title: ChIP-Seq analysis of H3K4me1 in human Mobilized CD34 cells; DNA_Lib 256

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 256
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.7527
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.2397
****************
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: GSM772734_BI.Mobilized_CD34_Primary_Cells.H3K4me1.RO_01536.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 256.hg19.level.1.release.4
ANALYSIS TITLE: Mapping of Mobilized CD34 Primary Cells Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me1 ChIP-Seq on Mobilized CD34 Primary Cells, Donor RO 01536 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.8234
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: 9,168,042
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 12
FINDPEAKS_SCORE: 0.629
FINDPEAKS_PERCENTILE: 92
HOTSPOT_SCORE: 0.6316
HOTSPOT_PERCENTILE: 92
IROC_SCORE: 0.9994
IROC_PERCENTILE: 83
POISSON_SCORE: 0.6949
POISSON_PERCENTILE: 92
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

ANALYSIS FILE NAME: GSM772734_BI.Mobilized_CD34_Primary_Cells.H3K4me1.RO_01536.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 256.hg19.level.2.release.4
ANALYSIS TITLE: Raw Signal Density Graphs of Mobilized CD34 Primary Cells Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me1 ChIP-Seq read mappings from Mobilized CD34 Primary Cells, Donor RO 01536 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.8261
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 H3K4me1 36 56
BROWSER_TRACK_DESCRIPTION: BI Mobilized CD34 Primary Cells Histone H3K4me1 Donor RO 01536 Library DNA_Lib 256 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 9,168,042
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 12
FINDPEAKS_SCORE: 0.629
FINDPEAKS_PERCENTILE: 92
HOTSPOT_SCORE: 0.6316
HOTSPOT_PERCENTILE: 92
IROC_SCORE: 0.9994
IROC_PERCENTILE: 83
POISSON_SCORE: 0.6949
POISSON_PERCENTILE: 92
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

ANALYSIS FILE NAME: GSM772734_BI.Mobilized_CD34_Primary_Cells.H3K4me1.RO_01536_release5.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 256-DNA_Lib 256-DNA_Lib 256-DNA_Lib 256-DNA_Lib 256.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Mobilized CD34 Primary Cells Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me1 ChIP-Seq on Mobilized CD34 Primary Cells, Donor RO 01536, 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.10750
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: 9,307,060
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.6258
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.6276
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9994
IROC_PERCENTILE: 98
POISSON_SCORE: 0.6924
POISSON_PERCENTILE: 98
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

ANALYSIS FILE NAME: GSM772734_BI.Mobilized_CD34_Primary_Cells.H3K4me1.RO_01536_release5.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 256-DNA_Lib 256-DNA_Lib 256-DNA_Lib 256-DNA_Lib 256.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Mobilized CD34 Primary Cells Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me1 ChIP-Seq read mappings from Mobilized CD34 Primary Cells, Donor RO 01536, 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.11014
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: MCD34 H3K4me1 36 56
BROWSER_TRACK_DESCRIPTION: BI Mobilized CD34 Primary Cells Histone H3K4me1 Donor RO 01536 Library DNA_Lib 256 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 9,307,060
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.6258
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.6276
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9994
IROC_PERCENTILE: 98
POISSON_SCORE: 0.6924
POISSON_PERCENTILE: 98
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

source_name: flow sorted CD34+ cells from cord blood; DNA_Lib 256

value: CD34 Primary Cells

value: genomic DNA

value: FHCRC HEIMFELD

value: Primary Cell

tag: markers

value: 27 years

value: Female

value: Hispanic

value: Protein A-Sepharose 4B

value: 10 million cells

value: 70 ul bed volume

value: Abcam

value: Histone H3K4me1


title: ChIP-Seq analysis of H3K4me1 in human fetal heart cells; DNA_Lib 466

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_0000948
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 466
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.7525
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.7547
****************
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: GSM772732_BI.Fetal_Heart.H3K4me1.UW_H23914.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 466.hg19.level.1.release.4
ANALYSIS TITLE: Mapping of Fetal Heart Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me1 ChIP-Seq on Fetal Heart, Donor UW H23914 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.8230
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: 16,123,785
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 12
FINDPEAKS_SCORE: 0.4452
FINDPEAKS_PERCENTILE: 77
HOTSPOT_SCORE: 0.492
HOTSPOT_PERCENTILE: 77
IROC_SCORE: 0.9949
IROC_PERCENTILE: 75
POISSON_SCORE: 0.5844
POISSON_PERCENTILE: 69
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

ANALYSIS FILE NAME: GSM772732_BI.Fetal_Heart.H3K4me1.UW_H23914.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 466.hg19.level.2.release.4
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Heart Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me1 ChIP-Seq read mappings from Fetal Heart, Donor UW H23914 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.8257
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: FH H3K4me1 14 66
BROWSER_TRACK_DESCRIPTION: BI Fetal Heart Histone H3K4me1 Donor UW H23914 Library DNA_Lib 466 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 16,123,785
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 12
FINDPEAKS_SCORE: 0.4452
FINDPEAKS_PERCENTILE: 77
HOTSPOT_SCORE: 0.492
HOTSPOT_PERCENTILE: 77
IROC_SCORE: 0.9949
IROC_PERCENTILE: 75
POISSON_SCORE: 0.5844
POISSON_PERCENTILE: 69
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

molecule: genomic DNA

organism: Homo sapiens

source_name: Primary fetal heart tissue; DNA_Lib 466

extract_protocol: Library construction protocol: Single read - Illumina

tag: sample alias

value: BioSam 201

tag: sample common name

value: Fetal Heart

value: Post-Mortem

value: presumed normal

tag: molecule

tag: disease

value: Male

value: Primary Tissue

value: Heart

value: University of Washington

value: SDS lysis

value: Bioruptor


title: ChIP-Seq analysis of H3K9me3 in Mobilized CD34 cells; Lib:RI:20100603:10--ChIP:MA:20100517:10:Mobilized CD34:H3K9Me3

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: Lib:RI:20100603:10--ChIP:MA:20100517:10:Mobilized CD34:H3K9Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.7515
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.2422
****************
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: GSM773049_BI.Mobilized_CD34_Primary_Cells.H3K9me3.RO_01562.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:RI:20100603:10--ChIP:MA:20100517:10:Mobilized CD34:H3K9Me3.hg19.level.1.release.4
ANALYSIS TITLE: Mapping of Mobilized CD34 Primary Cells Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9me3 ChIP-Seq on Mobilized CD34 Primary Cells, Donor RO 01562 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.8235
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: 24,502,146
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 6
FINDPEAKS_SCORE: 0.2949
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.3242
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9656
IROC_PERCENTILE: 100
POISSON_SCORE: 0.5206
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.92

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

ANALYSIS FILE NAME: GSM773049_BI.Mobilized_CD34_Primary_Cells.H3K9me3.RO_01562.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:RI:20100603:10--ChIP:MA:20100517:10:Mobilized CD34:H3K9Me3.hg19.level.2.release.4
ANALYSIS TITLE: Raw Signal Density Graphs of Mobilized CD34 Primary Cells Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9me3 ChIP-Seq read mappings from Mobilized CD34 Primary Cells, Donor RO 01562 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.8262
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 H3K9me3 62
BROWSER_TRACK_DESCRIPTION: BI Mobilized CD34 Primary Cells Histone H3K9me3 Donor RO 01562 Library Lib:RI:20100603:10--ChIP:MA:20100517:10:Mobilized Mobilized CD34:H3K9Me3 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 24,502,146
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 6
FINDPEAKS_SCORE: 0.2949
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.3242
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9656
IROC_PERCENTILE: 100
POISSON_SCORE: 0.5206
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.92

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

source_name: flow sorted CD34+ cells from cord blood; Lib:RI:20100603:10--ChIP:MA:20100517:10:Mobilized CD34:H3K9Me3

value: CD34 Primary Cells

value: genomic DNA

value: FHCRC HEIMFELD

value: Primary Cell

value: 42 years

value: Caucasian

value: Histone H3K9me3


title: ChIP-Seq analysis of H3K4me1 in human fetal lung cells; DNA_Lib 392

description:
sample_term_id: UBERON_0002048
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 392
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.7134
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.7162
****************
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: GSM706853_BI.Fetal_Lung.H3K4me1.UW_H22772.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 392.hg19.level.1.release.4
ANALYSIS TITLE: Mapping of Fetal Lung Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me1 ChIP-Seq on Fetal Lung, Donor UW H22772 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.8247
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: 21,911,851
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 12
FINDPEAKS_SCORE: 0.3385
FINDPEAKS_PERCENTILE: 46
HOTSPOT_SCORE: 0.4224
HOTSPOT_PERCENTILE: 46
IROC_SCORE: 0.9766
IROC_PERCENTILE: 33
POISSON_SCORE: 0.5787
POISSON_PERCENTILE: 62
MAXIMUM_REPLICATE_CORRELATION: 0.93

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

ANALYSIS FILE NAME: GSM706853_BI.Fetal_Lung.H3K4me1.UW_H22772.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 392.hg19.level.2.release.4
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Lung Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me1 ChIP-Seq read mappings from Fetal Lung, Donor UW H22772 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.8274
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: FL H3K4me1 72 92
BROWSER_TRACK_DESCRIPTION: BI Fetal Lung Histone H3K4me1 Donor UW H22772 Library DNA_Lib 392 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 21,911,851
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 12
FINDPEAKS_SCORE: 0.3385
FINDPEAKS_PERCENTILE: 46
HOTSPOT_SCORE: 0.4224
HOTSPOT_PERCENTILE: 46
IROC_SCORE: 0.9766
IROC_PERCENTILE: 33
POISSON_SCORE: 0.5787
POISSON_PERCENTILE: 62
MAXIMUM_REPLICATE_CORRELATION: 0.93

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

source_name: Primary fetal lung tissue; DNA_Lib 392

value: BioSAli 187

value: Fetal Lung

value: Female

value: Lung

value: 82 Days

value: Protein A-Sepharose 4B

value: 10 million cells

value: 70 ul bed volume

value: Abcam

value: Histone H3K4me1


title: ChIP-Seq analysis of H3K27me3 in human fetal lung cells; DNA_Lib 391

description:
sample_term_id: UBERON_0002048
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 391
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.7133
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.7162
****************
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: GSM706852_BI.Fetal_Lung.H3K27me3.UW_H22772.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 391.hg19.level.1.release.4
ANALYSIS TITLE: Mapping of Fetal Lung Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27me3 ChIP-Seq on Fetal Lung, Donor UW H22772 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.8244
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: 30,098,042
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 11
FINDPEAKS_SCORE: 0.2195
FINDPEAKS_PERCENTILE: 73
HOTSPOT_SCORE: 0.2539
HOTSPOT_PERCENTILE: 55
IROC_SCORE: 0.9684
IROC_PERCENTILE: 73
POISSON_SCORE: 0.463
POISSON_PERCENTILE: 91
MAXIMUM_REPLICATE_CORRELATION: 0.91

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

ANALYSIS FILE NAME: GSM706852_BI.Fetal_Lung.H3K27me3.UW_H22772.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 391.hg19.level.2.release.4
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Lung Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27me3 ChIP-Seq read mappings from Fetal Lung, Donor UW H22772 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.8271
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: FL H3K27me3 72 91
BROWSER_TRACK_DESCRIPTION: BI Fetal Lung Histone H3K27me3 Donor UW H22772 Library DNA_Lib 391 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 30,098,042
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 11
FINDPEAKS_SCORE: 0.2195
FINDPEAKS_PERCENTILE: 73
HOTSPOT_SCORE: 0.2539
HOTSPOT_PERCENTILE: 55
IROC_SCORE: 0.9684
IROC_PERCENTILE: 73
POISSON_SCORE: 0.463
POISSON_PERCENTILE: 91
MAXIMUM_REPLICATE_CORRELATION: 0.91

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

source_name: Primary fetal lung tissue; DNA_Lib 391

value: Post-Mortem

value: presumed normal

value: Primary Tissue

value: University of Washington

value: SDS lysis

value: Millipore

value: Histone H3K27me3

value: Bioruptor


title: ChIP-Seq analysis of WCE in human fetal heart cells; DNA_Lib 399

description:
sample_term_id: UBERON_0000948
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 399
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.7137
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.5290
****************
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: GSM706856_BI.Fetal_Heart.Input.H-23468.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 399.hg19.level.1.release.4
ANALYSIS TITLE: Mapping of Fetal Heart ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on Fetal Heart, Donor H-23468 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.8232
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: 8,454,527
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 14
FINDPEAKS_SCORE: 0.0101
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.1218
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.4706
IROC_PERCENTILE: 25
POISSON_SCORE: 0.1909
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.65

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

ANALYSIS FILE NAME: GSM706856_BI.Fetal_Heart.Input.H-23468.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 399.hg19.level.2.release.4
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Heart ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from Fetal Heart, Donor H-23468 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.8259
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: FH Input 68 99
BROWSER_TRACK_DESCRIPTION: BI Fetal Heart ChIP-Seq Input Donor H-23468 Library DNA_Lib 399 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 8,454,527
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 14
FINDPEAKS_SCORE: 0.0101
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.1218
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.4706
IROC_PERCENTILE: 25
POISSON_SCORE: 0.1909
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.65

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

source_name: Fetal Heart primary tissue, day 96; DNA_Lib 399

value: Fetal Heart

value: genomic DNA

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

value: UW

value: fetal

value: day 96

value: Male

value: standard

value: ChIP-Seq Input

value: Input


title: ChIP-Seq analysis of H3K9ac in human fetal lung cells; DNA_Lib 393

description:
sample_term_id: UBERON_0002048
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 393
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.7135
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.7162
****************
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: GSM706854_BI.Fetal_Lung.H3K9ac.UW_H22772.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 393.hg19.level.1.release.4
ANALYSIS TITLE: Mapping of Fetal Lung Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9ac ChIP-Seq on Fetal Lung, Donor UW H22772 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.8240
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: 17,321,198
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 3
FINDPEAKS_SCORE: 0.1404
FINDPEAKS_PERCENTILE: 67
HOTSPOT_SCORE: 0.2297
HOTSPOT_PERCENTILE: 33
IROC_SCORE: 0.9834
IROC_PERCENTILE: 67
POISSON_SCORE: 0.2941
POISSON_PERCENTILE: 33
MAXIMUM_REPLICATE_CORRELATION: 0.89

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

ANALYSIS FILE NAME: GSM706854_BI.Fetal_Lung.H3K9ac.UW_H22772.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 393.hg19.level.2.release.4
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Lung Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9ac ChIP-Seq read mappings from Fetal Lung, Donor UW H22772 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.8267
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: FL H3K9ac 72 93
BROWSER_TRACK_DESCRIPTION: BI Fetal Lung Histone H3K9ac Donor UW H22772 Library DNA_Lib 393 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 17,321,198
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 3
FINDPEAKS_SCORE: 0.1404
FINDPEAKS_PERCENTILE: 67
HOTSPOT_SCORE: 0.2297
HOTSPOT_PERCENTILE: 33
IROC_SCORE: 0.9834
IROC_PERCENTILE: 67
POISSON_SCORE: 0.2941
POISSON_PERCENTILE: 33
MAXIMUM_REPLICATE_CORRELATION: 0.89

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

source_name: Primary fetal lung tissue; DNA_Lib 393

value: BioSAli 187

value: Fetal Lung

value: Post-Mortem

value: presumed normal

value: Female

value: Lung

value: 82 Days

value: Protein A-Sepharose 4B

value: 10 million cells

value: 70 ul bed volume

value: Abcam

value: Histone H3K9ac


title: ChIP-Seq analysis of WCE in Mobilized CD34 cells; Lib:RI:20100524:15--ChIP:MA:20100517:15:Mobilized CD34:WCE

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: Lib:RI:20100524:15--ChIP:MA:20100517:15:Mobilized CD34:WCE
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.7510
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.1659
****************
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: GSM773044_BI.Mobilized_CD34_Primary_Cells.Input.RO_01535.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:RI:20100524:15--ChIP:MA:20100517:15:Mobilized CD34:WCE.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 01535 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.8245
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: 26,022,378
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 14
FINDPEAKS_SCORE: 0.0053
FINDPEAKS_PERCENTILE: 33
HOTSPOT_SCORE: 0.0136
HOTSPOT_PERCENTILE: 50
IROC_SCORE: 0.0
IROC_PERCENTILE: 17
POISSON_SCORE: 0.0427
POISSON_PERCENTILE: 50
MAXIMUM_REPLICATE_CORRELATION: 0.91

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

ANALYSIS FILE NAME: GSM773044_BI.Mobilized_CD34_Primary_Cells.Input.RO_01535.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:RI:20100524:15--ChIP:MA:20100517:15:Mobilized CD34:WCE.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 01535 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.8272
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 35
BROWSER_TRACK_DESCRIPTION: BI Mobilized CD34 Primary Cells ChIP-Seq Input Donor RO 01535 Library Lib:RI:20100524:15--ChIP:MA:20100517:15:Mobilized Mobilized CD34:WCE EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 26,022,378
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 14
FINDPEAKS_SCORE: 0.0053
FINDPEAKS_PERCENTILE: 33
HOTSPOT_SCORE: 0.0136
HOTSPOT_PERCENTILE: 50
IROC_SCORE: 0.0
IROC_PERCENTILE: 17
POISSON_SCORE: 0.0427
POISSON_PERCENTILE: 50
MAXIMUM_REPLICATE_CORRELATION: 0.91

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

source_name: flow sorted CD34+ cells from cord blood; Lib:RI:20100524:15--ChIP:MA:20100517:15:Mobilized CD34:WCE

value: CD34 Primary Cells

value: genomic DNA

value: FHCRC HEIMFELD

value: Primary Cell

value: Unknown

value: SDS lysis

value: Bioruptor


title: Ribominus total RNA from ES 2

status: Public on Dec 06 2011

city: Klosterneuburg

first: Florian

middle: M

last: Pauler

address: Am Campus 1

country: Austria

institute: IST Austria

description: Ribominus total RNA, Trizol isolated

library_source: transcriptomic

data_processing: Alignment: Sequence reads were obtained using the Illumina Genome Analyzer Pipeline and mapped to the mouse genome (mm9, July 2007) using Bowtie. All reads mapping with two or fewer mismatches were retained.

molecule: total RNA

organism: Mus musculus

source_name: Day5 differentiated CCE

growth_protocol: CCE feeder-independent ES cells were grown under standard conditions, and differentiation was induced by withdrawal of LIF and addition of 0.266µM retinoic acid (RA). Mouse fetal heads were dissected at 14.5 days postcoitum.

extract_protocol: DNase I treated 10µg of high quality total RNA from cells or tissues was subjected to ribosomal RNA depletion by using the RiboMinus Transcriptome Isolation Kit (Human/Mouse) according to the manufacturer’s  protocol. The quality of the purified RNA was checked on Agilent 2100 Bioanalyzer with Agilent RNA 6000 Pico Kit according to the manufacturer’s protocol. The purified Ribominus RNA fraction (100ng) was subsequently fragmented by addition of 5× fragmentation buffer (200mM Tris pH8.2, 500mM KAc and 150mM MgAc2) and heating at 94°C for 3.5min in a total volume of 100µl. The reaction was stopped by putting the sample on ice. The fragmented RNA was purified by RNeasy Mini Kit according to the manufacturer protocol, and subsequently ethanol precipitated and dissolved in 10µl nuclease-free ddH2O.The fragmented RNA was used as template for cDNA synthesis using 5µg random hexamers in a total volume of 20µl according to the Superscript II Reverse Transcriptase standard protocol. Second-strand synthesis was performed by adding 91.8µl water, 30µl 5× Second strand buffer, 3µl 10mM dNTP, 4µl DNA polymerase I, 1µl E. coli DNA ligase and 0.2µl RNase H, followed by incubation at 16°C for 2hour. T4 DNA Polymerase (1µl) was added followed by an additional 10 min at 16 °C. The ds-cDNA was purified by using the MinElute Reaction Cleanup Kit according to the manufacturer’s  protocol.

tag: strain

tag: cell type

value: differentiated ES cells induced by retinoic acid for 5 days

tag: fragmentation method

value: RNA hydrolysis

tag: rrna depletion

value: 1 round

tag: sequencing facility

value: IMP Solexa Sequencing facility, Vienna


title: ChIP-Seq analysis of H3K4me1 in Mobilized CD34 cells; Lib:RI:20100603:07--ChIP:MA:20100517:07:Mobilized CD34:H3K4Me1

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: Lib:RI:20100603:07--ChIP:MA:20100517:07:Mobilized CD34:H3K4Me1
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.7509
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.2422
****************
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: GSM773043_BI.Mobilized_CD34_Primary_Cells.H3K4me1.RO_01562.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:RI:20100603:07--ChIP:MA:20100517:07:Mobilized CD34:H3K4Me1.hg19.level.1.release.4
ANALYSIS TITLE: Mapping of Mobilized CD34 Primary Cells Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me1 ChIP-Seq on Mobilized CD34 Primary Cells, Donor RO 01562 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.8239
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: 30,730,425
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 12
FINDPEAKS_SCORE: 0.6924
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.6649
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9998
IROC_PERCENTILE: 100
POISSON_SCORE: 0.7374
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM773043_BI.Mobilized_CD34_Primary_Cells.H3K4me1.RO_01562.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:RI:20100603:07--ChIP:MA:20100517:07:Mobilized CD34:H3K4Me1.hg19.level.2.release.4
ANALYSIS TITLE: Raw Signal Density Graphs of Mobilized CD34 Primary Cells Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me1 ChIP-Seq read mappings from Mobilized CD34 Primary Cells, Donor RO 01562 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.8266
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 H3K4me1 62
BROWSER_TRACK_DESCRIPTION: BI Mobilized CD34 Primary Cells Histone H3K4me1 Donor RO 01562 Library Lib:RI:20100603:07--ChIP:MA:20100517:07:Mobilized Mobilized CD34:H3K4Me1 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 30,730,425
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 12
FINDPEAKS_SCORE: 0.6924
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.6649
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9998
IROC_PERCENTILE: 100
POISSON_SCORE: 0.7374
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

source_name: flow sorted CD34+ cells from cord blood; Lib:RI:20100603:07--ChIP:MA:20100517:07:Mobilized CD34:H3K4Me1

value: 42 years

value: Male

value: Caucasian

value: Histone H3K4me1


title: ChIP-Seq analysis of WCE in human fetal brain cells; DNA_Lib 390

description:
sample_term_id: UBERON_0000955
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 390
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.7132
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.7163
****************
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: GSM706851_BI.Fetal_Brain.Input.UW_H22676.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 390.hg19.level.1.release.4
ANALYSIS TITLE: Mapping of Fetal Brain ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on Fetal Brain, Donor UW H22676 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.8237
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: 15,984,962
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 14
FINDPEAKS_SCORE: 0.0079
FINDPEAKS_PERCENTILE: 67
HOTSPOT_SCORE: 0.0749
HOTSPOT_PERCENTILE: 92
IROC_SCORE: 0.9676
IROC_PERCENTILE: 42
POISSON_SCORE: 0.099
POISSON_PERCENTILE: 92
MAXIMUM_REPLICATE_CORRELATION: 0.56

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

ANALYSIS FILE NAME: GSM706851_BI.Fetal_Brain.Input.UW_H22676.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 390.hg19.level.2.release.4
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Brain ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from Fetal Brain, Donor UW H22676 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.8264
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: FB Input 76 90
BROWSER_TRACK_DESCRIPTION: BI Fetal Brain ChIP-Seq Input Donor UW H22676 Library DNA_Lib 390 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 15,984,962
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 14
FINDPEAKS_SCORE: 0.0079
FINDPEAKS_PERCENTILE: 67
HOTSPOT_SCORE: 0.0749
HOTSPOT_PERCENTILE: 92
IROC_SCORE: 0.9676
IROC_PERCENTILE: 42
POISSON_SCORE: 0.099
POISSON_PERCENTILE: 92
MAXIMUM_REPLICATE_CORRELATION: 0.56

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

source_name: Primary fetal brain tissue; DNA_Lib 390

value: BioSAli 186

value: Fetal Brain

value: Post-Mortem

value: presumed normal

value: Primary Tissue

value: Brain

value: University of Washington

value: standard

value: ChIP-Seq Input

value: Input


title: ChIP-Seq analysis of H3K9ac in human fetal heart cells; DNA_Lib 396

description:
sample_term_id: UBERON_0000948
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 396
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.7130
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.5274
****************
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: GSM706849_BI.Fetal_Heart.H3K9ac.H-23524.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 396.hg19.level.1.release.4
ANALYSIS TITLE: Mapping of Fetal Heart Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9ac ChIP-Seq on Fetal Heart, Donor H-23524 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.8238
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: 15,697,133
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 3
FINDPEAKS_SCORE: 0.3888
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.4454
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9957
IROC_PERCENTILE: 100
POISSON_SCORE: 0.4827
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM706849_BI.Fetal_Heart.H3K9ac.H-23524.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 396.hg19.level.2.release.4
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Heart Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9ac ChIP-Seq read mappings from Fetal Heart, Donor H-23524 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.8265
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: FH H3K9ac 24 96
BROWSER_TRACK_DESCRIPTION: BI Fetal Heart Histone H3K9ac Donor H-23524 Library DNA_Lib 396 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 15,697,133
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 3
FINDPEAKS_SCORE: 0.3888
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.4454
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9957
IROC_PERCENTILE: 100
POISSON_SCORE: 0.4827
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: Fetal Heart primary tissue, day 105; DNA_Lib 396

value: Fetal Heart

value: genomic DNA

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

value: UW

value: fetal

value: day 105

value: Protein A-Sepharose 4B

value: 10 million cells

value: SDS lysis

value: 70 ul bed volume

value: Abcam

value: Histone H3K9ac

value: Bioruptor


title: Bisulfite-Seq analysis of RRBS1242 derived from human Mobilized CD34 cells; RRBS1242

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: RRBS1242
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.7486
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.2422
****************
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: GSM772730_BI.Mobilized_CD34_Primary_Cells.RRBS.RO_01562.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RRBS1242.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 01562 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.8334
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 62 42
BROWSER_TRACK_DESCRIPTION: BI Mobilized CD34 Primary Cells RRBS Donor RO 01562 Library RRBS1242 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 22,330,680
NUMBER_OF_RRBS_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 21
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 99.76
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.87

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

source_name: flow sorted CD34+ cells from cord blood; RRBS1242

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

value: CD34 Primary Cells

value: FHCRC HEIMFELD

value: Primary Cell

value: 42 years

value: Male

value: Caucasian

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: ChIP-Seq analysis of H3K4me1 in human fetal brain cells; DNA_Lib 384

description:
sample_term_id: UBERON_0000955
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 384
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.7131
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.7163
****************
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: GSM706850_BI.Fetal_Brain.H3K4me1.UW_H22676.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 384.hg19.level.1.release.4
ANALYSIS TITLE: Mapping of Fetal Brain Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me1 ChIP-Seq on Fetal Brain, Donor UW H22676 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.8249
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: 16,695,767
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 12
FINDPEAKS_SCORE: 0.4201
FINDPEAKS_PERCENTILE: 69
HOTSPOT_SCORE: 0.4809
HOTSPOT_PERCENTILE: 69
IROC_SCORE: 0.9899
IROC_PERCENTILE: 58
POISSON_SCORE: 0.5718
POISSON_PERCENTILE: 54
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM706850_BI.Fetal_Brain.H3K4me1.UW_H22676.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 384.hg19.level.2.release.4
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Brain Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me1 ChIP-Seq read mappings from Fetal Brain, Donor UW H22676 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.8276
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: FB H3K4me1 76 84
BROWSER_TRACK_DESCRIPTION: BI Fetal Brain Histone H3K4me1 Donor UW H22676 Library DNA_Lib 384 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 16,695,767
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 12
FINDPEAKS_SCORE: 0.4201
FINDPEAKS_PERCENTILE: 69
HOTSPOT_SCORE: 0.4809
HOTSPOT_PERCENTILE: 69
IROC_SCORE: 0.9899
IROC_PERCENTILE: 58
POISSON_SCORE: 0.5718
POISSON_PERCENTILE: 54
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: Primary fetal brain tissue; DNA_Lib 384

value: BioSAli 186

value: Fetal Brain

value: Post-Mortem

value: presumed normal

value: genomic DNA

value: Unknown

value: Primary Tissue

value: Brain

value: University of Washington

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: Bisulfite-Seq analysis of RRBS1201 and RRBS1205 derived from HUES64-derived CD184 positive cells; RRBS1201 and RRBS1205

description:
sample_term_id: CL_0000223
assay_term_id: OBI_0001862
nucleic_acid_term_id: SO_0000352
Design description: RRBS REMC Sequencing on Illumina
Library name: RRBS1201 and RRBS1205
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.7481
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.7504
****************
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: GSM772725_BI.hESC_Derived_CD184+_Endoderm_Cultured_Cells.RRBS.RRBS1201_and_RRBS1205.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RRBS1201 and RRBS1205.hg19.level.2.release.4
ANALYSIS TITLE: Methylation Proportion Graphs of hESC Derived CD184+ Endoderm Cultured Cells RRBS Data
ANALYSIS DESCRIPTION: Illumina RRBS read mappings from hESC Derived CD184+ Endoderm Cultured Cells, Donor RRBS1201 and RRBS1205 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.8328
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: hDCE RRBS 05
BROWSER_TRACK_DESCRIPTION: BI hESC Derived CD184+ Endoderm Cultured Cells RRBS Libraries RRBS1201 and RRBS1205 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 30,152,506
NUMBER_OF_RRBS_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 21
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 99.33
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE: 14
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

source_name: CD184+ endothelial cells; RRBS1201 and RRBS1205

value: CD184+ endoderm cultured cells

value: BioSam 138

tag: lineage

value: endoderm

tag: medium

tag: passage

tag: line

value: HUES64-derived CD184 positive cells

value: HUES64 was differentiated in feeder free conditions, using RPMI containing 100ng/mL of Activin A and 50ng/mL of Wnt3a, for 5 days. On day 5, the CD184 positive population was sorted via FACS.

tag: batch

value: Cell Line

value: differentiated

tag: Sex

value: Male

value: Harvard University

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 RRBS1089 derived from human Neurons derived from ES H9 cell cells; RRBS1089

description:
sample_term_id: CL_0000540
assay_term_id: OBI_0001862
nucleic_acid_term_id: SO_0000352
Design description: RRBS REMC Sequencing on Illumina
Library name: RRBS1089
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.7484
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.7502
****************
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: GSM772728_BI.H9_Derived_Neuron_Cultured_Cells.RRBS.RRBS1089.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RRBS1089.hg19.level.2.release.4
ANALYSIS TITLE: Methylation Proportion Graphs of H9 Derived Neuron Cultured Cells RRBS Data
ANALYSIS DESCRIPTION: Illumina RRBS read mappings from H9 Derived Neuron Cultured Cells, Donor RRBS1089 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.8340
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: HDN RRBS 89
BROWSER_TRACK_DESCRIPTION: BI H9 Derived Neuron Cultured Cells RRBS Library RRBS1089 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 24,715,093
NUMBER_OF_RRBS_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 21
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 99.72
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE: 86
MAXIMUM_REPLICATE_CORRELATION: 0.85

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

source_name: neurons derived from H9 (WA09) human stem cells; RRBS1089

value: H9 Derived Neuron Cultured Cells

value: ectoderm

value: Differentiated from hNP1(trademark) for 2 weeks under defined (feeder & serum free) conditions – AB2+ANS+LIF on Matrigel (i.e., differentiation medium)

value: genomic DNA

value: Neurons derived from ES H9 cell

value: differentiated in vitro by vendor

value: Primary Cell Culture

value: Female

value: ArunA Biomedical, Athens, GA


title: ChIP-Seq analysis of H3K4me1 in human fetal heart cells; DNA_Lib 395

description:
sample_term_id: UBERON_0000948
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 395
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.7129
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.5274
****************
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: GSM706848_BI.Fetal_Heart.H3K4me1.H-23524.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 395.hg19.level.1.release.4
ANALYSIS TITLE: Mapping of Fetal Heart Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me1 ChIP-Seq on Fetal Heart, Donor H-23524 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.8231
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: 28,150,254
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 12
FINDPEAKS_SCORE: 0.3988
FINDPEAKS_PERCENTILE: 54
HOTSPOT_SCORE: 0.441
HOTSPOT_PERCENTILE: 54
IROC_SCORE: 0.9907
IROC_PERCENTILE: 50
POISSON_SCORE: 0.5706
POISSON_PERCENTILE: 46
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

ANALYSIS FILE NAME: GSM706848_BI.Fetal_Heart.H3K4me1.H-23524.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 395.hg19.level.2.release.4
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Heart Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me1 ChIP-Seq read mappings from Fetal Heart, Donor H-23524 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.8258
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: FH H3K4me1 24 95
BROWSER_TRACK_DESCRIPTION: BI Fetal Heart Histone H3K4me1 Donor H-23524 Library DNA_Lib 395 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 28,150,254
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 12
FINDPEAKS_SCORE: 0.3988
FINDPEAKS_PERCENTILE: 54
HOTSPOT_SCORE: 0.441
HOTSPOT_PERCENTILE: 54
IROC_SCORE: 0.9907
IROC_PERCENTILE: 50
POISSON_SCORE: 0.5706
POISSON_PERCENTILE: 46
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

source_name: Fetal Heart primary tissue, day 105; DNA_Lib 395

value: Fetal Heart

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

value: Primary Tissue

value: UW

value: fetal

value: day 105

value: Male

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: Bisulfite-Seq analysis of RRBS1202 and RRBS1206 derived from HUES64-derived CD184 positive cells; RRBS1202 and RRBS1206

description:
sample_term_id: CL_0000223
assay_term_id: OBI_0001862
nucleic_acid_term_id: SO_0000352
Design description: RRBS REMC Sequencing on Illumina
Library name: RRBS1202 and RRBS1206
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.7479
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.7503
****************
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: GSM772723_BI.hESC_Derived_CD184+_Endoderm_Cultured_Cells.RRBS.RRBS1202_and_RRBS1206.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RRBS1202 and RRBS1206.hg19.level.2.release.4
ANALYSIS TITLE: Methylation Proportion Graphs of hESC Derived CD184+ Endoderm Cultured Cells RRBS Data
ANALYSIS DESCRIPTION: Illumina RRBS read mappings from hESC Derived CD184+ Endoderm Cultured Cells, Donor RRBS1202 and RRBS1206 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.8335
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: hDCE RRBS 06
BROWSER_TRACK_DESCRIPTION: BI hESC Derived CD184+ Endoderm Cultured Cells RRBS Libraries RRBS1202 and RRBS1206 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 31,052,390
NUMBER_OF_RRBS_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 21
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 99.44
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE: 19
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

source_name: CD184+ endothelial cells; RRBS1202 and RRBS1206

value: CD184+ endoderm cultured cells

value: BioSam 139

value: endoderm

value: genomic DNA

value: HUES64-derived CD184 positive cells

value: HUES64 was differentiated in feeder free conditions, using RPMI containing 100ng/mL of Activin A and 50ng/mL of Wnt3a, for 5 days. On day 5, the CD184 positive population was sorted via FACS.

value: Cell Line

value: differentiated

value: Harvard University

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 RRBS1241 derived from human Mobilized CD34 cells; RRBS1241

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: RRBS1241
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.7485
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.2397
****************
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: GSM772729_BI.Mobilized_CD34_Primary_Cells.RRBS.RO_01536.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RRBS1241.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 01536 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.8325
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 36 41
BROWSER_TRACK_DESCRIPTION: BI Mobilized CD34 Primary Cells RRBS Donor RO 01536 Library RRBS1241 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 21,926,201
NUMBER_OF_RRBS_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 21
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 99.76
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.86

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

source_name: flow sorted CD34+ cells from cord blood; RRBS1241

value: CD34 Primary Cells

value: FHCRC HEIMFELD

value: Primary Cell

value: 27 years

value: Female

value: Hispanic


title: Bisulfite-Seq analysis of RRBS1088 derived from human Neurons derived from ES H9 cell cells; RRBS1088

description:
sample_term_id: CL_0000540
assay_term_id: OBI_0001862
nucleic_acid_term_id: SO_0000352
Design description: RRBS REMC Sequencing on Illumina
Library name: RRBS1088
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.7483
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.7501
****************
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: GSM772727_BI.H9_Derived_Neuron_Cultured_Cells.RRBS.RRBS1088.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RRBS1088.hg19.level.2.release.4
ANALYSIS TITLE: Methylation Proportion Graphs of H9 Derived Neuron Cultured Cells RRBS Data
ANALYSIS DESCRIPTION: Illumina RRBS read mappings from H9 Derived Neuron Cultured Cells, Donor RRBS1088 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.8339
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: HDN RRBS 88
BROWSER_TRACK_DESCRIPTION: BI H9 Derived Neuron Cultured Cells RRBS Library RRBS1088 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 21,943,274
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: 0.85

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

source_name: neurons derived from H9 (WA09) human stem cells; RRBS1088

value: H9 Derived Neuron Cultured Cells

value: ectoderm

value: Differentiated from hNP1(trademark) for 2 weeks under defined (feeder & serum free) conditions – AB2+ANS+LIF on Matrigel (i.e., differentiation medium)

value: genomic DNA

value: Neurons derived from ES H9 cell

value: differentiated in vitro by vendor

value: Primary Cell Culture

value: differentiated

value: ArunA Biomedical, Athens, GA


title: Control replicate 2

status: Public on Dec 04 2011

city: Ann Arbor

first: Jay

last: Hess

state: MI

address: 1301 Catherine

department: Pathology

institute: University of Michigan

description:
input DNA
MM0339

data_processing: Alignment: Sequence reads were obtained and mapped to the mouse (mm8; Feb 2006) genomes using the Illumina Genome Analyzer Pipeline. We determine for each profile a threshold peak height as the smallest height that corresponds to FDR < 0.001 for peaks of that height.

source_name: myeloblastic cell lines transformed with an MSCV-based retrovirus expressing untagged Hoxa9 and untagged Meis1

growth_protocol: Bone marrow cells were harvested from 5-Fluorouracil treated female 6-8 week old C57BL/6 mice and transformed into myeloblastic cell lines with an MSCV-based retrovirus expressing HA-tagged or untagged Hoxa9 or Meis1 (HM2 cells). For conditional activation of Hoxa9, cells were transformed with Hoxa9 fused to a modified estrogen receptor ligand-binding domain (Hoxa9-ER).  Cells were cultured in Iscove’s Modified Dulbecco’s Medium with 15% fetal bovine serum (Stem Cell Technologies) and penicillin/streptomycin.IL-3 (R&D) was added to media; alternatively cells were transduced with an IL-3-expressing retroviral vector (pMFGmIL3, obtained from RIKEN DNA Bank with consent of Dr. Hirofumi Hamada); Hoxa9-ER cells were also supplemented with 4-OHT (Sigma). Hoxa9 is required for continued mouse hematopoietic progenitor (MHP) survival, so positive selection of transduced clones was not necessary; double Hoxa9/Meis1 transductants were selected by fluorescence-activated cell sorting (bicistronic Meis1+GFP expression using MigR1 vector; a gift from Dr. Warren Pear).

extract_protocol: A total of 150 million cells were cross-linked sequentially with disuccinimidylglutarate (45 min RT) and 1% formaldehyde (15 min RT).  Hoxa9 and Meis1 immunoprecipitation was performed with anti-HA antibody (Abcam) pre-conjugated to Protein G magnetic beads (Dynal/Invitrogen).  4-hour incubation (4°C with gentle rotation) was followed by washes using Low Salt, High Salt, LiCl, and Tris-EDTA buffers (Upstate/Millipore).  Immunoprecipitateswere eluted with 0.1% SDS/0.1M NaHCO3 and cross-links were reversed overnight at 65° in 0.2M NaCl.  DNA was RNAse-treated and column purified (Qiaquick, Qiagen).  For ChIP-Seq, size selection and sequencing were performed as described previously (Robertson et. al 2007)

tag: chip antibody

value: anti-HA

tag: chip antibody vendor

value: Abcam

tag: chip antibody catalog#


title: Hoxa replicate 2

description:
Chromatin IP against Hoxa9
MM0338

source_name: myeloblastic cell lines transformed with an MSCV-based retrovirus expressing HA-Hoxa9 and Flag-Meis1


title: Control replicate 1

description:
input DNA
MM0305

value: myeloblastic cell lines transformed with an MSCV-based retrovirus expressing untagged Hoxa9 and untagged Meis1


title: Meis1 replicate 1

description:
Chromatin IP against Meis1
MM0301

source_name: myeloblastic cell lines transformed with an MSCV-based retrovirus expressing Flag-Hoxa9 and HA-Meis1


title: Hoxa replicate 1

description:
Chromatin IP against Hoxa9
MM0303

value: myeloblastic cell lines transformed with an MSCV-based retrovirus expressing HA-Hoxa9 and Flag-Meis1


title: Meis1 replicate 2

description:
Chromatin IP against Meis1
MM0337

value: myeloblastic cell lines transformed with an MSCV-based retrovirus expressing Flag-Hoxa9 and HA-Meis1


title: ChIP-Seq analysis of H3K36me3 in Mobilized CD34 cells; Lib:RI:20100603:12--ChIP:MA:20100517:12:Mobilized CD34:H3K36Me3

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: Lib:RI:20100603:12--ChIP:MA:20100517:12:Mobilized CD34:H3K36Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.7508
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.2422
****************
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: GSM773042_BI.Mobilized_CD34_Primary_Cells.H3K36me3.RO_01562.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:RI:20100603:12--ChIP:MA:20100517:12:Mobilized CD34:H3K36Me3.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 01562 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.8243
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: 27,857,736
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 7
FINDPEAKS_SCORE: 0.5827
FINDPEAKS_PERCENTILE: 86
HOTSPOT_SCORE: 0.4961
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9985
IROC_PERCENTILE: 86
POISSON_SCORE: 0.7086
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM773042_BI.Mobilized_CD34_Primary_Cells.H3K36me3.RO_01562.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:RI:20100603:12--ChIP:MA:20100517:12:Mobilized CD34:H3K36Me3.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 01562 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.8270
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 62
BROWSER_TRACK_DESCRIPTION: BI Mobilized CD34 Primary Cells Histone H3K36me3 Donor RO 01562 Library Lib:RI:20100603:12--ChIP:MA:20100517:12:Mobilized Mobilized CD34:H3K36Me3 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 27,857,736
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 7
FINDPEAKS_SCORE: 0.5827
FINDPEAKS_PERCENTILE: 86
HOTSPOT_SCORE: 0.4961
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9985
IROC_PERCENTILE: 86
POISSON_SCORE: 0.7086
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

source_name: flow sorted CD34+ cells from cord blood; Lib:RI:20100603:12--ChIP:MA:20100517:12:Mobilized CD34:H3K36Me3

tag: sample alias

tag: sample common name

value: CD34 Primary Cells

value: FHCRC HEIMFELD

value: Primary Cell

tag: markers

value: 42 years

value: Male

value: Caucasian

value: Protein A-Sepharose 4B

value: 10 million cells

value: SDS lysis

value: 70 ul bed volume

value: Histone H3K36me3

value: Bioruptor


title: wild type, 52 h, untreated

status: Public on Dec 10 2011

city: Boston

first: Taiowa

last: Montgomery

address: 185 Cambridge Street, CPZN-7250

department: Molecular Biology

institute: Massachusetts General Hospital

description: Small RNA

data_processing: Raw datasets are fastq files generated using Illumina software. The sequence of the 3' adapter used during library preparation is 5'-TGGAATTCTCGGGTGCCAAGG. For processed datasets, small RNA sequences were parsed from fastq files using CASHX v. 2.0 with a Q value threshold of 20. Sequences were not filtered for alignment to a genome. Tab-delimited files containing unique sequences and corresponding read counts were generated using custom Perl scripts.

organism: Caenorhabditis elegans

source_name: Whole worms, larvae, untreated

growth_protocol: Animals were grown at 20˚C on E. coli strain OP50.

extract_protocol: Total RNA was isolated from synchronized animals, and small RNAs were size selected, either treated with sodium periodate followed by beta elimination or untreated, tobacco acid pyrophosphatase (TAP)-treated to remove 5' di- and triphosphate groups, ligated to 3' and 5' adapters and subjected to RT-PCR.

tag: strain

tag: genotype

value: wild type

tag: tissue

value: whole body

tag: developmental stage

value: L4 larvae

tag: treatment


title: Bisulfite-Seq analysis of RRBS1085 derived from human Mobilized CD34 cells; RRBS1085

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: RRBS1085
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.7487
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.2417
****************
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: GSM772731_BI.Mobilized_CD34_Primary_Cells.RRBS.RO_01520.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RRBS1085.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 01520 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.8336
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 20 85
BROWSER_TRACK_DESCRIPTION: BI Mobilized CD34 Primary Cells RRBS Donor RO 01520 Library RRBS1085 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 21,355,945
NUMBER_OF_RRBS_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 21
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 99.68
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE: 71
MAXIMUM_REPLICATE_CORRELATION: 0.88

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

source_name: flow sorted CD34+ cells from cord blood; RRBS1085

tag: molecule

value: genomic DNA

tag: disease

value: 50 years

value: Female

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: MouseP2Heart_acCBP-p300_ChIP-seq

city: Berkeley

first: Matthew

middle: James

last: Blow

state: CA

address: 1 Cyclotron Road

department: Genomics Division

institute: Lawrence Berkeley National Laboratory

description: Tissue pooled from 15 postnatal day2 mice, Chromatin IP against AcCBP/p300

data_processing:
Bed: Sequence reads were  mapped to the human (hg18) and mouse (mm9) genome using bwa version 0.5.8c with default parameters except for a seed length of 25 bp and allowing for at most 2 mismatches to the reference. Reads mapping to multiple sites in the genome with an equivalent score, and duplicate reads with identical start sites were discarded.
Wig: Aligned read coordinates were extended to 300bp in the direction of the alignment. Coverage depth was calculated from extended reads at 25bp intervals throughout the genome.
peaks: CBP/p300 bound regions were identified from the intersection of two independent peak calling approaches: MACS 13 version 1.4, with default settings except --bw=300 --pvalue=1e-5 --mfold=10,30 --llocal=20000 --off-auto --shiftsize=100 (Zhang et al, Genome Biology, 2008) and Grizzly (Capaldi et al, Nature Genetics, 2008).  Peaks overlapping repeats, or duplicated regions of the genome were removed as likely mapping artifacts.

extract_protocol: Human adult heart, human fetal heart and pooled mouse postnatal heart tissues were cross linked and cells were dissociated and subject to  chromatin isolation and sonication as described previously (Visel et al, Nature, 2009) . Chromatin was subject to immunoprecipitation using anti-acCBP/p300 or anti-RNA Polymerase II antibodies. ChIP DNA was sheared by sonication, end-repaired, ligated to solexa sequencing adapters and amplified by emulsion PCR.  Gel purified amplified ChIP DNA between 300 and 500bp was sequenced on the Solexa / Illumina Genome Analyzer to generate 36 bp reads.

tag: gender

value: mixed

value: postnatal day 2

value: heart

value: Cell signaling technology

tag: catalog/batch number


title: HumanFetaltHeart_acCBP-p300_ChIP-seq

description: Chromatin IP against AcCBP/p300

value: fetus (gestational week 16)


title: HumanAdultHeart_acCBP-p300_ChIP-seq

description: Chromatin IP against AcCBP/p300

value: male

value: adult (45yr)


title: HumanFetaltHeart_polII_ChIP-seq

description: Chromatin IP against PolII

value: anti-RNA polymerase II (mouse monoclonal)

value: Abcam


title: wild type, 68 h, untreated

description: Small RNA

source_name: Whole worms, adult, untreated

value: wild type

value: whole body

value: adult


title: Total nuclei DNA 1 (Nuc10_20110313_3)

city: Seattle

first: Jorja

last: Henikoff

state: WA

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

description:
MNase-protected DNA fragments in total nuclei
Illumina HiSeq 2000, Flow cell:v2.5, Software:HCS1.3.8/RTA 1.10.36
average insert size is 139.63
In addition to worm DNA, Total_nuclei_20110313_3 raw files contain pooled fruit fly and yeast DNA from unrelated experiments. Paired
end reads that mapped to multiple organisms have been removed
from the sam and wig supplementary files.

data_processing: 1. We used Novoalign to map paired-end 25bp reads to release W220 of the C. elegans genomic sequence obtained from WormBase. If a read was mapped to multiple locations, one location was picked at random. (Supplementary file Total_nuclei_20110313_3.sam) 2. For each base pair in the genome, we counted the number of paired-end fragments aligned over it. 3. We normalized base pair counts by dividing by the total number of counts for all base pairs and then multiplying by the total number of base pairs in the genome. (Supplementary file Total_nuclei_20110313_3.wig) 4. We broke down aligned paired-end fragments into sub-groups by insert size length and repeated steps 2. and 3. for the paired-end fragments in each sub-group.

source_name: total nuclei

extract_protocol: INTACT (supplementary file INTACT_ChIP_protocol.rtf)

tag: age

value: whole organism

tag: sample type

value: total nuclei


title: Muscle nuclei DNA 1 (IP20_20110313_7)

description:
MNase-protected DNA fragments in muscle nuclei
Illumina HiSeq 2000, Flow cell:v2.5, Software:HCS1.3.8/RTA 1.10.36
average insert size is 132.08
In addition to worm DNA, Muscle_nuclei_20110313_7 raw files contain pooled fruit fly and yeast DNA from unrelated experiments. Paired
end reads that mapped to multiple organisms have been removed
from the sam  and wig supplementary files.

data_processing: 1. We used Novoalign to map paired-end 25bp reads to release W220 of the C. elegans genomic sequence obtained from WormBase. If a read was mapped to multiple locations, one location was picked at random. (Supplementary file Muscle_nuclei_20110313_7.sam) 2. For each base pair in the genome, we counted the number of paired-end fragments aligned over it. 3. We normalized base pair counts by dividing by the total number of counts for all base pairs and then multiplying by the total number of base pairs in the genome. (Supplementary file Muscle_nuclei_20110313_7.wig) 4. We broke down aligned paired-end fragments into sub-groups by insert size length and repeated steps 2. and 3. for the paired-end fragments in each sub-group.

source_name: INTACT-purified muscle nuclei

tag: cell type

value: muscle cell

value: INTACT affinity-purified muscle nuclei