title: ChIP-Seq analysis of WCE in human hiPS-18c cells; Lib:MC:20100108:07--ChIP:MC:20100105:07:hiPS-18c:WCE

description:
sample_term_id: NTR_0001167
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:MC:20100108:07--ChIP:MC:20100105:07:hiPS-18c:WCE
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3747
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3890
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************
BED and WIG files were replaced on April 29, 2014

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

ANALYSIS FILE NAME: GSM621407_BI.iPS-18c.Input.Lib_MC_20100108_07--ChIP_MC_20100105_07_hiPS-18c_WCE.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100108:07--ChIP:MC:20100105:07:hiPS-18c:WCE.hg19.level.1
ANALYSIS TITLE: Mapping of iPS-18c Cell Line ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on the iPS-18c Cell Line, Library Lib:MC:20100108:07--ChIP:MC:20100105:07:hiPS-18c:WCE were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.4619
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED: 67
FINDPEAKS_SCORE: 0.0056
FINDPEAKS_PERCENTILE: 13
HOTSPOT_SCORE: 0.006
HOTSPOT_PERCENTILE: 17
IROC_SCORE: 0.0
IROC_PERCENTILE: 18
POISSON_SCORE: 0.1972
POISSON_PERCENTILE: 25

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

ANALYSIS FILE NAME: GSM621407_BI.iPS-18c.Input.Lib_MC_20100108_07--ChIP_MC_20100105_07_hiPS-18c_WCE.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100108:07--ChIP:MC:20100105:07:hiPS-18c:WCE.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of iPS-18c Cell Line ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from the iPS-18c Cell Line, Library Lib:MC:20100108:07--ChIP:MC:20100105:07:hiPS-18c:WCE were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.4893
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: iPS18c Input CE
BROWSER_TRACK_DESCRIPTION: BI iPS-18c Cell Line ChIP-Seq Input Library Lib:MC:20100108:07--ChIP:MC:20100105:07:hiPS-18c:WCE EA Release 2

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED: 67
FINDPEAKS_SCORE: 0.0056
FINDPEAKS_PERCENTILE: 13
HOTSPOT_SCORE: 0.006
HOTSPOT_PERCENTILE: 17
IROC_SCORE: 0.0
IROC_PERCENTILE: 18
POISSON_SCORE: 0.1972
POISSON_PERCENTILE: 25

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

value: induced pluripotent stem cells

value: induced pluripotent cells

value: KSR

value: Cell Line

value: undifferentiated

value: Female

value: Harvard University

value: standard

value: ChIP-Seq Input

value: Input


title: ChIP-Seq analysis of H3K27me3 in human fetal brain cells; Lib:XZ:20100129:15--ChIP:XZ:20100125:15:fetal brain:H3K27me3

status: Public on Nov 12 2010

type: SRA

city: Cambridge

first: BROAD

last: INSTITUTE

state: MA

country: USA

institute: Broad Institute

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:20100129:15--ChIP:XZ:20100125:15:fetal brain:H3K27me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3733
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3878
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************
BED and WIG files were replaced on April 29, 2014

library_source: genomic

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

ANALYSIS FILE NAME: GSM621393_BI.Fetal_Brain.H3K27me3.UW_H-22510.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100129:15--ChIP:XZ:20100125:15:fetal brain:H3K27me3.hg19.level.1
ANALYSIS TITLE: Mapping of Fetal Brain Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27me3 ChIP-Seq on Fetal Brain, Donor H-22510 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.4828
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED: 52
FINDPEAKS_SCORE: 0.045
FINDPEAKS_PERCENTILE: 25
HOTSPOT_SCORE: 0.0944
HOTSPOT_PERCENTILE: 15
IROC_SCORE: 0.9062
IROC_PERCENTILE: 44
POISSON_SCORE: 0.3723
POISSON_PERCENTILE: 17

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

ANALYSIS FILE NAME: GSM621393_BI.Fetal_Brain.H3K27me3.UW_H-22510.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100129:15--ChIP:XZ:20100125:15:fetal brain:H3K27me3.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Brain Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27me3 ChIP-Seq read mappings from Fetal Brain, Donor H-22510 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.5102
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: FB H3K27me3 10
BROWSER_TRACK_DESCRIPTION: BI Fetal Brain Histone H3K27me3 Donor H-22510 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED: 52
FINDPEAKS_SCORE: 0.045
FINDPEAKS_PERCENTILE: 25
HOTSPOT_SCORE: 0.0944
HOTSPOT_PERCENTILE: 15
IROC_SCORE: 0.9062
IROC_PERCENTILE: 44
POISSON_SCORE: 0.3723
POISSON_PERCENTILE: 17

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

molecule: genomic DNA

organism: Homo sapiens

source_name: Primary fetal brain tissue; Lib:XZ:20100129:15--ChIP:XZ:20100125:15:fetal brain:H3K27me3

extract_protocol: Library construction protocol: Single read - Illumina

value: surgery

tag: molecule

value: genomic DNA

tag: disease

value: Fetal brain

value: Unknown

value: Primary Tissue

value: brain

value: UW

value: 122 days

value: Protein A-Sepharose 4B

value: 10 million cells

value: SDS lysis

value: 70 ul bed volume

value: Millipore

value: Histone H3K27me3

value: Bioruptor


title: ChIP-Seq analysis of H3K9me3 human fetal lung cells (superseded by GSE120321)

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:20100129:06--ChIP:XZ:20100125:06:fetal lung:H3K9Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3737
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3880
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************
BED and WIG files were replaced on April 29, 2014
****************************
This sample record's metadata may be obsolete; up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE120321
****************************

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

ANALYSIS FILE NAME: GSM621397_BI.Fetal_Lung.H3K9me3.UW_H-22727.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100129:06--ChIP:XZ:20100125:06:fetal lung:H3K9Me3.hg19.level.1
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 H-22727 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.4698
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED: 59
FINDPEAKS_SCORE: 0.0233
FINDPEAKS_PERCENTILE: 17
HOTSPOT_SCORE: 0.0411
HOTSPOT_PERCENTILE: 7
IROC_SCORE: 0.8968
IROC_PERCENTILE: 73
POISSON_SCORE: 0.2665
POISSON_PERCENTILE: 5

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

ANALYSIS FILE NAME: GSM621397_BI.Fetal_Lung.H3K9me3.UW_H-22727.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100129:06--ChIP:XZ:20100125:06:fetal lung:H3K9Me3.hg19.level.2
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 H-22727 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.4972
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: FL H3K9me3 27
BROWSER_TRACK_DESCRIPTION: BI Fetal Lung Histone H3K9me3 Donor H-22727 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED: 59
FINDPEAKS_SCORE: 0.0233
FINDPEAKS_PERCENTILE: 17
HOTSPOT_SCORE: 0.0411
HOTSPOT_PERCENTILE: 7
IROC_SCORE: 0.8968
IROC_PERCENTILE: 73
POISSON_SCORE: 0.2665
POISSON_PERCENTILE: 5

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

source_name: Primary fetal lung tissue; Lib:XZ:20100129:06--ChIP:XZ:20100125:06:fetal lung:H3K9Me3

value: Fetal lung

value: lung

value: 101 days

value: Abcam

value: Histone H3K9me3


title: ChIP-Seq analysis of H3K9ac human fetal lung cells (superseded by GSE120323)

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:20100129:05--ChIP:XZ:20100125:05:fetal lung:H3K9Ac
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3740
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3880
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************
BED and WIG files were replaced on April 29, 2014
****************************
This sample record's metadata may be obsolete; up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE120323
****************************

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

ANALYSIS FILE NAME: GSM621400_BI.Fetal_Lung.H3K9ac.UW_H-22727.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100129:05--ChIP:XZ:20100125:05:fetal lung:H3K9Ac.hg19.level.1
ANALYSIS TITLE: Mapping of Fetal Lung Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9ac ChIP-Seq on Fetal Lung, Donor H-22727 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.4737
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED: 35
FINDPEAKS_SCORE: 0.1063
FINDPEAKS_PERCENTILE: 23
HOTSPOT_SCORE: 0.1557
HOTSPOT_PERCENTILE: 23
IROC_SCORE: 0.9783
IROC_PERCENTILE: 43
POISSON_SCORE: 0.37
POISSON_PERCENTILE: 51

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

ANALYSIS FILE NAME: GSM621400_BI.Fetal_Lung.H3K9ac.UW_H-22727.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100129:05--ChIP:XZ:20100125:05:fetal lung:H3K9Ac.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Lung Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9ac ChIP-Seq read mappings from Fetal Lung, Donor H-22727 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.5011
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: FL H3K9ac 27
BROWSER_TRACK_DESCRIPTION: BI Fetal Lung Histone H3K9ac Donor H-22727 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED: 35
FINDPEAKS_SCORE: 0.1063
FINDPEAKS_PERCENTILE: 23
HOTSPOT_SCORE: 0.1557
HOTSPOT_PERCENTILE: 23
IROC_SCORE: 0.9783
IROC_PERCENTILE: 43
POISSON_SCORE: 0.37
POISSON_PERCENTILE: 51

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

source_name: Primary fetal lung tissue; Lib:XZ:20100129:05--ChIP:XZ:20100125:05:fetal lung:H3K9Ac

value: surgery

value: genomic DNA

value: Unknown

value: Histone H3K9ac


title: ChIP-Seq analysis of H3K4me3 human fetal lung cells (superseded by GSE120320)

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:20100129:25--ChIP:XZ:20100125:25:fetal lung:H3K4me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3745
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3879
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************
BED and WIG files were replaced on April 29, 2014
****************************
This sample record's metadata may be obsolete; up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE120320
****************************

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

ANALYSIS FILE NAME: GSM621405_BI.Fetal_Lung.H3K4me3.UW_H-22676.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100129:25--ChIP:XZ:20100125:25:fetal lung:H3K4me3.hg19.level.1
ANALYSIS TITLE: Mapping of Fetal Lung Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me3 ChIP-Seq on Fetal Lung, Donor H-22676 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.4807
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED: 62
FINDPEAKS_SCORE: 0.1925
FINDPEAKS_PERCENTILE: 8
HOTSPOT_SCORE: 0.2218
HOTSPOT_PERCENTILE: 13
IROC_SCORE: 0.9936
IROC_PERCENTILE: 16
POISSON_SCORE: 0.3757
POISSON_PERCENTILE: 24

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

ANALYSIS FILE NAME: GSM621405_BI.Fetal_Lung.H3K4me3.UW_H-22676.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100129:25--ChIP:XZ:20100125:25:fetal lung:H3K4me3.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Lung Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me3 ChIP-Seq read mappings from Fetal Lung, Donor H-22676 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.5081
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: FL H3K4me3 76
BROWSER_TRACK_DESCRIPTION: BI Fetal Lung Histone H3K4me3 Donor H-22676 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED: 62
FINDPEAKS_SCORE: 0.1925
FINDPEAKS_PERCENTILE: 8
HOTSPOT_SCORE: 0.2218
HOTSPOT_PERCENTILE: 13
IROC_SCORE: 0.9936
IROC_PERCENTILE: 16
POISSON_SCORE: 0.3757
POISSON_PERCENTILE: 24

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

source_name: Primary fetal lung tissue; Lib:XZ:20100129:25--ChIP:XZ:20100125:25:fetal lung:H3K4me3

value: Primary Tissue

value: UW

value: 120 days

value: Histone H3K4me3


title: ChIP-Seq analysis of H3K4me3 in human hiPS-20b cells; Lib:MC:20100119:05--ChIP:MC:20100113:05:hiPS-20b:H3K4Me3

description:
sample_term_id: NTR_0001168
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:MC:20100119:05--ChIP:MC:20100113:05:hiPS-20b:H3K4Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3763
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3892
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************
BED and WIG files were replaced on April 29, 2014

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

ANALYSIS FILE NAME: GSM621423_BI.iPS-20b.H3K4me3.Lib_MC_20100119_05--ChIP_MC_20100113_05_hiPS-20b_H3K4Me3.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100119:05--ChIP:MC:20100113:05:hiPS-20b:H3K4Me3.hg19.level.1
ANALYSIS TITLE: Mapping of iPS-20b Cell Line Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me3 ChIP-Seq on the iPS-20b Cell Line, Library Lib:MC:20100119:05--ChIP:MC:20100113:05:hiPS-20b:H3K4Me3 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.4779
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED: 62
FINDPEAKS_SCORE: 0.1906
FINDPEAKS_PERCENTILE: 6
HOTSPOT_SCORE: 0.2085
HOTSPOT_PERCENTILE: 7
IROC_SCORE: 0.9975
IROC_PERCENTILE: 31
POISSON_SCORE: 0.3856
POISSON_PERCENTILE: 29

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

ANALYSIS FILE NAME: GSM621423_BI.iPS-20b.H3K4me3.Lib_MC_20100119_05--ChIP_MC_20100113_05_hiPS-20b_H3K4Me3.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100119:05--ChIP:MC:20100113:05:hiPS-20b:H3K4Me3.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of iPS-20b Cell Line Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me3 ChIP-Seq read mappings from the iPS-20b Cell Line, Library Lib:MC:20100119:05--ChIP:MC:20100113:05:hiPS-20b:H3K4Me3 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.5053
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: iPS20b H3K4me3 e3
BROWSER_TRACK_DESCRIPTION: BI iPS-20b Cell Line Histone H3K4me3 Library Lib:MC:20100119:05--ChIP:MC:20100113:05:hiPS-20b:H3K4Me3 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED: 62
FINDPEAKS_SCORE: 0.1906
FINDPEAKS_PERCENTILE: 6
HOTSPOT_SCORE: 0.2085
HOTSPOT_PERCENTILE: 7
IROC_SCORE: 0.9975
IROC_PERCENTILE: 31
POISSON_SCORE: 0.3856
POISSON_PERCENTILE: 29

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

value: induced pluripotent stem cells 20b

tag: lineage

value: induced pluripotent cells

tag: medium

value: KSR

tag: passage

tag: line

tag: batch

value: Cell Line

value: undifferentiated

tag: Sex

value: Male

value: Harvard University

value: Protein A-Sepharose 4B

value: 10 million cells

value: SDS lysis

value: 70 ul bed volume


title: ChIP-Seq analysis of H3K36me3 in human fetal heart cells; Lib:XZ:20100129:21--ChIP:XZ:20100125:21:fetal heart:H3K36me3

description:
sample_term_id: UBERON_0000948
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:XZ:20100129:21--ChIP:XZ:20100125:21:fetal heart:H3K36me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3732
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3885
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************
BED and WIG files were replaced on April 29, 2014

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

ANALYSIS FILE NAME: GSM621392_BI.Fetal_Heart.H3K36me3.UW_H-22727.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100129:21--ChIP:XZ:20100125:21:fetal heart:H3K36me3.hg19.level.1
ANALYSIS TITLE: Mapping of Fetal Heart Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K36me3 ChIP-Seq on Fetal Heart, Donor H-22727 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.4723
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED: 54
FINDPEAKS_SCORE: 0.0154
FINDPEAKS_PERCENTILE: 4
HOTSPOT_SCORE: 0.107
HOTSPOT_PERCENTILE: 4
IROC_SCORE: 0.6775
IROC_PERCENTILE: 4
POISSON_SCORE: 0.317
POISSON_PERCENTILE: 7

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

ANALYSIS FILE NAME: GSM621392_BI.Fetal_Heart.H3K36me3.UW_H-22727.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100129:21--ChIP:XZ:20100125:21:fetal heart:H3K36me3.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Heart Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K36me3 ChIP-Seq read mappings from Fetal Heart, Donor H-22727 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.4997
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: FH H3K36me3 27
BROWSER_TRACK_DESCRIPTION: BI Fetal Heart Histone H3K36me3 Donor H-22727 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED: 54
FINDPEAKS_SCORE: 0.0154
FINDPEAKS_PERCENTILE: 4
HOTSPOT_SCORE: 0.107
HOTSPOT_PERCENTILE: 4
IROC_SCORE: 0.6775
IROC_PERCENTILE: 4
POISSON_SCORE: 0.317
POISSON_PERCENTILE: 7

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

source_name: Primary fetal heart tissue; Lib:XZ:20100129:21--ChIP:XZ:20100125:21:fetal heart:H3K36me3

value: surgery

value: genomic DNA

value: Fetal heart

value: Unknown

value: heart

value: 101 days

value: Abcam

value: Histone H3K36me3

value: Bioruptor


title: ChIP-Seq analysis of WCE in human Adult peripheral CD4 cells; Lib:MC:20100309:06--ChIP:MA:20100216:06:Mobilized CD4:WCE

description:
sample_term_id: CL_0000492
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:MC:20100309:06--ChIP:MA:20100216:06:Mobilized CD4:WCE
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3753
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3887
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************
BED and WIG files were replaced on April 29, 2014

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

ANALYSIS FILE NAME: GSM621413_BI.Mobilized_CD4_Primary_Cells.Input.37.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100309:06--ChIP:MA:20100216:06:Mobilized CD4:WCE.hg19.level.1
ANALYSIS TITLE: Mapping of Mobilized CD4 Primary Cells ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on Mobilized CD4 Primary Cells, Donor 37 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.4691
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED: 67
FINDPEAKS_SCORE: 0.0066
FINDPEAKS_PERCENTILE: 27
HOTSPOT_SCORE: 0.0049
HOTSPOT_PERCENTILE: 14
IROC_SCORE: 0.0
IROC_PERCENTILE: 18
POISSON_SCORE: 0.2392
POISSON_PERCENTILE: 55

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

ANALYSIS FILE NAME: GSM621413_BI.Mobilized_CD4_Primary_Cells.Input.37.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100309:06--ChIP:MA:20100216:06:Mobilized CD4:WCE.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Mobilized CD4 Primary Cells ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from Mobilized CD4 Primary Cells, Donor 37 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.4965
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: MCD4 Input 37
BROWSER_TRACK_DESCRIPTION: BI Mobilized CD4 Primary Cells ChIP-Seq Input Donor 37 EA Release 2

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED: 67
FINDPEAKS_SCORE: 0.0066
FINDPEAKS_PERCENTILE: 27
HOTSPOT_SCORE: 0.0049
HOTSPOT_PERCENTILE: 14
IROC_SCORE: 0.0
IROC_PERCENTILE: 18
POISSON_SCORE: 0.2392
POISSON_PERCENTILE: 55

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

source_name: CD4 cells mobilized into peripheral blood; Lib:MC:20100309:06--ChIP:MA:20100216:06:Mobilized CD4:WCE

tag: markers

value: Adult peripheral CD4

value: Primary Cell

value: UW

value: standard

value: ChIP-Seq Input

value: Input


title: ChIP-Seq analysis of H3K27me3 human fetal lung cells (superseded by GSE120317)

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:20100129:01--ChIP:XZ:20100125:01:fetal lung:H3K27me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3730
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3880
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************
BED and WIG files were replaced on April 29, 2014
****************************
This sample record's metadata may be obsolete; up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE120317
****************************

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

ANALYSIS FILE NAME: GSM621390_BI.Fetal_Lung.H3K27me3.UW_H-22727.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100129:01--ChIP:XZ:20100125:01:fetal lung:H3K27me3.hg19.level.1
ANALYSIS TITLE: Mapping of Fetal Lung Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27me3 ChIP-Seq on Fetal Lung, Donor H-22727 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.4666
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED: 52
FINDPEAKS_SCORE: 0.055
FINDPEAKS_PERCENTILE: 27
HOTSPOT_SCORE: 0.1037
HOTSPOT_PERCENTILE: 17
IROC_SCORE: 0.9104
IROC_PERCENTILE: 46
POISSON_SCORE: 0.3533
POISSON_PERCENTILE: 12

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

ANALYSIS FILE NAME: GSM621390_BI.Fetal_Lung.H3K27me3.UW_H-22727.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100129:01--ChIP:XZ:20100125:01:fetal lung:H3K27me3.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Lung Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27me3 ChIP-Seq read mappings from Fetal Lung, Donor H-22727 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.4940
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: FL H3K27me3 27
BROWSER_TRACK_DESCRIPTION: BI Fetal Lung Histone H3K27me3 Donor H-22727 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED: 52
FINDPEAKS_SCORE: 0.055
FINDPEAKS_PERCENTILE: 27
HOTSPOT_SCORE: 0.1037
HOTSPOT_PERCENTILE: 17
IROC_SCORE: 0.9104
IROC_PERCENTILE: 46
POISSON_SCORE: 0.3533
POISSON_PERCENTILE: 12

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

source_name: Primary fetal lung tissue; Lib:XZ:20100129:01--ChIP:XZ:20100125:01:fetal lung:H3K27me3

value: Fetal lung

value: Primary Tissue

value: lung

value: Protein A-Sepharose 4B

value: 10 million cells

value: SDS lysis

value: Millipore

value: Histone H3K27me3


status: Public on Nov 11 2010

city: San Francisco

first: UCSF-UBC

last: CENTER

state: CA

address: UCSF-UBC

institute: UCSF-UBC

description:
design description: ChIP-Seq input analysis of breast myoepithelial cell from RM080 (HS2765) using Illumina Genome Analyzer IIx
library name: HS2765
EXPERIMENT_TYPE: ChIP-Seq Input
EXTRACTION_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Fisher 550 Sonic Dismembrator
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 10 min
CHIP_PROTOCOL: Input
CHIP_PROTOCOL_CHROMATIN_AMOUNT: 2.08 ug
SIZE_FRACTION: 45-290 bp
****************
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: GSM613897_UCSF-UBC.Breast_Myoepithelial_Cells.Input.RM080.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: HS2765-1_629WHAAXX.hg19.level.1
ANALYSIS TITLE: Mapping of Breast Myoepithelial Cells ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on Breast Myoepithelial Cells, Donor RM080 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.4298
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED: 67
FINDPEAKS_SCORE: 0.0098
FINDPEAKS_PERCENTILE: 49
HOTSPOT_SCORE: 0.0094
HOTSPOT_PERCENTILE: 30
IROC_SCORE: 0.9746
IROC_PERCENTILE: 82
POISSON_SCORE: 0.1226
POISSON_PERCENTILE: 3

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

ANALYSIS FILE NAME: GSM613897_UCSF-UBC.Breast_Myoepithelial_Cells.Input.RM080.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: HS2765-1_629WHAAXX.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Breast Myoepithelial Cells ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from Breast Myoepithelial Cells, Donor RM080 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.4347
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: BMC Input 80
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-UCD Breast Myoepithelial Cells ChIP-Seq Input Donor RM080 EA Release 2

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED: 67
FINDPEAKS_SCORE: 0.0098
FINDPEAKS_PERCENTILE: 49
HOTSPOT_SCORE: 0.0094
HOTSPOT_PERCENTILE: 30
IROC_SCORE: 0.9746
IROC_PERCENTILE: 82
POISSON_SCORE: 0.1226
POISSON_PERCENTILE: 3

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

extract_protocol: library construction protocol: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)

tag: submitted sample id

value: female

tag: body site

value: Breast

tag: histological type

value: Myoepithelial cell

tag: is tumor

value: No

value: primary cell

value: breast myoepithelial cell


description:
design description: ChIP-Seq input analysis of peripheral mononuclear cell from TC012 (HS2743) using Illumina Genome Analyzer IIx
library name: HS2743
EXPERIMENT_TYPE: ChIP-Seq Input
EXTRACTION_PROTOCOL: Refer to document 'REMC ChIP and Library Construction Protocol' from the Farnham Lab at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Bioruptor
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 30 min
CHIP_PROTOCOL: Input
CHIP_PROTOCOL_CHROMATIN_AMOUNT: 0.1 ug
SIZE_FRACTION: 92-314 bp
****************
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: GSM613896_UCSF-UBC.Peripheral_Blood_Mononuclear_Primary_Cells.Input.TC012.HS2743.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: HS2743-1_62H26AAXX.hg19.level.1
ANALYSIS TITLE: Mapping of Peripheral Blood Mononuclear Primary Cells ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on Peripheral Blood Mononuclear Primary Cells, Donor TC012, Library HS2743 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.4301
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED: 67
FINDPEAKS_SCORE: 0.0259
FINDPEAKS_PERCENTILE: 79
HOTSPOT_SCORE: 0.0725
HOTSPOT_PERCENTILE: 56
IROC_SCORE: 0.8608
IROC_PERCENTILE: 55
POISSON_SCORE: 0.2357
POISSON_PERCENTILE: 49

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

ANALYSIS FILE NAME: GSM613896_UCSF-UBC.Peripheral_Blood_Mononuclear_Primary_Cells.Input.TC012.HS2743.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: HS2743-1_62H26AAXX.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Peripheral Blood Mononuclear Primary Cells ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from Peripheral Blood Mononuclear Primary Cells, Donor TC012, Library HS2743 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.4350
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: PBM Input 12 43
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-UCD Peripheral Blood Mononuclear Primary Cells ChIP-Seq Input Donor TC012 Library HS2743 EA Release 2

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED: 67
FINDPEAKS_SCORE: 0.0259
FINDPEAKS_PERCENTILE: 79
HOTSPOT_SCORE: 0.0725
HOTSPOT_PERCENTILE: 56
IROC_SCORE: 0.8608
IROC_PERCENTILE: 55
POISSON_SCORE: 0.2357
POISSON_PERCENTILE: 49

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

extract_protocol: library construction protocol: Refer to document 'REMC ChIP and Library Construction Protocol' from the Farnham Lab at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)

value: male

value: Blood

value: Peripheral blood mononuclear cell


description:
design description: ChIP-Seq input analysis of peripheral mononuclear cell from TC010 (HS2626) using Illumina Genome Analyzer IIx
library name: HS2626
EXPERIMENT_TYPE: ChIP-Seq Input
EXTRACTION_PROTOCOL: Refer to document 'REMC ChIP and Library Construction Protocol' from the Farnham Lab at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Bioruptor
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 30 min
CHIP_PROTOCOL: Input
CHIP_PROTOCOL_CHROMATIN_AMOUNT: 1 ug
SIZE_FRACTION: 37-268 bp
****************
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: GSM613894_UCSF-UBC.Peripheral_Blood_Mononuclear_Primary_Cells.Input.TC010.HS2626.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: HS2626-1_70601AAXX.hg19.level.1
ANALYSIS TITLE: Mapping of Peripheral Blood Mononuclear Primary Cells ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on Peripheral Blood Mononuclear Primary Cells, Donor TC010, Library HS2626 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.4295
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED: 67
FINDPEAKS_SCORE: 0.011
FINDPEAKS_PERCENTILE: 58
HOTSPOT_SCORE: 0.0434
HOTSPOT_PERCENTILE: 45
IROC_SCORE: 0.0
IROC_PERCENTILE: 18
POISSON_SCORE: 0.3034
POISSON_PERCENTILE: 76

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

ANALYSIS FILE NAME: GSM613894_UCSF-UBC.Peripheral_Blood_Mononuclear_Primary_Cells.Input.TC010.HS2626.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: HS2626-1_70601AAXX.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Peripheral Blood Mononuclear Primary Cells ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from Peripheral Blood Mononuclear Primary Cells, Donor TC010, Library HS2626 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.4344
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: PBM Input 10 26
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-UCD Peripheral Blood Mononuclear Primary Cells ChIP-Seq Input Donor TC010 Library HS2626 EA Release 2

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED: 67
FINDPEAKS_SCORE: 0.011
FINDPEAKS_PERCENTILE: 58
HOTSPOT_SCORE: 0.0434
HOTSPOT_PERCENTILE: 45
IROC_SCORE: 0.0
IROC_PERCENTILE: 18
POISSON_SCORE: 0.3034
POISSON_PERCENTILE: 76

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


description:
design description: ChIP-Seq input analysis of peripheral mononuclear cell from TC010 (HS2625) using Illumina Genome Analyzer IIx
library name: HS2625
EXPERIMENT_TYPE: ChIP-Seq Input
EXTRACTION_PROTOCOL: Refer to document 'REMC ChIP and Library Construction Protocol' from the Farnham Lab at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Bioruptor
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 30 min
CHIP_PROTOCOL: Input
CHIP_PROTOCOL_CHROMATIN_AMOUNT: 1 ug
SIZE_FRACTION: 171-450 bp
****************
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: GSM613893_UCSF-UBC.Peripheral_Blood_Mononuclear_Primary_Cells.Input.TC010.HS2625.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: HS2625-1_623WAAAXX.hg19.level.1
ANALYSIS TITLE: Mapping of Peripheral Blood Mononuclear Primary Cells ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on Peripheral Blood Mononuclear Primary Cells, Donor TC010, Library HS2625 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.4341
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED: 67
FINDPEAKS_SCORE: 0.0133
FINDPEAKS_PERCENTILE: 64
HOTSPOT_SCORE: 0.0645
HOTSPOT_PERCENTILE: 53
IROC_SCORE: 0.7506
IROC_PERCENTILE: 44
POISSON_SCORE: 0.236
POISSON_PERCENTILE: 51

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

ANALYSIS FILE NAME: GSM613893_UCSF-UBC.Peripheral_Blood_Mononuclear_Primary_Cells.Input.TC010.HS2625.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: HS2625-1_623WAAAXX.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Peripheral Blood Mononuclear Primary Cells ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from Peripheral Blood Mononuclear Primary Cells, Donor TC010, Library HS2625 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.4390
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: PBM Input 10 25
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-UCD Peripheral Blood Mononuclear Primary Cells ChIP-Seq Input Donor TC010 Library HS2625 EA Release 2

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED: 67
FINDPEAKS_SCORE: 0.0133
FINDPEAKS_PERCENTILE: 64
HOTSPOT_SCORE: 0.0645
HOTSPOT_PERCENTILE: 53
IROC_SCORE: 0.7506
IROC_PERCENTILE: 44
POISSON_SCORE: 0.236
POISSON_PERCENTILE: 51

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


description:
design description: ChIP-Seq input analysis of breast variant human mammary epithelial cell from RM035 (HS2620) using Illumina Genome Analyzer IIx
library name: HS2620
EXPERIMENT_TYPE: ChIP-Seq Input
EXTRACTION_PROTOCOL: Refer to document 'REMC ChIP and Library Construction Protocol' from the Farnham Lab at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Bioruptor
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 30 min
CHIP_PROTOCOL: Input
CHIP_PROTOCOL_CHROMATIN_AMOUNT: 0.5 ug
SIZE_FRACTION: 38-321 bp
****************
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: GSM613892_UCSF-UBC.Breast_vHMEC.Input.RM035.HS2620.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: HS2620-1_623YCAAXX.hg19.level.1
ANALYSIS TITLE: Mapping of Breast vHMEC ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on Breast vHMEC, Donor RM035, Library HS2620 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.4328
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED: 67
FINDPEAKS_SCORE: 0.0101
FINDPEAKS_PERCENTILE: 54
HOTSPOT_SCORE: 0.0258
HOTSPOT_PERCENTILE: 39
IROC_SCORE: 0.9517
IROC_PERCENTILE: 73
POISSON_SCORE: 0.2172
POISSON_PERCENTILE: 39

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

ANALYSIS FILE NAME: GSM613892_UCSF-UBC.Breast_vHMEC.Input.RM035.HS2620.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: HS2620-1_623YCAAXX.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Breast vHMEC ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from Breast vHMEC, Donor RM035, Library HS2620 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.4377
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: Bv Input 35 20
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-UCD Breast vHMEC ChIP-Seq Input Donor RM035 Library HS2620 EA Release 2

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED: 67
FINDPEAKS_SCORE: 0.0101
FINDPEAKS_PERCENTILE: 54
HOTSPOT_SCORE: 0.0258
HOTSPOT_PERCENTILE: 39
IROC_SCORE: 0.9517
IROC_PERCENTILE: 73
POISSON_SCORE: 0.2172
POISSON_PERCENTILE: 39

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

value: Variant human mammary epithelial cell culture

value: primary cell culture

tag: cell type


title: Small_RNA

city: beijing

first: Jinsong

last: Zhang

address: No.1 West Beichen Road,Chaoyang District

country: China

institute: IGDB

description: collect small RNA from total RNA of soybean seed by page by PAGE

library_source: transcriptomic

data_processing:
The raw data was preprocessed by Fastx-toolkit pipeline to remove low quality reads and clip adapter sequence. As to small RNA library, small RNAs ranged from 18-25 nt were collected and mapped to the soybean genome using SOAP2. The unique RNA sequences that perfectly matched the genome were subjected to the subsequent analysis. RNA reads, showing identical sequences to the known miRNAs from miRBase database, were picked up as the miRNA dataset of soybean. Sequences matching noncoding rRNA, tRNA, snRNA and snoRNA at Rfam database were removed. Reads overlapped with exons of protein-coding genes were excluded to avoid mRNA contamination. The remaining sequences were considered for prediction to find new miRNAs
processed data file: 1st column: length of small RNA
2nd column: the counts of small RNA by solexa sequencing,
3rd column: unique sequence of small RNA

molecule: total RNA

organism: Glycine max

source_name: soybean seed

growth_protocol: Soybean seeds of (Glycine max) cultivar Heinong44 were directly planted in the Experimental Station of Institute of Genetics and Developmental Biology, Chinese Academy of Sciences in Beijing on May. Soybean seeds of 15 days after flowering (DAF) were collected

extract_protocol: By polyacrylamide gel electrophoresis, the small RNAs (~17-27 nt) were purified from 100 μg of total RNA and ligated to a 5’ RNA adapter and a 3’ RNA adapter. Reverse transcriptase reaction followed by low cycle PCR was performed to obtain sufficient product for SBS sequencing. PCR products were collected by gel purification and sequenced by Solexa technology.

tag: developmental stage

value: 15 days after flowering

tag: cultivar


description:
design description: H3K36me3 ChIP-Seq analysis of breast myoepithelial cell from RM080 (HS2763) using Illumina Genome Analyzer IIx
library name: HS2763
EXPERIMENT_TYPE: Histone H3K36me3
EXTRACTION_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Fisher 550 Sonic Dismembrator
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 10 min
CHIP_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
CHIP_PROTOCOL_CHROMATIN_AMOUNT: 3.5 ug
SIZE_FRACTION: 36-265 bp
CHIP_PROTOCOL_BEAD_TYPE: Sepharose A/G Bead Mix
CHIP_PROTOCOL_BEAD_AMOUNT: 20 ul
CHIP_PROTOCOL_ANTIBODY_AMOUNT: 2.5 ug
CHIP_ANTIBODY: H3K36me3
CHIP_ANTIBODY_PROVIDER: Abcam
CHIP_ANTIBODY_CATALOG: ab9050
CHIP_ANTIBODY_LOT: 134025
****************
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: GSM613888_UCSF-UBC.Breast_Myoepithelial_Cells.H3K36me3.RM080.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: HS2763-1_629WHAAXX.hg19.level.1
ANALYSIS TITLE: Mapping of Breast Myoepithelial Cells Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K36me3 ChIP-Seq on Breast Myoepithelial Cells, Donor RM080 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.4323
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED: 54
FINDPEAKS_SCORE: 0.3895
FINDPEAKS_PERCENTILE: 78
HOTSPOT_SCORE: 0.324
HOTSPOT_PERCENTILE: 72
IROC_SCORE: 0.9837
IROC_PERCENTILE: 74
POISSON_SCORE: 0.6604
POISSON_PERCENTILE: 83

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

ANALYSIS FILE NAME: GSM613888_UCSF-UBC.Breast_Myoepithelial_Cells.H3K36me3.RM080.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: HS2763-1_629WHAAXX.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Breast Myoepithelial Cells Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K36me3 ChIP-Seq read mappings from Breast Myoepithelial Cells, Donor RM080 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.4372
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: BMC H3K36me3 80
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-UCD Breast Myoepithelial Cells Histone H3K36me3 Donor RM080 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED: 54
FINDPEAKS_SCORE: 0.3895
FINDPEAKS_PERCENTILE: 78
HOTSPOT_SCORE: 0.324
HOTSPOT_PERCENTILE: 72
IROC_SCORE: 0.9837
IROC_PERCENTILE: 74
POISSON_SCORE: 0.6604
POISSON_PERCENTILE: 83

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


description:
design description: H3K27me3 ChIP-Seq analysis of breast myoepithelial cell from RM080 (HS2762) using Illumina Genome Analyzer IIx
library name: HS2762
EXPERIMENT_TYPE: Histone H3K27me3
EXTRACTION_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Fisher 550 Sonic Dismembrator
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 10 min
CHIP_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
CHIP_PROTOCOL_CHROMATIN_AMOUNT: 3.5 ug
SIZE_FRACTION: 49-275 bp
CHIP_PROTOCOL_BEAD_TYPE: Sepharose A/G Bead Mix
CHIP_PROTOCOL_BEAD_AMOUNT: 20 ul
CHIP_PROTOCOL_ANTIBODY_AMOUNT: 5 ug
CHIP_ANTIBODY: H3K27me3
CHIP_ANTIBODY_PROVIDER: Diagenode
CHIP_ANTIBODY_CATALOG: pAb-069-050
CHIP_ANTIBODY_LOT: A299-00241
****************
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: GSM613887_UCSF-UBC.Breast_Myoepithelial_Cells.H3K27me3.RM080.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: HS2762-1_629WHAAXX.hg19.level.1
ANALYSIS TITLE: Mapping of Breast Myoepithelial Cells Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27me3 ChIP-Seq on Breast Myoepithelial Cells, Donor RM080 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.4297
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED: 52
FINDPEAKS_SCORE: 0.1937
FINDPEAKS_PERCENTILE: 62
HOTSPOT_SCORE: 0.2704
HOTSPOT_PERCENTILE: 65
IROC_SCORE: 0.9476
IROC_PERCENTILE: 71
POISSON_SCORE: 0.51
POISSON_PERCENTILE: 69

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

ANALYSIS FILE NAME: GSM613887_UCSF-UBC.Breast_Myoepithelial_Cells.H3K27me3.RM080.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: HS2762-1_629WHAAXX.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Breast Myoepithelial Cells Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27me3 ChIP-Seq read mappings from Breast Myoepithelial Cells, Donor RM080 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.4346
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: BMC H3K27me3 80
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-UCD Breast Myoepithelial Cells Histone H3K27me3 Donor RM080 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED: 52
FINDPEAKS_SCORE: 0.1937
FINDPEAKS_PERCENTILE: 62
HOTSPOT_SCORE: 0.2704
HOTSPOT_PERCENTILE: 65
IROC_SCORE: 0.9476
IROC_PERCENTILE: 71
POISSON_SCORE: 0.51
POISSON_PERCENTILE: 69

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


title: ChIP-Seq analysis of H3K36me3 human fetal lung cells (superseded by GSE120318)

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:20100129:02--ChIP:XZ:20100125:02:fetal lung:H3K36me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3727
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3880
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************
BED and WIG files were replaced on April 29, 2014
****************************
This sample record's metadata may be obsolete; up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE120318
****************************

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

ANALYSIS FILE NAME: GSM621387_BI.Fetal_Lung.H3K36me3.UW_H-22727.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100129:02--ChIP:XZ:20100125:02:fetal lung:H3K36me3.hg19.level.1
ANALYSIS TITLE: Mapping of Fetal Lung Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K36me3 ChIP-Seq on Fetal Lung, Donor H-22727 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.4569
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED: 54
FINDPEAKS_SCORE: 0.1375
FINDPEAKS_PERCENTILE: 26
HOTSPOT_SCORE: 0.1924
HOTSPOT_PERCENTILE: 25
IROC_SCORE: 0.9404
IROC_PERCENTILE: 39
POISSON_SCORE: 0.5072
POISSON_PERCENTILE: 54

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

ANALYSIS FILE NAME: GSM621387_BI.Fetal_Lung.H3K36me3.UW_H-22727.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100129:02--ChIP:XZ:20100125:02:fetal lung:H3K36me3.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Lung Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K36me3 ChIP-Seq read mappings from Fetal Lung, Donor H-22727 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.4843
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: FL H3K36me3 27
BROWSER_TRACK_DESCRIPTION: BI Fetal Lung Histone H3K36me3 Donor H-22727 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED: 54
FINDPEAKS_SCORE: 0.1375
FINDPEAKS_PERCENTILE: 26
HOTSPOT_SCORE: 0.1924
HOTSPOT_PERCENTILE: 25
IROC_SCORE: 0.9404
IROC_PERCENTILE: 39
POISSON_SCORE: 0.5072
POISSON_PERCENTILE: 54

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

source_name: Primary fetal lung tissue; Lib:XZ:20100129:02--ChIP:XZ:20100125:02:fetal lung:H3K36me3

value: surgery

value: genomic DNA

value: Fetal lung

value: Unknown

value: Primary Tissue

value: lung

value: UW

value: 101 days

value: Protein A-Sepharose 4B

value: 70 ul bed volume

value: Abcam

value: Histone H3K36me3

value: Bioruptor


description:
design description: H3K9me3 ChIP-Seq analysis of breast myoepithelial cell from RM080 (HS2761) using Illumina Genome Analyzer IIx
library name: HS2761
EXPERIMENT_TYPE: Histone H3K9me3
EXTRACTION_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Fisher 550 Sonic Dismembrator
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 10 min
CHIP_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
CHIP_PROTOCOL_CHROMATIN_AMOUNT: 3.5 ug
SIZE_FRACTION: 62-270 bp
CHIP_PROTOCOL_BEAD_TYPE: Sepharose A/G Bead Mix
CHIP_PROTOCOL_BEAD_AMOUNT: 20 ul
CHIP_PROTOCOL_ANTIBODY_AMOUNT: 5 ug
CHIP_ANTIBODY: H3K9me3
CHIP_ANTIBODY_PROVIDER: Diagenode
CHIP_ANTIBODY_CATALOG: pAb-056-050
CHIP_ANTIBODY_LOT: A93-0042
****************
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: GSM613886_UCSF-UBC.Breast_Myoepithelial_Cells.H3K9me3.RM080.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: HS2761-1_629WHAAXX.hg19.level.1
ANALYSIS TITLE: Mapping of Breast Myoepithelial Cells Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9me3 ChIP-Seq on Breast Myoepithelial Cells, Donor RM080 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.4318
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED: 59
FINDPEAKS_SCORE: 0.2335
FINDPEAKS_PERCENTILE: 83
HOTSPOT_SCORE: 0.2698
HOTSPOT_PERCENTILE: 86
IROC_SCORE: 0.9278
IROC_PERCENTILE: 80
POISSON_SCORE: 0.5306
POISSON_PERCENTILE: 90

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

ANALYSIS FILE NAME: GSM613886_UCSF-UBC.Breast_Myoepithelial_Cells.H3K9me3.RM080.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: HS2761-1_629WHAAXX.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Breast Myoepithelial Cells Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9me3 ChIP-Seq read mappings from Breast Myoepithelial Cells, Donor RM080 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.4367
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: BMC H3K9me3 80
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-UCD Breast Myoepithelial Cells Histone H3K9me3 Donor RM080 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED: 59
FINDPEAKS_SCORE: 0.2335
FINDPEAKS_PERCENTILE: 83
HOTSPOT_SCORE: 0.2698
HOTSPOT_PERCENTILE: 86
IROC_SCORE: 0.9278
IROC_PERCENTILE: 80
POISSON_SCORE: 0.5306
POISSON_PERCENTILE: 90

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

value: female

value: Breast

value: Myoepithelial cell

value: No

value: primary cell

value: breast myoepithelial cell


description:
design description: H3K9ac ChIP-Seq analysis of breast myoepithelial cell from RM080 (HS2764) using Illumina Genome Analyzer IIx
library name: HS2764
EXPERIMENT_TYPE: Histone H3K9ac
EXTRACTION_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Fisher 550 Sonic Dismembrator
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 10 min
CHIP_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
CHIP_PROTOCOL_CHROMATIN_AMOUNT: 3.5 ug
SIZE_FRACTION: 43-290 bp
CHIP_PROTOCOL_BEAD_TYPE: Sepharose A/G Bead Mix
CHIP_PROTOCOL_BEAD_AMOUNT: 20 ul
CHIP_PROTOCOL_ANTIBODY_AMOUNT: 10 ul
CHIP_ANTIBODY: H3K9ac
CHIP_ANTIBODY_PROVIDER: Cell Signaling Technology
CHIP_ANTIBODY_CATALOG: 9649S
CHIP_ANTIBODY_LOT: 1
****************
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: GSM613889_UCSF-UBC.Breast_Myoepithelial_Cells.H3K9ac.RM080.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: HS2764-1_629WHAAXX.hg19.level.1
ANALYSIS TITLE: Mapping of Breast Myoepithelial Cells Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9ac ChIP-Seq on Breast Myoepithelial Cells, Donor RM080 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.4333
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED: 35
FINDPEAKS_SCORE: 0.0568
FINDPEAKS_PERCENTILE: 6
HOTSPOT_SCORE: 0.1622
HOTSPOT_PERCENTILE: 26
IROC_SCORE: 0.8096
IROC_PERCENTILE: 3
POISSON_SCORE: 0.3481
POISSON_PERCENTILE: 40

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

ANALYSIS FILE NAME: GSM613889_UCSF-UBC.Breast_Myoepithelial_Cells.H3K9ac.RM080.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: HS2764-1_629WHAAXX.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Breast Myoepithelial Cells Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9ac ChIP-Seq read mappings from Breast Myoepithelial Cells, Donor RM080 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.4382
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: BMC H3K9ac 80
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-UCD Breast Myoepithelial Cells Histone H3K9ac Donor RM080 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED: 35
FINDPEAKS_SCORE: 0.0568
FINDPEAKS_PERCENTILE: 6
HOTSPOT_SCORE: 0.1622
HOTSPOT_PERCENTILE: 26
IROC_SCORE: 0.8096
IROC_PERCENTILE: 3
POISSON_SCORE: 0.3481
POISSON_PERCENTILE: 40

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


description:
design description: ChIP-Seq input analysis of breast myoepithelial cell from RM066 (HS2445) using Illumina Genome Analyzer IIx
library name: HS2445
EXPERIMENT_TYPE: ChIP-Seq Input
EXTRACTION_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Fisher 550 Sonic Dismembrator
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 10 min
CHIP_PROTOCOL: Input
CHIP_PROTOCOL_CHROMATIN_AMOUNT: 1.16 ug
SIZE_FRACTION: 65-265 bp
****************
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: GSM613891_UCSF-UBC.Breast_Myoepithelial_Cells.Input.RM066.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: HS2445-1_624UKAAXX.hg19.level.1
ANALYSIS TITLE: Mapping of Breast Myoepithelial Cells ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on Breast Myoepithelial Cells, Donor RM066 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.4330
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED: 67
FINDPEAKS_SCORE: 0.0103
FINDPEAKS_PERCENTILE: 57
HOTSPOT_SCORE: 0.0159
HOTSPOT_PERCENTILE: 32
IROC_SCORE: 0.9658
IROC_PERCENTILE: 77
POISSON_SCORE: 0.1617
POISSON_PERCENTILE: 9

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

ANALYSIS FILE NAME: GSM613891_UCSF-UBC.Breast_Myoepithelial_Cells.Input.RM066.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: HS2445-1_624UKAAXX.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Breast Myoepithelial Cells ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from Breast Myoepithelial Cells, Donor RM066 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.4379
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: BMC Input 66
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-UCD Breast Myoepithelial Cells ChIP-Seq Input Donor RM066 EA Release 2

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED: 67
FINDPEAKS_SCORE: 0.0103
FINDPEAKS_PERCENTILE: 57
HOTSPOT_SCORE: 0.0159
HOTSPOT_PERCENTILE: 32
IROC_SCORE: 0.9658
IROC_PERCENTILE: 77
POISSON_SCORE: 0.1617
POISSON_PERCENTILE: 9

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


description:
design description: ChIP-Seq input analysis of breast variant human mammary epithelial cell from RM035 (HS1995) using Illumina Genome Analyzer IIx
library name: HS1995
EXPERIMENT_TYPE: ChIP-Seq Input
EXTRACTION_PROTOCOL: Refer to document 'REMC ChIP and Library Construction Protocol' from the Farnham Lab at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Bioruptor
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 25 min
CHIP_PROTOCOL: Input
CHIP_PROTOCOL_CHROMATIN_AMOUNT: 0.1 ug
SIZE_FRACTION: 212-562 bp
****************
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: GSM613890_UCSF-UBC.Breast_vHMEC.Input.RM035.HS1995.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: HS1995-1_60065AAXX.hg19.level.1
ANALYSIS TITLE: Mapping of Breast vHMEC ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on Breast vHMEC, Donor RM035, Library HS1995 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.4332
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED: 67
FINDPEAKS_SCORE: 0.0131
FINDPEAKS_PERCENTILE: 63
HOTSPOT_SCORE: 0.019
HOTSPOT_PERCENTILE: 33
IROC_SCORE: 0.0
IROC_PERCENTILE: 18
POISSON_SCORE: 0.2241
POISSON_PERCENTILE: 43

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

ANALYSIS FILE NAME: GSM613890_UCSF-UBC.Breast_vHMEC.Input.RM035.HS1995.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: HS1995-1_60065AAXX.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Breast vHMEC ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from Breast vHMEC, Donor RM035, Library HS1995 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.4381
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: Bv Input 35 95
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-UCD Breast vHMEC ChIP-Seq Input Donor RM035 Library HS1995 EA Release 2

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED: 67
FINDPEAKS_SCORE: 0.0131
FINDPEAKS_PERCENTILE: 63
HOTSPOT_SCORE: 0.019
HOTSPOT_PERCENTILE: 33
IROC_SCORE: 0.0
IROC_PERCENTILE: 18
POISSON_SCORE: 0.2241
POISSON_PERCENTILE: 43

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

value: Variant human mammary epithelial cell culture

value: primary cell culture


description:
design description: H3K4me1 ChIP-Seq analysis of breast myoepithelial cell from RM080 (HS2759) using Illumina Genome Analyzer IIx
library name: HS2759
EXPERIMENT_TYPE: Histone H3K4me1
EXTRACTION_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Fisher 550 Sonic Dismembrator
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 10 min
CHIP_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
CHIP_PROTOCOL_CHROMATIN_AMOUNT: 3.5 ug
SIZE_FRACTION: 58-294 bp
CHIP_PROTOCOL_BEAD_TYPE: Sepharose A/G Bead Mix
CHIP_PROTOCOL_BEAD_AMOUNT: 20 ul
CHIP_PROTOCOL_ANTIBODY_AMOUNT: 3.75 ug
CHIP_ANTIBODY: H3K4me1
CHIP_ANTIBODY_PROVIDER: Diagenode
CHIP_ANTIBODY_CATALOG: pAb-037-050
CHIP_ANTIBODY_LOT: A399-0011
****************
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: GSM613885_UCSF-UBC.Breast_Myoepithelial_Cells.H3K4me1.RM080.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: HS2759-1_62A26AAXX.hg19.level.1
ANALYSIS TITLE: Mapping of Breast Myoepithelial Cells Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me1 ChIP-Seq on Breast Myoepithelial Cells, Donor RM080 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.4299
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED: 43
FINDPEAKS_SCORE: 0.3829
FINDPEAKS_PERCENTILE: 60
HOTSPOT_SCORE: 0.3773
HOTSPOT_PERCENTILE: 51
IROC_SCORE: 0.9889
IROC_PERCENTILE: 55
POISSON_SCORE: 0.6235
POISSON_PERCENTILE: 77

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

ANALYSIS FILE NAME: GSM613885_UCSF-UBC.Breast_Myoepithelial_Cells.H3K4me1.RM080.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: HS2759-1_62A26AAXX.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Breast Myoepithelial Cells Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me1 ChIP-Seq read mappings from Breast Myoepithelial Cells, Donor RM080 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.4348
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: BMC H3K4me1 80
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-UCD Breast Myoepithelial Cells Histone H3K4me1 Donor RM080 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED: 43
FINDPEAKS_SCORE: 0.3829
FINDPEAKS_PERCENTILE: 60
HOTSPOT_SCORE: 0.3773
HOTSPOT_PERCENTILE: 51
IROC_SCORE: 0.9889
IROC_PERCENTILE: 55
POISSON_SCORE: 0.6235
POISSON_PERCENTILE: 77

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