title: Bisulfite-Seq analysis of RRBS1087 derived from human mobilized CD34 cells; RRBS1087

status: Public on Sep 02 2011

description:
sample_term_id: CL_0000837
assay_term_id: OBI_0001862
nucleic_acid_term_id: SO_0000352
Design description: RRBS REMC Sequencing on Illumina
Library name: RRBS1087
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.6856
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.2401
****************
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: GSM706857_BI.Mobilized_CD34_Primary_Cells.RRBS.RO_01549.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RRBS1087.hg19.level.2.release.4
ANALYSIS TITLE: Methylation Proportion Graphs of Mobilized CD34 Primary Cells RRBS Data
ANALYSIS DESCRIPTION: Illumina RRBS read mappings from Mobilized CD34 Primary Cells, Donor RO 01549 were processed into graphs of methylation proportions. Methylation proportions were calculated as (methylated calls / (methylated calls + unmethylated calls)) for all CpGs covered by at least 4 reads.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.8329
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Reduced Representation Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19 MspI restriction fragments 40-220bp
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
GENOMIC_WINDOW: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 4
BROWSER_TRACK_NAME: MCD34 RRBS 49 87
BROWSER_TRACK_DESCRIPTION: BI Mobilized CD34 Primary Cells RRBS Donor RO 01549 Library RRBS1087 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 22,112,986
NUMBER_OF_RRBS_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 21
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 99.51
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE: 29
MAXIMUM_REPLICATE_CORRELATION: 0.92

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

source_name: flow sorted CD34+ cells from cord blood; RRBS1087

value: CD34 Primary Cells

value: genomic DNA

value: FHCRC HEIMFELD

value: Primary Cell

value: 33 years

value: Female

value: Caucasian


title: Bisulfite-Seq analysis of RRBS1082 derived from human fetal kidney cells; RRBS1082

status: Public on Dec 05 2011

type: SRA

city: Cambridge

first: BROAD

last: INSTITUTE

state: MA

country: USA

institute: Broad Institute

description:
sample_term_id: UBERON_0002113
assay_term_id: OBI_0001862
nucleic_acid_term_id: SO_0000352
Design description: RRBS REMC Sequencing on Illumina
Library name: RRBS1082
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.6999
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.2461
****************
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: GSM706841_BI.Fetal_Kidney.RRBS.H-22676.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RRBS1082.hg19.level.2.release.4
ANALYSIS TITLE: Methylation Proportion Graphs of Fetal Kidney RRBS Data
ANALYSIS DESCRIPTION: Illumina RRBS read mappings from Fetal Kidney, Donor H-22676 were processed into graphs of methylation proportions. Methylation proportions were calculated as (methylated calls / (methylated calls + unmethylated calls)) for all CpGs covered by at least 4 reads.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.8323
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Reduced Representation Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19 MspI restriction fragments 40-220bp
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
GENOMIC_WINDOW: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 4
BROWSER_TRACK_NAME: FK RRBS 76 82
BROWSER_TRACK_DESCRIPTION: BI Fetal Kidney RRBS Donor H-22676 Library RRBS1082 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 23,095,861
NUMBER_OF_RRBS_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 21
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 99.52
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE: 33
MAXIMUM_REPLICATE_CORRELATION: NA

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

molecule: genomic DNA

organism: Homo sapiens

source_name: Fetal Kidney primary tissue, day 122; RRBS1082

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

tag: sample alias

tag: sample common name

value: Fetal Kidney

tag: molecule

tag: disease

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

value: Primary Tissue

value: fetal kidney

value: UW

value: fetal

value: 122 days

value: Unknown

value: 2x5hrs Epitect Kit

value: 20 ng

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

value: 5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT

value: 5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT

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

value: DNA Methylation

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

value: Gel size selection

value: Pfu Turbo Cx hot start


title: Bisulfite-Seq analysis of RRBS1225 derived from human CD15 cells; RRBS1225

description:
sample_term_id: CL_0000775
assay_term_id: OBI_0001862
nucleic_acid_term_id: SO_0000352
Design description: RRBS REMC Sequencing on Illumina
Library name: RRBS1225
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.6995
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.7011
****************
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: GSM706837_BI.CD15_Primary_Cells.RRBS.9-16-2009_Cord_Blood_B.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RRBS1225.hg19.level.2.release.4
ANALYSIS TITLE: Methylation Proportion Graphs of CD15 Primary Cells RRBS Data
ANALYSIS DESCRIPTION: Illumina RRBS read mappings from CD15 Primary Cells, Donor 9-16-2009 Cord Blood B were processed into graphs of methylation proportions. Methylation proportions were calculated as (methylated calls / (methylated calls + unmethylated calls)) for all CpGs covered by at least 4 reads.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.8327
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Reduced Representation Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19 MspI restriction fragments 40-220bp
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
GENOMIC_WINDOW: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 4
BROWSER_TRACK_NAME: CD15 RRBS  B 25
BROWSER_TRACK_DESCRIPTION: BI CD15 Primary Cells RRBS Donor 9-16-2009 Cord Blood B Library RRBS1225 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 21,411,192
NUMBER_OF_RRBS_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 21
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 99.56
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE: 52
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: flow sorted CD15+ cells from cord blood; RRBS1225

value: BioSam 146

value: CD15 Primary Cells

value: genomic DNA

tag: markers

value: CD15 Cord Blood B

value: Male

value: Primary Cell

value: 9-16-2009 Cord Blood B

value: FHCRC


title: ChIP-Seq analysis of WCE in human Mobilized CD34 cells; DNA_Lib 252

description:
sample_term_id: CL_0000837
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 252
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.7087
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.2407
****************
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: GSM706847_BI.Mobilized_CD34_Primary_Cells.Input.RO_01480.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 252.hg19.level.1.release.4
ANALYSIS TITLE: Mapping of Mobilized CD34 Primary Cells ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on Mobilized CD34 Primary Cells, Donor RO 01480 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.8227
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 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 60,056,459
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 14
FINDPEAKS_SCORE: 0.0057
FINDPEAKS_PERCENTILE: 42
HOTSPOT_SCORE: 0.0032
HOTSPOT_PERCENTILE: 17
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.0164
POISSON_PERCENTILE: 17
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

ANALYSIS FILE NAME: GSM706847_BI.Mobilized_CD34_Primary_Cells.Input.RO_01480.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 252.hg19.level.2.release.4
ANALYSIS TITLE: Raw Signal Density Graphs of Mobilized CD34 Primary Cells ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from Mobilized CD34 Primary Cells, Donor RO 01480 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.8254
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 4
BROWSER_TRACK_NAME: MCD34 Input 80 52
BROWSER_TRACK_DESCRIPTION: BI Mobilized CD34 Primary Cells ChIP-Seq Input Donor RO 01480 Library DNA_Lib 252 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 60,056,459
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 14
FINDPEAKS_SCORE: 0.0057
FINDPEAKS_PERCENTILE: 42
HOTSPOT_SCORE: 0.0032
HOTSPOT_PERCENTILE: 17
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.0164
POISSON_PERCENTILE: 17
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

source_name: flow sorted CD34+ cells from cord blood; DNA_Lib 252

extract_protocol: Library construction protocol: Single read - Illumina

value: CD34 Primary Cells

value: FHCRC HEIMFELD

value: 27 years

value: Female

value: Caucasian

value: standard

value: SDS lysis

value: ChIP-Seq Input

value: Input

value: Bioruptor


title: Bisulfite-Seq analysis of RRBS1139andRRBS1080 derived from human fetal brain cells; RRBS1139andRRBS1080

description:
sample_term_id: UBERON_0000955
assay_term_id: OBI_0001862
nucleic_acid_term_id: SO_0000352
Design description: RRBS REMC Sequencing on Illumina
Library name: RRBS1139andRRBS1080
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.6998
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.3113
****************
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: GSM706840_BI.Fetal_Brain.RRBS.H-23284.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RRBS1139andRRBS1080.hg19.level.2.release.4
ANALYSIS TITLE: Methylation Proportion Graphs of Fetal Brain RRBS Data
ANALYSIS DESCRIPTION: Illumina RRBS read mappings from Fetal Brain, Donor H-23284 were processed into graphs of methylation proportions. Methylation proportions were calculated as (methylated calls / (methylated calls + unmethylated calls)) for all CpGs covered by at least 4 reads.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.8338
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Reduced Representation Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19 MspI restriction fragments 40-220bp
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
GENOMIC_WINDOW: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 4
BROWSER_TRACK_NAME: FB RRBS 84 80
BROWSER_TRACK_DESCRIPTION: BI Fetal Brain RRBS Donor H-23284 Library RRBS1139andRRBS1080 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 43,770,700
NUMBER_OF_RRBS_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 21
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 99.67
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE: 67
MAXIMUM_REPLICATE_CORRELATION: 0.71

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

source_name: Fetal Brain primary tissue, day 96; RRBS1139andRRBS1080

value: Fetal Brain

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

value: Primary Tissue

value: fetal brain

value: UW

value: fetal

value: day 96

value: 2x5hrs Epitect Kit

value: 20 ng

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

value: 5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT

value: 5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT

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

value: DNA Methylation

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

value: Gel size selection

value: Pfu Turbo Cx hot start


title: Bisulfite-Seq analysis of RRBS1084 derived from human mobilized CD34 cells; RRBS1084

description:
sample_term_id: CL_0000837
assay_term_id: OBI_0001862
nucleic_acid_term_id: SO_0000352
Design description: RRBS REMC Sequencing on Illumina
Library name: RRBS1084
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.6857
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.2407
****************
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: GSM706858_BI.Mobilized_CD34_Primary_Cells.RRBS.RO_01480.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RRBS1084.hg19.level.2.release.4
ANALYSIS TITLE: Methylation Proportion Graphs of Mobilized CD34 Primary Cells RRBS Data
ANALYSIS DESCRIPTION: Illumina RRBS read mappings from Mobilized CD34 Primary Cells, Donor RO 01480 were processed into graphs of methylation proportions. Methylation proportions were calculated as (methylated calls / (methylated calls + unmethylated calls)) for all CpGs covered by at least 4 reads.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.8322
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Reduced Representation Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19 MspI restriction fragments 40-220bp
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
GENOMIC_WINDOW: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 4
BROWSER_TRACK_NAME: MCD34 RRBS 80 84
BROWSER_TRACK_DESCRIPTION: BI Mobilized CD34 Primary Cells RRBS Donor RO 01480 Library RRBS1084 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 23,898,170
NUMBER_OF_RRBS_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 21
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 99.69
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE: 81
MAXIMUM_REPLICATE_CORRELATION: 0.92

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

source_name: flow sorted CD34+ cells from cord blood; RRBS1084

value: CD34 Primary Cells

value: genomic DNA

value: FHCRC HEIMFELD

value: Primary Cell

value: 27 years

value: Female

value: Caucasian


title: Bisulfite-Seq analysis of RRBS1223 derived from human CD3 cells; RRBS1223

description:
sample_term_id: CL_0000084
assay_term_id: OBI_0001862
nucleic_acid_term_id: SO_0000352
Design description: RRBS REMC Sequencing on Illumina
Library name: RRBS1223
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.6993
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.7010
****************
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: GSM706835_BI.CD3_Primary_Cells.RRBS.64.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RRBS1223.hg19.level.2.release.4
ANALYSIS TITLE: Methylation Proportion Graphs of CD3 Primary Cells RRBS Data
ANALYSIS DESCRIPTION: Illumina RRBS read mappings from CD3 Primary Cells, Donor 64 were processed into graphs of methylation proportions. Methylation proportions were calculated as (methylated calls / (methylated calls + unmethylated calls)) for all CpGs covered by at least 4 reads.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.8330
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Reduced Representation Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19 MspI restriction fragments 40-220bp
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
GENOMIC_WINDOW: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 4
BROWSER_TRACK_NAME: CD3 RRBS 64 23
BROWSER_TRACK_DESCRIPTION: BI CD3 Primary Cells RRBS Donor 64 Library RRBS1223 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 8,734,913
NUMBER_OF_RRBS_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 21
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 99.11
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE: 5
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: flow sorted CD3+ cells from cord blood; RRBS1223

value: CD3 Primary Cells

value: Unknown

value: FHCRC

value: 2x5hrs Epitect Kit


title: Bisulfite-Seq analysis of RRBS1086 derived from human mobilized CD34 cells; RRBS1086

description:
sample_term_id: CL_0000837
assay_term_id: OBI_0001862
nucleic_acid_term_id: SO_0000352
Design description: RRBS REMC Sequencing on Illumina
Library name: RRBS1086
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.6997
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.3100
****************
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: GSM706839_BI.Mobilized_CD34_Primary_Cells.RRBS.RO_01517.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RRBS1086.hg19.level.2.release.4
ANALYSIS TITLE: Methylation Proportion Graphs of Mobilized CD34 Primary Cells RRBS Data
ANALYSIS DESCRIPTION: Illumina RRBS read mappings from Mobilized CD34 Primary Cells, Donor RO 01517 were processed into graphs of methylation proportions. Methylation proportions were calculated as (methylated calls / (methylated calls + unmethylated calls)) for all CpGs covered by at least 4 reads.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.8331
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Reduced Representation Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19 MspI restriction fragments 40-220bp
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
GENOMIC_WINDOW: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 4
BROWSER_TRACK_NAME: MCD34 RRBS 17 86
BROWSER_TRACK_DESCRIPTION: BI Mobilized CD34 Primary Cells RRBS Donor RO 01517 Library RRBS1086 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 24,582,905
NUMBER_OF_RRBS_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 21
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 99.54
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE: 38
MAXIMUM_REPLICATE_CORRELATION: 0.91

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

source_name: flow sorted CD34+ cells, mobilized; RRBS1086

value: year 43

value: Male

value: 20 ng

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

value: 5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT

value: 5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT


title: ChIP-Seq analysis of H3K36me3 in human Mobilized CD34 cells; DNA_Lib 261

description:
sample_term_id: CL_0000837
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 261
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.7083
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.2401
****************
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: GSM706843_BI.Mobilized_CD34_Primary_Cells.H3K36me3.RO_01549.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 261.hg19.level.1.release.4
ANALYSIS TITLE: Mapping of Mobilized CD34 Primary Cells Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K36me3 ChIP-Seq on Mobilized CD34 Primary Cells, Donor RO 01549 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.8246
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 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 18,171,743
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 7
FINDPEAKS_SCORE: 0.5987
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.4892
HOTSPOT_PERCENTILE: 86
IROC_SCORE: 0.9986
IROC_PERCENTILE: 100
POISSON_SCORE: 0.7004
POISSON_PERCENTILE: 86
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM706843_BI.Mobilized_CD34_Primary_Cells.H3K36me3.RO_01549.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 261.hg19.level.2.release.4
ANALYSIS TITLE: Raw Signal Density Graphs of Mobilized CD34 Primary Cells Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K36me3 ChIP-Seq read mappings from Mobilized CD34 Primary Cells, Donor RO 01549 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.8273
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 4
BROWSER_TRACK_NAME: MCD34 H3K36me3 49 61
BROWSER_TRACK_DESCRIPTION: BI Mobilized CD34 Primary Cells Histone H3K36me3 Donor RO 01549 Library DNA_Lib 261 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 18,171,743
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 7
FINDPEAKS_SCORE: 0.5987
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.4892
HOTSPOT_PERCENTILE: 86
IROC_SCORE: 0.9986
IROC_PERCENTILE: 100
POISSON_SCORE: 0.7004
POISSON_PERCENTILE: 86
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

source_name: flow sorted CD34+ cells from cord blood; DNA_Lib 261

value: CD34 Primary Cells

value: 33 years

value: Protein A-Sepharose 4B

value: 10 million cells

value: SDS lysis

value: 70 ul bed volume

value: Abcam

value: Histone H3K36me3

value: Bioruptor


title: Bisulfite-Seq analysis of RRBS1079 derived from human fetal brain cells; RRBS1079

description:
sample_term_id: UBERON_0000955
assay_term_id: OBI_0001862
nucleic_acid_term_id: SO_0000352
Design description: RRBS REMC Sequencing on Illumina
Library name: RRBS1079
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.6996
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.2448
****************
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: GSM706838_BI.Fetal_Brain.RRBS.H-22510.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RRBS1079.hg19.level.2.release.4
ANALYSIS TITLE: Methylation Proportion Graphs of Fetal Brain RRBS Data
ANALYSIS DESCRIPTION: Illumina RRBS read mappings from Fetal Brain, Donor H-22510 were processed into graphs of methylation proportions. Methylation proportions were calculated as (methylated calls / (methylated calls + unmethylated calls)) for all CpGs covered by at least 4 reads.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.8332
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Reduced Representation Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19 MspI restriction fragments 40-220bp
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
GENOMIC_WINDOW: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 4
BROWSER_TRACK_NAME: FB RRBS 10 79
BROWSER_TRACK_DESCRIPTION: BI Fetal Brain RRBS Donor H-22510 Library RRBS1079 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 23,231,079
NUMBER_OF_RRBS_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 21
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 99.3
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE: 10
MAXIMUM_REPLICATE_CORRELATION: 0.71

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

source_name: Fetal Brain primary tissue, day 122; RRBS1079

value: Fetal Brain

value: genomic DNA

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

value: Primary Tissue

value: fetal brain

value: UW

value: fetal

value: 122 days

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

value: DNA Methylation

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

value: Gel size selection

value: Pfu Turbo Cx hot start


title: ChIP-Seq analysis of H3K27me3 in human Mobilized CD34 cells; DNA_Lib 262

description:
sample_term_id: CL_0000837
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 262
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.7084
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.2401
****************
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: GSM706844_BI.Mobilized_CD34_Primary_Cells.H3K27me3.RO_01549.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 262.hg19.level.1.release.4
ANALYSIS TITLE: Mapping of Mobilized CD34 Primary Cells Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27me3 ChIP-Seq on Mobilized CD34 Primary Cells, Donor RO 01549 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.8236
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 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 15,769,151
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 11
FINDPEAKS_SCORE: 0.2382
FINDPEAKS_PERCENTILE: 82
HOTSPOT_SCORE: 0.3081
HOTSPOT_PERCENTILE: 82
IROC_SCORE: 0.9771
IROC_PERCENTILE: 82
POISSON_SCORE: 0.4494
POISSON_PERCENTILE: 82
MAXIMUM_REPLICATE_CORRELATION: 0.95

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

ANALYSIS FILE NAME: GSM706844_BI.Mobilized_CD34_Primary_Cells.H3K27me3.RO_01549.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 262.hg19.level.2.release.4
ANALYSIS TITLE: Raw Signal Density Graphs of Mobilized CD34 Primary Cells Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27me3 ChIP-Seq read mappings from Mobilized CD34 Primary Cells, Donor RO 01549 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.8263
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 4
BROWSER_TRACK_NAME: MCD34 H3K27me3 49 62
BROWSER_TRACK_DESCRIPTION: BI Mobilized CD34 Primary Cells Histone H3K27me3 Donor RO 01549 Library DNA_Lib 262 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 15,769,151
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 11
FINDPEAKS_SCORE: 0.2382
FINDPEAKS_PERCENTILE: 82
HOTSPOT_SCORE: 0.3081
HOTSPOT_PERCENTILE: 82
IROC_SCORE: 0.9771
IROC_PERCENTILE: 82
POISSON_SCORE: 0.4494
POISSON_PERCENTILE: 82
MAXIMUM_REPLICATE_CORRELATION: 0.95

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

source_name: flow sorted CD34+ cells from cord blood; DNA_Lib 262

value: CD34 Primary Cells

value: FHCRC HEIMFELD

value: Primary Cell

value: 33 years

value: Female

value: Caucasian

value: Protein A-Sepharose 4B

value: 10 million cells

value: SDS lysis

value: 70 ul bed volume

value: Millipore

value: Histone H3K27me3


title: ChIP-Seq analysis of WCE in human Mobilized CD34 cells; DNA_Lib 259

description:
sample_term_id: CL_0000837
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 259
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.7086
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.2401
****************
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: GSM706846_BI.Mobilized_CD34_Primary_Cells.Input.RO_01549.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 259.hg19.level.1.release.4
ANALYSIS TITLE: Mapping of Mobilized CD34 Primary Cells ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on Mobilized CD34 Primary Cells, Donor RO 01549 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.8233
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 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 76,441,568
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 14
FINDPEAKS_SCORE: 0.0047
FINDPEAKS_PERCENTILE: 25
HOTSPOT_SCORE: 0.0025
HOTSPOT_PERCENTILE: 8
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.0124
POISSON_PERCENTILE: 8
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

ANALYSIS FILE NAME: GSM706846_BI.Mobilized_CD34_Primary_Cells.Input.RO_01549.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 259.hg19.level.2.release.4
ANALYSIS TITLE: Raw Signal Density Graphs of Mobilized CD34 Primary Cells ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from Mobilized CD34 Primary Cells, Donor RO 01549 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.8260
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 4
BROWSER_TRACK_NAME: MCD34 Input 49 59
BROWSER_TRACK_DESCRIPTION: BI Mobilized CD34 Primary Cells ChIP-Seq Input Donor RO 01549 Library DNA_Lib 259 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 76,441,568
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 14
FINDPEAKS_SCORE: 0.0047
FINDPEAKS_PERCENTILE: 25
HOTSPOT_SCORE: 0.0025
HOTSPOT_PERCENTILE: 8
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.0124
POISSON_PERCENTILE: 8
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

source_name: flow sorted CD34+ cells from cord blood; DNA_Lib 259

value: genomic DNA

value: standard

value: ChIP-Seq Input

value: Input

value: Bioruptor


title: Bisulfite-Seq analysis of RRBS1140 derived from human mobilized CD34 cells; RRBS1140

description:
sample_term_id: CL_0000837
assay_term_id: OBI_0001862
nucleic_acid_term_id: SO_0000352
Design description: RRBS REMC Sequencing on Illumina
Library name: RRBS1140
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.6858
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.1645
****************
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: GSM706859_BI.Mobilized_CD34_Primary_Cells.RRBS.RO_01508.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RRBS1140.hg19.level.2.release.4
ANALYSIS TITLE: Methylation Proportion Graphs of Mobilized CD34 Primary Cells RRBS Data
ANALYSIS DESCRIPTION: Illumina RRBS read mappings from Mobilized CD34 Primary Cells, Donor RO 01508 were processed into graphs of methylation proportions. Methylation proportions were calculated as (methylated calls / (methylated calls + unmethylated calls)) for all CpGs covered by at least 4 reads.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.8337
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Reduced Representation Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19 MspI restriction fragments 40-220bp
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
GENOMIC_WINDOW: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 4
BROWSER_TRACK_NAME: MCD34 RRBS 08 40
BROWSER_TRACK_DESCRIPTION: BI Mobilized CD34 Primary Cells RRBS Donor RO 01508 Library RRBS1140 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 18,832,559
NUMBER_OF_RRBS_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 21
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 99.73
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE: 90
MAXIMUM_REPLICATE_CORRELATION: 0.88

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

source_name: flow sorted CD34+ cells from cord blood; RRBS1140

value: CD34 Primary Cells

value: Unknown

value: 2x5hrs Epitect Kit

value: 20 ng

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

value: 5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT

value: 5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT

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

value: DNA Methylation

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

value: Gel size selection

value: Pfu Turbo Cx hot start


title: 30d replicate 2 (miRNA)

status: Public on Dec 23 2011

type: RNA

city: Philadelphia

first: Bonini

last: Nancy

state: PA

address: 415 S University Ave

institute: University of Pennsylvania

description:
small RNA profiling
miRNA0529H 30 Days #2 (Hy3) vs Pool (Hy5) 050407.gpr

hyb_protocol: Tecan Hybridization with Exiqon Hybridization Program

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

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

molecule: total RNA

organism: Drosophila melanogaster

source_name: dissected brain tissue

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

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

extract_protocol: Ambion miRvana miRNA isolation kit

treatment_protocol: natural aging

tag: tissue

value: dissected brain

tag: time

source_name: common reference pool

tag: common reference

value: pooled RNA from all samples


title: 30d replicate 1 (miRNA)

description:
small RNA profiling
miRNA0528H 30 Days #1 (Hy3) vs Pool (Hy5) 050407.gpr


title: 3d replicate 1 (miRNA)

description:
small RNA profiling
miRNA0525H 3 Days #1 (Hy3) vs Pool (Hy5) 050407.gpr


title: 3d replicate 3 (miRNA)

description:
small RNA profiling
miRNA0527H 3 Days #3 (Hy3) vs Pool (Hy5) 050407.gpr


title: 60d replicate 3 (miRNA)

description:
small RNA profiling
miRNA0533H 60 Days #3 (Hy3) vs Pool (Hy5) 050407.gpr


title: Bisulfite-Seq analysis of RRBS1083 derived from human fetal lung cells; RRBS1083

description:
sample_term_id: UBERON_0002048
assay_term_id: OBI_0001862
nucleic_acid_term_id: SO_0000352
Design description: RRBS REMC Sequencing on Illumina
Library name: RRBS1083
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.6859
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.2470
****************
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: GSM706860_BI.Fetal_Lung.RRBS.H-22727.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RRBS1083.hg19.level.2.release.4
ANALYSIS TITLE: Methylation Proportion Graphs of Fetal Lung RRBS Data
ANALYSIS DESCRIPTION: Illumina RRBS read mappings from Fetal Lung, Donor H-22727 were processed into graphs of methylation proportions. Methylation proportions were calculated as (methylated calls / (methylated calls + unmethylated calls)) for all CpGs covered by at least 4 reads.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.8326
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Reduced Representation Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19 MspI restriction fragments 40-220bp
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
GENOMIC_WINDOW: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 4
BROWSER_TRACK_NAME: FL RRBS 27 83
BROWSER_TRACK_DESCRIPTION: BI Fetal Lung RRBS Donor H-22727 Library RRBS1083 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 23,081,601
NUMBER_OF_RRBS_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 21
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 99.49
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE: 24
MAXIMUM_REPLICATE_CORRELATION: 0.76

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

source_name: Fetal Lung primary tissue, day 101; RRBS1083

value: Fetal Lung

value: genomic DNA

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

value: Primary Tissue

value: fetal lung

value: UW

value: fetal

value: 101 days


title: ChIP-Seq analysis of H3K27me3 in human ADMSC Diff Day20 cells; Lib EpiLabSPL Row 1753

status: Public on Dec 28 2011

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 1753
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8005
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.8182
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM772744_BI.Mesenchymal_Stem_Cell_Derived_Adipocyte_Cultured_Cells.H3K27me3.93.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib EpiLabSPL Row 1753.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 93, were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.10644
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: 30,312,749
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.0113
FINDPEAKS_PERCENTILE: 24
HOTSPOT_SCORE: 0.1245
HOTSPOT_PERCENTILE: 57
IROC_SCORE: 0.7406
IROC_PERCENTILE: 47
POISSON_SCORE: 0.3821
POISSON_PERCENTILE: 82
MAXIMUM_REPLICATE_CORRELATION: 0.93

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

ANALYSIS FILE NAME: GSM772744_BI.Mesenchymal_Stem_Cell_Derived_Adipocyte_Cultured_Cells.H3K27me3.93.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib EpiLabSPL Row 1753.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 93, were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.10908
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 93 53
BROWSER_TRACK_DESCRIPTION: BI Mesenchymal Stem Cell Derived Adipocyte Cultured Cells Histone H3K27me3 Donor 93 Library Lib EpiLabSPL Row 1753 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 30,312,749
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.0113
FINDPEAKS_PERCENTILE: 24
HOTSPOT_SCORE: 0.1245
HOTSPOT_PERCENTILE: 57
IROC_SCORE: 0.7406
IROC_PERCENTILE: 47
POISSON_SCORE: 0.3821
POISSON_PERCENTILE: 82
MAXIMUM_REPLICATE_CORRELATION: 0.93

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

source_name: Adipose-derived mesenchymal stem cells were cultured in adipocyte differentiation medium for 20 days; Lib EpiLabSPL Row 1753

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

value: ADMSC Diff Day20

value: Female

value: Primary Cell Culture

value: Harvard University

value: Protein A-Sepharose 4B

value: 10 million cells

value: SDS lysis

value: 70 ul bed volume

value: Millipore

value: Histone H3K27me3

value: Bioruptor


title: 60d replicate 1 (miRNA)

description:
small RNA profiling
miRNA0531H 60 Days #1 (Hy3) vs Pool (Hy5) 050407.gpr

value: dissected brain

value: pooled RNA from all samples


title: 3d replicate 2 (miRNA)

description:
small RNA profiling
miRNA0526H 3 Days #2 (Hy3) vs Pool (Hy5) 050407.gpr


title: 30d replicate 3 (miRNA)

description:
small RNA profiling
miRNA0530H 30 Days #3 (Hy3) vs Pool (Hy5) 050407.gpr


title: Calbicans_EMC120B12_3h_Biolrep2_Techrep2

status: Public on Jul 15 2011

city: Stuttgart

first: Steffen

last: Rupp

address: Nobelstr. 12

department: MBT

country: Germany

institute: Fraunhofer IGB

description: Dye Swap to Sample 3

hyb_protocol: 30 µL cDNA eluate, 6.5 µL SDS solution (1 %), 13 µL 20 x SSC and 15.5 µL RNase-free ddH2O were mixed and denatured at 100°C for 3 min. Hybridization was done over night (16 – 20 h) at 65 °C using LifterSlips (25 x 44 mm, VWR, Darmstadt, Germany). After hybridization, the LifterSlips were removed while rinsing for 1 min using 2 x SSC, 0.2 % SDS. Subsequently, DNA microarrays were washed for 10 min 2 x SSC, 0.2 % SDS, for 10 min in 2 x SSC and for 10 min in 0.2 x SSC. Afterwards, DNA microarrays were dried with compressed N2 gas, and stored protected from light in the dark until scanned.

scan_protocol: The completely dried DNA microarrays were scanned using the Genepix microarray scanner 4300A (Molecular Devices, Sunnyvale, CA) (resolution,  10 µm; PMT setting: auto-PMT). Pictures of both channels were saved as 16-bit TIFF files.

data_processing: Raw data were created using Molecular Devices imaging software GenePix Pro 7.0 (Molecular Devices, Sunnyvale, CA).  The data were statistically analyzed using the software R (V. 2.10.1), the limma package (V. 3.2.1) and the statmod package (V. 1.4.2) (1, 2). An empirical Bayes method was chosen to take into account that in the classical t test, small variance values of the gene of interest tend to lead to high t-test statistics and therefore, erroneously, to a higher probability of significant differential expression (3). Background correction was performed using “normexp” with an offset of 50 (4). The data was normalized “print-tip-loess” (5). Spots which were classified as not found by the image analysis software were ignored for fitting of the linear model.  As thousands of hypotheses can be tested with DNA microarrays, the chance to make an α error increases with the number of hypotheses. Therefore, multiple-hypothesis testing was performed (6). Multiple-hypothesis testing correction was performed by the method of Benjamini and Hochberg, which controls the false discovery rate (FDR) (7). The quotient between expected false-positive genes and all differentially expressed genes allows an adjusted P value to be calculated, which can be used to make predictions about differential gene expression. Genes were regarded as differentially expressed and followed up, when the adjusted P values were 0.001, therefore nominally controlling the expected FDR to less than 0.001.  [1. R. (2009) R: A language and environment for statistical computing. R Foundation for Statistical Computing., RDevelopment Core Team.] [2. Smyth, G. K. (2005) Limma: Linear models for microarray data., In Bioinformatics and Computational Biology Solutions using R and Bioconductor (Gentleman, R., Carrey, V., Dudoit, S., Irizzary, I., Huber, W., Ed.), pp 397-420, Springer, New York.] [3. Lönnstedt, I., and Speed, T. P. (2002) Replicated microarray data., Stat.Sin. 12, 31-46.] [4. Ritchie, M. E., Silver, J., Oshlack, A., Holmes, M., Diyagama, D., Holloway, A., and Smyth, G. K. (2007) A comparison of background correction methods for two-colour microarrays, Bioinformatics 23, 2700-2707.] [5. Smyth, G. K., and Speed, T. (2003) Normalization of cDNA microarray data, Methods 31, 265-273.] [6. Dudoit, S., Popper Schaffer, J., and Boldrick, J. C. (2003) Multiple hypothesis testing in microarray experiments, Stat. Sci. 28, 71-103.] [7. Benjamini, Y., and Hochberg, Y. (1995) Controlling the false discovery rate: A practical and powerful approach to multiple testing., J. R. Stat. Soc. B 57, 289-300.]

organism: Candida albicans

source_name: cultured cells, ECM120B12 treated, 3h

label_protocol: Identical amounts of concentrated total RNA were reverse transcribed using LabelStar-Kit (Qiagen, Hilden, Germany) and labeled with Cy3-dCTPs or Cy5-dCTPs. All reactions were performed on ice according to manufacturers’ protocol. After reverse transcription, reference (Cy3 or Cy5 labeled, respectively) and sample (Cy5 or Cy3 labeled, respectively) were combined, purified and eluted using 30 µL buffer EB.

growth_protocol: 100 mL RPMI 1640 Medium (Invitrogen, Karlsruhe, Germany) + 10 % Fetal Calf Serum (FCS, Gibco Life Technologies GmbH, Karlsruhe, Germany) were inoculated with C. albicans SC5314 to an OD of 0.4 from an ON culture (10 mL YPD medium (1 % yeast extract, 2 %bacto peptone, 2 % glucose), 30°C) and grown for 3 h at 37 °C with or without ECM120B12 (IC50: 0.4 µM).

extract_protocol: Cell beads were destroyed using mortar and pestle. Grounded cell powder was transferred to a 15 mL falcon tube filled with 4 mL RLT-buffer (RNeasy Midi Kit, Qiagen, Hilden, Germany) and 40 µL ß-mercaptoethanol (Merck, Darmstadt, Germany) using an applicator. Prior to use, mortar, pestle, and applicator were cooled with liquid nitrogen. Liquid nitrogen was added during the cell destruction process whenever needed to avoid thawing.   RNA was isolated using RNeasy-Midi-Kit (Qiagen, Hilden, Germany) according to manufacturers protocol (Yeast II). On column DNAse digestion was performed (RNase-free DNase set; Qiagen, Hilden, Germany). RNA concentration and quality were assessed photometrically (Spectra-Photometer V630, Jasco, Gross-Umstadt, Germany) and by bioanalyzer analysis (RNA 6000 Nano LabChip kit, Agilent Bioanalyzer 2100; Agilent Technologies, CA). The RNA was precipitated using lithium chloride: 500 µL 4 M LiCl-solution was added to 500 µL RNA-solution and incubated at -20°C over night. RNA was centrifuged at 4°C and 13,000 g for 30 min, washed three times with 70 % ethanol and the precipitate dried for 5 min at 37 °C. RNA was redissolved in 50 µL RNase free ddH2O. Only RNA with a 260 nm/280 nm ratio of 1.8 to 2 as well as a 260 nm/230 nm ratio of 1.8 was used for DNA microarrays.   25 μg of total-RNA in a volume of maximal 19 μL was used for reverse transcription and labeling.

treatment_protocol: Cells were centrifuged (1200 g, 3 min) and the supernatant discarded. Subsequently, cells were resuspended in the remaining medium and dropped into liquid N2 to generate cell beads for RNA isolation. The experiment was performed three times.

tag: strain

source_name: cultured cells, untreated, 3h


title: Calbicans_EMC120B12_3h_Biolrep1_Techrep1

description: Dye Swap to Sample 2


title: Calbicans_EMC120B12_3h_Biolrep2_Techrep1

description: Dye Swap to Sample 4


title: Calbicans_EMC120B12_3h_Biolrep3_Techrep2

description: Dye Swap to Sample 5


title: Calbicans_EMC120B12_3h_Biolrep1_Techrep2

description: Dye Swap to Sample 1


title: Calbicans_EMC120B12_3h_Biolrep3_Techrep1

description: Dye Swap to Sample 6


title: Brg-KO ES cells, rep3

status: Public on Aug 01 2011

city: RTP

first: Raja

last: Jothi

state: NC

address: 111 TW Alexander Drive; A314

department: National Institute of Environmental Health Sciences

institute: National Institutes of Health

hyb_protocol: 20 micrograms of biotin labeled RNA was fragmented to ~100 bp fragments by incubating in a buffer containing 200 mM Tris-Acetate pH 8.2, 500 mM Potassium Acetate and 500 Magnesium Acetate for 35 minutes at 95C. Fragments were hybridized to Affymetrix 430 2.0 chips for 16 hrs, washed and stained on an Affymetrix fluidics station.

scan_protocol: Scanning was performed with the Affymetrix GeneChip scanner using default settings.

data_processing: Raw signal values were normalized using RMAExpress.

label: biotin

organism: Mus musculus

source_name: Brg(lox/lox);Actin-CreER mice

label_protocol: Labeling was performed using Affymetrix's IVT labeling kit following manufacturer's directions.

extract_protocol: Total RNA was extracted using Trizol reagent (Invitrogen), followed by RNeasy kit with DNaseI digestion to eliminate genomic DNA

tag: cell line

value: Brg conditional ES cells prepared from Brg(lox/lox);Actin-CreER mice that allow conditional deletion of Brg upon addition of 4-hydroxytamoxifen (4OHT, Sigma)

tag: treatment

value: 4OHT for 72 hours to delete Brg


title: WT ES cells, rep3

value: untreated


title: Brg-KO ES cells, rep2


title: Brg-KO ES cells, rep1


title: WT ES cells, rep2


title: WT ES cells, rep1


title: IC+H_S981

status: Public on Jun 29 2011

city: Erlangen

first: Roland

last: Lang

address: Wasserturmstr. 3-5

institute: University Hospital Erlangen

description: Gene expression data from bone marrow derived DC

hyb_protocol: 5 µg of biotinylated DNA were hybridized to Mouse Gene ST 1.0 GeneChips overnight, followed by washing and staining procedures, and scanning, following Affymetrix protocols.

data_processing: For generation of probe set expression values, CEL files containing probe level data were normalized using RMA (Affymetrix Expression Console).

source_name: bone marrow derived Dendritic Cells from C57Bl/6 mice

label_protocol: RNA samples were processed and hybridised to Affymetrix Mouse Gene ST 1.0 GeneChips according to the manufacturer’s protocols. In brief, 200 ng total RNA and 100 ng nascent RNA were reverse transcribed introducing by random priming a T7-binding site into the cDNA that allows in vitro transcription. The resulting cRNA was subjected to a second round of random primed cDNA synthesis in the presence of dUTP, that allows fragmentation of the cDNA with uracil DNA glycosylase and apurinic/apyrimidinic endonuclease 1. Biotinylation of the fragmented cDNA was accomplished by incubation with Terminal Deoxynucleotidyltransferase (TdT).

growth_protocol: Bone marrow cells from C57Bl/6 mice were differentiated to BM-DC with GM-CSF.

extract_protocol: Total RNA was extracted with Trizol (Invitrogen Life Technologies, Carlsbad, CA) according to the manufacturer’s instruction. Concentration and integrity of total RNA were determined by spectrophotometry (Nanodrop) and Experion automated electrophoresis system (Biorad, Munich, Germany).

treatment_protocol: DC were plated at a density of approx. 0.2 x 10e6 cells/ cm2 (2 x 10e6 DC per 6 well [9.6cm2]) and stimulated with poly I:C (10µg/ml), hypoxia (0.5%) or both for 16h

tag: condition

value: Hypoxia, poly I:C


title: H_S980

scan_protocol: 5 µg of biotinylated DNA were hybridized to Mouse Gene ST 1.0 GeneChips overnight, followed by washing and staining procedures, and scanning, following Affymetrix protocols.

value: Hypoxia, media


title: un_S978

value: Normoxia, media


title: IC_S979

value: Normoxia, poly I:C


title: ChIP-Seq analysis of WCE; chondr. dif cls; Lib:MC:20100729:07--ChIP:MC:20100726:07:chondrogenic dif cells:WCE

status: Public on Mar 31 2011

description:
sample_term_id: CL_0000138
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:MC:20100729:07--ChIP:MC:20100726:07:chondrogenic dif cells:WCE
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5785
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5935
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM670044_BI.Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.Input.59.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100729:07--ChIP:MC:20100726:07:chondrogenic dif cells:WCE.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells, Donor 59 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6470
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 3

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 61
FINDPEAKS_SCORE: 0.0067
FINDPEAKS_PERCENTILE: 53
HOTSPOT_SCORE: 0.0129
HOTSPOT_PERCENTILE: 47
IROC_SCORE: 0.0
IROC_PERCENTILE: 38
POISSON_SCORE: 0.0519
POISSON_PERCENTILE: 43

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

ANALYSIS FILE NAME: GSM670044_BI.Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.Input.59.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100729:07--ChIP:MC:20100726:07:chondrogenic dif cells:WCE.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells, Donor 59 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6680
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 3
BROWSER_TRACK_NAME: CfBMDMSC Input 59
BROWSER_TRACK_DESCRIPTION: BI Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells ChIP-Seq Input Donor 59 Library Lib:MC:20100729:07--ChIP:MC:20100726:07:chondrogenic dif cells:WCE EA Release 3

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 61
FINDPEAKS_SCORE: 0.0067
FINDPEAKS_PERCENTILE: 53
HOTSPOT_SCORE: 0.0129
HOTSPOT_PERCENTILE: 47
IROC_SCORE: 0.0
IROC_PERCENTILE: 38
POISSON_SCORE: 0.0519
POISSON_PERCENTILE: 43

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

source_name: chondrocytes derived via in vitro culture from mesenchymal stem cells; Lib:MC:20100729:07--ChIP:MC:20100726:07:chondrogenic dif cells:WCE

value: healthy

value: genomic DNA

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

value: chondrogenic dif cells

value: Unknown

value: Primary Cell Culture

value: Rikshospitalet University Hospital

value: standard

value: ChIP-Seq Input

value: Input


title: ChIP-Seq analysis of H3K4me1 in AdiposeNuclei cells; Lib:XZ:20100731:08--ChIP:XZ:20100726:08:AdiposeNuclei:H3K4Me1

description:
sample_term_id: UBERON_0014455
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:XZ:20100731:08--ChIP:XZ:20100726:08:AdiposeNuclei:H3K4Me1
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5786
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5947
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM670045_BI.Adipose_Nuclei.H3K4me1.93.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100731:08--ChIP:XZ:20100726:08:AdiposeNuclei:H3K4Me1.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Adipose Nuclei Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me1 ChIP-Seq on Adipose Nuclei, Donor 93 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6597
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 3

QUALITY SCORES:
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 50
FINDPEAKS_SCORE: 0.4466
FINDPEAKS_PERCENTILE: 75
HOTSPOT_SCORE: 0.474
HOTSPOT_PERCENTILE: 75
IROC_SCORE: 0.9948
IROC_PERCENTILE: 68
POISSON_SCORE: 0.5791
POISSON_PERCENTILE: 64

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

ANALYSIS FILE NAME: GSM670045_BI.Adipose_Nuclei.H3K4me1.93.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100731:08--ChIP:XZ:20100726:08:AdiposeNuclei:H3K4Me1.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of Adipose Nuclei Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me1 ChIP-Seq read mappings from Adipose Nuclei, Donor 93 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6807
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 3
BROWSER_TRACK_NAME: AN H3K4me1 93
BROWSER_TRACK_DESCRIPTION: BI Adipose Nuclei Histone H3K4me1 Donor 93 Library Lib:XZ:20100731:08--ChIP:XZ:20100726:08:AdiposeNuclei:H3K4Me1 EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 50
FINDPEAKS_SCORE: 0.4466
FINDPEAKS_PERCENTILE: 75
HOTSPOT_SCORE: 0.474
HOTSPOT_PERCENTILE: 75
IROC_SCORE: 0.9948
IROC_PERCENTILE: 68
POISSON_SCORE: 0.5791
POISSON_PERCENTILE: 64

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

source_name: Nuclei derived from crude preps of adipose tissue; Lib:XZ:20100731:08--ChIP:XZ:20100726:08:AdiposeNuclei:H3K4Me1

value: Adipose Nuclei

value: surgery

value: Female

value: Primary Tissue

value: abdomen

value: Harvard University

value: Protein A-Sepharose 4B

value: 10 million cells

value: SDS lysis

value: 70 ul bed volume

value: Abcam

value: Histone H3K4me1

value: Bioruptor


title: ChIP-Seq analysis of WCE in AdiposeNuclei cells; Lib:XZ:20100731:14--ChIP:XZ:20100726:14:AdiposeNuclei:WCE

description:
sample_term_id: UBERON_0014455
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:XZ:20100731:14--ChIP:XZ:20100726:14:AdiposeNuclei:WCE
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5784
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5947
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM670043_BI.Adipose_Nuclei.Input.93.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100731:14--ChIP:XZ:20100726:14:AdiposeNuclei:WCE.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Adipose Nuclei ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on Adipose Nuclei, Donor 93 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6498
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 3

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 61
FINDPEAKS_SCORE: 0.0072
FINDPEAKS_PERCENTILE: 77
HOTSPOT_SCORE: 0.015
HOTSPOT_PERCENTILE: 57
IROC_SCORE: 0.0
IROC_PERCENTILE: 38
POISSON_SCORE: 0.0531
POISSON_PERCENTILE: 47

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

ANALYSIS FILE NAME: GSM670043_BI.Adipose_Nuclei.Input.93.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100731:14--ChIP:XZ:20100726:14:AdiposeNuclei:WCE.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of Adipose Nuclei ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from Adipose Nuclei, Donor 93 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6708
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 3
BROWSER_TRACK_NAME: AN Input 93
BROWSER_TRACK_DESCRIPTION: BI Adipose Nuclei ChIP-Seq Input Donor 93 Library Lib:XZ:20100731:14--ChIP:XZ:20100726:14:AdiposeNuclei:WCE EA Release 3

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 61
FINDPEAKS_SCORE: 0.0072
FINDPEAKS_PERCENTILE: 77
HOTSPOT_SCORE: 0.015
HOTSPOT_PERCENTILE: 57
IROC_SCORE: 0.0
IROC_PERCENTILE: 38
POISSON_SCORE: 0.0531
POISSON_PERCENTILE: 47

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

source_name: Nuclei derived from crude preps of adipose tissue; Lib:XZ:20100731:14--ChIP:XZ:20100726:14:AdiposeNuclei:WCE

value: genomic DNA


title: ChIP-Seq analysis of H3K4me3 in AdiposeNuclei cells; Lib:XZ:20100731:16--ChIP:XZ:20100726:16:AdiposeNuclei:H3K4Me3

description:
sample_term_id: UBERON_0014455
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:XZ:20100731:16--ChIP:XZ:20100726:16:AdiposeNuclei:H3K4Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5782
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5944
****************
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: GSM670041_BI.Adipose_Nuclei.H3K4me3.94.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100731:16--ChIP:XZ:20100726:16:AdiposeNuclei:H3K4Me3.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Adipose Nuclei Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me3 ChIP-Seq on Adipose Nuclei, Donor 94 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.6504
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 3

QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.3095
FINDPEAKS_PERCENTILE: 40
HOTSPOT_SCORE: 0.3591
HOTSPOT_PERCENTILE: 40
IROC_SCORE: 0.981
IROC_PERCENTILE: 12
POISSON_SCORE: 0.4053
POISSON_PERCENTILE: 48

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

ANALYSIS FILE NAME: GSM670041_BI.Adipose_Nuclei.H3K4me3.94.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100731:16--ChIP:XZ:20100726:16:AdiposeNuclei:H3K4Me3.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of Adipose Nuclei Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me3 ChIP-Seq read mappings from Adipose Nuclei, Donor 94 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.6714
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 3
BROWSER_TRACK_NAME: AN H3K4me3 94
BROWSER_TRACK_DESCRIPTION: BI Adipose Nuclei Histone H3K4me3 Donor 94 Library Lib:XZ:20100731:16--ChIP:XZ:20100726:16:AdiposeNuclei:H3K4Me3 EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.3095
FINDPEAKS_PERCENTILE: 40
HOTSPOT_SCORE: 0.3591
HOTSPOT_PERCENTILE: 40
IROC_SCORE: 0.981
IROC_PERCENTILE: 12
POISSON_SCORE: 0.4053
POISSON_PERCENTILE: 48

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

source_name: Nuclei derived from crude preps of adipose tissue; Lib:XZ:20100731:16--ChIP:XZ:20100726:16:AdiposeNuclei:H3K4Me3

value: Millipore

value: Histone H3K4me3


title: ChIP-Seq analysis of H3K9me3; chondr. dif cls; Lib:MC:20100726:06--ChIP:MC:20100713:06:chondrogenic dif cells:H3K9Me3

description:
sample_term_id: CL_0000138
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:MC:20100726:06--ChIP:MC:20100713:06:chondrogenic dif cells:H3K9Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5781
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5949
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM670040_BI.Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K9me3.57.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100726:06--ChIP:MC:20100713:06:chondrogenic dif cells:H3K9Me3.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9me3 ChIP-Seq on Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells, Donor 57 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6527
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 3

QUALITY SCORES:
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 60
FINDPEAKS_SCORE: 0.0433
FINDPEAKS_PERCENTILE: 46
HOTSPOT_SCORE: 0.1124
HOTSPOT_PERCENTILE: 42
IROC_SCORE: 0.6884
IROC_PERCENTILE: 4
POISSON_SCORE: 0.306
POISSON_PERCENTILE: 50

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

ANALYSIS FILE NAME: GSM670040_BI.Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K9me3.57.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100726:06--ChIP:MC:20100713:06:chondrogenic dif cells:H3K9Me3.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9me3 ChIP-Seq read mappings from Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells, Donor 57 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6737
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 3
BROWSER_TRACK_NAME: CfBMDMSC H3K9me3 57
BROWSER_TRACK_DESCRIPTION: BI Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K9me3 Donor 57 Library Lib:MC:20100726:06--ChIP:MC:20100713:06:chondrogenic dif cells:H3K9Me3 EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 60
FINDPEAKS_SCORE: 0.0433
FINDPEAKS_PERCENTILE: 46
HOTSPOT_SCORE: 0.1124
HOTSPOT_PERCENTILE: 42
IROC_SCORE: 0.6884
IROC_PERCENTILE: 4
POISSON_SCORE: 0.306
POISSON_PERCENTILE: 50

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

source_name: chondrocytes derived via in vitro culture from mesenchymal stem cells; Lib:MC:20100726:06--ChIP:MC:20100713:06:chondrogenic dif cells:H3K9Me3

value: healthy

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

value: chondrogenic dif cells

value: Unknown

value: Primary Cell Culture

value: Rikshospitalet University Hospital

value: Histone H3K9me3


title: ChIP-Seq analysis of H3K36me3 in BM-MSC cells; Lib:MC:20100706:10--ChIP:MC:20100628:10:BM-MSC:H3K36Me3

description:
sample_term_id: EFO_0000586
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:MC:20100706:10--ChIP:MC:20100628:10:BM-MSC:H3K36Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5778
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5953
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM670037_BI.Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K36me3.58.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100706:10--ChIP:MC:20100628:10:BM-MSC:H3K36Me3.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K36me3 ChIP-Seq on Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells, Donor 58 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6484
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 3

QUALITY SCORES:
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 59
FINDPEAKS_SCORE: 0.3022
FINDPEAKS_PERCENTILE: 54
HOTSPOT_SCORE: 0.2855
HOTSPOT_PERCENTILE: 50
IROC_SCORE: 0.985
IROC_PERCENTILE: 54
POISSON_SCORE: 0.5102
POISSON_PERCENTILE: 65

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

ANALYSIS FILE NAME: GSM670037_BI.Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K36me3.58.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100706:10--ChIP:MC:20100628:10:BM-MSC:H3K36Me3.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K36me3 ChIP-Seq read mappings from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells, Donor 58 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6694
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 3
BROWSER_TRACK_NAME: BMDMSC H3K36me3 58
BROWSER_TRACK_DESCRIPTION: BI Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K36me3 Donor 58 Library Lib:MC:20100706:10--ChIP:MC:20100628:10:BM-MSC:H3K36Me3 EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 59
FINDPEAKS_SCORE: 0.3022
FINDPEAKS_PERCENTILE: 54
HOTSPOT_SCORE: 0.2855
HOTSPOT_PERCENTILE: 50
IROC_SCORE: 0.985
IROC_PERCENTILE: 54
POISSON_SCORE: 0.5102
POISSON_PERCENTILE: 65

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

source_name: bone marrow was aspirated from the iliac crest, isolated by density gradient and adhesion to plastic, and expanded in monolayer culture, containing 10% FBS; Lib:MC:20100706:10--ChIP:MC:20100628:10:BM-MSC:H3K36Me3

value: BM-MSC

value: Protein A-Sepharose 4B

value: Histone H3K36me3


title: Exon arrays of Roadmap cell types; Fetal  primary tissue, day 108; DS17381-exon

status: Public on Apr 14 2011

city: Seattle

first: Northwest

last: REMC

state: WA

institute: University of Washington

description:
sample_term_id: UBERON_0001224
assay_term_id: OBI_0001463
nucleic_acid_term_id: SO_0000356
Exon profiling of NREMC cell types, these coincide with chromatin accessibility sequencing assays.
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.7189
sample alias: fKidney_renal_pelvis.H-23790d108
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.7116

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

scan_protocol: Affymetrix Gene Chip Scanner 3000

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

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

growth_protocol: Followed vendor recommendations for growth protocol/media

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

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

value: Primary Tissue

value: Fetal Renal Pelvis

value: UW

value: fetal

value: day 108

value: Male


title: Exon arrays of Roadmap cell types; Fetal  primary tissue, day 115; DS17429-exon

description:
sample_term_id: UBERON_0001383
assay_term_id: OBI_0001463
nucleic_acid_term_id: SO_0000356
Exon profiling of NREMC cell types, these coincide with chromatin accessibility sequencing assays.
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.7291
sample alias: fMuscle_Leg.H-23808d115
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.7281

value: Fetal Muscle, Leg

value: day 115


title: ChIP-Seq analysis of H3K9ac; chondr. dif cls; Lib:MC:20100729:05--ChIP:MC:20100726:05:chondrogenic dif cells:H3K9Ac

description:
sample_term_id: CL_0000138
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:MC:20100729:05--ChIP:MC:20100726:05:chondrogenic dif cells:H3K9Ac
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5771
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5935
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM670030_BI.Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K9ac.59.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100729:05--ChIP:MC:20100726:05:chondrogenic dif cells:H3K9Ac.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9ac ChIP-Seq on Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells, Donor 59 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6580
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 3

QUALITY SCORES:
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 40
FINDPEAKS_SCORE: 0.2527
FINDPEAKS_PERCENTILE: 72
HOTSPOT_SCORE: 0.3063
HOTSPOT_PERCENTILE: 72
IROC_SCORE: 0.9944
IROC_PERCENTILE: 60
POISSON_SCORE: 0.3743
POISSON_PERCENTILE: 76

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

ANALYSIS FILE NAME: GSM670030_BI.Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K9ac.59.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100729:05--ChIP:MC:20100726:05:chondrogenic dif cells:H3K9Ac.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9ac ChIP-Seq read mappings from Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells, Donor 59 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.6790
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 3
BROWSER_TRACK_NAME: CfBMDMSC H3K9ac 59
BROWSER_TRACK_DESCRIPTION: BI Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K9ac Donor 59 Library Lib:MC:20100729:05--ChIP:MC:20100726:05:chondrogenic dif cells:H3K9Ac EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 40
FINDPEAKS_SCORE: 0.2527
FINDPEAKS_PERCENTILE: 72
HOTSPOT_SCORE: 0.3063
HOTSPOT_PERCENTILE: 72
IROC_SCORE: 0.9944
IROC_PERCENTILE: 60
POISSON_SCORE: 0.3743
POISSON_PERCENTILE: 76

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

source_name: chondrocytes derived via in vitro culture from mesenchymal stem cells; Lib:MC:20100729:05--ChIP:MC:20100726:05:chondrogenic dif cells:H3K9Ac

value: healthy

value: genomic DNA

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

value: chondrogenic dif cells

value: 10 million cells

value: SDS lysis

value: 70 ul bed volume

value: Abcam

value: Histone H3K9ac

value: Bioruptor


title: Exon arrays of Roadmap cell types; Fetal  primary tissue, day 113; DS17455-exon

description:
sample_term_id: UBERON_0001225
assay_term_id: OBI_0001463
nucleic_acid_term_id: SO_0000356
Exon profiling of NREMC cell types, these coincide with chromatin accessibility sequencing assays.
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.7191
sample alias: fKidney_renal_cortex.H-23833d113
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.7077

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

value: Primary Tissue

value: Fetal Renal Cortex

value: day 113


title: Exon arrays of Roadmap cell types; Fetal  primary tissue, day 115; DS17432-exon

description:
sample_term_id: UBERON_0001499
assay_term_id: OBI_0001463
nucleic_acid_term_id: SO_0000356
Exon profiling of NREMC cell types, these coincide with chromatin accessibility sequencing assays.
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.7289
sample alias: fMuscle_Arm.H-23808d115
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.7271

value: Fetal Muscle, Arm

value: UW

value: fetal

value: Male