title: ChIP-Seq analysis of H3K36me3 in hLiver cells; Lib:XZ:20100827:02--ChIP:XZ:20100824:02:hLiver:H3K36Me3

description:
sample_term_id: UBERON_0002107
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:XZ:20100827:02--ChIP:XZ:20100824:02:hLiver:H3K36Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5672
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3345
****************
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: GSM669931_BI.Adult_Liver.H3K36me3.4.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100827:02--ChIP:XZ:20100824:02:hLiver:H3K36Me3.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Adult Liver Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K36me3 ChIP-Seq on Adult Liver, Donor 4 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.6588
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 3

QUALITY SCORES:
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 59
FINDPEAKS_SCORE: 0.5477
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.4527
HOTSPOT_PERCENTILE: 96
IROC_SCORE: 0.9979
IROC_PERCENTILE: 96
POISSON_SCORE: 0.6952
POISSON_PERCENTILE: 100

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

ANALYSIS FILE NAME: GSM669931_BI.Adult_Liver.H3K36me3.4.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100827:02--ChIP:XZ:20100824:02:hLiver:H3K36Me3.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of Adult Liver Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K36me3 ChIP-Seq read mappings from Adult Liver, Donor 4 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.6798
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 3
BROWSER_TRACK_NAME: AL H3K36me3 4
BROWSER_TRACK_DESCRIPTION: BI Adult Liver Histone H3K36me3 Donor 4 Library Lib:XZ:20100827:02--ChIP:XZ:20100824:02:hLiver:H3K36Me3 EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 59
FINDPEAKS_SCORE: 0.5477
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.4527
HOTSPOT_PERCENTILE: 96
IROC_SCORE: 0.9979
IROC_PERCENTILE: 96
POISSON_SCORE: 0.6952
POISSON_PERCENTILE: 100

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

source_name: normal adult liver; Lib:XZ:20100827:02--ChIP:XZ:20100824:02:hLiver:H3K36Me3

value: Adult Liver

value: Unknown

value: liver

value: MGH Pathology

value: Protein A-Sepharose 4B

value: 10 million cells

value: SDS lysis

value: 70 ul bed volume

value: Histone H3K36me3


title: ChIP-Seq analysis of H3K36me3; chondr. dif cls; Lib:MC:20100729:10--ChIP:MC:20100726:10:chondrogenic dif cells:H3K36Me3

status: Public on Mar 31 2011

type: SRA

city: Cambridge

first: BROAD

last: INSTITUTE

state: MA

country: USA

institute: Broad Institute

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:MC:20100729:10--ChIP:MC:20100726:10:chondrogenic dif cells:H3K36Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5676
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
****************

library_source: genomic

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

ANALYSIS FILE NAME: GSM669935_BI.Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K36me3.60.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100729:10--ChIP:MC:20100726:10:chondrogenic dif cells:H3K36Me3.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K36me3 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.6542
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 3

QUALITY SCORES:
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 59
FINDPEAKS_SCORE: 0.4295
FINDPEAKS_PERCENTILE: 88
HOTSPOT_SCORE: 0.3514
HOTSPOT_PERCENTILE: 85
IROC_SCORE: 0.9949
IROC_PERCENTILE: 85
POISSON_SCORE: 0.5925
POISSON_PERCENTILE: 88

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

ANALYSIS FILE NAME: GSM669935_BI.Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K36me3.60.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100729:10--ChIP:MC:20100726:10:chondrogenic dif cells:H3K36Me3.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K36me3 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.6752
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 3
BROWSER_TRACK_NAME: CfBMDMSC H3K36me3 60
BROWSER_TRACK_DESCRIPTION: BI Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K36me3 Donor 60 Library Lib:MC:20100729:10--ChIP:MC:20100726:10:chondrogenic dif cells:H3K36Me3 EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 59
FINDPEAKS_SCORE: 0.4295
FINDPEAKS_PERCENTILE: 88
HOTSPOT_SCORE: 0.3514
HOTSPOT_PERCENTILE: 85
IROC_SCORE: 0.9949
IROC_PERCENTILE: 85
POISSON_SCORE: 0.5925
POISSON_PERCENTILE: 88

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

molecule: genomic DNA

organism: Homo sapiens

source_name: chondrocytes derived via in vitro culture from mesenchymal stem cells; Lib:MC:20100729:10--ChIP:MC:20100726:10:chondrogenic dif cells:H3K36Me3

extract_protocol: Library construction protocol: Single read - Illumina

tag: sample alias

tag: sample common name

value: healthy

tag: molecule

value: genomic DNA

tag: disease

tag: markers

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: Abcam

value: Bioruptor


title: ChIP-Seq analysis of WCE in AdiposeNuclei cells; Lib:XZ:20100731:28--ChIP:XZ:20100726:28:AdiposeNuclei:WCE

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:20100731:28--ChIP:XZ:20100726:28:AdiposeNuclei:WCE
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5725
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5945
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM669984_BI.Adipose_Nuclei.Input.95.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100731:28--ChIP:XZ:20100726:28:AdiposeNuclei:WCE.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Adipose Nuclei ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on Adipose Nuclei, Donor 95 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6502
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 3

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 61
FINDPEAKS_SCORE: 0.0064
FINDPEAKS_PERCENTILE: 40
HOTSPOT_SCORE: 0.005
HOTSPOT_PERCENTILE: 23
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.0274
POISSON_PERCENTILE: 20

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

ANALYSIS FILE NAME: GSM669984_BI.Adipose_Nuclei.Input.95.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100731:28--ChIP:XZ:20100726:28:AdiposeNuclei:WCE.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of Adipose Nuclei ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from Adipose Nuclei, Donor 95 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6712
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 3
BROWSER_TRACK_NAME: AN Input 95
BROWSER_TRACK_DESCRIPTION: BI Adipose Nuclei ChIP-Seq Input Donor 95 Library Lib:XZ:20100731:28--ChIP:XZ:20100726:28:AdiposeNuclei:WCE EA Release 3

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 61
FINDPEAKS_SCORE: 0.0064
FINDPEAKS_PERCENTILE: 40
HOTSPOT_SCORE: 0.005
HOTSPOT_PERCENTILE: 23
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.0274
POISSON_PERCENTILE: 20

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

source_name: Nuclei derived from crude preps of adipose tissue; Lib:XZ:20100731:28--ChIP:XZ:20100726:28:AdiposeNuclei:WCE

value: Adipose Nuclei

value: surgery

value: Female

value: Primary Tissue

value: abdomen

value: Harvard University

value: standard

value: ChIP-Seq Input

value: Input


title: ChIP-Seq analysis of H3K27me3 in AdiposeNuclei cells; Lib:XZ:20100731:04--ChIP:XZ:20100726:04: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:20100731:04--ChIP:XZ:20100726:04:AdiposeNuclei:H3K27Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5671
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5946
****************
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: GSM669930_BI.Adipose_Nuclei.H3K27me3.92.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100731:04--ChIP:XZ:20100726:04:AdiposeNuclei:H3K27Me3.hg19.level.1.release.3
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 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.6530
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 3

QUALITY SCORES:
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 52
FINDPEAKS_SCORE: 0.0296
FINDPEAKS_PERCENTILE: 30
HOTSPOT_SCORE: 0.1136
HOTSPOT_PERCENTILE: 30
IROC_SCORE: 0.776
IROC_PERCENTILE: 10
POISSON_SCORE: 0.2993
POISSON_PERCENTILE: 35

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

ANALYSIS FILE NAME: GSM669930_BI.Adipose_Nuclei.H3K27me3.92.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100731:04--ChIP:XZ:20100726:04:AdiposeNuclei:H3K27Me3.hg19.level.2.release.3
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 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.6740
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 3
BROWSER_TRACK_NAME: AN H3K27me3 92
BROWSER_TRACK_DESCRIPTION: BI Adipose Nuclei Histone H3K27me3 Donor 92 Library Lib:XZ:20100731:04--ChIP:XZ:20100726:04:AdiposeNuclei:H3K27Me3 EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 52
FINDPEAKS_SCORE: 0.0296
FINDPEAKS_PERCENTILE: 30
HOTSPOT_SCORE: 0.1136
HOTSPOT_PERCENTILE: 30
IROC_SCORE: 0.776
IROC_PERCENTILE: 10
POISSON_SCORE: 0.2993
POISSON_PERCENTILE: 35

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

source_name: Nuclei derived from crude preps of adipose tissue; Lib:XZ:20100731:04--ChIP:XZ:20100726:04:AdiposeNuclei:H3K27Me3

value: Protein A-Sepharose 4B

value: 10 million cells

value: SDS lysis

value: 70 ul bed volume

value: Millipore

value: Histone H3K27me3


title: Exon arrays of Roadmap cell types; Fetal Kidney, Right primary tissue, day 115; DS16801-exon

status: Public on Apr 14 2011

type: RNA

city: Seattle

first: Northwest

last: REMC

state: WA

institute: University of Washington

description:
sample_term_id: UBERON_0004539
assay_term_id: OBI_0001463
nucleic_acid_term_id: SO_0000356
Exon profiling of NREMC cell types, these coincide with chromatin accessibility sequencing assays.
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.7185
sample alias: fKidney_Right.H-23640d115
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.5389

hyb_protocol: Hybridizations were carried out according the manufacturer (Affymetrix) protocol

scan_protocol: Affymetrix Gene Chip Scanner 3000

data_processing: Intensity files from the scanned exon arrays were analyzed at the exon level (Affymetrix ExACT 1.2.1 software). Sample data were quantile normalized with PM-GCBG background correction and PLIER (Probe Logarithmic Intensity Error) summarized

label: biotin

molecule: total RNA

label_protocol: A Whole Transcript Sense Target Labeling Assay (Affymetrix) was used to reduce the rRNA, perform in vitro transcription (IVT) and create labeled sense strand DNA for hybridization to the arrays.

growth_protocol: Followed vendor recommendations for growth protocol/media

extract_protocol: At cell harvest, a subset of cells was stored at -20 C in RNALater. Total RNA from 5 X 10^6 cells were purified using Ribopure (Ambion) according to vendor recommended protocols. Total RNA quality was assessed on RNA 6000 Nano Chips (Agilent) using a Bioanalyzer (Agilent).

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

value: Fetal Kidney, Right

value: UW

value: fetal

value: day 115

value: Male


title: ChIP-Seq analysis of WCE in AdiposeNuclei cells; Lib:XZ:20100731:07--ChIP:XZ:20100726:07:AdiposeNuclei:WCE

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:20100731:07--ChIP:XZ:20100726:07:AdiposeNuclei:WCE
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5675
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5946
****************
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: GSM669934_BI.Adipose_Nuclei.Input.92.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100731:07--ChIP:XZ:20100726:07:AdiposeNuclei:WCE.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Adipose Nuclei ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on Adipose Nuclei, 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.6494
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 3

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 61
FINDPEAKS_SCORE: 0.0067
FINDPEAKS_PERCENTILE: 53
HOTSPOT_SCORE: 0.0046
HOTSPOT_PERCENTILE: 17
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.0248
POISSON_PERCENTILE: 7

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

ANALYSIS FILE NAME: GSM669934_BI.Adipose_Nuclei.Input.92.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100731:07--ChIP:XZ:20100726:07:AdiposeNuclei:WCE.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of Adipose Nuclei ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from Adipose Nuclei, 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.6704
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 3
BROWSER_TRACK_NAME: AN Input 92
BROWSER_TRACK_DESCRIPTION: BI Adipose Nuclei ChIP-Seq Input Donor 92 Library Lib:XZ:20100731:07--ChIP:XZ:20100726:07:AdiposeNuclei:WCE EA Release 3

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 61
FINDPEAKS_SCORE: 0.0067
FINDPEAKS_PERCENTILE: 53
HOTSPOT_SCORE: 0.0046
HOTSPOT_PERCENTILE: 17
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.0248
POISSON_PERCENTILE: 7

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

source_name: Nuclei derived from crude preps of adipose tissue; Lib:XZ:20100731:07--ChIP:XZ:20100726:07:AdiposeNuclei:WCE

value: Adipose Nuclei

value: surgery

value: genomic DNA

value: Female

value: Primary Tissue

value: abdomen

value: Bioruptor


title: ChIP-Seq analysis of H3K9me3 in AdiposeNuclei cells; Lib:XZ:20100731:27--ChIP:XZ:20100726:27:AdiposeNuclei:H3K9Me3

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:20100731:27--ChIP:XZ:20100726:27:AdiposeNuclei:H3K9Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5674
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5945
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM669933_BI.Adipose_Nuclei.H3K9me3.95.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100731:27--ChIP:XZ:20100726:27:AdiposeNuclei:H3K9Me3.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Adipose Nuclei Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9me3 ChIP-Seq on Adipose Nuclei, Donor 95 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6487
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 3

QUALITY SCORES:
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 60
FINDPEAKS_SCORE: 0.1924
FINDPEAKS_PERCENTILE: 92
HOTSPOT_SCORE: 0.2458
HOTSPOT_PERCENTILE: 96
IROC_SCORE: 0.9244
IROC_PERCENTILE: 88
POISSON_SCORE: 0.4211
POISSON_PERCENTILE: 88

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

ANALYSIS FILE NAME: GSM669933_BI.Adipose_Nuclei.H3K9me3.95.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100731:27--ChIP:XZ:20100726:27:AdiposeNuclei:H3K9Me3.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of Adipose Nuclei Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9me3 ChIP-Seq read mappings from Adipose Nuclei, Donor 95 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6697
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 3
BROWSER_TRACK_NAME: AN H3K9me3 95
BROWSER_TRACK_DESCRIPTION: BI Adipose Nuclei Histone H3K9me3 Donor 95 Library Lib:XZ:20100731:27--ChIP:XZ:20100726:27:AdiposeNuclei:H3K9Me3 EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 60
FINDPEAKS_SCORE: 0.1924
FINDPEAKS_PERCENTILE: 92
HOTSPOT_SCORE: 0.2458
HOTSPOT_PERCENTILE: 96
IROC_SCORE: 0.9244
IROC_PERCENTILE: 88
POISSON_SCORE: 0.4211
POISSON_PERCENTILE: 88

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

source_name: Nuclei derived from crude preps of adipose tissue; Lib:XZ:20100731:27--ChIP:XZ:20100726:27:AdiposeNuclei:H3K9Me3

value: Harvard University

value: Protein A-Sepharose 4B

value: 10 million cells

value: SDS lysis

value: Abcam

value: Histone H3K9me3


title: ChIP-Seq analysis of H3K4me3 in BM-MSC cells; Lib:MC:20100706:09--ChIP:MC:20100628:09:BM-MSC:H3K4Me3

description:
sample_term_id: EFO_0000586
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:MC:20100706:09--ChIP:MC:20100628:09:BM-MSC:H3K4Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5665
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5953
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM669924_BI.Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K4me3.58.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100706:09--ChIP:MC:20100628:09:BM-MSC:H3K4Me3.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me3 ChIP-Seq on Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells, Donor 58 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6573
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 3

QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.4313
FINDPEAKS_PERCENTILE: 64
HOTSPOT_SCORE: 0.461
HOTSPOT_PERCENTILE: 64
IROC_SCORE: 0.9927
IROC_PERCENTILE: 20
POISSON_SCORE: 0.4979
POISSON_PERCENTILE: 64

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

ANALYSIS FILE NAME: GSM669924_BI.Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K4me3.58.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100706:09--ChIP:MC:20100628:09:BM-MSC:H3K4Me3.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me3 ChIP-Seq read mappings from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells, Donor 58 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6783
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 3
BROWSER_TRACK_NAME: BMDMSC H3K4me3 58
BROWSER_TRACK_DESCRIPTION: BI Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K4me3 Donor 58 Library Lib:MC:20100706:09--ChIP:MC:20100628:09:BM-MSC:H3K4Me3 EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.4313
FINDPEAKS_PERCENTILE: 64
HOTSPOT_SCORE: 0.461
HOTSPOT_PERCENTILE: 64
IROC_SCORE: 0.9927
IROC_PERCENTILE: 20
POISSON_SCORE: 0.4979
POISSON_PERCENTILE: 64

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

source_name: bone marrow was aspirated from the iliac crest, isolated by density gradient and adhesion to plastic, and expanded in monolayer culture, containing 10% FBS; Lib:MC:20100706:09--ChIP:MC:20100628:09:BM-MSC:H3K4Me3

value: healthy

value: BM-MSC

value: Unknown

value: Primary Cell Culture

value: Rikshospitalet University Hospital

value: 70 ul bed volume

value: Millipore

value: Histone H3K4me3


title: ChIP-Seq analysis of H3K4me3 in AdiposeNuclei cells; Lib:XZ:20100731:02--ChIP:XZ:20100726:02:AdiposeNuclei:H3K4Me3

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:20100731:02--ChIP:XZ:20100726:02:AdiposeNuclei:H3K4Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5666
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5946
****************
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: GSM669925_BI.Adipose_Nuclei.H3K4me3.92.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100731:02--ChIP:XZ:20100726:02:AdiposeNuclei:H3K4Me3.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Adipose Nuclei Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me3 ChIP-Seq on Adipose Nuclei, 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.6497
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 3

QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.4303
FINDPEAKS_PERCENTILE: 60
HOTSPOT_SCORE: 0.4353
HOTSPOT_PERCENTILE: 60
IROC_SCORE: 0.9997
IROC_PERCENTILE: 76
POISSON_SCORE: 0.4553
POISSON_PERCENTILE: 56

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

ANALYSIS FILE NAME: GSM669925_BI.Adipose_Nuclei.H3K4me3.92.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100731:02--ChIP:XZ:20100726:02:AdiposeNuclei:H3K4Me3.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of Adipose Nuclei Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me3 ChIP-Seq read mappings from Adipose Nuclei, 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.6707
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 3
BROWSER_TRACK_NAME: AN H3K4me3 92
BROWSER_TRACK_DESCRIPTION: BI Adipose Nuclei Histone H3K4me3 Donor 92 Library Lib:XZ:20100731:02--ChIP:XZ:20100726:02:AdiposeNuclei:H3K4Me3 EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.4303
FINDPEAKS_PERCENTILE: 60
HOTSPOT_SCORE: 0.4353
HOTSPOT_PERCENTILE: 60
IROC_SCORE: 0.9997
IROC_PERCENTILE: 76
POISSON_SCORE: 0.4553
POISSON_PERCENTILE: 56

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

source_name: Nuclei derived from crude preps of adipose tissue; Lib:XZ:20100731:02--ChIP:XZ:20100726:02:AdiposeNuclei:H3K4Me3

value: Adipose Nuclei

value: surgery

value: genomic DNA

value: Female

value: Primary Tissue


title: ChIP-Seq analysis of H3K4me1; chondr. dif cls; Lib:MC:20100729:08--ChIP:MC:20100726:08:chondrogenic dif cells:H3K4Me1

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:MC:20100729:08--ChIP:MC:20100726:08:chondrogenic dif cells:H3K4Me1
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5668
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: GSM669927_BI.Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K4me1.60.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100729:08--ChIP:MC:20100726:08:chondrogenic dif cells:H3K4Me1.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me1 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.6601
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 3

QUALITY SCORES:
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 50
FINDPEAKS_SCORE: 0.5446
FINDPEAKS_PERCENTILE: 86
HOTSPOT_SCORE: 0.5556
HOTSPOT_PERCENTILE: 86
IROC_SCORE: 0.9974
IROC_PERCENTILE: 89
POISSON_SCORE: 0.6642
POISSON_PERCENTILE: 86

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

ANALYSIS FILE NAME: GSM669927_BI.Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K4me1.60.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100729:08--ChIP:MC:20100726:08:chondrogenic dif cells:H3K4Me1.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me1 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.6811
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 3
BROWSER_TRACK_NAME: CfBMDMSC H3K4me1 60
BROWSER_TRACK_DESCRIPTION: BI Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K4me1 Donor 60 Library Lib:MC:20100729:08--ChIP:MC:20100726:08:chondrogenic dif cells:H3K4Me1 EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 50
FINDPEAKS_SCORE: 0.5446
FINDPEAKS_PERCENTILE: 86
HOTSPOT_SCORE: 0.5556
HOTSPOT_PERCENTILE: 86
IROC_SCORE: 0.9974
IROC_PERCENTILE: 89
POISSON_SCORE: 0.6642
POISSON_PERCENTILE: 86

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

source_name: chondrocytes derived via in vitro culture from mesenchymal stem cells; Lib:MC:20100729:08--ChIP:MC:20100726:08:chondrogenic dif cells:H3K4Me1

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

value: chondrogenic dif cells

value: Protein A-Sepharose 4B

value: 10 million cells

value: Histone H3K4me1

value: Bioruptor


title: ChIP-Seq analysis of H3K9ac in BM-MSC cells; Lib:MC:20100713:12--ChIP:MC:20100706:12:BM-MSC:H3K9Ac

description:
sample_term_id: EFO_0000586
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:MC:20100713:12--ChIP:MC:20100706:12:BM-MSC:H3K9Ac
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5724
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5950
****************
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: GSM669983_BI.Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K9ac.60.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100713:12--ChIP:MC:20100706:12:BM-MSC:H3K9Ac.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9ac ChIP-Seq on 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.6467
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 3

QUALITY SCORES:
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 40
FINDPEAKS_SCORE: 0.3734
FINDPEAKS_PERCENTILE: 92
HOTSPOT_SCORE: 0.4019
HOTSPOT_PERCENTILE: 84
IROC_SCORE: 0.9981
IROC_PERCENTILE: 96
POISSON_SCORE: 0.431
POISSON_PERCENTILE: 84

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

ANALYSIS FILE NAME: GSM669983_BI.Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K9ac.60.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100713:12--ChIP:MC:20100706:12:BM-MSC:H3K9Ac.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9ac ChIP-Seq read mappings 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.6677
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 3
BROWSER_TRACK_NAME: BMDMSC H3K9ac 60
BROWSER_TRACK_DESCRIPTION: BI Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K9ac Donor 60 Library Lib:MC:20100713:12--ChIP:MC:20100706:12:BM-MSC:H3K9Ac EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 40
FINDPEAKS_SCORE: 0.3734
FINDPEAKS_PERCENTILE: 92
HOTSPOT_SCORE: 0.4019
HOTSPOT_PERCENTILE: 84
IROC_SCORE: 0.9981
IROC_PERCENTILE: 96
POISSON_SCORE: 0.431
POISSON_PERCENTILE: 84

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

source_name: bone marrow was aspirated from the iliac crest, isolated by density gradient and adhesion to plastic, and expanded in monolayer culture, containing 10% FBS; Lib:MC:20100713:12--ChIP:MC:20100706:12:BM-MSC:H3K9Ac

value: healthy

value: BM-MSC

value: Unknown

value: SDS lysis

value: Abcam

value: Histone H3K9ac


title: ChIP-Seq analysis of H3K9ac; stomach sm musc cls; Lib:XZ:20100827:05--ChIP:XZ:20100824:05:stomach smooth muscle:H3K9Ac

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: Lib:XZ:20100827:05--ChIP:XZ:20100824:05:stomach smooth muscle:H3K9Ac
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5662
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3346
****************
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: GSM669921_BI.Stomach_Smooth_Muscle.H3K9ac.28.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100827:05--ChIP:XZ:20100824:05:stomach smooth muscle:H3K9Ac.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Stomach Smooth Muscle Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9ac ChIP-Seq on Stomach Smooth Muscle, Donor 28 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6453
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 3

QUALITY SCORES:
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 40
FINDPEAKS_SCORE: 0.1022
FINDPEAKS_PERCENTILE: 12
HOTSPOT_SCORE: 0.1402
HOTSPOT_PERCENTILE: 12
IROC_SCORE: 0.9959
IROC_PERCENTILE: 76
POISSON_SCORE: 0.204
POISSON_PERCENTILE: 8

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

ANALYSIS FILE NAME: GSM669921_BI.Stomach_Smooth_Muscle.H3K9ac.28.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100827:05--ChIP:XZ:20100824:05:stomach smooth muscle:H3K9Ac.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of Stomach Smooth Muscle Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9ac ChIP-Seq read mappings from Stomach Smooth Muscle, Donor 28 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6663
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 3
BROWSER_TRACK_NAME: SSM H3K9ac 28
BROWSER_TRACK_DESCRIPTION: BI Stomach Smooth Muscle Histone H3K9ac Donor 28 Library Lib:XZ:20100827:05--ChIP:XZ:20100824:05:stomach smooth muscle:H3K9Ac EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 40
FINDPEAKS_SCORE: 0.1022
FINDPEAKS_PERCENTILE: 12
HOTSPOT_SCORE: 0.1402
HOTSPOT_PERCENTILE: 12
IROC_SCORE: 0.9959
IROC_PERCENTILE: 76
POISSON_SCORE: 0.204
POISSON_PERCENTILE: 8

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

source_name: Primary gastric smooth muscle tissue; Lib:XZ:20100827:05--ChIP:XZ:20100824:05:stomach smooth muscle:H3K9Ac

value: Stomach Smooth Muscle

value: normal smooth muscle

value: smooth muscle

value: white

value: stomach

value: MGH Pathology

value: 70 ul bed volume


title: ChIP-Seq analysis of H3K4me1 in BM-MSC cells; Lib:MC:20100713:01--ChIP:MC:20100706:01:BM-MSC:H3K4Me1

description:
sample_term_id: EFO_0000586
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:MC:20100713:01--ChIP:MC:20100706:01:BM-MSC:H3K4Me1
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5661
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5948
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM669920_BI.Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K4me1.59.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100713:01--ChIP:MC:20100706:01:BM-MSC:H3K4Me1.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me1 ChIP-Seq on Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells, Donor 59 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6522
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 3

QUALITY SCORES:
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 50
FINDPEAKS_SCORE: 0.2691
FINDPEAKS_PERCENTILE: 43
HOTSPOT_SCORE: 0.3279
HOTSPOT_PERCENTILE: 36
IROC_SCORE: 0.9796
IROC_PERCENTILE: 54
POISSON_SCORE: 0.438
POISSON_PERCENTILE: 36

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

ANALYSIS FILE NAME: GSM669920_BI.Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K4me1.59.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100713:01--ChIP:MC:20100706:01:BM-MSC:H3K4Me1.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me1 ChIP-Seq read mappings from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells, Donor 59 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6732
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 3
BROWSER_TRACK_NAME: BMDMSC H3K4me1 59
BROWSER_TRACK_DESCRIPTION: BI Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K4me1 Donor 59 Library Lib:MC:20100713:01--ChIP:MC:20100706:01:BM-MSC:H3K4Me1 EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 50
FINDPEAKS_SCORE: 0.2691
FINDPEAKS_PERCENTILE: 43
HOTSPOT_SCORE: 0.3279
HOTSPOT_PERCENTILE: 36
IROC_SCORE: 0.9796
IROC_PERCENTILE: 54
POISSON_SCORE: 0.438
POISSON_PERCENTILE: 36

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

source_name: bone marrow was aspirated from the iliac crest, isolated by density gradient and adhesion to plastic, and expanded in monolayer culture, containing 10% FBS; Lib:MC:20100713:01--ChIP:MC:20100706:01:BM-MSC:H3K4Me1

value: genomic DNA

value: Primary Cell Culture

value: Rikshospitalet University Hospital

value: Protein A-Sepharose 4B


title: ChIP-Seq analysis of H3K9me3; chondr. dif cls; Lib:MC:20100726:07--ChIP:MC:20100713:07:chondrogenic dif cells:WCE

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:MC:20100726:07--ChIP:MC:20100713:07:chondrogenic dif cells:WCE
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5660
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5949
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM669919_BI.Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K9me3.58.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100726:07--ChIP:MC:20100713:07:chondrogenic dif cells:WCE.hg19.level.1.release.3
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 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.6528
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 3

QUALITY SCORES:
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 60
FINDPEAKS_SCORE: 0.0408
FINDPEAKS_PERCENTILE: 42
HOTSPOT_SCORE: 0.1024
HOTSPOT_PERCENTILE: 38
IROC_SCORE: 0.7108
IROC_PERCENTILE: 8
POISSON_SCORE: 0.282
POISSON_PERCENTILE: 38

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

ANALYSIS FILE NAME: GSM669919_BI.Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K9me3.58.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100726:07--ChIP:MC:20100713:07:chondrogenic dif cells:WCE.hg19.level.2.release.3
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 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.6738
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 3
BROWSER_TRACK_NAME: CfBMDMSC H3K9me3 58
BROWSER_TRACK_DESCRIPTION: BI Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K9me3 Donor 58 Library Lib:MC:20100726:07--ChIP:MC:20100713:07:chondrogenic dif cells:WCE EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 60
FINDPEAKS_SCORE: 0.0408
FINDPEAKS_PERCENTILE: 42
HOTSPOT_SCORE: 0.1024
HOTSPOT_PERCENTILE: 38
IROC_SCORE: 0.7108
IROC_PERCENTILE: 8
POISSON_SCORE: 0.282
POISSON_PERCENTILE: 38

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

source_name: chondrocytes derived via in vitro culture from mesenchymal stem cells; Lib:MC:20100726:07--ChIP:MC:20100713:07:chondrogenic dif cells:WCE

value: healthy

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

value: chondrogenic dif cells

value: 10 million cells

value: Histone H3K9me3

value: Bioruptor


title: ChIP-Seq analysis of H3K9ac; chondr. dif cls; Lib:MC:20100726:05--ChIP:MC:20100713:05:chondrogenic dif cells:H3K9Ac

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:MC:20100726:05--ChIP:MC:20100713:05:chondrogenic dif cells:H3K9Ac
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5658
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5949
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM669917_BI.Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K9ac.57.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100726:05--ChIP:MC:20100713:05:chondrogenic dif cells:H3K9Ac.hg19.level.1.release.3
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 57 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6574
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 3

QUALITY SCORES:
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 40
FINDPEAKS_SCORE: 0.3625
FINDPEAKS_PERCENTILE: 84
HOTSPOT_SCORE: 0.4024
HOTSPOT_PERCENTILE: 88
IROC_SCORE: 0.9899
IROC_PERCENTILE: 32
POISSON_SCORE: 0.4566
POISSON_PERCENTILE: 92

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

ANALYSIS FILE NAME: GSM669917_BI.Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K9ac.57.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100726:05--ChIP:MC:20100713:05:chondrogenic dif cells:H3K9Ac.hg19.level.2.release.3
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 57 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6784
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 3
BROWSER_TRACK_NAME: CfBMDMSC H3K9ac 57
BROWSER_TRACK_DESCRIPTION: BI Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K9ac Donor 57 Library Lib:MC:20100726:05--ChIP:MC:20100713:05:chondrogenic dif cells:H3K9Ac EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 40
FINDPEAKS_SCORE: 0.3625
FINDPEAKS_PERCENTILE: 84
HOTSPOT_SCORE: 0.4024
HOTSPOT_PERCENTILE: 88
IROC_SCORE: 0.9899
IROC_PERCENTILE: 32
POISSON_SCORE: 0.4566
POISSON_PERCENTILE: 92

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

source_name: chondrocytes derived via in vitro culture from mesenchymal stem cells; Lib:MC:20100726:05--ChIP:MC:20100713:05:chondrogenic dif cells:H3K9Ac

value: Unknown

value: SDS lysis

value: Abcam

value: Histone H3K9ac


title: ChIP-Seq analysis of H3K36me3; chondr. dif cls; Lib:MC:20100729:03--ChIP:MC:20100726:03:chondrogenic dif cells:H3K36Me3

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:MC:20100729:03--ChIP:MC:20100726:03:chondrogenic dif cells:H3K36Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5655
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5935
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM669914_BI.Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K36me3.59.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100729:03--ChIP:MC:20100726:03:chondrogenic dif cells:H3K36Me3.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K36me3 ChIP-Seq on Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells, Donor 59 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6449
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 3

QUALITY SCORES:
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 59
FINDPEAKS_SCORE: 0.4005
FINDPEAKS_PERCENTILE: 85
HOTSPOT_SCORE: 0.3415
HOTSPOT_PERCENTILE: 77
IROC_SCORE: 0.992
IROC_PERCENTILE: 73
POISSON_SCORE: 0.5752
POISSON_PERCENTILE: 85

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

ANALYSIS FILE NAME: GSM669914_BI.Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K36me3.59.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100729:03--ChIP:MC:20100726:03:chondrogenic dif cells:H3K36Me3.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K36me3 ChIP-Seq read mappings from Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells, Donor 59 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6659
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 3
BROWSER_TRACK_NAME: CfBMDMSC H3K36me3 59
BROWSER_TRACK_DESCRIPTION: BI Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K36me3 Donor 59 Library Lib:MC:20100729:03--ChIP:MC:20100726:03:chondrogenic dif cells:H3K36Me3 EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 59
FINDPEAKS_SCORE: 0.4005
FINDPEAKS_PERCENTILE: 85
HOTSPOT_SCORE: 0.3415
HOTSPOT_PERCENTILE: 77
IROC_SCORE: 0.992
IROC_PERCENTILE: 73
POISSON_SCORE: 0.5752
POISSON_PERCENTILE: 85

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

source_name: chondrocytes derived via in vitro culture from mesenchymal stem cells; Lib:MC:20100729:03--ChIP:MC:20100726:03:chondrogenic dif cells:H3K36Me3

value: Histone H3K36me3


title: ChIP-Seq analysis of H3K27me3; chondr. dif cls; Lib:MC:20100729:04--ChIP:MC:20100726:04:chondrogenic dif cells:H3K27Me3

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:MC:20100729:04--ChIP:MC:20100726:04:chondrogenic dif cells:H3K27Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5657
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5935
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM669916_BI.Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K27me3.59.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100729:04--ChIP:MC:20100726:04:chondrogenic dif cells:H3K27Me3.hg19.level.1.release.3
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 59 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6550
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 3

QUALITY SCORES:
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 52
FINDPEAKS_SCORE: 0.1474
FINDPEAKS_PERCENTILE: 75
HOTSPOT_SCORE: 0.214
HOTSPOT_PERCENTILE: 75
IROC_SCORE: 0.927
IROC_PERCENTILE: 75
POISSON_SCORE: 0.5054
POISSON_PERCENTILE: 95

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

ANALYSIS FILE NAME: GSM669916_BI.Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K27me3.59.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100729:04--ChIP:MC:20100726:04:chondrogenic dif cells:H3K27Me3.hg19.level.2.release.3
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 59 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6760
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 3
BROWSER_TRACK_NAME: CfBMDMSC H3K27me3 59
BROWSER_TRACK_DESCRIPTION: BI Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K27me3 Donor 59 Library Lib:MC:20100729:04--ChIP:MC:20100726:04:chondrogenic dif cells:H3K27Me3 EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 52
FINDPEAKS_SCORE: 0.1474
FINDPEAKS_PERCENTILE: 75
HOTSPOT_SCORE: 0.214
HOTSPOT_PERCENTILE: 75
IROC_SCORE: 0.927
IROC_PERCENTILE: 75
POISSON_SCORE: 0.5054
POISSON_PERCENTILE: 95

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

source_name: chondrocytes derived via in vitro culture from mesenchymal stem cells; Lib:MC:20100729:04--ChIP:MC:20100726:04:chondrogenic dif cells:H3K27Me3

value: Millipore

value: Histone H3K27me3


title: ChIP-Seq analysis of H3K4me1 in AdiposeNuclei cells; Lib:XZ:20100731:01--ChIP:XZ:20100726:01:AdiposeNuclei:H3K4Me1

description:
sample_term_id: UBERON_0014455
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:XZ:20100731:01--ChIP:XZ:20100726:01:AdiposeNuclei:H3K4Me1
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5649
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5946
****************
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: GSM669908_BI.Adipose_Nuclei.H3K4me1.92.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100731:01--ChIP:XZ:20100726:01:AdiposeNuclei:H3K4Me1.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Adipose Nuclei Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me1 ChIP-Seq on Adipose Nuclei, Donor 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.6594
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 3

QUALITY SCORES:
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 50
FINDPEAKS_SCORE: 0.427
FINDPEAKS_PERCENTILE: 71
HOTSPOT_SCORE: 0.4587
HOTSPOT_PERCENTILE: 68
IROC_SCORE: 0.9931
IROC_PERCENTILE: 64
POISSON_SCORE: 0.591
POISSON_PERCENTILE: 75

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

ANALYSIS FILE NAME: GSM669908_BI.Adipose_Nuclei.H3K4me1.92.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100731:01--ChIP:XZ:20100726:01:AdiposeNuclei:H3K4Me1.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of Adipose Nuclei Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me1 ChIP-Seq read mappings from Adipose Nuclei, Donor 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.6804
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 3
BROWSER_TRACK_NAME: AN H3K4me1 92
BROWSER_TRACK_DESCRIPTION: BI Adipose Nuclei Histone H3K4me1 Donor 92 Library Lib:XZ:20100731:01--ChIP:XZ:20100726:01:AdiposeNuclei:H3K4Me1 EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 50
FINDPEAKS_SCORE: 0.427
FINDPEAKS_PERCENTILE: 71
HOTSPOT_SCORE: 0.4587
HOTSPOT_PERCENTILE: 68
IROC_SCORE: 0.9931
IROC_PERCENTILE: 64
POISSON_SCORE: 0.591
POISSON_PERCENTILE: 75

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

source_name: Nuclei derived from crude preps of adipose tissue; Lib:XZ:20100731:01--ChIP:XZ:20100726:01:AdiposeNuclei:H3K4Me1

value: Adipose Nuclei

value: surgery

value: genomic DNA

value: Female

value: Primary Tissue

value: abdomen

value: Harvard University

value: 70 ul bed volume

value: Histone H3K4me1


title: ChIP-Seq analysis of H3K4me1 in BM-MSC cells; Lib:MC:20100706:08--ChIP:MC:20100628:08:BM-MSC:H3K4Me1

description:
sample_term_id: EFO_0000586
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:MC:20100706:08--ChIP:MC:20100628:08:BM-MSC:H3K4Me1
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5652
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5953
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM669911_BI.Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K4me1.58.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100706:08--ChIP:MC:20100628:08:BM-MSC:H3K4Me1.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me1 ChIP-Seq on Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells, Donor 58 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6517
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 3

QUALITY SCORES:
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 50
FINDPEAKS_SCORE: 0.5675
FINDPEAKS_PERCENTILE: 89
HOTSPOT_SCORE: 0.5693
HOTSPOT_PERCENTILE: 89
IROC_SCORE: 0.9985
IROC_PERCENTILE: 96
POISSON_SCORE: 0.6662
POISSON_PERCENTILE: 89

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

ANALYSIS FILE NAME: GSM669911_BI.Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K4me1.58.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100706:08--ChIP:MC:20100628:08:BM-MSC:H3K4Me1.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me1 ChIP-Seq read mappings from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells, Donor 58 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6727
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 3
BROWSER_TRACK_NAME: BMDMSC H3K4me1 58
BROWSER_TRACK_DESCRIPTION: BI Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K4me1 Donor 58 Library Lib:MC:20100706:08--ChIP:MC:20100628:08:BM-MSC:H3K4Me1 EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 50
FINDPEAKS_SCORE: 0.5675
FINDPEAKS_PERCENTILE: 89
HOTSPOT_SCORE: 0.5693
HOTSPOT_PERCENTILE: 89
IROC_SCORE: 0.9985
IROC_PERCENTILE: 96
POISSON_SCORE: 0.6662
POISSON_PERCENTILE: 89

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

source_name: bone marrow was aspirated from the iliac crest, isolated by density gradient and adhesion to plastic, and expanded in monolayer culture, containing 10% FBS; Lib:MC:20100706:08--ChIP:MC:20100628:08:BM-MSC:H3K4Me1

value: healthy

value: BM-MSC

value: Primary Cell Culture

value: Rikshospitalet University Hospital

value: Protein A-Sepharose 4B

value: 10 million cells

value: Bioruptor


title: ChIP-Seq analysis of H3K9ac in AdiposeNuclei cells; Lib:XZ:20100731:05--ChIP:XZ:20100726:05: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:20100731:05--ChIP:XZ:20100726:05:AdiposeNuclei:H3K9Ac
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5645
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5946
****************
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: GSM669904_BI.Adipose_Nuclei.H3K9ac.92.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100731:05--ChIP:XZ:20100726:05:AdiposeNuclei:H3K9Ac.hg19.level.1.release.3
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 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.6456
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 3

QUALITY SCORES:
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 40
FINDPEAKS_SCORE: 0.1151
FINDPEAKS_PERCENTILE: 16
HOTSPOT_SCORE: 0.1718
HOTSPOT_PERCENTILE: 16
IROC_SCORE: 0.995
IROC_PERCENTILE: 68
POISSON_SCORE: 0.2523
POISSON_PERCENTILE: 20

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

ANALYSIS FILE NAME: GSM669904_BI.Adipose_Nuclei.H3K9ac.92.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100731:05--ChIP:XZ:20100726:05:AdiposeNuclei:H3K9Ac.hg19.level.2.release.3
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 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.6666
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 3
BROWSER_TRACK_NAME: AN H3K9ac 92
BROWSER_TRACK_DESCRIPTION: BI Adipose Nuclei Histone H3K9ac Donor 92 Library Lib:XZ:20100731:05--ChIP:XZ:20100726:05:AdiposeNuclei:H3K9Ac EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 40
FINDPEAKS_SCORE: 0.1151
FINDPEAKS_PERCENTILE: 16
HOTSPOT_SCORE: 0.1718
HOTSPOT_PERCENTILE: 16
IROC_SCORE: 0.995
IROC_PERCENTILE: 68
POISSON_SCORE: 0.2523
POISSON_PERCENTILE: 20

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

source_name: Nuclei derived from crude preps of adipose tissue; Lib:XZ:20100731:05--ChIP:XZ:20100726:05:AdiposeNuclei:H3K9Ac

value: SDS lysis

value: Abcam

value: Histone H3K9ac


title: ChIP-Seq analysis of H3K9me3; chondr. dif cls; Lib:MC:20100729:06--ChIP:MC:20100726:06:chondrogenic dif cells:H3K9Me3

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:MC:20100729:06--ChIP:MC:20100726:06:chondrogenic dif cells:H3K9Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5764
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5935
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM670023_BI.Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K9me3.59.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100729:06--ChIP:MC:20100726:06:chondrogenic dif cells:H3K9Me3.hg19.level.1.release.3
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 59 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6531
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 3

QUALITY SCORES:
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 60
FINDPEAKS_SCORE: 0.0457
FINDPEAKS_PERCENTILE: 50
HOTSPOT_SCORE: 0.1132
HOTSPOT_PERCENTILE: 46
IROC_SCORE: 0.7126
IROC_PERCENTILE: 12
POISSON_SCORE: 0.3397
POISSON_PERCENTILE: 65

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

ANALYSIS FILE NAME: GSM670023_BI.Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K9me3.59.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100729:06--ChIP:MC:20100726:06:chondrogenic dif cells:H3K9Me3.hg19.level.2.release.3
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 59 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6741
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 3
BROWSER_TRACK_NAME: CfBMDMSC H3K9me3 59
BROWSER_TRACK_DESCRIPTION: BI Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K9me3 Donor 59 Library Lib:MC:20100729:06--ChIP:MC:20100726:06:chondrogenic dif cells:H3K9Me3 EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 60
FINDPEAKS_SCORE: 0.0457
FINDPEAKS_PERCENTILE: 50
HOTSPOT_SCORE: 0.1132
HOTSPOT_PERCENTILE: 46
IROC_SCORE: 0.7126
IROC_PERCENTILE: 12
POISSON_SCORE: 0.3397
POISSON_PERCENTILE: 65

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

source_name: chondrocytes derived via in vitro culture from mesenchymal stem cells; Lib:MC:20100729:06--ChIP:MC:20100726:06:chondrogenic dif cells:H3K9Me3

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: Unknown

value: Histone H3K9me3


title: ChIP-Seq analysis of H3K9ac in AdiposeNuclei cells; Lib:XZ:20100731:12--ChIP:XZ:20100726:12: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:20100731:12--ChIP:XZ:20100726:12:AdiposeNuclei:H3K9Ac
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5663
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: GSM669922_BI.Adipose_Nuclei.H3K9ac.93.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100731:12--ChIP:XZ:20100726:12:AdiposeNuclei:H3K9Ac.hg19.level.1.release.3
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 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.6457
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 3

QUALITY SCORES:
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 40
FINDPEAKS_SCORE: 0.1408
FINDPEAKS_PERCENTILE: 36
HOTSPOT_SCORE: 0.2159
HOTSPOT_PERCENTILE: 44
IROC_SCORE: 0.9889
IROC_PERCENTILE: 24
POISSON_SCORE: 0.2975
POISSON_PERCENTILE: 44

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

ANALYSIS FILE NAME: GSM669922_BI.Adipose_Nuclei.H3K9ac.93.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100731:12--ChIP:XZ:20100726:12:AdiposeNuclei:H3K9Ac.hg19.level.2.release.3
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 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.6667
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 3
BROWSER_TRACK_NAME: AN H3K9ac 93
BROWSER_TRACK_DESCRIPTION: BI Adipose Nuclei Histone H3K9ac Donor 93 Library Lib:XZ:20100731:12--ChIP:XZ:20100726:12:AdiposeNuclei:H3K9Ac EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 40
FINDPEAKS_SCORE: 0.1408
FINDPEAKS_PERCENTILE: 36
HOTSPOT_SCORE: 0.2159
HOTSPOT_PERCENTILE: 44
IROC_SCORE: 0.9889
IROC_PERCENTILE: 24
POISSON_SCORE: 0.2975
POISSON_PERCENTILE: 44

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

source_name: Nuclei derived from crude preps of adipose tissue; Lib:XZ:20100731:12--ChIP:XZ:20100726:12:AdiposeNuclei:H3K9Ac

value: Adipose Nuclei

value: surgery

value: Female

value: Primary Tissue

value: abdomen

value: Harvard University

value: 70 ul bed volume