title: ChIP-Seq analysis of H3K36me3; mobilized CD34 cells; Lib:RI:20100517:07--ChIP:Thanh:20100504:07: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:20100517:07--ChIP:Thanh:20100504:07:Mobilized CD34:H3K36Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3250
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3352
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************
BED and WIG files were replaced on April 29, 2014

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

ANALYSIS FILE NAME: GSM621666_BI.Mobilized_CD34_Primary_Cells.H3K36me3.UW_RO_01536.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:RI:20100517:07--ChIP:Thanh:20100504:07:Mobilized CD34:H3K36Me3.hg19.level.1
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 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.4827
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 2

QUALITY SCORES:
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED: 54
FINDPEAKS_SCORE: 0.027
FINDPEAKS_PERCENTILE: 7
HOTSPOT_SCORE: 0.1295
HOTSPOT_PERCENTILE: 8
IROC_SCORE: 0.709
IROC_PERCENTILE: 6
POISSON_SCORE: 0.2408
POISSON_PERCENTILE: 2

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

ANALYSIS FILE NAME: GSM621666_BI.Mobilized_CD34_Primary_Cells.H3K36me3.UW_RO_01536.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:RI:20100517:07--ChIP:Thanh:20100504:07:Mobilized CD34:H3K36Me3.hg19.level.2
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 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.5101
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 2
BROWSER_TRACK_NAME: MCD34 H3K36me3 36
BROWSER_TRACK_DESCRIPTION: BI Mobilized CD34 Primary Cells Histone H3K36me3 Donor RO 01536 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED: 54
FINDPEAKS_SCORE: 0.027
FINDPEAKS_PERCENTILE: 7
HOTSPOT_SCORE: 0.1295
HOTSPOT_PERCENTILE: 8
IROC_SCORE: 0.709
IROC_PERCENTILE: 6
POISSON_SCORE: 0.2408
POISSON_PERCENTILE: 2

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

source_name: CD34 cells mobilized into peripheral blood; Lib:RI:20100517:07--ChIP:Thanh:20100504:07:Mobilized CD34:H3K36Me3

value: genomic DNA

value: Mobilized CD34

value: Hisp

value: Primary Cell

value: Bioruptor


title: ChIP-Seq analysis of H3K4me3 in mobilized CD34 cells; Lib:RI:20100517:10--ChIP:Thanh:20100504:10:Mobilized CD34:H3K4Me3

status: Public on Nov 12 2010

type: SRA

city: Cambridge

first: BROAD

last: INSTITUTE

state: MA

country: USA

institute: Broad Institute

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:20100517:10--ChIP:Thanh:20100504:10:Mobilized CD34:H3K4Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3251
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3353
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************
BED and WIG files were replaced on April 29, 2014

library_source: genomic

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

ANALYSIS FILE NAME: GSM621667_BI.Mobilized_CD34_Primary_Cells.H3K4me3.UW_RO_01492.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:RI:20100517:10--ChIP:Thanh:20100504:10:Mobilized CD34:H3K4Me3.hg19.level.1
ANALYSIS TITLE: Mapping of Mobilized CD34 Primary Cells Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me3 ChIP-Seq on Mobilized CD34 Primary Cells, Donor RO 01492 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.4776
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 2

QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED: 62
FINDPEAKS_SCORE: 0.223
FINDPEAKS_PERCENTILE: 16
HOTSPOT_SCORE: 0.2857
HOTSPOT_PERCENTILE: 28
IROC_SCORE: 0.9999
IROC_PERCENTILE: 74
POISSON_SCORE: 0.3146
POISSON_PERCENTILE: 6

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

ANALYSIS FILE NAME: GSM621667_BI.Mobilized_CD34_Primary_Cells.H3K4me3.UW_RO_01492.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:RI:20100517:10--ChIP:Thanh:20100504:10:Mobilized CD34:H3K4Me3.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Mobilized CD34 Primary Cells Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me3 ChIP-Seq read mappings from Mobilized CD34 Primary Cells, Donor RO 01492 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.5050
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 2
BROWSER_TRACK_NAME: MCD34 H3K4me3 92
BROWSER_TRACK_DESCRIPTION: BI Mobilized CD34 Primary Cells Histone H3K4me3 Donor RO 01492 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED: 62
FINDPEAKS_SCORE: 0.223
FINDPEAKS_PERCENTILE: 16
HOTSPOT_SCORE: 0.2857
HOTSPOT_PERCENTILE: 28
IROC_SCORE: 0.9999
IROC_PERCENTILE: 74
POISSON_SCORE: 0.3146
POISSON_PERCENTILE: 6

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

molecule: genomic DNA

organism: Homo sapiens

source_name: CD34 cells mobilized into peripheral blood; Lib:RI:20100517:10--ChIP:Thanh:20100504:10:Mobilized CD34:H3K4Me3

extract_protocol: Library construction protocol: Single read - Illumina

tag: molecule

tag: disease

tag: markers

value: Cauc

value: Male

value: UW

value: Protein A-Sepharose 4B

value: 10 million cells

value: SDS lysis

value: 70 ul bed volume

value: Millipore

value: Histone H3K4me3


title: ChIP-Seq analysis of H3K9me3 in mobilized CD34 cells; Lib:RI:20100517:05--ChIP:Thanh:20100504:05: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:20100517:05--ChIP:Thanh:20100504:05:Mobilized CD34:H3K9Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3247
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3352
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************
BED and WIG files were replaced on April 29, 2014

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

ANALYSIS FILE NAME: GSM621663_BI.Mobilized_CD34_Primary_Cells.H3K9me3.UW_RO_01536.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:RI:20100517:05--ChIP:Thanh:20100504:05:Mobilized CD34:H3K9Me3.hg19.level.1
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 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.4775
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 2

QUALITY SCORES:
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED: 59
FINDPEAKS_SCORE: 0.0497
FINDPEAKS_PERCENTILE: 36
HOTSPOT_SCORE: 0.1396
HOTSPOT_PERCENTILE: 41
IROC_SCORE: 0.7058
IROC_PERCENTILE: 15
POISSON_SCORE: 0.2718
POISSON_PERCENTILE: 10

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

ANALYSIS FILE NAME: GSM621663_BI.Mobilized_CD34_Primary_Cells.H3K9me3.UW_RO_01536.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:RI:20100517:05--ChIP:Thanh:20100504:05:Mobilized CD34:H3K9Me3.hg19.level.2
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 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.5049
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 2
BROWSER_TRACK_NAME: MCD34 H3K9me3 36
BROWSER_TRACK_DESCRIPTION: BI Mobilized CD34 Primary Cells Histone H3K9me3 Donor RO 01536 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED: 59
FINDPEAKS_SCORE: 0.0497
FINDPEAKS_PERCENTILE: 36
HOTSPOT_SCORE: 0.1396
HOTSPOT_PERCENTILE: 41
IROC_SCORE: 0.7058
IROC_PERCENTILE: 15
POISSON_SCORE: 0.2718
POISSON_PERCENTILE: 10

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

source_name: CD34 cells mobilized into peripheral blood; Lib:RI:20100517:05--ChIP:Thanh:20100504:05:Mobilized CD34:H3K9Me3

value: Female

value: Abcam

value: Histone H3K9me3


title: ChIP-Seq analysis of H3K4me3 in Mobilized CD34 cells; Lib:RI:20100308:06--ChIP:MA:20100216:06:Mobilized CD34:H3K4Me3

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:20100308:06--ChIP:MA:20100216:06:Mobilized CD34:H3K4Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3777
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3877
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************
BED and WIG files were replaced on April 29, 2014

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

ANALYSIS FILE NAME: GSM621437_BI.Mobilized_CD34_Primary_Cells.H3K4me3.UW_RO_01480.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:RI:20100308:06--ChIP:MA:20100216:06:Mobilized CD34:H3K4Me3.hg19.level.1
ANALYSIS TITLE: Mapping of Mobilized CD34 Primary Cells Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me3 ChIP-Seq on Mobilized CD34 Primary Cells, Donor RO 01480 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.4729
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 2

QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED: 62
FINDPEAKS_SCORE: 0.241
FINDPEAKS_PERCENTILE: 23
HOTSPOT_SCORE: 0.2457
HOTSPOT_PERCENTILE: 16
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.3322
POISSON_PERCENTILE: 10

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

ANALYSIS FILE NAME: GSM621437_BI.Mobilized_CD34_Primary_Cells.H3K4me3.UW_RO_01480.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:RI:20100308:06--ChIP:MA:20100216:06:Mobilized CD34:H3K4Me3.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Mobilized CD34 Primary Cells Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me3 ChIP-Seq read mappings from Mobilized CD34 Primary Cells, Donor RO 01480 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.5003
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 2
BROWSER_TRACK_NAME: MCD34 H3K4me3 80
BROWSER_TRACK_DESCRIPTION: BI Mobilized CD34 Primary Cells Histone H3K4me3 Donor RO 01480 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED: 62
FINDPEAKS_SCORE: 0.241
FINDPEAKS_PERCENTILE: 23
HOTSPOT_SCORE: 0.2457
HOTSPOT_PERCENTILE: 16
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.3322
POISSON_PERCENTILE: 10

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

source_name: CD34 cells mobilized into peripheral blood; Lib:RI:20100308:06--ChIP:MA:20100216:06:Mobilized CD34:H3K4Me3

value: genomic DNA

value: Unknown


title: ChIP-Seq analysis of H3K9me3 in human fetal heart cells; Lib:XZ:20100129:23--ChIP:XZ:20100125:23:fetal heart:H3K9Me3

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: Lib:XZ:20100129:23--ChIP:XZ:20100125:23:fetal heart:H3K9Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3774
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3885
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************
BED and WIG files were replaced on April 29, 2014

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

ANALYSIS FILE NAME: GSM621434_BI.Fetal_Heart.H3K9me3.UW_H-22727.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100129:23--ChIP:XZ:20100125:23:fetal heart:H3K9Me3.hg19.level.1
ANALYSIS TITLE: Mapping of Fetal Heart Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9me3 ChIP-Seq on Fetal Heart, Donor H-22727 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.4580
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 2

QUALITY SCORES:
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED: 59
FINDPEAKS_SCORE: 0.0263
FINDPEAKS_PERCENTILE: 22
HOTSPOT_SCORE: 0.0676
HOTSPOT_PERCENTILE: 22
IROC_SCORE: 0.6603
IROC_PERCENTILE: 10
POISSON_SCORE: 0.2935
POISSON_PERCENTILE: 17

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

ANALYSIS FILE NAME: GSM621434_BI.Fetal_Heart.H3K9me3.UW_H-22727.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100129:23--ChIP:XZ:20100125:23:fetal heart:H3K9Me3.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Heart Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9me3 ChIP-Seq read mappings from Fetal Heart, Donor H-22727 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.4854
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 2
BROWSER_TRACK_NAME: FH H3K9me3 27
BROWSER_TRACK_DESCRIPTION: BI Fetal Heart Histone H3K9me3 Donor H-22727 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED: 59
FINDPEAKS_SCORE: 0.0263
FINDPEAKS_PERCENTILE: 22
HOTSPOT_SCORE: 0.0676
HOTSPOT_PERCENTILE: 22
IROC_SCORE: 0.6603
IROC_PERCENTILE: 10
POISSON_SCORE: 0.2935
POISSON_PERCENTILE: 17

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

source_name: Primary fetal heart tissue; Lib:XZ:20100129:23--ChIP:XZ:20100125:23:fetal heart:H3K9Me3

value: surgery

value: Fetal heart

value: Primary Tissue

value: heart

value: 101 days


title: ChIP-Seq analysis of H3K9me3 in Mobilized CD34 cells; Lib:RI:20100524:12--ChIP:MA:20100517:12: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:20100524:12--ChIP:MA:20100517:12:Mobilized CD34:H3K9Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3776
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3881
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************
BED and WIG files were replaced on April 29, 2014

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

ANALYSIS FILE NAME: GSM621436_BI.Mobilized_CD34_Primary_Cells.H3K9me3.UW_RO_01549.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:RI:20100524:12--ChIP:MA:20100517:12:Mobilized CD34:H3K9Me3.hg19.level.1
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 01549 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.4581
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 2

QUALITY SCORES:
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED: 59
FINDPEAKS_SCORE: 0.2508
FINDPEAKS_PERCENTILE: 85
HOTSPOT_SCORE: 0.3224
HOTSPOT_PERCENTILE: 92
IROC_SCORE: 0.9368
IROC_PERCENTILE: 81
POISSON_SCORE: 0.5107
POISSON_PERCENTILE: 86

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

ANALYSIS FILE NAME: GSM621436_BI.Mobilized_CD34_Primary_Cells.H3K9me3.UW_RO_01549.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:RI:20100524:12--ChIP:MA:20100517:12:Mobilized CD34:H3K9Me3.hg19.level.2
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 01549 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.4855
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 2
BROWSER_TRACK_NAME: MCD34 H3K9me3 49
BROWSER_TRACK_DESCRIPTION: BI Mobilized CD34 Primary Cells Histone H3K9me3 Donor RO 01549 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED: 59
FINDPEAKS_SCORE: 0.2508
FINDPEAKS_PERCENTILE: 85
HOTSPOT_SCORE: 0.3224
HOTSPOT_PERCENTILE: 92
IROC_SCORE: 0.9368
IROC_PERCENTILE: 81
POISSON_SCORE: 0.5107
POISSON_PERCENTILE: 86

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

source_name: CD34 cells mobilized into peripheral blood; Lib:RI:20100524:12--ChIP:MA:20100517:12:Mobilized CD34:H3K9Me3

value: Mobilized CD34

value: Cauc

value: Primary Cell

value: UW

value: Bioruptor


title: ChIP-Seq analysis of H3K4me3 in human fetal kidney cells; Lib:XZ:20100129:11--ChIP:XZ:20100125:11:fetal kidney:H3K4me3

description:
sample_term_id: UBERON_0002113
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:XZ:20100129:11--ChIP:XZ:20100125:11:fetal kidney:H3K4me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3778
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3886
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************
BED and WIG files were replaced on April 29, 2014

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

ANALYSIS FILE NAME: GSM621438_BI.Fetal_Kidney.H3K4me3.UW_H-22676.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100129:11--ChIP:XZ:20100125:11:fetal kidney:H3K4me3.hg19.level.1
ANALYSIS TITLE: Mapping of Fetal Kidney Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me3 ChIP-Seq on Fetal Kidney, Donor H-22676 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.4738
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 2

QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED: 62
FINDPEAKS_SCORE: 0.2099
FINDPEAKS_PERCENTILE: 15
HOTSPOT_SCORE: 0.2123
HOTSPOT_PERCENTILE: 10
IROC_SCORE: 0.9998
IROC_PERCENTILE: 63
POISSON_SCORE: 0.3331
POISSON_PERCENTILE: 11

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

ANALYSIS FILE NAME: GSM621438_BI.Fetal_Kidney.H3K4me3.UW_H-22676.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100129:11--ChIP:XZ:20100125:11:fetal kidney:H3K4me3.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Kidney Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me3 ChIP-Seq read mappings from Fetal Kidney, Donor H-22676 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.5012
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 2
BROWSER_TRACK_NAME: FK H3K4me3 76
BROWSER_TRACK_DESCRIPTION: BI Fetal Kidney Histone H3K4me3 Donor H-22676 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED: 62
FINDPEAKS_SCORE: 0.2099
FINDPEAKS_PERCENTILE: 15
HOTSPOT_SCORE: 0.2123
HOTSPOT_PERCENTILE: 10
IROC_SCORE: 0.9998
IROC_PERCENTILE: 63
POISSON_SCORE: 0.3331
POISSON_PERCENTILE: 11

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

source_name: Primary fetal kidney tissue; Lib:XZ:20100129:11--ChIP:XZ:20100125:11:fetal kidney:H3K4me3

value: Fetal kidney

value: kidney

value: 120 days

value: Protein A-Sepharose 4B

value: 10 million cells

value: SDS lysis

value: 70 ul bed volume

value: Millipore


title: ChIP-Seq analysis of H3K27me3 in human hiPS-15b cells; Lib:MC:20100128:05--ChIP:MC:20100125:05:hiPS-15b:H3K27Me3

description:
sample_term_id: NTR_0001162
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:MC:20100128:05--ChIP:MC:20100125:05:hiPS-15b:H3K27Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3773
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3888
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************
BED and WIG files were replaced on April 29, 2014

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

ANALYSIS FILE NAME: GSM621433_BI.iPS-15b.H3K27me3.Lib_MC_20100128_05--ChIP_MC_20100125_05_hiPS-15b_H3K27Me3.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100128:05--ChIP:MC:20100125:05:hiPS-15b:H3K27Me3.hg19.level.1
ANALYSIS TITLE: Mapping of iPS-15b Cell Line Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27me3 ChIP-Seq on the iPS-15b Cell Line, Library Lib:MC:20100128:05--ChIP:MC:20100125:05:hiPS-15b:H3K27Me3 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.4831
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 2

QUALITY SCORES:
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED: 52
FINDPEAKS_SCORE: 0.2711
FINDPEAKS_PERCENTILE: 77
HOTSPOT_SCORE: 0.2758
HOTSPOT_PERCENTILE: 67
IROC_SCORE: 0.9918
IROC_PERCENTILE: 94
POISSON_SCORE: 0.4558
POISSON_PERCENTILE: 52

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

ANALYSIS FILE NAME: GSM621433_BI.iPS-15b.H3K27me3.Lib_MC_20100128_05--ChIP_MC_20100125_05_hiPS-15b_H3K27Me3.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100128:05--ChIP:MC:20100125:05:hiPS-15b:H3K27Me3.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of iPS-15b Cell Line Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27me3 ChIP-Seq read mappings from the iPS-15b Cell Line, Library Lib:MC:20100128:05--ChIP:MC:20100125:05:hiPS-15b:H3K27Me3 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.5105
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 2
BROWSER_TRACK_NAME: iPS15b H3K27me3 e3
BROWSER_TRACK_DESCRIPTION: BI iPS-15b Cell Line Histone H3K27me3 Library Lib:MC:20100128:05--ChIP:MC:20100125:05:hiPS-15b:H3K27Me3 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED: 52
FINDPEAKS_SCORE: 0.2711
FINDPEAKS_PERCENTILE: 77
HOTSPOT_SCORE: 0.2758
HOTSPOT_PERCENTILE: 67
IROC_SCORE: 0.9918
IROC_PERCENTILE: 94
POISSON_SCORE: 0.4558
POISSON_PERCENTILE: 52

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

tag: lineage

value: induced pluripotent cells

tag: medium

value: KSR

value: genomic DNA

tag: passage

tag: line

tag: batch

value: Cell Line

value: undifferentiated

tag: Sex

value: Female

value: Harvard University

value: Histone H3K27me3


title: ZNF274_HepG2_ChIP-seq_rep1

status: Public on Nov 15 2010

city: Palo Alto

first: Philip

last: Cayting

state: CA

address: 1501 S California Ave

department: Genetics

institute: Stanford University

description: Chromatin IP against ZNF274

data_processing:
Alignment: Sequence reads were obtained and mapped to the human genome assembly hg18 (March, 2006) or hg19 (February, 2009) using the Illumina Genome Analyzer Pipeline. All reads mapping with two or fewer mismatches were retained and read starts were summed in sliding windows of 400 bp to create summary windows.
Peaks were called with Sole-Search (http://chipseq.genomecenter.ucdavis.edu/cgi-bin/chipseq.cgi)

source_name: hepatocellular carcinoma

growth_protocol: All cells were grown according to ENCODE standards (http://genomewiki.ucsc.edu/EncodeDCC/index.php/Cell_lines)

extract_protocol: Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.  Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (3 to 5 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

tag: cell line

tag: harvest date

tag: chip antibody

value: abnova mouse polyclonal anti-ZNF274

tag: vendor

value: Abnova

tag: lot#


title: ChIP-Seq analysis of H3K9me3 in human fetal brain cells; Lib:XZ:20100129:18--ChIP:XZ:20100125:18:fetal brain:H3K9Me3

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: Lib:XZ:20100129:18--ChIP:XZ:20100125:18:fetal brain:H3K9Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3767
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3878
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************
BED and WIG files were replaced on April 29, 2014

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

ANALYSIS FILE NAME: GSM621427_BI.Fetal_Brain.H3K9me3.UW_H-22510.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100129:18--ChIP:XZ:20100125:18:fetal brain:H3K9Me3.hg19.level.1
ANALYSIS TITLE: Mapping of Fetal Brain Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9me3 ChIP-Seq on Fetal Brain, Donor H-22510 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.4793
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 2

QUALITY SCORES:
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED: 59
FINDPEAKS_SCORE: 0.029
FINDPEAKS_PERCENTILE: 25
HOTSPOT_SCORE: 0.0596
HOTSPOT_PERCENTILE: 19
IROC_SCORE: 0.9415
IROC_PERCENTILE: 85
POISSON_SCORE: 0.2393
POISSON_PERCENTILE: 2

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

ANALYSIS FILE NAME: GSM621427_BI.Fetal_Brain.H3K9me3.UW_H-22510.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100129:18--ChIP:XZ:20100125:18:fetal brain:H3K9Me3.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Brain Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9me3 ChIP-Seq read mappings from Fetal Brain, Donor H-22510 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.5067
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 2
BROWSER_TRACK_NAME: FB H3K9me3 10
BROWSER_TRACK_DESCRIPTION: BI Fetal Brain Histone H3K9me3 Donor H-22510 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED: 59
FINDPEAKS_SCORE: 0.029
FINDPEAKS_PERCENTILE: 25
HOTSPOT_SCORE: 0.0596
HOTSPOT_PERCENTILE: 19
IROC_SCORE: 0.9415
IROC_PERCENTILE: 85
POISSON_SCORE: 0.2393
POISSON_PERCENTILE: 2

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

source_name: Primary fetal brain tissue; Lib:XZ:20100129:18--ChIP:XZ:20100125:18:fetal brain:H3K9Me3

value: surgery

value: Fetal brain

value: Unknown

value: Primary Tissue

value: brain

value: UW

value: 122 days

value: Abcam

value: Histone H3K9me3

value: Bioruptor


title: ChIP-Seq analysis of H3K9ac in human fetal kidney cells; Lib:XZ:20100129:12--ChIP:XZ:20100125:12:fetal kidney:H3K9Ac

description:
sample_term_id: UBERON_0002113
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:XZ:20100129:12--ChIP:XZ:20100125:12:fetal kidney:H3K9Ac
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3770
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3886
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************
BED and WIG files were replaced on April 29, 2014

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

ANALYSIS FILE NAME: GSM621430_BI.Fetal_Kidney.H3K9ac.UW_H-22676.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100129:12--ChIP:XZ:20100125:12:fetal kidney:H3K9Ac.hg19.level.1
ANALYSIS TITLE: Mapping of Fetal Kidney Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9ac ChIP-Seq on Fetal Kidney, Donor H-22676 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.4784
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 2

QUALITY SCORES:
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED: 35
FINDPEAKS_SCORE: 0.1389
FINDPEAKS_PERCENTILE: 46
HOTSPOT_SCORE: 0.154
HOTSPOT_PERCENTILE: 20
IROC_SCORE: 0.9995
IROC_PERCENTILE: 100
POISSON_SCORE: 0.2985
POISSON_PERCENTILE: 11

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

ANALYSIS FILE NAME: GSM621430_BI.Fetal_Kidney.H3K9ac.UW_H-22676.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100129:12--ChIP:XZ:20100125:12:fetal kidney:H3K9Ac.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Kidney Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9ac ChIP-Seq read mappings from Fetal Kidney, Donor H-22676 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.5058
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 2
BROWSER_TRACK_NAME: FK H3K9ac 76
BROWSER_TRACK_DESCRIPTION: BI Fetal Kidney Histone H3K9ac Donor H-22676 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED: 35
FINDPEAKS_SCORE: 0.1389
FINDPEAKS_PERCENTILE: 46
HOTSPOT_SCORE: 0.154
HOTSPOT_PERCENTILE: 20
IROC_SCORE: 0.9995
IROC_PERCENTILE: 100
POISSON_SCORE: 0.2985
POISSON_PERCENTILE: 11

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

source_name: Primary fetal kidney tissue; Lib:XZ:20100129:12--ChIP:XZ:20100125:12:fetal kidney:H3K9Ac

value: genomic DNA

value: Fetal kidney

value: kidney

value: 120 days

value: Protein A-Sepharose 4B

value: 10 million cells

value: SDS lysis

value: 70 ul bed volume

value: Histone H3K9ac


title: ChIP-Seq analysis of H3K27me3 in human fetal kidney cells; Lib:XZ:20100129:08--ChIP:XZ:20100125:08:fetal kidney:H3K27me3

description:
sample_term_id: UBERON_0002113
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:XZ:20100129:08--ChIP:XZ:20100125:08:fetal kidney:H3K27me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3764
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3886
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************
BED and WIG files were replaced on April 29, 2014

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

ANALYSIS FILE NAME: GSM621424_BI.Fetal_Kidney.H3K27me3.UW_H-22676.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100129:08--ChIP:XZ:20100125:08:fetal kidney:H3K27me3.hg19.level.1
ANALYSIS TITLE: Mapping of Fetal Kidney Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27me3 ChIP-Seq on Fetal Kidney, Donor H-22676 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.4700
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 2

QUALITY SCORES:
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED: 52
FINDPEAKS_SCORE: 0.0431
FINDPEAKS_PERCENTILE: 23
HOTSPOT_SCORE: 0.0827
HOTSPOT_PERCENTILE: 10
IROC_SCORE: 0.9537
IROC_PERCENTILE: 75
POISSON_SCORE: 0.3283
POISSON_PERCENTILE: 4

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

ANALYSIS FILE NAME: GSM621424_BI.Fetal_Kidney.H3K27me3.UW_H-22676.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100129:08--ChIP:XZ:20100125:08:fetal kidney:H3K27me3.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Kidney Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27me3 ChIP-Seq read mappings from Fetal Kidney, Donor H-22676 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.4974
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 2
BROWSER_TRACK_NAME: FK H3K27me3 76
BROWSER_TRACK_DESCRIPTION: BI Fetal Kidney Histone H3K27me3 Donor H-22676 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED: 52
FINDPEAKS_SCORE: 0.0431
FINDPEAKS_PERCENTILE: 23
HOTSPOT_SCORE: 0.0827
HOTSPOT_PERCENTILE: 10
IROC_SCORE: 0.9537
IROC_PERCENTILE: 75
POISSON_SCORE: 0.3283
POISSON_PERCENTILE: 4

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

source_name: Primary fetal kidney tissue; Lib:XZ:20100129:08--ChIP:XZ:20100125:08:fetal kidney:H3K27me3

value: surgery

value: Unknown

value: Millipore

value: Histone H3K27me3


title: ChIP-Seq analysis of H3K4me1 human fetal lung cells (superseded by GSE120322)

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: Lib:XZ:20100129:03--ChIP:XZ:20100125:03:fetal lung:H3K4me1
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3769
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3880
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************
BED and WIG files were replaced on April 29, 2014
****************************
This sample record's metadata may be obsolete; up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE120322
****************************

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

ANALYSIS FILE NAME: GSM621429_BI.Fetal_Lung.H3K4me1.UW_H-22727.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100129:03--ChIP:XZ:20100125:03:fetal lung:H3K4me1.hg19.level.1
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 H-22727 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.4682
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 2

QUALITY SCORES:
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED: 43
FINDPEAKS_SCORE: 0.0957
FINDPEAKS_PERCENTILE: 16
HOTSPOT_SCORE: 0.2044
HOTSPOT_PERCENTILE: 14
IROC_SCORE: 0.9192
IROC_PERCENTILE: 14
POISSON_SCORE: 0.4825
POISSON_PERCENTILE: 23

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

ANALYSIS FILE NAME: GSM621429_BI.Fetal_Lung.H3K4me1.UW_H-22727.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100129:03--ChIP:XZ:20100125:03:fetal lung:H3K4me1.hg19.level.2
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 H-22727 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.4956
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 2
BROWSER_TRACK_NAME: FL H3K4me1 27
BROWSER_TRACK_DESCRIPTION: BI Fetal Lung Histone H3K4me1 Donor H-22727 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED: 43
FINDPEAKS_SCORE: 0.0957
FINDPEAKS_PERCENTILE: 16
HOTSPOT_SCORE: 0.2044
HOTSPOT_PERCENTILE: 14
IROC_SCORE: 0.9192
IROC_PERCENTILE: 14
POISSON_SCORE: 0.4825
POISSON_PERCENTILE: 23

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

source_name: Primary fetal lung tissue; Lib:XZ:20100129:03--ChIP:XZ:20100125:03:fetal lung:H3K4me1

value: Fetal lung

value: Primary Tissue

value: lung

value: UW

value: 101 days

value: Histone H3K4me1


title: ChIP-Seq analysis of WCE in human hiPS-20b cells; Lib:MC:20100119:07--ChIP:MC:20100113:07:hiPS-20b:WCE

description:
sample_term_id: NTR_0001168
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:MC:20100119:07--ChIP:MC:20100113:07:hiPS-20b:WCE
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3752
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3892
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************
BED and WIG files were replaced on April 29, 2014

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

ANALYSIS FILE NAME: GSM621412_BI.iPS-20b.Input.Lib_MC_20100119_07--ChIP_MC_20100113_07_hiPS-20b_WCE.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100119:07--ChIP:MC:20100113:07:hiPS-20b:WCE.hg19.level.1
ANALYSIS TITLE: Mapping of iPS-20b Cell Line ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on the iPS-20b Cell Line, Library Lib:MC:20100119:07--ChIP:MC:20100113:07:hiPS-20b:WCE 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.4578
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 2

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED: 67
FINDPEAKS_SCORE: 0.007
FINDPEAKS_PERCENTILE: 33
HOTSPOT_SCORE: 0.0083
HOTSPOT_PERCENTILE: 26
IROC_SCORE: 0.9855
IROC_PERCENTILE: 89
POISSON_SCORE: 0.2211
POISSON_PERCENTILE: 40

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

ANALYSIS FILE NAME: GSM621412_BI.iPS-20b.Input.Lib_MC_20100119_07--ChIP_MC_20100113_07_hiPS-20b_WCE.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100119:07--ChIP:MC:20100113:07:hiPS-20b:WCE.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of iPS-20b Cell Line ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from the iPS-20b Cell Line, Library Lib:MC:20100119:07--ChIP:MC:20100113:07:hiPS-20b:WCE 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.4852
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 2
BROWSER_TRACK_NAME: iPS20b Input CE
BROWSER_TRACK_DESCRIPTION: BI iPS-20b Cell Line ChIP-Seq Input Library Lib:MC:20100119:07--ChIP:MC:20100113:07:hiPS-20b:WCE EA Release 2

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED: 67
FINDPEAKS_SCORE: 0.007
FINDPEAKS_PERCENTILE: 33
HOTSPOT_SCORE: 0.0083
HOTSPOT_PERCENTILE: 26
IROC_SCORE: 0.9855
IROC_PERCENTILE: 89
POISSON_SCORE: 0.2211
POISSON_PERCENTILE: 40

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

value: induced pluripotent stem cells 20b

value: induced pluripotent cells

value: KSR

value: genomic DNA

value: Cell Line

value: undifferentiated

value: Male

value: Harvard University

value: standard

value: ChIP-Seq Input

value: Input

value: Bioruptor


title: ChIP-Seq analysis of H3K4me3 in human fetal brain cells; Lib:XZ:20100129:17--ChIP:XZ:20100125:17:fetal brain:H3K4me3

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: Lib:XZ:20100129:17--ChIP:XZ:20100125:17:fetal brain:H3K4me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3797
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3878
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************
BED and WIG files were replaced on April 29, 2014

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

ANALYSIS FILE NAME: GSM621457_BI.Fetal_Brain.H3K4me3.UW_H-22510.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100129:17--ChIP:XZ:20100125:17:fetal brain:H3K4me3.hg19.level.1
ANALYSIS TITLE: Mapping of Fetal Brain Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me3 ChIP-Seq on Fetal Brain, Donor H-22510 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.4593
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 2

QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED: 62
FINDPEAKS_SCORE: 0.0817
FINDPEAKS_PERCENTILE: 2
HOTSPOT_SCORE: 0.1128
HOTSPOT_PERCENTILE: 2
IROC_SCORE: 0.9915
IROC_PERCENTILE: 8
POISSON_SCORE: 0.2941
POISSON_PERCENTILE: 2

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

ANALYSIS FILE NAME: GSM621457_BI.Fetal_Brain.H3K4me3.UW_H-22510.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100129:17--ChIP:XZ:20100125:17:fetal brain:H3K4me3.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Brain Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me3 ChIP-Seq read mappings from Fetal Brain, Donor H-22510 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.4867
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 2
BROWSER_TRACK_NAME: FB H3K4me3 10
BROWSER_TRACK_DESCRIPTION: BI Fetal Brain Histone H3K4me3 Donor H-22510 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED: 62
FINDPEAKS_SCORE: 0.0817
FINDPEAKS_PERCENTILE: 2
HOTSPOT_SCORE: 0.1128
HOTSPOT_PERCENTILE: 2
IROC_SCORE: 0.9915
IROC_PERCENTILE: 8
POISSON_SCORE: 0.2941
POISSON_PERCENTILE: 2

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

source_name: Primary fetal brain tissue; Lib:XZ:20100129:17--ChIP:XZ:20100125:17:fetal brain:H3K4me3

value: surgery

value: Fetal brain

value: Unknown

value: Primary Tissue

value: brain

value: 122 days

value: Protein A-Sepharose 4B

value: 10 million cells

value: SDS lysis

value: 70 ul bed volume

value: Millipore

value: Histone H3K4me3


title: ChIP-Seq analysis of H3K4me3 human fetal lung cells (superseded by GSE120324)

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: Lib:XZ:20100129:04--ChIP:XZ:20100125:04:fetal lung:H3K4me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3757
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3880
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************
BED and WIG files were replaced on April 29, 2014
****************************
This sample record's metadata may be obsolete; up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE120324
****************************

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

ANALYSIS FILE NAME: GSM621417_BI.Fetal_Lung.H3K4me3.UW_H-22727.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100129:04--ChIP:XZ:20100125:04:fetal lung:H3K4me3.hg19.level.1
ANALYSIS TITLE: Mapping of Fetal Lung Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me3 ChIP-Seq on Fetal Lung, Donor H-22727 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.4794
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 2

QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED: 62
FINDPEAKS_SCORE: 0.1714
FINDPEAKS_PERCENTILE: 3
HOTSPOT_SCORE: 0.1892
HOTSPOT_PERCENTILE: 3
IROC_SCORE: 0.9995
IROC_PERCENTILE: 60
POISSON_SCORE: 0.3494
POISSON_PERCENTILE: 16

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

ANALYSIS FILE NAME: GSM621417_BI.Fetal_Lung.H3K4me3.UW_H-22727.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100129:04--ChIP:XZ:20100125:04:fetal lung:H3K4me3.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Lung Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me3 ChIP-Seq read mappings from Fetal Lung, Donor H-22727 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.5068
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 2
BROWSER_TRACK_NAME: FL H3K4me3 27
BROWSER_TRACK_DESCRIPTION: BI Fetal Lung Histone H3K4me3 Donor H-22727 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED: 62
FINDPEAKS_SCORE: 0.1714
FINDPEAKS_PERCENTILE: 3
HOTSPOT_SCORE: 0.1892
HOTSPOT_PERCENTILE: 3
IROC_SCORE: 0.9995
IROC_PERCENTILE: 60
POISSON_SCORE: 0.3494
POISSON_PERCENTILE: 16

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

source_name: Primary fetal lung tissue; Lib:XZ:20100129:04--ChIP:XZ:20100125:04:fetal lung:H3K4me3

value: genomic DNA

value: Fetal lung

value: lung

value: UW

value: 101 days


title: ChIP-Seq analysis of H3K27me3 in human hiPS-20b cells; Lib:MC:20100119:06--ChIP:MC:20100113:06:hiPS-20b:H3K27Me3

description:
sample_term_id: NTR_0001168
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:MC:20100119:06--ChIP:MC:20100113:06:hiPS-20b:H3K27Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3756
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3892
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************
BED and WIG files were replaced on April 29, 2014

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

ANALYSIS FILE NAME: GSM621416_BI.iPS-20b.H3K27me3.Lib_MC_20100119_06--ChIP_MC_20100113_06_hiPS-20b_H3K27Me3.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100119:06--ChIP:MC:20100113:06:hiPS-20b:H3K27Me3.hg19.level.1
ANALYSIS TITLE: Mapping of iPS-20b Cell Line Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27me3 ChIP-Seq on the iPS-20b Cell Line, Library Lib:MC:20100119:06--ChIP:MC:20100113:06:hiPS-20b:H3K27Me3 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.4736
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 2

QUALITY SCORES:
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED: 52
FINDPEAKS_SCORE: 0.244
FINDPEAKS_PERCENTILE: 69
HOTSPOT_SCORE: 0.2568
HOTSPOT_PERCENTILE: 62
IROC_SCORE: 0.9863
IROC_PERCENTILE: 90
POISSON_SCORE: 0.4423
POISSON_PERCENTILE: 48

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

ANALYSIS FILE NAME: GSM621416_BI.iPS-20b.H3K27me3.Lib_MC_20100119_06--ChIP_MC_20100113_06_hiPS-20b_H3K27Me3.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100119:06--ChIP:MC:20100113:06:hiPS-20b:H3K27Me3.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of iPS-20b Cell Line Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27me3 ChIP-Seq read mappings from the iPS-20b Cell Line, Library Lib:MC:20100119:06--ChIP:MC:20100113:06:hiPS-20b:H3K27Me3 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.5010
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 2
BROWSER_TRACK_NAME: iPS20b H3K27me3 e3
BROWSER_TRACK_DESCRIPTION: BI iPS-20b Cell Line Histone H3K27me3 Library Lib:MC:20100119:06--ChIP:MC:20100113:06:hiPS-20b:H3K27Me3 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED: 52
FINDPEAKS_SCORE: 0.244
FINDPEAKS_PERCENTILE: 69
HOTSPOT_SCORE: 0.2568
HOTSPOT_PERCENTILE: 62
IROC_SCORE: 0.9863
IROC_PERCENTILE: 90
POISSON_SCORE: 0.4423
POISSON_PERCENTILE: 48

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

value: induced pluripotent stem cells 20b

value: induced pluripotent cells

value: KSR

value: Cell Line

value: undifferentiated

value: Male

value: Harvard University

value: Histone H3K27me3

value: Bioruptor


title: ChIP-Seq analysis of H3K36me3 in human fetal kidney cells; Lib:XZ:20100129:09--ChIP:XZ:20100125:09:fetal kidney:H3K36me3

description:
sample_term_id: UBERON_0002113
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:XZ:20100129:09--ChIP:XZ:20100125:09:fetal kidney:H3K36me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3755
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3886
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************
BED and WIG files were replaced on April 29, 2014

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

ANALYSIS FILE NAME: GSM621415_BI.Fetal_Kidney.H3K36me3.UW_H-22676.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100129:09--ChIP:XZ:20100125:09:fetal kidney:H3K36me3.hg19.level.1
ANALYSIS TITLE: Mapping of Fetal Kidney Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K36me3 ChIP-Seq on Fetal Kidney, Donor H-22676 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.4597
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 2

QUALITY SCORES:
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED: 54
FINDPEAKS_SCORE: 0.0228
FINDPEAKS_PERCENTILE: 6
HOTSPOT_SCORE: 0.1113
HOTSPOT_PERCENTILE: 6
IROC_SCORE: 0.7772
IROC_PERCENTILE: 11
POISSON_SCORE: 0.3823
POISSON_PERCENTILE: 17

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

ANALYSIS FILE NAME: GSM621415_BI.Fetal_Kidney.H3K36me3.UW_H-22676.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100129:09--ChIP:XZ:20100125:09:fetal kidney:H3K36me3.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Kidney Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K36me3 ChIP-Seq read mappings from Fetal Kidney, Donor H-22676 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.4871
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 2
BROWSER_TRACK_NAME: FK H3K36me3 76
BROWSER_TRACK_DESCRIPTION: BI Fetal Kidney Histone H3K36me3 Donor H-22676 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED: 54
FINDPEAKS_SCORE: 0.0228
FINDPEAKS_PERCENTILE: 6
HOTSPOT_SCORE: 0.1113
HOTSPOT_PERCENTILE: 6
IROC_SCORE: 0.7772
IROC_PERCENTILE: 11
POISSON_SCORE: 0.3823
POISSON_PERCENTILE: 17

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

source_name: Primary fetal kidney tissue; Lib:XZ:20100129:09--ChIP:XZ:20100125:09:fetal kidney:H3K36me3

value: surgery

value: Fetal kidney

value: Unknown

value: Primary Tissue

value: kidney

value: 120 days

value: Protein A-Sepharose 4B

value: 10 million cells

value: SDS lysis

value: 70 ul bed volume

value: Abcam

value: Histone H3K36me3


title: ChIP-Seq analysis of WCE in human hiPS-18b cells; Lib:MC:20090720:02--ChIP:MC:20090715:02:hiPS-18b:WCE

description:
sample_term_id: NTR_0001166
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:MC:20090720:02--ChIP:MC:20090715:02:hiPS-18b:WCE
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3751
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3897
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************
BED and WIG files were replaced on April 29, 2014

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

ANALYSIS FILE NAME: GSM621411_BI.iPS-18b.Input.Lib_MC_20090720_02--ChIP_MC_20090715_02_hiPS-18b_WCE.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20090720:02--ChIP:MC:20090715:02:hiPS-18b:WCE.hg19.level.1
ANALYSIS TITLE: Mapping of iPS-18b Cell Line ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on the iPS-18b Cell Line, Library Lib:MC:20090720:02--ChIP:MC:20090715:02:hiPS-18b:WCE 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.4618
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 2

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED: 67
FINDPEAKS_SCORE: 0.0077
FINDPEAKS_PERCENTILE: 36
HOTSPOT_SCORE: 0.1046
HOTSPOT_PERCENTILE: 76
IROC_SCORE: 0.5844
IROC_PERCENTILE: 37
POISSON_SCORE: 0.3183
POISSON_PERCENTILE: 79

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

ANALYSIS FILE NAME: GSM621411_BI.iPS-18b.Input.Lib_MC_20090720_02--ChIP_MC_20090715_02_hiPS-18b_WCE.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20090720:02--ChIP:MC:20090715:02:hiPS-18b:WCE.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of iPS-18b Cell Line ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from the iPS-18b Cell Line, Library Lib:MC:20090720:02--ChIP:MC:20090715:02:hiPS-18b:WCE 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.4892
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 2
BROWSER_TRACK_NAME: iPS18b Input CE
BROWSER_TRACK_DESCRIPTION: BI iPS-18b Cell Line ChIP-Seq Input Library Lib:MC:20090720:02--ChIP:MC:20090715:02:hiPS-18b:WCE EA Release 2

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED: 67
FINDPEAKS_SCORE: 0.0077
FINDPEAKS_PERCENTILE: 36
HOTSPOT_SCORE: 0.1046
HOTSPOT_PERCENTILE: 76
IROC_SCORE: 0.5844
IROC_PERCENTILE: 37
POISSON_SCORE: 0.3183
POISSON_PERCENTILE: 79

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

value: induced pluripotent stem cells

value: induced pluripotent cells

value: KSR

value: genomic DNA

value: Cell Line

value: undifferentiated

value: Female

value: standard

value: ChIP-Seq Input

value: Input


title: ChIP-Seq analysis of H3K36me3 in human fetal brain cells; Lib:XZ:20100129:16--ChIP:XZ:20100125:16:fetal brain:H3K36me3

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: Lib:XZ:20100129:16--ChIP:XZ:20100125:16:fetal brain:H3K36me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3750
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3878
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************
BED and WIG files were replaced on April 29, 2014

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

ANALYSIS FILE NAME: GSM621410_BI.Fetal_Brain.H3K36me3.UW_H-22510.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100129:16--ChIP:XZ:20100125:16:fetal brain:H3K36me3.hg19.level.1
ANALYSIS TITLE: Mapping of Fetal Brain Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K36me3 ChIP-Seq on Fetal Brain, Donor H-22510 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.4645
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 2

QUALITY SCORES:
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED: 54
FINDPEAKS_SCORE: 0.009
FINDPEAKS_PERCENTILE: 2
HOTSPOT_SCORE: 0.0753
HOTSPOT_PERCENTILE: 2
IROC_SCORE: 0.5705
IROC_PERCENTILE: 2
POISSON_SCORE: 0.341
POISSON_PERCENTILE: 11

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

ANALYSIS FILE NAME: GSM621410_BI.Fetal_Brain.H3K36me3.UW_H-22510.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100129:16--ChIP:XZ:20100125:16:fetal brain:H3K36me3.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Brain Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K36me3 ChIP-Seq read mappings from Fetal Brain, Donor H-22510 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.4919
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 2
BROWSER_TRACK_NAME: FB H3K36me3 10
BROWSER_TRACK_DESCRIPTION: BI Fetal Brain Histone H3K36me3 Donor H-22510 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED: 54
FINDPEAKS_SCORE: 0.009
FINDPEAKS_PERCENTILE: 2
HOTSPOT_SCORE: 0.0753
HOTSPOT_PERCENTILE: 2
IROC_SCORE: 0.5705
IROC_PERCENTILE: 2
POISSON_SCORE: 0.341
POISSON_PERCENTILE: 11

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

source_name: Primary fetal brain tissue; Lib:XZ:20100129:16--ChIP:XZ:20100125:16:fetal brain:H3K36me3

value: surgery

value: Fetal brain

value: Unknown

value: Primary Tissue

value: brain

value: UW

value: 122 days

value: Bioruptor


title: ChIP-Seq analysis of H3K4me1 in human fetal kidney cells; Lib:XZ:20100129:10--ChIP:XZ:20100125:10:fetal kidney:H3K4me1

description:
sample_term_id: UBERON_0002113
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:XZ:20100129:10--ChIP:XZ:20100125:10:fetal kidney:H3K4me1
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3749
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3886
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************
BED and WIG files were replaced on April 29, 2014

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

ANALYSIS FILE NAME: GSM621409_BI.Fetal_Kidney.H3K4me1.UW_H-22676.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100129:10--ChIP:XZ:20100125:10:fetal kidney:H3K4me1.hg19.level.1
ANALYSIS TITLE: Mapping of Fetal Kidney Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me1 ChIP-Seq on Fetal Kidney, Donor H-22676 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.4709
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 2

QUALITY SCORES:
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED: 43
FINDPEAKS_SCORE: 0.0156
FINDPEAKS_PERCENTILE: 5
HOTSPOT_SCORE: 0.1268
HOTSPOT_PERCENTILE: 5
IROC_SCORE: 0.7718
IROC_PERCENTILE: 7
POISSON_SCORE: 0.4282
POISSON_PERCENTILE: 7

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

ANALYSIS FILE NAME: GSM621409_BI.Fetal_Kidney.H3K4me1.UW_H-22676.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100129:10--ChIP:XZ:20100125:10:fetal kidney:H3K4me1.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Kidney Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me1 ChIP-Seq read mappings from Fetal Kidney, Donor H-22676 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.4983
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 2
BROWSER_TRACK_NAME: FK H3K4me1 76
BROWSER_TRACK_DESCRIPTION: BI Fetal Kidney Histone H3K4me1 Donor H-22676 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED: 43
FINDPEAKS_SCORE: 0.0156
FINDPEAKS_PERCENTILE: 5
HOTSPOT_SCORE: 0.1268
HOTSPOT_PERCENTILE: 5
IROC_SCORE: 0.7718
IROC_PERCENTILE: 7
POISSON_SCORE: 0.4282
POISSON_PERCENTILE: 7

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

source_name: Primary fetal kidney tissue; Lib:XZ:20100129:10--ChIP:XZ:20100125:10:fetal kidney:H3K4me1

value: Fetal kidney

value: kidney

value: 120 days

value: Protein A-Sepharose 4B

value: 10 million cells

value: SDS lysis

value: 70 ul bed volume

value: Abcam

value: Histone H3K4me1


title: ChIP-Seq analysis of H3K9me3 in human fetal kidney cells; Lib:XZ:20100129:13--ChIP:XZ:20100125:13:fetal kidney:H3K9Me3

description:
sample_term_id: UBERON_0002113
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:XZ:20100129:13--ChIP:XZ:20100125:13:fetal kidney:H3K9Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3781
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3886
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************
BED and WIG files were replaced on April 29, 2014

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

ANALYSIS FILE NAME: GSM621441_BI.Fetal_Kidney.H3K9me3.UW_H-22676.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100129:13--ChIP:XZ:20100125:13:fetal kidney:H3K9Me3.hg19.level.1
ANALYSIS TITLE: Mapping of Fetal Kidney Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9me3 ChIP-Seq on Fetal Kidney, Donor H-22676 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.4648
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 2

QUALITY SCORES:
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED: 59
FINDPEAKS_SCORE: 0.0203
FINDPEAKS_PERCENTILE: 12
HOTSPOT_SCORE: 0.0385
HOTSPOT_PERCENTILE: 2
IROC_SCORE: 0.9004
IROC_PERCENTILE: 75
POISSON_SCORE: 0.256
POISSON_PERCENTILE: 3

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

ANALYSIS FILE NAME: GSM621441_BI.Fetal_Kidney.H3K9me3.UW_H-22676.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100129:13--ChIP:XZ:20100125:13:fetal kidney:H3K9Me3.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Kidney Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9me3 ChIP-Seq read mappings from Fetal Kidney, Donor H-22676 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.4922
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 2
BROWSER_TRACK_NAME: FK H3K9me3 76
BROWSER_TRACK_DESCRIPTION: BI Fetal Kidney Histone H3K9me3 Donor H-22676 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED: 59
FINDPEAKS_SCORE: 0.0203
FINDPEAKS_PERCENTILE: 12
HOTSPOT_SCORE: 0.0385
HOTSPOT_PERCENTILE: 2
IROC_SCORE: 0.9004
IROC_PERCENTILE: 75
POISSON_SCORE: 0.256
POISSON_PERCENTILE: 3

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

source_name: Primary fetal kidney tissue; Lib:XZ:20100129:13--ChIP:XZ:20100125:13:fetal kidney:H3K9Me3

value: surgery

value: genomic DNA

value: Histone H3K9me3


title: ChIP-Seq analysis of H3K9me3 in Mobilized CD34 cells; Lib:RI:20100308:08--ChIP:MA:20100216:08: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:20100308:08--ChIP:MA:20100216:08:Mobilized CD34:H3K9Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3739
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3877
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************
BED and WIG files were replaced on April 29, 2014

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

ANALYSIS FILE NAME: GSM621399_BI.Mobilized_CD34_Primary_Cells.H3K9me3.UW_RO_01480.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:RI:20100308:08--ChIP:MA:20100216:08:Mobilized CD34:H3K9Me3.hg19.level.1
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 01480 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.4634
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 2

QUALITY SCORES:
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED: 59
FINDPEAKS_SCORE: 0.0413
FINDPEAKS_PERCENTILE: 31
HOTSPOT_SCORE: 0.0994
HOTSPOT_PERCENTILE: 34
IROC_SCORE: 0.8102
IROC_PERCENTILE: 44
POISSON_SCORE: 0.3298
POISSON_PERCENTILE: 32

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

ANALYSIS FILE NAME: GSM621399_BI.Mobilized_CD34_Primary_Cells.H3K9me3.UW_RO_01480.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:RI:20100308:08--ChIP:MA:20100216:08:Mobilized CD34:H3K9Me3.hg19.level.2
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 01480 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.4908
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 2
BROWSER_TRACK_NAME: MCD34 H3K9me3 80
BROWSER_TRACK_DESCRIPTION: BI Mobilized CD34 Primary Cells Histone H3K9me3 Donor RO 01480 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED: 59
FINDPEAKS_SCORE: 0.0413
FINDPEAKS_PERCENTILE: 31
HOTSPOT_SCORE: 0.0994
HOTSPOT_PERCENTILE: 34
IROC_SCORE: 0.8102
IROC_PERCENTILE: 44
POISSON_SCORE: 0.3298
POISSON_PERCENTILE: 32

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

source_name: CD34 cells mobilized into peripheral blood; Lib:RI:20100308:08--ChIP:MA:20100216:08:Mobilized CD34:H3K9Me3

value: Mobilized CD34

value: Unknown

value: Primary Cell