title: ChIP-Seq analysis of H3K36me3 in human colonic mucosa cells; DNA_Lib 365

description:
sample_term_id: UBERON_0000317
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 365
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.9616
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9761
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM916042_BI.Colonic_Mucosa.H3K36me3.155.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 365-DNA_Lib 365-DNA_Lib 365-DNA_Lib 365.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of Colonic Mucosa Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K36me3 ChIP-Seq on Colonic Mucosa, Donor 155, 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.12320
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 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 20,200,754
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 13
FINDPEAKS_SCORE: 0.0159
FINDPEAKS_PERCENTILE: 8
HOTSPOT_SCORE: 0.1207
HOTSPOT_PERCENTILE: 23
IROC_SCORE: 0.7492
IROC_PERCENTILE: 8
POISSON_SCORE: 0.2245
POISSON_PERCENTILE: 15
MAXIMUM_REPLICATE_CORRELATION: 0.87

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

ANALYSIS FILE NAME: GSM916042_BI.Colonic_Mucosa.H3K36me3.155.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 365-DNA_Lib 365-DNA_Lib 365-DNA_Lib 365.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of Colonic Mucosa Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K36me3 ChIP-Seq read mappings from Colonic Mucosa, Donor 155, 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.12367
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 6
BROWSER_TRACK_NAME: CM H3K36me3 55 65
BROWSER_TRACK_DESCRIPTION: BI Colonic Mucosa Histone H3K36me3 Donor 155 Library DNA_Lib 365 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 20,200,754
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 13
FINDPEAKS_SCORE: 0.0159
FINDPEAKS_PERCENTILE: 8
HOTSPOT_SCORE: 0.1207
HOTSPOT_PERCENTILE: 23
IROC_SCORE: 0.7492
IROC_PERCENTILE: 8
POISSON_SCORE: 0.2245
POISSON_PERCENTILE: 15
MAXIMUM_REPLICATE_CORRELATION: 0.87

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

source_name: Primary colonic mucosal tissue obtained during surgery and confirmed by pathology examination to be healthy tissue; DNA_Lib 365

value: BioSam 157 REMC 19

value: Colonic Mucosa

value: NL colonic mucosa, colon rmvd as part of abmnl Sarc

value: Female

value: Primary Tissue

value: Colon

value: MGH

value: 56.0 Years

value: Protein A-Sepharose 4B

value: cell/nuclei lysis

value: ~1 ug


title: ChIP-Seq analysis of H3K36me3 in human colon smooth muscle cells; DNA_Lib 928

status: Public on Apr 17 2012

type: SRA

city: Cambridge

first: BROAD

last: INSTITUTE

state: MA

country: USA

institute: Broad Institute

description:
sample_term_id: UBERON_0012489
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 928
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.9605
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9758
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

library_source: genomic

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

ANALYSIS FILE NAME: GSM916031_BI.Colon_Smooth_Muscle.H3K36me3.156.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 928-DNA_Lib 928.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of Colon Smooth Muscle Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K36me3 ChIP-Seq on Colon Smooth Muscle, Donor 156, 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.12290
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 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 12,253,130
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 13
FINDPEAKS_SCORE: 0.0474
FINDPEAKS_PERCENTILE: 23
HOTSPOT_SCORE: 0.197
HOTSPOT_PERCENTILE: 54
IROC_SCORE: 0.7837
IROC_PERCENTILE: 23
POISSON_SCORE: 0.2969
POISSON_PERCENTILE: 38
MAXIMUM_REPLICATE_CORRELATION: 0.9

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

ANALYSIS FILE NAME: GSM916031_BI.Colon_Smooth_Muscle.H3K36me3.156.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 928-DNA_Lib 928.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of Colon Smooth Muscle Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K36me3 ChIP-Seq read mappings from Colon Smooth Muscle, Donor 156, 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.12337
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 6
BROWSER_TRACK_NAME: CSM H3K36me3 56 28
BROWSER_TRACK_DESCRIPTION: BI Colon Smooth Muscle Histone H3K36me3 Donor 156 Library DNA_Lib 928 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 12,253,130
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 13
FINDPEAKS_SCORE: 0.0474
FINDPEAKS_PERCENTILE: 23
HOTSPOT_SCORE: 0.197
HOTSPOT_PERCENTILE: 54
IROC_SCORE: 0.7837
IROC_PERCENTILE: 23
POISSON_SCORE: 0.2969
POISSON_PERCENTILE: 38
MAXIMUM_REPLICATE_CORRELATION: 0.9

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

molecule: genomic DNA

organism: Homo sapiens

source_name: Smooth muscle from wall of colon obtained during surgery and confirmed by pathology examination to be healthy tissue; DNA_Lib 928

extract_protocol: Library construction protocol: Single read - Illumina

tag: sample alias

tag: sample common name

value: Colon Smooth Muscle

value: Surgery

value: NL smooth muscle, colon rmvd as part of abdmnl Sarc.

tag: molecule

value: genomic DNA

tag: disease

value: Smooth Muscle

value: Caucasian

value: 0.5 to 3 million cells

value: 10 ul bed volume

value: Abcam

value: Histone H3K36me3

value: Branson


title: ChIP-Seq analysis of H3K4me3 in human colon smooth muscle cells; DNA_Lib 925

description:
sample_term_id: UBERON_0012489
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 925
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.9603
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9758
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM916029_BI.Colon_Smooth_Muscle.H3K4me3.156.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 925-DNA_Lib 925.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of Colon Smooth Muscle Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me3 ChIP-Seq on Colon Smooth Muscle, Donor 156, 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.12285
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 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 15,019,126
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 11
FINDPEAKS_SCORE: 0.1624
FINDPEAKS_PERCENTILE: 27
HOTSPOT_SCORE: 0.2441
HOTSPOT_PERCENTILE: 36
IROC_SCORE: 0.9997
IROC_PERCENTILE: 73
POISSON_SCORE: 0.2653
POISSON_PERCENTILE: 36
MAXIMUM_REPLICATE_CORRELATION: 0.95

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

ANALYSIS FILE NAME: GSM916029_BI.Colon_Smooth_Muscle.H3K4me3.156.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 925-DNA_Lib 925.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of Colon Smooth Muscle Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me3 ChIP-Seq read mappings from Colon Smooth Muscle, Donor 156, 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.12332
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 6
BROWSER_TRACK_NAME: CSM H3K4me3 56 25
BROWSER_TRACK_DESCRIPTION: BI Colon Smooth Muscle Histone H3K4me3 Donor 156 Library DNA_Lib 925 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 15,019,126
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 11
FINDPEAKS_SCORE: 0.1624
FINDPEAKS_PERCENTILE: 27
HOTSPOT_SCORE: 0.2441
HOTSPOT_PERCENTILE: 36
IROC_SCORE: 0.9997
IROC_PERCENTILE: 73
POISSON_SCORE: 0.2653
POISSON_PERCENTILE: 36
MAXIMUM_REPLICATE_CORRELATION: 0.95

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

source_name: Smooth muscle from wall of colon obtained during surgery and confirmed by pathology examination to be healthy tissue; DNA_Lib 925

value: Female

value: Primary Tissue

value: Colon

value: Millipore

value: Histone H3K4me3


title: ChIP-Seq analysis of WCE in human colon smooth muscle cells; DNA_Lib 924

description:
sample_term_id: UBERON_0012489
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 924
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.9604
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9758
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM916030_BI.Colon_Smooth_Muscle.Input.156.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 924-DNA_Lib 924.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of Colon Smooth Muscle ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on Colon Smooth Muscle, Donor 156, 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.12323
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 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 25,828,649
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 15
FINDPEAKS_SCORE: 0.0053
FINDPEAKS_PERCENTILE: 40
HOTSPOT_SCORE: 0.0113
HOTSPOT_PERCENTILE: 60
IROC_SCORE: 0.0
IROC_PERCENTILE: 7
POISSON_SCORE: 0.0418
POISSON_PERCENTILE: 60
MAXIMUM_REPLICATE_CORRELATION: 0.91

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

ANALYSIS FILE NAME: GSM916030_BI.Colon_Smooth_Muscle.Input.156.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 924-DNA_Lib 924.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of Colon Smooth Muscle ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from Colon Smooth Muscle, Donor 156, 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.12370
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 6
BROWSER_TRACK_NAME: CSM Input 56 24
BROWSER_TRACK_DESCRIPTION: BI Colon Smooth Muscle ChIP-Seq Input Donor 156 Library DNA_Lib 924 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 25,828,649
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 15
FINDPEAKS_SCORE: 0.0053
FINDPEAKS_PERCENTILE: 40
HOTSPOT_SCORE: 0.0113
HOTSPOT_PERCENTILE: 60
IROC_SCORE: 0.0
IROC_PERCENTILE: 7
POISSON_SCORE: 0.0418
POISSON_PERCENTILE: 60
MAXIMUM_REPLICATE_CORRELATION: 0.91

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

source_name: Smooth muscle from wall of colon obtained during surgery and confirmed by pathology examination to be healthy tissue; DNA_Lib 924

value: MGH

value: 56.0 Years

value: standard

value: cell/nuclei lysis

value: ChIP-Seq Input

value: Input


title: Normal Muscle individual 7

status: Public on Sep 14 2012

type: RNA

city: rotterdam

first: Mario

last: Pescatori

address: Westplein 11

country: Netherlands

institute: Health e-genomics

hyb_protocol: Hybridization was performed on an illumina air hybridization owen. Slides were washed  and stained using reagents and protocols provided by Illumina.

scan_protocol: Slides were scanned on an Illumina Iscan BeadChip reader, following the protocol provided by illumina for the HumanHT-12_V3_0_R1  BeadChip.

data_processing: Data were extracted from the scan files using Illumina Genome Studio and exported both as raw and preprocessed expression data. Before analysis, the dataset was quantile normalized, local background was not subtracted, and the expression values for the missing bead were imputed using the GenomeStudio imputation algoritm

label: biotin

molecule: total RNA

source_name: Muscle tissue

label_protocol: Biotin labelled cRNA was produced using the Ambion TotalPrep RNA amplification kit

extract_protocol: Total RNA was extracted from muscle biopsies using the Trizol reagent followed by an additional clean up step on Qiagen RNAeasy column, following protocols provided by the manufacturer

tag: individual

tag: tissue

value: quadriceps

tag: gender

value: F

tag: disease state

value: Normal Muscle


title: ChIP-Seq analysis of H3K4me3 in human Duodenum mucosa cells; DNA_Lib 374

description:
sample_term_id: UBERON_0000320
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 374
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.9593
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9454
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM916019_BI.Duodenum_Mucosa.H3K4me3.159.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 374-DNA_Lib 374-DNA_Lib 374-DNA_Lib 374.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of Duodenum Mucosa Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me3 ChIP-Seq on Duodenum Mucosa, Donor 159, were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.12324
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 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 18,974,670
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 11
FINDPEAKS_SCORE: 0.3348
FINDPEAKS_PERCENTILE: 73
HOTSPOT_SCORE: 0.3756
HOTSPOT_PERCENTILE: 73
IROC_SCORE: 0.9972
IROC_PERCENTILE: 27
POISSON_SCORE: 0.4149
POISSON_PERCENTILE: 73
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM916019_BI.Duodenum_Mucosa.H3K4me3.159.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 374-DNA_Lib 374-DNA_Lib 374-DNA_Lib 374.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of Duodenum Mucosa Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me3 ChIP-Seq read mappings from Duodenum Mucosa, Donor 159, were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.12371
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 6
BROWSER_TRACK_NAME: DM H3K4me3 59 74
BROWSER_TRACK_DESCRIPTION: BI Duodenum Mucosa Histone H3K4me3 Donor 159 Library DNA_Lib 374 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 18,974,670
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 11
FINDPEAKS_SCORE: 0.3348
FINDPEAKS_PERCENTILE: 73
HOTSPOT_SCORE: 0.3756
HOTSPOT_PERCENTILE: 73
IROC_SCORE: 0.9972
IROC_PERCENTILE: 27
POISSON_SCORE: 0.4149
POISSON_PERCENTILE: 73
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

source_name: Primary duodenum mucosal tissue; DNA_Lib 374

value: Duodenum Mucosa

value: Surgery

value: presumed normal

value: genomic DNA

value: Caucasian

value: Male

value: Duodenum

value: 59.0 Years

value: Protein A-Sepharose 4B

value: 0.5 to 3 million cells

value: ~1 ug

value: 10 ul bed volume


title: ChIP-Seq analysis of H3K36me3 in human Duodenum mucosa cells; DNA_Lib 375

description:
sample_term_id: UBERON_0000320
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 375
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.9594
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9454
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM916020_BI.Duodenum_Mucosa.H3K36me3.159.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 375-DNA_Lib 375-DNA_Lib 375.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of Duodenum Mucosa Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K36me3 ChIP-Seq on Duodenum Mucosa, Donor 159, were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.12312
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 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 14,426,278
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 13
FINDPEAKS_SCORE: 0.1892
FINDPEAKS_PERCENTILE: 85
HOTSPOT_SCORE: 0.2683
HOTSPOT_PERCENTILE: 92
IROC_SCORE: 0.9352
IROC_PERCENTILE: 62
POISSON_SCORE: 0.4083
POISSON_PERCENTILE: 69
MAXIMUM_REPLICATE_CORRELATION: 0.94

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

ANALYSIS FILE NAME: GSM916020_BI.Duodenum_Mucosa.H3K36me3.159.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 375-DNA_Lib 375-DNA_Lib 375.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of Duodenum Mucosa Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K36me3 ChIP-Seq read mappings from Duodenum Mucosa, Donor 159, were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.12359
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 6
BROWSER_TRACK_NAME: DM H3K36me3 59 75
BROWSER_TRACK_DESCRIPTION: BI Duodenum Mucosa Histone H3K36me3 Donor 159 Library DNA_Lib 375 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 14,426,278
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 13
FINDPEAKS_SCORE: 0.1892
FINDPEAKS_PERCENTILE: 85
HOTSPOT_SCORE: 0.2683
HOTSPOT_PERCENTILE: 92
IROC_SCORE: 0.9352
IROC_PERCENTILE: 62
POISSON_SCORE: 0.4083
POISSON_PERCENTILE: 69
MAXIMUM_REPLICATE_CORRELATION: 0.94

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

source_name: Primary duodenum mucosal tissue; DNA_Lib 375

value: Primary Tissue

value: MGH

value: cell/nuclei lysis

value: Abcam

value: Histone H3K36me3

value: Branson


title: ChIP-Seq analysis of H3K9ac in human Duodenum mucosa cells; DNA_Lib 371

description:
sample_term_id: UBERON_0000320
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 371
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.9592
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9454
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM916018_BI.Duodenum_Mucosa.H3K9ac.159.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 371-DNA_Lib 371-DNA_Lib 371-DNA_Lib 371.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of Duodenum Mucosa Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9ac ChIP-Seq on Duodenum Mucosa, Donor 159, were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.12286
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 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 13,542,291
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 9
FINDPEAKS_SCORE: 0.2469
FINDPEAKS_PERCENTILE: 89
HOTSPOT_SCORE: 0.3329
HOTSPOT_PERCENTILE: 78
IROC_SCORE: 0.99
IROC_PERCENTILE: 67
POISSON_SCORE: 0.3628
POISSON_PERCENTILE: 89
MAXIMUM_REPLICATE_CORRELATION: 0.93

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

ANALYSIS FILE NAME: GSM916018_BI.Duodenum_Mucosa.H3K9ac.159.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 371-DNA_Lib 371-DNA_Lib 371-DNA_Lib 371.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of Duodenum Mucosa Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9ac ChIP-Seq read mappings from Duodenum Mucosa, Donor 159, were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.12333
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 6
BROWSER_TRACK_NAME: DM H3K9ac 59 71
BROWSER_TRACK_DESCRIPTION: BI Duodenum Mucosa Histone H3K9ac Donor 159 Library DNA_Lib 371 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 13,542,291
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 9
FINDPEAKS_SCORE: 0.2469
FINDPEAKS_PERCENTILE: 89
HOTSPOT_SCORE: 0.3329
HOTSPOT_PERCENTILE: 78
IROC_SCORE: 0.99
IROC_PERCENTILE: 67
POISSON_SCORE: 0.3628
POISSON_PERCENTILE: 89
MAXIMUM_REPLICATE_CORRELATION: 0.93

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

source_name: Primary duodenum mucosal tissue; DNA_Lib 371

value: Duodenum Mucosa

value: Surgery

value: Histone H3K9ac


title: WT-TBP-H3K4me3

status: Public on Mar 01 2012

city: Illkirch

first: Celine

last: Keime

address: 1 rue Laurent Fries

country: France

institute: IGBMC (CNRS/INSERM/UDS)

description: ChIP with antibody against trimethyated lysine 4 of histone H3

data_processing:
Alignment: Sequence reads were obtained and mapped to the mouse genomes mm9/NCBI37(July, 2007) using the Illumina Genome Analyzer Pipeline. All reads mapping with two or fewer mismatches were retained.
Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/). Peak annotation was performed with GPAT(http://bips.u-strasbg.fr/GPAT/).

organism: Mus musculus

source_name: Embryonic fibroblast

growth_protocol: MEF cells were cultured in DMEM with 10% FCS.

extract_protocol: TheChIP-seq libraries were prepared following the Illumina protocol.  After PCR amplification, surplus PCR primers and dimer adapters were removed by purification using AMPure beads (Agencourt Biosciences Corporation). Size selection was performed by electrophoresis on a 2% agarose gel and DNA fragments in the range of 200bp were excised and purified using QIAquick Gel Extraction Kit (Qiagen). DNA libraries were checked for quality and quantified using 2100 Bioanalyzer (Agilent). The libraries were loaded in the flowcell at 6pM concentration and clusters generated and sequenced on the Illumina Genome  Analyzer IIx as single-end 36 base reads

treatment_protocol: MEFs were grown to 80% confluence and fixed with 0.4% formaldehyde

tag: cell line

value: TBP-null MEFs

tag: genotype/variation

value: expressing exogenous wild-type human TBP

tag: antibody

value: trimethyated lysine 4 of histone H3


title: R188E-TBP-H3K4me3

value: expressing exogenous human TBP R188E


title: R188E-TBP-TBP

description: ChIP with antibody against TBP

value: TBP


title: WT-TBP-Pol II

description: ChIP with antibody against RNA polymerase II

value: RNA polymerase II


title: R188E-TBP-Pol II


title: ChIP-Seq analysis of H3K27me3 in human Duodenum smooth muscle cells; DNA_Lib 989

description:
sample_term_id: UBERON_0012488
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 989
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.9606
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9762
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM916032_BI.Duodenum_Smooth_Muscle.H3K27me3.Donor_174_REMC_28.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 989-DNA_Lib 989.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of Duodenum Smooth Muscle Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27me3 ChIP-Seq on Duodenum Smooth Muscle, Donor Donor 174 REMC 28, were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.12280
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 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 13,226,776
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 10
FINDPEAKS_SCORE: 0.2869
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.3683
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9611
IROC_PERCENTILE: 90
POISSON_SCORE: 0.5046
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.71

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

ANALYSIS FILE NAME: GSM916032_BI.Duodenum_Smooth_Muscle.H3K27me3.Donor_174_REMC_28.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 989-DNA_Lib 989.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of Duodenum Smooth Muscle Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27me3 ChIP-Seq read mappings from Duodenum Smooth Muscle, Donor Donor 174 REMC 28, were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.12327
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 6
BROWSER_TRACK_NAME: DSM H3K27me3 74 89
BROWSER_TRACK_DESCRIPTION: BI Duodenum Smooth Muscle Histone H3K27me3 Donor 174 REMC 28 Library DNA_Lib 989 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 13,226,776
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 10
FINDPEAKS_SCORE: 0.2869
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.3683
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9611
IROC_PERCENTILE: 90
POISSON_SCORE: 0.5046
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.71

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

source_name: Smooth muscle from wall of duodenum obtained during surgery and confirmed by pathology examination to be healthy tissue; DNA_Lib 989

value: BioSam 309

value: Duodenum Smooth Muscle

value: NL smth muscle,  ddnum rmvd as part of whipple operation  because of autoimmune pancreatitis (type1)

value: genomic DNA

value: Smooth Muscle

value: Caucasian

value: Male

value: Duodenum

value: Donor 174 REMC 28

value: Protein A-Sepharose 4B

value: 0.5 to 3 million cells

value: ~1 ug

value: Millipore

value: Histone H3K27me3


title: ChIP-Seq analysis of H3K27me3 in human colonic mucosa cells; DNA_Lib 364

description:
sample_term_id: UBERON_0000317
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 364
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.9617
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9761
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM916043_BI.Colonic_Mucosa.H3K27me3.155.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 364-DNA_Lib 364-DNA_Lib 364-DNA_Lib 364.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of Colonic Mucosa Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27me3 ChIP-Seq on Colonic Mucosa, Donor 155, 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.12318
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 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 25,564,809
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 10
FINDPEAKS_SCORE: 0.0048
FINDPEAKS_PERCENTILE: 10
HOTSPOT_SCORE: 0.0757
HOTSPOT_PERCENTILE: 20
IROC_SCORE: 0.543
IROC_PERCENTILE: 10
POISSON_SCORE: 0.1963
POISSON_PERCENTILE: 20
MAXIMUM_REPLICATE_CORRELATION: 0.86

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

ANALYSIS FILE NAME: GSM916043_BI.Colonic_Mucosa.H3K27me3.155.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 364-DNA_Lib 364-DNA_Lib 364-DNA_Lib 364.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of Colonic Mucosa Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27me3 ChIP-Seq read mappings from Colonic Mucosa, Donor 155, 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.12365
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 6
BROWSER_TRACK_NAME: CM H3K27me3 55 64
BROWSER_TRACK_DESCRIPTION: BI Colonic Mucosa Histone H3K27me3 Donor 155 Library DNA_Lib 364 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 25,564,809
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 10
FINDPEAKS_SCORE: 0.0048
FINDPEAKS_PERCENTILE: 10
HOTSPOT_SCORE: 0.0757
HOTSPOT_PERCENTILE: 20
IROC_SCORE: 0.543
IROC_PERCENTILE: 10
POISSON_SCORE: 0.1963
POISSON_PERCENTILE: 20
MAXIMUM_REPLICATE_CORRELATION: 0.86

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

source_name: Primary colonic mucosal tissue obtained during surgery and confirmed by pathology examination to be healthy tissue; DNA_Lib 364

value: BioSam 157 REMC 19

value: Colonic Mucosa

value: Surgery

value: NL colonic mucosa, colon rmvd as part of abmnl Sarc

value: Female

value: Primary Tissue

value: Colon

value: MGH

value: 56.0 Years

value: cell/nuclei lysis

value: 10 ul bed volume

value: Branson


title: WT-TBP-TBP

description: ChIP with antibody against TBP

value: TBP-null MEFs

value: expressing exogenous wild-type human TBP

value: TBP


title: GFP-control

description: ChIP with antibody against GFP

value: GFP


title: ChIP-Seq analysis of H3K4me3 in human Duodenum smooth muscle cells; DNA_Lib 990

description:
sample_term_id: UBERON_0012488
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 990
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.9588
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9762
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM916014_BI.Duodenum_Smooth_Muscle.H3K4me3.Donor_174_REMC_28.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 990-DNA_Lib 990.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of Duodenum Smooth Muscle Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me3 ChIP-Seq on Duodenum Smooth Muscle, Donor Donor 174 REMC 28, were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.12296
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 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 19,656,673
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 11
FINDPEAKS_SCORE: 0.4578
FINDPEAKS_PERCENTILE: 91
HOTSPOT_SCORE: 0.4778
HOTSPOT_PERCENTILE: 91
IROC_SCORE: 0.9943
IROC_PERCENTILE: 18
POISSON_SCORE: 0.5339
POISSON_PERCENTILE: 82
MAXIMUM_REPLICATE_CORRELATION: 0.9

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

ANALYSIS FILE NAME: GSM916014_BI.Duodenum_Smooth_Muscle.H3K4me3.Donor_174_REMC_28.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 990-DNA_Lib 990.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of Duodenum Smooth Muscle Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me3 ChIP-Seq read mappings from Duodenum Smooth Muscle, Donor Donor 174 REMC 28, were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.12343
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 6
BROWSER_TRACK_NAME: DSM H3K4me3 74 90
BROWSER_TRACK_DESCRIPTION: BI Duodenum Smooth Muscle Histone H3K4me3 Donor 174 REMC 28 Library DNA_Lib 990 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 19,656,673
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 11
FINDPEAKS_SCORE: 0.4578
FINDPEAKS_PERCENTILE: 91
HOTSPOT_SCORE: 0.4778
HOTSPOT_PERCENTILE: 91
IROC_SCORE: 0.9943
IROC_PERCENTILE: 18
POISSON_SCORE: 0.5339
POISSON_PERCENTILE: 82
MAXIMUM_REPLICATE_CORRELATION: 0.9

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

source_name: Smooth muscle from wall of duodenum obtained during surgery and confirmed by pathology examination to be healthy tissue; DNA_Lib 990

value: BioSam 309

value: Duodenum Smooth Muscle

value: NL smth muscle,  ddnum rmvd as part of whipple operation  because of autoimmune pancreatitis (type1)

value: genomic DNA

value: Smooth Muscle

value: Caucasian

value: Male

value: Duodenum

value: Donor 174 REMC 28

value: Protein A-Sepharose 4B

value: 0.5 to 3 million cells

value: ~1 ug

value: Millipore

value: Histone H3K4me3


title: ChIP-Seq analysis of H3K27me3 in human Duodenum mucosa cells; DNA_Lib 372

description:
sample_term_id: UBERON_0000320
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 372
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.9590
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9454
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM916016_BI.Duodenum_Mucosa.H3K27me3.159.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 372-DNA_Lib 372-DNA_Lib 372-DNA_Lib 372.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of Duodenum Mucosa Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27me3 ChIP-Seq on Duodenum Mucosa, Donor 159, were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.12284
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 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 24,999,789
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 10
FINDPEAKS_SCORE: 0.0375
FINDPEAKS_PERCENTILE: 50
HOTSPOT_SCORE: 0.1205
HOTSPOT_PERCENTILE: 60
IROC_SCORE: 0.8361
IROC_PERCENTILE: 50
POISSON_SCORE: 0.2699
POISSON_PERCENTILE: 50
MAXIMUM_REPLICATE_CORRELATION: 0.95

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

ANALYSIS FILE NAME: GSM916016_BI.Duodenum_Mucosa.H3K27me3.159.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 372-DNA_Lib 372-DNA_Lib 372-DNA_Lib 372.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of Duodenum Mucosa Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27me3 ChIP-Seq read mappings from Duodenum Mucosa, Donor 159, were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.12331
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 6
BROWSER_TRACK_NAME: DM H3K27me3 59 72
BROWSER_TRACK_DESCRIPTION: BI Duodenum Mucosa Histone H3K27me3 Donor 159 Library DNA_Lib 372 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 24,999,789
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 10
FINDPEAKS_SCORE: 0.0375
FINDPEAKS_PERCENTILE: 50
HOTSPOT_SCORE: 0.1205
HOTSPOT_PERCENTILE: 60
IROC_SCORE: 0.8361
IROC_PERCENTILE: 50
POISSON_SCORE: 0.2699
POISSON_PERCENTILE: 50
MAXIMUM_REPLICATE_CORRELATION: 0.95

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

source_name: Primary duodenum mucosal tissue; DNA_Lib 372

value: Duodenum Mucosa

value: Surgery

value: presumed normal

value: Primary Tissue

value: MGH

value: 59.0 Years

value: cell/nuclei lysis

value: 10 ul bed volume

value: Histone H3K27me3

value: Branson


title: ChIP-Seq analysis of H3K4me1 in human Duodenum mucosa cells; DNA_Lib 370

description:
sample_term_id: UBERON_0000320
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 370
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.9591
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9454
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM916017_BI.Duodenum_Mucosa.H3K4me1.159.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 370-DNA_Lib 370-DNA_Lib 370-DNA_Lib 370.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of Duodenum Mucosa Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me1 ChIP-Seq on Duodenum Mucosa, Donor 159, were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.12303
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 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 24,966,597
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 14
FINDPEAKS_SCORE: 0.2963
FINDPEAKS_PERCENTILE: 71
HOTSPOT_SCORE: 0.3654
HOTSPOT_PERCENTILE: 79
IROC_SCORE: 0.9763
IROC_PERCENTILE: 71
POISSON_SCORE: 0.513
POISSON_PERCENTILE: 71
MAXIMUM_REPLICATE_CORRELATION: 0.95

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

ANALYSIS FILE NAME: GSM916017_BI.Duodenum_Mucosa.H3K4me1.159.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 370-DNA_Lib 370-DNA_Lib 370-DNA_Lib 370.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of Duodenum Mucosa Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me1 ChIP-Seq read mappings from Duodenum Mucosa, Donor 159, were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.12350
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 6
BROWSER_TRACK_NAME: DM H3K4me1 59 70
BROWSER_TRACK_DESCRIPTION: BI Duodenum Mucosa Histone H3K4me1 Donor 159 Library DNA_Lib 370 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 24,966,597
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 14
FINDPEAKS_SCORE: 0.2963
FINDPEAKS_PERCENTILE: 71
HOTSPOT_SCORE: 0.3654
HOTSPOT_PERCENTILE: 79
IROC_SCORE: 0.9763
IROC_PERCENTILE: 71
POISSON_SCORE: 0.513
POISSON_PERCENTILE: 71
MAXIMUM_REPLICATE_CORRELATION: 0.95

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

source_name: Primary duodenum mucosal tissue; DNA_Lib 370

value: genomic DNA

value: Caucasian

value: Male

value: Duodenum

value: Abcam

value: Histone H3K4me1


title: Normal Breast Sample [ATM_27]

status: Public on Feb 01 2012

first: Ana Teresa

last: Maia

state: Cambridgeshire

address: Robinson Way

department: Department of Oncology

country: United Kingdom

institute: University of Cambridge

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The bead-level data were preprocessed using BASH (Cairns et al. (2008) Bioinformatics 24(24):2921-2), a function from the beadarray package (Dunning et al (2007) Bioinformatics 23(16):2183-4) in Bioconductor, and also log base 2 transformed and quantile normalised using the beadarray package.

source_name: Normal Breast Sample

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina

extract_protocol: Total RNA was extracted from all samples using Qiazol (Invitrogen, Carlsbad, CA, USA) following manufacturer's instructions. The RNA was subsequently treated with DNaseI and repurified using acidic phenol-chlorophorm, and ethanol precipitation. DNA and RNA integrity were checked using the Agilent Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).

value: breast

value: female


title: Normal Breast Sample [ATM_36]


title: Normal Breast Sample [ATM_29]


title: Normal Breast Sample [ATM_26]


title: Normal Breast Sample [ATM_24]


title: Normal Breast Sample [ATM_31]


title: Normal Breast Sample [ATM_33]


title: Normal Breast Sample [ATM_32]


title: Exon arrays of Roadmap cell types; Fetal Intestine, Small primary tissue, day 87; DS16975-exon

status: Public on Jun 06 2012

city: Seattle

first: Northwest

last: REMC

state: WA

institute: University of Washington

description:
sample_term_id: UBERON_0002108
assay_term_id: OBI_0001463
nucleic_acid_term_id: SO_0000356
Exon profiling of NREMC cell types, these coincide with chromatin accessibility sequencing assays.
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.12952
sample alias: fIntestine_Small.H-23724d87
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.10042

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

scan_protocol: Affymetrix Gene Chip Scanner 3000

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

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

growth_protocol: Followed vendor recommendations for growth protocol/media

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

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

value: Fetal Intestine, Small

value: UW

value: fetal

value: day 87


title: Exon arrays of Roadmap cell types; Fetal Kidney, Right primary tissue, day 107; DS17144-exon

description:
sample_term_id: UBERON_0004539
assay_term_id: OBI_0001463
nucleic_acid_term_id: SO_0000356
Exon profiling of NREMC cell types, these coincide with chromatin accessibility sequencing assays.
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.12944
sample alias: fKidney_Right.H-23758d107
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.10125

value: Primary Tissue

value: Fetal Kidney, Right

value: day 107

value: Female


title: Exon arrays of Roadmap cell types; Fetal Kidney, Left primary tissue, day 107; DS17140-exon

description:
sample_term_id: UBERON_0004538
assay_term_id: OBI_0001463
nucleic_acid_term_id: SO_0000356
Exon profiling of NREMC cell types, these coincide with chromatin accessibility sequencing assays.
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.12946
sample alias: fKidney_Left.H-23758d107
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.8356

value: genomic DNA

value: Fetal Kidney, Left


title: Exon arrays of Roadmap cell types; flow sorted CD34+ Cells, year 37; DS17112-exon

description:
sample_term_id: CL_0000837
assay_term_id: OBI_0001463
nucleic_acid_term_id: SO_0000356
Exon profiling of NREMC cell types, these coincide with chromatin accessibility sequencing assays.
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.12966
sample alias: CD34.RO_01701
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.8369

value: FHCRC HEIMFELD

value: Primary Cell

value: CD34 Primary Cells

tag: markers

value: year 37

value: Male

value: Hispanic


title: Normal Breast Sample [ATM_25]

value: breast

value: female


title: Exon arrays of Roadmap cell types; Fetal Lung, Right primary tissue, day 107; DS17162-exon

description:
sample_term_id: UBERON_0002167
assay_term_id: OBI_0001463
nucleic_acid_term_id: SO_0000356
Exon profiling of NREMC cell types, these coincide with chromatin accessibility sequencing assays.
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.12936
sample alias: fLung_Right.H-23758d107
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.9916

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

value: Fetal Lung, Right

value: UW


title: Normal Breast Sample [ATM_28]


title: Exon arrays of Roadmap cell types; flow sorted CD3+ Primary Cells, from cord blood; DS17702-exon

description:
sample_term_id: CL_0000084
assay_term_id: OBI_0001463
nucleic_acid_term_id: SO_0000356
Exon profiling of NREMC cell types, these coincide with chromatin accessibility sequencing assays.
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.12964
sample alias: CD3.CB1_1-3-2011
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.7024

value: CD3 Primary Cells

value: Unknown


title: Exon arrays of Roadmap cell types; Fetal Lung, Left primary tissue, day 107; DS17154-exon

description:
sample_term_id: UBERON_0002168
assay_term_id: OBI_0001463
nucleic_acid_term_id: SO_0000356
Exon profiling of NREMC cell types, these coincide with chromatin accessibility sequencing assays.
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.12940
sample alias: fLung_Left.H-23758d107
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.8394

value: Primary Tissue

value: Fetal Lung, Left

value: fetal

value: day 107


title: Exon arrays of Roadmap cell types; Fetal Intestine, Small primary tissue, day 107; DS17150-exon

description:
sample_term_id: UBERON_0002108
assay_term_id: OBI_0001463
nucleic_acid_term_id: SO_0000356
Exon profiling of NREMC cell types, these coincide with chromatin accessibility sequencing assays.
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.12948
sample alias: fIntestine_Small.H-23758d107
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.8417

value: genomic DNA

value: Fetal Intestine, Small

value: Female


title: Normal Breast Sample [ATM_22]


title: Exon arrays of Roadmap cell types; flow sorted CD14+ Cells, year 37; DS17889-exon

description:
sample_term_id: CL_0001054
assay_term_id: OBI_0001463
nucleic_acid_term_id: SO_0000356
Exon profiling of NREMC cell types, these coincide with chromatin accessibility sequencing assays.
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.12968
sample alias: CD14.RO_01736
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.6962

value: FHCRC HEIMFELD

value: Primary Cell

value: CD14 Primary Cells

value: year 37


title: Normal Breast Sample [ATM_19]

value: breast

value: female


title: Normal Breast Sample [ATM_15]


title: Exon arrays of Roadmap cell types; flow sorted CD3+ Primary Cells, from cord blood; DS17706-exon

description:
sample_term_id: CL_0000084
assay_term_id: OBI_0001463
nucleic_acid_term_id: SO_0000356
Exon profiling of NREMC cell types, these coincide with chromatin accessibility sequencing assays.
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.12962
sample alias: CD3.CB6_1-4-2011
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.7021


title: Exon arrays of Roadmap cell types; Fetal Lung, Right primary tissue, day 91; DS17101-exon

description:
sample_term_id: UBERON_0002167
assay_term_id: OBI_0001463
nucleic_acid_term_id: SO_0000356
Exon profiling of NREMC cell types, these coincide with chromatin accessibility sequencing assays.
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.12938
sample alias: fLung_Right.H-23744d91
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.8385

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

value: Fetal Lung, Right

value: day 91


title: Normal Breast Sample [ATM_30]


title: Normal Breast Sample [ATM_23]


title: Normal Breast Sample [ATM_14]


title: Exon arrays of Roadmap cell types; flow sorted CD3+ Cells, year 37; DS17534-exon

description:
sample_term_id: CL_0000084
assay_term_id: OBI_0001463
nucleic_acid_term_id: SO_0000356
Exon profiling of NREMC cell types, these coincide with chromatin accessibility sequencing assays.
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.12958
sample alias: CD3.RO_01736
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.6984

value: CD3 Primary Cells

value: Male

value: Hispanic


title: Normal Breast Sample [ATM_20]


title: Normal Breast Sample [ATM_17]


title: Normal Breast Sample [ATM_21]


title: Exon arrays of Roadmap cell types; Fetal Heart primary tissue, day 105; DS16819-exon

description:
sample_term_id: UBERON_0000948
assay_term_id: OBI_0001463
nucleic_acid_term_id: SO_0000356
Exon profiling of NREMC cell types, these coincide with chromatin accessibility sequencing assays.
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.12954
sample alias: fHeart.H-23663d105
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.8365

value: Primary Tissue

value: Fetal Heart

value: UW

value: fetal

value: day 105


title: Normal Breast Sample [ATM_13]


title: Exon arrays of Roadmap cell types; flow sorted CD8+ Cells, year 37; DS17885-exon

description:
sample_term_id: CL_0000625
assay_term_id: OBI_0001463
nucleic_acid_term_id: SO_0000356
Exon profiling of NREMC cell types, these coincide with chromatin accessibility sequencing assays.
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.12956
sample alias: CD8.RO_01736
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.7035

value: genomic DNA

value: FHCRC HEIMFELD

value: CD8 Primary Cells


title: Normal Breast Sample [ATM_12]


title: Exon arrays of Roadmap cell types; flow sorted CD3+ Primary Cells, Mobilized, year 36; DS11148-exon

description:
sample_term_id: CL_0000084
assay_term_id: OBI_0001463
nucleic_acid_term_id: SO_0000356
Exon profiling of NREMC cell types, these coincide with chromatin accessibility sequencing assays.
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.12960
sample alias: CD3.RO_01508
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.8318

value: Primary Cell

value: Mobilized CD3 Primary Cells

value: year 36


title: Exon arrays of Roadmap cell types; Fetal Lung, Left primary tissue, day 91; DS17105-exon

description:
sample_term_id: UBERON_0002168
assay_term_id: OBI_0001463
nucleic_acid_term_id: SO_0000356
Exon profiling of NREMC cell types, these coincide with chromatin accessibility sequencing assays.
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.12942
sample alias: fLung_Left.H-23744d91
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.8399

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

value: Fetal Lung, Left

value: Female


title: Normal Breast Sample [ATM_9]

value: breast

value: female


title: Normal Breast Sample [ATM_10]


title: Exon arrays of Roadmap cell types; Fetal Intestine, Small primary tissue, day 91; DS17092-exon

description:
sample_term_id: UBERON_0002108
assay_term_id: OBI_0001463
nucleic_acid_term_id: SO_0000356
Exon profiling of NREMC cell types, these coincide with chromatin accessibility sequencing assays.
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.12950
sample alias: fIntestine_Small.H-23744d91
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.8421

value: Fetal Intestine, Small

value: day 91


title: Normal Breast Sample [ATM_8]


title: Normal Breast Sample [ATM_11]


title: ChIP-Seq analysis of H3K4me3 in human kidney cells; DNA_Lib 338

status: Public on Dec 28 2011

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: DNA_Lib 338
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8695
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9455
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM773005_BI.Adult_Kidney.H3K4me3.153.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 338-DNA_Lib 338-DNA_Lib 338-DNA_Lib 338.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Adult Kidney Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me3 ChIP-Seq on Adult Kidney, Donor 153, 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.10639
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 32,450,359
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.2968
FINDPEAKS_PERCENTILE: 61
HOTSPOT_SCORE: 0.3255
HOTSPOT_PERCENTILE: 54
IROC_SCORE: 0.9997
IROC_PERCENTILE: 76
POISSON_SCORE: 0.3645
POISSON_PERCENTILE: 48
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

ANALYSIS FILE NAME: GSM773005_BI.Adult_Kidney.H3K4me3.153.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 338-DNA_Lib 338-DNA_Lib 338-DNA_Lib 338.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Adult Kidney Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me3 ChIP-Seq read mappings from Adult Kidney, Donor 153, 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.10903
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 5
BROWSER_TRACK_NAME: AK H3K4me3 53 38
BROWSER_TRACK_DESCRIPTION: BI Adult Kidney Histone H3K4me3 Donor 153 Library DNA_Lib 338 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 32,450,359
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.2968
FINDPEAKS_PERCENTILE: 61
HOTSPOT_SCORE: 0.3255
HOTSPOT_PERCENTILE: 54
IROC_SCORE: 0.9997
IROC_PERCENTILE: 76
POISSON_SCORE: 0.3645
POISSON_PERCENTILE: 48
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

source_name: Primary kidney tissue; DNA_Lib 338

value: Adult Kidney

value: Surgery

value: NL kidney,right kidney resection for RCC

value: Caucasian

value: Male

value: Primary Tissue

value: Kidney

value: MGH

value: 50.0 Years

value: Protein A-Sepharose 4B

value: 0.5 to 3 million cells

value: cell/nuclei lysis

value: ~1 ug

value: 10 ul bed volume

value: Millipore

value: Histone H3K4me3

value: Branson


title: ChIP-Seq analysis of H3K9ac in human kidney cells; DNA_Lib 339

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: DNA_Lib 339
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8696
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9455
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM773006_BI.Adult_Kidney.H3K9ac.153.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 339-DNA_Lib 339-DNA_Lib 339-DNA_Lib 339.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Adult Kidney Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9ac ChIP-Seq on Adult Kidney, Donor 153, 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.10811
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 31,799,936
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 19
FINDPEAKS_SCORE: 0.1035
FINDPEAKS_PERCENTILE: 26
HOTSPOT_SCORE: 0.1643
HOTSPOT_PERCENTILE: 32
IROC_SCORE: 0.9854
IROC_PERCENTILE: 26
POISSON_SCORE: 0.2503
POISSON_PERCENTILE: 32
MAXIMUM_REPLICATE_CORRELATION: 0.95

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

ANALYSIS FILE NAME: GSM773006_BI.Adult_Kidney.H3K9ac.153.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 339-DNA_Lib 339-DNA_Lib 339-DNA_Lib 339.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Adult Kidney Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9ac ChIP-Seq read mappings from Adult Kidney, Donor 153, 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.11075
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 5
BROWSER_TRACK_NAME: AK H3K9ac 53 39
BROWSER_TRACK_DESCRIPTION: BI Adult Kidney Histone H3K9ac Donor 153 Library DNA_Lib 339 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 31,799,936
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 19
FINDPEAKS_SCORE: 0.1035
FINDPEAKS_PERCENTILE: 26
HOTSPOT_SCORE: 0.1643
HOTSPOT_PERCENTILE: 32
IROC_SCORE: 0.9854
IROC_PERCENTILE: 26
POISSON_SCORE: 0.2503
POISSON_PERCENTILE: 32
MAXIMUM_REPLICATE_CORRELATION: 0.95

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

source_name: Primary kidney tissue; DNA_Lib 339

value: Adult Kidney

value: genomic DNA

value: Abcam

value: Histone H3K9ac


title: Exon arrays of Roadmap cell types; Fetal Thymus primary tissue, day 105; DS16841-exon

description:
sample_term_id: UBERON_0002370
assay_term_id: OBI_0001463
nucleic_acid_term_id: SO_0000356
Exon profiling of NREMC cell types, these coincide with chromatin accessibility sequencing assays.
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.12934
sample alias: fThymus.H-23663d105
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.8478

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

value: Fetal Thymus

value: UW

value: fetal

value: day 105

value: Female


title: ChIP-Seq analysis of H3K4me1 in human kidney cells; DNA_Lib 335

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: DNA_Lib 335
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8691
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9455
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM773001_BI.Adult_Kidney.H3K4me1.153.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 335-DNA_Lib 335-DNA_Lib 335-DNA_Lib 335.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Adult Kidney Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me1 ChIP-Seq on Adult Kidney, Donor 153, 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.10802
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 24,703,910
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.0744
FINDPEAKS_PERCENTILE: 13
HOTSPOT_SCORE: 0.2048
HOTSPOT_PERCENTILE: 13
IROC_SCORE: 0.8864
IROC_PERCENTILE: 15
POISSON_SCORE: 0.3755
POISSON_PERCENTILE: 19
MAXIMUM_REPLICATE_CORRELATION: 0.91

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

ANALYSIS FILE NAME: GSM773001_BI.Adult_Kidney.H3K4me1.153.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 335-DNA_Lib 335-DNA_Lib 335-DNA_Lib 335.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Adult Kidney Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me1 ChIP-Seq read mappings from Adult Kidney, Donor 153, 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.11066
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 5
BROWSER_TRACK_NAME: AK H3K4me1 53 35
BROWSER_TRACK_DESCRIPTION: BI Adult Kidney Histone H3K4me1 Donor 153 Library DNA_Lib 335 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 24,703,910
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.0744
FINDPEAKS_PERCENTILE: 13
HOTSPOT_SCORE: 0.2048
HOTSPOT_PERCENTILE: 13
IROC_SCORE: 0.8864
IROC_PERCENTILE: 15
POISSON_SCORE: 0.3755
POISSON_PERCENTILE: 19
MAXIMUM_REPLICATE_CORRELATION: 0.91

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

source_name: Primary kidney tissue; DNA_Lib 335

value: Surgery

value: NL kidney,right kidney resection for RCC

value: Caucasian

value: Male

value: Primary Tissue

value: Kidney

value: MGH

value: 50.0 Years

value: Protein A-Sepharose 4B

value: 0.5 to 3 million cells

value: Histone H3K4me1


title: ChIP-Seq analysis of H3K27me3 in human CD45RO CD4 cells; DNA_Lib 537

description:
sample_term_id: CL_0000897
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 537
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8688
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9467
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM772998_BI.CD4_Memory_Primary_Cells.H3K27me3.Donor_100_7_pooled_leukopaks_Jan_7_2011.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 537-DNA_Lib 537-DNA_Lib 537.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of CD4 Memory Primary Cells Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27me3 ChIP-Seq on CD4 Memory Primary Cells, Donor Donor 100 7 pooled leukopaks Jan 7 2011, 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.10729
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 18,398,874
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.0078
FINDPEAKS_PERCENTILE: 14
HOTSPOT_SCORE: 0.1046
HOTSPOT_PERCENTILE: 33
IROC_SCORE: 0.5216
IROC_PERCENTILE: 6
POISSON_SCORE: 0.2103
POISSON_PERCENTILE: 31
MAXIMUM_REPLICATE_CORRELATION: 0.92

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

ANALYSIS FILE NAME: GSM772998_BI.CD4_Memory_Primary_Cells.H3K27me3.Donor_100_7_pooled_leukopaks_Jan_7_2011.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 537-DNA_Lib 537-DNA_Lib 537.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of CD4 Memory Primary Cells Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27me3 ChIP-Seq read mappings from CD4 Memory Primary Cells, Donor Donor 100 7 pooled leukopaks Jan 7 2011, 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.10993
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 5
BROWSER_TRACK_NAME: CD4M H3K27me3 00 37
BROWSER_TRACK_DESCRIPTION: BI CD4 Memory Primary Cells Histone H3K27me3 Donor 100 7 pooled leukopaks Jan 7 2011 Library DNA_Lib 537 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 18,398,874
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.0078
FINDPEAKS_PERCENTILE: 14
HOTSPOT_SCORE: 0.1046
HOTSPOT_PERCENTILE: 33
IROC_SCORE: 0.5216
IROC_PERCENTILE: 6
POISSON_SCORE: 0.2103
POISSON_PERCENTILE: 31
MAXIMUM_REPLICATE_CORRELATION: 0.92

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

source_name: Memory CD4+ T cells; DNA_Lib 537

value: BioSam 181

value: CD4 Memory Primary Cells

value: presumed normal

value: genomic DNA

value: CD45RO CD4

value: Unknown

value: Primary Cell

value: Donor 100 7 pooled leukopaks Jan 7 2011

value: Dana Farber

value: cell/nuclei lysis

value: ~1 ug

value: 10 ul bed volume

value: Millipore

value: Histone H3K27me3

value: Branson


title: Normal Breast Sample [ATM_38]

value: breast

value: female


title: Normal Breast Sample [ATM_6]


title: ChIP-Seq analysis of H3K27ac in human CD45RO CD4 cells; DNA_Lib 486

description:
sample_term_id: CL_0000897
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 486
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8687
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9464
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM772997_BI.CD4_Memory_Primary_Cells.H3K27ac.Donor_101_8_pooled_leukopaks_Jan_20_2011.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 486-DNA_Lib 486-DNA_Lib 486-DNA_Lib 486.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of CD4 Memory Primary Cells Histone H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27ac ChIP-Seq on CD4 Memory Primary Cells, Donor Donor 101 8 pooled leukopaks Jan 20 2011, 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.10684
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 12,703,793
NUMBER_OF_H3K27ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 34
FINDPEAKS_SCORE: 0.1851
FINDPEAKS_PERCENTILE: 50
HOTSPOT_SCORE: 0.2622
HOTSPOT_PERCENTILE: 53
IROC_SCORE: 0.9989
IROC_PERCENTILE: 85
POISSON_SCORE: 0.2654
POISSON_PERCENTILE: 26
MAXIMUM_REPLICATE_CORRELATION: 0.88

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

ANALYSIS FILE NAME: GSM772997_BI.CD4_Memory_Primary_Cells.H3K27ac.Donor_101_8_pooled_leukopaks_Jan_20_2011.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 486-DNA_Lib 486-DNA_Lib 486-DNA_Lib 486.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of CD4 Memory Primary Cells Histone H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27ac ChIP-Seq read mappings from CD4 Memory Primary Cells, Donor Donor 101 8 pooled leukopaks Jan 20 2011, 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.10948
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 5
BROWSER_TRACK_NAME: CD4M H3K27ac 01 86
BROWSER_TRACK_DESCRIPTION: BI CD4 Memory Primary Cells Histone H3K27ac Donor 101 8 pooled leukopaks Jan 20 2011 Library DNA_Lib 486 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 12,703,793
NUMBER_OF_H3K27ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 34
FINDPEAKS_SCORE: 0.1851
FINDPEAKS_PERCENTILE: 50
HOTSPOT_SCORE: 0.2622
HOTSPOT_PERCENTILE: 53
IROC_SCORE: 0.9989
IROC_PERCENTILE: 85
POISSON_SCORE: 0.2654
POISSON_PERCENTILE: 26
MAXIMUM_REPLICATE_CORRELATION: 0.88

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

source_name: Memory CD4+ T cells; DNA_Lib 486

value: BioSam 185

value: Protein A-Sepharose 4B

value: 0.5 to 3 million cells

value: Abcam

value: Histone H3K27ac


title: ChIP-Seq analysis of H3K36me3 in human kidney cells; DNA_Lib 337

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: DNA_Lib 337
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8690
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9455
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM773000_BI.Adult_Kidney.H3K36me3.153.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 337-DNA_Lib 337-DNA_Lib 337-DNA_Lib 337.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Adult Kidney Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K36me3 ChIP-Seq on Adult Kidney, Donor 153, 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.10706
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 30,423,110
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.0615
FINDPEAKS_PERCENTILE: 29
HOTSPOT_SCORE: 0.16
HOTSPOT_PERCENTILE: 24
IROC_SCORE: 0.8906
IROC_PERCENTILE: 29
POISSON_SCORE: 0.334
POISSON_PERCENTILE: 37
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

ANALYSIS FILE NAME: GSM773000_BI.Adult_Kidney.H3K36me3.153.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 337-DNA_Lib 337-DNA_Lib 337-DNA_Lib 337.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Adult Kidney Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K36me3 ChIP-Seq read mappings from Adult Kidney, Donor 153, 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.10970
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 5
BROWSER_TRACK_NAME: AK H3K36me3 53 37
BROWSER_TRACK_DESCRIPTION: BI Adult Kidney Histone H3K36me3 Donor 153 Library DNA_Lib 337 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 30,423,110
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.0615
FINDPEAKS_PERCENTILE: 29
HOTSPOT_SCORE: 0.16
HOTSPOT_PERCENTILE: 24
IROC_SCORE: 0.8906
IROC_PERCENTILE: 29
POISSON_SCORE: 0.334
POISSON_PERCENTILE: 37
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

source_name: Primary kidney tissue; DNA_Lib 337

value: Adult Kidney

value: Surgery

value: NL kidney,right kidney resection for RCC

value: genomic DNA

value: Caucasian

value: Male

value: Primary Tissue

value: Kidney

value: MGH

value: 50.0 Years

value: Histone H3K36me3