title: ChIP-Seq analysis of WCE in human CD45RO CD4 cells; DNA_Lib 541

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 541
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8571
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9467
****************
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: GSM772881_BI.CD4_Memory_Primary_Cells.Input.Donor_100_7_pooled_leukopaks_Jan_7_2011.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 541-DNA_Lib 541-DNA_Lib 541.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of CD4 Memory Primary Cells ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on CD4 Memory Primary Cells, Donor Donor 100 7 pooled leukopaks Jan 7 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.10769
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: 43,694,709
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 56
FINDPEAKS_SCORE: 0.0054
FINDPEAKS_PERCENTILE: 56
HOTSPOT_SCORE: 0.0042
HOTSPOT_PERCENTILE: 20
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.0361
POISSON_PERCENTILE: 25
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

ANALYSIS FILE NAME: GSM772881_BI.CD4_Memory_Primary_Cells.Input.Donor_100_7_pooled_leukopaks_Jan_7_2011.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 541-DNA_Lib 541-DNA_Lib 541.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of CD4 Memory Primary Cells ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from CD4 Memory Primary Cells, Donor Donor 100 7 pooled leukopaks Jan 7 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.11033
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 Input 00 41
BROWSER_TRACK_DESCRIPTION: BI CD4 Memory Primary Cells ChIP-Seq Input Donor 100 7 pooled leukopaks Jan 7 2011 Library DNA_Lib 541 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 43,694,709
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 56
FINDPEAKS_SCORE: 0.0054
FINDPEAKS_PERCENTILE: 56
HOTSPOT_SCORE: 0.0042
HOTSPOT_PERCENTILE: 20
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.0361
POISSON_PERCENTILE: 25
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

source_name: Memory CD4+ T cells; DNA_Lib 541

value: BioSam 181

value: CD4 Memory Primary Cells

value: presumed normal

value: CD45RO CD4

value: Unknown

value: Primary Cell

value: Donor 100 7 pooled leukopaks Jan 7 2011

value: Dana Farber

value: standard

value: cell/nuclei lysis

value: ChIP-Seq Input

value: Input

value: Branson


title: ChIP-Seq analysis of H3K9me3 in human CD45RO CD8 cells; DNA_Lib 547

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: CL_0000909
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 547
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8569
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9468
****************
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: GSM772879_BI.CD8_Memory_Primary_Cells.H3K9me3.Donor_100_7_pooled_leukopaks_Jan_7_2011.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 547-DNA_Lib 547-DNA_Lib 547.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of CD8 Memory Primary Cells Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9me3 ChIP-Seq on CD8 Memory Primary Cells, Donor Donor 100 7 pooled leukopaks Jan 7 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.10640
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: 23,438,929
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.0184
FINDPEAKS_PERCENTILE: 22
HOTSPOT_SCORE: 0.0763
HOTSPOT_PERCENTILE: 29
IROC_SCORE: 0.8839
IROC_PERCENTILE: 67
POISSON_SCORE: 0.165
POISSON_PERCENTILE: 22
MAXIMUM_REPLICATE_CORRELATION: 0.95

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

ANALYSIS FILE NAME: GSM772879_BI.CD8_Memory_Primary_Cells.H3K9me3.Donor_100_7_pooled_leukopaks_Jan_7_2011.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 547-DNA_Lib 547-DNA_Lib 547.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of CD8 Memory Primary Cells Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9me3 ChIP-Seq read mappings from CD8 Memory Primary Cells, Donor Donor 100 7 pooled leukopaks Jan 7 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.10904
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: CD8M H3K9me3 00 47
BROWSER_TRACK_DESCRIPTION: BI CD8 Memory Primary Cells Histone H3K9me3 Donor 100 7 pooled leukopaks Jan 7 2011 Library DNA_Lib 547 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 23,438,929
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.0184
FINDPEAKS_PERCENTILE: 22
HOTSPOT_SCORE: 0.0763
HOTSPOT_PERCENTILE: 29
IROC_SCORE: 0.8839
IROC_PERCENTILE: 67
POISSON_SCORE: 0.165
POISSON_PERCENTILE: 22
MAXIMUM_REPLICATE_CORRELATION: 0.95

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

molecule: genomic DNA

organism: Homo sapiens

source_name: Memory CD8+ T cells; DNA_Lib 547

extract_protocol: Library construction protocol: Single read - Illumina

tag: sample alias

value: BioSam 182

tag: sample common name

value: CD8 Memory Primary Cells

tag: molecule

value: genomic DNA

tag: disease

tag: markers

value: CD45RO CD8

value: Protein A-Sepharose 4B

value: 0.5 to 3 million cells

value: ~1 ug

value: 10 ul bed volume

value: Abcam

value: Histone H3K9me3


title: ChIP-Seq analysis of H3K9ac in human AdiposeNuclei cells; Lib:XZ:20100107:12--ChIP:XZ:20100104:10:AdiposeNuclei:H3K9Ac

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:20100107:12--ChIP:XZ:20100104:10:AdiposeNuclei:H3K9Ac
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8063
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3891
****************
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: GSM772802_BI.Adipose_Nuclei.H3K9ac.7.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100107:12--ChIP:XZ:20100104:10:AdiposeNuclei:H3K9Ac.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Adipose Nuclei Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9ac ChIP-Seq on Adipose Nuclei, Donor 7, 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.10720
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: 29,823,711
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 19
FINDPEAKS_SCORE: 0.0296
FINDPEAKS_PERCENTILE: 5
HOTSPOT_SCORE: 0.0902
HOTSPOT_PERCENTILE: 11
IROC_SCORE: 0.9242
IROC_PERCENTILE: 5
POISSON_SCORE: 0.1519
POISSON_PERCENTILE: 11
MAXIMUM_REPLICATE_CORRELATION: 0.89

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

ANALYSIS FILE NAME: GSM772802_BI.Adipose_Nuclei.H3K9ac.7.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100107:12--ChIP:XZ:20100104:10:AdiposeNuclei:H3K9Ac.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Adipose Nuclei Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9ac ChIP-Seq read mappings from Adipose Nuclei, Donor 7, 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.10984
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 H3K9ac 7
BROWSER_TRACK_DESCRIPTION: BI Adipose Nuclei Histone H3K9ac Donor 7 Library Lib:XZ:20100107:12--ChIP:XZ:20100104:10:AdiposeNuclei:H3K9Ac EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 29,823,711
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 19
FINDPEAKS_SCORE: 0.0296
FINDPEAKS_PERCENTILE: 5
HOTSPOT_SCORE: 0.0902
HOTSPOT_PERCENTILE: 11
IROC_SCORE: 0.9242
IROC_PERCENTILE: 5
POISSON_SCORE: 0.1519
POISSON_PERCENTILE: 11
MAXIMUM_REPLICATE_CORRELATION: 0.89

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

source_name: Nuclei derived from crude preps of adipose tissue; Lib:XZ:20100107:12--ChIP:XZ:20100104:10:AdiposeNuclei:H3K9Ac

value: Adipose Nuclei

value: surgery

value: Female

value: Primary Tissue

value: abdomen

value: Harvard University

value: 10 million cells

value: SDS lysis

value: 70 ul bed volume

value: Histone H3K9ac

value: Bioruptor


title: ChIP-Seq analysis of H3K4me1 in human ADMSC Diff Day20 cells; Lib EpiLabSPL Row 1734

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 1734
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8077
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.8181
****************
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: GSM772816_BI.Mesenchymal_Stem_Cell_Derived_Adipocyte_Cultured_Cells.H3K4me1.92.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib EpiLabSPL Row 1734.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 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.10714
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: 32,256,205
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.4945
FINDPEAKS_PERCENTILE: 89
HOTSPOT_SCORE: 0.5323
HOTSPOT_PERCENTILE: 93
IROC_SCORE: 0.9933
IROC_PERCENTILE: 76
POISSON_SCORE: 0.6602
POISSON_PERCENTILE: 93
MAXIMUM_REPLICATE_CORRELATION: 0.9

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

ANALYSIS FILE NAME: GSM772816_BI.Mesenchymal_Stem_Cell_Derived_Adipocyte_Cultured_Cells.H3K4me1.92.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib EpiLabSPL Row 1734.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 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.10978
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 92 34
BROWSER_TRACK_DESCRIPTION: BI Mesenchymal Stem Cell Derived Adipocyte Cultured Cells Histone H3K4me1 Donor 92 Library Lib EpiLabSPL Row 1734 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 32,256,205
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.4945
FINDPEAKS_PERCENTILE: 89
HOTSPOT_SCORE: 0.5323
HOTSPOT_PERCENTILE: 93
IROC_SCORE: 0.9933
IROC_PERCENTILE: 76
POISSON_SCORE: 0.6602
POISSON_PERCENTILE: 93
MAXIMUM_REPLICATE_CORRELATION: 0.9

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

source_name: Adipose-derived mesenchymal stem cells were cultured in adipocyte differentiation medium for 20 days; Lib EpiLabSPL Row 1734

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: Primary Cell Culture

value: Protein A-Sepharose 4B

value: Histone H3K4me1


title: ChIP-Seq analysis of H3K27ac in human CD45RO CD8 cells; DNA_Lib 546

description:
sample_term_id: CL_0000909
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 546
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8570
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9468
****************
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: GSM772880_BI.CD8_Memory_Primary_Cells.H3K27ac.Donor_100_7_pooled_leukopaks_Jan_7_2011.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 546-DNA_Lib 546-DNA_Lib 546.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of CD8 Memory Primary Cells Histone H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27ac ChIP-Seq on CD8 Memory Primary Cells, Donor Donor 100 7 pooled leukopaks Jan 7 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.10649
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: 13,953,415
NUMBER_OF_H3K27ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 34
FINDPEAKS_SCORE: 0.2534
FINDPEAKS_PERCENTILE: 68
HOTSPOT_SCORE: 0.3251
HOTSPOT_PERCENTILE: 68
IROC_SCORE: 0.9972
IROC_PERCENTILE: 71
POISSON_SCORE: 0.3378
POISSON_PERCENTILE: 50
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM772880_BI.CD8_Memory_Primary_Cells.H3K27ac.Donor_100_7_pooled_leukopaks_Jan_7_2011.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 546-DNA_Lib 546-DNA_Lib 546.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of CD8 Memory Primary Cells Histone H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27ac ChIP-Seq read mappings from CD8 Memory Primary Cells, Donor Donor 100 7 pooled leukopaks Jan 7 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.10913
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: CD8M H3K27ac 00 46
BROWSER_TRACK_DESCRIPTION: BI CD8 Memory Primary Cells Histone H3K27ac Donor 100 7 pooled leukopaks Jan 7 2011 Library DNA_Lib 546 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 13,953,415
NUMBER_OF_H3K27ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 34
FINDPEAKS_SCORE: 0.2534
FINDPEAKS_PERCENTILE: 68
HOTSPOT_SCORE: 0.3251
HOTSPOT_PERCENTILE: 68
IROC_SCORE: 0.9972
IROC_PERCENTILE: 71
POISSON_SCORE: 0.3378
POISSON_PERCENTILE: 50
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: Memory CD8+ T cells; DNA_Lib 546

value: BioSam 182

value: CD8 Memory Primary Cells

value: presumed normal

value: CD45RO CD8

value: Unknown

value: Primary Cell

value: Donor 100 7 pooled leukopaks Jan 7 2011

value: Dana Farber

value: 0.5 to 3 million cells

value: cell/nuclei lysis

value: ~1 ug

value: 10 ul bed volume

value: Abcam

value: Histone H3K27ac

value: Branson


title: ChIP-Seq analysis of H3K27me3 in human CD45RO CD8 cells; DNA_Lib 544

description:
sample_term_id: CL_0000909
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 544
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8568
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9468
****************
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: GSM772878_BI.CD8_Memory_Primary_Cells.H3K27me3.Donor_100_7_pooled_leukopaks_Jan_7_2011.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 544-DNA_Lib 544-DNA_Lib 544.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of CD8 Memory Primary Cells Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27me3 ChIP-Seq on CD8 Memory Primary Cells, Donor Donor 100 7 pooled leukopaks Jan 7 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.10636
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: 26,412,322
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.0071
FINDPEAKS_PERCENTILE: 10
HOTSPOT_SCORE: 0.0768
HOTSPOT_PERCENTILE: 10
IROC_SCORE: 0.6733
IROC_PERCENTILE: 24
POISSON_SCORE: 0.1995
POISSON_PERCENTILE: 27
MAXIMUM_REPLICATE_CORRELATION: 0.82

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

ANALYSIS FILE NAME: GSM772878_BI.CD8_Memory_Primary_Cells.H3K27me3.Donor_100_7_pooled_leukopaks_Jan_7_2011.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 544-DNA_Lib 544-DNA_Lib 544.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of CD8 Memory Primary Cells Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27me3 ChIP-Seq read mappings from CD8 Memory Primary Cells, Donor Donor 100 7 pooled leukopaks Jan 7 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.10900
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: CD8M H3K27me3 00 44
BROWSER_TRACK_DESCRIPTION: BI CD8 Memory Primary Cells Histone H3K27me3 Donor 100 7 pooled leukopaks Jan 7 2011 Library DNA_Lib 544 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 26,412,322
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.0071
FINDPEAKS_PERCENTILE: 10
HOTSPOT_SCORE: 0.0768
HOTSPOT_PERCENTILE: 10
IROC_SCORE: 0.6733
IROC_PERCENTILE: 24
POISSON_SCORE: 0.1995
POISSON_PERCENTILE: 27
MAXIMUM_REPLICATE_CORRELATION: 0.82

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

source_name: Memory CD8+ T cells; DNA_Lib 544

value: genomic DNA

value: Protein A-Sepharose 4B

value: Millipore

value: Histone H3K27me3


title: ChIP-Seq analysis of H3K27me3 in human chondrogenic dif cells; Lib EpiLabSPL Row 1389

description:
sample_term_id: CL_0000138
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib EpiLabSPL Row 1389
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8049
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5951
****************
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: GSM772788_BI.Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K27me3.58.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib EpiLabSPL Row 1389.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27me3 ChIP-Seq on Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells, Donor 58, were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.10775
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: 30,348,937
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.1282
FINDPEAKS_PERCENTILE: 82
HOTSPOT_SCORE: 0.2005
HOTSPOT_PERCENTILE: 80
IROC_SCORE: 0.9205
IROC_PERCENTILE: 65
POISSON_SCORE: 0.4842
POISSON_PERCENTILE: 94
MAXIMUM_REPLICATE_CORRELATION: 0.94

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

ANALYSIS FILE NAME: GSM772788_BI.Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K27me3.58.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib EpiLabSPL Row 1389.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27me3 ChIP-Seq read mappings from Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells, Donor 58, were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.11039
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: CfBMDMSC H3K27me3 58 89
BROWSER_TRACK_DESCRIPTION: BI Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K27me3 Donor 58 Library Lib EpiLabSPL Row 1389 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 30,348,937
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.1282
FINDPEAKS_PERCENTILE: 82
HOTSPOT_SCORE: 0.2005
HOTSPOT_PERCENTILE: 80
IROC_SCORE: 0.9205
IROC_PERCENTILE: 65
POISSON_SCORE: 0.4842
POISSON_PERCENTILE: 94
MAXIMUM_REPLICATE_CORRELATION: 0.94

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

source_name: chondrocytes derived via in vitro culture from mesenchymal stem cells; Lib EpiLabSPL Row 1389

value: healthy

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

value: chondrogenic dif cells

value: Primary Cell Culture

value: Rikshospitalet University Hospital

value: 10 million cells

value: SDS lysis

value: 70 ul bed volume

value: Bioruptor


title: ChIP-Seq analysis of WCE in human CD45RO CD8 cells; DNA_Lib 548

description:
sample_term_id: CL_0000909
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 548
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8564
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9468
****************
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: GSM772874_BI.CD8_Memory_Primary_Cells.Input.Donor_100_7_pooled_leukopaks_Jan_7_2011.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 548-DNA_Lib 548-DNA_Lib 548.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of CD8 Memory Primary Cells ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on CD8 Memory Primary Cells, Donor Donor 100 7 pooled leukopaks Jan 7 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.10646
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: 23,051,947
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 56
FINDPEAKS_SCORE: 0.0071
FINDPEAKS_PERCENTILE: 82
HOTSPOT_SCORE: 0.0307
HOTSPOT_PERCENTILE: 74
IROC_SCORE: 0.9643
IROC_PERCENTILE: 48
POISSON_SCORE: 0.0789
POISSON_PERCENTILE: 72
MAXIMUM_REPLICATE_CORRELATION: 0.93

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

ANALYSIS FILE NAME: GSM772874_BI.CD8_Memory_Primary_Cells.Input.Donor_100_7_pooled_leukopaks_Jan_7_2011.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 548-DNA_Lib 548-DNA_Lib 548.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of CD8 Memory Primary Cells ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from CD8 Memory Primary Cells, Donor Donor 100 7 pooled leukopaks Jan 7 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.10910
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: CD8M Input 00 48
BROWSER_TRACK_DESCRIPTION: BI CD8 Memory Primary Cells ChIP-Seq Input Donor 100 7 pooled leukopaks Jan 7 2011 Library DNA_Lib 548 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 23,051,947
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 56
FINDPEAKS_SCORE: 0.0071
FINDPEAKS_PERCENTILE: 82
HOTSPOT_SCORE: 0.0307
HOTSPOT_PERCENTILE: 74
IROC_SCORE: 0.9643
IROC_PERCENTILE: 48
POISSON_SCORE: 0.0789
POISSON_PERCENTILE: 72
MAXIMUM_REPLICATE_CORRELATION: 0.93

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

source_name: Memory CD8+ T cells; DNA_Lib 548

value: BioSam 182

value: CD8 Memory Primary Cells

value: presumed normal

value: CD45RO CD8

value: Unknown

value: Primary Cell

value: Donor 100 7 pooled leukopaks Jan 7 2011

value: Dana Farber

value: standard

value: cell/nuclei lysis

value: ChIP-Seq Input

value: Input


title: ChIP-Seq analysis of H3K9ac in human chondrogenic dif cells; Lib EpiLabSPL Row 1390

description:
sample_term_id: CL_0000138
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib EpiLabSPL Row 1390
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8047
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5951
****************
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: GSM772786_BI.Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K9ac.58.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib EpiLabSPL Row 1390.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9ac ChIP-Seq on Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells, Donor 58, were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.10840
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: 30,793,260
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 19
FINDPEAKS_SCORE: 0.2608
FINDPEAKS_PERCENTILE: 79
HOTSPOT_SCORE: 0.3076
HOTSPOT_PERCENTILE: 79
IROC_SCORE: 0.9966
IROC_PERCENTILE: 63
POISSON_SCORE: 0.3663
POISSON_PERCENTILE: 79
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

ANALYSIS FILE NAME: GSM772786_BI.Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K9ac.58.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib EpiLabSPL Row 1390.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9ac ChIP-Seq read mappings from Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells, Donor 58, were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.11104
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: CfBMDMSC H3K9ac 58 90
BROWSER_TRACK_DESCRIPTION: BI Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K9ac Donor 58 Library Lib EpiLabSPL Row 1390 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 30,793,260
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 19
FINDPEAKS_SCORE: 0.2608
FINDPEAKS_PERCENTILE: 79
HOTSPOT_SCORE: 0.3076
HOTSPOT_PERCENTILE: 79
IROC_SCORE: 0.9966
IROC_PERCENTILE: 63
POISSON_SCORE: 0.3663
POISSON_PERCENTILE: 79
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

source_name: chondrocytes derived via in vitro culture from mesenchymal stem cells; Lib EpiLabSPL Row 1390

value: healthy

value: genomic DNA

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

value: chondrogenic dif cells

value: Primary Cell Culture

value: Rikshospitalet University Hospital

value: Protein A-Sepharose 4B

value: Abcam

value: Histone H3K9ac


title: ChIP-Seq analysis of H3K36me3 in human CD45RO CD8 cells; DNA_Lib 545

description:
sample_term_id: CL_0000909
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 545
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8567
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9468
****************
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: GSM772877_BI.CD8_Memory_Primary_Cells.H3K36me3.Donor_100_7_pooled_leukopaks_Jan_7_2011.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 545-DNA_Lib 545-DNA_Lib 545.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of CD8 Memory Primary Cells Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K36me3 ChIP-Seq on CD8 Memory Primary Cells, Donor Donor 100 7 pooled leukopaks Jan 7 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.10591
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: 29,439,667
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.0142
FINDPEAKS_PERCENTILE: 8
HOTSPOT_SCORE: 0.1022
HOTSPOT_PERCENTILE: 8
IROC_SCORE: 0.7845
IROC_PERCENTILE: 6
POISSON_SCORE: 0.2347
POISSON_PERCENTILE: 8
MAXIMUM_REPLICATE_CORRELATION: 0.94

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

ANALYSIS FILE NAME: GSM772877_BI.CD8_Memory_Primary_Cells.H3K36me3.Donor_100_7_pooled_leukopaks_Jan_7_2011.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 545-DNA_Lib 545-DNA_Lib 545.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of CD8 Memory Primary Cells Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K36me3 ChIP-Seq read mappings from CD8 Memory Primary Cells, Donor Donor 100 7 pooled leukopaks Jan 7 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.10855
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: CD8M H3K36me3 00 45
BROWSER_TRACK_DESCRIPTION: BI CD8 Memory Primary Cells Histone H3K36me3 Donor 100 7 pooled leukopaks Jan 7 2011 Library DNA_Lib 545 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 29,439,667
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.0142
FINDPEAKS_PERCENTILE: 8
HOTSPOT_SCORE: 0.1022
HOTSPOT_PERCENTILE: 8
IROC_SCORE: 0.7845
IROC_PERCENTILE: 6
POISSON_SCORE: 0.2347
POISSON_PERCENTILE: 8
MAXIMUM_REPLICATE_CORRELATION: 0.94

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

source_name: Memory CD8+ T cells; DNA_Lib 545

value: BioSam 182

value: CD8 Memory Primary Cells

value: presumed normal

value: CD45RO CD8

value: Unknown

value: 0.5 to 3 million cells

value: ~1 ug

value: 10 ul bed volume

value: Histone H3K36me3

value: Branson


title: ChIP-Seq analysis of WCE in human stomach smooth muscle cells; DNA_Lib 381

description:
sample_term_id: UBERON_0008856
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 381
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8573
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9451
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM772883_BI.Stomach_Smooth_Muscle.Input.161.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 381-DNA_Lib 381-DNA_Lib 381-DNA_Lib 381.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Stomach Smooth Muscle ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on Stomach Smooth Muscle, Donor 161, were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.10643
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: 22,407,956
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 56
FINDPEAKS_SCORE: 0.0064
FINDPEAKS_PERCENTILE: 75
HOTSPOT_SCORE: 0.0344
HOTSPOT_PERCENTILE: 77
IROC_SCORE: 0.9666
IROC_PERCENTILE: 50
POISSON_SCORE: 0.0799
POISSON_PERCENTILE: 75
MAXIMUM_REPLICATE_CORRELATION: 0.65

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

ANALYSIS FILE NAME: GSM772883_BI.Stomach_Smooth_Muscle.Input.161.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 381-DNA_Lib 381-DNA_Lib 381-DNA_Lib 381.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Stomach Smooth Muscle ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from Stomach Smooth Muscle, Donor 161, were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.10907
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: SSM Input 61 81
BROWSER_TRACK_DESCRIPTION: BI Stomach Smooth Muscle ChIP-Seq Input Donor 161 Library DNA_Lib 381 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 22,407,956
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 56
FINDPEAKS_SCORE: 0.0064
FINDPEAKS_PERCENTILE: 75
HOTSPOT_SCORE: 0.0344
HOTSPOT_PERCENTILE: 77
IROC_SCORE: 0.9666
IROC_PERCENTILE: 50
POISSON_SCORE: 0.0799
POISSON_PERCENTILE: 75
MAXIMUM_REPLICATE_CORRELATION: 0.65

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

source_name: Primary stomach smooth muscle tissue; DNA_Lib 381

value: Stomach Smooth Muscle

value: Surgery

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

value: genomic DNA

value: Smooth Muscle

value: Caucasian

value: Male

value: Primary Tissue

value: Stomach

value: MGH

value: 59.0 Years

value: standard

value: cell/nuclei lysis

value: ChIP-Seq Input

value: Input


title: ChIP-Seq analysis of H3K9me3 in human chondrogenic dif cells; Lib EpiLabSPL Row 1405

description:
sample_term_id: CL_0000138
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib EpiLabSPL Row 1405
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8036
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5932
****************
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: GSM772775_BI.Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K9me3.60.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib EpiLabSPL Row 1405.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9me3 ChIP-Seq on Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells, Donor 60, 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.10781
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: 27,904,004
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.0428
FINDPEAKS_PERCENTILE: 55
HOTSPOT_SCORE: 0.1121
HOTSPOT_PERCENTILE: 53
IROC_SCORE: 0.7284
IROC_PERCENTILE: 22
POISSON_SCORE: 0.3397
POISSON_PERCENTILE: 73
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

ANALYSIS FILE NAME: GSM772775_BI.Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K9me3.60.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib EpiLabSPL Row 1405.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9me3 ChIP-Seq read mappings from Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells, Donor 60, 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.11045
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: CfBMDMSC H3K9me3 60 05
BROWSER_TRACK_DESCRIPTION: BI Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K9me3 Donor 60 Library Lib EpiLabSPL Row 1405 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 27,904,004
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.0428
FINDPEAKS_PERCENTILE: 55
HOTSPOT_SCORE: 0.1121
HOTSPOT_PERCENTILE: 53
IROC_SCORE: 0.7284
IROC_PERCENTILE: 22
POISSON_SCORE: 0.3397
POISSON_PERCENTILE: 73
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

source_name: chondrocytes derived via in vitro culture from mesenchymal stem cells; Lib EpiLabSPL Row 1405

value: healthy

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

value: chondrogenic dif cells

value: Unknown

value: Primary Cell Culture

value: Rikshospitalet University Hospital

value: Protein A-Sepharose 4B

value: 10 million cells

value: SDS lysis

value: 70 ul bed volume

value: Abcam

value: Histone H3K9me3

value: Bioruptor


title: ChIP-Seq analysis of H3K4me3 in human colon smooth muscle cells; DNA_Lib 324

description:
sample_term_id: UBERON_0012489
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 324
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8551
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: GSM772861_BI.Colon_Smooth_Muscle.H3K4me3.Donor_83_REMC_18.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 324-DNA_Lib 324-DNA_Lib 324-DNA_Lib 324.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Colon Smooth Muscle Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me3 ChIP-Seq on Colon Smooth Muscle, Donor Donor 83 REMC 18, 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.10618
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: 29,461,096
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.1674
FINDPEAKS_PERCENTILE: 31
HOTSPOT_SCORE: 0.207
HOTSPOT_PERCENTILE: 30
IROC_SCORE: 0.9994
IROC_PERCENTILE: 59
POISSON_SCORE: 0.2667
POISSON_PERCENTILE: 26
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM772861_BI.Colon_Smooth_Muscle.H3K4me3.Donor_83_REMC_18.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 324-DNA_Lib 324-DNA_Lib 324-DNA_Lib 324.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Colon Smooth Muscle Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me3 ChIP-Seq read mappings from Colon Smooth Muscle, Donor Donor 83 REMC 18, 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.10882
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: CSM H3K4me3 83 24
BROWSER_TRACK_DESCRIPTION: BI Colon Smooth Muscle Histone H3K4me3 Donor 83 REMC 18 Library DNA_Lib 324 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 29,461,096
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.1674
FINDPEAKS_PERCENTILE: 31
HOTSPOT_SCORE: 0.207
HOTSPOT_PERCENTILE: 30
IROC_SCORE: 0.9994
IROC_PERCENTILE: 59
POISSON_SCORE: 0.2667
POISSON_PERCENTILE: 26
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: Primary colonic smooth muscle tissue; DNA_Lib 324

value: BioSam 156 REMC 18

value: Colon Smooth Muscle

value: surgery

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

value: genomic DNA

value: smooth muscle

value: caucasian

value: Female

value: Primary Tissue

value: colon

value: Donor 83 REMC 18

value: MGH Pathology

value: 77 years

value: 0.5 to 3 million cells

value: ~1 ug

value: 10 ul bed volume

value: Millipore

value: Histone H3K4me3

value: Branson


title: ChIP-Seq analysis of H3K9me3 in human CD45RO CD4 cells; DNA_Lib 485

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 485
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8547
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: GSM772857_BI.CD4_Memory_Primary_Cells.H3K9me3.Donor_101_8_pooled_leukopaks_Jan_20_2011.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 485-DNA_Lib 485-DNA_Lib 485-DNA_Lib 485.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of CD4 Memory Primary Cells Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9me3 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.10676
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: 21,205,340
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.0123
FINDPEAKS_PERCENTILE: 6
HOTSPOT_SCORE: 0.051
HOTSPOT_PERCENTILE: 10
IROC_SCORE: 0.0
IROC_PERCENTILE: 4
POISSON_SCORE: 0.1078
POISSON_PERCENTILE: 4
MAXIMUM_REPLICATE_CORRELATION: 0.93

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

ANALYSIS FILE NAME: GSM772857_BI.CD4_Memory_Primary_Cells.H3K9me3.Donor_101_8_pooled_leukopaks_Jan_20_2011.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 485-DNA_Lib 485-DNA_Lib 485-DNA_Lib 485.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of CD4 Memory Primary Cells Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9me3 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.10940
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 H3K9me3 01 85
BROWSER_TRACK_DESCRIPTION: BI CD4 Memory Primary Cells Histone H3K9me3 Donor 101 8 pooled leukopaks Jan 20 2011 Library DNA_Lib 485 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 21,205,340
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.0123
FINDPEAKS_PERCENTILE: 6
HOTSPOT_SCORE: 0.051
HOTSPOT_PERCENTILE: 10
IROC_SCORE: 0.0
IROC_PERCENTILE: 4
POISSON_SCORE: 0.1078
POISSON_PERCENTILE: 4
MAXIMUM_REPLICATE_CORRELATION: 0.93

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

source_name: Memory CD4+ T cells; DNA_Lib 485

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: cell/nuclei lysis

value: Abcam

value: Histone H3K9me3


title: ChIP-Seq analysis of H3K9me3 in human colon smooth muscle cells; DNA_Lib 322

description:
sample_term_id: UBERON_0012489
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 322
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8548
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: GSM772858_BI.Colon_Smooth_Muscle.H3K9me3.Donor_83_REMC_18.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 322-DNA_Lib 322-DNA_Lib 322-DNA_Lib 322.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Colon Smooth Muscle Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9me3 ChIP-Seq on Colon Smooth Muscle, Donor Donor 83 REMC 18, 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.10635
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: 26,371,587
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.0137
FINDPEAKS_PERCENTILE: 10
HOTSPOT_SCORE: 0.0474
HOTSPOT_PERCENTILE: 6
IROC_SCORE: 0.9088
IROC_PERCENTILE: 78
POISSON_SCORE: 0.1184
POISSON_PERCENTILE: 6
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM772858_BI.Colon_Smooth_Muscle.H3K9me3.Donor_83_REMC_18.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 322-DNA_Lib 322-DNA_Lib 322-DNA_Lib 322.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Colon Smooth Muscle Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9me3 ChIP-Seq read mappings from Colon Smooth Muscle, Donor Donor 83 REMC 18, 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.10899
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: CSM H3K9me3 83 22
BROWSER_TRACK_DESCRIPTION: BI Colon Smooth Muscle Histone H3K9me3 Donor 83 REMC 18 Library DNA_Lib 322 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 26,371,587
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.0137
FINDPEAKS_PERCENTILE: 10
HOTSPOT_SCORE: 0.0474
HOTSPOT_PERCENTILE: 6
IROC_SCORE: 0.9088
IROC_PERCENTILE: 78
POISSON_SCORE: 0.1184
POISSON_PERCENTILE: 6
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: Primary colonic smooth muscle tissue; DNA_Lib 322

value: BioSam 156 REMC 18

value: Colon Smooth Muscle

value: surgery

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

value: genomic DNA

value: smooth muscle

value: caucasian

value: Female

value: Primary Tissue

value: colon

value: Donor 83 REMC 18

value: MGH Pathology

value: 77 years

value: 0.5 to 3 million cells


title: ChIP-Seq analysis of H3K27me3 in human chondrogenic dif cells; Lib EpiLabSPL Row 1403

description:
sample_term_id: CL_0000138
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib EpiLabSPL Row 1403
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8034
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5932
****************
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: GSM772773_BI.Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K27me3.60.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib EpiLabSPL Row 1403.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27me3 ChIP-Seq on Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells, Donor 60, 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.10783
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: 31,438,838
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.1227
FINDPEAKS_PERCENTILE: 80
HOTSPOT_SCORE: 0.1977
HOTSPOT_PERCENTILE: 73
IROC_SCORE: 0.9215
IROC_PERCENTILE: 67
POISSON_SCORE: 0.4843
POISSON_PERCENTILE: 96
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

ANALYSIS FILE NAME: GSM772773_BI.Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K27me3.60.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib EpiLabSPL Row 1403.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27me3 ChIP-Seq read mappings from Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells, Donor 60, 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.11047
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: CfBMDMSC H3K27me3 60 03
BROWSER_TRACK_DESCRIPTION: BI Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K27me3 Donor 60 Library Lib EpiLabSPL Row 1403 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 31,438,838
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.1227
FINDPEAKS_PERCENTILE: 80
HOTSPOT_SCORE: 0.1977
HOTSPOT_PERCENTILE: 73
IROC_SCORE: 0.9215
IROC_PERCENTILE: 67
POISSON_SCORE: 0.4843
POISSON_PERCENTILE: 96
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

source_name: chondrocytes derived via in vitro culture from mesenchymal stem cells; Lib EpiLabSPL Row 1403

value: healthy

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

value: chondrogenic dif cells

value: Unknown

value: Primary Cell Culture

value: Rikshospitalet University Hospital

value: Protein A-Sepharose 4B

value: 10 million cells

value: SDS lysis

value: 70 ul bed volume

value: Millipore

value: Histone H3K27me3

value: Bioruptor


title: ChIP-Seq analysis of H3K27me3 in AdiposeNuclei cells; Lib:XZ:20100731:11--ChIP:XZ:20100726:11:AdiposeNuclei:H3K27Me3

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:20100731:11--ChIP:XZ:20100726:11:AdiposeNuclei:H3K27Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8032
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5947
****************
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: GSM772771_BI.Adipose_Nuclei.H3K27me3.93.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100731:11--ChIP:XZ:20100726:11:AdiposeNuclei:H3K27Me3.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Adipose Nuclei Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27me3 ChIP-Seq on Adipose Nuclei, 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.10654
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: 30,743,845
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.015
FINDPEAKS_PERCENTILE: 31
HOTSPOT_SCORE: 0.112
HOTSPOT_PERCENTILE: 49
IROC_SCORE: 0.7209
IROC_PERCENTILE: 41
POISSON_SCORE: 0.3204
POISSON_PERCENTILE: 61
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

ANALYSIS FILE NAME: GSM772771_BI.Adipose_Nuclei.H3K27me3.93.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100731:11--ChIP:XZ:20100726:11:AdiposeNuclei:H3K27Me3.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Adipose Nuclei Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27me3 ChIP-Seq read mappings from Adipose Nuclei, 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.10918
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 H3K27me3 93
BROWSER_TRACK_DESCRIPTION: BI Adipose Nuclei Histone H3K27me3 Donor 93 Library Lib:XZ:20100731:11--ChIP:XZ:20100726:11:AdiposeNuclei:H3K27Me3 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 30,743,845
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.015
FINDPEAKS_PERCENTILE: 31
HOTSPOT_SCORE: 0.112
HOTSPOT_PERCENTILE: 49
IROC_SCORE: 0.7209
IROC_PERCENTILE: 41
POISSON_SCORE: 0.3204
POISSON_PERCENTILE: 61
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

source_name: Nuclei derived from crude preps of adipose tissue; Lib:XZ:20100731:11--ChIP:XZ:20100726:11:AdiposeNuclei:H3K27Me3

value: Adipose Nuclei

value: surgery

value: genomic DNA

value: Female

value: Primary Tissue

value: abdomen

value: Harvard University


title: ChIP-Seq analysis of H3K9ac in human chondrogenic dif cells; Lib EpiLabSPL Row 1404

description:
sample_term_id: CL_0000138
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib EpiLabSPL Row 1404
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8035
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5932
****************
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: GSM772774_BI.Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K9ac.60.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib EpiLabSPL Row 1404.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9ac ChIP-Seq on Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells, Donor 60, 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.10844
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: 32,793,789
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 19
FINDPEAKS_SCORE: 0.1866
FINDPEAKS_PERCENTILE: 58
HOTSPOT_SCORE: 0.241
HOTSPOT_PERCENTILE: 58
IROC_SCORE: 0.9967
IROC_PERCENTILE: 68
POISSON_SCORE: 0.3188
POISSON_PERCENTILE: 58
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

ANALYSIS FILE NAME: GSM772774_BI.Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K9ac.60.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib EpiLabSPL Row 1404.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9ac ChIP-Seq read mappings from Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells, Donor 60, 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.11108
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: CfBMDMSC H3K9ac 60 04
BROWSER_TRACK_DESCRIPTION: BI Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K9ac Donor 60 Library Lib EpiLabSPL Row 1404 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 32,793,789
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 19
FINDPEAKS_SCORE: 0.1866
FINDPEAKS_PERCENTILE: 58
HOTSPOT_SCORE: 0.241
HOTSPOT_PERCENTILE: 58
IROC_SCORE: 0.9967
IROC_PERCENTILE: 68
POISSON_SCORE: 0.3188
POISSON_PERCENTILE: 58
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

source_name: chondrocytes derived via in vitro culture from mesenchymal stem cells; Lib EpiLabSPL Row 1404

value: healthy

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

value: chondrogenic dif cells

value: Unknown

value: Abcam

value: Histone H3K9ac


title: ChIP-Seq analysis of WCE in human ADMSC undiff Day0 cells; Lib EpiLabSPL Row 1740

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 1740
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8026
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: GSM772765_BI.Adipose_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.Input.92.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib EpiLabSPL Row 1740.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 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.10659
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: 36,816,101
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 56
FINDPEAKS_SCORE: 0.0044
FINDPEAKS_PERCENTILE: 26
HOTSPOT_SCORE: 0.0033
HOTSPOT_PERCENTILE: 11
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.0214
POISSON_PERCENTILE: 7
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

ANALYSIS FILE NAME: GSM772765_BI.Adipose_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.Input.92.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib EpiLabSPL Row 1740.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 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.10923
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 92 40
BROWSER_TRACK_DESCRIPTION: BI Adipose Derived Mesenchymal Stem Cell Cultured Cells ChIP-Seq Input Donor 92 Library Lib EpiLabSPL Row 1740 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 36,816,101
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 56
FINDPEAKS_SCORE: 0.0044
FINDPEAKS_PERCENTILE: 26
HOTSPOT_SCORE: 0.0033
HOTSPOT_PERCENTILE: 11
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.0214
POISSON_PERCENTILE: 7
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

source_name: Adherent cells derived following short term serial passage from adipose tissue; Lib EpiLabSPL Row 1740

value: ADMSC undiff Day0

value: Primary Cell Culture

value: standard

value: SDS lysis

value: ChIP-Seq Input

value: Input


title: ChIP-Seq analysis of WCE in human ADMSC Diff Day20 cells; Lib EpiLabSPL Row 1741

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 1741
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8025
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.8181
****************
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: GSM772764_BI.Mesenchymal_Stem_Cell_Derived_Adipocyte_Cultured_Cells.Input.92.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib EpiLabSPL Row 1741.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 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.10742
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: 33,424,127
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 56
FINDPEAKS_SCORE: 0.0052
FINDPEAKS_PERCENTILE: 49
HOTSPOT_SCORE: 0.0066
HOTSPOT_PERCENTILE: 34
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.039
POISSON_PERCENTILE: 30
MAXIMUM_REPLICATE_CORRELATION: 0.95

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

ANALYSIS FILE NAME: GSM772764_BI.Mesenchymal_Stem_Cell_Derived_Adipocyte_Cultured_Cells.Input.92.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib EpiLabSPL Row 1741.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 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.11006
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 92 41
BROWSER_TRACK_DESCRIPTION: BI Mesenchymal Stem Cell Derived Adipocyte Cultured Cells ChIP-Seq Input Donor 92 Library Lib EpiLabSPL Row 1741 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 33,424,127
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 56
FINDPEAKS_SCORE: 0.0052
FINDPEAKS_PERCENTILE: 49
HOTSPOT_SCORE: 0.0066
HOTSPOT_PERCENTILE: 34
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.039
POISSON_PERCENTILE: 30
MAXIMUM_REPLICATE_CORRELATION: 0.95

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

source_name: Adipose-derived mesenchymal stem cells were cultured in adipocyte differentiation medium for 20 days; Lib EpiLabSPL Row 1741

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: Bioruptor


title: ChIP-Seq analysis of H3K36me3 in human ADMSC undiff Day0 cells; Lib EpiLabSPL Row 1746

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 1746
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8024
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: GSM772763_BI.Adipose_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K36me3.93.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib EpiLabSPL Row 1746.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Adipose Derived Mesenchymal Stem Cell Cultured Cells Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K36me3 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.10733
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: 20,097,664
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.3039
FINDPEAKS_PERCENTILE: 78
HOTSPOT_SCORE: 0.3083
HOTSPOT_PERCENTILE: 73
IROC_SCORE: 0.9796
IROC_PERCENTILE: 67
POISSON_SCORE: 0.477
POISSON_PERCENTILE: 71
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

ANALYSIS FILE NAME: GSM772763_BI.Adipose_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K36me3.93.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib EpiLabSPL Row 1746.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Adipose Derived Mesenchymal Stem Cell Cultured Cells Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K36me3 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.10997
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 H3K36me3 93 46
BROWSER_TRACK_DESCRIPTION: BI Adipose Derived Mesenchymal Stem Cell Cultured Cells Histone H3K36me3 Donor 93 Library Lib EpiLabSPL Row 1746 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 20,097,664
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.3039
FINDPEAKS_PERCENTILE: 78
HOTSPOT_SCORE: 0.3083
HOTSPOT_PERCENTILE: 73
IROC_SCORE: 0.9796
IROC_PERCENTILE: 67
POISSON_SCORE: 0.477
POISSON_PERCENTILE: 71
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

source_name: Adherent cells derived following short term serial passage from adipose tissue; Lib EpiLabSPL Row 1746

value: Female

value: Harvard University

value: Protein A-Sepharose 4B

value: 10 million cells

value: 70 ul bed volume

value: Histone H3K36me3