title: ChIP-Seq analysis of H3K9me3 in human ADMSC undiff Day0 cells; Lib EpiLabSPL Row 1749

description:
sample_term_id: EFO_0005023
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib EpiLabSPL Row 1749
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8020
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.8180
****************
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: GSM772759_BI.Adipose_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K9me3.93.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib EpiLabSPL Row 1749.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Adipose Derived Mesenchymal Stem Cell Cultured Cells Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9me3 ChIP-Seq on Adipose Derived Mesenchymal Stem Cell Cultured Cells, Donor 93, 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.10718
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 26,538,416
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.0721
FINDPEAKS_PERCENTILE: 73
HOTSPOT_SCORE: 0.1594
HOTSPOT_PERCENTILE: 76
IROC_SCORE: 0.8145
IROC_PERCENTILE: 41
POISSON_SCORE: 0.402
POISSON_PERCENTILE: 82
MAXIMUM_REPLICATE_CORRELATION: 0.95

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

ANALYSIS FILE NAME: GSM772759_BI.Adipose_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K9me3.93.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib EpiLabSPL Row 1749.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Adipose Derived Mesenchymal Stem Cell Cultured Cells Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9me3 ChIP-Seq read mappings from Adipose Derived Mesenchymal Stem Cell Cultured Cells, Donor 93, 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.10982
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 5
BROWSER_TRACK_NAME: ADMSC H3K9me3 93 49
BROWSER_TRACK_DESCRIPTION: BI Adipose Derived Mesenchymal Stem Cell Cultured Cells Histone H3K9me3 Donor 93 Library Lib EpiLabSPL Row 1749 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 26,538,416
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.0721
FINDPEAKS_PERCENTILE: 73
HOTSPOT_SCORE: 0.1594
HOTSPOT_PERCENTILE: 76
IROC_SCORE: 0.8145
IROC_PERCENTILE: 41
POISSON_SCORE: 0.402
POISSON_PERCENTILE: 82
MAXIMUM_REPLICATE_CORRELATION: 0.95

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

source_name: Adherent cells derived following short term serial passage from adipose tissue; Lib EpiLabSPL Row 1749

value: Abcam

value: Histone H3K9me3


title: ChIP-Seq analysis of H3K4me1 in human ADMSC undiff Day0 cells; Lib EpiLabSPL Row 1744

status: Public on Dec 28 2011

type: SRA

city: Cambridge

first: BROAD

last: INSTITUTE

state: MA

country: USA

institute: Broad Institute

description:
sample_term_id: EFO_0005023
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib EpiLabSPL Row 1744
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8023
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.8180
****************
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: GSM772762_BI.Adipose_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K4me1.93.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib EpiLabSPL Row 1744.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Adipose Derived Mesenchymal Stem Cell Cultured Cells Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me1 ChIP-Seq on Adipose Derived Mesenchymal Stem Cell Cultured Cells, Donor 93, 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.10664
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 27,515,887
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.5205
FINDPEAKS_PERCENTILE: 93
HOTSPOT_SCORE: 0.5443
HOTSPOT_PERCENTILE: 94
IROC_SCORE: 0.9916
IROC_PERCENTILE: 70
POISSON_SCORE: 0.6789
POISSON_PERCENTILE: 96
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

ANALYSIS FILE NAME: GSM772762_BI.Adipose_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K4me1.93.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib EpiLabSPL Row 1744.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Adipose Derived Mesenchymal Stem Cell Cultured Cells Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me1 ChIP-Seq read mappings from Adipose Derived Mesenchymal Stem Cell Cultured Cells, Donor 93, 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.10928
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 5
BROWSER_TRACK_NAME: ADMSC H3K4me1 93 44
BROWSER_TRACK_DESCRIPTION: BI Adipose Derived Mesenchymal Stem Cell Cultured Cells Histone H3K4me1 Donor 93 Library Lib EpiLabSPL Row 1744 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 27,515,887
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.5205
FINDPEAKS_PERCENTILE: 93
HOTSPOT_SCORE: 0.5443
HOTSPOT_PERCENTILE: 94
IROC_SCORE: 0.9916
IROC_PERCENTILE: 70
POISSON_SCORE: 0.6789
POISSON_PERCENTILE: 96
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

molecule: genomic DNA

organism: Homo sapiens

source_name: Adherent cells derived following short term serial passage from adipose tissue; Lib EpiLabSPL Row 1744

extract_protocol: Library construction protocol: Single read - Illumina

tag: sample alias

tag: sample common name

tag: molecule

value: genomic DNA

tag: disease

tag: markers

value: ADMSC undiff Day0

value: Female

value: Primary Cell Culture

value: Harvard University

value: Protein A-Sepharose 4B

value: 10 million cells

value: SDS lysis

value: 70 ul bed volume

value: Histone H3K4me1

value: Bioruptor


title: ChIP-Seq analysis of H3K4me3 in human ADMSC undiff Day0 cells; Lib EpiLabSPL Row 1745

description:
sample_term_id: EFO_0005023
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib EpiLabSPL Row 1745
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8022
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.8180
****************
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: GSM772761_BI.Adipose_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K4me3.93.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib EpiLabSPL Row 1745.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Adipose Derived Mesenchymal Stem Cell Cultured Cells Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me3 ChIP-Seq on Adipose Derived Mesenchymal Stem Cell Cultured Cells, Donor 93, 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.10670
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 26,533,469
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.2734
FINDPEAKS_PERCENTILE: 59
HOTSPOT_SCORE: 0.3342
HOTSPOT_PERCENTILE: 56
IROC_SCORE: 0.9891
IROC_PERCENTILE: 24
POISSON_SCORE: 0.4222
POISSON_PERCENTILE: 65
MAXIMUM_REPLICATE_CORRELATION: 0.93

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

ANALYSIS FILE NAME: GSM772761_BI.Adipose_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K4me3.93.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib EpiLabSPL Row 1745.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Adipose Derived Mesenchymal Stem Cell Cultured Cells Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me3 ChIP-Seq read mappings from Adipose Derived Mesenchymal Stem Cell Cultured Cells, Donor 93, 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.10934
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 5
BROWSER_TRACK_NAME: ADMSC H3K4me3 93 45
BROWSER_TRACK_DESCRIPTION: BI Adipose Derived Mesenchymal Stem Cell Cultured Cells Histone H3K4me3 Donor 93 Library Lib EpiLabSPL Row 1745 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 26,533,469
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.2734
FINDPEAKS_PERCENTILE: 59
HOTSPOT_SCORE: 0.3342
HOTSPOT_PERCENTILE: 56
IROC_SCORE: 0.9891
IROC_PERCENTILE: 24
POISSON_SCORE: 0.4222
POISSON_PERCENTILE: 65
MAXIMUM_REPLICATE_CORRELATION: 0.93

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

source_name: Adherent cells derived following short term serial passage from adipose tissue; Lib EpiLabSPL Row 1745

value: Millipore

value: Histone H3K4me3


title: ChIP-Seq analysis of H3K4me1 in human AdiposeNuclei cells; Lib:XZ:20100731:22--ChIP:XZ:20100726:22:AdiposeNuclei:H3K4Me1

description:
sample_term_id: UBERON_0014455
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:XZ:20100731:22--ChIP:XZ:20100726:22:AdiposeNuclei:H3K4Me1
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8018
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5945
****************
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: GSM772757_BI.Adipose_Nuclei.H3K4me1.95.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100731:22--ChIP:XZ:20100726:22:AdiposeNuclei:H3K4Me1.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Adipose Nuclei Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me1 ChIP-Seq on Adipose Nuclei, Donor 95, 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.10763
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 28,205,425
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.5698
FINDPEAKS_PERCENTILE: 96
HOTSPOT_SCORE: 0.5675
HOTSPOT_PERCENTILE: 96
IROC_SCORE: 0.9972
IROC_PERCENTILE: 91
POISSON_SCORE: 0.6763
POISSON_PERCENTILE: 94
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

ANALYSIS FILE NAME: GSM772757_BI.Adipose_Nuclei.H3K4me1.95.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100731:22--ChIP:XZ:20100726:22:AdiposeNuclei:H3K4Me1.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Adipose Nuclei Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me1 ChIP-Seq read mappings from Adipose Nuclei, Donor 95, 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.11027
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 5
BROWSER_TRACK_NAME: AN H3K4me1 95
BROWSER_TRACK_DESCRIPTION: BI Adipose Nuclei Histone H3K4me1 Donor 95 Library Lib:XZ:20100731:22--ChIP:XZ:20100726:22:AdiposeNuclei:H3K4Me1 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 28,205,425
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.5698
FINDPEAKS_PERCENTILE: 96
HOTSPOT_SCORE: 0.5675
HOTSPOT_PERCENTILE: 96
IROC_SCORE: 0.9972
IROC_PERCENTILE: 91
POISSON_SCORE: 0.6763
POISSON_PERCENTILE: 94
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

source_name: Nuclei derived from crude preps of adipose tissue; Lib:XZ:20100731:22--ChIP:XZ:20100726:22:AdiposeNuclei:H3K4Me1

value: Adipose Nuclei

value: surgery

value: Primary Tissue

value: abdomen


title: ChIP-Seq analysis of H3K4me1 in human Duodenum smooth muscle cells; DNA_Lib 459

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 459
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8527
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9450
****************
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: GSM772837_BI.Duodenum_Smooth_Muscle.H3K4me1.160.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 459-DNA_Lib 459-DNA_Lib 459-DNA_Lib 459.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Duodenum Smooth Muscle Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me1 ChIP-Seq on Duodenum Smooth Muscle, Donor 160, 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.10745
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 36,283,429
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.0047
FINDPEAKS_PERCENTILE: 6
HOTSPOT_SCORE: 0.0962
HOTSPOT_PERCENTILE: 4
IROC_SCORE: 0.6635
IROC_PERCENTILE: 4
POISSON_SCORE: 0.2236
POISSON_PERCENTILE: 2
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM772837_BI.Duodenum_Smooth_Muscle.H3K4me1.160.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 459-DNA_Lib 459-DNA_Lib 459-DNA_Lib 459.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Duodenum Smooth Muscle Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me1 ChIP-Seq read mappings from Duodenum Smooth Muscle, Donor 160, 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.11009
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 5
BROWSER_TRACK_NAME: DSM H3K4me1 60 59
BROWSER_TRACK_DESCRIPTION: BI Duodenum Smooth Muscle Histone H3K4me1 Donor 160 Library DNA_Lib 459 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 36,283,429
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.0047
FINDPEAKS_PERCENTILE: 6
HOTSPOT_SCORE: 0.0962
HOTSPOT_PERCENTILE: 4
IROC_SCORE: 0.6635
IROC_PERCENTILE: 4
POISSON_SCORE: 0.2236
POISSON_PERCENTILE: 2
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: Primary duodenum smooth muscle tissue; DNA_Lib 459

value: Duodenum Smooth Muscle

value: Surgery

value: NL smooth muscle, duodenum rmvd as part of pancr.,VA

value: genomic DNA

value: Smooth Muscle

value: Caucasian

value: Male

value: Duodenum

value: MGH

value: 59.0 Years

value: 0.5 to 3 million cells

value: cell/nuclei lysis

value: ~1 ug

value: 10 ul bed volume

value: Abcam

value: Branson


title: ChIP-Seq analysis of H3K4me3 in human Duodenum smooth muscle cells; DNA_Lib 457

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 457
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8529
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9450
****************
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: GSM772839_BI.Duodenum_Smooth_Muscle.H3K4me3.160.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 457-DNA_Lib 457-DNA_Lib 457-DNA_Lib 457.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Duodenum Smooth Muscle Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me3 ChIP-Seq on Duodenum Smooth Muscle, Donor 160, 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.10741
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 36,792,677
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.1641
FINDPEAKS_PERCENTILE: 28
HOTSPOT_SCORE: 0.1923
HOTSPOT_PERCENTILE: 24
IROC_SCORE: 0.9995
IROC_PERCENTILE: 63
POISSON_SCORE: 0.2339
POISSON_PERCENTILE: 22
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM772839_BI.Duodenum_Smooth_Muscle.H3K4me3.160.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 457-DNA_Lib 457-DNA_Lib 457-DNA_Lib 457.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Duodenum Smooth Muscle Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me3 ChIP-Seq read mappings from Duodenum Smooth Muscle, Donor 160, 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.11005
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 5
BROWSER_TRACK_NAME: DSM H3K4me3 60 57
BROWSER_TRACK_DESCRIPTION: BI Duodenum Smooth Muscle Histone H3K4me3 Donor 160 Library DNA_Lib 457 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 36,792,677
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.1641
FINDPEAKS_PERCENTILE: 28
HOTSPOT_SCORE: 0.1923
HOTSPOT_PERCENTILE: 24
IROC_SCORE: 0.9995
IROC_PERCENTILE: 63
POISSON_SCORE: 0.2339
POISSON_PERCENTILE: 22
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: Primary duodenum smooth muscle tissue; DNA_Lib 457

value: Primary Tissue

value: Protein A-Sepharose 4B

value: Millipore

value: Histone H3K4me3


title: ChIP-Seq analysis of H3K4me3 in human ADMSC undiff Day0 cells; Lib EpiLabSPL Row 1729

description:
sample_term_id: EFO_0005023
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib EpiLabSPL Row 1729
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8008
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.8179
****************
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: GSM772747_BI.Adipose_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K4me3.92.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib EpiLabSPL Row 1729.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Adipose Derived Mesenchymal Stem Cell Cultured Cells Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me3 ChIP-Seq on Adipose Derived Mesenchymal Stem Cell Cultured Cells, Donor 92, 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.10667
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 28,898,337
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.5063
FINDPEAKS_PERCENTILE: 87
HOTSPOT_SCORE: 0.5236
HOTSPOT_PERCENTILE: 85
IROC_SCORE: 0.9966
IROC_PERCENTILE: 33
POISSON_SCORE: 0.5549
POISSON_PERCENTILE: 91
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM772747_BI.Adipose_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K4me3.92.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib EpiLabSPL Row 1729.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Adipose Derived Mesenchymal Stem Cell Cultured Cells Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me3 ChIP-Seq read mappings from Adipose Derived Mesenchymal Stem Cell Cultured Cells, Donor 92, 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.10931
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 5
BROWSER_TRACK_NAME: ADMSC H3K4me3 92 29
BROWSER_TRACK_DESCRIPTION: BI Adipose Derived Mesenchymal Stem Cell Cultured Cells Histone H3K4me3 Donor 92 Library Lib EpiLabSPL Row 1729 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 28,898,337
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.5063
FINDPEAKS_PERCENTILE: 87
HOTSPOT_SCORE: 0.5236
HOTSPOT_PERCENTILE: 85
IROC_SCORE: 0.9966
IROC_PERCENTILE: 33
POISSON_SCORE: 0.5549
POISSON_PERCENTILE: 91
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

source_name: Adherent cells derived following short term serial passage from adipose tissue; Lib EpiLabSPL Row 1729

value: genomic DNA

value: ADMSC undiff Day0

value: Female

value: Primary Cell Culture

value: Harvard University

value: 10 million cells

value: SDS lysis

value: 70 ul bed volume

value: Bioruptor


title: ChIP-Seq analysis of H3K9ac in human ADMSC undiff Day0 cells; Lib EpiLabSPL Row 1748

description:
sample_term_id: EFO_0005023
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib EpiLabSPL Row 1748
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8021
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.8180
****************
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: GSM772760_BI.Adipose_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K9ac.93.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib EpiLabSPL Row 1748.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Adipose Derived Mesenchymal Stem Cell Cultured Cells Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9ac ChIP-Seq on Adipose Derived Mesenchymal Stem Cell Cultured Cells, Donor 93, 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.10791
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 22,560,175
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 19
FINDPEAKS_SCORE: 0.2871
FINDPEAKS_PERCENTILE: 84
HOTSPOT_SCORE: 0.3453
HOTSPOT_PERCENTILE: 84
IROC_SCORE: 0.9935
IROC_PERCENTILE: 47
POISSON_SCORE: 0.4055
POISSON_PERCENTILE: 84
MAXIMUM_REPLICATE_CORRELATION: 0.95

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

ANALYSIS FILE NAME: GSM772760_BI.Adipose_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K9ac.93.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib EpiLabSPL Row 1748.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Adipose Derived Mesenchymal Stem Cell Cultured Cells Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9ac ChIP-Seq read mappings from Adipose Derived Mesenchymal Stem Cell Cultured Cells, Donor 93, 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.11055
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 5
BROWSER_TRACK_NAME: ADMSC H3K9ac 93 48
BROWSER_TRACK_DESCRIPTION: BI Adipose Derived Mesenchymal Stem Cell Cultured Cells Histone H3K9ac Donor 93 Library Lib EpiLabSPL Row 1748 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 22,560,175
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 19
FINDPEAKS_SCORE: 0.2871
FINDPEAKS_PERCENTILE: 84
HOTSPOT_SCORE: 0.3453
HOTSPOT_PERCENTILE: 84
IROC_SCORE: 0.9935
IROC_PERCENTILE: 47
POISSON_SCORE: 0.4055
POISSON_PERCENTILE: 84
MAXIMUM_REPLICATE_CORRELATION: 0.95

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

source_name: Adherent cells derived following short term serial passage from adipose tissue; Lib EpiLabSPL Row 1748

value: Histone H3K9ac


title: ChIP-Seq analysis of H3K36me3 in human Duodenum smooth muscle cells; DNA_Lib 458

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 458
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8528
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9450
****************
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: GSM772838_BI.Duodenum_Smooth_Muscle.H3K36me3.160.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 458-DNA_Lib 458-DNA_Lib 458-DNA_Lib 458.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Duodenum Smooth Muscle Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K36me3 ChIP-Seq on Duodenum Smooth Muscle, Donor 160, 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.10780
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 33,657,257
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.0652
FINDPEAKS_PERCENTILE: 33
HOTSPOT_SCORE: 0.1696
HOTSPOT_PERCENTILE: 33
IROC_SCORE: 0.9053
IROC_PERCENTILE: 39
POISSON_SCORE: 0.3375
POISSON_PERCENTILE: 41
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM772838_BI.Duodenum_Smooth_Muscle.H3K36me3.160.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 458-DNA_Lib 458-DNA_Lib 458-DNA_Lib 458.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Duodenum Smooth Muscle Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K36me3 ChIP-Seq read mappings from Duodenum Smooth Muscle, Donor 160, 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.11044
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 5
BROWSER_TRACK_NAME: DSM H3K36me3 60 58
BROWSER_TRACK_DESCRIPTION: BI Duodenum Smooth Muscle Histone H3K36me3 Donor 160 Library DNA_Lib 458 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 33,657,257
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.0652
FINDPEAKS_PERCENTILE: 33
HOTSPOT_SCORE: 0.1696
HOTSPOT_PERCENTILE: 33
IROC_SCORE: 0.9053
IROC_PERCENTILE: 39
POISSON_SCORE: 0.3375
POISSON_PERCENTILE: 41
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: Primary duodenum smooth muscle tissue; DNA_Lib 458

value: Duodenum Smooth Muscle

value: Surgery

value: NL smooth muscle, duodenum rmvd as part of pancr.,VA

value: Smooth Muscle

value: Caucasian

value: Male

value: Duodenum

value: MGH

value: 59.0 Years

value: 0.5 to 3 million cells

value: cell/nuclei lysis

value: ~1 ug

value: 10 ul bed volume

value: Histone H3K36me3


title: ChIP-Seq analysis of H3K4me3 in human ADMSC Diff Day20 cells; Lib EpiLabSPL Row 1751

description:
sample_term_id: CL_0000136
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib EpiLabSPL Row 1751
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8007
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.8182
****************
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: GSM772746_BI.Mesenchymal_Stem_Cell_Derived_Adipocyte_Cultured_Cells.H3K4me3.93.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib EpiLabSPL Row 1751.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Mesenchymal Stem Cell Derived Adipocyte Cultured Cells Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me3 ChIP-Seq on Mesenchymal Stem Cell Derived Adipocyte Cultured Cells, Donor 93, 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.10685
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 26,717,070
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.3826
FINDPEAKS_PERCENTILE: 74
HOTSPOT_SCORE: 0.428
HOTSPOT_PERCENTILE: 76
IROC_SCORE: 0.9884
IROC_PERCENTILE: 22
POISSON_SCORE: 0.4946
POISSON_PERCENTILE: 81
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

ANALYSIS FILE NAME: GSM772746_BI.Mesenchymal_Stem_Cell_Derived_Adipocyte_Cultured_Cells.H3K4me3.93.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib EpiLabSPL Row 1751.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Mesenchymal Stem Cell Derived Adipocyte Cultured Cells Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me3 ChIP-Seq read mappings from Mesenchymal Stem Cell Derived Adipocyte Cultured Cells, Donor 93, 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.10949
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 5
BROWSER_TRACK_NAME: MSCDA H3K4me3 93 51
BROWSER_TRACK_DESCRIPTION: BI Mesenchymal Stem Cell Derived Adipocyte Cultured Cells Histone H3K4me3 Donor 93 Library Lib EpiLabSPL Row 1751 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 26,717,070
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.3826
FINDPEAKS_PERCENTILE: 74
HOTSPOT_SCORE: 0.428
HOTSPOT_PERCENTILE: 76
IROC_SCORE: 0.9884
IROC_PERCENTILE: 22
POISSON_SCORE: 0.4946
POISSON_PERCENTILE: 81
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

source_name: Adipose-derived mesenchymal stem cells were cultured in adipocyte differentiation medium for 20 days; Lib EpiLabSPL Row 1751

value: genomic DNA

value: Differentiation Method:Mesenchymal stem cells were differentiated into adipocytes by using 3-isobutyl-1-methyl xanthine (IBMX), rosiglitazone, insulin, and dexamethasone

value: ADMSC Diff Day20

value: Female

value: Primary Cell Culture

value: Harvard University

value: Protein A-Sepharose 4B

value: 10 million cells

value: SDS lysis

value: 70 ul bed volume

value: Millipore

value: Histone H3K4me3


title: ChIP-Seq analysis of H3K4me1 in human ADMSC undiff Day0 cells; Lib EpiLabSPL Row 1728

description:
sample_term_id: EFO_0005023
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib EpiLabSPL Row 1728
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8009
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.8179
****************
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: GSM772748_BI.Adipose_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K4me1.92.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib EpiLabSPL Row 1728.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Adipose Derived Mesenchymal Stem Cell Cultured Cells Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me1 ChIP-Seq on Adipose Derived Mesenchymal Stem Cell Cultured Cells, Donor 92, 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.10661
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 32,352,465
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.6078
FINDPEAKS_PERCENTILE: 98
HOTSPOT_SCORE: 0.5938
HOTSPOT_PERCENTILE: 98
IROC_SCORE: 0.9958
IROC_PERCENTILE: 81
POISSON_SCORE: 0.7242
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

ANALYSIS FILE NAME: GSM772748_BI.Adipose_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K4me1.92.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib EpiLabSPL Row 1728.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Adipose Derived Mesenchymal Stem Cell Cultured Cells Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me1 ChIP-Seq read mappings from Adipose Derived Mesenchymal Stem Cell Cultured Cells, Donor 92, 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.10925
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 5
BROWSER_TRACK_NAME: ADMSC H3K4me1 92 28
BROWSER_TRACK_DESCRIPTION: BI Adipose Derived Mesenchymal Stem Cell Cultured Cells Histone H3K4me1 Donor 92 Library Lib EpiLabSPL Row 1728 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 32,352,465
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.6078
FINDPEAKS_PERCENTILE: 98
HOTSPOT_SCORE: 0.5938
HOTSPOT_PERCENTILE: 98
IROC_SCORE: 0.9958
IROC_PERCENTILE: 81
POISSON_SCORE: 0.7242
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

source_name: Adherent cells derived following short term serial passage from adipose tissue; Lib EpiLabSPL Row 1728

value: ADMSC undiff Day0

value: Abcam

value: Histone H3K4me1

value: Bioruptor


title: ChIP-Seq analysis of H3K36me3 in human ADMSC Diff Day20 cells; Lib EpiLabSPL Row 1752

description:
sample_term_id: CL_0000136
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib EpiLabSPL Row 1752
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8004
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.8182
****************
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: GSM772743_BI.Mesenchymal_Stem_Cell_Derived_Adipocyte_Cultured_Cells.H3K36me3.93.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib EpiLabSPL Row 1752.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Mesenchymal Stem Cell Derived Adipocyte Cultured Cells Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K36me3 ChIP-Seq on Mesenchymal Stem Cell Derived Adipocyte Cultured Cells, Donor 93, 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.10680
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 21,057,686
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.2463
FINDPEAKS_PERCENTILE: 65
HOTSPOT_SCORE: 0.2758
HOTSPOT_PERCENTILE: 65
IROC_SCORE: 0.9727
IROC_PERCENTILE: 61
POISSON_SCORE: 0.4297
POISSON_PERCENTILE: 61
MAXIMUM_REPLICATE_CORRELATION: 0.93

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

ANALYSIS FILE NAME: GSM772743_BI.Mesenchymal_Stem_Cell_Derived_Adipocyte_Cultured_Cells.H3K36me3.93.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib EpiLabSPL Row 1752.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Mesenchymal Stem Cell Derived Adipocyte Cultured Cells Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K36me3 ChIP-Seq read mappings from Mesenchymal Stem Cell Derived Adipocyte Cultured Cells, Donor 93, 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.10944
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 5
BROWSER_TRACK_NAME: MSCDA H3K36me3 93 52
BROWSER_TRACK_DESCRIPTION: BI Mesenchymal Stem Cell Derived Adipocyte Cultured Cells Histone H3K36me3 Donor 93 Library Lib EpiLabSPL Row 1752 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 21,057,686
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.2463
FINDPEAKS_PERCENTILE: 65
HOTSPOT_SCORE: 0.2758
HOTSPOT_PERCENTILE: 65
IROC_SCORE: 0.9727
IROC_PERCENTILE: 61
POISSON_SCORE: 0.4297
POISSON_PERCENTILE: 61
MAXIMUM_REPLICATE_CORRELATION: 0.93

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

source_name: Adipose-derived mesenchymal stem cells were cultured in adipocyte differentiation medium for 20 days; Lib EpiLabSPL Row 1752

value: Histone H3K36me3


title: ChIP-Seq analysis of WCE in human ADMSC undiff Day0 cells; Lib EpiLabSPL Row 1756

description:
sample_term_id: EFO_0005023
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib EpiLabSPL Row 1756
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8000
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.8180
****************
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: GSM772739_BI.Adipose_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.Input.93.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib EpiLabSPL Row 1756.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Adipose Derived Mesenchymal Stem Cell Cultured Cells ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on Adipose Derived Mesenchymal Stem Cell Cultured Cells, Donor 93, 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.10663
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 34,533,722
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 56
FINDPEAKS_SCORE: 0.0044
FINDPEAKS_PERCENTILE: 26
HOTSPOT_SCORE: 0.0037
HOTSPOT_PERCENTILE: 18
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.0252
POISSON_PERCENTILE: 11
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

ANALYSIS FILE NAME: GSM772739_BI.Adipose_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.Input.93.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib EpiLabSPL Row 1756.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Adipose Derived Mesenchymal Stem Cell Cultured Cells ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from Adipose Derived Mesenchymal Stem Cell Cultured Cells, Donor 93, 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.10927
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 5
BROWSER_TRACK_NAME: ADMSC Input 93 56
BROWSER_TRACK_DESCRIPTION: BI Adipose Derived Mesenchymal Stem Cell Cultured Cells ChIP-Seq Input Donor 93 Library Lib EpiLabSPL Row 1756 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 34,533,722
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 56
FINDPEAKS_SCORE: 0.0044
FINDPEAKS_PERCENTILE: 26
HOTSPOT_SCORE: 0.0037
HOTSPOT_PERCENTILE: 18
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.0252
POISSON_PERCENTILE: 11
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

source_name: Adherent cells derived following short term serial passage from adipose tissue; Lib EpiLabSPL Row 1756

value: genomic DNA

value: standard

value: ChIP-Seq Input

value: Input


title: ChIP-Seq analysis of WCE in human ADMSC Diff Day20 cells; Lib EpiLabSPL Row 1757

description:
sample_term_id: CL_0000136
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib EpiLabSPL Row 1757
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8001
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.8182
****************
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: GSM772740_BI.Mesenchymal_Stem_Cell_Derived_Adipocyte_Cultured_Cells.Input.93.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib EpiLabSPL Row 1757.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Mesenchymal Stem Cell Derived Adipocyte Cultured Cells ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on Mesenchymal Stem Cell Derived Adipocyte Cultured Cells, Donor 93, 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.10743
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 36,969,381
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 56
FINDPEAKS_SCORE: 0.0047
FINDPEAKS_PERCENTILE: 34
HOTSPOT_SCORE: 0.0044
HOTSPOT_PERCENTILE: 23
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.0324
POISSON_PERCENTILE: 21
MAXIMUM_REPLICATE_CORRELATION: 0.95

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

ANALYSIS FILE NAME: GSM772740_BI.Mesenchymal_Stem_Cell_Derived_Adipocyte_Cultured_Cells.Input.93.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib EpiLabSPL Row 1757.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Mesenchymal Stem Cell Derived Adipocyte Cultured Cells ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from Mesenchymal Stem Cell Derived Adipocyte Cultured Cells, Donor 93, 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.11007
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 5
BROWSER_TRACK_NAME: MSCDA Input 93 57
BROWSER_TRACK_DESCRIPTION: BI Mesenchymal Stem Cell Derived Adipocyte Cultured Cells ChIP-Seq Input Donor 93 Library Lib EpiLabSPL Row 1757 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 36,969,381
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 56
FINDPEAKS_SCORE: 0.0047
FINDPEAKS_PERCENTILE: 34
HOTSPOT_SCORE: 0.0044
HOTSPOT_PERCENTILE: 23
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.0324
POISSON_PERCENTILE: 21
MAXIMUM_REPLICATE_CORRELATION: 0.95

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

source_name: Adipose-derived mesenchymal stem cells were cultured in adipocyte differentiation medium for 20 days; Lib EpiLabSPL Row 1757

value: Differentiation Method:Mesenchymal stem cells were differentiated into adipocytes by using 3-isobutyl-1-methyl xanthine (IBMX), rosiglitazone, insulin, and dexamethasone

value: ADMSC Diff Day20

value: Female

value: Primary Cell Culture


title: ChIP-Seq analysis of H3K27me3 in human CD45RO CD4 cells; DNA_Lib 484

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 484
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8545
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9464
****************
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: GSM772855_BI.CD4_Memory_Primary_Cells.H3K27me3.Donor_101_8_pooled_leukopaks_Jan_20_2011.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 484-DNA_Lib 484-DNA_Lib 484-DNA_Lib 484.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of CD4 Memory Primary Cells Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27me3 ChIP-Seq on CD4 Memory Primary Cells, Donor Donor 101 8 pooled leukopaks Jan 20 2011, 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.10818
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 19,464,225
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.006
FINDPEAKS_PERCENTILE: 6
HOTSPOT_SCORE: 0.0756
HOTSPOT_PERCENTILE: 8
IROC_SCORE: 0.668
IROC_PERCENTILE: 18
POISSON_SCORE: 0.1535
POISSON_PERCENTILE: 10
MAXIMUM_REPLICATE_CORRELATION: 0.92

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

ANALYSIS FILE NAME: GSM772855_BI.CD4_Memory_Primary_Cells.H3K27me3.Donor_101_8_pooled_leukopaks_Jan_20_2011.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 484-DNA_Lib 484-DNA_Lib 484-DNA_Lib 484.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of CD4 Memory Primary Cells Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27me3 ChIP-Seq read mappings from CD4 Memory Primary Cells, Donor Donor 101 8 pooled leukopaks Jan 20 2011, 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.11082
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 5
BROWSER_TRACK_NAME: CD4M H3K27me3 01 84
BROWSER_TRACK_DESCRIPTION: BI CD4 Memory Primary Cells Histone H3K27me3 Donor 101 8 pooled leukopaks Jan 20 2011 Library DNA_Lib 484 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 19,464,225
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.006
FINDPEAKS_PERCENTILE: 6
HOTSPOT_SCORE: 0.0756
HOTSPOT_PERCENTILE: 8
IROC_SCORE: 0.668
IROC_PERCENTILE: 18
POISSON_SCORE: 0.1535
POISSON_PERCENTILE: 10
MAXIMUM_REPLICATE_CORRELATION: 0.92

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

source_name: Memory CD4+ T cells; DNA_Lib 484

value: BioSam 185

value: CD4 Memory Primary Cells

value: presumed normal

value: CD45RO CD4

value: Unknown

value: Primary Cell

value: Dana Farber

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: Histone H3K27me3

value: Branson


title: ChIP-Seq analysis of H3K9me3 in human ADMSC Diff Day20 cells; Lib EpiLabSPL Row 1755

description:
sample_term_id: CL_0000136
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib EpiLabSPL Row 1755
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8003
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.8182
****************
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: GSM772742_BI.Mesenchymal_Stem_Cell_Derived_Adipocyte_Cultured_Cells.H3K9me3.93.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib EpiLabSPL Row 1755.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Mesenchymal Stem Cell Derived Adipocyte Cultured Cells Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9me3 ChIP-Seq on Mesenchymal Stem Cell Derived Adipocyte Cultured Cells, Donor 93, 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.10758
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 25,200,608
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.1053
FINDPEAKS_PERCENTILE: 84
HOTSPOT_SCORE: 0.1719
HOTSPOT_PERCENTILE: 82
IROC_SCORE: 0.9021
IROC_PERCENTILE: 71
POISSON_SCORE: 0.3415
POISSON_PERCENTILE: 76
MAXIMUM_REPLICATE_CORRELATION: 0.95

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

ANALYSIS FILE NAME: GSM772742_BI.Mesenchymal_Stem_Cell_Derived_Adipocyte_Cultured_Cells.H3K9me3.93.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib EpiLabSPL Row 1755.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Mesenchymal Stem Cell Derived Adipocyte Cultured Cells Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9me3 ChIP-Seq read mappings from Mesenchymal Stem Cell Derived Adipocyte Cultured Cells, Donor 93, 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.11022
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 5
BROWSER_TRACK_NAME: MSCDA H3K9me3 93 55
BROWSER_TRACK_DESCRIPTION: BI Mesenchymal Stem Cell Derived Adipocyte Cultured Cells Histone H3K9me3 Donor 93 Library Lib EpiLabSPL Row 1755 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 25,200,608
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.1053
FINDPEAKS_PERCENTILE: 84
HOTSPOT_SCORE: 0.1719
HOTSPOT_PERCENTILE: 82
IROC_SCORE: 0.9021
IROC_PERCENTILE: 71
POISSON_SCORE: 0.3415
POISSON_PERCENTILE: 76
MAXIMUM_REPLICATE_CORRELATION: 0.95

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

source_name: Adipose-derived mesenchymal stem cells were cultured in adipocyte differentiation medium for 20 days; Lib EpiLabSPL Row 1755

value: genomic DNA

value: Differentiation Method:Mesenchymal stem cells were differentiated into adipocytes by using 3-isobutyl-1-methyl xanthine (IBMX), rosiglitazone, insulin, and dexamethasone

value: ADMSC Diff Day20

value: Harvard University

value: 10 million cells

value: SDS lysis

value: 70 ul bed volume

value: Abcam

value: Histone H3K9me3

value: Bioruptor


title: ChIP-Seq analysis of H3K9ac in human ADMSC Diff Day20 cells; Lib EpiLabSPL Row 1754

description:
sample_term_id: CL_0000136
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib EpiLabSPL Row 1754
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8002
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.8182
****************
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: GSM772741_BI.Mesenchymal_Stem_Cell_Derived_Adipocyte_Cultured_Cells.H3K9ac.93.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib EpiLabSPL Row 1754.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Mesenchymal Stem Cell Derived Adipocyte Cultured Cells Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9ac ChIP-Seq on Mesenchymal Stem Cell Derived Adipocyte Cultured Cells, Donor 93, 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.10847
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 23,874,748
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 19
FINDPEAKS_SCORE: 0.3186
FINDPEAKS_PERCENTILE: 89
HOTSPOT_SCORE: 0.3652
HOTSPOT_PERCENTILE: 89
IROC_SCORE: 0.9963
IROC_PERCENTILE: 58
POISSON_SCORE: 0.412
POISSON_PERCENTILE: 89
MAXIMUM_REPLICATE_CORRELATION: 0.94

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

ANALYSIS FILE NAME: GSM772741_BI.Mesenchymal_Stem_Cell_Derived_Adipocyte_Cultured_Cells.H3K9ac.93.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib EpiLabSPL Row 1754.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Mesenchymal Stem Cell Derived Adipocyte Cultured Cells Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9ac ChIP-Seq read mappings from Mesenchymal Stem Cell Derived Adipocyte Cultured Cells, Donor 93, 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.11111
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 5
BROWSER_TRACK_NAME: MSCDA H3K9ac 93 54
BROWSER_TRACK_DESCRIPTION: BI Mesenchymal Stem Cell Derived Adipocyte Cultured Cells Histone H3K9ac Donor 93 Library Lib EpiLabSPL Row 1754 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 23,874,748
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 19
FINDPEAKS_SCORE: 0.3186
FINDPEAKS_PERCENTILE: 89
HOTSPOT_SCORE: 0.3652
HOTSPOT_PERCENTILE: 89
IROC_SCORE: 0.9963
IROC_PERCENTILE: 58
POISSON_SCORE: 0.412
POISSON_PERCENTILE: 89
MAXIMUM_REPLICATE_CORRELATION: 0.94

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

source_name: Adipose-derived mesenchymal stem cells were cultured in adipocyte differentiation medium for 20 days; Lib EpiLabSPL Row 1754

value: Female

value: Primary Cell Culture

value: Protein A-Sepharose 4B

value: Histone H3K9ac


title: ChIP-Seq analysis of H3K4me1 in human ADMSC Diff Day20 cells; Lib EpiLabSPL Row 1750

description:
sample_term_id: CL_0000136
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib EpiLabSPL Row 1750
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8006
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.8182
****************
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: GSM772745_BI.Mesenchymal_Stem_Cell_Derived_Adipocyte_Cultured_Cells.H3K4me1.93.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib EpiLabSPL Row 1750.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Mesenchymal Stem Cell Derived Adipocyte Cultured Cells Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me1 ChIP-Seq on Mesenchymal Stem Cell Derived Adipocyte Cultured Cells, Donor 93, 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.10717
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 22,598,812
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.34
FINDPEAKS_PERCENTILE: 76
HOTSPOT_SCORE: 0.4149
HOTSPOT_PERCENTILE: 78
IROC_SCORE: 0.9786
IROC_PERCENTILE: 56
POISSON_SCORE: 0.5225
POISSON_PERCENTILE: 76
MAXIMUM_REPLICATE_CORRELATION: 0.9

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

ANALYSIS FILE NAME: GSM772745_BI.Mesenchymal_Stem_Cell_Derived_Adipocyte_Cultured_Cells.H3K4me1.93.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib EpiLabSPL Row 1750.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Mesenchymal Stem Cell Derived Adipocyte Cultured Cells Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me1 ChIP-Seq read mappings from Mesenchymal Stem Cell Derived Adipocyte Cultured Cells, Donor 93, 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.10981
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 5
BROWSER_TRACK_NAME: MSCDA H3K4me1 93 50
BROWSER_TRACK_DESCRIPTION: BI Mesenchymal Stem Cell Derived Adipocyte Cultured Cells Histone H3K4me1 Donor 93 Library Lib EpiLabSPL Row 1750 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 22,598,812
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.34
FINDPEAKS_PERCENTILE: 76
HOTSPOT_SCORE: 0.4149
HOTSPOT_PERCENTILE: 78
IROC_SCORE: 0.9786
IROC_PERCENTILE: 56
POISSON_SCORE: 0.5225
POISSON_PERCENTILE: 76
MAXIMUM_REPLICATE_CORRELATION: 0.9

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

source_name: Adipose-derived mesenchymal stem cells were cultured in adipocyte differentiation medium for 20 days; Lib EpiLabSPL Row 1750

value: Histone H3K4me1


title: ChIP-Seq analysis of H3K27me3 in human Duodenum smooth muscle cells; DNA_Lib 456

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 456
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8530
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9450
****************
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: GSM772840_BI.Duodenum_Smooth_Muscle.H3K27me3.160.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 456-DNA_Lib 456-DNA_Lib 456-DNA_Lib 456.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Duodenum Smooth Muscle Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27me3 ChIP-Seq on Duodenum Smooth Muscle, Donor 160, 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.10753
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 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 35,928,745
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.0057
FINDPEAKS_PERCENTILE: 4
HOTSPOT_SCORE: 0.0363
HOTSPOT_PERCENTILE: 4
IROC_SCORE: 0.8126
IROC_PERCENTILE: 53
POISSON_SCORE: 0.1159
POISSON_PERCENTILE: 6
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM772840_BI.Duodenum_Smooth_Muscle.H3K27me3.160.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 456-DNA_Lib 456-DNA_Lib 456-DNA_Lib 456.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Duodenum Smooth Muscle Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27me3 ChIP-Seq read mappings from Duodenum Smooth Muscle, Donor 160, 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.11017
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 5
BROWSER_TRACK_NAME: DSM H3K27me3 60 56
BROWSER_TRACK_DESCRIPTION: BI Duodenum Smooth Muscle Histone H3K27me3 Donor 160 Library DNA_Lib 456 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 35,928,745
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.0057
FINDPEAKS_PERCENTILE: 4
HOTSPOT_SCORE: 0.0363
HOTSPOT_PERCENTILE: 4
IROC_SCORE: 0.8126
IROC_PERCENTILE: 53
POISSON_SCORE: 0.1159
POISSON_PERCENTILE: 6
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: Primary duodenum smooth muscle tissue; DNA_Lib 456

value: Duodenum Smooth Muscle

value: Surgery

value: NL smooth muscle, duodenum rmvd as part of pancr.,VA

value: Smooth Muscle

value: Caucasian

value: Male

value: Primary Tissue

value: Duodenum

value: MGH

value: 59.0 Years

value: 0.5 to 3 million cells

value: cell/nuclei lysis

value: ~1 ug

value: 10 ul bed volume

value: Millipore

value: Histone H3K27me3


title: Bisulfite-Seq analysis of RRBS1204 and RRBS1208 derived from human stomach mucosa cells; RRBS1204 and RRBS1208

status: Public on Dec 05 2011

description:
sample_term_id: UBERON_0001199
assay_term_id: OBI_0001862
nucleic_acid_term_id: SO_0000352
Design description: RRBS REMC Sequencing on Illumina
Library name: RRBS1204 and RRBS1208
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.7482
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.7506
****************
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: GSM772726_BI.Stomach_Mucosa.RRBS.157.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RRBS1204 and RRBS1208.hg19.level.2.release.4
ANALYSIS TITLE: Methylation Proportion Graphs of Stomach Mucosa RRBS Data
ANALYSIS DESCRIPTION: Illumina RRBS read mappings from Stomach Mucosa, Donor 157 were processed into graphs of methylation proportions. Methylation proportions were calculated as (methylated calls / (methylated calls + unmethylated calls)) for all CpGs covered by at least 4 reads.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.8333
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Reduced Representation Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19 MspI restriction fragments 40-220bp
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
GENOMIC_WINDOW: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 4
BROWSER_TRACK_NAME: SM RRBS 57 08
BROWSER_TRACK_DESCRIPTION: BI Stomach Mucosa RRBS Donor 157 Library RRBS1204 and RRBS1208 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 28,101,460
NUMBER_OF_RRBS_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 21
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 99.64
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE: 62
MAXIMUM_REPLICATE_CORRELATION: 0.68

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

source_name: Primary gastric mucosa tissue; RRBS1204 and RRBS1208

extract_protocol: Library construction protocol: Smith et al., Methods 48, 226-232

value: BioSam 149

value: Stomach Mucosa

value: surgery

value: NK stomach mucosa, stomach rmvd as part of pancr. CA

value: genomic DNA

value: mucosa

value: white

value: stomach

value: MGH Pathology

value: 59 years

value: 2x5hrs Epitect Kit

value: 20 ng

value: T4 Ligase (2,000U/ul) 16C o/n

value: 5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT

value: 5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT

value: Standard Protocol (Smith et al., Methods 48, 226-232)

value: DNA Methylation

value: Smith et al., Methods 48, 226-232

value: Gel size selection

value: Pfu Turbo Cx hot start


title: Bisulfite-Seq analysis of RRBS1203 and RRBS1207 derived from human smooth muscle cells; RRBS1203 and RRBS1207

description:
sample_term_id: UBERON_0012489
assay_term_id: OBI_0001862
nucleic_acid_term_id: SO_0000352
Design description: RRBS REMC Sequencing on Illumina
Library name: RRBS1203 and RRBS1207
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.7480
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.7505
****************
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: GSM772724_BI.Colon_Smooth_Muscle.RRBS.Donor_83_REMC_18.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RRBS1203 and RRBS1207.hg19.level.2.release.4
ANALYSIS TITLE: Methylation Proportion Graphs of Colon Smooth Muscle RRBS Data
ANALYSIS DESCRIPTION: Illumina RRBS read mappings from Colon Smooth Muscle, Donor Donor 83 REMC 18 were processed into graphs of methylation proportions. Methylation proportions were calculated as (methylated calls / (methylated calls + unmethylated calls)) for all CpGs covered by at least 4 reads.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.8342
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Reduced Representation Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19 MspI restriction fragments 40-220bp
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
GENOMIC_WINDOW: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 4
BROWSER_TRACK_NAME: CSM RRBS 18 07
BROWSER_TRACK_DESCRIPTION: BI Colon Smooth Muscle RRBS Donor Donor 83 REMC 18 Library RRBS1203 and RRBS1207 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 30,629,506
NUMBER_OF_RRBS_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 21
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 99.63
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE: 57
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: Primary colonic smooth muscle tissue; RRBS1203 and RRBS1207

value: BioSam 156 REMC 18

value: Colon Smooth Muscle

value: surgery

value: NL smooth muscle, colon rsctn for Adeno CA of cecum

value: smooth muscle

value: caucasian

value: Female

value: Primary Tissue

value: colon

value: Donor 83 REMC 18

value: 77 years


title: 60d replicate 2 (miRNA)

status: Public on Dec 23 2011

type: RNA

city: Philadelphia

first: Bonini

last: Nancy

state: PA

address: 415 S University Ave

institute: University of Pennsylvania

description:
small RNA profiling
miRNA0532H 60 Days #2 (Hy3) vs Pool (Hy5) 050407.gpr

hyb_protocol: Tecan Hybridization with Exiqon Hybridization Program

scan_protocol: Axon Instruments 4000B Scanner using GenePix Pro 6.0 image acquisition software

data_processing:
Global LOESS regression algorithm (locally weighted scatterplot smoothing).
~80 array features listed below are meaningful data for Drosophila miRNAs, all others are either unrelated sequences or human miRNA sequences that Exiqon used for test/development of new products.  So we consider only those 80 or so probesets are useful.

molecule: total RNA

organism: Drosophila melanogaster

source_name: dissected brain tissue

label_protocol: miRCURY Labeling Kit (Exiqon) for use with Exiqon miRNA arrays

growth_protocol: Fly were grown in standard cornmeal molasses agar medium with dry yeast, at 25°C

extract_protocol: Ambion miRvana miRNA isolation kit

treatment_protocol: natural aging

tag: tissue

value: dissected brain

tag: time

source_name: common reference pool

tag: common reference

value: pooled RNA from all samples


title: Bisulfite-Seq analysis of RRBS1224 derived from human fetal lung cells; RRBS1224

description:
sample_term_id: UBERON_0002048
assay_term_id: OBI_0001862
nucleic_acid_term_id: SO_0000352
Design description: RRBS REMC Sequencing on Illumina
Library name: RRBS1224
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.6994
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.3130
****************
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: GSM706836_BI.Fetal_Lung.RRBS.H-23266.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RRBS1224.hg19.level.2.release.4
ANALYSIS TITLE: Methylation Proportion Graphs of Fetal Lung RRBS Data
ANALYSIS DESCRIPTION: Illumina RRBS read mappings from Fetal Lung, Donor H-23266 were processed into graphs of methylation proportions. Methylation proportions were calculated as (methylated calls / (methylated calls + unmethylated calls)) for all CpGs covered by at least 4 reads.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.8324
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Reduced Representation Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19 MspI restriction fragments 40-220bp
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
GENOMIC_WINDOW: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 4
BROWSER_TRACK_NAME: FL RRBS 66 24
BROWSER_TRACK_DESCRIPTION: BI Fetal Lung RRBS Donor H-23266 Library RRBS1224 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 21,939,176
NUMBER_OF_RRBS_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 21
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 99.56
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE: 52
MAXIMUM_REPLICATE_CORRELATION: 0.76

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

source_name: Fetal Lung primary tissue, day 85; RRBS1224

value: Fetal Lung

value: genomic DNA

value: University of Washington, Congenital Defects Lab. Ian Glass

value: fetal lung

value: UW

value: fetal

value: day 85

value: 2x5hrs Epitect Kit

value: 20 ng

value: T4 Ligase (2,000U/ul) 16C o/n

value: 5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT

value: 5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT

value: Standard Protocol (Smith et al., Methods 48, 226-232)

value: DNA Methylation


title: Bisulfite-Seq analysis of RRBS1081 derived from human fetal heart cells; RRBS1081

description:
sample_term_id: UBERON_0000948
assay_term_id: OBI_0001862
nucleic_acid_term_id: SO_0000352
Design description: RRBS REMC Sequencing on Illumina
Library name: RRBS1081
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.7000
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.2456
****************
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: GSM706842_BI.Fetal_Heart.RRBS.H-22727.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RRBS1081.hg19.level.2.release.4
ANALYSIS TITLE: Methylation Proportion Graphs of Fetal Heart RRBS Data
ANALYSIS DESCRIPTION: Illumina RRBS read mappings from Fetal Heart, Donor H-22727 were processed into graphs of methylation proportions. Methylation proportions were calculated as (methylated calls / (methylated calls + unmethylated calls)) for all CpGs covered by at least 4 reads.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.8341
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Reduced Representation Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19 MspI restriction fragments 40-220bp
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
GENOMIC_WINDOW: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 4
BROWSER_TRACK_NAME: FH RRBS 27 81
BROWSER_TRACK_DESCRIPTION: BI Fetal Heart RRBS Donor H-22727 Library RRBS1081 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 20,501,835
NUMBER_OF_RRBS_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 21
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 99.56
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE: 52
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: Fetal Heart primary tissue, day 101; RRBS1081

value: Fetal Heart

value: Primary Tissue

value: fetal heart

value: 101 days

value: Unknown

value: Smith et al., Methods 48, 226-232

value: Gel size selection

value: Pfu Turbo Cx hot start