 3

QUALITY SCORES:
NUMBER_OF_MRNA-SEQ_EXPERIMENTS_SCORED: 7
PERCENT_READS_MAPPING_TO_UCSC_GENES: 88.4
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 14

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

molecule: total RNA

extract_protocol: library construction protocol: Refer to document 'Strand Specific 96-well Library Construction for Illumina Sequencing' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)

tag: submitted sample id

value: female

tag: body site

value: Breast

tag: histological type

value: Progenitor enriched cell

tag: is tumor

value: No

value: primary cell

value: breast progenitor enriched cell