description:
design description: H3K4me3 ChIP-Seq analysis of placenta (amniotic membrane) tissue from CTL02 (A21718) using Illumina HiSeq 2000
library name: A21718
EXPERIMENT_TYPE: Histone H3K4me3
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: 15 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: 4.5 ug
SIZE_FRACTION: 152-438 bp
CHIP_PROTOCOL_BEAD_TYPE: Sepharose A/G Bead Mix
CHIP_PROTOCOL_BEAD_AMOUNT: 20 ul
CHIP_PROTOCOL_ANTIBODY_AMOUNT: 5 ul
CHIP_ANTIBODY: H3K4me3
CHIP_ANTIBODY_PROVIDER: Cell Signaling Technology
CHIP_ANTIBODY_CATALOG: 9751S
CHIP_ANTIBODY_LOT: 4
****************
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: GSM1127138_UCSF-UBC.Placenta_Amnion.H3K4me3.CTL02.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A21718-1.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Placenta Amnion H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K4me3 ChIP-Seq on Placenta Amnion, Donor CTL02 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.17050
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 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 23,358,398
FINDPEAKS_SCORE: 0.0925
FINDPEAKS_PERCENTILE: 5
HOTSPOT_SCORE: 0.1064
HOTSPOT_PERCENTILE: 2
IROC_SCORE: 0.9993
IROC_PERCENTILE: 20
POISSON_SCORE: 0.1188
POISSON_PERCENTILE: 2
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1127138_UCSF-UBC.Placenta_Amnion.H3K4me3.CTL02.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A21718-1.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Placenta Amnion H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K4me3 ChIP-Seq read mappings from Placenta Amnion, Donor CTL02 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.17109
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 9
BROWSER_TRACK_NAME: PA H3K4me3 02 18
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Placenta Amnion Histone H3K4me3 Donor CTL02 Library A21718 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 23,358,398
FINDPEAKS_SCORE: 0.0925
FINDPEAKS_PERCENTILE: 5
HOTSPOT_SCORE: 0.1064
HOTSPOT_PERCENTILE: 2
IROC_SCORE: 0.9993
IROC_PERCENTILE: 20
POISSON_SCORE: 0.1188
POISSON_PERCENTILE: 2
MAXIMUM_REPLICATE_CORRELATION: NA

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

value: male

value: Placenta


status: Public on Jun 22 2013

type: SRA

city: San Francisco

first: UCSF-UBC

last: CENTER

state: CA

address: UCSF-UBC

country: USA

institute: UCSF-UBC

description:
design description: H3K27ac ChIP-Seq analysis of peripheral mononuclear cell from TC016 (A21638) using Illumina HiSeq 2000
library name: A21638
EXPERIMENT_TYPE: Histone H3K27ac
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: 5 ug
SIZE_FRACTION: 94-294 bp
CHIP_PROTOCOL_BEAD_TYPE: Sepharose A/G Bead Mix
CHIP_PROTOCOL_BEAD_AMOUNT: 20 ul
CHIP_PROTOCOL_ANTIBODY_AMOUNT: 2.5 ug
CHIP_ANTIBODY: H3K27ac
CHIP_ANTIBODY_PROVIDER: Abcam
CHIP_ANTIBODY_CATALOG: ab4729
CHIP_ANTIBODY_LOT: GR28147-1
****************
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: GSM1127137_UCSF-UBC.Peripheral_Blood_Mononuclear_Primary_Cells.H3K27ac.TC016.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A21638-1.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Peripheral Blood Mononuclear Primary Cells H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27ac ChIP-Seq on Peripheral Blood Mononuclear Primary Cells, Donor TC016, Library A21638 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.17031
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 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 24,518,890
FINDPEAKS_SCORE: 0.0609
FINDPEAKS_PERCENTILE: 4
HOTSPOT_SCORE: 0.112
HOTSPOT_PERCENTILE: 8
IROC_SCORE: 0.9724
IROC_PERCENTILE: 13
POISSON_SCORE: 0.1732
POISSON_PERCENTILE: 1
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

ANALYSIS FILE NAME: GSM1127137_UCSF-UBC.Peripheral_Blood_Mononuclear_Primary_Cells.H3K27ac.TC016.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A21638-1.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Peripheral Blood Mononuclear Primary Cells H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27ac ChIP-Seq read mappings from Peripheral Blood Mononuclear Primary Cells, Donor TC016, Library A21638 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.17090
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 9
BROWSER_TRACK_NAME: PBM H3K27ac 16 38
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Peripheral Blood Mononuclear Primary Cells Histone H3K27ac Donor TC016 Library A21638 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 24,518,890
FINDPEAKS_SCORE: 0.0609
FINDPEAKS_PERCENTILE: 4
HOTSPOT_SCORE: 0.112
HOTSPOT_PERCENTILE: 8
IROC_SCORE: 0.9724
IROC_PERCENTILE: 13
POISSON_SCORE: 0.1732
POISSON_PERCENTILE: 1
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

molecule: genomic DNA

organism: Homo sapiens

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

tag: submitted sample id

tag: Sex

value: female

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 placenta (smooth chorionic membrane) tissue from CTL02 (A21710) using Illumina HiSeq 2000
library name: A21710
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: 4.5 ug
SIZE_FRACTION: 159-435 bp
CHIP_PROTOCOL_BEAD_TYPE: Sepharose A/G Bead Mix
CHIP_PROTOCOL_BEAD_AMOUNT: 20 ul
CHIP_PROTOCOL_ANTIBODY_AMOUNT: 5 ug
CHIP_ANTIBODY: H3K4me1
CHIP_ANTIBODY_PROVIDER: Diagenode
CHIP_ANTIBODY_CATALOG: pAb-037-050
CHIP_ANTIBODY_LOT: A399-002341P
****************
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: GSM1127136_UCSF-UBC.Placenta_Chorion_Smooth.H3K4me1.CTL02.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A21710-1.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Placenta Chorion Smooth H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K4me1 ChIP-Seq on Placenta Chorion Smooth, Donor CTL02 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.17052
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 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 24,950,545
FINDPEAKS_SCORE: 0.1209
FINDPEAKS_PERCENTILE: 27
HOTSPOT_SCORE: 0.235
HOTSPOT_PERCENTILE: 23
IROC_SCORE: 0.9276
IROC_PERCENTILE: 29
POISSON_SCORE: 0.4146
POISSON_PERCENTILE: 30
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1127136_UCSF-UBC.Placenta_Chorion_Smooth.H3K4me1.CTL02.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A21710-1.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Placenta Chorion Smooth H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K4me1 ChIP-Seq read mappings from Placenta Chorion Smooth, Donor CTL02 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.17111
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 9
BROWSER_TRACK_NAME: PCS H3K4me1 02 10
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Placenta Chorion Smooth Histone H3K4me1 Donor CTL02 Library A21710 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 24,950,545
FINDPEAKS_SCORE: 0.1209
FINDPEAKS_PERCENTILE: 27
HOTSPOT_SCORE: 0.235
HOTSPOT_PERCENTILE: 23
IROC_SCORE: 0.9276
IROC_PERCENTILE: 29
POISSON_SCORE: 0.4146
POISSON_PERCENTILE: 30
MAXIMUM_REPLICATE_CORRELATION: NA

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

value: Chorion smooth tissue

value: primary tissue


description:
design description: H3K9me3 ChIP-Seq analysis of peripheral mononuclear cell from TC016 (A21635) using Illumina HiSeq 2000
library name: A21635
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: 5 ug
SIZE_FRACTION: 94-294 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: GSM1127135_UCSF-UBC.Peripheral_Blood_Mononuclear_Primary_Cells.H3K9me3.TC016.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A21635-1.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Peripheral Blood Mononuclear Primary Cells H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K9me3 ChIP-Seq on Peripheral Blood Mononuclear Primary Cells, Donor TC016, Library A21635 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.17059
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 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 17,936,973
FINDPEAKS_SCORE: 0.0216
FINDPEAKS_PERCENTILE: 24
HOTSPOT_SCORE: 0.0953
HOTSPOT_PERCENTILE: 28
IROC_SCORE: 0.5748
IROC_PERCENTILE: 4
POISSON_SCORE: 0.1663
POISSON_PERCENTILE: 8
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM1127135_UCSF-UBC.Peripheral_Blood_Mononuclear_Primary_Cells.H3K9me3.TC016.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A21635-1.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Peripheral Blood Mononuclear Primary Cells H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K9me3 ChIP-Seq read mappings from Peripheral Blood Mononuclear Primary Cells, Donor TC016, Library A21635 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.17118
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 9
BROWSER_TRACK_NAME: PBM H3K9me3 16 35
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Peripheral Blood Mononuclear Primary Cells Histone H3K9me3 Donor TC016 Library A21635 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 17,936,973
FINDPEAKS_SCORE: 0.0216
FINDPEAKS_PERCENTILE: 24
HOTSPOT_SCORE: 0.0953
HOTSPOT_PERCENTILE: 28
IROC_SCORE: 0.5748
IROC_PERCENTILE: 4
POISSON_SCORE: 0.1663
POISSON_PERCENTILE: 8
MAXIMUM_REPLICATE_CORRELATION: 0.98

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


description:
design description: H3K27me3 ChIP-Seq analysis of breast fibroblast from RM071 (A21643) using Illumina HiSeq 2000
library name: A21643
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: 5 ug
SIZE_FRACTION: 94-294 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: A299-00242
****************
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: GSM1127134_UCSF-UBC.Breast_Fibroblast_Primary_Cells.H3K27me3.RM071.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A21643-1.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Breast Fibroblast Primary Cells H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27me3 ChIP-Seq on Breast Fibroblast Primary Cells, Donor RM071 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.17071
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 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 37,763,741
FINDPEAKS_SCORE: 0.037
FINDPEAKS_PERCENTILE: 30
HOTSPOT_SCORE: 0.0846
HOTSPOT_PERCENTILE: 11
IROC_SCORE: 0.873
IROC_PERCENTILE: 44
POISSON_SCORE: 0.2583
POISSON_PERCENTILE: 32
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1127134_UCSF-UBC.Breast_Fibroblast_Primary_Cells.H3K27me3.RM071.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A21643-1.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Breast Fibroblast Primary Cells H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27me3 ChIP-Seq read mappings from Breast Fibroblast Primary Cells, Donor RM071 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.17130
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 9
BROWSER_TRACK_NAME: BF H3K27me3 71 43
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Breast Fibroblast Primary Cells Histone H3K27me3 Donor RM071 Library A21643 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 37,763,741
FINDPEAKS_SCORE: 0.037
FINDPEAKS_PERCENTILE: 30
HOTSPOT_SCORE: 0.0846
HOTSPOT_PERCENTILE: 11
IROC_SCORE: 0.873
IROC_PERCENTILE: 44
POISSON_SCORE: 0.2583
POISSON_PERCENTILE: 32
MAXIMUM_REPLICATE_CORRELATION: NA

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

value: Breast

value: Fibroblast cultured cell

value: primary cell culture

tag: cell type

value: breast fibroblast


description:
design description: H3K27ac ChIP-Seq analysis of placenta (amniotic membrane) tissue from CTL02 (A21722) using Illumina HiSeq 2000
library name: A21722
EXPERIMENT_TYPE: Histone H3K27ac
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: 15 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: 4.5 ug
SIZE_FRACTION: 151-463 bp
CHIP_PROTOCOL_BEAD_TYPE: Sepharose A/G Bead Mix
CHIP_PROTOCOL_BEAD_AMOUNT: 20 ul
CHIP_PROTOCOL_ANTIBODY_AMOUNT: 2.5 ug
CHIP_ANTIBODY: H3K27ac
CHIP_ANTIBODY_PROVIDER: Abcam
CHIP_ANTIBODY_CATALOG: ab4729
CHIP_ANTIBODY_LOT: GR55451-1
****************
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: GSM1127132_UCSF-UBC.Placenta_Amnion.H3K27ac.CTL02.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A21722-1.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Placenta Amnion H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27ac ChIP-Seq on Placenta Amnion, Donor CTL02 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.17055
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 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 28,256,387
FINDPEAKS_SCORE: 0.0041
FINDPEAKS_PERCENTILE: 1
HOTSPOT_SCORE: 0.0754
HOTSPOT_PERCENTILE: 7
IROC_SCORE: 0.658
IROC_PERCENTILE: 1
POISSON_SCORE: 0.1914
POISSON_PERCENTILE: 4
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1127132_UCSF-UBC.Placenta_Amnion.H3K27ac.CTL02.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A21722-1.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Placenta Amnion H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27ac ChIP-Seq read mappings from Placenta Amnion, Donor CTL02 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.17114
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 9
BROWSER_TRACK_NAME: PA H3K27ac 02 22
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Placenta Amnion Histone H3K27ac Donor CTL02 Library A21722 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 28,256,387
FINDPEAKS_SCORE: 0.0041
FINDPEAKS_PERCENTILE: 1
HOTSPOT_SCORE: 0.0754
HOTSPOT_PERCENTILE: 7
IROC_SCORE: 0.658
IROC_PERCENTILE: 1
POISSON_SCORE: 0.1914
POISSON_PERCENTILE: 4
MAXIMUM_REPLICATE_CORRELATION: NA

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

value: Amnion tissue

value: placenta (amniotic membrane) tissue


title: Histone H3K27me3 ChIP-Seq of CD19 Primary Cells; Histone.DS23315

city: Seattle

first: Northwest

last: REMC

state: WA

institute: University of Washington

description:
sample_term_id: CL_0000236
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Histone H3K27me3 ChIP-Seq
Library name: Histone.DS23315
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.16302
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.6973
****************
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: GSM1160194_UW.CD19_Primary_Cells.H3K27me3.RO_01701.Histone.DS23315.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS23315-Histone.DS23315.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of CD19 Primary Cells H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27me3 ChIP-Seq on CD19 Primary Cells, Donor RO 01701, 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.16870
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 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 26,596,940
FINDPEAKS_SCORE: 0.0785
FINDPEAKS_PERCENTILE: 57
HOTSPOT_SCORE: 0.1885
HOTSPOT_PERCENTILE: 52
IROC_SCORE: 0.8657
IROC_PERCENTILE: 41
POISSON_SCORE: 0.3758
POISSON_PERCENTILE: 61
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM1160194_UW.CD19_Primary_Cells.H3K27me3.RO_01701.Histone.DS23315.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS23315-Histone.DS23315.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of CD19 Primary Cells H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27me3 ChIP-Seq read mappings from CD19 Primary Cells, Donor RO 01701, 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.16966
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 9
BROWSER_TRACK_NAME: CD19 H3K27me3 01 15
BROWSER_TRACK_DESCRIPTION: UW CD19 Primary Cells Histone H3K27me3 Donor RO 01701 Library Histone.DS23315 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 26,596,940
FINDPEAKS_SCORE: 0.0785
FINDPEAKS_PERCENTILE: 57
HOTSPOT_SCORE: 0.1885
HOTSPOT_PERCENTILE: 52
IROC_SCORE: 0.8657
IROC_PERCENTILE: 41
POISSON_SCORE: 0.3758
POISSON_PERCENTILE: 61
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

source_name: flow sorted CD19+ Cells, year 37; Histone.DS23315

extract_protocol: Library construction protocol: Single read - Illumina

tag: sra sample accession

tag: disease

value: FHCRC HEIMFELD

value: Primary Cell

value: CD19 Primary Cells

tag: markers

value: year 37

value: Male

value: Hispanic

value: Histone H3K27me3

value: Diagenode Bioruptor

value: 20-40 cycles of 0.5 minute on and 0.5 minute off

value: Millipore A/G agarose beads

value: 30ul A/G bead slurry

value: Millipore


description:
design description: H3K9me3 ChIP-Seq analysis of peripheral mononuclear cell from TC015 (A21628) using Illumina HiSeq 2000
library name: A21628
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: 5 ug
SIZE_FRACTION: 94-294 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: GSM1127133_UCSF-UBC.Peripheral_Blood_Mononuclear_Primary_Cells.H3K9me3.TC015.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A21628-1.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Peripheral Blood Mononuclear Primary Cells H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K9me3 ChIP-Seq on Peripheral Blood Mononuclear Primary Cells, Donor TC015, Library A21628 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.17062
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 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 18,234,895
FINDPEAKS_SCORE: 0.0291
FINDPEAKS_PERCENTILE: 36
HOTSPOT_SCORE: 0.0866
HOTSPOT_PERCENTILE: 24
IROC_SCORE: 0.7172
IROC_PERCENTILE: 32
POISSON_SCORE: 0.1878
POISSON_PERCENTILE: 18
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM1127133_UCSF-UBC.Peripheral_Blood_Mononuclear_Primary_Cells.H3K9me3.TC015.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A21628-1.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Peripheral Blood Mononuclear Primary Cells H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K9me3 ChIP-Seq read mappings from Peripheral Blood Mononuclear Primary Cells, Donor TC015, Library A21628 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.17121
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 9
BROWSER_TRACK_NAME: PBM H3K9me3 15 28
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Peripheral Blood Mononuclear Primary Cells Histone H3K9me3 Donor TC015 Library A21628 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 18,234,895
FINDPEAKS_SCORE: 0.0291
FINDPEAKS_PERCENTILE: 36
HOTSPOT_SCORE: 0.0866
HOTSPOT_PERCENTILE: 24
IROC_SCORE: 0.7172
IROC_PERCENTILE: 32
POISSON_SCORE: 0.1878
POISSON_PERCENTILE: 18
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

value: male

value: Blood

value: Peripheral blood mononuclear cell

value: No

value: primary cell


description:
design description: H3K36me3 ChIP-Seq analysis of peripheral mononuclear cell from TC015 (A21630) using Illumina HiSeq 2000
library name: A21630
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: 5 ug
SIZE_FRACTION: 94-294 bp
CHIP_PROTOCOL_BEAD_TYPE: Sepharose A/G Bead Mix
CHIP_PROTOCOL_BEAD_AMOUNT: 20 ul
CHIP_PROTOCOL_ANTIBODY_AMOUNT: 2.5 ug
CHIP_ANTIBODY: H3K36me3
CHIP_ANTIBODY_PROVIDER: Abcam
CHIP_ANTIBODY_CATALOG: ab9050
CHIP_ANTIBODY_LOT: 947467
****************
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: GSM1127131_UCSF-UBC.Peripheral_Blood_Mononuclear_Primary_Cells.H3K36me3.TC015.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A21630-1.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Peripheral Blood Mononuclear Primary Cells H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K36me3 ChIP-Seq on Peripheral Blood Mononuclear Primary Cells, Donor TC015, Library A21630 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.17046
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 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 18,965,336
FINDPEAKS_SCORE: 0.2061
FINDPEAKS_PERCENTILE: 34
HOTSPOT_SCORE: 0.2385
HOTSPOT_PERCENTILE: 19
IROC_SCORE: 0.968
IROC_PERCENTILE: 43
POISSON_SCORE: 0.4122
POISSON_PERCENTILE: 28
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM1127131_UCSF-UBC.Peripheral_Blood_Mononuclear_Primary_Cells.H3K36me3.TC015.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A21630-1.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Peripheral Blood Mononuclear Primary Cells H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K36me3 ChIP-Seq read mappings from Peripheral Blood Mononuclear Primary Cells, Donor TC015, Library A21630 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.17105
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 9
BROWSER_TRACK_NAME: PBM H3K36me3 15 30
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Peripheral Blood Mononuclear Primary Cells Histone H3K36me3 Donor TC015 Library A21630 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 18,965,336
FINDPEAKS_SCORE: 0.2061
FINDPEAKS_PERCENTILE: 34
HOTSPOT_SCORE: 0.2385
HOTSPOT_PERCENTILE: 19
IROC_SCORE: 0.968
IROC_PERCENTILE: 43
POISSON_SCORE: 0.4122
POISSON_PERCENTILE: 28
MAXIMUM_REPLICATE_CORRELATION: 0.98

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


description:
design description: H3K27me3 ChIP-Seq analysis of peripheral mononuclear cell from TC015 (A21629) using Illumina HiSeq 2000
library name: A21629
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: 5 ug
SIZE_FRACTION: 94-294 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: A299-00242
****************
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: GSM1127130_UCSF-UBC.Peripheral_Blood_Mononuclear_Primary_Cells.H3K27me3.TC015.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A21629-1.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Peripheral Blood Mononuclear Primary Cells H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27me3 ChIP-Seq on Peripheral Blood Mononuclear Primary Cells, Donor TC015, Library A21629 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.17051
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 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 23,762,527
FINDPEAKS_SCORE: 0.0287
FINDPEAKS_PERCENTILE: 20
HOTSPOT_SCORE: 0.0936
HOTSPOT_PERCENTILE: 14
IROC_SCORE: 0.8759
IROC_PERCENTILE: 46
POISSON_SCORE: 0.1991
POISSON_PERCENTILE: 9
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM1127130_UCSF-UBC.Peripheral_Blood_Mononuclear_Primary_Cells.H3K27me3.TC015.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A21629-1.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Peripheral Blood Mononuclear Primary Cells H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27me3 ChIP-Seq read mappings from Peripheral Blood Mononuclear Primary Cells, Donor TC015, Library A21629 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.17110
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 9
BROWSER_TRACK_NAME: PBM H3K27me3 15 29
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Peripheral Blood Mononuclear Primary Cells Histone H3K27me3 Donor TC015 Library A21629 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 23,762,527
FINDPEAKS_SCORE: 0.0287
FINDPEAKS_PERCENTILE: 20
HOTSPOT_SCORE: 0.0936
HOTSPOT_PERCENTILE: 14
IROC_SCORE: 0.8759
IROC_PERCENTILE: 46
POISSON_SCORE: 0.1991
POISSON_PERCENTILE: 9
MAXIMUM_REPLICATE_CORRELATION: 0.98

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


description:
design description: H3K4me3 ChIP-Seq analysis of placenta (smooth chorionic membrane) tissue from CTL02 (A21711) using Illumina HiSeq 2000
library name: A21711
EXPERIMENT_TYPE: Histone H3K4me3
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: 4.5 ug
SIZE_FRACTION: 147-479 bp
CHIP_PROTOCOL_BEAD_TYPE: Sepharose A/G Bead Mix
CHIP_PROTOCOL_BEAD_AMOUNT: 20 ul
CHIP_PROTOCOL_ANTIBODY_AMOUNT: 5 ul
CHIP_ANTIBODY: H3K4me3
CHIP_ANTIBODY_PROVIDER: Cell Signaling Technology
CHIP_ANTIBODY_CATALOG: 9751S
CHIP_ANTIBODY_LOT: 4
****************
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: GSM1127128_UCSF-UBC.Placenta_Chorion_Smooth.H3K4me3.CTL02.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A21711-1.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Placenta Chorion Smooth H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K4me3 ChIP-Seq on Placenta Chorion Smooth, Donor CTL02 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.17022
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 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 20,979,984
FINDPEAKS_SCORE: 0.1817
FINDPEAKS_PERCENTILE: 13
HOTSPOT_SCORE: 0.1909
HOTSPOT_PERCENTILE: 7
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.2025
POISSON_PERCENTILE: 4
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1127128_UCSF-UBC.Placenta_Chorion_Smooth.H3K4me3.CTL02.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A21711-1.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Placenta Chorion Smooth H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K4me3 ChIP-Seq read mappings from Placenta Chorion Smooth, Donor CTL02 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.17081
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 9
BROWSER_TRACK_NAME: PCS H3K4me3 02 11
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Placenta Chorion Smooth Histone H3K4me3 Donor CTL02 Library A21711 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 20,979,984
FINDPEAKS_SCORE: 0.1817
FINDPEAKS_PERCENTILE: 13
HOTSPOT_SCORE: 0.1909
HOTSPOT_PERCENTILE: 7
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.2025
POISSON_PERCENTILE: 4
MAXIMUM_REPLICATE_CORRELATION: NA

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

value: Placenta

value: Chorion smooth tissue

value: primary tissue


description:
design description: H3K4me3 ChIP-Seq analysis of peripheral mononuclear cell from TC016 (A21634) using Illumina HiSeq 2000
library name: A21634
EXPERIMENT_TYPE: Histone H3K4me3
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: 5 ug
SIZE_FRACTION: 94-294 bp
CHIP_PROTOCOL_BEAD_TYPE: Sepharose A/G Bead Mix
CHIP_PROTOCOL_BEAD_AMOUNT: 20 ul
CHIP_PROTOCOL_ANTIBODY_AMOUNT: 5 ul
CHIP_ANTIBODY: H3K4me3
CHIP_ANTIBODY_PROVIDER: Cell Signaling Technology
CHIP_ANTIBODY_CATALOG: 9751S
CHIP_ANTIBODY_LOT: 4
****************
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: GSM1127127_UCSF-UBC.Peripheral_Blood_Mononuclear_Primary_Cells.H3K4me3.TC016.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A21634-1.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Peripheral Blood Mononuclear Primary Cells H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K4me3 ChIP-Seq on Peripheral Blood Mononuclear Primary Cells, Donor TC016, Library A21634 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.17053
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 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 18,618,618
FINDPEAKS_SCORE: 0.1908
FINDPEAKS_PERCENTILE: 14
HOTSPOT_SCORE: 0.2049
HOTSPOT_PERCENTILE: 9
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.2149
POISSON_PERCENTILE: 5
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

ANALYSIS FILE NAME: GSM1127127_UCSF-UBC.Peripheral_Blood_Mononuclear_Primary_Cells.H3K4me3.TC016.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A21634-1.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Peripheral Blood Mononuclear Primary Cells H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K4me3 ChIP-Seq read mappings from Peripheral Blood Mononuclear Primary Cells, Donor TC016, Library A21634 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.17112
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 9
BROWSER_TRACK_NAME: PBM H3K4me3 16 34
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Peripheral Blood Mononuclear Primary Cells Histone H3K4me3 Donor TC016 Library A21634 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 18,618,618
FINDPEAKS_SCORE: 0.1908
FINDPEAKS_PERCENTILE: 14
HOTSPOT_SCORE: 0.2049
HOTSPOT_PERCENTILE: 9
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.2149
POISSON_PERCENTILE: 5
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

value: female


description:
design description: H3K4me1 ChIP-Seq analysis of placenta (amniotic membrane) tissue from CTL02 (A21717) using Illumina HiSeq 2000
library name: A21717
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: 15 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: 4.5 ug
SIZE_FRACTION: 161-486 bp
CHIP_PROTOCOL_BEAD_TYPE: Sepharose A/G Bead Mix
CHIP_PROTOCOL_BEAD_AMOUNT: 20 ul
CHIP_PROTOCOL_ANTIBODY_AMOUNT: 5 ug
CHIP_ANTIBODY: H3K4me1
CHIP_ANTIBODY_PROVIDER: Diagenode
CHIP_ANTIBODY_CATALOG: pAb-037-050
CHIP_ANTIBODY_LOT: A399-002341P
****************
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: GSM1127129_UCSF-UBC.Placenta_Amnion.H3K4me1.CTL02.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A21717-1.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Placenta Amnion H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K4me1 ChIP-Seq on Placenta Amnion, Donor CTL02 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.17024
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 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 24,134,126
FINDPEAKS_SCORE: 0.0638
FINDPEAKS_PERCENTILE: 13
HOTSPOT_SCORE: 0.1897
HOTSPOT_PERCENTILE: 13
IROC_SCORE: 0.8993
IROC_PERCENTILE: 21
POISSON_SCORE: 0.3196
POISSON_PERCENTILE: 7
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1127129_UCSF-UBC.Placenta_Amnion.H3K4me1.CTL02.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A21717-1.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Placenta Amnion H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K4me1 ChIP-Seq read mappings from Placenta Amnion, Donor CTL02 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.17083
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 9
BROWSER_TRACK_NAME: PA H3K4me1 02 17
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Placenta Amnion Histone H3K4me1 Donor CTL02 Library A21717 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 24,134,126
FINDPEAKS_SCORE: 0.0638
FINDPEAKS_PERCENTILE: 13
HOTSPOT_SCORE: 0.1897
HOTSPOT_PERCENTILE: 13
IROC_SCORE: 0.8993
IROC_PERCENTILE: 21
POISSON_SCORE: 0.3196
POISSON_PERCENTILE: 7
MAXIMUM_REPLICATE_CORRELATION: NA

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

value: Amnion tissue

value: placenta (amniotic membrane) tissue


description:
design description: H3K4me3 ChIP-Seq analysis of peripheral mononuclear cell from TC015 (A21627) using Illumina HiSeq 2000
library name: A21627
EXPERIMENT_TYPE: Histone H3K4me3
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: 5 ug
SIZE_FRACTION: 94-294 bp
CHIP_PROTOCOL_BEAD_TYPE: Sepharose A/G Bead Mix
CHIP_PROTOCOL_BEAD_AMOUNT: 20 ul
CHIP_PROTOCOL_ANTIBODY_AMOUNT: 5 ul
CHIP_ANTIBODY: H3K4me3
CHIP_ANTIBODY_PROVIDER: Cell Signaling Technology
CHIP_ANTIBODY_CATALOG: 9751S
CHIP_ANTIBODY_LOT: 4
****************
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: GSM1127126_UCSF-UBC.Peripheral_Blood_Mononuclear_Primary_Cells.H3K4me3.TC015.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A21627-1.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Peripheral Blood Mononuclear Primary Cells H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K4me3 ChIP-Seq on Peripheral Blood Mononuclear Primary Cells, Donor TC015, Library A21627 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.17064
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 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 18,728,810
FINDPEAKS_SCORE: 0.2315
FINDPEAKS_PERCENTILE: 23
HOTSPOT_SCORE: 0.2438
HOTSPOT_PERCENTILE: 18
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.2523
POISSON_PERCENTILE: 14
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

ANALYSIS FILE NAME: GSM1127126_UCSF-UBC.Peripheral_Blood_Mononuclear_Primary_Cells.H3K4me3.TC015.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A21627-1.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Peripheral Blood Mononuclear Primary Cells H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K4me3 ChIP-Seq read mappings from Peripheral Blood Mononuclear Primary Cells, Donor TC015, Library A21627 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.17123
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 9
BROWSER_TRACK_NAME: PBM H3K4me3 15 27
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Peripheral Blood Mononuclear Primary Cells Histone H3K4me3 Donor TC015 Library A21627 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 18,728,810
FINDPEAKS_SCORE: 0.2315
FINDPEAKS_PERCENTILE: 23
HOTSPOT_SCORE: 0.2438
HOTSPOT_PERCENTILE: 18
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.2523
POISSON_PERCENTILE: 14
MAXIMUM_REPLICATE_CORRELATION: 0.96

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


description:
design description: ChIP-Seq input analysis of pancreas islet from ZGI 213 (A22474) using Illumina HiSeq 2000
library name: A22474
EXPERIMENT_TYPE: ChIP-Seq Input
EXTRACTION_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Bioruptor
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 30 min
CHIP_PROTOCOL: Input
CHIP_PROTOCOL_CHROMATIN_AMOUNT: 0.1 ug
SIZE_FRACTION: 124-199 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: GSM1127092_UCSF-UBC.Pancreatic_Islets.Input.ZGI_213.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A22474-1.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Pancreatic Islets Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Input ChIP-Seq on Pancreatic Islets, Donor ZGI 213 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.17039
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 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 26,161,644
FINDPEAKS_SCORE: 0.0017
FINDPEAKS_PERCENTILE: 3
HOTSPOT_SCORE: 0.0025
HOTSPOT_PERCENTILE: 5
IROC_SCORE: 0.0
IROC_PERCENTILE: 25
POISSON_SCORE: 0.0195
POISSON_PERCENTILE: 8
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

ANALYSIS FILE NAME: GSM1127092_UCSF-UBC.Pancreatic_Islets.Input.ZGI_213.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A22474-1.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Pancreatic Islets Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Input ChIP-Seq read mappings from Pancreatic Islets, Donor ZGI 213 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.17098
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 9
BROWSER_TRACK_NAME: PI Input 13 74
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Pancreatic Islets ChIP-Seq Input Donor ZGI 213 Library A22474 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 26,161,644
FINDPEAKS_SCORE: 0.0017
FINDPEAKS_PERCENTILE: 3
HOTSPOT_SCORE: 0.0025
HOTSPOT_PERCENTILE: 5
IROC_SCORE: 0.0
IROC_PERCENTILE: 25
POISSON_SCORE: 0.0195
POISSON_PERCENTILE: 8
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

value: Pancreas

value: Islet

value: pancreas islet


description:
design description: ChIP-Seq input analysis of ganglionic eminence neural stem and progenitor cells from HuFNSC03 (A16057) using Illumina HiSeq 2000
library name: A16057
EXPERIMENT_TYPE: ChIP-Seq Input
EXTRACTION_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Fisher 550 Sonic Dismembrator
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 10 min
CHIP_PROTOCOL: Input
CHIP_PROTOCOL_CHROMATIN_AMOUNT: N/A
SIZE_FRACTION: 74-441 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: GSM1127088_UCSF-UBC.Neurosphere_Cultured_Cells_Ganglionic_Eminence_Derived.Input.HuFNSC03.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A16057-1.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Neurosphere Cultured Cells Ganglionic Eminence Derived Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Input ChIP-Seq on Neurosphere Cultured Cells Ganglionic Eminence Derived, Donor HuFNSC03 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.17066
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 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 24,250,518
FINDPEAKS_SCORE: 0.0047
FINDPEAKS_PERCENTILE: 25
HOTSPOT_SCORE: 0.0737
HOTSPOT_PERCENTILE: 80
IROC_SCORE: 0.6062
IROC_PERCENTILE: 29
POISSON_SCORE: 0.0955
POISSON_PERCENTILE: 72
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM1127088_UCSF-UBC.Neurosphere_Cultured_Cells_Ganglionic_Eminence_Derived.Input.HuFNSC03.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A16057-1.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Neurosphere Cultured Cells Ganglionic Eminence Derived Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Input ChIP-Seq read mappings from Neurosphere Cultured Cells Ganglionic Eminence Derived, Donor HuFNSC03 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.17125
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 9
BROWSER_TRACK_NAME: NGED Input 03 57
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Neurosphere Cultured Cells Ganglionic Eminence Derived ChIP-Seq Input Donor HuFNSC03 Library A16057 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 24,250,518
FINDPEAKS_SCORE: 0.0047
FINDPEAKS_PERCENTILE: 25
HOTSPOT_SCORE: 0.0737
HOTSPOT_PERCENTILE: 80
IROC_SCORE: 0.6062
IROC_PERCENTILE: 29
POISSON_SCORE: 0.0955
POISSON_PERCENTILE: 72
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

value: Brain

value: Ganglionic eminence neurosphere culture

value: primary cell culture


description:
design description: H3K27me3 ChIP-Seq analysis of placenta (amniotic membrane) tissue from CTL02 (A21720) using Illumina HiSeq 2000
library name: A21720
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: 15 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: 4.5 ug
SIZE_FRACTION: 158-479 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: A1456-004P
****************
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: GSM1127139_UCSF-UBC.Placenta_Amnion.H3K27me3.CTL02.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A21720-1.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Placenta Amnion H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27me3 ChIP-Seq on Placenta Amnion, Donor CTL02 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.17029
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 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 27,757,878
FINDPEAKS_SCORE: 0.018
FINDPEAKS_PERCENTILE: 14
HOTSPOT_SCORE: 0.0551
HOTSPOT_PERCENTILE: 5
IROC_SCORE: 0.8982
IROC_PERCENTILE: 56
POISSON_SCORE: 0.1416
POISSON_PERCENTILE: 2
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1127139_UCSF-UBC.Placenta_Amnion.H3K27me3.CTL02.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A21720-1.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Placenta Amnion H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27me3 ChIP-Seq read mappings from Placenta Amnion, Donor CTL02 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.17088
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 9
BROWSER_TRACK_NAME: PA H3K27me3 02 20
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Placenta Amnion Histone H3K27me3 Donor CTL02 Library A21720 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 27,757,878
FINDPEAKS_SCORE: 0.018
FINDPEAKS_PERCENTILE: 14
HOTSPOT_SCORE: 0.0551
HOTSPOT_PERCENTILE: 5
IROC_SCORE: 0.8982
IROC_PERCENTILE: 56
POISSON_SCORE: 0.1416
POISSON_PERCENTILE: 2
MAXIMUM_REPLICATE_CORRELATION: NA

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

value: male


description:
design description: H3K4me1 ChIP-Seq analysis of pancreas islet from ZGI 213 (A22468) using Illumina HiSeq 2000
library name: A22468
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: Bioruptor
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 30 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: 9 ug
SIZE_FRACTION: 124-199 bp
CHIP_PROTOCOL_BEAD_TYPE: Pierce Magnetic Protein A/G
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: A399-002341P
****************
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: GSM1127087_UCSF-UBC.Pancreatic_Islets.H3K4me1.ZGI_213.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A22468-1.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Pancreatic Islets H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K4me1 ChIP-Seq on Pancreatic Islets, Donor ZGI 213 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.17040
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 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 25,255,924
FINDPEAKS_SCORE: 0.088
FINDPEAKS_PERCENTILE: 14
HOTSPOT_SCORE: 0.2107
HOTSPOT_PERCENTILE: 16
IROC_SCORE: 0.9047
IROC_PERCENTILE: 23
POISSON_SCORE: 0.4013
POISSON_PERCENTILE: 27
MAXIMUM_REPLICATE_CORRELATION: 0.95

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

ANALYSIS FILE NAME: GSM1127087_UCSF-UBC.Pancreatic_Islets.H3K4me1.ZGI_213.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A22468-1.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Pancreatic Islets H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K4me1 ChIP-Seq read mappings from Pancreatic Islets, Donor ZGI 213 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.17099
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 9
BROWSER_TRACK_NAME: PI H3K4me1 13 68
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Pancreatic Islets Histone H3K4me1 Donor ZGI 213 Library A22468 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 25,255,924
FINDPEAKS_SCORE: 0.088
FINDPEAKS_PERCENTILE: 14
HOTSPOT_SCORE: 0.2107
HOTSPOT_PERCENTILE: 16
IROC_SCORE: 0.9047
IROC_PERCENTILE: 23
POISSON_SCORE: 0.4013
POISSON_PERCENTILE: 27
MAXIMUM_REPLICATE_CORRELATION: 0.95

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


description:
design description: ChIP-Seq input analysis of breast fibroblast from RM071 (A21646) using Illumina HiSeq 2000
library name: A21646
EXPERIMENT_TYPE: ChIP-Seq Input
EXTRACTION_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Fisher 550 Sonic Dismembrator
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 10 min
CHIP_PROTOCOL: Input
CHIP_PROTOCOL_CHROMATIN_AMOUNT: N/A
SIZE_FRACTION: 94-294 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: GSM1127089_UCSF-UBC.Breast_Fibroblast_Primary_Cells.Input.RM071.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A21646-1.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Breast Fibroblast Primary Cells Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Input ChIP-Seq on Breast Fibroblast Primary Cells, Donor RM071 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.17026
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 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 18,638,078
FINDPEAKS_SCORE: 0.0234
FINDPEAKS_PERCENTILE: 97
HOTSPOT_SCORE: 0.2273
HOTSPOT_PERCENTILE: 98
IROC_SCORE: 0.862
IROC_PERCENTILE: 41
POISSON_SCORE: 0.4806
POISSON_PERCENTILE: 98
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1127089_UCSF-UBC.Breast_Fibroblast_Primary_Cells.Input.RM071.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A21646-1.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Breast Fibroblast Primary Cells Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Input ChIP-Seq read mappings from Breast Fibroblast Primary Cells, Donor RM071 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.17085
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 9
BROWSER_TRACK_NAME: BF Input 71 46
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Breast Fibroblast Primary Cells ChIP-Seq Input Donor RM071 Library A21646 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 18,638,078
FINDPEAKS_SCORE: 0.0234
FINDPEAKS_PERCENTILE: 97
HOTSPOT_SCORE: 0.2273
HOTSPOT_PERCENTILE: 98
IROC_SCORE: 0.862
IROC_PERCENTILE: 41
POISSON_SCORE: 0.4806
POISSON_PERCENTILE: 98
MAXIMUM_REPLICATE_CORRELATION: NA

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

value: Breast

value: Fibroblast cultured cell

value: breast fibroblast


description:
design description: H3K36me3 ChIP-Seq analysis of placenta (smooth chorionic membrane) tissue from CTL02 (A21714) using Illumina HiSeq 2000
library name: A21714
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: 4.5 ug
SIZE_FRACTION: 156-466 bp
CHIP_PROTOCOL_BEAD_TYPE: Sepharose A/G Bead Mix
CHIP_PROTOCOL_BEAD_AMOUNT: 20 ul
CHIP_PROTOCOL_ANTIBODY_AMOUNT: 2.5 ug
CHIP_ANTIBODY: H3K36me3
CHIP_ANTIBODY_PROVIDER: Abcam
CHIP_ANTIBODY_CATALOG: ab9050
CHIP_ANTIBODY_LOT: 947467
****************
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: GSM1127141_UCSF-UBC.Placenta_Chorion_Smooth.H3K36me3.CTL02.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A21714-1.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Placenta Chorion Smooth H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K36me3 ChIP-Seq on Placenta Chorion Smooth, Donor CTL02 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.17063
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 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 26,264,997
FINDPEAKS_SCORE: 0.1325
FINDPEAKS_PERCENTILE: 21
HOTSPOT_SCORE: 0.1776
HOTSPOT_PERCENTILE: 10
IROC_SCORE: 0.9389
IROC_PERCENTILE: 29
POISSON_SCORE: 0.3996
POISSON_PERCENTILE: 22
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1127141_UCSF-UBC.Placenta_Chorion_Smooth.H3K36me3.CTL02.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A21714-1.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Placenta Chorion Smooth H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K36me3 ChIP-Seq read mappings from Placenta Chorion Smooth, Donor CTL02 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.17122
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 9
BROWSER_TRACK_NAME: PCS H3K36me3 02 14
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Placenta Chorion Smooth Histone H3K36me3 Donor CTL02 Library A21714 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 26,264,997
FINDPEAKS_SCORE: 0.1325
FINDPEAKS_PERCENTILE: 21
HOTSPOT_SCORE: 0.1776
HOTSPOT_PERCENTILE: 10
IROC_SCORE: 0.9389
IROC_PERCENTILE: 29
POISSON_SCORE: 0.3996
POISSON_PERCENTILE: 22
MAXIMUM_REPLICATE_CORRELATION: NA

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

value: No


description:
design description: H3K4me3 ChIP-Seq analysis of breast fibroblast from RM071 (A21641) using Illumina HiSeq 2000
library name: A21641
EXPERIMENT_TYPE: Histone H3K4me3
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: 5 ug
SIZE_FRACTION: 94-294 bp
CHIP_PROTOCOL_BEAD_TYPE: Sepharose A/G Bead Mix
CHIP_PROTOCOL_BEAD_AMOUNT: 20 ul
CHIP_PROTOCOL_ANTIBODY_AMOUNT: 5 ul
CHIP_ANTIBODY: H3K4me3
CHIP_ANTIBODY_PROVIDER: Cell Signaling Technology
CHIP_ANTIBODY_CATALOG: 9751S
CHIP_ANTIBODY_LOT: 4
****************
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: GSM1127085_UCSF-UBC.Breast_Fibroblast_Primary_Cells.H3K4me3.RM071.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A21641-1.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Breast Fibroblast Primary Cells H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K4me3 ChIP-Seq on Breast Fibroblast Primary Cells, Donor RM071 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.17070
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 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 18,886,092
FINDPEAKS_SCORE: 0.2059
FINDPEAKS_PERCENTILE: 16
HOTSPOT_SCORE: 0.2175
HOTSPOT_PERCENTILE: 13
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.2197
POISSON_PERCENTILE: 7
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1127085_UCSF-UBC.Breast_Fibroblast_Primary_Cells.H3K4me3.RM071.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A21641-1.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Breast Fibroblast Primary Cells H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K4me3 ChIP-Seq read mappings from Breast Fibroblast Primary Cells, Donor RM071 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.17129
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 9
BROWSER_TRACK_NAME: BF H3K4me3 71 41
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Breast Fibroblast Primary Cells Histone H3K4me3 Donor RM071 Library A21641 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 18,886,092
FINDPEAKS_SCORE: 0.2059
FINDPEAKS_PERCENTILE: 16
HOTSPOT_SCORE: 0.2175
HOTSPOT_PERCENTILE: 13
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.2197
POISSON_PERCENTILE: 7
MAXIMUM_REPLICATE_CORRELATION: NA

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


description:
design description: H3K9me3 ChIP-Seq analysis of UCSF-4 embryonic stem cell line (A19298) using Illumina HiSeq 2000
library name: A19298
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: 5 ug
SIZE_FRACTION: 80-385 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: GSM1127081_UCSF-UBC.UCSF-4Star.H3K9me3.A19298.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A19298-1.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of UCSF-4* Cell Line H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K9me3 ChIP-Seq on the UCSF-4* Cell Line, Library A19298 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.17019
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 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 27,977,217
FINDPEAKS_SCORE: 0.1396
FINDPEAKS_PERCENTILE: 78
HOTSPOT_SCORE: 0.1717
HOTSPOT_PERCENTILE: 60
IROC_SCORE: 0.922
IROC_PERCENTILE: 86
POISSON_SCORE: 0.3644
POISSON_PERCENTILE: 80
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

ANALYSIS FILE NAME: GSM1127081_UCSF-UBC.UCSF-4Star.H3K9me3.A19298.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A19298-1.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of UCSF-4Star Cell Line H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K9me3 ChIP-Seq read mappings from the UCSF-4Star Cell Line, Library A19298 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.17078
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 9
BROWSER_TRACK_NAME: UCSF4* H3K9me3 98
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC UCSF-4* Cell Line Histone H3K9me3 Library A19298 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 27,977,217
FINDPEAKS_SCORE: 0.1396
FINDPEAKS_PERCENTILE: 78
HOTSPOT_SCORE: 0.1717
HOTSPOT_PERCENTILE: 60
IROC_SCORE: 0.922
IROC_PERCENTILE: 86
POISSON_SCORE: 0.3644
POISSON_PERCENTILE: 80
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

value: cell line

tag: line

value: Embryo ICM

value: Embryonic stem cell