title: ChIP-Seq analysis of H3K27ac in human BM-MSC cells; DNA_Lib 998

description:
sample_term_id: EFO_0000586
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 998
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.14624
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5948
****************
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: GSM1112797_BI.Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K27ac.59.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 998.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27ac ChIP-Seq on Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells, Donor 59, 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.17293
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: 23,007,362
FINDPEAKS_SCORE: 0.7717
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.7583
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9997
IROC_PERCENTILE: 96
POISSON_SCORE: 0.7914
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.95

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

ANALYSIS FILE NAME: GSM1112797_BI.Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K27ac.59.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 998.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27ac ChIP-Seq read mappings from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells, Donor 59, 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.17476
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: BMDMSC H3K27ac 59 98
BROWSER_TRACK_DESCRIPTION: BI Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K27ac Donor 59 Library DNA_Lib 998 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 23,007,362
FINDPEAKS_SCORE: 0.7717
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.7583
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9997
IROC_PERCENTILE: 96
POISSON_SCORE: 0.7914
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.95

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

source_name: bone marrow was aspirated from the iliac crest, isolated by density gradient and adhesion to plastic, and expanded in monolayer culture, containing 10% FBS; DNA_Lib 998


title: ChIP-Seq analysis of H3K27ac in human anterior caudate cells; DNA_Lib 1050

status: Public on Jul 18 2013

type: SRA

city: Cambridge

first: BROAD

last: INSTITUTE

state: MA

country: USA

institute: Broad Institute

description:
sample_term_id: UBERON_0001873
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 1050
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.14638
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5936
****************
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: GSM1112811_BI.Brain_Anterior_Caudate.H3K27ac.112.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 1050.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Brain Anterior Caudate H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27ac ChIP-Seq on Brain Anterior Caudate, Donor 112, 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.17250
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: 16,424,681
FINDPEAKS_SCORE: 0.3903
FINDPEAKS_PERCENTILE: 58
HOTSPOT_SCORE: 0.4406
HOTSPOT_PERCENTILE: 61
IROC_SCORE: 0.9935
IROC_PERCENTILE: 46
POISSON_SCORE: 0.5097
POISSON_PERCENTILE: 64
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

ANALYSIS FILE NAME: GSM1112811_BI.Brain_Anterior_Caudate.H3K27ac.112.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 1050.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Brain Anterior Caudate H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27ac ChIP-Seq read mappings from Brain Anterior Caudate, Donor 112, 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.17433
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: BAC H3K27ac 12 50
BROWSER_TRACK_DESCRIPTION: BI Brain Anterior Caudate Histone H3K27ac Donor 112 Library DNA_Lib 1050 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 16,424,681
FINDPEAKS_SCORE: 0.3903
FINDPEAKS_PERCENTILE: 58
HOTSPOT_SCORE: 0.4406
HOTSPOT_PERCENTILE: 61
IROC_SCORE: 0.9935
IROC_PERCENTILE: 46
POISSON_SCORE: 0.5097
POISSON_PERCENTILE: 64
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

molecule: genomic DNA

organism: Homo sapiens

source_name: human post mortem brain region from a non Alzheimer's donor; DNA_Lib 1050

extract_protocol: Library construction protocol: Single read - Illumina

tag: sample common name

value: Brain, Anterior Caudate

tag: sra sample accession

value: post-mortem

tag: disease

value: Anterior Caudate

value: Female

value: Primary Tissue

value: brain

value: Rush University Medical Center

value: Protein A-Sepharose 4B

value: 0.5 to 3 million cells

value: cell/nuclei lysis

value: ~1 ug

value: 10 ul bed volume

value: Active Motif

value: Histone H3K27ac

value: Branson


title: ChIP-Seq analysis of H3K27ac in human Duodenum mucosa cells; DNA_Lib 1048

description:
sample_term_id: UBERON_0000320
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 1048
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.14617
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9454
****************
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: GSM1112790_BI.Duodenum_Mucosa.H3K27ac.159.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 1048.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Duodenum Mucosa H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27ac ChIP-Seq on Duodenum Mucosa, Donor 159, 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.17270
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: 13,836,118
FINDPEAKS_SCORE: 0.1852
FINDPEAKS_PERCENTILE: 21
HOTSPOT_SCORE: 0.2679
HOTSPOT_PERCENTILE: 25
IROC_SCORE: 0.9878
IROC_PERCENTILE: 32
POISSON_SCORE: 0.2974
POISSON_PERCENTILE: 12
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1112790_BI.Duodenum_Mucosa.H3K27ac.159.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 1048.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Duodenum Mucosa H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27ac ChIP-Seq read mappings from Duodenum Mucosa, Donor 159, 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.17453
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: DM H3K27ac 59 48
BROWSER_TRACK_DESCRIPTION: BI Duodenum Mucosa Histone H3K27ac Donor 159 Library DNA_Lib 1048 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 13,836,118
FINDPEAKS_SCORE: 0.1852
FINDPEAKS_PERCENTILE: 21
HOTSPOT_SCORE: 0.2679
HOTSPOT_PERCENTILE: 25
IROC_SCORE: 0.9878
IROC_PERCENTILE: 32
POISSON_SCORE: 0.2974
POISSON_PERCENTILE: 12
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: Primary duodenum mucosal tissue; DNA_Lib 1048

value: Duodenum Mucosa

value: Surgery

value: presumed normal

value: Caucasian

value: Male

value: Duodenum

value: MGH

value: 59.0 Years


title: ChIP-Seq analysis of H3K9me3 in human Duodenum smooth muscle cells; DNA_Lib 992

description:
sample_term_id: UBERON_0012488
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 992
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.14615
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9762
****************
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: GSM1112788_BI.Duodenum_Smooth_Muscle.H3K9me3.Donor_174_REMC_28.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 992.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Duodenum Smooth Muscle H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K9me3 ChIP-Seq on Duodenum Smooth Muscle, Donor Donor 174 REMC 28, 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.17263
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: 12,822,470
FINDPEAKS_SCORE: 0.2662
FINDPEAKS_PERCENTILE: 94
HOTSPOT_SCORE: 0.3395
HOTSPOT_PERCENTILE: 94
IROC_SCORE: 0.9377
IROC_PERCENTILE: 96
POISSON_SCORE: 0.4922
POISSON_PERCENTILE: 98
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

ANALYSIS FILE NAME: GSM1112788_BI.Duodenum_Smooth_Muscle.H3K9me3.Donor_174_REMC_28.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 992.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Duodenum Smooth Muscle H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K9me3 ChIP-Seq read mappings from Duodenum Smooth Muscle, Donor Donor 174 REMC 28, 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.17446
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: DSM H3K9me3 74 92
BROWSER_TRACK_DESCRIPTION: BI Duodenum Smooth Muscle Histone H3K9me3 Donor 174 REMC 28 Library DNA_Lib 992 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 12,822,470
FINDPEAKS_SCORE: 0.2662
FINDPEAKS_PERCENTILE: 94
HOTSPOT_SCORE: 0.3395
HOTSPOT_PERCENTILE: 94
IROC_SCORE: 0.9377
IROC_PERCENTILE: 96
POISSON_SCORE: 0.4922
POISSON_PERCENTILE: 98
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

source_name: Smooth muscle from wall of duodenum obtained during surgery and confirmed by pathology examination to be healthy tissue; DNA_Lib 992

value: Duodenum Smooth Muscle

value: NL smth muscle,  ddnum rmvd as part of whipple operation  because of autoimmune pancreatitis (type1)

value: Smooth Muscle

value: Primary Tissue

value: Donor 174 REMC 28

value: Abcam

value: Histone H3K9me3


title: ChIP-Seq analysis of H3K27ac in human chondrogenic dif cells; DNA_Lib 1001

description:
sample_term_id: CL_0000138
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 1001
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.14614
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5935
****************
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: GSM1112787_BI.Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K27ac.59.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 1001.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27ac ChIP-Seq on Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells, Donor 59, 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.17284
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 20,449,388
FINDPEAKS_SCORE: 0.7022
FINDPEAKS_PERCENTILE: 95
HOTSPOT_SCORE: 0.6987
HOTSPOT_PERCENTILE: 95
IROC_SCORE: 0.9992
IROC_PERCENTILE: 86
POISSON_SCORE: 0.7404
POISSON_PERCENTILE: 95
MAXIMUM_REPLICATE_CORRELATION: 0.95

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

ANALYSIS FILE NAME: GSM1112787_BI.Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K27ac.59.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 1001.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27ac ChIP-Seq read mappings from Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells, Donor 59, 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.17467
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: CfBMDMSC H3K27ac 59 01
BROWSER_TRACK_DESCRIPTION: BI Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K27ac Donor 59 Library DNA_Lib 1001 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 20,449,388
FINDPEAKS_SCORE: 0.7022
FINDPEAKS_PERCENTILE: 95
HOTSPOT_SCORE: 0.6987
HOTSPOT_PERCENTILE: 95
IROC_SCORE: 0.9992
IROC_PERCENTILE: 86
POISSON_SCORE: 0.7404
POISSON_PERCENTILE: 95
MAXIMUM_REPLICATE_CORRELATION: 0.95

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

source_name: chondrocytes derived via in vitro culture from mesenchymal stem cells; DNA_Lib 1001

value: healthy

tag: markers

value: Medium:NA; Differentiation Method:alginate hydrogel scaffold (SR Herlofsen et al, Tissue Eng Part A. 2011)

value: chondrogenic dif cells

value: Unknown

value: Primary Cell Culture

value: Rikshospitalet University Hospital

value: Protein A-Sepharose 4B

value: 0.5 to 3 million cells

value: cell/nuclei lysis

value: ~1 ug

value: 10 ul bed volume

value: Active Motif

value: Histone H3K27ac


title: ChIP-Seq analysis of H3K27ac in human inferior temporal lobe cells; DNA_Lib 1053

description:
sample_term_id: UBERON_0001871
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 1053
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.14639
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5933
****************
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: GSM1112812_BI.Brain_Inferior_Temporal_Lobe.H3K27ac.112.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 1053.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Brain Inferior Temporal Lobe H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27ac ChIP-Seq on Brain Inferior Temporal Lobe, Donor 112, 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.17235
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: 13,350,951
FINDPEAKS_SCORE: 0.3341
FINDPEAKS_PERCENTILE: 44
HOTSPOT_SCORE: 0.4056
HOTSPOT_PERCENTILE: 51
IROC_SCORE: 0.9838
IROC_PERCENTILE: 25
POISSON_SCORE: 0.4694
POISSON_PERCENTILE: 53
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

ANALYSIS FILE NAME: GSM1112812_BI.Brain_Inferior_Temporal_Lobe.H3K27ac.112.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 1053.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Brain Inferior Temporal Lobe H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27ac ChIP-Seq read mappings from Brain Inferior Temporal Lobe, Donor 112, 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.17418
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: BITL H3K27ac 12 53
BROWSER_TRACK_DESCRIPTION: BI Brain Inferior Temporal Lobe Histone H3K27ac Donor 112 Library DNA_Lib 1053 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 13,350,951
FINDPEAKS_SCORE: 0.3341
FINDPEAKS_PERCENTILE: 44
HOTSPOT_SCORE: 0.4056
HOTSPOT_PERCENTILE: 51
IROC_SCORE: 0.9838
IROC_PERCENTILE: 25
POISSON_SCORE: 0.4694
POISSON_PERCENTILE: 53
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

source_name: human post mortem brain region from a non Alzheimer's donor; DNA_Lib 1053

value: Brain, Inferior Temporal Lobe

value: post-mortem

value: Inferior Temporal Lobe

value: Female

value: Primary Tissue

value: brain

value: Rush University Medical Center

value: Branson


title: ChIP-Seq analysis of H3K27ac in human BM-MSC cells; DNA_Lib 997

description:
sample_term_id: EFO_0000586
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 997
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.14620
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5953
****************
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: GSM1112793_BI.Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K27ac.58.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 997.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27ac ChIP-Seq on Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells, Donor 58, 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.17290
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: 22,060,696
FINDPEAKS_SCORE: 0.7262
FINDPEAKS_PERCENTILE: 96
HOTSPOT_SCORE: 0.7145
HOTSPOT_PERCENTILE: 96
IROC_SCORE: 0.9997
IROC_PERCENTILE: 96
POISSON_SCORE: 0.7491
POISSON_PERCENTILE: 96
MAXIMUM_REPLICATE_CORRELATION: 0.95

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

ANALYSIS FILE NAME: GSM1112793_BI.Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K27ac.58.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 997.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27ac ChIP-Seq read mappings from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells, Donor 58, 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.17473
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: BMDMSC H3K27ac 58 97
BROWSER_TRACK_DESCRIPTION: BI Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K27ac Donor 58 Library DNA_Lib 997 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 22,060,696
FINDPEAKS_SCORE: 0.7262
FINDPEAKS_PERCENTILE: 96
HOTSPOT_SCORE: 0.7145
HOTSPOT_PERCENTILE: 96
IROC_SCORE: 0.9997
IROC_PERCENTILE: 96
POISSON_SCORE: 0.7491
POISSON_PERCENTILE: 96
MAXIMUM_REPLICATE_CORRELATION: 0.95

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

source_name: bone marrow was aspirated from the iliac crest, isolated by density gradient and adhesion to plastic, and expanded in monolayer culture, containing 10% FBS; DNA_Lib 997

value: healthy

value: BM-MSC

value: Unknown

value: Primary Cell Culture


title: Adult control cerebellum [AC3]

status: Public on Jul 29 2013

type: RNA

city: London

first: Denise

last: Sheer

address: Blizard Institute, 4 Newark Street

department: Neuroscience & Trauma

country: United Kingdom

institute: Barts & The London School of Medicine & Dentistry

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation in GenomeStudio

molecule: total RNA

source_name: Adult control cerebellum AC3  (BioChain #A911104)

label_protocol: Cy3 Standard illumina prorocol

extract_protocol: RNA was extracted with QIAGEN miRNeasy mini kit in accordance with the prescribed protocol provided with the kit.

tag: tissue

value: Adult control cerebellum

tag: Sex

value: M

tag: age


title: ChIP-Seq analysis of WCE in human CD25- IL17- Th stim MACS cells; DNA_Lib 2276

description:
sample_term_id: CL_0000492
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 2276
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.14611
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.13309
****************
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: GSM1112784_BI.CD4+_CD25-_IL17-_PMA-Ionomycin_stimulated_MACS_purified_Th_Primary_Cells.Input.Donor_332.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 2276.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of CD4+ CD25- IL17- PMA-Ionomycin stimulated MACS purified Th Primary Cells Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Input ChIP-Seq on CD4+ CD25- IL17- PMA-Ionomycin stimulated MACS purified Th Primary Cells, Donor Donor 332, 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.17304
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: 32,954,555
FINDPEAKS_SCORE: 0.0058
FINDPEAKS_PERCENTILE: 51
HOTSPOT_SCORE: 0.0047
HOTSPOT_PERCENTILE: 25
IROC_SCORE: 0.0
IROC_PERCENTILE: 26
POISSON_SCORE: 0.027
POISSON_PERCENTILE: 21
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM1112784_BI.CD4+_CD25-_IL17-_PMA-Ionomycin_stimulated_MACS_purified_Th_Primary_Cells.Input.Donor_332.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 2276.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of CD4+ CD25- IL17- PMA-Ionomycin stimulated MACS purified Th Primary Cells Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Input ChIP-Seq read mappings from CD4+ CD25- IL17- PMA-Ionomycin stimulated MACS purified Th Primary Cells, Donor Donor 332, 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.17487
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: CCIPsMpT Input 32 76
BROWSER_TRACK_DESCRIPTION: BI CD4+ CD25- IL17- PMA-Ionomycin stimulated MACS purified Th Primary Cells ChIP-Seq Input Donor 332 Library DNA_Lib 2276 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 32,954,555
FINDPEAKS_SCORE: 0.0058
FINDPEAKS_PERCENTILE: 51
HOTSPOT_SCORE: 0.0047
HOTSPOT_PERCENTILE: 25
IROC_SCORE: 0.0
IROC_PERCENTILE: 26
POISSON_SCORE: 0.027
POISSON_PERCENTILE: 21
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

source_name: CD25- IL17- Th stim MACS is one of  CD4+  T cell subsets  that purified by microbeads, LS column  ; DNA_Lib 2276

value: normal

value: CD4+ T cell

value: CD25- IL17- Th stim MACS

value: Primary Cell

value: Donor 332

value: Dana Farber

value: standard

value: cell/nuclei lysis

value: ChIP-Seq Input

value: Input


title: ChIP-Seq analysis of WCE in human CD25int CD127+ Tmem cells; DNA_Lib 2277

description:
sample_term_id: CL_0000897
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 2277
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.14612
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.13316
****************
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: GSM1112785_BI.CD4+_CD25int_CD127+_Tmem_Primary_Cells.Input.Donor_332.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 2277.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of CD4+ CD25int CD127+ Tmem Primary Cells Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Input ChIP-Seq on CD4+ CD25int CD127+ Tmem Primary Cells, Donor Donor 332, 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.17211
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: 32,354,909
FINDPEAKS_SCORE: 0.0058
FINDPEAKS_PERCENTILE: 51
HOTSPOT_SCORE: 0.0046
HOTSPOT_PERCENTILE: 24
IROC_SCORE: 0.0
IROC_PERCENTILE: 26
POISSON_SCORE: 0.0259
POISSON_PERCENTILE: 19
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM1112785_BI.CD4+_CD25int_CD127+_Tmem_Primary_Cells.Input.Donor_332.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 2277.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of CD4+ CD25int CD127+ Tmem Primary Cells Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Input ChIP-Seq read mappings from CD4+ CD25int CD127+ Tmem Primary Cells, Donor Donor 332, 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.17394
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: CCCTmemmem Input 32 77
BROWSER_TRACK_DESCRIPTION: BI CD4+ CD25int CD127+ Tmem Primary Cells ChIP-Seq Input Donor 332 Library DNA_Lib 2277 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 32,354,909
FINDPEAKS_SCORE: 0.0058
FINDPEAKS_PERCENTILE: 51
HOTSPOT_SCORE: 0.0046
HOTSPOT_PERCENTILE: 24
IROC_SCORE: 0.0
IROC_PERCENTILE: 26
POISSON_SCORE: 0.0259
POISSON_PERCENTILE: 19
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: CD25int CD127+ Tmem is one of  CD4+  T cell subsets  that purified by microbeads, LS column and FACS ; DNA_Lib 2277

value: CD4+ CD25int CD127+ Tmem Primary Cells

value: CD25int CD127+ Tmem

value: Branson


title: Adult control cerebellum [AC1]

source_name: Adult control cerebellum AC1  (BioChain #A510131)


title: ChIP-Seq analysis of H3K27ac in human rectal mucosa cells; DNA_Lib 1044

description:
sample_term_id: UBERON_0003346
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 1044
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.14628
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3351
****************
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: GSM1112801_BI.Rectal_Mucosa.H3K27ac.31.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 1044.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Rectal Mucosa H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27ac ChIP-Seq on Rectal Mucosa, Donor 31, 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.17253
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: 15,905,900
FINDPEAKS_SCORE: 0.5844
FINDPEAKS_PERCENTILE: 86
HOTSPOT_SCORE: 0.596
HOTSPOT_PERCENTILE: 86
IROC_SCORE: 0.998
IROC_PERCENTILE: 73
POISSON_SCORE: 0.6281
POISSON_PERCENTILE: 85
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

ANALYSIS FILE NAME: GSM1112801_BI.Rectal_Mucosa.H3K27ac.31.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 1044.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Rectal Mucosa H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27ac ChIP-Seq read mappings from Rectal Mucosa, Donor 31, 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.17436
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: RM H3K27ac 31 44
BROWSER_TRACK_DESCRIPTION: BI Rectal Mucosa Histone H3K27ac Donor 31 Library DNA_Lib 1044 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 15,905,900
FINDPEAKS_SCORE: 0.5844
FINDPEAKS_PERCENTILE: 86
HOTSPOT_SCORE: 0.596
HOTSPOT_PERCENTILE: 86
IROC_SCORE: 0.998
IROC_PERCENTILE: 73
POISSON_SCORE: 0.6281
POISSON_PERCENTILE: 85
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

source_name: Primary rectal mucosal tissue; DNA_Lib 1044

value: Rectal Mucosa

value: surgery

value: "normal mucosa, diverticular disease"

value: mucosa

value: white

value: Female

value: Primary Tissue

value: rectum

value: MGH Pathology

value: Protein A-Sepharose 4B

value: 0.5 to 3 million cells

value: ~1 ug

value: 10 ul bed volume

value: Active Motif

value: Histone H3K27ac


title: Adult control cerebellum [AC8]

source_name: Adult control cerebellum AC8  (BioChain #A911105)

value: Adult control cerebellum

value: M


title: ChIP-Seq analysis of H3K27ac in human rectal smooth muscle cells; DNA_Lib 1043

description:
sample_term_id: NTR_0001404
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 1043
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.14623
EDACC Genboree Sample Page:

****************
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: GSM1112796_BI.Rectal_Smooth_Muscle.H3K27ac.30.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 1043.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Rectal Smooth Muscle H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27ac ChIP-Seq on Rectal Smooth Muscle, Donor 30, 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.17228
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: 18,669,303
FINDPEAKS_SCORE: 0.4231
FINDPEAKS_PERCENTILE: 64
HOTSPOT_SCORE: 0.4451
HOTSPOT_PERCENTILE: 64
IROC_SCORE: 0.9982
IROC_PERCENTILE: 75
POISSON_SCORE: 0.4948
POISSON_PERCENTILE: 56
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1112796_BI.Rectal_Smooth_Muscle.H3K27ac.30.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 1043.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Rectal Smooth Muscle H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27ac ChIP-Seq read mappings from Rectal Smooth Muscle, Donor 30, 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.17411
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: RSM H3K27ac 30 43
BROWSER_TRACK_DESCRIPTION: BI Rectal Smooth Muscle Histone H3K27ac Donor 30 Library DNA_Lib 1043 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 18,669,303
FINDPEAKS_SCORE: 0.4231
FINDPEAKS_PERCENTILE: 64
HOTSPOT_SCORE: 0.4451
HOTSPOT_PERCENTILE: 64
IROC_SCORE: 0.9982
IROC_PERCENTILE: 75
POISSON_SCORE: 0.4948
POISSON_PERCENTILE: 56
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: Primary rectal smooth muscle tissue; DNA_Lib 1043

value: Rectal Smooth Muscle

value: normal smooth muscle

value: smooth muscle

value: cell/nuclei lysis

value: Branson


title: ChIP-Seq analysis of H3K27ac in human hippocampus middle cells; DNA_Lib 1049

description:
sample_term_id: EFO_0000530
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 1049
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.14618
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5937
****************
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: GSM1112791_BI.Brain_Hippocampus_Middle.H3K27ac.112.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 1049.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Brain Hippocampus Middle H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27ac ChIP-Seq on Brain Hippocampus Middle, Donor 112, 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.17313
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: 13,331,274
FINDPEAKS_SCORE: 0.3963
FINDPEAKS_PERCENTILE: 59
HOTSPOT_SCORE: 0.4545
HOTSPOT_PERCENTILE: 65
IROC_SCORE: 0.9914
IROC_PERCENTILE: 39
POISSON_SCORE: 0.5032
POISSON_PERCENTILE: 61
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

ANALYSIS FILE NAME: GSM1112791_BI.Brain_Hippocampus_Middle.H3K27ac.112.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 1049.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Brain Hippocampus Middle H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27ac ChIP-Seq read mappings from Brain Hippocampus Middle, Donor 112, 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.17496
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: BHM H3K27ac 12 49
BROWSER_TRACK_DESCRIPTION: BI Brain Hippocampus Middle Histone H3K27ac Donor 112 Library DNA_Lib 1049 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 13,331,274
FINDPEAKS_SCORE: 0.3963
FINDPEAKS_PERCENTILE: 59
HOTSPOT_SCORE: 0.4545
HOTSPOT_PERCENTILE: 65
IROC_SCORE: 0.9914
IROC_PERCENTILE: 39
POISSON_SCORE: 0.5032
POISSON_PERCENTILE: 61
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

source_name: human post mortem brain region from a non Alzheimer's donor; DNA_Lib 1049

value: Brain, Hippocampus Middle

value: post-mortem

value: Hippocampus Middle

value: Female

value: brain

value: Rush University Medical Center


title: Adult control cerebellum [AC4]

source_name: Adult control cerebellum AC4  (BioChain #A508112)


title: ChIP-Seq analysis of WCE in human CD25- CD45RA+ naive cells; DNA_Lib 2279

description:
sample_term_id: CL_0000492
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 2279
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.14609
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.13318
****************
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: GSM1112782_BI.CD4+_CD25-_CD45RA+_Naive_Primary_Cells.Input.Donor_332.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 2279.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of CD4+ CD25- CD45RA+ Naive Primary Cells Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Input ChIP-Seq on CD4+ CD25- CD45RA+ Naive Primary Cells, Donor Donor 332, 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.17247
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: 42,880,298
FINDPEAKS_SCORE: 0.0049
FINDPEAKS_PERCENTILE: 25
HOTSPOT_SCORE: 0.0032
HOTSPOT_PERCENTILE: 16
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.016
POISSON_PERCENTILE: 3
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM1112782_BI.CD4+_CD25-_CD45RA+_Naive_Primary_Cells.Input.Donor_332.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 2279.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of CD4+ CD25- CD45RA+ Naive Primary Cells Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Input ChIP-Seq read mappings from CD4+ CD25- CD45RA+ Naive Primary Cells, Donor Donor 332, 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.17430
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: CCCNN Input 32 79
BROWSER_TRACK_DESCRIPTION: BI CD4+ CD25- CD45RA+ Naive Primary Cells ChIP-Seq Input Donor 332 Library DNA_Lib 2279 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 42,880,298
FINDPEAKS_SCORE: 0.0049
FINDPEAKS_PERCENTILE: 25
HOTSPOT_SCORE: 0.0032
HOTSPOT_PERCENTILE: 16
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.016
POISSON_PERCENTILE: 3
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: CD25- CD45RA+ naive is one of  CD4+  T cell subsets  that purified by microbeads, LS column and FACS ; DNA_Lib 2279

value: CD4+ CD25- CD45RA+ Naive Primary Cells

value: normal

value: CD4+ T cell

value: CD25- CD45RA+ naive

value: Unknown

value: Primary Cell

value: Donor 332

value: Dana Farber

value: standard

value: ChIP-Seq Input

value: Input


title: ChIP-Seq analysis of H3K27me3 in human stomach smooth muscle cells; DNA_Lib 383

description:
sample_term_id: UBERON_0008856
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 383
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.14610
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9451
****************
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: GSM1112783_BI.Stomach_Smooth_Muscle.H3K27me3.161.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 383.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Stomach Smooth Muscle H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27me3 ChIP-Seq on Stomach Smooth Muscle, Donor 161, 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.17297
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: 29,667,244
FINDPEAKS_SCORE: 0.0437
FINDPEAKS_PERCENTILE: 41
HOTSPOT_SCORE: 0.1129
HOTSPOT_PERCENTILE: 23
IROC_SCORE: 0.9196
IROC_PERCENTILE: 65
POISSON_SCORE: 0.2549
POISSON_PERCENTILE: 30
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

ANALYSIS FILE NAME: GSM1112783_BI.Stomach_Smooth_Muscle.H3K27me3.161.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 383.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Stomach Smooth Muscle H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27me3 ChIP-Seq read mappings from Stomach Smooth Muscle, Donor 161, 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.17480
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: SSM H3K27me3 61 83
BROWSER_TRACK_DESCRIPTION: BI Stomach Smooth Muscle Histone H3K27me3 Donor 161 Library DNA_Lib 383 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 29,667,244
FINDPEAKS_SCORE: 0.0437
FINDPEAKS_PERCENTILE: 41
HOTSPOT_SCORE: 0.1129
HOTSPOT_PERCENTILE: 23
IROC_SCORE: 0.9196
IROC_PERCENTILE: 65
POISSON_SCORE: 0.2549
POISSON_PERCENTILE: 30
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

source_name: Primary stomach smooth muscle tissue; DNA_Lib 383

value: Stomach Smooth Muscle

value: Surgery

value: NL smooth muscle, stomach rmvd as part of pancr., CA

value: Smooth Muscle

value: Caucasian

value: Male

value: Primary Tissue

value: Stomach

value: MGH

value: 59.0 Years

value: Protein A-Sepharose 4B

value: 0.5 to 3 million cells

value: cell/nuclei lysis

value: ~1 ug

value: 10 ul bed volume

value: Millipore

value: Histone H3K27me3

value: Branson


title: ChIP-Seq analysis of H3K27ac in human colon smooth muscle cells; DNA_Lib 930

description:
sample_term_id: UBERON_0012489
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 930
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.14607
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9758
****************
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: GSM1112780_BI.Colon_Smooth_Muscle.H3K27ac.156.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 930.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Colon Smooth Muscle H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27ac ChIP-Seq on Colon Smooth Muscle, Donor 156, 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.17291
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: 13,764,059
FINDPEAKS_SCORE: 0.3423
FINDPEAKS_PERCENTILE: 46
HOTSPOT_SCORE: 0.4067
HOTSPOT_PERCENTILE: 52
IROC_SCORE: 0.9957
IROC_PERCENTILE: 54
POISSON_SCORE: 0.4597
POISSON_PERCENTILE: 49
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1112780_BI.Colon_Smooth_Muscle.H3K27ac.156.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 930.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Colon Smooth Muscle H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27ac ChIP-Seq read mappings from Colon Smooth Muscle, Donor 156, 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.17474
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: CSM H3K27ac 56 30
BROWSER_TRACK_DESCRIPTION: BI Colon Smooth Muscle Histone H3K27ac Donor 156 Library DNA_Lib 930 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 13,764,059
FINDPEAKS_SCORE: 0.3423
FINDPEAKS_PERCENTILE: 46
HOTSPOT_SCORE: 0.4067
HOTSPOT_PERCENTILE: 52
IROC_SCORE: 0.9957
IROC_PERCENTILE: 54
POISSON_SCORE: 0.4597
POISSON_PERCENTILE: 49
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: Smooth muscle from wall of colon obtained during surgery and confirmed by pathology examination to be healthy tissue; DNA_Lib 930

value: Colon Smooth Muscle

value: Surgery

value: NL smooth muscle, colon rmvd as part of abdmnl Sarc.

value: Female

value: Colon

value: 56.0 Years

value: Abcam

value: Histone H3K27ac


title: ChIP-Seq analysis of H3K27ac in human HUES 6 cells; DNA_Lib 837

description:
sample_term_id: NTR_0000841
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 837
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.14603
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5644
****************
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: GSM1112776_BI.HUES6.H3K27ac.DNA_Lib_837.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 837.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of HUES6 Cell Line H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27ac ChIP-Seq on the HUES6 Cell Line, Library DNA_Lib 837, 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.17307
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: 21,015,892
FINDPEAKS_SCORE: 0.1701
FINDPEAKS_PERCENTILE: 18
HOTSPOT_SCORE: 0.2344
HOTSPOT_PERCENTILE: 20
IROC_SCORE: 0.9878
IROC_PERCENTILE: 32
POISSON_SCORE: 0.3021
POISSON_PERCENTILE: 13
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

ANALYSIS FILE NAME: GSM1112776_BI.HUES6.H3K27ac.DNA_Lib_837.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 837.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of HUES6 Cell Line H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27ac ChIP-Seq read mappings from the HUES6 Cell Line, Library DNA_Lib 837, 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.17490
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: HUES6 H3K27ac 37
BROWSER_TRACK_DESCRIPTION: BI HUES6 Cell Line Histone H3K27ac Library DNA_Lib 837 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 21,015,892
FINDPEAKS_SCORE: 0.1701
FINDPEAKS_PERCENTILE: 18
HOTSPOT_SCORE: 0.2344
HOTSPOT_PERCENTILE: 20
IROC_SCORE: 0.9878
IROC_PERCENTILE: 32
POISSON_SCORE: 0.3021
POISSON_PERCENTILE: 13
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

source_name: Harvard University Embryonic Stem Cells; DNA_Lib 837

value: HUES6 Cell Line

tag: lineage

value: embrionic stem cell

tag: medium

value: KSR

tag: passage

tag: line

value: HUES 6

tag: batch

value: ES cell HUES_6-2

value: Cell Line

value: undifferentiated

value: Unknown

value: Harvard University


title: ChIP-Seq analysis of H3K27ac in human substantia nigra cells; DNA_Lib 1060

description:
sample_term_id: UBERON_0002038
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 1060
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.14605
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9444
****************
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: GSM1112778_BI.Brain_Substantia_Nigra.H3K27ac.149.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 1060.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Brain Substantia Nigra H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27ac ChIP-Seq on Brain Substantia Nigra, Donor 149, were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.17324
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 26,067,386
FINDPEAKS_SCORE: 0.2736
FINDPEAKS_PERCENTILE: 35
HOTSPOT_SCORE: 0.316
HOTSPOT_PERCENTILE: 29
IROC_SCORE: 0.9908
IROC_PERCENTILE: 35
POISSON_SCORE: 0.4398
POISSON_PERCENTILE: 42
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1112778_BI.Brain_Substantia_Nigra.H3K27ac.149.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 1060.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Brain Substantia Nigra H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27ac ChIP-Seq read mappings from Brain Substantia Nigra, Donor 149, were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.17507
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: BSN H3K27ac 49 60
BROWSER_TRACK_DESCRIPTION: BI Brain Substantia Nigra Histone H3K27ac Donor 149 Library DNA_Lib 1060 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 26,067,386
FINDPEAKS_SCORE: 0.2736
FINDPEAKS_PERCENTILE: 35
HOTSPOT_SCORE: 0.316
HOTSPOT_PERCENTILE: 29
IROC_SCORE: 0.9908
IROC_PERCENTILE: 35
POISSON_SCORE: 0.4398
POISSON_PERCENTILE: 42
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: specified brain region obtained by post-mortem collection in a longitudinal study; DNA_Lib 1060

value: Brain, Substantia Nigra

value: Post-Mortem

value: no AD evident at demise

value: Substantia Nigra

value: Male

value: Primary Tissue

value: Brain

value: Rush University Medical Center

value: 81.0 Years

value: Protein A-Sepharose 4B

value: 0.5 to 3 million cells

value: cell/nuclei lysis

value: ~1 ug

value: 10 ul bed volume

value: Branson


title: ChIP-Seq analysis of WCE in human chondrogenic dif cells; DNA_Lib 839

description:
sample_term_id: CL_0000138
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 839
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.14604
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5949
****************
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: GSM1112777_BI.Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.Input.57.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 839.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Input ChIP-Seq on Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells, Donor 57, 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.17256
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 25,505,849
FINDPEAKS_SCORE: 0.0056
FINDPEAKS_PERCENTILE: 41
HOTSPOT_SCORE: 0.0187
HOTSPOT_PERCENTILE: 56
IROC_SCORE: 0.0
IROC_PERCENTILE: 26
POISSON_SCORE: 0.0597
POISSON_PERCENTILE: 48
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM1112777_BI.Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.Input.57.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 839.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Input ChIP-Seq read mappings from Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells, Donor 57, 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.17439
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: CfBMDMSC Input 57 39
BROWSER_TRACK_DESCRIPTION: BI Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells ChIP-Seq Input Donor 57 Library DNA_Lib 839 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 25,505,849
FINDPEAKS_SCORE: 0.0056
FINDPEAKS_PERCENTILE: 41
HOTSPOT_SCORE: 0.0187
HOTSPOT_PERCENTILE: 56
IROC_SCORE: 0.0
IROC_PERCENTILE: 26
POISSON_SCORE: 0.0597
POISSON_PERCENTILE: 48
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

source_name: chondrocytes derived via in vitro culture from mesenchymal stem cells; DNA_Lib 839

value: healthy

value: Medium:NA; Differentiation Method:alginate hydrogel scaffold (SR Herlofsen et al, Tissue Eng Part A. 2011)

value: chondrogenic dif cells

value: Unknown

value: Primary Cell Culture

value: Rikshospitalet University Hospital

value: standard

value: ChIP-Seq Input

value: Input


title: ChIP-Seq analysis of H3K27ac in human colonic mucosa cells; DNA_Lib 1047

description:
sample_term_id: UBERON_0000317
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 1047
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.14606
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.14740
****************
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: GSM1112779_BI.Colonic_Mucosa.H3K27ac.155.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 1047.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Colonic Mucosa H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27ac ChIP-Seq on Colonic Mucosa, Donor 155, 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.17260
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: 15,374,718
FINDPEAKS_SCORE: 0.3668
FINDPEAKS_PERCENTILE: 53
HOTSPOT_SCORE: 0.4161
HOTSPOT_PERCENTILE: 55
IROC_SCORE: 0.9962
IROC_PERCENTILE: 61
POISSON_SCORE: 0.4586
POISSON_PERCENTILE: 48
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

ANALYSIS FILE NAME: GSM1112779_BI.Colonic_Mucosa.H3K27ac.155.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 1047.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Colonic Mucosa H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27ac ChIP-Seq read mappings from Colonic Mucosa, Donor 155, 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.17443
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: CM H3K27ac 55 47
BROWSER_TRACK_DESCRIPTION: BI Colonic Mucosa Histone H3K27ac Donor 155 Library DNA_Lib 1047 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 15,374,718
FINDPEAKS_SCORE: 0.3668
FINDPEAKS_PERCENTILE: 53
HOTSPOT_SCORE: 0.4161
HOTSPOT_PERCENTILE: 55
IROC_SCORE: 0.9962
IROC_PERCENTILE: 61
POISSON_SCORE: 0.4586
POISSON_PERCENTILE: 48
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

source_name: Primary colonic mucosal tissue obtained during surgery and confirmed by pathology examination to be healthy tissue; DNA_Lib 1047

tag: sample alias

value: Colonic Mucosa

value: Surgery

value: NL colonic mucosa, colon rmvd as part of abmnl Sarc

value: Caucasian

value: Female

value: Primary Tissue

value: Colon

value: MGH

value: 56.0 Years

value: Active Motif

value: Histone H3K27ac


title: ChIP-Seq analysis of H3K27ac in human substantia nigra cells; DNA_Lib 1847

description:
sample_term_id: UBERON_0002038
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 1847
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.13171
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.13311
****************
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: GSM997258_BI.Brain_Substantia_Nigra.H3K27ac.149.DNA_Lib_1847.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 1847.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Brain Substantia Nigra H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27ac ChIP-Seq on Brain Substantia Nigra, Donor 149, were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.17225
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: 15,229,303
FINDPEAKS_SCORE: 0.3617
FINDPEAKS_PERCENTILE: 52
HOTSPOT_SCORE: 0.4049
HOTSPOT_PERCENTILE: 49
IROC_SCORE: 0.9959
IROC_PERCENTILE: 58
POISSON_SCORE: 0.4503
POISSON_PERCENTILE: 47
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM997258_BI.Brain_Substantia_Nigra.H3K27ac.149.DNA_Lib_1847.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 1847.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Brain Substantia Nigra H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27ac ChIP-Seq read mappings from Brain Substantia Nigra, Donor 149, were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.17408
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: BSN H3K27ac 49 47
BROWSER_TRACK_DESCRIPTION: BI Brain Substantia Nigra Histone H3K27ac Donor 149 Library DNA_Lib 1847 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 15,229,303
FINDPEAKS_SCORE: 0.3617
FINDPEAKS_PERCENTILE: 52
HOTSPOT_SCORE: 0.4049
HOTSPOT_PERCENTILE: 49
IROC_SCORE: 0.9959
IROC_PERCENTILE: 58
POISSON_SCORE: 0.4503
POISSON_PERCENTILE: 47
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: specified brain region obtained by post-mortem collection in a longitudinal study; DNA_Lib 1847

value: BioSam 752

value: Brain, Substantia Nigra

value: Post-Mortem

value: no AD evident at demise

tag: molecule

value: genomic DNA

value: Substantia Nigra

value: Male

value: Brain

value: Rush University Medical Center

value: 81.0 Years

value: Protein A-Sepharose 4B

value: 0.5 to 3 million cells

value: cell/nuclei lysis

value: ~1 ug

value: 10 ul bed volume

value: Branson


title: ChIP-Seq analysis of H3K4me3 in human CD25- CD45RA+ naive cells; DNA_Lib 2208

description:
sample_term_id: CL_0000492
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 2208
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.13169
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.13318
****************
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: GSM997256_BI.CD4+_CD25-_CD45RA+_Naive_Primary_Cells.H3K4me3.Donor_332.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 2208.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of CD4+ CD25- CD45RA+ Naive Primary Cells H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K4me3 ChIP-Seq on CD4+ CD25- CD45RA+ Naive Primary Cells, Donor Donor 332, 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.17309
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: 10,025,835
FINDPEAKS_SCORE: 0.4842
FINDPEAKS_PERCENTILE: 75
HOTSPOT_SCORE: 0.499
HOTSPOT_PERCENTILE: 73
IROC_SCORE: 0.9983
IROC_PERCENTILE: 9
POISSON_SCORE: 0.5114
POISSON_PERCENTILE: 79
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

ANALYSIS FILE NAME: GSM997256_BI.CD4+_CD25-_CD45RA+_Naive_Primary_Cells.H3K4me3.Donor_332.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 2208.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of CD4+ CD25- CD45RA+ Naive Primary Cells H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K4me3 ChIP-Seq read mappings from CD4+ CD25- CD45RA+ Naive Primary Cells, Donor Donor 332, 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.17492
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: CCCNN H3K4me3 32 08
BROWSER_TRACK_DESCRIPTION: BI CD4+ CD25- CD45RA+ Naive Primary Cells Histone H3K4me3 Donor 332 Library DNA_Lib 2208 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 10,025,835
FINDPEAKS_SCORE: 0.4842
FINDPEAKS_PERCENTILE: 75
HOTSPOT_SCORE: 0.499
HOTSPOT_PERCENTILE: 73
IROC_SCORE: 0.9983
IROC_PERCENTILE: 9
POISSON_SCORE: 0.5114
POISSON_PERCENTILE: 79
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: CD25- CD45RA+ naive is one of  CD4+  T cell subsets  that purified by microbeads, LS column and FACS ; DNA_Lib 2208

value: BioSam 718

value: CD4+ CD25- CD45RA+ Naive Primary Cells

value: normal

value: CD4+ T cell

value: CD25- CD45RA+ naive

value: Unknown

value: Primary Cell

value: Donor 332

value: Dana Farber

value: Millipore

value: Histone H3K4me3


title: ChIP-Seq analysis of H3K36me3 in human CD25- IL17- Th stim MACS cells; DNA_Lib 2259

description:
sample_term_id: CL_0000492
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 2259
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.13187
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.13309
****************
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: GSM997274_BI.CD4+_CD25-_IL17-_PMA-Ionomycin_stimulated_MACS_purified_Th_Primary_Cells.H3K36me3.Donor_332.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 2259.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of CD4+ CD25- IL17- PMA-Ionomycin stimulated MACS purified Th Primary Cells H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K36me3 ChIP-Seq on CD4+ CD25- IL17- PMA-Ionomycin stimulated MACS purified Th Primary Cells, Donor Donor 332, 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.17292
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: 14,514,010
FINDPEAKS_SCORE: 0.354
FINDPEAKS_PERCENTILE: 69
HOTSPOT_SCORE: 0.3535
HOTSPOT_PERCENTILE: 76
IROC_SCORE: 0.9865
IROC_PERCENTILE: 69
POISSON_SCORE: 0.5315
POISSON_PERCENTILE: 64
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

ANALYSIS FILE NAME: GSM997274_BI.CD4+_CD25-_IL17-_PMA-Ionomycin_stimulated_MACS_purified_Th_Primary_Cells.H3K36me3.Donor_332.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 2259.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of CD4+ CD25- IL17- PMA-Ionomycin stimulated MACS purified Th Primary Cells H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K36me3 ChIP-Seq read mappings from CD4+ CD25- IL17- PMA-Ionomycin stimulated MACS purified Th Primary Cells, Donor Donor 332, 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.17475
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: CCIPsMpT H3K36me3 32 59
BROWSER_TRACK_DESCRIPTION: BI CD4+ CD25- IL17- PMA-Ionomycin stimulated MACS purified Th Primary Cells Histone H3K36me3 Donor 332 Library DNA_Lib 2259 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 14,514,010
FINDPEAKS_SCORE: 0.354
FINDPEAKS_PERCENTILE: 69
HOTSPOT_SCORE: 0.3535
HOTSPOT_PERCENTILE: 76
IROC_SCORE: 0.9865
IROC_PERCENTILE: 69
POISSON_SCORE: 0.5315
POISSON_PERCENTILE: 64
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

source_name: CD25- IL17- Th stim MACS is one of  CD4+  T cell subsets  that purified by microbeads, LS column  ; DNA_Lib 2259

value: BioSam 720

value: genomic DNA

value: CD25- IL17- Th stim MACS

value: Protein A-Sepharose 4B

value: Abcam

value: Histone H3K36me3