description:
design description: H3K4me1 ChIP-Seq analysis of UCSF-4 embryonic stem cell line (A19296) using Illumina HiSeq 2000
library name: A19296
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: 81-365 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: GSM1127080_UCSF-UBC.UCSF-4Star.H3K4me1.A19296.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A19296-1.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of UCSF-4* Cell Line H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K4me1 ChIP-Seq on the UCSF-4* Cell Line, Library A19296 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.17034
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 51,385,031
FINDPEAKS_SCORE: 0.1149
FINDPEAKS_PERCENTILE: 23
HOTSPOT_SCORE: 0.2389
HOTSPOT_PERCENTILE: 25
IROC_SCORE: 0.8904
IROC_PERCENTILE: 16
POISSON_SCORE: 0.439
POISSON_PERCENTILE: 43
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

ANALYSIS FILE NAME: GSM1127080_UCSF-UBC.UCSF-4Star.H3K4me1.A19296.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A19296-1.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of UCSF-4Star Cell Line H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K4me1 ChIP-Seq read mappings from the UCSF-4Star Cell Line, Library A19296 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.17093
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: UCSF4* H3K4me1 96
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC UCSF-4* Cell Line Histone H3K4me1 Library A19296 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 51,385,031
FINDPEAKS_SCORE: 0.1149
FINDPEAKS_PERCENTILE: 23
HOTSPOT_SCORE: 0.2389
HOTSPOT_PERCENTILE: 25
IROC_SCORE: 0.8904
IROC_PERCENTILE: 16
POISSON_SCORE: 0.439
POISSON_PERCENTILE: 43
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

value: female


status: Public on Jun 22 2013

type: SRA

city: San Francisco

first: UCSF-UBC

last: CENTER

state: CA

address: UCSF-UBC

country: USA

institute: UCSF-UBC

description:
design description: H3K9me3 ChIP-Seq analysis of pancreas islet from ZGI 213 (A22470) using Illumina HiSeq 2000
library name: A22470
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: Bioruptor
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 30 min
CHIP_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
CHIP_PROTOCOL_CHROMATIN_AMOUNT: 10 ug
SIZE_FRACTION: 124-199 bp
CHIP_PROTOCOL_BEAD_TYPE: Pierce Magnetic Protein A/G
CHIP_PROTOCOL_BEAD_AMOUNT: 15 ul
CHIP_PROTOCOL_ANTIBODY_AMOUNT: 8 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
****************

library_source: genomic

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

ANALYSIS FILE NAME: GSM1127086_UCSF-UBC.Pancreatic_Islets.H3K9me3.ZGI_213.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A22470-1.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Pancreatic Islets H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K9me3 ChIP-Seq on Pancreatic Islets, Donor ZGI 213 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.17027
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 23,532,309
FINDPEAKS_SCORE: 0.0164
FINDPEAKS_PERCENTILE: 10
HOTSPOT_SCORE: 0.1112
HOTSPOT_PERCENTILE: 38
IROC_SCORE: 0.6892
IROC_PERCENTILE: 28
POISSON_SCORE: 0.3276
POISSON_PERCENTILE: 58
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

ANALYSIS FILE NAME: GSM1127086_UCSF-UBC.Pancreatic_Islets.H3K9me3.ZGI_213.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A22470-1.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Pancreatic Islets H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K9me3 ChIP-Seq read mappings from Pancreatic Islets, Donor ZGI 213 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.17086
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: PI H3K9me3 13 70
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Pancreatic Islets Histone H3K9me3 Donor ZGI 213 Library A22470 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 23,532,309
FINDPEAKS_SCORE: 0.0164
FINDPEAKS_PERCENTILE: 10
HOTSPOT_SCORE: 0.1112
HOTSPOT_PERCENTILE: 38
IROC_SCORE: 0.6892
IROC_PERCENTILE: 28
POISSON_SCORE: 0.3276
POISSON_PERCENTILE: 58
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

tag: body site

value: Pancreas

tag: histological type

value: Islet

tag: is tumor

value: No

value: primary cell

value: pancreas islet


description:
design description: H3K27me3 ChIP-Seq analysis of UCSF-4 embryonic stem cell line (A19299) using Illumina HiSeq 2000
library name: A19299
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: 10 ug
SIZE_FRACTION: 77-340 bp
CHIP_PROTOCOL_BEAD_TYPE: Sepharose A/G Bead Mix
CHIP_PROTOCOL_BEAD_AMOUNT: 20 ul
CHIP_PROTOCOL_ANTIBODY_AMOUNT: 5 ug
CHIP_ANTIBODY: H3K27me3
CHIP_ANTIBODY_PROVIDER: Diagenode
CHIP_ANTIBODY_CATALOG: pAb-069-050
CHIP_ANTIBODY_LOT: A299-00242
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM1127084_UCSF-UBC.UCSF-4Star.H3K27me3.A19299.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A19299-1.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of UCSF-4* Cell Line H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27me3 ChIP-Seq on the UCSF-4* Cell Line, Library A19299 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.17023
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 32,333,206
FINDPEAKS_SCORE: 0.0762
FINDPEAKS_PERCENTILE: 52
HOTSPOT_SCORE: 0.1388
HOTSPOT_PERCENTILE: 39
IROC_SCORE: 0.9884
IROC_PERCENTILE: 94
POISSON_SCORE: 0.2662
POISSON_PERCENTILE: 36
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

ANALYSIS FILE NAME: GSM1127084_UCSF-UBC.UCSF-4Star.H3K27me3.A19299.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A19299-1.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of UCSF-4Star Cell Line H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27me3 ChIP-Seq read mappings from the UCSF-4Star Cell Line, Library A19299 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.17082
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: UCSF4* H3K27me3 99
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC UCSF-4* Cell Line Histone H3K27me3 Library A19299 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 32,333,206
FINDPEAKS_SCORE: 0.0762
FINDPEAKS_PERCENTILE: 52
HOTSPOT_SCORE: 0.1388
HOTSPOT_PERCENTILE: 39
IROC_SCORE: 0.9884
IROC_PERCENTILE: 94
POISSON_SCORE: 0.2662
POISSON_PERCENTILE: 36
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

value: cell line

tag: line

value: Embryo ICM

value: Embryonic stem cell


description:
design description: H3K4me3 ChIP-Seq analysis of pancreas islet from ZGI 213 (A22469) using Illumina HiSeq 2000
library name: A22469
EXPERIMENT_TYPE: Histone H3K4me3
EXTRACTION_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Bioruptor
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 30 min
CHIP_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
CHIP_PROTOCOL_CHROMATIN_AMOUNT: 5 ug
SIZE_FRACTION: 124-199 bp
CHIP_PROTOCOL_BEAD_TYPE: Pierce Magnetic Protein A/G
CHIP_PROTOCOL_BEAD_AMOUNT: 15 ul
CHIP_PROTOCOL_ANTIBODY_AMOUNT: 10 ul
CHIP_ANTIBODY: H3K4me3
CHIP_ANTIBODY_PROVIDER: Cell Signaling Technology
CHIP_ANTIBODY_CATALOG: 9751S
CHIP_ANTIBODY_LOT: 4
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM1127082_UCSF-UBC.Pancreatic_Islets.H3K4me3.ZGI_213.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A22469-1.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Pancreatic Islets H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K4me3 ChIP-Seq on Pancreatic Islets, Donor ZGI 213 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.17067
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 22,164,192
FINDPEAKS_SCORE: 0.4545
FINDPEAKS_PERCENTILE: 68
HOTSPOT_SCORE: 0.4606
HOTSPOT_PERCENTILE: 66
IROC_SCORE: 0.9999
IROC_PERCENTILE: 47
POISSON_SCORE: 0.4683
POISSON_PERCENTILE: 68
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

ANALYSIS FILE NAME: GSM1127082_UCSF-UBC.Pancreatic_Islets.H3K4me3.ZGI_213.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A22469-1.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Pancreatic Islets H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K4me3 ChIP-Seq read mappings from Pancreatic Islets, Donor ZGI 213 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.17126
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: PI H3K4me3 13 69
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Pancreatic Islets Histone H3K4me3 Donor ZGI 213 Library A22469 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 22,164,192
FINDPEAKS_SCORE: 0.4545
FINDPEAKS_PERCENTILE: 68
HOTSPOT_SCORE: 0.4606
HOTSPOT_PERCENTILE: 66
IROC_SCORE: 0.9999
IROC_PERCENTILE: 47
POISSON_SCORE: 0.4683
POISSON_PERCENTILE: 68
MAXIMUM_REPLICATE_CORRELATION: 0.96

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


description:
design description: H3K9me3 ChIP-Seq analysis of ganglionic eminence neural stem and progenitor cells from HuFNSC04 (A19305) using Illumina HiSeq 2000
library name: A19305
EXPERIMENT_TYPE: Histone H3K9me3
EXTRACTION_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Fisher 550 Sonic Dismembrator
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 10 min
CHIP_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
CHIP_PROTOCOL_CHROMATIN_AMOUNT: 5 ug
SIZE_FRACTION: 62-413 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: GSM1127079_UCSF-UBC.Neurosphere_Cultured_Cells_Ganglionic_Eminence_Derived.H3K9me3.HuFNSC04.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A19305-1.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Neurosphere Cultured Cells Ganglionic Eminence Derived H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K9me3 ChIP-Seq on Neurosphere Cultured Cells Ganglionic Eminence Derived, Donor HuFNSC04 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.17025
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 23,330,048
FINDPEAKS_SCORE: 0.0656
FINDPEAKS_PERCENTILE: 60
HOTSPOT_SCORE: 0.1453
HOTSPOT_PERCENTILE: 54
IROC_SCORE: 0.8613
IROC_PERCENTILE: 68
POISSON_SCORE: 0.2795
POISSON_PERCENTILE: 42
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM1127079_UCSF-UBC.Neurosphere_Cultured_Cells_Ganglionic_Eminence_Derived.H3K9me3.HuFNSC04.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A19305-1.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Neurosphere Cultured Cells Ganglionic Eminence Derived H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K9me3 ChIP-Seq read mappings from Neurosphere Cultured Cells Ganglionic Eminence Derived, Donor HuFNSC04 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.17084
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: NGED H3K9me3 04 05
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Neurosphere Cultured Cells Ganglionic Eminence Derived Histone H3K9me3 Donor HuFNSC04 Library A19305 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 23,330,048
FINDPEAKS_SCORE: 0.0656
FINDPEAKS_PERCENTILE: 60
HOTSPOT_SCORE: 0.1453
HOTSPOT_PERCENTILE: 54
IROC_SCORE: 0.8613
IROC_PERCENTILE: 68
POISSON_SCORE: 0.2795
POISSON_PERCENTILE: 42
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

value: Brain

value: Ganglionic eminence neurosphere culture

value: primary cell culture

tag: cell type


description:
design description: H3K27ac ChIP-Seq analysis of foreskin fibroblast from skin01 (A18460) using Illumina HiSeq 2000
library name: A18460
EXPERIMENT_TYPE: Histone H3K27ac
EXTRACTION_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Fisher 550 Sonic Dismembrator
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 10 min
CHIP_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
CHIP_PROTOCOL_CHROMATIN_AMOUNT: 5 ug
SIZE_FRACTION: 28-299 bp
CHIP_PROTOCOL_BEAD_TYPE: Sepharose A/G Bead Mix
CHIP_PROTOCOL_BEAD_AMOUNT: 20 ul
CHIP_PROTOCOL_ANTIBODY_AMOUNT: 2.5 ug
CHIP_ANTIBODY: H3K27ac
CHIP_ANTIBODY_PROVIDER: Abcam
CHIP_ANTIBODY_CATALOG: ab4729
CHIP_ANTIBODY_LOT: GR28147-1
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM1127076_UCSF-UBC.Penis_Foreskin_Fibroblast_Primary_Cells.H3K27ac.skin01.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A18460-1.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Penis Foreskin Fibroblast Primary Cells H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27ac ChIP-Seq 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.17054
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 29,702,339
FINDPEAKS_SCORE: 0.2365
FINDPEAKS_PERCENTILE: 28
HOTSPOT_SCORE: 0.3021
HOTSPOT_PERCENTILE: 27
IROC_SCORE: 0.9959
IROC_PERCENTILE: 58
POISSON_SCORE: 0.3934
POISSON_PERCENTILE: 31
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

ANALYSIS FILE NAME: GSM1127076_UCSF-UBC.Penis_Foreskin_Fibroblast_Primary_Cells.H3K27ac.skin01.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A18460-1.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Penis Foreskin Fibroblast Primary Cells H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27ac ChIP-Seq 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.17113
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: PFF H3K27ac 01 60
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells Histone H3K27ac Donor skin01 Library A18460 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 29,702,339
FINDPEAKS_SCORE: 0.2365
FINDPEAKS_PERCENTILE: 28
HOTSPOT_SCORE: 0.3021
HOTSPOT_PERCENTILE: 27
IROC_SCORE: 0.9959
IROC_PERCENTILE: 58
POISSON_SCORE: 0.3934
POISSON_PERCENTILE: 31
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

value: male

value: Penis

value: Fibroblast

value: foreskin fibroblast


description:
design description: H3K36me3 ChIP-Seq analysis of ganglionic eminence neural stem and progenitor cells from HuFNSC04 (A19307) using Illumina HiSeq 2000
library name: A19307
EXPERIMENT_TYPE: Histone H3K36me3
EXTRACTION_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Fisher 550 Sonic Dismembrator
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 10 min
CHIP_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
CHIP_PROTOCOL_CHROMATIN_AMOUNT: 5 ug
SIZE_FRACTION: 93-324 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: GSM1127075_UCSF-UBC.Neurosphere_Cultured_Cells_Ganglionic_Eminence_Derived.H3K36me3.HuFNSC04.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A19307-1.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Neurosphere Cultured Cells Ganglionic Eminence Derived H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K36me3 ChIP-Seq on Neurosphere Cultured Cells Ganglionic Eminence Derived, Donor HuFNSC04 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.17021
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 49,001,087
FINDPEAKS_SCORE: 0.351
FINDPEAKS_PERCENTILE: 67
HOTSPOT_SCORE: 0.3024
HOTSPOT_PERCENTILE: 52
IROC_SCORE: 0.9774
IROC_PERCENTILE: 52
POISSON_SCORE: 0.5755
POISSON_PERCENTILE: 78
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM1127075_UCSF-UBC.Neurosphere_Cultured_Cells_Ganglionic_Eminence_Derived.H3K36me3.HuFNSC04.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A19307-1.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Neurosphere Cultured Cells Ganglionic Eminence Derived H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K36me3 ChIP-Seq read mappings from Neurosphere Cultured Cells Ganglionic Eminence Derived, Donor HuFNSC04 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.17080
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: NGED H3K36me3 04 07
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Neurosphere Cultured Cells Ganglionic Eminence Derived Histone H3K36me3 Donor HuFNSC04 Library A19307 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 49,001,087
FINDPEAKS_SCORE: 0.351
FINDPEAKS_PERCENTILE: 67
HOTSPOT_SCORE: 0.3024
HOTSPOT_PERCENTILE: 52
IROC_SCORE: 0.9774
IROC_PERCENTILE: 52
POISSON_SCORE: 0.5755
POISSON_PERCENTILE: 78
MAXIMUM_REPLICATE_CORRELATION: 0.98

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


description:
design description: H3K27ac ChIP-Seq analysis of foreskin melanocyte from skin03 (A18468) using Illumina HiSeq 2000
library name: A18468
EXPERIMENT_TYPE: Histone H3K27ac
EXTRACTION_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Fisher 550 Sonic Dismembrator
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 10 min
CHIP_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
CHIP_PROTOCOL_CHROMATIN_AMOUNT: 5 ug
SIZE_FRACTION: 85-332 bp
CHIP_PROTOCOL_BEAD_TYPE: Sepharose A/G Bead Mix
CHIP_PROTOCOL_BEAD_AMOUNT: 20 ul
CHIP_PROTOCOL_ANTIBODY_AMOUNT: 2.5 ug
CHIP_ANTIBODY: H3K27ac
CHIP_ANTIBODY_PROVIDER: Abcam
CHIP_ANTIBODY_CATALOG: ab4729
CHIP_ANTIBODY_LOT: GR28147-1
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM1127073_UCSF-UBC.Penis_Foreskin_Melanocyte_Primary_Cells.H3K27ac.skin03.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A15584-1-A18468-1.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Penis Foreskin Melanocyte Primary Cells H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27ac ChIP-Seq on Penis Foreskin Melanocyte Primary Cells, Donor skin03 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.17075
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 23,732,736
FINDPEAKS_SCORE: 0.1501
FINDPEAKS_PERCENTILE: 14
HOTSPOT_SCORE: 0.2458
HOTSPOT_PERCENTILE: 21
IROC_SCORE: 0.9855
IROC_PERCENTILE: 26
POISSON_SCORE: 0.3192
POISSON_PERCENTILE: 15
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

ANALYSIS FILE NAME: GSM1127073_UCSF-UBC.Penis_Foreskin_Melanocyte_Primary_Cells.H3K27ac.skin03.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A15584-1-A18468-1.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Penis Foreskin Melanocyte Primary Cells H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27ac ChIP-Seq read mappings from Penis Foreskin Melanocyte Primary Cells, Donor skin03 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.17134
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: PFM H3K27ac 03 84
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells Histone H3K27ac Donor skin03 Library A15584 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 23,732,736
FINDPEAKS_SCORE: 0.1501
FINDPEAKS_PERCENTILE: 14
HOTSPOT_SCORE: 0.2458
HOTSPOT_PERCENTILE: 21
IROC_SCORE: 0.9855
IROC_PERCENTILE: 26
POISSON_SCORE: 0.3192
POISSON_PERCENTILE: 15
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

value: Melanocyte

value: foreskin melanocyte


description:
design description: H3K27me3 ChIP-Seq analysis of pancreas islet from ZGI 213 (A22472) using Illumina HiSeq 2000
library name: A22472
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: Bioruptor
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 30 min
CHIP_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
CHIP_PROTOCOL_CHROMATIN_AMOUNT: 9 ug
SIZE_FRACTION: 124-199 bp
CHIP_PROTOCOL_BEAD_TYPE: Pierce Magnetic Protein A/G
CHIP_PROTOCOL_BEAD_AMOUNT: 15 ul
CHIP_PROTOCOL_ANTIBODY_AMOUNT: 10 ul
CHIP_ANTIBODY: H3K27me3
CHIP_ANTIBODY_PROVIDER: Cell Signaling Technology
CHIP_ANTIBODY_CATALOG: 9733S
CHIP_ANTIBODY_LOT: 5
****************
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: GSM1127074_UCSF-UBC.Pancreatic_Islets.H3K27me3.ZGI_213.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A22472-1.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Pancreatic Islets H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27me3 ChIP-Seq on Pancreatic Islets, Donor ZGI 213 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.17041
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 22,450,856
FINDPEAKS_SCORE: 0.012
FINDPEAKS_PERCENTILE: 11
HOTSPOT_SCORE: 0.0998
HOTSPOT_PERCENTILE: 18
IROC_SCORE: 0.6563
IROC_PERCENTILE: 7
POISSON_SCORE: 0.3785
POISSON_PERCENTILE: 63
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

ANALYSIS FILE NAME: GSM1127074_UCSF-UBC.Pancreatic_Islets.H3K27me3.ZGI_213.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A22472-1.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Pancreatic Islets H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27me3 ChIP-Seq read mappings from Pancreatic Islets, Donor ZGI 213 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.17100
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: PI H3K27me3 13 72
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Pancreatic Islets Histone H3K27me3 Donor ZGI 213 Library A22472 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 22,450,856
FINDPEAKS_SCORE: 0.012
FINDPEAKS_PERCENTILE: 11
HOTSPOT_SCORE: 0.0998
HOTSPOT_PERCENTILE: 18
IROC_SCORE: 0.6563
IROC_PERCENTILE: 7
POISSON_SCORE: 0.3785
POISSON_PERCENTILE: 63
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

value: female

value: Pancreas


description:
design description: H3K27ac ChIP-Seq analysis of pancreas islet from ZD4 273 (A19680) using Illumina HiSeq 2000
library name: A19680
EXPERIMENT_TYPE: Histone H3K27ac
EXTRACTION_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Bioruptor
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 30 min
CHIP_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
CHIP_PROTOCOL_CHROMATIN_AMOUNT: 7.5 ug
SIZE_FRACTION: 74-374 bp
CHIP_PROTOCOL_BEAD_TYPE: Pierce Magnetic Protein A/G
CHIP_PROTOCOL_BEAD_AMOUNT: 15 ul
CHIP_PROTOCOL_ANTIBODY_AMOUNT: 6 ug
CHIP_ANTIBODY: H3K27ac
CHIP_ANTIBODY_PROVIDER: Active Motif
CHIP_ANTIBODY_CATALOG: 39133
CHIP_ANTIBODY_LOT: 21311004
****************
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: GSM1127071_UCSF-UBC.Pancreatic_Islets.H3K27ac.ZD4_273.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A19680-1.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Pancreatic Islets H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27ac ChIP-Seq on Pancreatic Islets, Donor ZD4 273 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.17057
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 18,180,811
FINDPEAKS_SCORE: 0.2263
FINDPEAKS_PERCENTILE: 26
HOTSPOT_SCORE: 0.2786
HOTSPOT_PERCENTILE: 26
IROC_SCORE: 0.9781
IROC_PERCENTILE: 18
POISSON_SCORE: 0.3979
POISSON_PERCENTILE: 34
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

ANALYSIS FILE NAME: GSM1127071_UCSF-UBC.Pancreatic_Islets.H3K27ac.ZD4_273.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A19680-1.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Pancreatic Islets H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27ac ChIP-Seq read mappings from Pancreatic Islets, Donor ZD4 273 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.17116
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: PI H3K27ac 73 80
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Pancreatic Islets Histone H3K27ac Donor ZD4 273 Library A19680 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 18,180,811
FINDPEAKS_SCORE: 0.2263
FINDPEAKS_PERCENTILE: 26
HOTSPOT_SCORE: 0.2786
HOTSPOT_PERCENTILE: 26
IROC_SCORE: 0.9781
IROC_PERCENTILE: 18
POISSON_SCORE: 0.3979
POISSON_PERCENTILE: 34
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

value: Islet

value: No


description:
design description: H3K27ac ChIP-Seq analysis of foreskin melanocyte from skin01 (A18462) using Illumina HiSeq 2000
library name: A18462
EXPERIMENT_TYPE: Histone H3K27ac
EXTRACTION_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Fisher 550 Sonic Dismembrator
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 10 min
CHIP_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
CHIP_PROTOCOL_CHROMATIN_AMOUNT: 5 ug
SIZE_FRACTION: 101-367 bp
CHIP_PROTOCOL_BEAD_TYPE: Sepharose A/G Bead Mix
CHIP_PROTOCOL_BEAD_AMOUNT: 20 ul
CHIP_PROTOCOL_ANTIBODY_AMOUNT: 2.5 ug
CHIP_ANTIBODY: H3K27ac
CHIP_ANTIBODY_PROVIDER: Abcam
CHIP_ANTIBODY_CATALOG: ab4729
CHIP_ANTIBODY_LOT: GR28147-1
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM1127072_UCSF-UBC.Penis_Foreskin_Melanocyte_Primary_Cells.H3K27ac.skin01.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A18462-1.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Penis Foreskin Melanocyte Primary Cells H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27ac ChIP-Seq on Penis Foreskin Melanocyte 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.17074
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 41,197,031
FINDPEAKS_SCORE: 0.0676
FINDPEAKS_PERCENTILE: 6
HOTSPOT_SCORE: 0.1303
HOTSPOT_PERCENTILE: 12
IROC_SCORE: 0.9781
IROC_PERCENTILE: 18
POISSON_SCORE: 0.2338
POISSON_PERCENTILE: 7
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1127072_UCSF-UBC.Penis_Foreskin_Melanocyte_Primary_Cells.H3K27ac.skin01.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A18462-1.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Penis Foreskin Melanocyte Primary Cells H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27ac ChIP-Seq read mappings from Penis Foreskin Melanocyte 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.17133
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: PFM H3K27ac 01 62
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells Histone H3K27ac Donor skin01 Library A18462 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 41,197,031
FINDPEAKS_SCORE: 0.0676
FINDPEAKS_PERCENTILE: 6
HOTSPOT_SCORE: 0.1303
HOTSPOT_PERCENTILE: 12
IROC_SCORE: 0.9781
IROC_PERCENTILE: 18
POISSON_SCORE: 0.2338
POISSON_PERCENTILE: 7
MAXIMUM_REPLICATE_CORRELATION: NA

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


description:
design description: ChIP-Seq input analysis of ganglionic eminence neural stem and progenitor cells from HuFNSC04 (A19309) using Illumina HiSeq 2000
library name: A19309
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: 81-121 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: GSM1127091_UCSF-UBC.Neurosphere_Cultured_Cells_Ganglionic_Eminence_Derived.Input.HuFNSC04.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A19309-1.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Neurosphere Cultured Cells Ganglionic Eminence Derived Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Input ChIP-Seq on Neurosphere Cultured Cells Ganglionic Eminence Derived, Donor HuFNSC04 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.17068
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 41,200,072
FINDPEAKS_SCORE: 0.0051
FINDPEAKS_PERCENTILE: 31
HOTSPOT_SCORE: 0.1242
HOTSPOT_PERCENTILE: 88
IROC_SCORE: NA
IROC_PERCENTILE: NA
POISSON_SCORE: 0.3717
POISSON_PERCENTILE: 95
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM1127091_UCSF-UBC.Neurosphere_Cultured_Cells_Ganglionic_Eminence_Derived.Input.HuFNSC04.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A19309-1.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Neurosphere Cultured Cells Ganglionic Eminence Derived Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Input ChIP-Seq read mappings from Neurosphere Cultured Cells Ganglionic Eminence Derived, Donor HuFNSC04 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.17127
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: NGED Input 04 09
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Neurosphere Cultured Cells Ganglionic Eminence Derived ChIP-Seq Input Donor HuFNSC04 Library A19309 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 41,200,072
FINDPEAKS_SCORE: 0.0051
FINDPEAKS_PERCENTILE: 31
HOTSPOT_SCORE: 0.1242
HOTSPOT_PERCENTILE: 88
IROC_SCORE: NA
IROC_PERCENTILE: NA
POISSON_SCORE: 0.3717
POISSON_PERCENTILE: 95
MAXIMUM_REPLICATE_CORRELATION: 0.98

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


description:
design description: ChIP-Seq input analysis of UCSF-4 embryonic stem cell line (A19302) using Illumina HiSeq 2000
library name: A19302
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: 91-396 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: GSM1127090_UCSF-UBC.UCSF-4Star.Input.A19302.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A19302-1.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of UCSF-4* Cell Line Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Input ChIP-Seq on the UCSF-4* Cell Line, Library A19302 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.17072
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 48,433,958
FINDPEAKS_SCORE: 0.003
FINDPEAKS_PERCENTILE: 12
HOTSPOT_SCORE: 0.0089
HOTSPOT_PERCENTILE: 45
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.043
POISSON_PERCENTILE: 42
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1127090_UCSF-UBC.UCSF-4Star.Input.A19302.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A19302-1.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of UCSF-4Star Cell Line Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Input ChIP-Seq read mappings from the UCSF-4Star Cell Line, Library A19302 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.17131
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: UCSF4* Input 02
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC UCSF-4* Cell Line ChIP-Seq Input Library A19302 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 48,433,958
FINDPEAKS_SCORE: 0.003
FINDPEAKS_PERCENTILE: 12
HOTSPOT_SCORE: 0.0089
HOTSPOT_PERCENTILE: 45
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.043
POISSON_PERCENTILE: 42
MAXIMUM_REPLICATE_CORRELATION: NA

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


description:
design description: H3K36me3 ChIP-Seq analysis of breast fibroblast from RM071 (A21644) using Illumina HiSeq 2000
library name: A21644
EXPERIMENT_TYPE: Histone H3K36me3
EXTRACTION_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Fisher 550 Sonic Dismembrator
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 10 min
CHIP_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
CHIP_PROTOCOL_CHROMATIN_AMOUNT: 5 ug
SIZE_FRACTION: 94-294 bp
CHIP_PROTOCOL_BEAD_TYPE: Sepharose A/G Bead Mix
CHIP_PROTOCOL_BEAD_AMOUNT: 20 ul
CHIP_PROTOCOL_ANTIBODY_AMOUNT: 2.5 ug
CHIP_ANTIBODY: H3K36me3
CHIP_ANTIBODY_PROVIDER: Abcam
CHIP_ANTIBODY_CATALOG: ab9050
CHIP_ANTIBODY_LOT: 947467
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM1127068_UCSF-UBC.Breast_Fibroblast_Primary_Cells.H3K36me3.RM071.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A21644-1.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Breast Fibroblast Primary Cells H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K36me3 ChIP-Seq on Breast Fibroblast Primary Cells, Donor RM071 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.17020
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 24,245,121
FINDPEAKS_SCORE: 0.3004
FINDPEAKS_PERCENTILE: 60
HOTSPOT_SCORE: 0.2671
HOTSPOT_PERCENTILE: 40
IROC_SCORE: 0.9807
IROC_PERCENTILE: 59
POISSON_SCORE: 0.5113
POISSON_PERCENTILE: 59
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1127068_UCSF-UBC.Breast_Fibroblast_Primary_Cells.H3K36me3.RM071.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A21644-1.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Breast Fibroblast Primary Cells H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K36me3 ChIP-Seq read mappings from Breast Fibroblast Primary Cells, Donor RM071 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.17079
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: BF H3K36me3 71 44
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Breast Fibroblast Primary Cells Histone H3K36me3 Donor RM071 Library A21644 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 24,245,121
FINDPEAKS_SCORE: 0.3004
FINDPEAKS_PERCENTILE: 60
HOTSPOT_SCORE: 0.2671
HOTSPOT_PERCENTILE: 40
IROC_SCORE: 0.9807
IROC_PERCENTILE: 59
POISSON_SCORE: 0.5113
POISSON_PERCENTILE: 59
MAXIMUM_REPLICATE_CORRELATION: NA

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

value: Breast

value: Fibroblast cultured cell

value: breast fibroblast


description:
design description: H3K27ac ChIP-Seq analysis of foreskin keratinocyte from skin03 (A18467) using Illumina HiSeq 2000
library name: A18467
EXPERIMENT_TYPE: Histone H3K27ac
EXTRACTION_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Fisher 550 Sonic Dismembrator
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 10 min
CHIP_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
CHIP_PROTOCOL_CHROMATIN_AMOUNT: 5 ug
SIZE_FRACTION: 75-356 bp
CHIP_PROTOCOL_BEAD_TYPE: Sepharose A/G Bead Mix
CHIP_PROTOCOL_BEAD_AMOUNT: 20 ul
CHIP_PROTOCOL_ANTIBODY_AMOUNT: 2.5 ug
CHIP_ANTIBODY: H3K27ac
CHIP_ANTIBODY_PROVIDER: Abcam
CHIP_ANTIBODY_CATALOG: ab4729
CHIP_ANTIBODY_LOT: GR28147-1
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM1127077_UCSF-UBC.Penis_Foreskin_Keratinocyte_Primary_Cells.H3K27ac.skin03.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A15577-1-A18467-1.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Penis Foreskin Keratinocyte Primary Cells H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27ac ChIP-Seq on Penis Foreskin Keratinocyte Primary Cells, Donor skin03 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.17065
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 23,576,030
FINDPEAKS_SCORE: 0.0837
FINDPEAKS_PERCENTILE: 8
HOTSPOT_SCORE: 0.1812
HOTSPOT_PERCENTILE: 14
IROC_SCORE: 0.9827
IROC_PERCENTILE: 24
POISSON_SCORE: 0.2322
POISSON_PERCENTILE: 6
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1127077_UCSF-UBC.Penis_Foreskin_Keratinocyte_Primary_Cells.H3K27ac.skin03.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A15577-1-A18467-1.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Penis Foreskin Keratinocyte Primary Cells H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27ac ChIP-Seq read mappings from Penis Foreskin Keratinocyte Primary Cells, Donor skin03 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.17124
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: PFK H3K27ac 03 77
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells Histone H3K27ac Donor skin03 Library A15577 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 23,576,030
FINDPEAKS_SCORE: 0.0837
FINDPEAKS_PERCENTILE: 8
HOTSPOT_SCORE: 0.1812
HOTSPOT_PERCENTILE: 14
IROC_SCORE: 0.9827
IROC_PERCENTILE: 24
POISSON_SCORE: 0.2322
POISSON_PERCENTILE: 6
MAXIMUM_REPLICATE_CORRELATION: NA

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

value: Keratinocyte

value: foreskin keratinocyte


description:
design description: H3K4me1 ChIP-Seq analysis of breast fibroblast from RM071 (A21640) using Illumina HiSeq 2000
library name: A21640
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: 94-294 bp
CHIP_PROTOCOL_BEAD_TYPE: Sepharose A/G Bead Mix
CHIP_PROTOCOL_BEAD_AMOUNT: 20 ul
CHIP_PROTOCOL_ANTIBODY_AMOUNT: 5 ug
CHIP_ANTIBODY: 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: GSM1127065_UCSF-UBC.Breast_Fibroblast_Primary_Cells.H3K4me1.RM071.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A21640-1.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Breast Fibroblast Primary Cells H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K4me1 ChIP-Seq on Breast Fibroblast Primary Cells, Donor RM071 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.17045
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 17,418,859
FINDPEAKS_SCORE: 0.2368
FINDPEAKS_PERCENTILE: 50
HOTSPOT_SCORE: 0.3155
HOTSPOT_PERCENTILE: 48
IROC_SCORE: 0.9571
IROC_PERCENTILE: 48
POISSON_SCORE: 0.4632
POISSON_PERCENTILE: 50
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1127065_UCSF-UBC.Breast_Fibroblast_Primary_Cells.H3K4me1.RM071.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A21640-1.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Breast Fibroblast Primary Cells H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K4me1 ChIP-Seq read mappings from Breast Fibroblast Primary Cells, Donor RM071 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.17104
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: BF H3K4me1 71 40
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Breast Fibroblast Primary Cells Histone H3K4me1 Donor RM071 Library A21640 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 17,418,859
FINDPEAKS_SCORE: 0.2368
FINDPEAKS_PERCENTILE: 50
HOTSPOT_SCORE: 0.3155
HOTSPOT_PERCENTILE: 48
IROC_SCORE: 0.9571
IROC_PERCENTILE: 48
POISSON_SCORE: 0.4632
POISSON_PERCENTILE: 50
MAXIMUM_REPLICATE_CORRELATION: NA

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


description:
design description: H3K36me3 ChIP-Seq analysis of UCSF-4 embryonic stem cell line (A19300) using Illumina HiSeq 2000
library name: A19300
EXPERIMENT_TYPE: Histone H3K36me3
EXTRACTION_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Fisher 550 Sonic Dismembrator
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 10 min
CHIP_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
CHIP_PROTOCOL_CHROMATIN_AMOUNT: 5 ug
SIZE_FRACTION: 86-371 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: GSM1127070_UCSF-UBC.UCSF-4Star.H3K36me3.A19300.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A19300-1.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of UCSF-4* Cell Line H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K36me3 ChIP-Seq on the UCSF-4* Cell Line, Library A19300 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.17032
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 50,648,102
FINDPEAKS_SCORE: 0.2653
FINDPEAKS_PERCENTILE: 48
HOTSPOT_SCORE: 0.251
HOTSPOT_PERCENTILE: 29
IROC_SCORE: 0.9788
IROC_PERCENTILE: 55
POISSON_SCORE: 0.4638
POISSON_PERCENTILE: 43
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

ANALYSIS FILE NAME: GSM1127070_UCSF-UBC.UCSF-4Star.H3K36me3.A19300.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A19300-1.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of UCSF-4Star Cell Line H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K36me3 ChIP-Seq read mappings from the UCSF-4Star Cell Line, Library A19300 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.17091
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: UCSF4* H3K36me3 00
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC UCSF-4* Cell Line Histone H3K36me3 Library A19300 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 50,648,102
FINDPEAKS_SCORE: 0.2653
FINDPEAKS_PERCENTILE: 48
HOTSPOT_SCORE: 0.251
HOTSPOT_PERCENTILE: 29
IROC_SCORE: 0.9788
IROC_PERCENTILE: 55
POISSON_SCORE: 0.4638
POISSON_PERCENTILE: 43
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

value: cell line

value: Embryo ICM

value: Embryonic stem cell


description:
design description: H3K36me3 ChIP-Seq analysis of pancreas islet from ZGI 213 (A22473) using Illumina HiSeq 2000
library name: A22473
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: Bioruptor
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 30 min
CHIP_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
CHIP_PROTOCOL_CHROMATIN_AMOUNT: 9 ug
SIZE_FRACTION: 124-199 bp
CHIP_PROTOCOL_BEAD_TYPE: Pierce Magnetic Protein A/G
CHIP_PROTOCOL_BEAD_AMOUNT: 15 ul
CHIP_PROTOCOL_ANTIBODY_AMOUNT: 4 ug
CHIP_ANTIBODY: H3K36me3
CHIP_ANTIBODY_PROVIDER: Diagenode
CHIP_ANTIBODY_CATALOG: pAb-058-050
CHIP_ANTIBODY_LOT: A241-0011
****************
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: GSM1127069_UCSF-UBC.Pancreatic_Islets.H3K36me3.ZGI_213.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A22473-1.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Pancreatic Islets H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K36me3 ChIP-Seq on Pancreatic Islets, Donor ZGI 213 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.17044
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 27,874,742
FINDPEAKS_SCORE: 0.303
FINDPEAKS_PERCENTILE: 62
HOTSPOT_SCORE: 0.2644
HOTSPOT_PERCENTILE: 34
IROC_SCORE: 0.9782
IROC_PERCENTILE: 53
POISSON_SCORE: 0.5508
POISSON_PERCENTILE: 69
MAXIMUM_REPLICATE_CORRELATION: 0.95

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

ANALYSIS FILE NAME: GSM1127069_UCSF-UBC.Pancreatic_Islets.H3K36me3.ZGI_213.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A22473-1.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Pancreatic Islets H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K36me3 ChIP-Seq read mappings from Pancreatic Islets, Donor ZGI 213 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.17103
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: PI H3K36me3 13 73
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Pancreatic Islets Histone H3K36me3 Donor ZGI 213 Library A22473 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 27,874,742
FINDPEAKS_SCORE: 0.303
FINDPEAKS_PERCENTILE: 62
HOTSPOT_SCORE: 0.2644
HOTSPOT_PERCENTILE: 34
IROC_SCORE: 0.9782
IROC_PERCENTILE: 53
POISSON_SCORE: 0.5508
POISSON_PERCENTILE: 69
MAXIMUM_REPLICATE_CORRELATION: 0.95

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

value: primary cell

value: pancreas islet


description:
design description: H3K27ac ChIP-Seq analysis of breast fibroblast from RM071 (A21645) using Illumina HiSeq 2000
library name: A21645
EXPERIMENT_TYPE: Histone H3K27ac
EXTRACTION_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Fisher 550 Sonic Dismembrator
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 10 min
CHIP_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
CHIP_PROTOCOL_CHROMATIN_AMOUNT: 5 ug
SIZE_FRACTION: 94-294 bp
CHIP_PROTOCOL_BEAD_TYPE: Sepharose A/G Bead Mix
CHIP_PROTOCOL_BEAD_AMOUNT: 20 ul
CHIP_PROTOCOL_ANTIBODY_AMOUNT: 2.5 ug
CHIP_ANTIBODY: H3K27ac
CHIP_ANTIBODY_PROVIDER: Abcam
CHIP_ANTIBODY_CATALOG: ab4729
CHIP_ANTIBODY_LOT: GR28147-1
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM1127064_UCSF-UBC.Breast_Fibroblast_Primary_Cells.H3K27ac.RM071.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A21645-1.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Breast Fibroblast Primary Cells H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27ac ChIP-Seq on Breast Fibroblast Primary Cells, Donor RM071 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.17033
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 23,665,688
FINDPEAKS_SCORE: 0.2144
FINDPEAKS_PERCENTILE: 24
HOTSPOT_SCORE: 0.2532
HOTSPOT_PERCENTILE: 24
IROC_SCORE: 0.9932
IROC_PERCENTILE: 45
POISSON_SCORE: 0.3251
POISSON_PERCENTILE: 16
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1127064_UCSF-UBC.Breast_Fibroblast_Primary_Cells.H3K27ac.RM071.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A21645-1.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Breast Fibroblast Primary Cells H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27ac ChIP-Seq read mappings from Breast Fibroblast Primary Cells, Donor RM071 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.17092
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: BF H3K27ac 71 45
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Breast Fibroblast Primary Cells Histone H3K27ac Donor RM071 Library A21645 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 23,665,688
FINDPEAKS_SCORE: 0.2144
FINDPEAKS_PERCENTILE: 24
HOTSPOT_SCORE: 0.2532
HOTSPOT_PERCENTILE: 24
IROC_SCORE: 0.9932
IROC_PERCENTILE: 45
POISSON_SCORE: 0.3251
POISSON_PERCENTILE: 16
MAXIMUM_REPLICATE_CORRELATION: NA

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

value: primary cell culture


description:
design description: H3K4me1 ChIP-Seq analysis of ganglionic eminence neural stem and progenitor cells from HuFNSC04 (A19303) using Illumina HiSeq 2000
library name: A19303
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: 67-380 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: GSM1127066_UCSF-UBC.Neurosphere_Cultured_Cells_Ganglionic_Eminence_Derived.H3K4me1.HuFNSC04.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A19303-1.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Neurosphere Cultured Cells Ganglionic Eminence Derived H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K4me1 ChIP-Seq on Neurosphere Cultured Cells Ganglionic Eminence Derived, Donor HuFNSC04 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.17030
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 28,974,659
FINDPEAKS_SCORE: 0.3495
FINDPEAKS_PERCENTILE: 68
HOTSPOT_SCORE: 0.4034
HOTSPOT_PERCENTILE: 66
IROC_SCORE: 0.9795
IROC_PERCENTILE: 57
POISSON_SCORE: 0.5149
POISSON_PERCENTILE: 64
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM1127066_UCSF-UBC.Neurosphere_Cultured_Cells_Ganglionic_Eminence_Derived.H3K4me1.HuFNSC04.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A19303-1.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Neurosphere Cultured Cells Ganglionic Eminence Derived H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K4me1 ChIP-Seq read mappings from Neurosphere Cultured Cells Ganglionic Eminence Derived, Donor HuFNSC04 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.17089
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: NGED H3K4me1 04 03
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Neurosphere Cultured Cells Ganglionic Eminence Derived Histone H3K4me1 Donor HuFNSC04 Library A19303 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 28,974,659
FINDPEAKS_SCORE: 0.3495
FINDPEAKS_PERCENTILE: 68
HOTSPOT_SCORE: 0.4034
HOTSPOT_PERCENTILE: 66
IROC_SCORE: 0.9795
IROC_PERCENTILE: 57
POISSON_SCORE: 0.5149
POISSON_PERCENTILE: 64
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

value: Brain

value: Ganglionic eminence neurosphere culture


description:
design description: H3K4me3 ChIP-Seq analysis of pancreas islet from ZD4 273 (A19678) using Illumina HiSeq 2000
library name: A19678
EXPERIMENT_TYPE: Histone H3K4me3
EXTRACTION_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Bioruptor
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 30 min
CHIP_PROTOCOL: Refer to document 'Chromatin Immunoprecipitation (ChIP)' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
CHIP_PROTOCOL_CHROMATIN_AMOUNT: 6 ug
SIZE_FRACTION: 74-374 bp
CHIP_PROTOCOL_BEAD_TYPE: Pierce Magnetic Protein A/G
CHIP_PROTOCOL_BEAD_AMOUNT: 15 ul
CHIP_PROTOCOL_ANTIBODY_AMOUNT: 10 ul
CHIP_ANTIBODY: H3K4me3
CHIP_ANTIBODY_PROVIDER: Cell Signaling Technology
CHIP_ANTIBODY_CATALOG: 9751S
CHIP_ANTIBODY_LOT: 4
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM1127067_UCSF-UBC.Pancreatic_Islets.H3K4me3.ZD4_273.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A19678-1.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Pancreatic Islets H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K4me3 ChIP-Seq on Pancreatic Islets, Donor ZD4 273 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.17043
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 21,257,029
FINDPEAKS_SCORE: 0.375
FINDPEAKS_PERCENTILE: 45
HOTSPOT_SCORE: 0.3765
HOTSPOT_PERCENTILE: 38
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.3771
POISSON_PERCENTILE: 38
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

ANALYSIS FILE NAME: GSM1127067_UCSF-UBC.Pancreatic_Islets.H3K4me3.ZD4_273.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A19678-1.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Pancreatic Islets H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K4me3 ChIP-Seq read mappings from Pancreatic Islets, Donor ZD4 273 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.17102
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: PI H3K4me3 73 78
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Pancreatic Islets Histone H3K4me3 Donor ZD4 273 Library A19678 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 21,257,029
FINDPEAKS_SCORE: 0.375
FINDPEAKS_PERCENTILE: 45
HOTSPOT_SCORE: 0.3765
HOTSPOT_PERCENTILE: 38
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.3771
POISSON_PERCENTILE: 38
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

value: male


description:
design description: H3K27me3 ChIP-Seq analysis of ganglionic eminence neural stem and progenitor cells from HuFNSC04 (A19306) using Illumina HiSeq 2000
library name: A19306
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: 10 ug
SIZE_FRACTION: 75-444 bp
CHIP_PROTOCOL_BEAD_TYPE: Sepharose A/G Bead Mix
CHIP_PROTOCOL_BEAD_AMOUNT: 20 ul
CHIP_PROTOCOL_ANTIBODY_AMOUNT: 5 ug
CHIP_ANTIBODY: H3K27me3
CHIP_ANTIBODY_PROVIDER: Diagenode
CHIP_ANTIBODY_CATALOG: pAb-069-050
CHIP_ANTIBODY_LOT: A299-00242
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM1127078_UCSF-UBC.Neurosphere_Cultured_Cells_Ganglionic_Eminence_Derived.H3K27me3.HuFNSC04.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A19306-1.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Neurosphere Cultured Cells Ganglionic Eminence Derived H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27me3 ChIP-Seq on Neurosphere Cultured Cells Ganglionic Eminence Derived, Donor HuFNSC04 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.17028
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 33,656,621
FINDPEAKS_SCORE: 0.0954
FINDPEAKS_PERCENTILE: 63
HOTSPOT_SCORE: 0.161
HOTSPOT_PERCENTILE: 46
IROC_SCORE: 0.9672
IROC_PERCENTILE: 81
POISSON_SCORE: 0.3431
POISSON_PERCENTILE: 52
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM1127078_UCSF-UBC.Neurosphere_Cultured_Cells_Ganglionic_Eminence_Derived.H3K27me3.HuFNSC04.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: A19306-1.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Neurosphere Cultured Cells Ganglionic Eminence Derived H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27me3 ChIP-Seq read mappings from Neurosphere Cultured Cells Ganglionic Eminence Derived, Donor HuFNSC04 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.17087
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: NGED H3K27me3 04 06
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-USC Neurosphere Cultured Cells Ganglionic Eminence Derived Histone H3K27me3 Donor HuFNSC04 Library A19306 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 33,656,621
FINDPEAKS_SCORE: 0.0954
FINDPEAKS_PERCENTILE: 63
HOTSPOT_SCORE: 0.161
HOTSPOT_PERCENTILE: 46
IROC_SCORE: 0.9672
IROC_PERCENTILE: 81
POISSON_SCORE: 0.3431
POISSON_PERCENTILE: 52
MAXIMUM_REPLICATE_CORRELATION: 0.98

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