title: ChIP-Seq analysis of H3K36me3; mid frontal lobe cls; Lib:XZ:20100924:03--ChIP:XZ:20100914:03:mid frontal lobe:H3K36Me3

description:
sample_term_id: UBERON_0006483
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:XZ:20100924:03--ChIP:XZ:20100914:03:mid frontal lobe:H3K36Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5723
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5939
****************
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: GSM669982_BI.Brain_Mid_Frontal_Lobe.H3K36me3.112.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100924:03--ChIP:XZ:20100914:03:mid frontal lobe:H3K36Me3.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Brain Mid Frontal Lobe Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K36me3 ChIP-Seq on Brain Mid Frontal 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.6471
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: 0.0536
FINDPEAKS_PERCENTILE: 12
HOTSPOT_SCORE: 0.1489
HOTSPOT_PERCENTILE: 12
IROC_SCORE: 0.89
IROC_PERCENTILE: 15
POISSON_SCORE: 0.298
POISSON_PERCENTILE: 12

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

ANALYSIS FILE NAME: GSM669982_BI.Brain_Mid_Frontal_Lobe.H3K36me3.112.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100924:03--ChIP:XZ:20100914:03:mid frontal lobe:H3K36Me3.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of Brain Mid Frontal Lobe Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K36me3 ChIP-Seq read mappings from Brain Mid Frontal 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.6681
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: BMFL H3K36me3 12
BROWSER_TRACK_DESCRIPTION: BI Brain Mid Frontal Lobe Histone H3K36me3 Donor 112 Library Lib:XZ:20100924:03--ChIP:XZ:20100914:03:mid frontal lobe:H3K36Me3 EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 59
FINDPEAKS_SCORE: 0.0536
FINDPEAKS_PERCENTILE: 12
HOTSPOT_SCORE: 0.1489
HOTSPOT_PERCENTILE: 12
IROC_SCORE: 0.89
IROC_PERCENTILE: 15
POISSON_SCORE: 0.298
POISSON_PERCENTILE: 12

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

source_name: human post mortem brain region from a non Alzheimer's donor; Lib:XZ:20100924:03--ChIP:XZ:20100914:03:mid frontal lobe:H3K36Me3

value: Brain, Mid Frontal Lobe

value: Mid Frontal Lobe

value: Female

value: Primary Tissue

value: Protein A-Sepharose 4B

value: 10 million cells

value: 70 ul bed volume


title: ChIP-Seq analysis of H3K9ac; substantia nigra cells; Lib:XZ:20100921:05--ChIP:XZ:20100914:05:substantia nigra: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_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:20100921:05--ChIP:XZ:20100914:05:substantia nigra:H3K9Ac
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5718
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
****************

library_source: genomic

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

ANALYSIS FILE NAME: GSM669977_BI.Brain_Substantia_Nigra.H3K9ac.112.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100921:05--ChIP:XZ:20100914:05:substantia nigra:H3K9Ac.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Brain Substantia Nigra Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9ac 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.6562
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: 0.1534
FINDPEAKS_PERCENTILE: 44
HOTSPOT_SCORE: 0.2078
HOTSPOT_PERCENTILE: 36
IROC_SCORE: 0.9887
IROC_PERCENTILE: 20
POISSON_SCORE: 0.2985
POISSON_PERCENTILE: 48

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

ANALYSIS FILE NAME: GSM669977_BI.Brain_Substantia_Nigra.H3K9ac.112.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100921:05--ChIP:XZ:20100914:05:substantia nigra:H3K9Ac.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of Brain Substantia Nigra Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9ac 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.6772
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 H3K9ac 12
BROWSER_TRACK_DESCRIPTION: BI Brain Substantia Nigra Histone H3K9ac Donor 112 Library Lib:XZ:20100921:05--ChIP:XZ:20100914:05:substantia nigra:H3K9Ac EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 40
FINDPEAKS_SCORE: 0.1534
FINDPEAKS_PERCENTILE: 44
HOTSPOT_SCORE: 0.2078
HOTSPOT_PERCENTILE: 36
IROC_SCORE: 0.9887
IROC_PERCENTILE: 20
POISSON_SCORE: 0.2985
POISSON_PERCENTILE: 48

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

molecule: genomic DNA

organism: Homo sapiens

source_name: human post mortem brain region from a non Alzheimer's donor; Lib:XZ:20100921:05--ChIP:XZ:20100914:05:substantia nigra:H3K9Ac

extract_protocol: Library construction protocol: Single read - Illumina

tag: sample alias

tag: sample common name

value: Brain, Substantia Nigra

value: post-mortem

tag: molecule

value: genomic DNA

tag: disease

value: Substantia Nigra

value: brain

value: Rush University Medical Center

value: SDS lysis

value: Abcam

value: Histone H3K9ac

value: Bioruptor


title: ChIP-Seq analysis of H3K9me3; ant. caudate cls; Lib:XZ:20100921:20--ChIP:XZ:20100914:20:anterior caudate :H3K9Me3

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:20100921:20--ChIP:XZ:20100914:20:anterior caudate :H3K9Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5735
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: GSM669994_BI.Brain_Anterior_Caudate.H3K9me3.112.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100921:20--ChIP:XZ:20100914:20:anterior caudate :H3K9Me3.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Brain Anterior Caudate Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9me3 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.6486
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: 0.0254
FINDPEAKS_PERCENTILE: 31
HOTSPOT_SCORE: 0.0818
HOTSPOT_PERCENTILE: 31
IROC_SCORE: 0.8004
IROC_PERCENTILE: 31
POISSON_SCORE: 0.2092
POISSON_PERCENTILE: 31

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

ANALYSIS FILE NAME: GSM669994_BI.Brain_Anterior_Caudate.H3K9me3.112.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100921:20--ChIP:XZ:20100914:20:anterior caudate :H3K9Me3.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of Brain Anterior Caudate Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9me3 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.6696
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 H3K9me3 12
BROWSER_TRACK_DESCRIPTION: BI Brain Anterior Caudate Histone H3K9me3 Donor 112 Library Lib:XZ:20100921:20--ChIP:XZ:20100914:20:anterior caudate :H3K9Me3 EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 60
FINDPEAKS_SCORE: 0.0254
FINDPEAKS_PERCENTILE: 31
HOTSPOT_SCORE: 0.0818
HOTSPOT_PERCENTILE: 31
IROC_SCORE: 0.8004
IROC_PERCENTILE: 31
POISSON_SCORE: 0.2092
POISSON_PERCENTILE: 31

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

source_name: human post mortem brain region from a non Alzheimer's donor; Lib:XZ:20100921:20--ChIP:XZ:20100914:20:anterior caudate :H3K9Me3

value: Brain, Anterior Caudate

value: Anterior Caudate

value: Histone H3K9me3


title: E15.5_whole_mouse_brain

status: Public on Apr 05 2011

city: UPM Serdang

first: King

middle: Hwa

last: Ling

state: Selangor Darul Ehsan

address: Faculty of Medicine and Health Sciences

department: Department of Obstetrics and Gynaecology

country: Malaysia

institute: Universiti Putra Malaysia

library_source: transcriptomic

data_processing: Image data was generated by the Genome Analyzer II and was processed using the Illumina pipeline software (Pipeline version 1.0 was used for the FASTQ data). This consists of an image analysis module (Firecrest), followed by basecalling using the BUSTARD module and finally production of a data file in FASTQ format using the GERALD module. The FASTQ data was ranked according to decreasing abundance of the unique tags. This file was created using a PERL script in Linux without taking into consideration any filters (adapter sequences) or quality.

molecule: total RNA

organism: Mus musculus

source_name: Whole brain, E15.5

growth_protocol: A pregnant mouse was bred under a 12-hour light and 12-hour dark cycle with access to unlimited food and water. Embryos were removed after 15.5 days (E15.5) of pregnancy. The developing whole brain was dissected from one of the embryos for total RNA extraction.

extract_protocol: Total RNA was isolated from a whole brain dissected from an E15.5 embryo of C57BL/6 background using TRIzol reagent (Invitrogen) according to the manufacturer’s protocol. Small RNAs with sizes ranging from 16-30nt were isolated from 10μg total RNA using polyacrylamide gel electrophoresis. The complementary small RNA library was constructed using the Small RNA Sample Prep Kit version 1.0 (Illumina) according to the manufacturer's protocol with 5’-GTTCAGAGTT CTACAGTCCG ACGATC-3’ and 5’- TCGTATGCCG TCTTCTGCTT GT-3’ adapters at the 5’ and 3’ ends, respectively.

treatment_protocol: No treatment.

tag: strain

tag: tissue

value: whole brain

tag: developmental stage

value: embryonic day 15.5


title: ChIP-Seq analysis of H3K4me1; hippocampus mid cls; Lib:XZ:20100921:08--ChIP:XZ:20100914:08:hippocampus middle:H3K4Me1

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:20100921:08--ChIP:XZ:20100914:08:hippocampus middle:H3K4Me1
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5703
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: GSM669962_BI.Brain_Hippocampus_Middle.H3K4me1.112.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100921:08--ChIP:XZ:20100914:08:hippocampus middle:H3K4Me1.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Brain Hippocampus Middle Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me1 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.6581
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: 0.1132
FINDPEAKS_PERCENTILE: 21
HOTSPOT_SCORE: 0.2108
HOTSPOT_PERCENTILE: 21
IROC_SCORE: 0.9181
IROC_PERCENTILE: 18
POISSON_SCORE: 0.3721
POISSON_PERCENTILE: 14

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

ANALYSIS FILE NAME: GSM669962_BI.Brain_Hippocampus_Middle.H3K4me1.112.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100921:08--ChIP:XZ:20100914:08:hippocampus middle:H3K4Me1.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of Brain Hippocampus Middle Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me1 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.6791
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 H3K4me1 12
BROWSER_TRACK_DESCRIPTION: BI Brain Hippocampus Middle Histone H3K4me1 Donor 112 Library Lib:XZ:20100921:08--ChIP:XZ:20100914:08:hippocampus middle:H3K4Me1 EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 50
FINDPEAKS_SCORE: 0.1132
FINDPEAKS_PERCENTILE: 21
HOTSPOT_SCORE: 0.2108
HOTSPOT_PERCENTILE: 21
IROC_SCORE: 0.9181
IROC_PERCENTILE: 18
POISSON_SCORE: 0.3721
POISSON_PERCENTILE: 14

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

source_name: human post mortem brain region from a non Alzheimer's donor; Lib:XZ:20100921:08--ChIP:XZ:20100914:08:hippocampus middle:H3K4Me1

value: Brain, Hippocampus Middle

value: Hippocampus Middle

value: Female

value: Primary Tissue

value: Protein A-Sepharose 4B

value: 10 million cells

value: Histone H3K4me1


title: ChIP-Seq analysis of H3K9me3; substantia nigra cells; Lib:XZ:20100921:06--ChIP:XZ:20100914:06:substantia nigra:H3K9Me3

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:20100921:06--ChIP:XZ:20100914:06:substantia nigra:H3K9Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5714
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: GSM669973_BI.Brain_Substantia_Nigra.H3K9me3.112.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100921:06--ChIP:XZ:20100914:06:substantia nigra:H3K9Me3.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Brain Substantia Nigra Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9me3 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.6495
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: 0.0186
FINDPEAKS_PERCENTILE: 12
HOTSPOT_SCORE: 0.0589
HOTSPOT_PERCENTILE: 15
IROC_SCORE: 0.8724
IROC_PERCENTILE: 54
POISSON_SCORE: 0.1508
POISSON_PERCENTILE: 12

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

ANALYSIS FILE NAME: GSM669973_BI.Brain_Substantia_Nigra.H3K9me3.112.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100921:06--ChIP:XZ:20100914:06:substantia nigra:H3K9Me3.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of Brain Substantia Nigra Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9me3 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.6705
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 H3K9me3 12
BROWSER_TRACK_DESCRIPTION: BI Brain Substantia Nigra Histone H3K9me3 Donor 112 Library Lib:XZ:20100921:06--ChIP:XZ:20100914:06:substantia nigra:H3K9Me3 EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 60
FINDPEAKS_SCORE: 0.0186
FINDPEAKS_PERCENTILE: 12
HOTSPOT_SCORE: 0.0589
HOTSPOT_PERCENTILE: 15
IROC_SCORE: 0.8724
IROC_PERCENTILE: 54
POISSON_SCORE: 0.1508
POISSON_PERCENTILE: 12

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

source_name: human post mortem brain region from a non Alzheimer's donor; Lib:XZ:20100921:06--ChIP:XZ:20100914:06:substantia nigra:H3K9Me3

value: Brain, Substantia Nigra

value: post-mortem

value: genomic DNA

value: Substantia Nigra

value: brain

value: Rush University Medical Center

value: 70 ul bed volume


title: ChIP-Seq analysis of H3K9ac in HUES64 cells; Lib:MC:20101025:05--ChIP:MC:20101020:05:ES cell HUES_64:H3K9Ac

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:20101025:05--ChIP:MC:20101020:05:ES cell HUES_64:H3K9Ac
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5704
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: GSM669963_BI.HUES64.H3K9ac.Lib_MC_20101025_05--ChIP_MC_20101020_05_ES_cell_HUES_64_H3K9Ac.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20101025:05--ChIP:MC:20101020:05:ES cell HUES_64:H3K9Ac.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of HUES64 Cell Line Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9ac ChIP-Seq on the HUES64 Cell Line, Library Lib:MC:20101025:05--ChIP:MC:20101020:05:ES cell HUES_64: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.6526
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: 0.1559
FINDPEAKS_PERCENTILE: 48
HOTSPOT_SCORE: 0.2265
HOTSPOT_PERCENTILE: 52
IROC_SCORE: 0.9947
IROC_PERCENTILE: 64
POISSON_SCORE: 0.2795
POISSON_PERCENTILE: 32

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

ANALYSIS FILE NAME: GSM669963_BI.HUES64.H3K9ac.Lib_MC_20101025_05--ChIP_MC_20101020_05_ES_cell_HUES_64_H3K9Ac.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20101025:05--ChIP:MC:20101020:05:ES cell HUES_64:H3K9Ac.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of HUES64 Cell Line Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9ac ChIP-Seq read mappings from the HUES64 Cell Line, Library Lib:MC:20101025:05--ChIP:MC:20101020:05:ES cell HUES_64: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.6736
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 H3K9ac Ac
BROWSER_TRACK_DESCRIPTION: BI HUES64 Cell Line Histone H3K9ac Library Lib:MC:20101025:05--ChIP:MC:20101020:05:ES cell HUES_64:H3K9Ac EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 40
FINDPEAKS_SCORE: 0.1559
FINDPEAKS_PERCENTILE: 48
HOTSPOT_SCORE: 0.2265
HOTSPOT_PERCENTILE: 52
IROC_SCORE: 0.9947
IROC_PERCENTILE: 64
POISSON_SCORE: 0.2795
POISSON_PERCENTILE: 32

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

source_name: Harvard University Embryonic Stem Cells; Lib:MC:20101025:05--ChIP:MC:20101020:05:ES cell HUES_64:H3K9Ac

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: SDS lysis

value: Abcam

value: Histone H3K9ac

value: Bioruptor


title: ChIP-Seq analysis of H3K4me1 in fetal lung cells; Lib:XZ:20100731:05--ChIP:XZ:20100726:05:fetal lung:H3K4Me1

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:20100731:05--ChIP:XZ:20100726:05:fetal lung:H3K4Me1
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5710
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5929
****************
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: GSM669969_BI.Fetal_Lung.H3K4me1.UW_H23266.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100731:05--ChIP:XZ:20100726:05:fetal lung:H3K4Me1.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Fetal Lung Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me1 ChIP-Seq on Fetal Lung, Donor UW H23266 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.6524
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: 0.41
FINDPEAKS_PERCENTILE: 64
HOTSPOT_SCORE: 0.4642
HOTSPOT_PERCENTILE: 71
IROC_SCORE: 0.9895
IROC_PERCENTILE: 61
POISSON_SCORE: 0.5819
POISSON_PERCENTILE: 68

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

ANALYSIS FILE NAME: GSM669969_BI.Fetal_Lung.H3K4me1.UW_H23266.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100731:05--ChIP:XZ:20100726:05:fetal lung:H3K4Me1.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Lung Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me1 ChIP-Seq read mappings from Fetal Lung, Donor UW H23266 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.6734
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 H3K4me1 66
BROWSER_TRACK_DESCRIPTION: BI Fetal Lung Histone H3K4me1 Donor UW H23266 Library Lib:XZ:20100731:05--ChIP:XZ:20100726:05:fetal lung:H3K4Me1 EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 50
FINDPEAKS_SCORE: 0.41
FINDPEAKS_PERCENTILE: 64
HOTSPOT_SCORE: 0.4642
HOTSPOT_PERCENTILE: 71
IROC_SCORE: 0.9895
IROC_PERCENTILE: 61
POISSON_SCORE: 0.5819
POISSON_PERCENTILE: 68

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

source_name: Primary fetal lung tissue; Lib:XZ:20100731:05--ChIP:XZ:20100726:05:fetal lung:H3K4Me1

value: Fetal Lung

value: surgery

value: genomic DNA

value: Fetal lung

value: Female

value: Primary Tissue

value: lung

value: UW

value: 85 days

value: Protein A-Sepharose 4B

value: 10 million cells

value: Histone H3K4me1


title: ChIP-Seq analysis of H3K36me3 in Cultured CD34 cells; Lib:RI:20101012:05--ChIP:MA:20100927:05:CD34 expanded:H3K36Me3

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:20101012:05--ChIP:MA:20100927:05:CD34 expanded:H3K36Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5696
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: GSM669955_BI.CD34_Cultured_Cells.H3K36me3.123.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:RI:20101012:05--ChIP:MA:20100927:05:CD34 expanded:H3K36Me3.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of CD34 Cultured Cells Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K36me3 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.6579
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: 0.4564
FINDPEAKS_PERCENTILE: 92
HOTSPOT_SCORE: 0.3843
HOTSPOT_PERCENTILE: 92
IROC_SCORE: 0.9961
IROC_PERCENTILE: 92
POISSON_SCORE: 0.605
POISSON_PERCENTILE: 92

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

ANALYSIS FILE NAME: GSM669955_BI.CD34_Cultured_Cells.H3K36me3.123.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:RI:20101012:05--ChIP:MA:20100927:05:CD34 expanded:H3K36Me3.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of CD34 Cultured Cells Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K36me3 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.6789
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 H3K36me3 23
BROWSER_TRACK_DESCRIPTION: BI CD34 Cultured Cells Histone H3K36me3 Donor 123 Library Lib:RI:20101012:05--ChIP:MA:20100927:05:CD34 expanded:H3K36Me3 EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 59
FINDPEAKS_SCORE: 0.4564
FINDPEAKS_PERCENTILE: 92
HOTSPOT_SCORE: 0.3843
HOTSPOT_PERCENTILE: 92
IROC_SCORE: 0.9961
IROC_PERCENTILE: 92
POISSON_SCORE: 0.605
POISSON_PERCENTILE: 92

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

source_name: flow sorted CD34+ cells from cord blood expanded in short term culture; Lib:RI:20101012:05--ChIP:MA:20100927:05:CD34 expanded:H3K36Me3

value: CD34 Cultured Cells

tag: markers

value: short term

value: cultured CD34

value: Unknown

value: Primary Cell

value: FHCRC

value: 70 ul bed volume

value: Histone H3K36me3


title: ChIP-Seq analysis of WCE in mid frontal lobe cells; Lib:XZ:20100924:07--ChIP:XZ:20100914:07:mid frontal lobe:WCE

description:
sample_term_id: UBERON_0006483
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:XZ:20100924:07--ChIP:XZ:20100914:07:mid frontal lobe:WCE
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5701
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5939
****************
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: GSM669960_BI.Brain_Mid_Frontal_Lobe.Input.112.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100924:07--ChIP:XZ:20100914:07:mid frontal lobe:WCE.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Brain Mid Frontal Lobe ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on Brain Mid Frontal 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.6536
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: 0.0064
FINDPEAKS_PERCENTILE: 40
HOTSPOT_SCORE: 0.0042
HOTSPOT_PERCENTILE: 7
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.0232
POISSON_PERCENTILE: 3

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

ANALYSIS FILE NAME: GSM669960_BI.Brain_Mid_Frontal_Lobe.Input.112.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100924:07--ChIP:XZ:20100914:07:mid frontal lobe:WCE.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of Brain Mid Frontal Lobe ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from Brain Mid Frontal 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.6746
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: BMFL Input 12
BROWSER_TRACK_DESCRIPTION: BI Brain Mid Frontal Lobe ChIP-Seq Input Donor 112 Library Lib:XZ:20100924:07--ChIP:XZ:20100914:07:mid frontal lobe:WCE EA Release 3

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 61
FINDPEAKS_SCORE: 0.0064
FINDPEAKS_PERCENTILE: 40
HOTSPOT_SCORE: 0.0042
HOTSPOT_PERCENTILE: 7
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.0232
POISSON_PERCENTILE: 3

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

source_name: human post mortem brain region from a non Alzheimer's donor; Lib:XZ:20100924:07--ChIP:XZ:20100914:07:mid frontal lobe:WCE

value: Brain, Mid Frontal Lobe

value: post-mortem

value: genomic DNA

value: Mid Frontal Lobe

value: brain

value: Rush University Medical Center

value: standard

value: SDS lysis

value: ChIP-Seq Input

value: Input

value: Bioruptor


title: ChIP-Seq analysis of WCE; hippocampus mid cls; Lib:XZ:20100921:14--ChIP:XZ:20100914:14:hippocampus middle:WCE

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:20100921:14--ChIP:XZ:20100914:14:hippocampus middle:WCE
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5712
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: GSM669971_BI.Brain_Hippocampus_Middle.Input.112.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100921:14--ChIP:XZ:20100914:14:hippocampus middle:WCE.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Brain Hippocampus Middle ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input 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.6503
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: 0.0062
FINDPEAKS_PERCENTILE: 33
HOTSPOT_SCORE: 0.0047
HOTSPOT_PERCENTILE: 20
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.0249
POISSON_PERCENTILE: 13

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

ANALYSIS FILE NAME: GSM669971_BI.Brain_Hippocampus_Middle.Input.112.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100921:14--ChIP:XZ:20100914:14:hippocampus middle:WCE.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of Brain Hippocampus Middle ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input 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.6713
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 Input 12
BROWSER_TRACK_DESCRIPTION: BI Brain Hippocampus Middle ChIP-Seq Input Donor 112 Library Lib:XZ:20100921:14--ChIP:XZ:20100914:14:hippocampus middle:WCE EA Release 3

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 61
FINDPEAKS_SCORE: 0.0062
FINDPEAKS_PERCENTILE: 33
HOTSPOT_SCORE: 0.0047
HOTSPOT_PERCENTILE: 20
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.0249
POISSON_PERCENTILE: 13

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

source_name: human post mortem brain region from a non Alzheimer's donor; Lib:XZ:20100921:14--ChIP:XZ:20100914:14:hippocampus middle:WCE

value: Brain, Hippocampus Middle

value: Hippocampus Middle

value: Female

value: Primary Tissue


title: ChIP-Seq analysis of H3K27me3; substantia nigra cells; Lib:XZ:20100921:04--ChIP:XZ:20100914:04:substantia nigra:H3K27Me3

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:20100921:04--ChIP:XZ:20100914:04:substantia nigra:H3K27Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5694
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: GSM669953_BI.Brain_Substantia_Nigra.H3K27me3.112.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100921:04--ChIP:XZ:20100914:04:substantia nigra:H3K27Me3.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Brain Substantia Nigra Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27me3 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.6483
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: 0.0066
FINDPEAKS_PERCENTILE: 5
HOTSPOT_SCORE: 0.0432
HOTSPOT_PERCENTILE: 10
IROC_SCORE: 0.8099
IROC_PERCENTILE: 20
POISSON_SCORE: 0.1401
POISSON_PERCENTILE: 5

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

ANALYSIS FILE NAME: GSM669953_BI.Brain_Substantia_Nigra.H3K27me3.112.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100921:04--ChIP:XZ:20100914:04:substantia nigra:H3K27Me3.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of Brain Substantia Nigra Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27me3 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.6693
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 H3K27me3 12
BROWSER_TRACK_DESCRIPTION: BI Brain Substantia Nigra Histone H3K27me3 Donor 112 Library Lib:XZ:20100921:04--ChIP:XZ:20100914:04:substantia nigra:H3K27Me3 EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 52
FINDPEAKS_SCORE: 0.0066
FINDPEAKS_PERCENTILE: 5
HOTSPOT_SCORE: 0.0432
HOTSPOT_PERCENTILE: 10
IROC_SCORE: 0.8099
IROC_PERCENTILE: 20
POISSON_SCORE: 0.1401
POISSON_PERCENTILE: 5

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

source_name: human post mortem brain region from a non Alzheimer's donor; Lib:XZ:20100921:04--ChIP:XZ:20100914:04:substantia nigra:H3K27Me3

value: Brain, Substantia Nigra

value: Substantia Nigra

value: Protein A-Sepharose 4B

value: 10 million cells

value: 70 ul bed volume

value: Millipore

value: Histone H3K27me3


title: ChIP-Seq analysis of H3K9me3 in mid frontal lobe cells; Lib:XZ:20100924:06--ChIP:XZ:20100914:06:mid frontal lobe:H3K9Me3

description:
sample_term_id: UBERON_0006483
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:XZ:20100924:06--ChIP:XZ:20100914:06:mid frontal lobe:H3K9Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5706
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5939
****************
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: GSM669965_BI.Brain_Mid_Frontal_Lobe.H3K9me3.112.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100924:06--ChIP:XZ:20100914:06:mid frontal lobe:H3K9Me3.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Brain Mid Frontal Lobe Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9me3 ChIP-Seq on Brain Mid Frontal 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.6518
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: 0.0209
FINDPEAKS_PERCENTILE: 23
HOTSPOT_SCORE: 0.0675
HOTSPOT_PERCENTILE: 23
IROC_SCORE: 0.8191
IROC_PERCENTILE: 38
POISSON_SCORE: 0.1686
POISSON_PERCENTILE: 19

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

ANALYSIS FILE NAME: GSM669965_BI.Brain_Mid_Frontal_Lobe.H3K9me3.112.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100924:06--ChIP:XZ:20100914:06:mid frontal lobe:H3K9Me3.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of Brain Mid Frontal Lobe Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9me3 ChIP-Seq read mappings from Brain Mid Frontal 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.6728
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: BMFL H3K9me3 12
BROWSER_TRACK_DESCRIPTION: BI Brain Mid Frontal Lobe Histone H3K9me3 Donor 112 Library Lib:XZ:20100924:06--ChIP:XZ:20100914:06:mid frontal lobe:H3K9Me3 EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 60
FINDPEAKS_SCORE: 0.0209
FINDPEAKS_PERCENTILE: 23
HOTSPOT_SCORE: 0.0675
HOTSPOT_PERCENTILE: 23
IROC_SCORE: 0.8191
IROC_PERCENTILE: 38
POISSON_SCORE: 0.1686
POISSON_PERCENTILE: 19

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

source_name: human post mortem brain region from a non Alzheimer's donor; Lib:XZ:20100924:06--ChIP:XZ:20100914:06:mid frontal lobe:H3K9Me3

value: Brain, Mid Frontal Lobe

value: post-mortem

value: genomic DNA

value: Mid Frontal Lobe

value: brain

value: Rush University Medical Center

value: Abcam

value: Histone H3K9me3


title: ChIP-Seq analysis of H3K4me1; ant. caudate cls; Lib:XZ:20100921:15--ChIP:XZ:20100914:15:anterior caudate :H3K4Me1

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:20100921:15--ChIP:XZ:20100914:15:anterior caudate :H3K4Me1
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5711
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: GSM669970_BI.Brain_Anterior_Caudate.H3K4me1.112.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100921:15--ChIP:XZ:20100914:15:anterior caudate :H3K4Me1.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Brain Anterior Caudate Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me1 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.6545
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: 0.0737
FINDPEAKS_PERCENTILE: 7
HOTSPOT_SCORE: 0.1892
HOTSPOT_PERCENTILE: 7
IROC_SCORE: 0.8915
IROC_PERCENTILE: 7
POISSON_SCORE: 0.3855
POISSON_PERCENTILE: 21

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

ANALYSIS FILE NAME: GSM669970_BI.Brain_Anterior_Caudate.H3K4me1.112.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100921:15--ChIP:XZ:20100914:15:anterior caudate :H3K4Me1.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of Brain Anterior Caudate Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me1 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.6755
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 H3K4me1 12
BROWSER_TRACK_DESCRIPTION: BI Brain Anterior Caudate Histone H3K4me1 Donor 112 Library Lib:XZ:20100921:15--ChIP:XZ:20100914:15:anterior caudate :H3K4Me1 EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 50
FINDPEAKS_SCORE: 0.0737
FINDPEAKS_PERCENTILE: 7
HOTSPOT_SCORE: 0.1892
HOTSPOT_PERCENTILE: 7
IROC_SCORE: 0.8915
IROC_PERCENTILE: 7
POISSON_SCORE: 0.3855
POISSON_PERCENTILE: 21

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

source_name: human post mortem brain region from a non Alzheimer's donor; Lib:XZ:20100921:15--ChIP:XZ:20100914:15:anterior caudate :H3K4Me1

value: Brain, Anterior Caudate

value: Anterior Caudate

value: Female

value: SDS lysis

value: Histone H3K4me1

value: Bioruptor


title: ChIP-Seq analysis of WCE in fetal lung cells; Lib:XZ:20100731:07--ChIP:XZ:20100726:07:fetal lung:WCE

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:20100731:07--ChIP:XZ:20100726:07:fetal lung:WCE
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5697
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5940
****************
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: GSM669956_BI.Fetal_Lung.Input.UW_H23266.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100731:07--ChIP:XZ:20100726:07:fetal lung:WCE.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Fetal Lung ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on Fetal Lung, Donor UW H23266 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.6482
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: 0.007
FINDPEAKS_PERCENTILE: 67
HOTSPOT_SCORE: 0.006
HOTSPOT_PERCENTILE: 30
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.0309
POISSON_PERCENTILE: 30

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

ANALYSIS FILE NAME: GSM669956_BI.Fetal_Lung.Input.UW_H23266.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100731:07--ChIP:XZ:20100726:07:fetal lung:WCE.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Lung ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from Fetal Lung, Donor UW H23266 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.6692
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 Input 66
BROWSER_TRACK_DESCRIPTION: BI Fetal Lung ChIP-Seq Input Donor UW H23266 Library Lib:XZ:20100731:07--ChIP:XZ:20100726:07:fetal lung:WCE EA Release 3

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 61
FINDPEAKS_SCORE: 0.007
FINDPEAKS_PERCENTILE: 67
HOTSPOT_SCORE: 0.006
HOTSPOT_PERCENTILE: 30
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.0309
POISSON_PERCENTILE: 30

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

source_name: Primary fetal lung tissue; Lib:XZ:20100731:07--ChIP:XZ:20100726:07:fetal lung:WCE

value: Fetal Lung

value: surgery

value: Fetal lung

value: Primary Tissue

value: lung

value: UW

value: 85 days

value: standard

value: ChIP-Seq Input

value: Input


title: ChIP-Seq analysis of WCE in mobilized CD34 cells; Lib:RI:20100517:08--ChIP:Thanh:20100504:08:Mobilized CD34:WCE

description:
sample_term_id: CL_0000837
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:RI:20100517:08--ChIP:Thanh:20100504:08:Mobilized CD34:WCE
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5702
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3353
****************
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: GSM669961_BI.CD34_Primary_Cells.Input.UW_RO_01492.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:RI:20100517:08--ChIP:Thanh:20100504:08:Mobilized CD34:WCE.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of CD34 Primary Cells ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on CD34 Primary Cells, Donor UW RO 01492 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.6561
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: 0.0083
FINDPEAKS_PERCENTILE: 90
HOTSPOT_SCORE: 0.0497
HOTSPOT_PERCENTILE: 87
IROC_SCORE: 0.0
IROC_PERCENTILE: 38
POISSON_SCORE: 0.1196
POISSON_PERCENTILE: 90

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

ANALYSIS FILE NAME: GSM669961_BI.CD34_Primary_Cells.Input.UW_RO_01492.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:RI:20100517:08--ChIP:Thanh:20100504:08:Mobilized CD34:WCE.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of CD34 Primary Cells ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from CD34 Primary Cells, Donor UW RO 01492 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.6771
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 92
BROWSER_TRACK_DESCRIPTION: BI CD34 Primary Cells ChIP-Seq Input Donor UW RO 01492 Library Lib:RI:20100517:08--ChIP:Thanh:20100504:08:Mobilized CD34:WCE EA Release 3

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 61
FINDPEAKS_SCORE: 0.0083
FINDPEAKS_PERCENTILE: 90
HOTSPOT_SCORE: 0.0497
HOTSPOT_PERCENTILE: 87
IROC_SCORE: 0.0
IROC_PERCENTILE: 38
POISSON_SCORE: 0.1196
POISSON_PERCENTILE: 90

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

source_name: CD34 cells mobilized into peripheral blood; Lib:RI:20100517:08--ChIP:Thanh:20100504:08:Mobilized CD34:WCE

value: Mobilized CD34 Primary Cells

value: genomic DNA

value: Mobilized CD34

value: Cauc

value: Male

value: Primary Cell


title: ChIP-Seq analysis of H3K4me1 in HUES64 cells; Lib:MC:20101025:01--ChIP:MC:20101020:01:ES cell HUES_64:H3K4Me1

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:20101025:01--ChIP:MC:20101020:01:ES cell HUES_64:H3K4Me1
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5707
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: GSM669966_BI.HUES64.H3K4me1.Lib_MC_20101025_01--ChIP_MC_20101020_01_ES_cell_HUES_64_H3K4Me1.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20101025:01--ChIP:MC:20101020:01:ES cell HUES_64:H3K4Me1.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of HUES64 Cell Line Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me1 ChIP-Seq on the HUES64 Cell Line, Library Lib:MC:20101025:01--ChIP:MC:20101020:01:ES cell HUES_64: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.6480
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: 0.2689
FINDPEAKS_PERCENTILE: 39
HOTSPOT_SCORE: 0.3525
HOTSPOT_PERCENTILE: 43
IROC_SCORE: 0.9604
IROC_PERCENTILE: 36
POISSON_SCORE: 0.5135
POISSON_PERCENTILE: 50

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

ANALYSIS FILE NAME: GSM669966_BI.HUES64.H3K4me1.Lib_MC_20101025_01--ChIP_MC_20101020_01_ES_cell_HUES_64_H3K4Me1.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20101025:01--ChIP:MC:20101020:01:ES cell HUES_64:H3K4Me1.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of HUES64 Cell Line Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me1 ChIP-Seq read mappings from the HUES64 Cell Line, Library Lib:MC:20101025:01--ChIP:MC:20101020:01:ES cell HUES_64: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.6690
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 H3K4me1 e1
BROWSER_TRACK_DESCRIPTION: BI HUES64 Cell Line Histone H3K4me1 Library Lib:MC:20101025:01--ChIP:MC:20101020:01:ES cell HUES_64:H3K4Me1 EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 50
FINDPEAKS_SCORE: 0.2689
FINDPEAKS_PERCENTILE: 39
HOTSPOT_SCORE: 0.3525
HOTSPOT_PERCENTILE: 43
IROC_SCORE: 0.9604
IROC_PERCENTILE: 36
POISSON_SCORE: 0.5135
POISSON_PERCENTILE: 50

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

source_name: Harvard University Embryonic Stem Cells; Lib:MC:20101025:01--ChIP:MC:20101020:01:ES cell HUES_64:H3K4Me1

value: HUES64 Cell Line

value: embrionic stem cell

value: KSR

value: ES cell HUES_64-1

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 H3K4me1

value: Bioruptor


title: ChIP-Seq analysis of H3K9me3 in fetal lung cells; Lib:XZ:20100731:01--ChIP:XZ:20100726:01:fetal lung:H3K9Me3

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:20100731:01--ChIP:XZ:20100726:01:fetal lung:H3K9Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5680
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5940
****************
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: GSM669939_BI.Fetal_Lung.H3K9me3.UW_H23266.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100731:01--ChIP:XZ:20100726:01:fetal lung:H3K9Me3.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Fetal Lung Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9me3 ChIP-Seq on Fetal Lung, Donor UW H23266 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.6461
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: 0.067
FINDPEAKS_PERCENTILE: 54
HOTSPOT_SCORE: 0.1397
HOTSPOT_PERCENTILE: 50
IROC_SCORE: 0.799
IROC_PERCENTILE: 27
POISSON_SCORE: 0.3137
POISSON_PERCENTILE: 54

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

ANALYSIS FILE NAME: GSM669939_BI.Fetal_Lung.H3K9me3.UW_H23266.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100731:01--ChIP:XZ:20100726:01:fetal lung:H3K9Me3.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Lung Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9me3 ChIP-Seq read mappings from Fetal Lung, Donor UW H23266 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.6671
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 H3K9me3 66
BROWSER_TRACK_DESCRIPTION: BI Fetal Lung Histone H3K9me3 Donor UW H23266 Library Lib:XZ:20100731:01--ChIP:XZ:20100726:01:fetal lung:H3K9Me3 EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 60
FINDPEAKS_SCORE: 0.067
FINDPEAKS_PERCENTILE: 54
HOTSPOT_SCORE: 0.1397
HOTSPOT_PERCENTILE: 50
IROC_SCORE: 0.799
IROC_PERCENTILE: 27
POISSON_SCORE: 0.3137
POISSON_PERCENTILE: 54

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

source_name: Primary fetal lung tissue; Lib:XZ:20100731:01--ChIP:XZ:20100726:01:fetal lung:H3K9Me3

value: Fetal Lung

value: surgery

value: genomic DNA

value: Fetal lung

value: Female

value: Primary Tissue

value: lung

value: UW

value: 85 days

value: Histone H3K9me3


title: ChIP-Seq analysis of WCE in fetal brain cells; Lib:XZ:20100731:09--ChIP:XZ:20100726:09:fetal brain:WCE

description:
sample_term_id: UBERON_0000955
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:XZ:20100731:09--ChIP:XZ:20100726:09:fetal brain:WCE
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5685
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5942
****************
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: GSM669944_BI.Fetal_Brain.Input.UW_H23284.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100731:09--ChIP:XZ:20100726:09:fetal brain:WCE.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Fetal Brain ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on Fetal Brain, 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.6492
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: 0.0028
FINDPEAKS_PERCENTILE: 3
HOTSPOT_SCORE: 0.0
HOTSPOT_PERCENTILE: 3
IROC_SCORE: 0.8899
IROC_PERCENTILE: 45
POISSON_SCORE: 0.0865
POISSON_PERCENTILE: 80

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

ANALYSIS FILE NAME: GSM669944_BI.Fetal_Brain.Input.UW_H23284.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100731:09--ChIP:XZ:20100726:09:fetal brain:WCE.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Brain ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from Fetal Brain, 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.6702
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: FB Input 84
BROWSER_TRACK_DESCRIPTION: BI Fetal Brain ChIP-Seq Input Donor UW H23284 Library Lib:XZ:20100731:09--ChIP:XZ:20100726:09:fetal brain:WCE EA Release 3

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 61
FINDPEAKS_SCORE: 0.0028
FINDPEAKS_PERCENTILE: 3
HOTSPOT_SCORE: 0.0
HOTSPOT_PERCENTILE: 3
IROC_SCORE: 0.8899
IROC_PERCENTILE: 45
POISSON_SCORE: 0.0865
POISSON_PERCENTILE: 80

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

source_name: Primary fetal brain tissue; Lib:XZ:20100731:09--ChIP:XZ:20100726:09:fetal brain:WCE

value: Fetal Brain

value: Fetal brain

value: brain

value: 96 days

value: standard

value: ChIP-Seq Input

value: Input


title: ChIP-Seq analysis of H3K36me3; substantia nigra cells; Lib:XZ:20100921:03--ChIP:XZ:20100914:03:substantia nigra:H3K36Me3

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:20100921:03--ChIP:XZ:20100914:03:substantia nigra:H3K36Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5688
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: GSM669947_BI.Brain_Substantia_Nigra.H3K36me3.112.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100921:03--ChIP:XZ:20100914:03:substantia nigra:H3K36Me3.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Brain Substantia Nigra Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K36me3 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.6543
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: 0.049
FINDPEAKS_PERCENTILE: 8
HOTSPOT_SCORE: 0.1426
HOTSPOT_PERCENTILE: 8
IROC_SCORE: 0.8812
IROC_PERCENTILE: 12
POISSON_SCORE: 0.2891
POISSON_PERCENTILE: 8

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

ANALYSIS FILE NAME: GSM669947_BI.Brain_Substantia_Nigra.H3K36me3.112.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100921:03--ChIP:XZ:20100914:03:substantia nigra:H3K36Me3.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of Brain Substantia Nigra Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K36me3 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.6753
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 H3K36me3 12
BROWSER_TRACK_DESCRIPTION: BI Brain Substantia Nigra Histone H3K36me3 Donor 112 Library Lib:XZ:20100921:03--ChIP:XZ:20100914:03:substantia nigra:H3K36Me3 EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 59
FINDPEAKS_SCORE: 0.049
FINDPEAKS_PERCENTILE: 8
HOTSPOT_SCORE: 0.1426
HOTSPOT_PERCENTILE: 8
IROC_SCORE: 0.8812
IROC_PERCENTILE: 12
POISSON_SCORE: 0.2891
POISSON_PERCENTILE: 8

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

source_name: human post mortem brain region from a non Alzheimer's donor; Lib:XZ:20100921:03--ChIP:XZ:20100914:03:substantia nigra:H3K36Me3

value: Brain, Substantia Nigra

value: post-mortem

value: Substantia Nigra

value: Rush University Medical Center

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 in Mobilized CD34 cells; Lib:RI:20100308:09--ChIP:MA:20100216:09:Mobilized CD34:H3K27Me3

description:
sample_term_id: CL_0000837
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:RI:20100308:09--ChIP:MA:20100216:09:Mobilized CD34:H3K27Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5686
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3877
****************
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: GSM669945_BI.Mobilized_CD34_Primary_Cells.H3K27me3.UW_RO_01480.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:RI:20100308:09--ChIP:MA:20100216:09:Mobilized CD34:H3K27Me3.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Mobilized CD34 Primary Cells Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27me3 ChIP-Seq on Mobilized CD34 Primary Cells, Donor UW RO 01480 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.6511
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: 0.0752
FINDPEAKS_PERCENTILE: 55
HOTSPOT_SCORE: 0.1454
HOTSPOT_PERCENTILE: 45
IROC_SCORE: 0.9259
IROC_PERCENTILE: 70
POISSON_SCORE: 0.2635
POISSON_PERCENTILE: 30

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

ANALYSIS FILE NAME: GSM669945_BI.Mobilized_CD34_Primary_Cells.H3K27me3.UW_RO_01480.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:RI:20100308:09--ChIP:MA:20100216:09:Mobilized CD34:H3K27Me3.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of Mobilized CD34 Primary Cells Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27me3 ChIP-Seq read mappings from Mobilized CD34 Primary Cells, Donor UW RO 01480 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.6721
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: MCD34 H3K27me3 80
BROWSER_TRACK_DESCRIPTION: BI Mobilized CD34 Primary Cells Histone H3K27me3 Donor UW RO 01480 Library Lib:RI:20100308:09--ChIP:MA:20100216:09:Mobilized CD34:H3K27Me3 EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 52
FINDPEAKS_SCORE: 0.0752
FINDPEAKS_PERCENTILE: 55
HOTSPOT_SCORE: 0.1454
HOTSPOT_PERCENTILE: 45
IROC_SCORE: 0.9259
IROC_PERCENTILE: 70
POISSON_SCORE: 0.2635
POISSON_PERCENTILE: 30

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

source_name: CD34 cells mobilized into peripheral blood; Lib:RI:20100308:09--ChIP:MA:20100216:09:Mobilized CD34:H3K27Me3

value: Mobilized CD34 Primary Cells

value: genomic DNA

value: Mobilized CD34

value: Unknown

value: Primary Cell

value: UW

value: Upstate

value: Histone H3K27me3


title: ChIP-Seq analysis of H3K4me3 in Cultured CD34 cells; Lib:RI:20101012:02--ChIP:MA:20100927:02:CD34 expanded:H3K4Me3

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:20101012:02--ChIP:MA:20100927:02:CD34 expanded:H3K4Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5684
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: GSM669943_BI.CD34_Cultured_Cells.H3K4me3.123.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:RI:20101012:02--ChIP:MA:20100927:02:CD34 expanded:H3K4Me3.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of CD34 Cultured Cells Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me3 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.6493
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: 0.2682
FINDPEAKS_PERCENTILE: 36
HOTSPOT_SCORE: 0.2771
HOTSPOT_PERCENTILE: 32
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.2788
POISSON_PERCENTILE: 24

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

ANALYSIS FILE NAME: GSM669943_BI.CD34_Cultured_Cells.H3K4me3.123.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:RI:20101012:02--ChIP:MA:20100927:02:CD34 expanded:H3K4Me3.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of CD34 Cultured Cells Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me3 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.6703
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 H3K4me3 23
BROWSER_TRACK_DESCRIPTION: BI CD34 Cultured Cells Histone H3K4me3 Donor 123 Library Lib:RI:20101012:02--ChIP:MA:20100927:02:CD34 expanded:H3K4Me3 EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.2682
FINDPEAKS_PERCENTILE: 36
HOTSPOT_SCORE: 0.2771
HOTSPOT_PERCENTILE: 32
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.2788
POISSON_PERCENTILE: 24

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

source_name: flow sorted CD34+ cells from cord blood expanded in short term culture; Lib:RI:20101012:02--ChIP:MA:20100927:02:CD34 expanded:H3K4Me3

value: CD34 Cultured Cells

value: short term

value: cultured CD34

value: FHCRC

value: Millipore

value: Histone H3K4me3