title: ChIP-Seq analysis of H3K9me3 in human Duodenum smooth muscle cells; DNA_Lib 460

description:
sample_term_id: UBERON_0012488
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 460
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8599
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9450
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM772909_BI.Duodenum_Smooth_Muscle.H3K9me3.160.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 460-DNA_Lib 460-DNA_Lib 460-DNA_Lib 460.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Duodenum Smooth Muscle Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9me3 ChIP-Seq on Duodenum Smooth Muscle, Donor 160, were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.10800
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 32,280,370
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.0206
FINDPEAKS_PERCENTILE: 29
HOTSPOT_SCORE: 0.0602
HOTSPOT_PERCENTILE: 16
IROC_SCORE: 0.872
IROC_PERCENTILE: 61
POISSON_SCORE: 0.1591
POISSON_PERCENTILE: 20
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM772909_BI.Duodenum_Smooth_Muscle.H3K9me3.160.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 460-DNA_Lib 460-DNA_Lib 460-DNA_Lib 460.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Duodenum Smooth Muscle Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9me3 ChIP-Seq read mappings from Duodenum Smooth Muscle, Donor 160, were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.11064
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 5
BROWSER_TRACK_NAME: DSM H3K9me3 60 60
BROWSER_TRACK_DESCRIPTION: BI Duodenum Smooth Muscle Histone H3K9me3 Donor 160 Library DNA_Lib 460 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 32,280,370
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.0206
FINDPEAKS_PERCENTILE: 29
HOTSPOT_SCORE: 0.0602
HOTSPOT_PERCENTILE: 16
IROC_SCORE: 0.872
IROC_PERCENTILE: 61
POISSON_SCORE: 0.1591
POISSON_PERCENTILE: 20
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: Primary duodenum smooth muscle tissue; DNA_Lib 460

value: Duodenum Smooth Muscle

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

value: Smooth Muscle

value: Duodenum

value: Protein A-Sepharose 4B

value: 0.5 to 3 million cells

value: cell/nuclei lysis

value: ~1 ug


title: ChIP-Seq analysis of H3K27ac in human Duodenum smooth muscle cells; DNA_Lib 462

status: Public on Dec 28 2011

type: SRA

city: Cambridge

first: BROAD

last: INSTITUTE

state: MA

country: USA

institute: Broad Institute

description:
sample_term_id: UBERON_0012488
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 462
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8598
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9450
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

library_source: genomic

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

ANALYSIS FILE NAME: GSM772908_BI.Duodenum_Smooth_Muscle.H3K27ac.160.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 462-DNA_Lib 462-DNA_Lib 462-DNA_Lib 462.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Duodenum Smooth Muscle Histone H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27ac ChIP-Seq on Duodenum Smooth Muscle, Donor 160, were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.10668
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 30,933,844
NUMBER_OF_H3K27ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 34
FINDPEAKS_SCORE: 0.1606
FINDPEAKS_PERCENTILE: 41
HOTSPOT_SCORE: 0.2224
HOTSPOT_PERCENTILE: 32
IROC_SCORE: 0.9855
IROC_PERCENTILE: 47
POISSON_SCORE: 0.2985
POISSON_PERCENTILE: 38
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM772908_BI.Duodenum_Smooth_Muscle.H3K27ac.160.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 462-DNA_Lib 462-DNA_Lib 462-DNA_Lib 462.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Duodenum Smooth Muscle Histone H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27ac ChIP-Seq read mappings from Duodenum Smooth Muscle, Donor 160, were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.10932
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 5
BROWSER_TRACK_NAME: DSM H3K27ac 60 62
BROWSER_TRACK_DESCRIPTION: BI Duodenum Smooth Muscle Histone H3K27ac Donor 160 Library DNA_Lib 462 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 30,933,844
NUMBER_OF_H3K27ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 34
FINDPEAKS_SCORE: 0.1606
FINDPEAKS_PERCENTILE: 41
HOTSPOT_SCORE: 0.2224
HOTSPOT_PERCENTILE: 32
IROC_SCORE: 0.9855
IROC_PERCENTILE: 47
POISSON_SCORE: 0.2985
POISSON_PERCENTILE: 38
MAXIMUM_REPLICATE_CORRELATION: NA

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

molecule: genomic DNA

organism: Homo sapiens

source_name: Primary duodenum smooth muscle tissue; DNA_Lib 462

extract_protocol: Library construction protocol: Single read - Illumina

tag: sample alias

tag: sample common name

value: Surgery

tag: molecule

value: genomic DNA

tag: disease

value: Caucasian

value: Male

value: Primary Tissue

value: MGH

value: 59.0 Years

value: 10 ul bed volume

value: Abcam

value: Histone H3K27ac

value: Branson


title: ChIP-Seq analysis of H3K4me1 in human stomach mucosa cells; DNA_Lib 318

description:
sample_term_id: UBERON_0001199
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 318
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8597
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9453
****************
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: GSM772907_BI.Stomach_Mucosa.H3K4me1.157.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 318-DNA_Lib 318-DNA_Lib 318-DNA_Lib 318.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Stomach Mucosa Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me1 ChIP-Seq on Stomach Mucosa, Donor 157, 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.10634
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 27,839,668
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.2296
FINDPEAKS_PERCENTILE: 33
HOTSPOT_SCORE: 0.3063
HOTSPOT_PERCENTILE: 39
IROC_SCORE: 0.9668
IROC_PERCENTILE: 48
POISSON_SCORE: 0.462
POISSON_PERCENTILE: 50
MAXIMUM_REPLICATE_CORRELATION: 0.69

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

ANALYSIS FILE NAME: GSM772907_BI.Stomach_Mucosa.H3K4me1.157.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 318-DNA_Lib 318-DNA_Lib 318-DNA_Lib 318.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Stomach Mucosa Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me1 ChIP-Seq read mappings from Stomach Mucosa, Donor 157, 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.10898
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 5
BROWSER_TRACK_NAME: SM H3K4me1 57 18
BROWSER_TRACK_DESCRIPTION: BI Stomach Mucosa Histone H3K4me1 Donor 157 Library DNA_Lib 318 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 27,839,668
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.2296
FINDPEAKS_PERCENTILE: 33
HOTSPOT_SCORE: 0.3063
HOTSPOT_PERCENTILE: 39
IROC_SCORE: 0.9668
IROC_PERCENTILE: 48
POISSON_SCORE: 0.462
POISSON_PERCENTILE: 50
MAXIMUM_REPLICATE_CORRELATION: 0.69

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

source_name: Primary stomach mucosal tissue; DNA_Lib 318

value: Stomach Mucosa

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

value: Stomach

value: Histone H3K4me1


title: ChIP-Seq analysis of WCE in human Duodenum smooth muscle cells; DNA_Lib 461

description:
sample_term_id: UBERON_0012488
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 461
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8600
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9450
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM772910_BI.Duodenum_Smooth_Muscle.Input.160.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 461-DNA_Lib 461-DNA_Lib 461-DNA_Lib 461.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Duodenum Smooth Muscle ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on Duodenum Smooth Muscle, Donor 160, were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.10592
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 55,001,186
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 56
FINDPEAKS_SCORE: 0.0048
FINDPEAKS_PERCENTILE: 38
HOTSPOT_SCORE: 0.0026
HOTSPOT_PERCENTILE: 3
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.0216
POISSON_PERCENTILE: 10
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM772910_BI.Duodenum_Smooth_Muscle.Input.160.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 461-DNA_Lib 461-DNA_Lib 461-DNA_Lib 461.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Duodenum Smooth Muscle ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from Duodenum Smooth Muscle, Donor 160, were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.10856
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 5
BROWSER_TRACK_NAME: DSM Input 60 61
BROWSER_TRACK_DESCRIPTION: BI Duodenum Smooth Muscle ChIP-Seq Input Donor 160 Library DNA_Lib 461 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 55,001,186
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 56
FINDPEAKS_SCORE: 0.0048
FINDPEAKS_PERCENTILE: 38
HOTSPOT_SCORE: 0.0026
HOTSPOT_PERCENTILE: 3
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.0216
POISSON_PERCENTILE: 10
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: Primary duodenum smooth muscle tissue; DNA_Lib 461

value: Duodenum Smooth Muscle

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

value: Smooth Muscle

value: Duodenum

value: standard

value: cell/nuclei lysis

value: ChIP-Seq Input

value: Input


title: ChIP-Seq analysis of H3K9ac in human stomach smooth muscle cells; DNA_Lib 380

description:
sample_term_id: UBERON_0008856
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 380
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8576
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9451
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM772886_BI.Stomach_Smooth_Muscle.H3K9ac.161.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 380-DNA_Lib 380-DNA_Lib 380-DNA_Lib 380.hg19.level.1.release.5
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 161, were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.10740
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 26,198,597
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 19
FINDPEAKS_SCORE: 0.2045
FINDPEAKS_PERCENTILE: 68
HOTSPOT_SCORE: 0.2581
HOTSPOT_PERCENTILE: 63
IROC_SCORE: 0.9973
IROC_PERCENTILE: 84
POISSON_SCORE: 0.3227
POISSON_PERCENTILE: 68
MAXIMUM_REPLICATE_CORRELATION: 0.95

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

ANALYSIS FILE NAME: GSM772886_BI.Stomach_Smooth_Muscle.H3K9ac.161.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 380-DNA_Lib 380-DNA_Lib 380-DNA_Lib 380.hg19.level.2.release.5
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 161, were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.11004
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 5
BROWSER_TRACK_NAME: SSM H3K9ac 61 80
BROWSER_TRACK_DESCRIPTION: BI Stomach Smooth Muscle Histone H3K9ac Donor 161 Library DNA_Lib 380 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 26,198,597
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 19
FINDPEAKS_SCORE: 0.2045
FINDPEAKS_PERCENTILE: 68
HOTSPOT_SCORE: 0.2581
HOTSPOT_PERCENTILE: 63
IROC_SCORE: 0.9973
IROC_PERCENTILE: 84
POISSON_SCORE: 0.3227
POISSON_PERCENTILE: 68
MAXIMUM_REPLICATE_CORRELATION: 0.95

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

source_name: Primary stomach smooth muscle tissue; DNA_Lib 380

value: Stomach Smooth Muscle

value: Surgery

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

value: genomic DNA

value: Caucasian

value: Male

value: Primary Tissue

value: MGH

value: 59.0 Years

value: Protein A-Sepharose 4B

value: 0.5 to 3 million cells

value: ~1 ug

value: Histone H3K9ac


title: ChIP-Seq analysis of H3K9me3 in human stomach smooth muscle cells; DNA_Lib 379

description:
sample_term_id: UBERON_0008856
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 379
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8578
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9451
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM772888_BI.Stomach_Smooth_Muscle.H3K9me3.161.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 379-DNA_Lib 379-DNA_Lib 379-DNA_Lib 379.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Stomach Smooth Muscle Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9me3 ChIP-Seq on Stomach Smooth Muscle, Donor 161, were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.10789
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 28,103,717
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.0248
FINDPEAKS_PERCENTILE: 39
HOTSPOT_SCORE: 0.0925
HOTSPOT_PERCENTILE: 39
IROC_SCORE: 0.777
IROC_PERCENTILE: 33
POISSON_SCORE: 0.2244
POISSON_PERCENTILE: 43
MAXIMUM_REPLICATE_CORRELATION: 0.86

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

ANALYSIS FILE NAME: GSM772888_BI.Stomach_Smooth_Muscle.H3K9me3.161.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 379-DNA_Lib 379-DNA_Lib 379-DNA_Lib 379.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Stomach Smooth Muscle Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9me3 ChIP-Seq read mappings from Stomach Smooth Muscle, Donor 161, were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.11053
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 5
BROWSER_TRACK_NAME: SSM H3K9me3 61 79
BROWSER_TRACK_DESCRIPTION: BI Stomach Smooth Muscle Histone H3K9me3 Donor 161 Library DNA_Lib 379 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 28,103,717
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.0248
FINDPEAKS_PERCENTILE: 39
HOTSPOT_SCORE: 0.0925
HOTSPOT_PERCENTILE: 39
IROC_SCORE: 0.777
IROC_PERCENTILE: 33
POISSON_SCORE: 0.2244
POISSON_PERCENTILE: 43
MAXIMUM_REPLICATE_CORRELATION: 0.86

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

source_name: Primary stomach smooth muscle tissue; DNA_Lib 379

value: Smooth Muscle

value: Stomach

value: 10 ul bed volume

value: Abcam

value: Histone H3K9me3

value: Branson


title: ChIP-Seq analysis of H3K36me3 in human stomach smooth muscle cells; DNA_Lib 377

description:
sample_term_id: UBERON_0008856
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 377
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8581
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9451
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM772891_BI.Stomach_Smooth_Muscle.H3K36me3.161.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 377-DNA_Lib 377-DNA_Lib 377-DNA_Lib 377.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Stomach Smooth Muscle Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K36me3 ChIP-Seq on Stomach Smooth Muscle, Donor 161, were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.10831
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 34,974,021
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.132
FINDPEAKS_PERCENTILE: 53
HOTSPOT_SCORE: 0.2117
HOTSPOT_PERCENTILE: 45
IROC_SCORE: 0.9427
IROC_PERCENTILE: 55
POISSON_SCORE: 0.3998
POISSON_PERCENTILE: 55
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM772891_BI.Stomach_Smooth_Muscle.H3K36me3.161.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 377-DNA_Lib 377-DNA_Lib 377-DNA_Lib 377.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Stomach Smooth Muscle Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K36me3 ChIP-Seq read mappings from Stomach Smooth Muscle, Donor 161, were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.11095
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 5
BROWSER_TRACK_NAME: SSM H3K36me3 61 77
BROWSER_TRACK_DESCRIPTION: BI Stomach Smooth Muscle Histone H3K36me3 Donor 161 Library DNA_Lib 377 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 34,974,021
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.132
FINDPEAKS_PERCENTILE: 53
HOTSPOT_SCORE: 0.2117
HOTSPOT_PERCENTILE: 45
IROC_SCORE: 0.9427
IROC_PERCENTILE: 55
POISSON_SCORE: 0.3998
POISSON_PERCENTILE: 55
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

source_name: Primary stomach smooth muscle tissue; DNA_Lib 377

value: Stomach Smooth Muscle

value: Surgery

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

value: cell/nuclei lysis

value: Histone H3K36me3


title: ChIP-Seq analysis of WCE in human Duodenum mucosa cells; DNA_Lib 376

description:
sample_term_id: UBERON_0000320
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 376
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8580
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9454
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM772890_BI.Duodenum_Mucosa.Input.159.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 376-DNA_Lib 376-DNA_Lib 376-DNA_Lib 376.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Duodenum Mucosa ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on Duodenum Mucosa, Donor 159, were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.10656
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 44,216,633
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 56
FINDPEAKS_SCORE: 0.0046
FINDPEAKS_PERCENTILE: 30
HOTSPOT_SCORE: 0.0034
HOTSPOT_PERCENTILE: 13
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.0323
POISSON_PERCENTILE: 20
MAXIMUM_REPLICATE_CORRELATION: 0.91

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

ANALYSIS FILE NAME: GSM772890_BI.Duodenum_Mucosa.Input.159.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 376-DNA_Lib 376-DNA_Lib 376-DNA_Lib 376.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Duodenum Mucosa ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from Duodenum Mucosa, Donor 159, were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.10920
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 5
BROWSER_TRACK_NAME: DM Input 59 76
BROWSER_TRACK_DESCRIPTION: BI Duodenum Mucosa ChIP-Seq Input Donor 159 Library DNA_Lib 376 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 44,216,633
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 56
FINDPEAKS_SCORE: 0.0046
FINDPEAKS_PERCENTILE: 30
HOTSPOT_SCORE: 0.0034
HOTSPOT_PERCENTILE: 13
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.0323
POISSON_PERCENTILE: 20
MAXIMUM_REPLICATE_CORRELATION: 0.91

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

source_name: Primary duodenum mucosal tissue; DNA_Lib 376

value: Duodenum Mucosa

value: presumed normal

value: genomic DNA

value: Caucasian

value: Male

value: Primary Tissue

value: Duodenum

value: MGH

value: standard

value: ChIP-Seq Input

value: Input


title: ChIP-Seq analysis of H3K4me3 in human stomach smooth muscle cells; DNA_Lib 378

description:
sample_term_id: UBERON_0008856
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 378
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8577
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9451
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM772887_BI.Stomach_Smooth_Muscle.H3K4me3.161.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 378-DNA_Lib 378-DNA_Lib 378-DNA_Lib 378.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Stomach Smooth Muscle Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me3 ChIP-Seq on Stomach Smooth Muscle, Donor 161, were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.10696
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 27,567,677
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.2195
FINDPEAKS_PERCENTILE: 44
HOTSPOT_SCORE: 0.2695
HOTSPOT_PERCENTILE: 39
IROC_SCORE: 0.998
IROC_PERCENTILE: 43
POISSON_SCORE: 0.3335
POISSON_PERCENTILE: 46
MAXIMUM_REPLICATE_CORRELATION: 0.91

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

ANALYSIS FILE NAME: GSM772887_BI.Stomach_Smooth_Muscle.H3K4me3.161.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 378-DNA_Lib 378-DNA_Lib 378-DNA_Lib 378.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Stomach Smooth Muscle Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me3 ChIP-Seq read mappings from Stomach Smooth Muscle, Donor 161, were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.10960
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 5
BROWSER_TRACK_NAME: SSM H3K4me3 61 78
BROWSER_TRACK_DESCRIPTION: BI Stomach Smooth Muscle Histone H3K4me3 Donor 161 Library DNA_Lib 378 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 27,567,677
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.2195
FINDPEAKS_PERCENTILE: 44
HOTSPOT_SCORE: 0.2695
HOTSPOT_PERCENTILE: 39
IROC_SCORE: 0.998
IROC_PERCENTILE: 43
POISSON_SCORE: 0.3335
POISSON_PERCENTILE: 46
MAXIMUM_REPLICATE_CORRELATION: 0.91

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

source_name: Primary stomach smooth muscle tissue; DNA_Lib 378

value: Smooth Muscle

value: Stomach

value: 59.0 Years

value: Protein A-Sepharose 4B

value: 0.5 to 3 million cells

value: ~1 ug

value: 10 ul bed volume

value: Millipore

value: Histone H3K4me3

value: Branson


title: ChIP-Seq analysis of H3K9me3 in human Duodenum mucosa cells; DNA_Lib 373

description:
sample_term_id: UBERON_0000320
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 373
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8579
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9454
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM772889_BI.Duodenum_Mucosa.H3K9me3.159.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 373-DNA_Lib 373-DNA_Lib 373-DNA_Lib 373.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Duodenum Mucosa Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9me3 ChIP-Seq on Duodenum Mucosa, Donor 159, were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.10823
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 25,125,248
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.0562
FINDPEAKS_PERCENTILE: 59
HOTSPOT_SCORE: 0.1255
HOTSPOT_PERCENTILE: 59
IROC_SCORE: 0.7535
IROC_PERCENTILE: 27
POISSON_SCORE: 0.3221
POISSON_PERCENTILE: 63
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

ANALYSIS FILE NAME: GSM772889_BI.Duodenum_Mucosa.H3K9me3.159.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 373-DNA_Lib 373-DNA_Lib 373-DNA_Lib 373.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Duodenum Mucosa Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9me3 ChIP-Seq read mappings from Duodenum Mucosa, Donor 159, were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.11087
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 5
BROWSER_TRACK_NAME: DM H3K9me3 59 73
BROWSER_TRACK_DESCRIPTION: BI Duodenum Mucosa Histone H3K9me3 Donor 159 Library DNA_Lib 373 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 25,125,248
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.0562
FINDPEAKS_PERCENTILE: 59
HOTSPOT_SCORE: 0.1255
HOTSPOT_PERCENTILE: 59
IROC_SCORE: 0.7535
IROC_PERCENTILE: 27
POISSON_SCORE: 0.3221
POISSON_PERCENTILE: 63
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

source_name: Primary duodenum mucosal tissue; DNA_Lib 373

value: Duodenum Mucosa

value: Surgery

value: presumed normal

value: genomic DNA

value: Caucasian

value: Male

value: cell/nuclei lysis

value: Abcam

value: Histone H3K9me3


title: ChIP-Seq analysis of H3K4me3 in human chondrogenic dif cells; Lib EpiLabSPL Row 1387

description:
sample_term_id: CL_0000138
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib EpiLabSPL Row 1387
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8053
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5951
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM772792_BI.Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K4me3.58.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib EpiLabSPL Row 1387.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me3 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.10709
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 31,594,948
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.5103
FINDPEAKS_PERCENTILE: 89
HOTSPOT_SCORE: 0.5267
HOTSPOT_PERCENTILE: 91
IROC_SCORE: 0.9957
IROC_PERCENTILE: 28
POISSON_SCORE: 0.5531
POISSON_PERCENTILE: 89
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

ANALYSIS FILE NAME: GSM772792_BI.Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K4me3.58.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib EpiLabSPL Row 1387.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me3 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.10973
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 5
BROWSER_TRACK_NAME: CfBMDMSC H3K4me3 58 87
BROWSER_TRACK_DESCRIPTION: BI Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K4me3 Donor 58 Library Lib EpiLabSPL Row 1387 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 31,594,948
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.5103
FINDPEAKS_PERCENTILE: 89
HOTSPOT_SCORE: 0.5267
HOTSPOT_PERCENTILE: 91
IROC_SCORE: 0.9957
IROC_PERCENTILE: 28
POISSON_SCORE: 0.5531
POISSON_PERCENTILE: 89
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

source_name: chondrocytes derived via in vitro culture from mesenchymal stem cells; Lib EpiLabSPL Row 1387

value: healthy

tag: markers

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

value: chondrogenic dif cells

value: Unknown

value: Primary Cell Culture

value: Rikshospitalet University Hospital

value: 10 million cells

value: SDS lysis

value: 70 ul bed volume

value: Bioruptor


title: ChIP-Seq analysis of H3K9me3 in human ADMSC Diff Day20 cells; Lib EpiLabSPL Row 1739

description:
sample_term_id: CL_0000136
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib EpiLabSPL Row 1739
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8074
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.8181
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM772813_BI.Mesenchymal_Stem_Cell_Derived_Adipocyte_Cultured_Cells.H3K9me3.92.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib EpiLabSPL Row 1739.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Mesenchymal Stem Cell Derived Adipocyte Cultured Cells Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9me3 ChIP-Seq on Mesenchymal Stem Cell Derived Adipocyte Cultured Cells, Donor 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.10756
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 23,249,793
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.0866
FINDPEAKS_PERCENTILE: 76
HOTSPOT_SCORE: 0.1632
HOTSPOT_PERCENTILE: 78
IROC_SCORE: 0.8471
IROC_PERCENTILE: 53
POISSON_SCORE: 0.3378
POISSON_PERCENTILE: 71
MAXIMUM_REPLICATE_CORRELATION: 0.95

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

ANALYSIS FILE NAME: GSM772813_BI.Mesenchymal_Stem_Cell_Derived_Adipocyte_Cultured_Cells.H3K9me3.92.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib EpiLabSPL Row 1739.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Mesenchymal Stem Cell Derived Adipocyte Cultured Cells Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9me3 ChIP-Seq read mappings from Mesenchymal Stem Cell Derived Adipocyte Cultured Cells, Donor 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.11020
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 5
BROWSER_TRACK_NAME: MSCDA H3K9me3 92 39
BROWSER_TRACK_DESCRIPTION: BI Mesenchymal Stem Cell Derived Adipocyte Cultured Cells Histone H3K9me3 Donor 92 Library Lib EpiLabSPL Row 1739 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 23,249,793
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.0866
FINDPEAKS_PERCENTILE: 76
HOTSPOT_SCORE: 0.1632
HOTSPOT_PERCENTILE: 78
IROC_SCORE: 0.8471
IROC_PERCENTILE: 53
POISSON_SCORE: 0.3378
POISSON_PERCENTILE: 71
MAXIMUM_REPLICATE_CORRELATION: 0.95

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

source_name: Adipose-derived mesenchymal stem cells were cultured in adipocyte differentiation medium for 20 days; Lib EpiLabSPL Row 1739

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

value: ADMSC Diff Day20

value: Female

value: Harvard University

value: Protein A-Sepharose 4B


title: ChIP-Seq analysis of H3K9ac in human adult kidney cells; Lib:XZ:20100827:07--ChIP:XZ:20100824:07:adult kidney:H3K9Ac

description:
sample_term_id: UBERON_0002113
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:XZ:20100827:07--ChIP:XZ:20100824:07:adult kidney:H3K9Ac
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8072
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3349
****************
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: GSM772811_BI.Adult_Kidney.H3K9ac.27.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100827:07--ChIP:XZ:20100824:07:adult kidney:H3K9Ac.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Adult Kidney Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9ac ChIP-Seq on Adult Kidney, Donor 27, 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.10619
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 38,225,656
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 19
FINDPEAKS_SCORE: 0.0439
FINDPEAKS_PERCENTILE: 11
HOTSPOT_SCORE: 0.0846
HOTSPOT_PERCENTILE: 5
IROC_SCORE: 0.957
IROC_PERCENTILE: 11
POISSON_SCORE: 0.1436
POISSON_PERCENTILE: 5
MAXIMUM_REPLICATE_CORRELATION: 0.95

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

ANALYSIS FILE NAME: GSM772811_BI.Adult_Kidney.H3K9ac.27.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100827:07--ChIP:XZ:20100824:07:adult kidney:H3K9Ac.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Adult Kidney Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9ac ChIP-Seq read mappings from Adult Kidney, Donor 27, 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.10883
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 5
BROWSER_TRACK_NAME: AK H3K9ac 27
BROWSER_TRACK_DESCRIPTION: BI Adult Kidney Histone H3K9ac Donor 27 Library Lib:XZ:20100827:07--ChIP:XZ:20100824:07:adult kidney:H3K9Ac EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 38,225,656
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 19
FINDPEAKS_SCORE: 0.0439
FINDPEAKS_PERCENTILE: 11
HOTSPOT_SCORE: 0.0846
HOTSPOT_PERCENTILE: 5
IROC_SCORE: 0.957
IROC_PERCENTILE: 11
POISSON_SCORE: 0.1436
POISSON_PERCENTILE: 5
MAXIMUM_REPLICATE_CORRELATION: 0.95

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

source_name: Primary kidney tissue; Lib:XZ:20100827:07--ChIP:XZ:20100824:07:adult kidney:H3K9Ac

value: Adult Kidney

value: surgery

value: "normal, renal cell CA (clear cell type)"

value: genomic DNA

value: white

value: Male

value: Primary Tissue

value: kidney

value: MGH Pathology

value: Abcam

value: Histone H3K9ac


title: ChIP-Seq analysis of H3K9ac in human ADMSC Diff Day20 cells; Lib EpiLabSPL Row 1738

description:
sample_term_id: CL_0000136
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib EpiLabSPL Row 1738
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8073
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.8181
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM772812_BI.Mesenchymal_Stem_Cell_Derived_Adipocyte_Cultured_Cells.H3K9ac.92.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib EpiLabSPL Row 1738.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Mesenchymal Stem Cell Derived Adipocyte Cultured Cells Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9ac ChIP-Seq on Mesenchymal Stem Cell Derived Adipocyte Cultured Cells, Donor 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.10845
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 26,241,263
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 19
FINDPEAKS_SCORE: 0.4634
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.4971
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9944
IROC_PERCENTILE: 53
POISSON_SCORE: 0.5522
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.94

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

ANALYSIS FILE NAME: GSM772812_BI.Mesenchymal_Stem_Cell_Derived_Adipocyte_Cultured_Cells.H3K9ac.92.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib EpiLabSPL Row 1738.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Mesenchymal Stem Cell Derived Adipocyte Cultured Cells Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9ac ChIP-Seq read mappings from Mesenchymal Stem Cell Derived Adipocyte Cultured Cells, Donor 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.11109
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 5
BROWSER_TRACK_NAME: MSCDA H3K9ac 92 38
BROWSER_TRACK_DESCRIPTION: BI Mesenchymal Stem Cell Derived Adipocyte Cultured Cells Histone H3K9ac Donor 92 Library Lib EpiLabSPL Row 1738 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 26,241,263
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 19
FINDPEAKS_SCORE: 0.4634
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.4971
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9944
IROC_PERCENTILE: 53
POISSON_SCORE: 0.5522
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.94

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

source_name: Adipose-derived mesenchymal stem cells were cultured in adipocyte differentiation medium for 20 days; Lib EpiLabSPL Row 1738

value: Primary Cell Culture

value: 10 million cells

value: SDS lysis

value: 70 ul bed volume

value: Bioruptor


title: ChIP-Seq analysis of H3K9ac in human ADMSC undiff Day0 cells; Lib EpiLabSPL Row 1732

description:
sample_term_id: EFO_0005023
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib EpiLabSPL Row 1732
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8083
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.8179
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM772822_BI.Adipose_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K9ac.92.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib EpiLabSPL Row 1732.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Adipose Derived Mesenchymal Stem Cell Cultured Cells Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9ac ChIP-Seq on Adipose Derived Mesenchymal Stem Cell Cultured Cells, Donor 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.10790
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 30,398,041
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 19
FINDPEAKS_SCORE: 0.3972
FINDPEAKS_PERCENTILE: 95
HOTSPOT_SCORE: 0.4347
HOTSPOT_PERCENTILE: 95
IROC_SCORE: 0.9928
IROC_PERCENTILE: 42
POISSON_SCORE: 0.5205
POISSON_PERCENTILE: 95
MAXIMUM_REPLICATE_CORRELATION: 0.95

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

ANALYSIS FILE NAME: GSM772822_BI.Adipose_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K9ac.92.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib EpiLabSPL Row 1732.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Adipose Derived Mesenchymal Stem Cell Cultured Cells Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9ac ChIP-Seq read mappings from Adipose Derived Mesenchymal Stem Cell Cultured Cells, Donor 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.11054
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 5
BROWSER_TRACK_NAME: ADMSC H3K9ac 92 32
BROWSER_TRACK_DESCRIPTION: BI Adipose Derived Mesenchymal Stem Cell Cultured Cells Histone H3K9ac Donor 92 Library Lib EpiLabSPL Row 1732 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 30,398,041
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 19
FINDPEAKS_SCORE: 0.3972
FINDPEAKS_PERCENTILE: 95
HOTSPOT_SCORE: 0.4347
HOTSPOT_PERCENTILE: 95
IROC_SCORE: 0.9928
IROC_PERCENTILE: 42
POISSON_SCORE: 0.5205
POISSON_PERCENTILE: 95
MAXIMUM_REPLICATE_CORRELATION: 0.95

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

source_name: Adherent cells derived following short term serial passage from adipose tissue; Lib EpiLabSPL Row 1732

value: ADMSC undiff Day0

value: Female

value: Harvard University

value: Protein A-Sepharose 4B


title: ChIP-Seq analysis of H3K4me3 in human ADMSC Diff Day20 cells; Lib EpiLabSPL Row 1735

description:
sample_term_id: CL_0000136
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib EpiLabSPL Row 1735
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8078
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.8181
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM772817_BI.Mesenchymal_Stem_Cell_Derived_Adipocyte_Cultured_Cells.H3K4me3.92.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib EpiLabSPL Row 1735.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Mesenchymal Stem Cell Derived Adipocyte Cultured Cells Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me3 ChIP-Seq on Mesenchymal Stem Cell Derived Adipocyte Cultured Cells, Donor 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.10683
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 27,613,863
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.4966
FINDPEAKS_PERCENTILE: 85
HOTSPOT_SCORE: 0.5242
HOTSPOT_PERCENTILE: 89
IROC_SCORE: 0.9904
IROC_PERCENTILE: 26
POISSON_SCORE: 0.5559
POISSON_PERCENTILE: 93
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

ANALYSIS FILE NAME: GSM772817_BI.Mesenchymal_Stem_Cell_Derived_Adipocyte_Cultured_Cells.H3K4me3.92.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib EpiLabSPL Row 1735.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Mesenchymal Stem Cell Derived Adipocyte Cultured Cells Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me3 ChIP-Seq read mappings from Mesenchymal Stem Cell Derived Adipocyte Cultured Cells, Donor 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.10947
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 5
BROWSER_TRACK_NAME: MSCDA H3K4me3 92 35
BROWSER_TRACK_DESCRIPTION: BI Mesenchymal Stem Cell Derived Adipocyte Cultured Cells Histone H3K4me3 Donor 92 Library Lib EpiLabSPL Row 1735 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 27,613,863
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.4966
FINDPEAKS_PERCENTILE: 85
HOTSPOT_SCORE: 0.5242
HOTSPOT_PERCENTILE: 89
IROC_SCORE: 0.9904
IROC_PERCENTILE: 26
POISSON_SCORE: 0.5559
POISSON_PERCENTILE: 93
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

source_name: Adipose-derived mesenchymal stem cells were cultured in adipocyte differentiation medium for 20 days; Lib EpiLabSPL Row 1735

value: genomic DNA

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

value: ADMSC Diff Day20

value: Millipore

value: Histone H3K4me3


title: ChIP-Seq analysis of H3K36me3 in human chondrogenic dif cells; Lib EpiLabSPL Row 1388

description:
sample_term_id: CL_0000138
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib EpiLabSPL Row 1388
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8086
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5951
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM772825_BI.Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K36me3.58.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib EpiLabSPL Row 1388.hg19.level.1.release.5
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 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.10686
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 31,838,510
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.3673
FINDPEAKS_PERCENTILE: 80
HOTSPOT_SCORE: 0.3196
HOTSPOT_PERCENTILE: 76
IROC_SCORE: 0.9909
IROC_PERCENTILE: 80
POISSON_SCORE: 0.5406
POISSON_PERCENTILE: 82
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

ANALYSIS FILE NAME: GSM772825_BI.Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K36me3.58.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib EpiLabSPL Row 1388.hg19.level.2.release.5
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 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.10950
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 5
BROWSER_TRACK_NAME: CfBMDMSC H3K36me3 58 88
BROWSER_TRACK_DESCRIPTION: BI Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K36me3 Donor 58 Library Lib EpiLabSPL Row 1388 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 31,838,510
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.3673
FINDPEAKS_PERCENTILE: 80
HOTSPOT_SCORE: 0.3196
HOTSPOT_PERCENTILE: 76
IROC_SCORE: 0.9909
IROC_PERCENTILE: 80
POISSON_SCORE: 0.5406
POISSON_PERCENTILE: 82
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

source_name: chondrocytes derived via in vitro culture from mesenchymal stem cells; Lib EpiLabSPL Row 1388

value: healthy

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

value: chondrogenic dif cells

value: Unknown

value: Rikshospitalet University Hospital

value: Histone H3K36me3


title: ChIP-Seq analysis of H3K27me3 in human ADMSC undiff Day0 cells; Lib EpiLabSPL Row 1731

description:
sample_term_id: EFO_0005023
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib EpiLabSPL Row 1731
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8082
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.8179
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM772821_BI.Adipose_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K27me3.92.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib EpiLabSPL Row 1731.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Adipose Derived Mesenchymal Stem Cell Cultured Cells Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27me3 ChIP-Seq on Adipose Derived Mesenchymal Stem Cell Cultured Cells, Donor 92, were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.10701
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 25,805,788
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.2213
FINDPEAKS_PERCENTILE: 90
HOTSPOT_SCORE: 0.2636
HOTSPOT_PERCENTILE: 88
IROC_SCORE: 0.953
IROC_PERCENTILE: 71
POISSON_SCORE: 0.5203
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.93

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

ANALYSIS FILE NAME: GSM772821_BI.Adipose_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K27me3.92.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib EpiLabSPL Row 1731.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Adipose Derived Mesenchymal Stem Cell Cultured Cells Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27me3 ChIP-Seq read mappings from Adipose Derived Mesenchymal Stem Cell Cultured Cells, Donor 92, were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.10965
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 5
BROWSER_TRACK_NAME: ADMSC H3K27me3 92 31
BROWSER_TRACK_DESCRIPTION: BI Adipose Derived Mesenchymal Stem Cell Cultured Cells Histone H3K27me3 Donor 92 Library Lib EpiLabSPL Row 1731 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 25,805,788
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.2213
FINDPEAKS_PERCENTILE: 90
HOTSPOT_SCORE: 0.2636
HOTSPOT_PERCENTILE: 88
IROC_SCORE: 0.953
IROC_PERCENTILE: 71
POISSON_SCORE: 0.5203
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.93

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

source_name: Adherent cells derived following short term serial passage from adipose tissue; Lib EpiLabSPL Row 1731

value: Primary Cell Culture

value: 10 million cells

value: SDS lysis

value: 70 ul bed volume

value: Histone H3K27me3


title: ChIP-Seq analysis of H3K36me3 in human ADMSC undiff Day0 cells; Lib EpiLabSPL Row 1730

description:
sample_term_id: EFO_0005023
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib EpiLabSPL Row 1730
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8081
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.8179
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM772820_BI.Adipose_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K36me3.92.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib EpiLabSPL Row 1730.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Adipose Derived Mesenchymal Stem Cell Cultured Cells Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K36me3 ChIP-Seq on Adipose Derived Mesenchymal Stem Cell Cultured Cells, Donor 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.10731
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 32,149,926
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.5323
FINDPEAKS_PERCENTILE: 96
HOTSPOT_SCORE: 0.446
HOTSPOT_PERCENTILE: 94
IROC_SCORE: 0.9978
IROC_PERCENTILE: 92
POISSON_SCORE: 0.6752
POISSON_PERCENTILE: 96
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

ANALYSIS FILE NAME: GSM772820_BI.Adipose_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K36me3.92.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib EpiLabSPL Row 1730.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Adipose Derived Mesenchymal Stem Cell Cultured Cells Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K36me3 ChIP-Seq read mappings from Adipose Derived Mesenchymal Stem Cell Cultured Cells, Donor 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.10995
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 5
BROWSER_TRACK_NAME: ADMSC H3K36me3 92 30
BROWSER_TRACK_DESCRIPTION: BI Adipose Derived Mesenchymal Stem Cell Cultured Cells Histone H3K36me3 Donor 92 Library Lib EpiLabSPL Row 1730 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 32,149,926
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.5323
FINDPEAKS_PERCENTILE: 96
HOTSPOT_SCORE: 0.446
HOTSPOT_PERCENTILE: 94
IROC_SCORE: 0.9978
IROC_PERCENTILE: 92
POISSON_SCORE: 0.6752
POISSON_PERCENTILE: 96
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

source_name: Adherent cells derived following short term serial passage from adipose tissue; Lib EpiLabSPL Row 1730

value: ADMSC undiff Day0

value: Female

value: Harvard University

value: Protein A-Sepharose 4B

value: Abcam

value: Bioruptor


title: ChIP-Seq analysis of H3K27me3 in human ADMSC Diff Day20 cells; Lib EpiLabSPL Row 1737

description:
sample_term_id: CL_0000136
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib EpiLabSPL Row 1737
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8080
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.8181
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM772819_BI.Mesenchymal_Stem_Cell_Derived_Adipocyte_Cultured_Cells.H3K27me3.92.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib EpiLabSPL Row 1737.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Mesenchymal Stem Cell Derived Adipocyte Cultured Cells Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27me3 ChIP-Seq on Mesenchymal Stem Cell Derived Adipocyte Cultured Cells, Donor 92, were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.10642
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 25,797,702
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.1048
FINDPEAKS_PERCENTILE: 76
HOTSPOT_SCORE: 0.2032
HOTSPOT_PERCENTILE: 82
IROC_SCORE: 0.8925
IROC_PERCENTILE: 61
POISSON_SCORE: 0.4693
POISSON_PERCENTILE: 92
MAXIMUM_REPLICATE_CORRELATION: 0.93

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

ANALYSIS FILE NAME: GSM772819_BI.Mesenchymal_Stem_Cell_Derived_Adipocyte_Cultured_Cells.H3K27me3.92.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib EpiLabSPL Row 1737.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Mesenchymal Stem Cell Derived Adipocyte Cultured Cells Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27me3 ChIP-Seq read mappings from Mesenchymal Stem Cell Derived Adipocyte Cultured Cells, Donor 92, were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.10906
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 5
BROWSER_TRACK_NAME: MSCDA H3K27me3 92 37
BROWSER_TRACK_DESCRIPTION: BI Mesenchymal Stem Cell Derived Adipocyte Cultured Cells Histone H3K27me3 Donor 92 Library Lib EpiLabSPL Row 1737 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 25,797,702
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.1048
FINDPEAKS_PERCENTILE: 76
HOTSPOT_SCORE: 0.2032
HOTSPOT_PERCENTILE: 82
IROC_SCORE: 0.8925
IROC_PERCENTILE: 61
POISSON_SCORE: 0.4693
POISSON_PERCENTILE: 92
MAXIMUM_REPLICATE_CORRELATION: 0.93

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

source_name: Adipose-derived mesenchymal stem cells were cultured in adipocyte differentiation medium for 20 days; Lib EpiLabSPL Row 1737

value: genomic DNA

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

value: ADMSC Diff Day20

value: Millipore


title: ChIP-Seq analysis of H3K9me3 in human ADMSC undiff Day0 cells; Lib EpiLabSPL Row 1733

description:
sample_term_id: EFO_0005023
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib EpiLabSPL Row 1733
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8084
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.8179
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM772823_BI.Adipose_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K9me3.92.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib EpiLabSPL Row 1733.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Adipose Derived Mesenchymal Stem Cell Cultured Cells Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9me3 ChIP-Seq on Adipose Derived Mesenchymal Stem Cell Cultured Cells, Donor 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.10715
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 24,461,162
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.0705
FINDPEAKS_PERCENTILE: 71
HOTSPOT_SCORE: 0.15
HOTSPOT_PERCENTILE: 71
IROC_SCORE: 0.7973
IROC_PERCENTILE: 35
POISSON_SCORE: 0.3783
POISSON_PERCENTILE: 80
MAXIMUM_REPLICATE_CORRELATION: 0.95

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

ANALYSIS FILE NAME: GSM772823_BI.Adipose_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K9me3.92.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib EpiLabSPL Row 1733.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Adipose Derived Mesenchymal Stem Cell Cultured Cells Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9me3 ChIP-Seq read mappings from Adipose Derived Mesenchymal Stem Cell Cultured Cells, Donor 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.10979
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 5
BROWSER_TRACK_NAME: ADMSC H3K9me3 92 33
BROWSER_TRACK_DESCRIPTION: BI Adipose Derived Mesenchymal Stem Cell Cultured Cells Histone H3K9me3 Donor 92 Library Lib EpiLabSPL Row 1733 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 24,461,162
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.0705
FINDPEAKS_PERCENTILE: 71
HOTSPOT_SCORE: 0.15
HOTSPOT_PERCENTILE: 71
IROC_SCORE: 0.7973
IROC_PERCENTILE: 35
POISSON_SCORE: 0.3783
POISSON_PERCENTILE: 80
MAXIMUM_REPLICATE_CORRELATION: 0.95

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

source_name: Adherent cells derived following short term serial passage from adipose tissue; Lib EpiLabSPL Row 1733

value: Histone H3K9me3


title: ChIP-Seq analysis of H3K36me3 in human ADMSC Diff Day20 cells; Lib EpiLabSPL Row 1736

description:
sample_term_id: CL_0000136
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib EpiLabSPL Row 1736
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8079
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.8181
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM772818_BI.Mesenchymal_Stem_Cell_Derived_Adipocyte_Cultured_Cells.H3K36me3.92.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib EpiLabSPL Row 1736.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Mesenchymal Stem Cell Derived Adipocyte Cultured Cells Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K36me3 ChIP-Seq on Mesenchymal Stem Cell Derived Adipocyte Cultured Cells, Donor 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.10678
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 27,567,948
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.411
FINDPEAKS_PERCENTILE: 88
HOTSPOT_SCORE: 0.3841
HOTSPOT_PERCENTILE: 88
IROC_SCORE: 0.9945
IROC_PERCENTILE: 90
POISSON_SCORE: 0.5673
POISSON_PERCENTILE: 86
MAXIMUM_REPLICATE_CORRELATION: 0.93

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

ANALYSIS FILE NAME: GSM772818_BI.Mesenchymal_Stem_Cell_Derived_Adipocyte_Cultured_Cells.H3K36me3.92.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib EpiLabSPL Row 1736.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Mesenchymal Stem Cell Derived Adipocyte Cultured Cells Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K36me3 ChIP-Seq read mappings from Mesenchymal Stem Cell Derived Adipocyte Cultured Cells, Donor 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.10942
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 5
BROWSER_TRACK_NAME: MSCDA H3K36me3 92 36
BROWSER_TRACK_DESCRIPTION: BI Mesenchymal Stem Cell Derived Adipocyte Cultured Cells Histone H3K36me3 Donor 92 Library Lib EpiLabSPL Row 1736 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 27,567,948
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.411
FINDPEAKS_PERCENTILE: 88
HOTSPOT_SCORE: 0.3841
HOTSPOT_PERCENTILE: 88
IROC_SCORE: 0.9945
IROC_PERCENTILE: 90
POISSON_SCORE: 0.5673
POISSON_PERCENTILE: 86
MAXIMUM_REPLICATE_CORRELATION: 0.93

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

source_name: Adipose-derived mesenchymal stem cells were cultured in adipocyte differentiation medium for 20 days; Lib EpiLabSPL Row 1736

value: Histone H3K36me3