title: ChIP-Seq analysis of WCE in human fetal heart cells; Lib:XZ:20100129:24--ChIP:XZ:20100125:24:fetal heart:WCE

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:20100129:24--ChIP:XZ:20100125:24:fetal heart:WCE
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3736
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: GSM621396_BI.Fetal_Heart.Input.UW_H-22727.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100129:24--ChIP:XZ:20100125:24:fetal heart:WCE.hg19.level.1
ANALYSIS TITLE: Mapping of Fetal Heart ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input 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.4592
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: 0.0111
FINDPEAKS_PERCENTILE: 60
HOTSPOT_SCORE: 0.0794
HOTSPOT_PERCENTILE: 58
IROC_SCORE: 0.0
IROC_PERCENTILE: NA
POISSON_SCORE: 0.2858
POISSON_PERCENTILE: 75

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

ANALYSIS FILE NAME: GSM621396_BI.Fetal_Heart.Input.UW_H-22727.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100129:24--ChIP:XZ:20100125:24:fetal heart:WCE.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Heart ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input 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.4866
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 Input 27
BROWSER_TRACK_DESCRIPTION: BI Fetal Heart ChIP-Seq Input Donor H-22727 EA Release 2

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED: 67
FINDPEAKS_SCORE: 0.0111
FINDPEAKS_PERCENTILE: 60
HOTSPOT_SCORE: 0.0794
HOTSPOT_PERCENTILE: 58
IROC_SCORE: 0.0
IROC_PERCENTILE: NA
POISSON_SCORE: 0.2858
POISSON_PERCENTILE: 75

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

source_name: Primary fetal heart tissue; Lib:XZ:20100129:24--ChIP:XZ:20100125:24:fetal heart:WCE

value: surgery

value: genomic DNA

value: Fetal heart

value: Unknown

value: Primary Tissue

value: heart

value: standard

value: SDS lysis

value: ChIP-Seq Input

value: Input


status: Public on Nov 11 2010

type: SRA

city: San Francisco

first: UCSF-UBC

last: CENTER

state: CA

address: UCSF-UBC

country: USA

institute: UCSF-UBC

description:
design description: H3K9me3 ChIP-Seq analysis of peripheral mononuclear cell from TC012 (HS2742) using Illumina Genome Analyzer IIx
library name: HS2742
EXPERIMENT_TYPE: Histone H3K9me3
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: 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/)
CHIP_PROTOCOL_CHROMATIN_AMOUNT: 5 ug
SIZE_FRACTION: 269-473 bp
CHIP_PROTOCOL_BEAD_TYPE: Protein G Mag Beads
CHIP_PROTOCOL_BEAD_AMOUNT: 15 ul
CHIP_PROTOCOL_ANTIBODY_AMOUNT: 20 ul
CHIP_ANTIBODY: H3K9me3
CHIP_ANTIBODY_PROVIDER: Cell Signaling Technology
CHIP_ANTIBODY_CATALOG: 9754S
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
****************

library_source: genomic

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

ANALYSIS FILE NAME: GSM613882_UCSF-UBC.Peripheral_Blood_Mononuclear_Primary_Cells.H3K9me3.TC012.HS2742.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: HS2742-1_62H0JAAXX.hg19.level.1
ANALYSIS TITLE: Mapping of Peripheral Blood Mononuclear Primary Cells Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9me3 ChIP-Seq on Peripheral Blood Mononuclear Primary Cells, Donor TC012, Library HS2742 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.4304
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: 0.1122
FINDPEAKS_PERCENTILE: 59
HOTSPOT_SCORE: 0.206
HOTSPOT_PERCENTILE: 69
IROC_SCORE: 0.783
IROC_PERCENTILE: 36
POISSON_SCORE: 0.3337
POISSON_PERCENTILE: 36

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

ANALYSIS FILE NAME: GSM613882_UCSF-UBC.Peripheral_Blood_Mononuclear_Primary_Cells.H3K9me3.TC012.HS2742.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: HS2742-1_62H0JAAXX.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Peripheral Blood Mononuclear Primary Cells Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9me3 ChIP-Seq read mappings from Peripheral Blood Mononuclear Primary Cells, Donor TC012, Library HS2742 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.4353
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 H3K9me3 12 42
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-UCD Peripheral Blood Mononuclear Primary Cells Histone H3K9me3 Donor TC012 Library HS2742 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED: 59
FINDPEAKS_SCORE: 0.1122
FINDPEAKS_PERCENTILE: 59
HOTSPOT_SCORE: 0.206
HOTSPOT_PERCENTILE: 69
IROC_SCORE: 0.783
IROC_PERCENTILE: 36
POISSON_SCORE: 0.3337
POISSON_PERCENTILE: 36

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

molecule: genomic DNA

organism: Homo sapiens

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/)

tag: submitted sample id

tag: Sex

value: male

tag: body site

value: Blood

tag: histological type

value: Peripheral blood mononuclear cell

tag: is tumor

value: No

value: primary cell


description:
design description: H3K4me1 ChIP-Seq analysis of peripheral mononuclear cell from TC012 (HS2745) using Illumina Genome Analyzer IIx
library name: HS2745
EXPERIMENT_TYPE: Histone H3K4me1
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: 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/)
CHIP_PROTOCOL_CHROMATIN_AMOUNT: 3 ug
SIZE_FRACTION: 80-330 bp
CHIP_PROTOCOL_BEAD_TYPE: Protein G Mag Beads
CHIP_PROTOCOL_BEAD_AMOUNT: 15 ul
CHIP_PROTOCOL_ANTIBODY_AMOUNT: 2 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: GSM613884_UCSF-UBC.Peripheral_Blood_Mononuclear_Primary_Cells.H3K4me1.TC012.HS2745.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: HS2745-1_62H0JAAXX.hg19.level.1
ANALYSIS TITLE: Mapping of Peripheral Blood Mononuclear Primary Cells Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me1 ChIP-Seq on Peripheral Blood Mononuclear Primary Cells, Donor TC012, Library HS2745 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.4340
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: 0.0869
FINDPEAKS_PERCENTILE: 14
HOTSPOT_SCORE: 0.1534
HOTSPOT_PERCENTILE: 7
IROC_SCORE: 0.956
IROC_PERCENTILE: 24
POISSON_SCORE: 0.4865
POISSON_PERCENTILE: 26

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

ANALYSIS FILE NAME: GSM613884_UCSF-UBC.Peripheral_Blood_Mononuclear_Primary_Cells.H3K4me1.TC012.HS2745.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: HS2745-1_62H0JAAXX.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Peripheral Blood Mononuclear Primary Cells Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me1 ChIP-Seq read mappings from Peripheral Blood Mononuclear Primary Cells, Donor TC012, Library HS2745 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.4389
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 H3K4me1 12 45
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-UCD Peripheral Blood Mononuclear Primary Cells Histone H3K4me1 Donor TC012 Library HS2745 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED: 43
FINDPEAKS_SCORE: 0.0869
FINDPEAKS_PERCENTILE: 14
HOTSPOT_SCORE: 0.1534
HOTSPOT_PERCENTILE: 7
IROC_SCORE: 0.956
IROC_PERCENTILE: 24
POISSON_SCORE: 0.4865
POISSON_PERCENTILE: 26

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


description:
design description: H3K4me3 ChIP-Seq analysis of peripheral cd8 naive from TC010 (HS2739) using Illumina Genome Analyzer IIx
library name: HS2739
EXPERIMENT_TYPE: Histone H3K4me3
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: 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/)
CHIP_PROTOCOL_CHROMATIN_AMOUNT: 9 ug
SIZE_FRACTION: 77-312 bp
CHIP_PROTOCOL_BEAD_TYPE: Protein G Mag Beads
CHIP_PROTOCOL_BEAD_AMOUNT: 15 ul
CHIP_PROTOCOL_ANTIBODY_AMOUNT: 5 ul
CHIP_ANTIBODY: H3K4me3
CHIP_ANTIBODY_PROVIDER: Cell Signaling Technology
CHIP_ANTIBODY_CATALOG: 9751S
CHIP_ANTIBODY_LOT: 2
****************
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: GSM613881_UCSF-UBC.CD8_Naive_Primary_Cells.H3K4me3.TC010.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: HS2739-1_62H0JAAXX.hg19.level.1
ANALYSIS TITLE: Mapping of CD8 Naive Primary Cells Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me3 ChIP-Seq on CD8 Naive Primary Cells, Donor TC010 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.4334
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: 0.26
FINDPEAKS_PERCENTILE: 24
HOTSPOT_SCORE: 0.2599
HOTSPOT_PERCENTILE: 21
IROC_SCORE: 0.9999
IROC_PERCENTILE: 74
POISSON_SCORE: 0.3526
POISSON_PERCENTILE: 18

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

ANALYSIS FILE NAME: GSM613881_UCSF-UBC.CD8_Naive_Primary_Cells.H3K4me3.TC010.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: HS2739-1_62H0JAAXX.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of CD8 Naive Primary Cells Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me3 ChIP-Seq read mappings from CD8 Naive Primary Cells, Donor TC010 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.4383
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: CD8N H3K4me3 10
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-UCD CD8 Naive Primary Cells Histone H3K4me3 Donor TC010 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED: 62
FINDPEAKS_SCORE: 0.26
FINDPEAKS_PERCENTILE: 24
HOTSPOT_SCORE: 0.2599
HOTSPOT_PERCENTILE: 21
IROC_SCORE: 0.9999
IROC_PERCENTILE: 74
POISSON_SCORE: 0.3526
POISSON_PERCENTILE: 18

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

value: CD8 naive cell


description:
design description: H3K9ac ChIP-Seq analysis of peripheral mononuclear cell from TC012 (HS2744) using Illumina Genome Analyzer IIx
library name: HS2744
EXPERIMENT_TYPE: Histone H3K9ac
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: 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/)
CHIP_PROTOCOL_CHROMATIN_AMOUNT: 2 ug
SIZE_FRACTION: 91-252 bp
CHIP_PROTOCOL_BEAD_TYPE: Protein G Mag Beads
CHIP_PROTOCOL_BEAD_AMOUNT: 15 ul
CHIP_PROTOCOL_ANTIBODY_AMOUNT: 15 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: GSM613883_UCSF-UBC.Peripheral_Blood_Mononuclear_Primary_Cells.H3K9ac.TC012.HS2744.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: HS2744-1_62H26AAXX.hg19.level.1
ANALYSIS TITLE: Mapping of Peripheral Blood Mononuclear Primary Cells Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9ac ChIP-Seq on Peripheral Blood Mononuclear Primary Cells, Donor TC012, Library HS2744 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.4305
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: 0.0881
FINDPEAKS_PERCENTILE: 17
HOTSPOT_SCORE: 0.1502
HOTSPOT_PERCENTILE: 17
IROC_SCORE: 0.9587
IROC_PERCENTILE: 26
POISSON_SCORE: 0.5284
POISSON_PERCENTILE: 71

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

ANALYSIS FILE NAME: GSM613883_UCSF-UBC.Peripheral_Blood_Mononuclear_Primary_Cells.H3K9ac.TC012.HS2744.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: HS2744-1_62H26AAXX.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Peripheral Blood Mononuclear Primary Cells Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9ac ChIP-Seq read mappings from Peripheral Blood Mononuclear Primary Cells, Donor TC012, Library HS2744 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.4354
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 H3K9ac 12 44
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-UCD Peripheral Blood Mononuclear Primary Cells Histone H3K9ac Donor TC012 Library HS2744 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED: 35
FINDPEAKS_SCORE: 0.0881
FINDPEAKS_PERCENTILE: 17
HOTSPOT_SCORE: 0.1502
HOTSPOT_PERCENTILE: 17
IROC_SCORE: 0.9587
IROC_PERCENTILE: 26
POISSON_SCORE: 0.5284
POISSON_PERCENTILE: 71

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


description:
design description: H3K9me3 ChIP-Seq analysis of peripheral mononuclear cell from TC010 (HS2622) using Illumina Genome Analyzer IIx
library name: HS2622
EXPERIMENT_TYPE: Histone H3K9me3
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: 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/)
CHIP_PROTOCOL_CHROMATIN_AMOUNT: 5 ug
SIZE_FRACTION: 222-530 bp
CHIP_PROTOCOL_BEAD_TYPE: Protein G Mag Beads
CHIP_PROTOCOL_BEAD_AMOUNT: 15 ul
CHIP_PROTOCOL_ANTIBODY_AMOUNT: 20 ul
CHIP_ANTIBODY: H3K9me3
CHIP_ANTIBODY_PROVIDER: Cell Signaling Technology
CHIP_ANTIBODY_CATALOG: 9754S
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: GSM613878_UCSF-UBC.Peripheral_Blood_Mononuclear_Primary_Cells.H3K9me3.TC010.HS2622.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: HS2622-1_623WAAAXX.hg19.level.1
ANALYSIS TITLE: Mapping of Peripheral Blood Mononuclear Primary Cells Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9me3 ChIP-Seq on Peripheral Blood Mononuclear Primary Cells, Donor TC010, Library HS2622 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.4313
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: 0.1328
FINDPEAKS_PERCENTILE: 64
HOTSPOT_SCORE: 0.1958
HOTSPOT_PERCENTILE: 66
IROC_SCORE: 0.8298
IROC_PERCENTILE: 53
POISSON_SCORE: 0.4341
POISSON_PERCENTILE: 66

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

ANALYSIS FILE NAME: GSM613878_UCSF-UBC.Peripheral_Blood_Mononuclear_Primary_Cells.H3K9me3.TC010.HS2622.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: HS2622-1_623WAAAXX.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Peripheral Blood Mononuclear Primary Cells Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9me3 ChIP-Seq read mappings from Peripheral Blood Mononuclear Primary Cells, Donor TC010, Library HS2622 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.4362
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 H3K9me3 10 22
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-UCD Peripheral Blood Mononuclear Primary Cells Histone H3K9me3 Donor TC010 Library HS2622 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED: 59
FINDPEAKS_SCORE: 0.1328
FINDPEAKS_PERCENTILE: 64
HOTSPOT_SCORE: 0.1958
HOTSPOT_PERCENTILE: 66
IROC_SCORE: 0.8298
IROC_PERCENTILE: 53
POISSON_SCORE: 0.4341
POISSON_PERCENTILE: 66

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


description:
design description: H3K27me3 ChIP-Seq analysis of peripheral mononuclear cell from TC010 (HS2621) using Illumina Genome Analyzer IIx
library name: HS2621
EXPERIMENT_TYPE: Histone H3K27me3
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: 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/)
CHIP_PROTOCOL_CHROMATIN_AMOUNT: 4 ug
SIZE_FRACTION: 270-516 bp
CHIP_PROTOCOL_BEAD_TYPE: Protein G Mag Beads
CHIP_PROTOCOL_BEAD_AMOUNT: 15 ul
CHIP_PROTOCOL_ANTIBODY_AMOUNT: 15 ul
CHIP_ANTIBODY: H3K27me3
CHIP_ANTIBODY_PROVIDER: Cell Signaling Technology
CHIP_ANTIBODY_CATALOG: 9733S
CHIP_ANTIBODY_LOT: 2
****************
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: GSM613877_UCSF-UBC.Peripheral_Blood_Mononuclear_Primary_Cells.H3K27me3.TC010.HS2621.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: HS2621-1_623YCAAXX.hg19.level.1
ANALYSIS TITLE: Mapping of Peripheral Blood Mononuclear Primary Cells Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27me3 ChIP-Seq on Peripheral Blood Mononuclear Primary Cells, Donor TC010, Library HS2621 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.4315
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: 0.1668
FINDPEAKS_PERCENTILE: 56
HOTSPOT_SCORE: 0.2764
HOTSPOT_PERCENTILE: 69
IROC_SCORE: 0.9243
IROC_PERCENTILE: 56
POISSON_SCORE: 0.5479
POISSON_PERCENTILE: 88

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

ANALYSIS FILE NAME: GSM613877_UCSF-UBC.Peripheral_Blood_Mononuclear_Primary_Cells.H3K27me3.TC010.HS2621.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: HS2621-1_623YCAAXX.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Peripheral Blood Mononuclear Primary Cells Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27me3 ChIP-Seq read mappings from Peripheral Blood Mononuclear Primary Cells, Donor TC010, Library HS2621 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.4364
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 H3K27me3 10 21
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-UCD Peripheral Blood Mononuclear Primary Cells Histone H3K27me3 Donor TC010 Library HS2621 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED: 52
FINDPEAKS_SCORE: 0.1668
FINDPEAKS_PERCENTILE: 56
HOTSPOT_SCORE: 0.2764
HOTSPOT_PERCENTILE: 69
IROC_SCORE: 0.9243
IROC_PERCENTILE: 56
POISSON_SCORE: 0.5479
POISSON_PERCENTILE: 88

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


description:
design description: H3K36me3 ChIP-Seq analysis of peripheral mononuclear cell from TC010 (HS2624) using Illumina Genome Analyzer IIx
library name: HS2624
EXPERIMENT_TYPE: Histone H3K36me3
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: 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/)
CHIP_PROTOCOL_CHROMATIN_AMOUNT: 5 ug
SIZE_FRACTION: 72-371 bp
CHIP_PROTOCOL_BEAD_TYPE: Protein G Mag Beads
CHIP_PROTOCOL_BEAD_AMOUNT: 15 ul
CHIP_PROTOCOL_ANTIBODY_AMOUNT: 20 ul
CHIP_ANTIBODY: H3K36me3
CHIP_ANTIBODY_PROVIDER: Cell Signaling Technology
CHIP_ANTIBODY_CATALOG: 9763S
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: GSM613880_UCSF-UBC.Peripheral_Blood_Mononuclear_Primary_Cells.H3K36me3.TC010.HS2624.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: HS2624-1_623WAAAXX.hg19.level.1
ANALYSIS TITLE: Mapping of Peripheral Blood Mononuclear Primary Cells Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K36me3 ChIP-Seq on Peripheral Blood Mononuclear Primary Cells, Donor TC010, Library HS2624 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.4325
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: 0.6117
FINDPEAKS_PERCENTILE: 94
HOTSPOT_SCORE: 0.4862
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9986
IROC_PERCENTILE: 98
POISSON_SCORE: 0.7176
POISSON_PERCENTILE: 98

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

ANALYSIS FILE NAME: GSM613880_UCSF-UBC.Peripheral_Blood_Mononuclear_Primary_Cells.H3K36me3.TC010.HS2624.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: HS2624-1_623WAAAXX.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Peripheral Blood Mononuclear Primary Cells Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K36me3 ChIP-Seq read mappings from Peripheral Blood Mononuclear Primary Cells, Donor TC010, Library HS2624 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.4374
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 H3K36me3 10 24
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-UCD Peripheral Blood Mononuclear Primary Cells Histone H3K36me3 Donor TC010 Library HS2624 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED: 54
FINDPEAKS_SCORE: 0.6117
FINDPEAKS_PERCENTILE: 94
HOTSPOT_SCORE: 0.4862
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9986
IROC_PERCENTILE: 98
POISSON_SCORE: 0.7176
POISSON_PERCENTILE: 98

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


description:
design description: H3K9ac ChIP-Seq analysis of peripheral mononuclear cell from TC010 (HS2623) using Illumina Genome Analyzer IIx
library name: HS2623
EXPERIMENT_TYPE: Histone H3K9ac
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: 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/)
CHIP_PROTOCOL_CHROMATIN_AMOUNT: 2 ug
SIZE_FRACTION: 49-371 bp
CHIP_PROTOCOL_BEAD_TYPE: Protein G Mag Beads
CHIP_PROTOCOL_BEAD_AMOUNT: 15 ul
CHIP_PROTOCOL_ANTIBODY_AMOUNT: 15 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: GSM613879_UCSF-UBC.Peripheral_Blood_Mononuclear_Primary_Cells.H3K9ac.TC010.HS2623.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: HS2623-1_623WAAAXX.hg19.level.1
ANALYSIS TITLE: Mapping of Peripheral Blood Mononuclear Primary Cells Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9ac ChIP-Seq on Peripheral Blood Mononuclear Primary Cells, Donor TC010, Library HS2623 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.4303
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: 0.2077
FINDPEAKS_PERCENTILE: 54
HOTSPOT_SCORE: 0.2855
HOTSPOT_PERCENTILE: 66
IROC_SCORE: 0.967
IROC_PERCENTILE: 31
POISSON_SCORE: 0.4143
POISSON_PERCENTILE: 63

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

ANALYSIS FILE NAME: GSM613879_UCSF-UBC.Peripheral_Blood_Mononuclear_Primary_Cells.H3K9ac.TC010.HS2623.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: HS2623-1_623WAAAXX.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Peripheral Blood Mononuclear Primary Cells Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9ac ChIP-Seq read mappings from Peripheral Blood Mononuclear Primary Cells, Donor TC010, Library HS2623 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.4352
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 H3K9ac 10 23
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-UCD Peripheral Blood Mononuclear Primary Cells Histone H3K9ac Donor TC010 Library HS2623 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED: 35
FINDPEAKS_SCORE: 0.2077
FINDPEAKS_PERCENTILE: 54
HOTSPOT_SCORE: 0.2855
HOTSPOT_PERCENTILE: 66
IROC_SCORE: 0.967
IROC_PERCENTILE: 31
POISSON_SCORE: 0.4143
POISSON_PERCENTILE: 63

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


description:
design description: H3K4me1 ChIP-Seq analysis of breast variant human mammary epithelial cell from RM035 (HS2618) using Illumina Genome Analyzer IIx
library name: HS2618
EXPERIMENT_TYPE: Histone H3K4me1
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: 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/)
CHIP_PROTOCOL_CHROMATIN_AMOUNT: 3 ug
SIZE_FRACTION: 36-278 bp
CHIP_PROTOCOL_BEAD_TYPE: Protein G Mag Beads
CHIP_PROTOCOL_BEAD_AMOUNT: 15 ul
CHIP_PROTOCOL_ANTIBODY_AMOUNT: 2 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: GSM613876_UCSF-UBC.Breast_vHMEC.H3K4me1.RM035.HS2618.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: HS2618-1_623YCAAXX.hg19.level.1
ANALYSIS TITLE: Mapping of Breast vHMEC Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me1 ChIP-Seq on Breast vHMEC, Donor RM035, Library HS2618 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.4296
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: 0.3292
FINDPEAKS_PERCENTILE: 44
HOTSPOT_SCORE: 0.3533
HOTSPOT_PERCENTILE: 37
IROC_SCORE: 0.9814
IROC_PERCENTILE: 43
POISSON_SCORE: 0.5801
POISSON_PERCENTILE: 60

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

ANALYSIS FILE NAME: GSM613876_UCSF-UBC.Breast_vHMEC.H3K4me1.RM035.HS2618.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: HS2618-1_623YCAAXX.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Breast vHMEC Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me1 ChIP-Seq read mappings from Breast vHMEC, Donor RM035, Library HS2618 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.4345
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 H3K4me1 35 18
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-UCD Breast vHMEC Histone H3K4me1 Donor RM035 Library HS2618 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED: 43
FINDPEAKS_SCORE: 0.3292
FINDPEAKS_PERCENTILE: 44
HOTSPOT_SCORE: 0.3533
HOTSPOT_PERCENTILE: 37
IROC_SCORE: 0.9814
IROC_PERCENTILE: 43
POISSON_SCORE: 0.5801
POISSON_PERCENTILE: 60

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

value: female

value: Breast

value: Variant human mammary epithelial cell culture

value: primary cell culture

tag: cell type


description:
design description: H3K9me3 ChIP-Seq analysis of breast variant human mammary epithelial cell from RM035 (HS2617) using Illumina Genome Analyzer IIx
library name: HS2617
EXPERIMENT_TYPE: Histone H3K9me3
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: 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/)
CHIP_PROTOCOL_CHROMATIN_AMOUNT: 5 ug
SIZE_FRACTION: 259-571 bp
CHIP_PROTOCOL_BEAD_TYPE: Protein G Mag Beads
CHIP_PROTOCOL_BEAD_AMOUNT: 15 ul
CHIP_PROTOCOL_ANTIBODY_AMOUNT: 20 ul
CHIP_ANTIBODY: H3K9me3
CHIP_ANTIBODY_PROVIDER: Cell Signaling Technology
CHIP_ANTIBODY_CATALOG: 9754S
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: GSM613875_UCSF-UBC.Breast_vHMEC.H3K9me3.RM035.HS2617.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: HS2617-1_623YCAAXX.hg19.level.1
ANALYSIS TITLE: Mapping of Breast vHMEC Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9me3 ChIP-Seq on Breast vHMEC, Donor RM035, Library HS2617 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.4316
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: 0.0725
FINDPEAKS_PERCENTILE: 47
HOTSPOT_SCORE: 0.1198
HOTSPOT_PERCENTILE: 37
IROC_SCORE: 0.8135
IROC_PERCENTILE: 47
POISSON_SCORE: 0.4678
POISSON_PERCENTILE: 76

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

ANALYSIS FILE NAME: GSM613875_UCSF-UBC.Breast_vHMEC.H3K9me3.RM035.HS2617.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: HS2617-1_623YCAAXX.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Breast vHMEC Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9me3 ChIP-Seq read mappings from Breast vHMEC, Donor RM035, Library HS2617 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.4365
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 H3K9me3 35 17
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-UCD Breast vHMEC Histone H3K9me3 Donor RM035 Library HS2617 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED: 59
FINDPEAKS_SCORE: 0.0725
FINDPEAKS_PERCENTILE: 47
HOTSPOT_SCORE: 0.1198
HOTSPOT_PERCENTILE: 37
IROC_SCORE: 0.8135
IROC_PERCENTILE: 47
POISSON_SCORE: 0.4678
POISSON_PERCENTILE: 76

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


description:
design description: H3K36me3 ChIP-Seq analysis of breast myoepithelial cell from RM066 (HS2443) using Illumina Genome Analyzer IIx
library name: HS2443
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: 3.3 ug
SIZE_FRACTION: 80-280 bp
CHIP_PROTOCOL_BEAD_TYPE: Sepharose A/G Bead Mix
CHIP_PROTOCOL_BEAD_AMOUNT: 20 ul
CHIP_PROTOCOL_ANTIBODY_AMOUNT: 6.25 ul
CHIP_ANTIBODY: H3K36me3
CHIP_ANTIBODY_PROVIDER: Abcam
CHIP_ANTIBODY_CATALOG: ab9050-100
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: GSM613873_UCSF-UBC.Breast_Myoepithelial_Cells.H3K36me3.RM066.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: HS2443-1_61YUCAAXX.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 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.4314
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: 0.3553
FINDPEAKS_PERCENTILE: 74
HOTSPOT_SCORE: 0.2882
HOTSPOT_PERCENTILE: 60
IROC_SCORE: 0.9756
IROC_PERCENTILE: 59
POISSON_SCORE: 0.6827
POISSON_PERCENTILE: 85

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

ANALYSIS FILE NAME: GSM613873_UCSF-UBC.Breast_Myoepithelial_Cells.H3K36me3.RM066.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: HS2443-1_61YUCAAXX.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 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.4363
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 66
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-UCD Breast Myoepithelial Cells Histone H3K36me3 Donor RM066 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED: 54
FINDPEAKS_SCORE: 0.3553
FINDPEAKS_PERCENTILE: 74
HOTSPOT_SCORE: 0.2882
HOTSPOT_PERCENTILE: 60
IROC_SCORE: 0.9756
IROC_PERCENTILE: 59
POISSON_SCORE: 0.6827
POISSON_PERCENTILE: 85

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

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/)

value: Myoepithelial cell

value: breast myoepithelial cell


description:
design description: H3K4me3 ChIP-Seq analysis of breast variant human mammary epithelial cell from RM035 (HS2615) using Illumina Genome Analyzer IIx
library name: HS2615
EXPERIMENT_TYPE: Histone H3K4me3
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: 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/)
CHIP_PROTOCOL_CHROMATIN_AMOUNT: 1 ug
SIZE_FRACTION: 80-280 bp
CHIP_PROTOCOL_BEAD_TYPE: Protein G Mag Beads
CHIP_PROTOCOL_BEAD_AMOUNT: 15 ul
CHIP_PROTOCOL_ANTIBODY_AMOUNT: 5 ul
CHIP_ANTIBODY: H3K4me3
CHIP_ANTIBODY_PROVIDER: Cell Signaling Technology
CHIP_ANTIBODY_CATALOG: 9751S
CHIP_ANTIBODY_LOT: 2
****************
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: GSM613874_UCSF-UBC.Breast_vHMEC.H3K4me3.RM035.HS2615.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: HS2615-1_623YCAAXX.hg19.level.1
ANALYSIS TITLE: Mapping of Breast vHMEC Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me3 ChIP-Seq on Breast vHMEC, Donor RM035, Library HS2615 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.4322
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: 0.47
FINDPEAKS_PERCENTILE: 66
HOTSPOT_SCORE: 0.5139
HOTSPOT_PERCENTILE: 72
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.5154
POISSON_PERCENTILE: 58

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

ANALYSIS FILE NAME: GSM613874_UCSF-UBC.Breast_vHMEC.H3K4me3.RM035.HS2615.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: HS2615-1_623YCAAXX.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Breast vHMEC Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me3 ChIP-Seq read mappings from Breast vHMEC, Donor RM035, Library HS2615 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.4371
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 H3K4me3 35 15
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-UCD Breast vHMEC Histone H3K4me3 Donor RM035 Library HS2615 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED: 62
FINDPEAKS_SCORE: 0.47
FINDPEAKS_PERCENTILE: 66
HOTSPOT_SCORE: 0.5139
HOTSPOT_PERCENTILE: 72
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.5154
POISSON_PERCENTILE: 58

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


description:
design description: H3K27me3 ChIP-Seq analysis of breast myoepithelial cell from RM066 (HS2442) using Illumina Genome Analyzer IIx
library name: HS2442
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: 3.33 ug
SIZE_FRACTION: 80-280 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: GSM613872_UCSF-UBC.Breast_Myoepithelial_Cells.H3K27me3.RM066.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: HS2442-1_61YUCAAXX.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 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.4329
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: 0.06
FINDPEAKS_PERCENTILE: 33
HOTSPOT_SCORE: 0.1583
HOTSPOT_PERCENTILE: 37
IROC_SCORE: 0.8353
IROC_PERCENTILE: 23
POISSON_SCORE: 0.4765
POISSON_PERCENTILE: 58

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

ANALYSIS FILE NAME: GSM613872_UCSF-UBC.Breast_Myoepithelial_Cells.H3K27me3.RM066.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: HS2442-1_61YUCAAXX.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 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.4378
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 66
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-UCD Breast Myoepithelial Cells Histone H3K27me3 Donor RM066 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED: 52
FINDPEAKS_SCORE: 0.06
FINDPEAKS_PERCENTILE: 33
HOTSPOT_SCORE: 0.1583
HOTSPOT_PERCENTILE: 37
IROC_SCORE: 0.8353
IROC_PERCENTILE: 23
POISSON_SCORE: 0.4765
POISSON_PERCENTILE: 58

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


description:
design description: H3K4me1 ChIP-Seq analysis of breast myoepithelial cell from RM066 (HS2440) using Illumina Genome Analyzer IIx
library name: HS2440
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: 2 ug
SIZE_FRACTION: 80-280 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: GSM613870_UCSF-UBC.Breast_Myoepithelial_Cells.H3K4me1.RM066.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: HS2440-1_61YUCAAXX.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 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.4337
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: 0.2487
FINDPEAKS_PERCENTILE: 30
HOTSPOT_SCORE: 0.2918
HOTSPOT_PERCENTILE: 28
IROC_SCORE: 0.9586
IROC_PERCENTILE: 26
POISSON_SCORE: 0.5648
POISSON_PERCENTILE: 53

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

ANALYSIS FILE NAME: GSM613870_UCSF-UBC.Breast_Myoepithelial_Cells.H3K4me1.RM066.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: HS2440-1_61YUCAAXX.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 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.4386
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 66
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-UCD Breast Myoepithelial Cells Histone H3K4me1 Donor RM066 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED: 43
FINDPEAKS_SCORE: 0.2487
FINDPEAKS_PERCENTILE: 30
HOTSPOT_SCORE: 0.2918
HOTSPOT_PERCENTILE: 28
IROC_SCORE: 0.9586
IROC_PERCENTILE: 26
POISSON_SCORE: 0.5648
POISSON_PERCENTILE: 53

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


description:
design description: H3K4me1 ChIP-Seq analysis of breast variant human mammary epithelial cell from RM035 (HS1994) using Illumina Genome Analyzer IIx
library name: HS1994
EXPERIMENT_TYPE: Histone H3K4me1
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: 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/)
CHIP_PROTOCOL_CHROMATIN_AMOUNT: 1 ug
SIZE_FRACTION: 46-346 bp
CHIP_PROTOCOL_BEAD_TYPE: Protein G Mag Beads
CHIP_PROTOCOL_BEAD_AMOUNT: 15 ul
CHIP_PROTOCOL_ANTIBODY_AMOUNT: 2 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: GSM613868_UCSF-UBC.Breast_vHMEC.H3K4me1.RM035.HS1994.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: HS1994-1_60065AAXX.hg19.level.1
ANALYSIS TITLE: Mapping of Breast vHMEC Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me1 ChIP-Seq on Breast vHMEC, Donor RM035, Library HS1994 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.4300
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: 0.2258
FINDPEAKS_PERCENTILE: 26
HOTSPOT_SCORE: 0.2869
HOTSPOT_PERCENTILE: 26
IROC_SCORE: 0.9516
IROC_PERCENTILE: 21
POISSON_SCORE: 0.518
POISSON_PERCENTILE: 37

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

ANALYSIS FILE NAME: GSM613868_UCSF-UBC.Breast_vHMEC.H3K4me1.RM035.HS1994.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: HS1994-1_60065AAXX.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Breast vHMEC Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me1 ChIP-Seq read mappings from Breast vHMEC, Donor RM035, Library HS1994 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.4349
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 H3K4me1 35 94
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-UCD Breast vHMEC Histone H3K4me1 Donor RM035 Library HS1994 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED: 43
FINDPEAKS_SCORE: 0.2258
FINDPEAKS_PERCENTILE: 26
HOTSPOT_SCORE: 0.2869
HOTSPOT_PERCENTILE: 26
IROC_SCORE: 0.9516
IROC_PERCENTILE: 21
POISSON_SCORE: 0.518
POISSON_PERCENTILE: 37

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


description:
design description: H3K27me3 ChIP-Seq analysis of peripheral cd8 naive from TC001 (HS2386) using Illumina Genome Analyzer IIx
library name: HS2386
EXPERIMENT_TYPE: Histone H3K27me3
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: 20 min
CHIP_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/)
CHIP_PROTOCOL_CHROMATIN_AMOUNT: 1 ug
SIZE_FRACTION: 30-280 bp
CHIP_PROTOCOL_BEAD_TYPE: Protein G Mag Beads
CHIP_PROTOCOL_BEAD_AMOUNT: 15 ul
CHIP_PROTOCOL_ANTIBODY_AMOUNT: 1 ug
CHIP_ANTIBODY: H3K27me3
CHIP_ANTIBODY_PROVIDER: Cell Signaling Technology
CHIP_ANTIBODY_CATALOG: 9733S
CHIP_ANTIBODY_LOT: 2
****************
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: GSM613815_UCSF-UBC.CD8_Naive_Primary_Cells.H3K27me3.TC001.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: HS2386-1_61YUCAAXX.hg19.level.1
ANALYSIS TITLE: Mapping of CD8 Naive Primary Cells Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27me3 ChIP-Seq on CD8 Naive Primary Cells, Donor TC001 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.4331
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: 0.0334
FINDPEAKS_PERCENTILE: 19
HOTSPOT_SCORE: 0.1489
HOTSPOT_PERCENTILE: 31
IROC_SCORE: 0.7582
IROC_PERCENTILE: 12
POISSON_SCORE: 0.493
POISSON_PERCENTILE: 62

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

ANALYSIS FILE NAME: GSM613815_UCSF-UBC.CD8_Naive_Primary_Cells.H3K27me3.TC001.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: HS2386-1_61YUCAAXX.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of CD8 Naive Primary Cells Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27me3 ChIP-Seq read mappings from CD8 Naive Primary Cells, Donor TC001 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.4380
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: CD8N H3K27me3 01
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-UCD CD8 Naive Primary Cells Histone H3K27me3 Donor TC001 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED: 52
FINDPEAKS_SCORE: 0.0334
FINDPEAKS_PERCENTILE: 19
HOTSPOT_SCORE: 0.1489
HOTSPOT_PERCENTILE: 31
IROC_SCORE: 0.7582
IROC_PERCENTILE: 12
POISSON_SCORE: 0.493
POISSON_PERCENTILE: 62

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


description:
design description: H3K4me1 ChIP-Seq analysis of peripheral cd8 naive from TC001 (HS2283) using Illumina Genome Analyzer IIx
library name: HS2283
EXPERIMENT_TYPE: Histone H3K4me1
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: 20 min
CHIP_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/)
CHIP_PROTOCOL_CHROMATIN_AMOUNT: 1 ug
SIZE_FRACTION: 256-576 bp
CHIP_PROTOCOL_BEAD_TYPE: Protein G Mag Beads
CHIP_PROTOCOL_BEAD_AMOUNT: 15 ul
CHIP_PROTOCOL_ANTIBODY_AMOUNT: 2 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: GSM613814_UCSF-UBC.CD8_Naive_Primary_Cells.H3K4me1.TC001.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: HS2283-1_61LH3AAXX.hg19.level.1
ANALYSIS TITLE: Mapping of CD8 Naive Primary Cells Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me1 ChIP-Seq on CD8 Naive Primary Cells, Donor TC001 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.4294
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: 0.3835
FINDPEAKS_PERCENTILE: 63
HOTSPOT_SCORE: 0.3514
HOTSPOT_PERCENTILE: 35
IROC_SCORE: 0.9954
IROC_PERCENTILE: 74
POISSON_SCORE: 0.5534
POISSON_PERCENTILE: 47

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

ANALYSIS FILE NAME: GSM613814_UCSF-UBC.CD8_Naive_Primary_Cells.H3K4me1.TC001.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: HS2283-1_61LH3AAXX.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of CD8 Naive Primary Cells Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me1 ChIP-Seq read mappings from CD8 Naive Primary Cells, Donor TC001 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.4343
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: CD8N H3K4me1 01
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-UCD CD8 Naive Primary Cells Histone H3K4me1 Donor TC001 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED: 43
FINDPEAKS_SCORE: 0.3835
FINDPEAKS_PERCENTILE: 63
HOTSPOT_SCORE: 0.3514
HOTSPOT_PERCENTILE: 35
IROC_SCORE: 0.9954
IROC_PERCENTILE: 74
POISSON_SCORE: 0.5534
POISSON_PERCENTILE: 47

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


description:
design description: H3K4me3 ChIP-Seq analysis of peripheral cd8 naive from TC001 (HS2280) using Illumina Genome Analyzer IIx
library name: HS2280
EXPERIMENT_TYPE: Histone H3K4me3
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: 20 min
CHIP_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/)
CHIP_PROTOCOL_CHROMATIN_AMOUNT: 1 ug
SIZE_FRACTION: 256-469 bp
CHIP_PROTOCOL_BEAD_TYPE: Protein G Mag Beads
CHIP_PROTOCOL_BEAD_AMOUNT: 15 ul
CHIP_PROTOCOL_ANTIBODY_AMOUNT: 5 ul
CHIP_ANTIBODY: H3K4me3
CHIP_ANTIBODY_PROVIDER: Cell Signaling Technology
CHIP_ANTIBODY_CATALOG: 9751S
CHIP_ANTIBODY_LOT: 2
****************
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: GSM613811_UCSF-UBC.CD8_Naive_Primary_Cells.H3K4me3.TC001.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: HS2280-1_61LH3AAXX.hg19.level.1
ANALYSIS TITLE: Mapping of CD8 Naive Primary Cells Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me3 ChIP-Seq on CD8 Naive Primary Cells, Donor TC001 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.4293
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: 0.203
FINDPEAKS_PERCENTILE: 11
HOTSPOT_SCORE: 0.2562
HOTSPOT_PERCENTILE: 20
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.3039
POISSON_PERCENTILE: 3

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

ANALYSIS FILE NAME: GSM613811_UCSF-UBC.CD8_Naive_Primary_Cells.H3K4me3.TC001.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: HS2280-1_61LH3AAXX.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of CD8 Naive Primary Cells Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me3 ChIP-Seq read mappings from CD8 Naive Primary Cells, Donor TC001 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.4342
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: CD8N H3K4me3 01
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-UCD CD8 Naive Primary Cells Histone H3K4me3 Donor TC001 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED: 62
FINDPEAKS_SCORE: 0.203
FINDPEAKS_PERCENTILE: 11
HOTSPOT_SCORE: 0.2562
HOTSPOT_PERCENTILE: 20
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.3039
POISSON_PERCENTILE: 3

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


description:
design description: H3K9me3 ChIP-Seq analysis of breast myoepithelial cell from RM066 (HS2441) using Illumina Genome Analyzer IIx
library name: HS2441
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: 3.3 ug
SIZE_FRACTION: 80-280 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: GSM613871_UCSF-UBC.Breast_Myoepithelial_Cells.H3K9me3.RM066.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: HS2441-1_61YUCAAXX.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 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.4310
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: 0.2958
FINDPEAKS_PERCENTILE: 92
HOTSPOT_SCORE: 0.3223
HOTSPOT_PERCENTILE: 90
IROC_SCORE: 0.9395
IROC_PERCENTILE: 83
POISSON_SCORE: 0.5409
POISSON_PERCENTILE: 93

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

ANALYSIS FILE NAME: GSM613871_UCSF-UBC.Breast_Myoepithelial_Cells.H3K9me3.RM066.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: HS2441-1_61YUCAAXX.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 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.4359
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 66
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-UCD Breast Myoepithelial Cells Histone H3K9me3 Donor RM066 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED: 59
FINDPEAKS_SCORE: 0.2958
FINDPEAKS_PERCENTILE: 92
HOTSPOT_SCORE: 0.3223
HOTSPOT_PERCENTILE: 90
IROC_SCORE: 0.9395
IROC_PERCENTILE: 83
POISSON_SCORE: 0.5409
POISSON_PERCENTILE: 93

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


title: S2-DRSC-CG8241_RNAi-2

status: Public on Nov 20 2010

city: Farmington

first: Brenton

middle: R

last: Graveley

state: CT

address: 400 Farmington Avenue

department: Genetics and Genome Sciences

institute: University of Connecticut Health Center

description:
dsRNA treatment: CG8241
read length: 78
library_source: RNA
library_selection: RT and size selection

library_source: transcriptomic

data_processing: Reads were aligned to the reference genome and a splice junction database to identify uniquely mapping reads and the data converted to SAM files and .bedgraph files which indicate the number of reads that map to each base in the genome.

molecule: total RNA

organism: Drosophila melanogaster

growth_protocol: Schneider's medium + 10% heat-inactivated FCS

extract_protocol:
Oligo-dT selected, double stranded cDNA, Single Read Sequencing
TRIzol Dnase Rneasy

treatment_protocol: Cells were treated with dsRNA to the indicated gene

tag: cell line


description:
design description: ChIP-Seq input analysis of peripheral cd8 naive from TC001 (HS2284) using Illumina Genome Analyzer IIx
library name: HS2284
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: 20 min
CHIP_PROTOCOL: Input
CHIP_PROTOCOL_CHROMATIN_AMOUNT: 1 ug
SIZE_FRACTION: 198-465 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: GSM613816_UCSF-UBC.CD8_Naive_Primary_Cells.Input.TC001.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: HS2284-1_61LH3AAXX.hg19.level.1
ANALYSIS TITLE: Mapping of CD8 Naive Primary Cells ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on CD8 Naive Primary Cells, Donor TC001 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.4306
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: 0.0093
FINDPEAKS_PERCENTILE: 43
HOTSPOT_SCORE: 0.0211
HOTSPOT_PERCENTILE: 35
IROC_SCORE: 0.9369
IROC_PERCENTILE: 69
POISSON_SCORE: 0.2339
POISSON_PERCENTILE: 46

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

ANALYSIS FILE NAME: GSM613816_UCSF-UBC.CD8_Naive_Primary_Cells.Input.TC001.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: HS2284-1_61LH3AAXX.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of CD8 Naive Primary Cells ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from CD8 Naive Primary Cells, Donor TC001 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.4355
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: CD8N Input 01
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-UCD CD8 Naive Primary Cells ChIP-Seq Input Donor TC001 EA Release 2

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED: 67
FINDPEAKS_SCORE: 0.0093
FINDPEAKS_PERCENTILE: 43
HOTSPOT_SCORE: 0.0211
HOTSPOT_PERCENTILE: 35
IROC_SCORE: 0.9369
IROC_PERCENTILE: 69
POISSON_SCORE: 0.2339
POISSON_PERCENTILE: 46

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


title: new_H4K8Ac_1H_minus

status: Public on Nov 10 2010

city: New York

first: Uwe

last: Schaefer

state: NY

address: 1230 York Ave.

institute: Rockefeller University

description: Chromatin Immunoprecipitation against H4K8Ac

data_processing: RTA 2.6, wig files contain alignments to mm9

organism: Mus musculus

source_name: Macrophages

extract_protocol:
For ChIP experiments, BMDMs were pre-incubated with 1 mM of GSK-BET compound in DMSO or DMSO only for 30 minutes. Cells were stimulated with 100 ng/ml LPS for 1 hours by adding LPS directly to the culture medium. ChIP experiments were performed as described previously 22. Cells were crosslinked with 1% formaldehyde. DNA was sonicated using a Biorupter (Diagenode) to generate DNA-fragments of approximately 200 to 600 bp. The following antibodies were pre-bound to Invitogen Dynal magnetic beads in 0.5% BSA/PBS (Invitrogen Dynabeads anti-mouse M-280 or Dynabeads anti-rabbit M-280): H3 (Abcam, ab1791), H3K4me3 (Millipore, 17-614), H4Acet (Millipore, 06-866), BRD4 (Abcam, ab84776), CDK9 (Santa Cruz, sc-8338x), Pol II (Abcam, ab5408) and Pol II S2 (Abcam, ab5095). Regular ChIP was performed using 1x106 cells (for H3, H3K4me3, Pol II and Pol II S2) or 2x106 cells (for H4Acet, BRD4 and CDK9) and 2 mg antibody coupled to 20 mL beads. ChIP-Seq was performed using 1x107 cells and 7 mg antibody coupled to 70 mL magnetic beads (for H3, H3K4me3 and Pol II) or 2x107 cells and 14 mg antibody coupled to 140 mL beads (for Pol II S2, H4Acet, BRD4 and CDK9). Beads were added to the cell lysates and incubation was allowed to proceed overnight. Beads were washed 8x in modified RIPA wash buffer (50 mM HEPES [pH 7.6], 100 mM LiCl [for H4Acet, BRD4 and CDK9] or 300 mM LiCl [H3, H3K4me3, Pol II and Pol II S2], 1mM EDTA, 1% NP-40 and 0.7% Na-deoxycholate) and 1x in TE containing 50 mM NaCl. Elution of DNA was performed in TE buffer containing 1% SDS. After overnight cross-link reversal at 650C, RNase digestion and Proteinase K digestion, ChIP DNA and input DNA was purified using the QIAGEN Quiaquick PCR purification kit. For regular ChIP and for validation of ChIP-Seq, ChIP DNA was analyzed via qPCR using SYBR Green master mix (Roche) and the LightCycler480 (Roche).
For ChIP-Seq, 30 mL of remaining ChIP DNA was used to generate blunt-ended DNA using the Epicenter DNA ENDRepair kit (Epicenter Biotechnologies). The end-repaired DNA was purified using the QIAGEN Quiaquick PCR purification kit. Using Klenow Fragment (NEB) A bases were added to the DNA. DNA was purified using the QIAGEN MinElute kit. T4 DNA ligase (NEB) was used for ligation of Illumina/Solexa adapters to the DNA fragments. The adaptor-ligated DNA was purified with the QIAGEN MinElute kit. The DNA fragments were subjected to 18 cycles of PCR using the Illumina/Solexa primers 1.0 and 2.0 to generate the ChIP-Seq libraries. The ChIP-Seq libraries were purified with the QIAGEN MinElute kit. Samples were sequenced on the Illumina GAIIx platform for 36 cycles, and raw sequencing data was processed using the onboard SCS/RTA software version 2.6 yielding 36bp reads. Sequencing kits used were version 4 sequencing kits.

tag: strain

value: Bone-marrow-derived macrophages

tag: treatment

tag: antibody

tag: antibody manufacturer

value: Millipore

tag: antibody catalog #

tag: antibody lot #

tag: time


title: new_H4K8Ac_1H_plus

treatment_protocol: For ChIP experiments, BMDMs were pre-incubated with 1 mM of GSK-BET compound in DMSO or DMSO only for 30 minutes. Cells were stimulated with 100 ng/ml LPS for 1 hours by adding LPS directly to the culture medium.


title: new_H4K8Ac_0H_minus


title: new_H4K5Ac_0H_minus

description: Chromatin Immunoprecipitation against H4K5Ac


title: new_H4K5Ac_1H_plus


title: new_H4K5Ac_1H_minus


title: new_H4K12Ac_1H_plus

description: Chromatin Immunoprecipitation against H4K12Ac


title: new_H4K12Ac_1H_minus


title: new_H4K12Ac_0H_plus


title: new_H3Ac_1H_plus

description: Chromatin Immunoprecipitation against H3Ac


title: new_H4K12Ac_0H_minus


title: new_H3Ac_0H_plus


title: new_H3Ac_0H_minus


title: new_H3Ac_1H_minus