title: LICR_ChipSeq_Liver_Input_adult-8wks

status: Public on Apr 19 2012

city: Stanford

first: ENCODE

last: DCC

address: 300 Pasteur Dr

institute: ENCODE DCC

organism: Mus musculus

source_name: Liver

tag: lab

value: LICR-m

tag: lab description

value: Ren - Ludwig Institue for Cancer Research

tag: datatype

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

value: tissue

tag: cell organism

value: mouse

value: liver

value: M

tag: antibody

value: Input

tag: antibody description

value: Control signal which may be subtracted from experimental raw signal before peaks are called.

tag: age

tag: age description

value: Adult 8 weeks

tag: control

value: std

tag: control description

value: Standard input signal for most experiments.

tag: controlid

tag: labversion

tag: replicate

tag: softwareversion

value: ELAND

tag: strain

tag: strain description

value: C57 black 6, the most common inbred strain of laboratory mouse


status: Public on Apr 17 2012

type: SRA

city: San Francisco

first: UCSF-UBC

last: CENTER

state: CA

address: UCSF-UBC

country: USA

institute: UCSF-UBC

description:
design description: H3K27me3 ChIP-Seq analysis of brain (germinal matrix) tissue from HuFGM02 (A03504) using Illumina HiSeq 2000
library name: A03504
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: 15 ug
SIZE_FRACTION: 74-264 bp
CHIP_PROTOCOL_BEAD_TYPE: Sepharose A/G Bead Mix
CHIP_PROTOCOL_BEAD_AMOUNT: 20 ul
CHIP_PROTOCOL_ANTIBODY_AMOUNT: 5 ug
CHIP_ANTIBODY: H3K27me3
CHIP_ANTIBODY_PROVIDER: Diagenode
CHIP_ANTIBODY_CATALOG: pAb-069-050
CHIP_ANTIBODY_LOT: A299-00241
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

library_source: genomic

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

ANALYSIS FILE NAME: GSM817226_UCSF-UBC.Brain_Germinal_Matrix.H3K27me3.HuFGM02.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A03504-1-A03504-1.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of Brain Germinal Matrix Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27me3 ChIP-Seq on Brain Germinal Matrix, Donor HuFGM02 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.12523
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 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 17,498,823
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 10
FINDPEAKS_SCORE: 0.1596
FINDPEAKS_PERCENTILE: 90
HOTSPOT_SCORE: 0.2494
HOTSPOT_PERCENTILE: 90
IROC_SCORE: 0.9676
IROC_PERCENTILE: 100
POISSON_SCORE: 0.3515
POISSON_PERCENTILE: 70
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

ANALYSIS FILE NAME: GSM817226_UCSF-UBC.Brain_Germinal_Matrix.H3K27me3.HuFGM02.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A03504-1-A03504-1.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of Brain Germinal Matrix Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27me3 ChIP-Seq read mappings from Brain Germinal Matrix, Donor HuFGM02 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.12546
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 6
BROWSER_TRACK_NAME: BGM H3K27me3 02 04
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Brain Germinal Matrix Histone H3K27me3 Donor HuFGM02 Library A03504 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 17,498,823
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 10
FINDPEAKS_SCORE: 0.1596
FINDPEAKS_PERCENTILE: 90
HOTSPOT_SCORE: 0.2494
HOTSPOT_PERCENTILE: 90
IROC_SCORE: 0.9676
IROC_PERCENTILE: 100
POISSON_SCORE: 0.3515
POISSON_PERCENTILE: 70
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: male

tag: body site

value: Brain

tag: histological type

value: Germinal matrix tissue

tag: is tumor

value: No

value: primary tissue

value: brain (germinal matrix) tissue


description:
design description: H3K4me1 ChIP-Seq analysis of brain (germinal matrix) tissue from HuFGM01 (A05150) using Illumina HiSeq 2000
library name: A05150
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: 15 ug
SIZE_FRACTION: 59-264 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: GSM817228_UCSF-UBC.Brain_Germinal_Matrix.H3K4me1.HuFGM01.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A05150-1-A05150-1.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of Brain Germinal Matrix Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me1 ChIP-Seq on Brain Germinal Matrix, Donor HuFGM01 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.12532
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 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 20,569,273
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 14
FINDPEAKS_SCORE: 0.0888
FINDPEAKS_PERCENTILE: 36
HOTSPOT_SCORE: 0.2169
HOTSPOT_PERCENTILE: 43
IROC_SCORE: 0.9081
IROC_PERCENTILE: 36
POISSON_SCORE: 0.365
POISSON_PERCENTILE: 43
MAXIMUM_REPLICATE_CORRELATION: 0.94

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

ANALYSIS FILE NAME: GSM817228_UCSF-UBC.Brain_Germinal_Matrix.H3K4me1.HuFGM01.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A05150-1-A05150-1.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of Brain Germinal Matrix Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me1 ChIP-Seq read mappings from Brain Germinal Matrix, Donor HuFGM01 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.12555
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 6
BROWSER_TRACK_NAME: BGM H3K4me1 01 50
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Brain Germinal Matrix Histone H3K4me1 Donor HuFGM01 Library A05150 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 20,569,273
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 14
FINDPEAKS_SCORE: 0.0888
FINDPEAKS_PERCENTILE: 36
HOTSPOT_SCORE: 0.2169
HOTSPOT_PERCENTILE: 43
IROC_SCORE: 0.9081
IROC_PERCENTILE: 36
POISSON_SCORE: 0.365
POISSON_PERCENTILE: 43
MAXIMUM_REPLICATE_CORRELATION: 0.94

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


description:
design description: H3K4me1 ChIP-Seq analysis of cortex neural stem and progenitor cells from HuFNSC01 (A03269) using Illumina HiSeq 2000
library name: A03269
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: 5 ug
SIZE_FRACTION: 84-304 bp
CHIP_PROTOCOL_BEAD_TYPE: Sepharose A/G Bead Mix
CHIP_PROTOCOL_BEAD_AMOUNT: 20 ul
CHIP_PROTOCOL_ANTIBODY_AMOUNT: 3.75 ug
CHIP_ANTIBODY: H3K4me1
CHIP_ANTIBODY_PROVIDER: Diagenode
CHIP_ANTIBODY_CATALOG: pAb-037-050
CHIP_ANTIBODY_LOT: A399-0011
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM817230_UCSF-UBC.Neurosphere_Cultured_Cells_Cortex_Derived.H3K4me1.HuFNSC01.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A03269-1.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of Neurosphere Cultured Cells Cortex Derived Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me1 ChIP-Seq on Neurosphere Cultured Cells Cortex Derived, Donor HuFNSC01 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.12531
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 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 80,732,149
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 14
FINDPEAKS_SCORE: 0.4722
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.4762
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9968
IROC_PERCENTILE: 100
POISSON_SCORE: 0.6006
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.93

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

ANALYSIS FILE NAME: GSM817230_UCSF-UBC.Neurosphere_Cultured_Cells_Cortex_Derived.H3K4me1.HuFNSC01.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A03269-1.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of Neurosphere Cultured Cells Cortex Derived Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me1 ChIP-Seq read mappings from Neurosphere Cultured Cells Cortex Derived, Donor HuFNSC01 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.12554
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 6
BROWSER_TRACK_NAME: NCD H3K4me1 01 69
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Neurosphere Cultured Cells Cortex Derived Histone H3K4me1 Donor HuFNSC01 Library A03269 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 80,732,149
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 14
FINDPEAKS_SCORE: 0.4722
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.4762
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9968
IROC_PERCENTILE: 100
POISSON_SCORE: 0.6006
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.93

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

value: female

value: Cortex neurosphere culture

value: primary cell culture

tag: cell type

value: cortex neural stem and progenitor cells


description:
design description: H3K36me3 ChIP-Seq analysis of brain (germinal matrix) tissue from HuFGM02 (A03505) using Illumina HiSeq 2000
library name: A03505
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: 15 ug
SIZE_FRACTION: 59-309 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: GSM817227_UCSF-UBC.Brain_Germinal_Matrix.H3K36me3.HuFGM02.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A03505-1-A03505-1.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of Brain Germinal Matrix Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K36me3 ChIP-Seq on Brain Germinal Matrix, Donor HuFGM02 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.12529
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 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 23,037,293
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 13
FINDPEAKS_SCORE: 0.1696
FINDPEAKS_PERCENTILE: 77
HOTSPOT_SCORE: 0.2081
HOTSPOT_PERCENTILE: 69
IROC_SCORE: 0.9507
IROC_PERCENTILE: 77
POISSON_SCORE: 0.4339
POISSON_PERCENTILE: 85
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

ANALYSIS FILE NAME: GSM817227_UCSF-UBC.Brain_Germinal_Matrix.H3K36me3.HuFGM02.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A03505-1-A03505-1.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of Brain Germinal Matrix Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K36me3 ChIP-Seq read mappings from Brain Germinal Matrix, Donor HuFGM02 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.12552
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 6
BROWSER_TRACK_NAME: BGM H3K36me3 02 05
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Brain Germinal Matrix Histone H3K36me3 Donor HuFGM02 Library A03505 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 23,037,293
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 13
FINDPEAKS_SCORE: 0.1696
FINDPEAKS_PERCENTILE: 77
HOTSPOT_SCORE: 0.2081
HOTSPOT_PERCENTILE: 69
IROC_SCORE: 0.9507
IROC_PERCENTILE: 77
POISSON_SCORE: 0.4339
POISSON_PERCENTILE: 85
MAXIMUM_REPLICATE_CORRELATION: 0.96

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


description:
design description: ChIP-Seq input analysis of ganglionic eminence neural stem and progenitor cells from HuFNSC01 (A03288) using Illumina HiSeq 2000
library name: A03288
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: 84-324 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: GSM817245_UCSF-UBC.Neurosphere_Cultured_Cells_Ganglionic_Eminence_Derived.Input.HuFNSC01.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A03288-1.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of Neurosphere Cultured Cells Ganglionic Eminence Derived ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on Neurosphere Cultured Cells Ganglionic Eminence Derived, Donor HuFNSC01 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.12520
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 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 41,851,331
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 15
FINDPEAKS_SCORE: 0.0012
FINDPEAKS_PERCENTILE: 20
HOTSPOT_SCORE: 0.0009
HOTSPOT_PERCENTILE: 27
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.0085
POISSON_PERCENTILE: 20
MAXIMUM_REPLICATE_CORRELATION: 0.78

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

ANALYSIS FILE NAME: GSM817245_UCSF-UBC.Neurosphere_Cultured_Cells_Ganglionic_Eminence_Derived.Input.HuFNSC01.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A03288-1.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of Neurosphere Cultured Cells Ganglionic Eminence Derived ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from Neurosphere Cultured Cells Ganglionic Eminence Derived, Donor HuFNSC01 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.12543
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 6
BROWSER_TRACK_NAME: NGED Input 01 88
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Neurosphere Cultured Cells Ganglionic Eminence Derived ChIP-Seq Input Donor HuFNSC01 Library A03288 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 41,851,331
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 15
FINDPEAKS_SCORE: 0.0012
FINDPEAKS_PERCENTILE: 20
HOTSPOT_SCORE: 0.0009
HOTSPOT_PERCENTILE: 27
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.0085
POISSON_PERCENTILE: 20
MAXIMUM_REPLICATE_CORRELATION: 0.78

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

value: Ganglionic eminence neurosphere culture


description:
design description: ChIP-Seq input analysis of foreskin fibroblast from skin01 (A08394) using Illumina HiSeq 2000
library name: A08394
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: 64-374 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: GSM817246_UCSF-UBC.Penis_Foreskin_Fibroblast_Primary_Cells.Input.skin01.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A08394-1.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of Penis Foreskin Fibroblast Primary Cells ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on Penis Foreskin Fibroblast Primary Cells, Donor skin01 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.12535
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 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 49,101,343
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 15
FINDPEAKS_SCORE: 0.0011
FINDPEAKS_PERCENTILE: 13
HOTSPOT_SCORE: 0.0008
HOTSPOT_PERCENTILE: 20
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.0089
POISSON_PERCENTILE: 27
MAXIMUM_REPLICATE_CORRELATION: 0.95

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

ANALYSIS FILE NAME: GSM817246_UCSF-UBC.Penis_Foreskin_Fibroblast_Primary_Cells.Input.skin01.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A08394-1.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of Penis Foreskin Fibroblast Primary Cells ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from Penis Foreskin Fibroblast Primary Cells, Donor skin01 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.12558
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 6
BROWSER_TRACK_NAME: PFF Input 01 94
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells ChIP-Seq Input Donor skin01 Library A08394 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 49,101,343
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 15
FINDPEAKS_SCORE: 0.0011
FINDPEAKS_PERCENTILE: 13
HOTSPOT_SCORE: 0.0008
HOTSPOT_PERCENTILE: 20
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.0089
POISSON_PERCENTILE: 27
MAXIMUM_REPLICATE_CORRELATION: 0.95

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

value: Penis

value: Fibroblast

value: foreskin fibroblast


title: ChIP-Seq analysis of H3K27ac in human mid frontal lobe cells; DNA_Lib 612

city: Cambridge

first: BROAD

last: INSTITUTE

state: MA

institute: Broad Institute

description:
sample_term_id: UBERON_0006483
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 612
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8705
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9448
****************
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: GSM773015_BI.Brain_Mid_Frontal_Lobe.H3K27ac.149.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 612-DNA_Lib 612-DNA_Lib 612.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of Brain Mid Frontal Lobe Histone H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27ac ChIP-Seq on Brain Mid Frontal Lobe, Donor 149, 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.12288
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 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 34,362,604
NUMBER_OF_H3K27ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 5
FINDPEAKS_SCORE: 0.1184
FINDPEAKS_PERCENTILE: 40
HOTSPOT_SCORE: 0.1967
HOTSPOT_PERCENTILE: 40
IROC_SCORE: 0.9367
IROC_PERCENTILE: 20
POISSON_SCORE: 0.3642
POISSON_PERCENTILE: 40
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM773015_BI.Brain_Mid_Frontal_Lobe.H3K27ac.149.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 612-DNA_Lib 612-DNA_Lib 612.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of Brain Mid Frontal Lobe Histone H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27ac ChIP-Seq read mappings from Brain Mid Frontal Lobe, Donor 149, 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.12335
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 6
BROWSER_TRACK_NAME: BMFL H3K27ac 49 12
BROWSER_TRACK_DESCRIPTION: BI Brain Mid Frontal Lobe Histone H3K27ac Donor 149 Library DNA_Lib 612 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 34,362,604
NUMBER_OF_H3K27ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 5
FINDPEAKS_SCORE: 0.1184
FINDPEAKS_PERCENTILE: 40
HOTSPOT_SCORE: 0.1967
HOTSPOT_PERCENTILE: 40
IROC_SCORE: 0.9367
IROC_PERCENTILE: 20
POISSON_SCORE: 0.3642
POISSON_PERCENTILE: 40
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: specified brain region obtained by post-mortem collection in a longitudinal study; DNA_Lib 612

extract_protocol: Library construction protocol: Single read - Illumina

tag: sample alias

tag: sample common name

value: Brain, Mid Frontal Lobe

value: Post-Mortem

value: no AD evident at demise

tag: molecule

value: genomic DNA

tag: disease

value: Mid Frontal Lobe

value: Male

value: Primary Tissue

value: Rush University Medical Center

value: 81.0 Years

value: Protein A-Sepharose 4B

value: 0.5 to 3 million cells

value: cell/nuclei lysis

value: ~1 ug

value: 10 ul bed volume

value: Abcam

value: Histone H3K27ac

value: Branson


title: ChIP-Seq analysis of H3K4me3 in human mid frontal lobe cells; DNA_Lib 611

description:
sample_term_id: UBERON_0006483
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 611
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8702
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9448
****************
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: GSM773012_BI.Brain_Mid_Frontal_Lobe.H3K4me3.149.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 611-DNA_Lib 611-DNA_Lib 611.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of Brain Mid Frontal Lobe Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me3 ChIP-Seq on Brain Mid Frontal Lobe, Donor 149, 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.12297
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 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 28,093,699
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 11
FINDPEAKS_SCORE: 0.2428
FINDPEAKS_PERCENTILE: 45
HOTSPOT_SCORE: 0.2731
HOTSPOT_PERCENTILE: 45
IROC_SCORE: 0.9999
IROC_PERCENTILE: 91
POISSON_SCORE: 0.3072
POISSON_PERCENTILE: 45
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

ANALYSIS FILE NAME: GSM773012_BI.Brain_Mid_Frontal_Lobe.H3K4me3.149.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 611-DNA_Lib 611-DNA_Lib 611.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of Brain Mid Frontal Lobe Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me3 ChIP-Seq read mappings from Brain Mid Frontal Lobe, Donor 149, 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.12344
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 6
BROWSER_TRACK_NAME: BMFL H3K4me3 49 11
BROWSER_TRACK_DESCRIPTION: BI Brain Mid Frontal Lobe Histone H3K4me3 Donor 149 Library DNA_Lib 611 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 28,093,699
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 11
FINDPEAKS_SCORE: 0.2428
FINDPEAKS_PERCENTILE: 45
HOTSPOT_SCORE: 0.2731
HOTSPOT_PERCENTILE: 45
IROC_SCORE: 0.9999
IROC_PERCENTILE: 91
POISSON_SCORE: 0.3072
POISSON_PERCENTILE: 45
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

source_name: specified brain region obtained by post-mortem collection in a longitudinal study; DNA_Lib 611

value: Brain, Mid Frontal Lobe

value: Brain

value: Millipore

value: Histone H3K4me3


title: ChIP-Seq analysis of H3K4me1 in human mid frontal lobe cells; DNA_Lib 613

description:
sample_term_id: UBERON_0006483
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 613
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8704
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9448
****************
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: GSM773014_BI.Brain_Mid_Frontal_Lobe.H3K4me1.149.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 613-DNA_Lib 613-DNA_Lib 613.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of Brain Mid Frontal Lobe Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me1 ChIP-Seq on Brain Mid Frontal Lobe, Donor 149, 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.12279
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 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 33,447,073
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 14
FINDPEAKS_SCORE: 0.0529
FINDPEAKS_PERCENTILE: 21
HOTSPOT_SCORE: 0.1751
HOTSPOT_PERCENTILE: 21
IROC_SCORE: 0.8682
IROC_PERCENTILE: 29
POISSON_SCORE: 0.3531
POISSON_PERCENTILE: 36
MAXIMUM_REPLICATE_CORRELATION: 0.95

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

ANALYSIS FILE NAME: GSM773014_BI.Brain_Mid_Frontal_Lobe.H3K4me1.149.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 613-DNA_Lib 613-DNA_Lib 613.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of Brain Mid Frontal Lobe Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me1 ChIP-Seq read mappings from Brain Mid Frontal Lobe, Donor 149, 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.12326
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 6
BROWSER_TRACK_NAME: BMFL H3K4me1 49 13
BROWSER_TRACK_DESCRIPTION: BI Brain Mid Frontal Lobe Histone H3K4me1 Donor 149 Library DNA_Lib 613 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 33,447,073
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 14
FINDPEAKS_SCORE: 0.0529
FINDPEAKS_PERCENTILE: 21
HOTSPOT_SCORE: 0.1751
HOTSPOT_PERCENTILE: 21
IROC_SCORE: 0.8682
IROC_PERCENTILE: 29
POISSON_SCORE: 0.3531
POISSON_PERCENTILE: 36
MAXIMUM_REPLICATE_CORRELATION: 0.95

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

source_name: specified brain region obtained by post-mortem collection in a longitudinal study; DNA_Lib 613

value: Post-Mortem

value: no AD evident at demise

value: genomic DNA

value: Mid Frontal Lobe

value: Histone H3K4me1


description:
design description: H3K9me3 ChIP-Seq analysis of foreskin fibroblast from skin02 (A08397) using Illumina HiSeq 2000
library name: A08397
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: 20 ug
SIZE_FRACTION: 94-374 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: GSM817239_UCSF-UBC.Penis_Foreskin_Fibroblast_Primary_Cells.H3K9me3.skin02.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A08397-1.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of Penis Foreskin Fibroblast Primary Cells Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9me3 ChIP-Seq on Penis Foreskin Fibroblast Primary Cells, Donor skin02 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.12522
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 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 53,308,458
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 13
FINDPEAKS_SCORE: 0.0162
FINDPEAKS_PERCENTILE: 8
HOTSPOT_SCORE: 0.0948
HOTSPOT_PERCENTILE: 31
IROC_SCORE: 0.7756
IROC_PERCENTILE: 38
POISSON_SCORE: 0.3925
POISSON_PERCENTILE: 77
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

ANALYSIS FILE NAME: GSM817239_UCSF-UBC.Penis_Foreskin_Fibroblast_Primary_Cells.H3K9me3.skin02.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A08397-1.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of Penis Foreskin Fibroblast Primary Cells Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9me3 ChIP-Seq read mappings from Penis Foreskin Fibroblast Primary Cells, Donor skin02 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.12545
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 6
BROWSER_TRACK_NAME: PFF H3K9me3 02 97
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells Histone H3K9me3 Donor skin02 Library A08397 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 53,308,458
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 13
FINDPEAKS_SCORE: 0.0162
FINDPEAKS_PERCENTILE: 8
HOTSPOT_SCORE: 0.0948
HOTSPOT_PERCENTILE: 31
IROC_SCORE: 0.7756
IROC_PERCENTILE: 38
POISSON_SCORE: 0.3925
POISSON_PERCENTILE: 77
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

value: male

value: Penis

value: Fibroblast

value: No

value: primary cell culture

value: foreskin fibroblast


title: ChIP-Seq analysis of H3K4me3 in human cingulate gyrus cells; DNA_Lib 618

description:
sample_term_id: UBERON_0002967
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 618
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8698
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9452
****************
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: GSM773008_BI.Brain_Cingulate_Gyrus.H3K4me3.149.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 618-DNA_Lib 618-DNA_Lib 618.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of Brain Cingulate Gyrus Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me3 ChIP-Seq on Brain Cingulate Gyrus, Donor 149, 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.12299
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 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 30,268,847
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 11
FINDPEAKS_SCORE: 0.2598
FINDPEAKS_PERCENTILE: 55
HOTSPOT_SCORE: 0.286
HOTSPOT_PERCENTILE: 55
IROC_SCORE: 0.9999
IROC_PERCENTILE: 91
POISSON_SCORE: 0.3233
POISSON_PERCENTILE: 55
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

ANALYSIS FILE NAME: GSM773008_BI.Brain_Cingulate_Gyrus.H3K4me3.149.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 618-DNA_Lib 618-DNA_Lib 618.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of Brain Cingulate Gyrus Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me3 ChIP-Seq read mappings from Brain Cingulate Gyrus, Donor 149, 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.12346
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 6
BROWSER_TRACK_NAME: BCG H3K4me3 49 18
BROWSER_TRACK_DESCRIPTION: BI Brain Cingulate Gyrus Histone H3K4me3 Donor 149 Library DNA_Lib 618 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 30,268,847
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 11
FINDPEAKS_SCORE: 0.2598
FINDPEAKS_PERCENTILE: 55
HOTSPOT_SCORE: 0.286
HOTSPOT_PERCENTILE: 55
IROC_SCORE: 0.9999
IROC_PERCENTILE: 91
POISSON_SCORE: 0.3233
POISSON_PERCENTILE: 55
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

source_name: specified brain region obtained by post-mortem collection in a longitudinal study; DNA_Lib 618

value: Brain, Cingulate Gyrus

value: Cingulate Gyrus

value: Male

value: Primary Tissue

value: Rush University Medical Center

value: 81.0 Years

value: Protein A-Sepharose 4B

value: 0.5 to 3 million cells

value: cell/nuclei lysis

value: ~1 ug

value: 10 ul bed volume


title: ChIP-Seq analysis of H3K36me3 in human cingulate gyrus cells; DNA_Lib 615

description:
sample_term_id: UBERON_0002967
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 615
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8699
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9452
****************
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: GSM773009_BI.Brain_Cingulate_Gyrus.H3K36me3.149.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 615-DNA_Lib 615-DNA_Lib 615.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of Brain Cingulate Gyrus Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K36me3 ChIP-Seq on Brain Cingulate Gyrus, Donor 149, 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.12315
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 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 33,123,753
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 13
FINDPEAKS_SCORE: 0.0532
FINDPEAKS_PERCENTILE: 38
HOTSPOT_SCORE: 0.1594
HOTSPOT_PERCENTILE: 31
IROC_SCORE: 0.8986
IROC_PERCENTILE: 54
POISSON_SCORE: 0.3107
POISSON_PERCENTILE: 46
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

ANALYSIS FILE NAME: GSM773009_BI.Brain_Cingulate_Gyrus.H3K36me3.149.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 615-DNA_Lib 615-DNA_Lib 615.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of Brain Cingulate Gyrus Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K36me3 ChIP-Seq read mappings from Brain Cingulate Gyrus, Donor 149, 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.12362
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 6
BROWSER_TRACK_NAME: BCG H3K36me3 49 15
BROWSER_TRACK_DESCRIPTION: BI Brain Cingulate Gyrus Histone H3K36me3 Donor 149 Library DNA_Lib 615 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 33,123,753
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 13
FINDPEAKS_SCORE: 0.0532
FINDPEAKS_PERCENTILE: 38
HOTSPOT_SCORE: 0.1594
HOTSPOT_PERCENTILE: 31
IROC_SCORE: 0.8986
IROC_PERCENTILE: 54
POISSON_SCORE: 0.3107
POISSON_PERCENTILE: 46
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

source_name: specified brain region obtained by post-mortem collection in a longitudinal study; DNA_Lib 615

value: Post-Mortem

value: no AD evident at demise

value: genomic DNA

value: Brain

value: Abcam

value: Histone H3K36me3

value: Branson


title: ChIP-Seq analysis of H3K27ac in human cingulate gyrus cells; DNA_Lib 617

description:
sample_term_id: UBERON_0002967
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 617
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8701
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9452
****************
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: GSM773011_BI.Brain_Cingulate_Gyrus.H3K27ac.149.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 617-DNA_Lib 617-DNA_Lib 617.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of Brain Cingulate Gyrus Histone H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27ac ChIP-Seq on Brain Cingulate Gyrus, Donor 149, 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.12289
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 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 34,537,642
NUMBER_OF_H3K27ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 5
FINDPEAKS_SCORE: 0.2019
FINDPEAKS_PERCENTILE: 60
HOTSPOT_SCORE: 0.2524
HOTSPOT_PERCENTILE: 60
IROC_SCORE: 0.9815
IROC_PERCENTILE: 40
POISSON_SCORE: 0.4
POISSON_PERCENTILE: 60
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM773011_BI.Brain_Cingulate_Gyrus.H3K27ac.149.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 617-DNA_Lib 617-DNA_Lib 617.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of Brain Cingulate Gyrus Histone H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27ac ChIP-Seq read mappings from Brain Cingulate Gyrus, Donor 149, 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.12336
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 6
BROWSER_TRACK_NAME: BCG H3K27ac 49 17
BROWSER_TRACK_DESCRIPTION: BI Brain Cingulate Gyrus Histone H3K27ac Donor 149 Library DNA_Lib 617 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 34,537,642
NUMBER_OF_H3K27ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 5
FINDPEAKS_SCORE: 0.2019
FINDPEAKS_PERCENTILE: 60
HOTSPOT_SCORE: 0.2524
HOTSPOT_PERCENTILE: 60
IROC_SCORE: 0.9815
IROC_PERCENTILE: 40
POISSON_SCORE: 0.4
POISSON_PERCENTILE: 60
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: specified brain region obtained by post-mortem collection in a longitudinal study; DNA_Lib 617

value: Brain, Cingulate Gyrus

value: Cingulate Gyrus

value: Histone H3K27ac


title: ChIP-Seq analysis of H3K4me1 in human cingulate gyrus cells; DNA_Lib 619

description:
sample_term_id: UBERON_0002967
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 619
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8697
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9452
****************
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: GSM773007_BI.Brain_Cingulate_Gyrus.H3K4me1.149.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 619-DNA_Lib 619-DNA_Lib 619.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of Brain Cingulate Gyrus Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me1 ChIP-Seq on Brain Cingulate Gyrus, Donor 149, 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.12300
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 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 36,720,929
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 14
FINDPEAKS_SCORE: 0.1868
FINDPEAKS_PERCENTILE: 50
HOTSPOT_SCORE: 0.2695
HOTSPOT_PERCENTILE: 50
IROC_SCORE: 0.9606
IROC_PERCENTILE: 50
POISSON_SCORE: 0.4417
POISSON_PERCENTILE: 50
MAXIMUM_REPLICATE_CORRELATION: 0.93

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

ANALYSIS FILE NAME: GSM773007_BI.Brain_Cingulate_Gyrus.H3K4me1.149.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 619-DNA_Lib 619-DNA_Lib 619.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of Brain Cingulate Gyrus Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me1 ChIP-Seq read mappings from Brain Cingulate Gyrus, Donor 149, 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.12347
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 6
BROWSER_TRACK_NAME: BCG H3K4me1 49 19
BROWSER_TRACK_DESCRIPTION: BI Brain Cingulate Gyrus Histone H3K4me1 Donor 149 Library DNA_Lib 619 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 36,720,929
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 14
FINDPEAKS_SCORE: 0.1868
FINDPEAKS_PERCENTILE: 50
HOTSPOT_SCORE: 0.2695
HOTSPOT_PERCENTILE: 50
IROC_SCORE: 0.9606
IROC_PERCENTILE: 50
POISSON_SCORE: 0.4417
POISSON_PERCENTILE: 50
MAXIMUM_REPLICATE_CORRELATION: 0.93

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

source_name: specified brain region obtained by post-mortem collection in a longitudinal study; DNA_Lib 619

value: Male

value: Primary Tissue

value: Rush University Medical Center

value: Histone H3K4me1


title: ChIP-Seq analysis of WCE in human mid frontal lobe cells; DNA_Lib 614

description:
sample_term_id: UBERON_0006483
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 614
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8700
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9448
****************
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: GSM773010_BI.Brain_Mid_Frontal_Lobe.Input.149.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 614-DNA_Lib 614-DNA_Lib 614.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of Brain Mid Frontal Lobe ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on Brain Mid Frontal Lobe, Donor 149, 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.12306
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 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 33,946,503
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 15
FINDPEAKS_SCORE: 0.0062
FINDPEAKS_PERCENTILE: 67
HOTSPOT_SCORE: 0.0054
HOTSPOT_PERCENTILE: 53
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.0376
POISSON_PERCENTILE: 53
MAXIMUM_REPLICATE_CORRELATION: 0.9

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

ANALYSIS FILE NAME: GSM773010_BI.Brain_Mid_Frontal_Lobe.Input.149.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 614-DNA_Lib 614-DNA_Lib 614.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of Brain Mid Frontal Lobe ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from Brain Mid Frontal Lobe, Donor 149, 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.12353
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 6
BROWSER_TRACK_NAME: BMFL Input 49 14
BROWSER_TRACK_DESCRIPTION: BI Brain Mid Frontal Lobe ChIP-Seq Input Donor 149 Library DNA_Lib 614 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 33,946,503
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 15
FINDPEAKS_SCORE: 0.0062
FINDPEAKS_PERCENTILE: 67
HOTSPOT_SCORE: 0.0054
HOTSPOT_PERCENTILE: 53
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.0376
POISSON_PERCENTILE: 53
MAXIMUM_REPLICATE_CORRELATION: 0.9

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

source_name: specified brain region obtained by post-mortem collection in a longitudinal study; DNA_Lib 614

value: Brain, Mid Frontal Lobe

value: Mid Frontal Lobe

value: 81.0 Years

value: standard

value: cell/nuclei lysis

value: ChIP-Seq Input

value: Input


title: ChIP-Seq analysis of H3K4me1 in human CD25- CD45RA+ naive cells; DNA_Lib 727

description:
sample_term_id: CL_0000492
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 727
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8541
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9443
****************
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: GSM772851_BI.CD4+_CD25-_CD45RA+_Naive_Primary_Cells.H3K4me1.Donor_62.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 727-DNA_Lib 727-DNA_Lib 727-DNA_Lib 727.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of CD4+ CD25- CD45RA+ Naive Primary Cells Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me1 ChIP-Seq on CD4+ CD25- CD45RA+ Naive Primary Cells, Donor Donor 62, 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.12302
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 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 24,268,476
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 14
FINDPEAKS_SCORE: 0.3574
FINDPEAKS_PERCENTILE: 86
HOTSPOT_SCORE: 0.3632
HOTSPOT_PERCENTILE: 71
IROC_SCORE: 0.9963
IROC_PERCENTILE: 93
POISSON_SCORE: 0.4691
POISSON_PERCENTILE: 57
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM772851_BI.CD4+_CD25-_CD45RA+_Naive_Primary_Cells.H3K4me1.Donor_62.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 727-DNA_Lib 727-DNA_Lib 727-DNA_Lib 727.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of CD4+ CD25- CD45RA+ Naive Primary Cells Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me1 ChIP-Seq read mappings from CD4+ CD25- CD45RA+ Naive Primary Cells, Donor Donor 62, 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.12349
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 6
BROWSER_TRACK_NAME: CCCN H3K4me1 62 27
BROWSER_TRACK_DESCRIPTION: BI CD4+ CD25- CD45RA+ Naive Primary Cells Histone H3K4me1 Donor 62 Library DNA_Lib 727 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 24,268,476
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 14
FINDPEAKS_SCORE: 0.3574
FINDPEAKS_PERCENTILE: 86
HOTSPOT_SCORE: 0.3632
HOTSPOT_PERCENTILE: 71
IROC_SCORE: 0.9963
IROC_PERCENTILE: 93
POISSON_SCORE: 0.4691
POISSON_PERCENTILE: 57
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: CD25- CD45RA+ naive is one of  CD4+  T cell subsets  that purified by microbeads, LS column and FACS ; DNA_Lib 727

value: BioSam 133

value: CD4+ CD25- CD45RA+ Naive Primary Cells

value: presumed normal

value: genomic DNA

tag: markers

value: CD4+ T cell

value: CD25- CD45RA+ naive

value: Unknown

value: Primary Cell

value: Donor 62

value: Dana Farber

value: Protein A-Sepharose 4B

value: 0.5 to 3 million cells

value: ~1 ug

value: 10 ul bed volume

value: Abcam


city: Copenhagen

first: Sheroy

last: Minocherhomji

state: Copenhagen N

address: Blegdamsvej 3B, Building 18.1

department: Nordea Centre for Healthy Aging, Faculty Of Health Sciences Department of Cellular and Molecular Medicine

country: Denmark

institute: University of Copenhagen

description: IP against H3K27me3 using a polyclonal H3K27me3 antibody (Cat # 39155 Abcam Plc)

data_processing:
Unique sequenced reads from all high-throughput experiments were re-aligned using Bowtie (Langmead et al., 2009) to an altered hg18 assembly that included sequence for all three chr20 gaps (termed hg18+chr20 gaps genome assembly) newly identified in this study. 709bp starting from the 5' end of gap 2 was not included in the re-alignment assembly (hg18+chr20 gaps) file so as to not change the genome base positions (chromosome offsets) on either side of the gap 2 during alignment. Importantly no significant reads were shown to align to this region in any high-throughput experiment. The required numbers of NNNs were maintained in gaps 1 and 3 as they were estimated to be 20kb and 110kb respectively in the hg18 human-genome assembly. MBD-Seq, MRE-Seq and ChIP-Seq reads were analyzed using Cisgenome software as published elsewhere using an FDR or <0.01 (Ji et al., 2008). ChIP-Seq data was analyzed using IgG as a negative control.
Alignment: Sequence reads were obtained and mapped to an edited human genome assembly having the sequence for human chromsome 20 gap regions (termed hg18+chr20 gaps) using the Illumina Genome Analyzer Pipeline. All reads mapping with two or fewer mismatches with the first 28-32 bases were retained and aligned. ChIP-Seq, MBD-Seq and MRE-Seq analysis was performed using Chromosome 20 gaps were sequenced here using touchdown PCR conditions, overlapping PCR primers and Sanger sequencing. These sequences have been deposited at GenBank with accessions: JN854134, JN854135 and JN854136. Reads were aligned using Bowtie and visuallised using the UCSC genome browser at UCSC.
Genome Build:
H3K27me3_Human_Peripheral_Blood_Lymphocytes.wig: hg18+chr20 gaps

source_name: Human Peripheral Blood Lymphocytes

extract_protocol:
Chromatin IP (ChIP-Seq): ChIP was performed using sonicated chromatin obtained from EBV transformed PBLs of a translocation carrier (Hertz et al., 2004), antibodies for H3K27me3 (Active Motif, Cat. #39155), IgG (Cell Signaling Technology Cat #2729S) and performed as previously published (Pasini et al., 2010) or using the ChIP-IT express kit (Cat # 53008, Active Motif) followed by high-throughput Illumina sequencing according to manufacturers instructions.  The average insert size (fragment length not including adapters) of the libraries was 300bp.
High-throughput Illumina Sequencing of gDNA libraries:  Library preparation of gDNA obtained from MBD-Seq, MRE-Seq and ChIP-Seq experiments were sequenced using single read or paired-end adapters and run on a Genome Analyzer II according to manufacturer’s instructions (Illumina) and as indicated.

value: Peripheral Blood Lymphocytes

tag: protocol

value: ChIP (polyclonal H3K27me3 antibody, Cat # 39155, Abcam Plc)


title: Human_Cerebellum_IgG

description: IP against IgG using a polyclonal IgG antibody (Cat # kch-819-015 Diagenode or 2729S: Cell Signalling Tech

data_processing:
Unique sequenced reads from all high-throughput experiments were re-aligned using Bowtie (Langmead et al., 2009) to an altered hg18 assembly that included sequence for all three chr20 gaps (termed hg18+chr20 gaps genome assembly) newly identified in this study. 709bp starting from the 5' end of gap 2 was not included in the re-alignment assembly (hg18+chr20 gaps) file so as to not change the genome base positions (chromosome offsets) on either side of the gap 2 during alignment. Importantly no significant reads were shown to align to this region in any high-throughput experiment. The required numbers of NNNs were maintained in gaps 1 and 3 as they were estimated to be 20kb and 110kb respectively in the hg18 human-genome assembly. MBD-Seq, MRE-Seq and ChIP-Seq reads were analyzed using Cisgenome software as published elsewhere using an FDR or <0.01 (Ji et al., 2008). ChIP-Seq data was analyzed using IgG as a negative control.
Alignment: Sequence reads were obtained and mapped to an edited human genome assembly having the sequence for human chromsome 20 gap regions (termed hg18+chr20 gaps) using the Illumina Genome Analyzer Pipeline. All reads mapping with two or fewer mismatches with the first 28-32 bases were retained and aligned. ChIP-Seq, MBD-Seq and MRE-Seq analysis was performed using Chromosome 20 gaps were sequenced here using touchdown PCR conditions, overlapping PCR primers and Sanger sequencing. These sequences have been deposited at GenBank with accessions: JN854134, JN854135 and JN854136. Reads were aligned using Bowtie and visuallised using the UCSC genome browser at UCSC.
Genome Build:
Human_Cerebellum_IgG.wig: hg18+chr20 gaps

source_name: Human Cerebellum tissue (Cat # TCB-4098, Capital Biosciences USA)

tag: tissue

value: Cebrellum

value: ChIP (polyclonal IgG antibody, Cat # kch-819-015 Diagenode or 2729S:Cell Signalling Tech)


title: Human_Peripheral_Blood_Lymphocytes_5mC

description: IP against hypermethylated gDNA using his-MBD2b antibody

data_processing:
Unique sequenced reads from all high-throughput experiments were re-aligned using Bowtie (Langmead et al., 2009) to an altered hg18 assembly that included sequence for all three chr20 gaps (termed hg18+chr20 gaps genome assembly) newly identified in this study. 709bp starting from the 5' end of gap 2 was not included in the re-alignment assembly (hg18+chr20 gaps) file so as to not change the genome base positions (chromosome offsets) on either side of the gap 2 during alignment. Importantly no significant reads were shown to align to this region in any high-throughput experiment. The required numbers of NNNs were maintained in gaps 1 and 3 as they were estimated to be 20kb and 110kb respectively in the hg18 human-genome assembly. MBD-Seq, MRE-Seq and ChIP-Seq reads were analyzed using Cisgenome software as published elsewhere using an FDR or <0.01 (Ji et al., 2008). ChIP-Seq data was analyzed using IgG as a negative control.
Alignment: Sequence reads were obtained and mapped to an edited human genome assembly having the sequence for human chromsome 20 gap regions (termed hg18+chr20 gaps) using the Illumina Genome Analyzer Pipeline. All reads mapping with two or fewer mismatches with the first 28-32 bases were retained and aligned. ChIP-Seq, MBD-Seq and MRE-Seq analysis was performed using Chromosome 20 gaps were sequenced here using touchdown PCR conditions, overlapping PCR primers and Sanger sequencing. These sequences have been deposited at GenBank with accessions: JN854134, JN854135 and JN854136. Reads were aligned using Bowtie and visuallised using the UCSC genome browser at UCSC.
Genome Build:
Human_Peripheral_Blood_Lymphocytes_5mC.wig: hg18+chr20 gaps

extract_protocol:
Immunoprecipitation (IP) of hypermethylated gDNA using his–MBD2b (MBD-Seq):  2–4µg of gDNA obtained from whole blood of either a translocation carrier (Hertz et al., 2004), phenotypically normal controls or purchased normal human cerebellum (41 year old male donor, Cat # TCB-4098, Capital Biosciences) and sonicated/nebulized, followed by purification using QIAquick columns and purification kits (Qiagen). Immunoprecipitation (IP) of hypermethylated CpG dinucleotides was performed using a his-tagged MBD2b (termed MBD) antibody (0.1µg/µl) and the MethylCollector kit (Cat # 5502, Active Motif) according to manufacturer’s instructions followed by high-throughput Illumina sequencing. The average insert size (fragment length not including adapters) of the libraries was 300bp.
High-throughput Illumina Sequencing of gDNA libraries:  Library preparation of gDNA obtained from MBD-Seq, MRE-Seq and ChIP-Seq experiments were sequenced using single read or paired-end adapters and run on a Genome Analyzer II according to manufacturer’s instructions (Illumina) and as indicated.

value: MBD (his-MBD2b antibody)


title: Mate-Pair reads_chr20_gaps

description: 2–5 kb mate pair genomic DNA libraries for cluster generation and analysis using the Illumina Mate Pair sequencing protocol

data_processing:
Unique sequenced reads from all high-throughput experiments were re-aligned using Bowtie (Langmead et al., 2009) to an altered hg18 assembly that included sequence for all three chr20 gaps (termed hg18+chr20 gaps genome assembly) newly identified in this study. 709bp starting from the 5' end of gap 2 was not included in the re-alignment assembly (hg18+chr20 gaps) file so as to not change the genome base positions (chromosome offsets) on either side of the gap 2 during alignment. Importantly no significant reads were shown to align to this region in any high-throughput experiment. The required numbers of NNNs were maintained in gaps 1 and 3 as they were estimated to be 20kb and 110kb respectively in the hg18 human-genome assembly. MBD-Seq, MRE-Seq and ChIP-Seq reads were analyzed using Cisgenome software as published elsewhere using an FDR or <0.01 (Ji et al., 2008). ChIP-Seq data was analyzed using IgG as a negative control.
Alignment: Sequence reads were obtained and mapped to an edited human genome assembly having the sequence for human chromsome 20 gap regions (termed hg18+chr20 gaps) using the Illumina Genome Analyzer Pipeline. All reads mapping with two or fewer mismatches with the first 28-32 bases were retained and aligned. ChIP-Seq, MBD-Seq and MRE-Seq analysis was performed using Chromosome 20 gaps were sequenced here using touchdown PCR conditions, overlapping PCR primers and Sanger sequencing. These sequences have been deposited at GenBank with accessions: JN854134, JN854135 and JN854136. Reads were aligned using Bowtie and visuallised using the UCSC genome browser at UCSC.
Genome Build:
Mate-Pair reads_chr20_gaps.bed: hg18+chr20 gaps

extract_protocol:
Mate-Pair paired-end Illumina sequencing of gDNA:  Mate-pair paired-end sequence libraries were prepared using the Mate Pair Library (v2) kit (Illumina, USA). Genomic DNA was isolated from peripheral blood lymphocytes (PBLs) of three translocation carriers having rearrangements involving chromosomes other than human chromosome 20 as previously published in Halgren Clinical Genetics 2011. Briefly, 10 µg genomic DNA was sheared using a Nebulizer (Illumina). Fragments measuring 2kb to 3kb in length were isolated using gel electrophoresis followed by end-repair using a mix of natural and biotinylated dNTPs, blunt-end ligation using circularization ligase and further fragmentation to a size of 200bp to 400bp. Biotinylated fragments were isolated and end-repaired. A-overhangs were added to the 3′ ends. Paired-end adapters were ligated to the fragments and the library was amplified by 18 cycles of PCR. Mate-pair libraries were subjected to 2 × 36 bases paired-end sequencing on a Genome Analyzer II (Illumina), using a manufacturer recommended protocol (Illumina). The average insert size (fragment length not including adapters) of the libraries was 300bp.
High-throughput Illumina Sequencing of gDNA libraries:  Library preparation of gDNA obtained from MBD-Seq, MRE-Seq and ChIP-Seq experiments were sequenced using single read or paired-end adapters and run on a Genome Analyzer II according to manufacturer’s instructions (Illumina) and as indicated.

value: Mate-pair paired-end genomic DNA libraries


title: Human_Cerebellum_5mC

data_processing:
Unique sequenced reads from all high-throughput experiments were re-aligned using Bowtie (Langmead et al., 2009) to an altered hg18 assembly that included sequence for all three chr20 gaps (termed hg18+chr20 gaps genome assembly) newly identified in this study. 709bp starting from the 5' end of gap 2 was not included in the re-alignment assembly (hg18+chr20 gaps) file so as to not change the genome base positions (chromosome offsets) on either side of the gap 2 during alignment. Importantly no significant reads were shown to align to this region in any high-throughput experiment. The required numbers of NNNs were maintained in gaps 1 and 3 as they were estimated to be 20kb and 110kb respectively in the hg18 human-genome assembly. MBD-Seq, MRE-Seq and ChIP-Seq reads were analyzed using Cisgenome software as published elsewhere using an FDR or <0.01 (Ji et al., 2008). ChIP-Seq data was analyzed using IgG as a negative control.
Alignment: Sequence reads were obtained and mapped to an edited human genome assembly having the sequence for human chromsome 20 gap regions (termed hg18+chr20 gaps) using the Illumina Genome Analyzer Pipeline. All reads mapping with two or fewer mismatches with the first 28-32 bases were retained and aligned. ChIP-Seq, MBD-Seq and MRE-Seq analysis was performed using Chromosome 20 gaps were sequenced here using touchdown PCR conditions, overlapping PCR primers and Sanger sequencing. These sequences have been deposited at GenBank with accessions: JN854134, JN854135 and JN854136. Reads were aligned using Bowtie and visuallised using the UCSC genome browser at UCSC.
Genome Build:
Human_Cerebellum_5mC_part_1.wig: hg18+chr20 gaps
Human_Cerebellum_5mC_part_2.wig: hg18+chr20 gaps


description: Restriction enzyme digestion using the methylation sensitive enzyme HpaII

data_processing:
Unique sequenced reads from all high-throughput experiments were re-aligned using Bowtie (Langmead et al., 2009) to an altered hg18 assembly that included sequence for all three chr20 gaps (termed hg18+chr20 gaps genome assembly) newly identified in this study. 709bp starting from the 5' end of gap 2 was not included in the re-alignment assembly (hg18+chr20 gaps) file so as to not change the genome base positions (chromosome offsets) on either side of the gap 2 during alignment. Importantly no significant reads were shown to align to this region in any high-throughput experiment. The required numbers of NNNs were maintained in gaps 1 and 3 as they were estimated to be 20kb and 110kb respectively in the hg18 human-genome assembly. MBD-Seq, MRE-Seq and ChIP-Seq reads were analyzed using Cisgenome software as published elsewhere using an FDR or <0.01 (Ji et al., 2008). ChIP-Seq data was analyzed using IgG as a negative control.
Alignment: Sequence reads were obtained and mapped to an edited human genome assembly having the sequence for human chromsome 20 gap regions (termed hg18+chr20 gaps) using the Illumina Genome Analyzer Pipeline. All reads mapping with two or fewer mismatches with the first 28-32 bases were retained and aligned. ChIP-Seq, MBD-Seq and MRE-Seq analysis was performed using Chromosome 20 gaps were sequenced here using touchdown PCR conditions, overlapping PCR primers and Sanger sequencing. These sequences have been deposited at GenBank with accessions: JN854134, JN854135 and JN854136. Reads were aligned using Bowtie and visuallised using the UCSC genome browser at UCSC.
Genome Build:
Human_Peripheral_Blood_Lymphocytes_MRE-Seq.wig: hg18+chr20 gaps

extract_protocol:
Methylation Sensitive Restriction Enzyme Digestion of gDNA (MRE-Seq):  Restriction enzyme (RE) digests were performed using the methylation sensitive HpaII enzyme according to manufacturer’s instructions (New England Biolabs). Digested gDNA was size selected using 2% agarose gel TBE electrophoresis. A region corresponding to 150-300bp on the gel was excised and purified using a gel purification kit (Qiagen) followed by high-throughput Illumina sequencing. The average insert size (fragment length not including adapters) of the libraries was 300bp.
High-throughput Illumina Sequencing of gDNA libraries:  Library preparation of gDNA obtained from MBD-Seq, MRE-Seq and ChIP-Seq experiments were sequenced using single read or paired-end adapters and run on a Genome Analyzer II according to manufacturer’s instructions (Illumina) and as indicated.

value: RE ENZYME HpaII


title: Crypt4_H3K4me3_ChIPSeq

status: Public on Apr 16 2012

city: Cleveland Heights

first: Peter

last: Scacheri

state: OH

address: 10900 Euclid Ave; BRB 647

institute: Case Western Reserve University

description:
Crypt4
processed data file: all_mFOLD7_MACS_peaks_H3K4me3.txt
genome build: hg18

data_processing: MACS peak calls: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/)[.txt processed files are available as Series Supplementary files]; paired end data files were treated as single end experiments.

source_name: Normal Colon Crypt_H3K4me3_ChIPSeq

growth_protocol: Primary colon cancer cell lines were grown in 15 cm dishes to 70% confluency prior to harvest for ChIP-seq and RNA extraction. Normal colon crypts were isolated from surgical specimens of colon excised past the normal margin of tumors. Specimens were verified by microscopy to be free of any cancer cells.  Samples were washed in cold PBS, placed in cold DMEM+10%FBS, and then transported from the operating room to the laboratory within 8 hours of surgery.  Extraction of colonic crypts was performed by EDTA fractionation.

extract_protocol: Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.  Libraries were prepared with NEB reagents as previously described. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 17 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

value: Normal Colon Crypt

tag: chip antibody

tag: chip antibody vendor

value: Active Motif

tag: chip antibody cat. #

tag: chip antibody lot #


title: Crypt3_H3K4me3_ChIPSeq

description:
Crypt3
processed data file: all_mFOLD7_MACS_peaks_H3K4me3.txt
genome build: hg18


title: ChIP-Seq analysis of H3K27me3 in human cingulate gyrus cells; DNA_Lib 620

description:
sample_term_id: UBERON_0002967
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 620
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8679
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9452
****************
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: GSM772989_BI.Brain_Cingulate_Gyrus.H3K27me3.149.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 620-DNA_Lib 620-DNA_Lib 620.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of Brain Cingulate Gyrus Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27me3 ChIP-Seq on Brain Cingulate Gyrus, Donor 149, 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.12310
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 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 30,662,087
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 10
FINDPEAKS_SCORE: 0.0212
FINDPEAKS_PERCENTILE: 30
HOTSPOT_SCORE: 0.0853
HOTSPOT_PERCENTILE: 30
IROC_SCORE: 0.8335
IROC_PERCENTILE: 40
POISSON_SCORE: 0.2415
POISSON_PERCENTILE: 40
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM772989_BI.Brain_Cingulate_Gyrus.H3K27me3.149.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 620-DNA_Lib 620-DNA_Lib 620.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of Brain Cingulate Gyrus Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27me3 ChIP-Seq read mappings from Brain Cingulate Gyrus, Donor 149, 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.12357
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 6
BROWSER_TRACK_NAME: BCG H3K27me3 49 20
BROWSER_TRACK_DESCRIPTION: BI Brain Cingulate Gyrus Histone H3K27me3 Donor 149 Library DNA_Lib 620 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 30,662,087
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 10
FINDPEAKS_SCORE: 0.0212
FINDPEAKS_PERCENTILE: 30
HOTSPOT_SCORE: 0.0853
HOTSPOT_PERCENTILE: 30
IROC_SCORE: 0.8335
IROC_PERCENTILE: 40
POISSON_SCORE: 0.2415
POISSON_PERCENTILE: 40
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: specified brain region obtained by post-mortem collection in a longitudinal study; DNA_Lib 620

value: Brain, Cingulate Gyrus

value: Post-Mortem

value: no AD evident at demise

value: genomic DNA

value: Cingulate Gyrus

value: Male

value: Primary Tissue

value: Brain

value: Rush University Medical Center

value: 81.0 Years

value: cell/nuclei lysis

value: Millipore

value: Histone H3K27me3

value: Branson


title: Crypt1_H3K4me3_ChIPSeq

description:
Crypt1
processed data file: all_mFOLD7_MACS_peaks_H3K4me3.txt
genome build: hg18


title: V400_H3K4me3_ChIPSeq

description:
V400
processed data file: all_mFOLD7_MACS_peaks_H3K4me3.txt
genome build: hg18

source_name: Colon cancer_H3K4me3_ChIPSeq

value: Colon Cancer