title: 171_CR

description: cerebellum


title: 166_CR

status: Public on Apr 25 2013

type: RNA

city: New York

first: Jun

last: Zhu

state: NY

address: One Gustave L Levy, Box 1498

department: Genetics and Genomic Sciences

country: USA

institute: Icahn Medical School at Mount Sinai

description: cerebellum

hyb_protocol: Microarrays are incubated at 40C for 48 hours in a rotating carousel. Hybridizations to custom Agilent microarrays are completed as previously described (Hughes et al.Nat Biotech (2001), 19(4):342-7). Microarrays are washed to remove non-specific hybridized sample. Afterwards, microarrays are dried in an ozone-free nitrogen chamber.

scan_protocol: Microarrays are scanned using the Agilent LP2 laser scanner. The scanner output is a Tiff file, which contains the quantitative hybridization data from each individual microarray. The Tiff files are then processed using Rosetta custom feature extraction software.

data_processing: Data were processed using the Rosetta Resolver system. Rosetta's custom feature extraction software performs error modeling before data are loaded into the Resolver system. The Resolver system performs a squeeze operation that combines replicates of the same sequence in an array while applying error weighting. The error weighting consists of adjusting for additive and multiplicative noise. A P-value is generated and propagated throughout the system. The P-value represents the probability that a gene is expressed. The Resolver system allows users to set thresholds, below which genes of a P-value are considered to be significantly expressed. The Resolver system also combines multiple arrays using a squeezing process. If multiple spots reference one sequence, summarization is performed using an error-weighted average as described in Roland Stoughton and Hongyue Dai, Statistical Combining of Cell Expression Profiles. US Patent #6,351,712, February 26, 2002.

molecule: total RNA

organism: Homo sapiens

label_protocol: Samples were amplified and labeled using a custom automated two-cycle version of the MessageAmp II kit from Ambion. Hybridizations to custom Agilent microarrays were completed as described in by Hughes et al. Nat Biotech (2001), 19(4):342-7. Sample amplification, labeling, and microarray processing were performed by the Rosetta Inpharmatics Gene Expression Laboratory in Seattle, Wash.

extract_protocol: Qiagen RNeasy spin columns with DNAse treatment  Qiagen RNeasy spin columns with DNAse treatment

tag: age

tag: tissue

value: brain

tag: gender

tag: disease

value: A

value: M

tag: pmi

tag: ph

tag: rin

tag: pres

value: LNV

tag: batch

tag: disease status


title: 168_CR

description: cerebellum

value: Dry-Ice


title: 179_CR

description: cerebellum


title: 165_CR

description: cerebellum


title: 159_CR

description: cerebellum

value: F


title: 154_CR

description: cerebellum


title: 156_CR

description: cerebellum

value: N


title: 161_CR

description: cerebellum


title: 164_CR

description: cerebellum


title: 155_CR

description: cerebellum


title: 169_CR

description: cerebellum


title: 158_CR

description: cerebellum


title: 162_CR

description: cerebellum


title: 152_CR

description: cerebellum


title: 153_CR

description: cerebellum


title: 149_CR

description: cerebellum


title: 150_CR

description: cerebellum


title: 151_CR

description: cerebellum


title: 138_CR

description: cerebellum


title: 132_CR

description: cerebellum


title: 146_CR

description: cerebellum


title: 137_CR

description: cerebellum


title: 143_CR

description: cerebellum


title: 140_CR

description: cerebellum


title: 134_CR

description: cerebellum


title: 147_CR

description: cerebellum


title: 141_CR

description: cerebellum


title: 148_CR

description: cerebellum


title: 126_CR

description: cerebellum


title: 142_CR

description: cerebellum


title: 131_CR

description: cerebellum


title: 136_CR

description: cerebellum


title: 145_CR

description: cerebellum


title: 128_CR

description: cerebellum


title: 139_CR

description: cerebellum


title: 144_CR

description: cerebellum


title: 125_CR

description: cerebellum


title: 122_CR

description: cerebellum


title: 119_CR

description: cerebellum


title: 133_CR

description: cerebellum


title: 116_CR

description: cerebellum


title: 129_CR

description: cerebellum


title: 120_CR

description: cerebellum


title: 104_CR

description: cerebellum


title: 127_CR

description: cerebellum


title: 110_CR

description: cerebellum


title: 113_CR

description: cerebellum


title: 107_CR

description: cerebellum


title: 135_CR

description: cerebellum


title: 111_CR

description: cerebellum


title: 130_CR

description: cerebellum


title: 114_CR

description: cerebellum


title: 117_CR

description: cerebellum


title: 105_CR

description: cerebellum


title: 102_CR

description: cerebellum


title: 115_CR

description: cerebellum


title: 108_CR

description: cerebellum


title: 112_CR

description: cerebellum


title: 123_CR

description: cerebellum


title: 118_CR

description: cerebellum


title: 124_CR

description: cerebellum


title: 109_CR

description: cerebellum


title: 106_CR

description: cerebellum


title: 103_CR

description: cerebellum


title: 100_CR

description: cerebellum


title: 97_CR

description: cerebellum


title: 95_CR

description: cerebellum


title: 99_CR

description: cerebellum


title: 88_CR

description: cerebellum


title: 90_CR

description: cerebellum


title: 89_CR

description: cerebellum


title: 85_CR

description: cerebellum


title: 94_CR

description: cerebellum


title: 82_CR

description: cerebellum


title: 83_CR

description: cerebellum


title: 77_CR

description: cerebellum


title: 98_CR

description: cerebellum


title: 93_CR

description: cerebellum


title: 74_CR

description: cerebellum


title: 79_CR

description: cerebellum


title: 92_CR

description: cerebellum


title: 86_CR

description: cerebellum


title: 81_CR

description: cerebellum


title: 78_CR

description: cerebellum


title: 96_CR

description: cerebellum


title: 73_CR

description: cerebellum


title: 91_CR

description: cerebellum


title: 84_CR

description: cerebellum


title: 75_CR

description: cerebellum


title: 80_CR

description: cerebellum


title: 87_CR

description: cerebellum


title: 76_CR

description: cerebellum


title: 121_CR

description: cerebellum


title: 69_CR

description: cerebellum


title: 51_CR

description: cerebellum


title: 65_CR

description: cerebellum


title: 72_CR

description: cerebellum


title: 49_CR

description: cerebellum


title: 71_CR

description: cerebellum


title: 57_CR

description: cerebellum


title: 64_CR

description: cerebellum


title: 45_CR

description: cerebellum


title: 56_CR

description: cerebellum


title: 48_CR

description: cerebellum


title: 46_CR

description: cerebellum


title: 58_CR

description: cerebellum


title: 54_CR

description: cerebellum


title: 55_CR

description: cerebellum


title: 62_CR

description: cerebellum


title: 66_CR

description: cerebellum


title: 59_CR

description: cerebellum


title: 63_CR

description: cerebellum


title: 67_CR

description: cerebellum


title: 70_CR

description: cerebellum


title: 52_CR

description: cerebellum


title: 61_CR

description: cerebellum


title: 47_CR

description: cerebellum


title: 50_CR

description: cerebellum


title: 44_CR

description: cerebellum


title: 60_CR

description: cerebellum


title: 68_CR

description: cerebellum


title: 53_CR

description: cerebellum


title: 101_CR

description: cerebellum


title: 43_CR

description: cerebellum


title: 41_CR

description: cerebellum


title: 38_CR

description: cerebellum


title: 35_CR

description: cerebellum


title: 28_CR

description: cerebellum


title: 34_CR

description: cerebellum


title: 24_CR

description: cerebellum


title: 31_CR

description: cerebellum


title: 37_CR

description: cerebellum


title: 27_CR

description: cerebellum


title: 36_CR

description: cerebellum


title: 32_CR

description: cerebellum


title: 42_CR

description: cerebellum


title: 25_CR

description: cerebellum


title: 26_CR

description: cerebellum


title: 39_CR

description: cerebellum


title: 23_CR

description: cerebellum


title: 30_CR

description: cerebellum


title: 18_CR

description: cerebellum


title: 33_CR

description: cerebellum


title: 29_CR

description: cerebellum


title: 20_CR

description: cerebellum


title: 40_CR

description: cerebellum


title: 19_CR

description: cerebellum


title: 16_CR

description: cerebellum


title: 21_CR

description: cerebellum


title: 14_CR

description: cerebellum


title: 22_CR

description: cerebellum


title: 15_CR

description: cerebellum


title: 17_CR

description: cerebellum


title: 13_CR

description: cerebellum


title: ChIP-Seq analysis of H3K9ac in human hLiver cells; Lib:XZ:20100104:05--ChIP:XZ:20091228:05:hLiver:H3K9Ac

status: Public on Nov 12 2010

type: SRA

city: Cambridge

first: BROAD

last: INSTITUTE

state: MA

institute: Broad Institute

description:
sample_term_id: UBERON_0002107
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:XZ:20100104:05--ChIP:XZ:20091228:05:hLiver:H3K9Ac
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3214
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3345
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************
BED and WIG files were replaced on April 29, 2014

library_source: genomic

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

ANALYSIS FILE NAME: GSM621630_BI.Adult_Liver.H3K9ac.4.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100104:05--ChIP:XZ:20091228:05:hLiver:H3K9Ac.hg19.level.1
ANALYSIS TITLE: Mapping of Adult Liver Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9ac ChIP-Seq on Adult Liver, Donor 4 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.4641
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED: 35
FINDPEAKS_SCORE: 0.1908
FINDPEAKS_PERCENTILE: 51
HOTSPOT_SCORE: 0.2282
HOTSPOT_PERCENTILE: 43
IROC_SCORE: 0.9921
IROC_PERCENTILE: 69
POISSON_SCORE: 0.4035
POISSON_PERCENTILE: 60

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

ANALYSIS FILE NAME: GSM621630_BI.Adult_Liver.H3K9ac.4.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100104:05--ChIP:XZ:20091228:05:hLiver:H3K9Ac.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Adult Liver Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9ac ChIP-Seq read mappings from Adult Liver, Donor 4 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.4915
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: AL H3K9ac 4
BROWSER_TRACK_DESCRIPTION: BI Adult Liver Histone H3K9ac Donor 4 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED: 35
FINDPEAKS_SCORE: 0.1908
FINDPEAKS_PERCENTILE: 51
HOTSPOT_SCORE: 0.2282
HOTSPOT_PERCENTILE: 43
IROC_SCORE: 0.9921
IROC_PERCENTILE: 69
POISSON_SCORE: 0.4035
POISSON_PERCENTILE: 60

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

molecule: genomic DNA

source_name: normal adult liver; Lib:XZ:20100104:05--ChIP:XZ:20091228:05:hLiver:H3K9Ac

extract_protocol: Library construction protocol: Single read - Illumina

value: surgery

tag: molecule

value: genomic DNA

value: Adult Liver

value: Unknown

value: Primary Tissue

value: liver

value: MGH Pathology

value: Protein A-Sepharose 4B

value: 10 million cells

value: SDS lysis

value: 70 ul bed volume

value: Abcam

value: Histone H3K9ac

value: Bioruptor


title: 10_CR

description: cerebellum

value: brain

value: A

value: LNV


title: 12_CR

description: cerebellum

value: M


title: human primary osteoblast passage 8 6 hours treated (1,25D3) Set2

status: Public on Aug 01 2012

city: Coral Gables

first: Thomas

last: Lisse

state: Florida

address: 1801 Memorial Drive

department: Biology

institute: University of Miami

hyb_protocol: standard Exiqon  protocol

scan_protocol: standard Exiqon  protocol

data_processing: Raw data were re-scaled to account for differences in individual array signal intensities (MIDAS). Statistical Analysis of Microarrays (SAM) was performed (MEV), two class unpaired analysis, arrays sorted into two groups. For normalization of raw data, we utilized the locally weighted regression method to re-scale to account for system-related variations in individual array signal intensities to reveal biological variations using the Midas software.

label_protocol: standard Exiqon  protocol

extract_protocol: standard Exiqon  protocol

tag: source tissue

value: femur

tag: cell type

value: primary osteoblast

tag: treatment


title: 6_CR

description: cerebellum

value: F


title: human primary osteoblast passage 8 6 hours vehicle (ethanol) Set3

value: ethanol


title: ChIP-Seq analysis of WCE in human hLiver cells; Lib:XZ:20100104:07--ChIP:XZ:20091228:07:hLiver:WCE

description:
sample_term_id: UBERON_0002107
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:XZ:20100104:07--ChIP:XZ:20091228:07:hLiver:WCE
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3213
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3345
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************
BED and WIG files were replaced on April 29, 2014

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

ANALYSIS FILE NAME: GSM621629_BI.Adult_Liver.Input.4.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100104:07--ChIP:XZ:20091228:07:hLiver:WCE.hg19.level.1
ANALYSIS TITLE: Mapping of Adult Liver ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on Adult Liver, Donor 4 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.4568
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED: 67
FINDPEAKS_SCORE: 0.0099
FINDPEAKS_PERCENTILE: 51
HOTSPOT_SCORE: 0.0846
HOTSPOT_PERCENTILE: 68
IROC_SCORE: 0.236
IROC_PERCENTILE: 21
POISSON_SCORE: 0.1851
POISSON_PERCENTILE: 16

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

ANALYSIS FILE NAME: GSM621629_BI.Adult_Liver.Input.4.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100104:07--ChIP:XZ:20091228:07:hLiver:WCE.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Adult Liver ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from Adult Liver, Donor 4 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.4842
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: AL Input 4
BROWSER_TRACK_DESCRIPTION: BI Adult Liver ChIP-Seq Input Donor 4 EA Release 2

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED: 67
FINDPEAKS_SCORE: 0.0099
FINDPEAKS_PERCENTILE: 51
HOTSPOT_SCORE: 0.0846
HOTSPOT_PERCENTILE: 68
IROC_SCORE: 0.236
IROC_PERCENTILE: 21
POISSON_SCORE: 0.1851
POISSON_PERCENTILE: 16

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

source_name: normal adult liver; Lib:XZ:20100104:07--ChIP:XZ:20091228:07:hLiver:WCE

value: surgery

value: genomic DNA

value: Adult Liver

value: Unknown

value: Primary Tissue

value: liver

value: standard

value: ChIP-Seq Input

value: Input


title: ChIP-Seq analysis of H3K9me3 in hLiver cells; Lib:XZ:20100827:03--ChIP:XZ:20100824:03:hLiver:H3K9Me3

status: Public on Mar 31 2011

description:
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:XZ:20100827:03--ChIP:XZ:20100824:03:hLiver:H3K9Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5727
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3345
****************
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: GSM669986_BI.Adult_Liver.H3K9me3.4.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100827:03--ChIP:XZ:20100824:03:hLiver:H3K9Me3.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Adult Liver Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9me3 ChIP-Seq on Adult Liver, Donor 4 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.6459
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 3

QUALITY SCORES:
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 60
FINDPEAKS_SCORE: 0.0918
FINDPEAKS_PERCENTILE: 62
HOTSPOT_SCORE: 0.1457
HOTSPOT_PERCENTILE: 54
IROC_SCORE: 0.8709
IROC_PERCENTILE: 50
POISSON_SCORE: 0.3566
POISSON_PERCENTILE: 73

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

ANALYSIS FILE NAME: GSM669986_BI.Adult_Liver.H3K9me3.4.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100827:03--ChIP:XZ:20100824:03:hLiver:H3K9Me3.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of Adult Liver Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9me3 ChIP-Seq read mappings from Adult Liver, Donor 4 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.6669
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 3
BROWSER_TRACK_NAME: AL H3K9me3 4
BROWSER_TRACK_DESCRIPTION: BI Adult Liver Histone H3K9me3 Donor 4 Library Lib:XZ:20100827:03--ChIP:XZ:20100824:03:hLiver:H3K9Me3 EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 60
FINDPEAKS_SCORE: 0.0918
FINDPEAKS_PERCENTILE: 62
HOTSPOT_SCORE: 0.1457
HOTSPOT_PERCENTILE: 54
IROC_SCORE: 0.8709
IROC_PERCENTILE: 50
POISSON_SCORE: 0.3566
POISSON_PERCENTILE: 73

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

source_name: normal adult liver; Lib:XZ:20100827:03--ChIP:XZ:20100824:03:hLiver:H3K9Me3

tag: sample alias

tag: sample common name

value: MGH Pathology

value: Protein A-Sepharose 4B

value: 10 million cells

value: SDS lysis

value: 70 ul bed volume

value: Abcam

value: Histone H3K9me3

value: Bioruptor


title: human primary osteoblast passage 8 6 hours vehicle (ethanol) Set2

value: femur

value: primary osteoblast

value: ethanol


title: 8_CR

description: cerebellum

value: brain

value: A

value: F

value: LNV


title: 7_CR

description: cerebellum

value: N

value: M


title: 9_CR

description: cerebellum


title: 11_CR

description: cerebellum


title: ChIP-Seq analysis of H3K27me3 in human hLiver cells; 61C9RAAXX100224-6-S

status: Public on Apr 28 2010

description:
sample_term_id: UBERON_0002107
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Solexa-20758
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.2522
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.2561
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************
BED and WIG files were replaced on April 29, 2014

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

ANALYSIS FILE NAME: GSM537698_BI.Adult_Liver.H3K27me3.3.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 61C9RAAXX100224-6-S.hg19.level.1
ANALYSIS TITLE: Mapping of Adult Liver Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27me3 ChIP-Seq on Adult Liver, Donor 3.0 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.4702
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED: 52
FINDPEAKS_SCORE: 0.1468
FINDPEAKS_PERCENTILE: 52
HOTSPOT_SCORE: 0.3609
HOTSPOT_PERCENTILE: 90
IROC_SCORE: 0.9408
IROC_PERCENTILE: 65
POISSON_SCORE: 0.6943
POISSON_PERCENTILE: 100

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

ANALYSIS FILE NAME: GSM537698_BI.Adult_Liver.H3K27me3.3.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 61C9RAAXX100224-6-S.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Adult Liver Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27me3 ChIP-Seq read mappings from Adult Liver, Donor 3.0 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.4976
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: AL H3K27me3 3.0
BROWSER_TRACK_DESCRIPTION: BI Adult Liver Histone H3K27me3 Donor 3.0 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED: 52
FINDPEAKS_SCORE: 0.1468
FINDPEAKS_PERCENTILE: 52
HOTSPOT_SCORE: 0.3609
HOTSPOT_PERCENTILE: 90
IROC_SCORE: 0.9408
IROC_PERCENTILE: 65
POISSON_SCORE: 0.6943
POISSON_PERCENTILE: 100

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

source_name: normal adult liver; 61C9RAAXX100224-6-S

value: genomic DNA

value: MGH Pathology

value: Primary Tissue

value: liver

value: surgery

value: Female

value: Histone H3K27me3

value: Millipore


title: ChIP-Seq analysis of H3K9me3 in human hLiver cells; 61C9RAAXX100224-8-S

description:
sample_term_id: UBERON_0002107
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Solexa-20740
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.2519
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.2561
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************
BED and WIG files were replaced on April 29, 2014

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

ANALYSIS FILE NAME: GSM537695_BI.Adult_Liver.H3K9me3.3.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 61C9RAAXX100224-8-S.hg19.level.1
ANALYSIS TITLE: Mapping of Adult Liver Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9me3 ChIP-Seq on Adult Liver, Donor 3.0 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.4727
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED: 59
FINDPEAKS_SCORE: 0.0724
FINDPEAKS_PERCENTILE: 44
HOTSPOT_SCORE: 0.1451
HOTSPOT_PERCENTILE: 44
IROC_SCORE: 0.7553
IROC_PERCENTILE: 31
POISSON_SCORE: 0.4323
POISSON_PERCENTILE: 64

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

ANALYSIS FILE NAME: GSM537695_BI.Adult_Liver.H3K9me3.3.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 61C9RAAXX100224-8-S.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Adult Liver Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9me3 ChIP-Seq read mappings from Adult Liver, Donor 3.0 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.5001
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: AL H3K9me3 3.0
BROWSER_TRACK_DESCRIPTION: BI Adult Liver Histone H3K9me3 Donor 3.0 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED: 59
FINDPEAKS_SCORE: 0.0724
FINDPEAKS_PERCENTILE: 44
HOTSPOT_SCORE: 0.1451
HOTSPOT_PERCENTILE: 44
IROC_SCORE: 0.7553
IROC_PERCENTILE: 31
POISSON_SCORE: 0.4323
POISSON_PERCENTILE: 64

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

source_name: normal adult liver; 61C9RAAXX100224-8-S

value: Histone H3K9me3

value: SDS lysis

value: Bioruptor

value: 10 million cells

value: Protein A-Sepharose 4B

value: 70 ul bed volume

value: Abcam


title: human primary osteoblast passage 8 6 hours vehicle (ethanol) Set1

value: femur

value: primary osteoblast

value: ethanol


title: human primary osteoblast passage 8 6 hours treated (1,25D3) Set3


title: ChIP-Seq analysis of H3K9ac in human hLiver cells; 61GKJAAXX100226-2-S

description:
sample_term_id: UBERON_0002107
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Solexa-20731
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.2529
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.2561
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************
BED and WIG files were replaced on April 29, 2014

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

ANALYSIS FILE NAME: GSM537705_BI.Adult_Liver.H3K9ac.3.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 61GKJAAXX100226-2-S.hg19.level.1
ANALYSIS TITLE: Mapping of Adult Liver Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9ac ChIP-Seq on Adult Liver, Donor 3.0 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.4759
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED: 35
FINDPEAKS_SCORE: 0.1017
FINDPEAKS_PERCENTILE: 20
HOTSPOT_SCORE: 0.1628
HOTSPOT_PERCENTILE: 29
IROC_SCORE: 0.9853
IROC_PERCENTILE: 54
POISSON_SCORE: 0.3224
POISSON_PERCENTILE: 23

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

ANALYSIS FILE NAME: GSM537705_BI.Adult_Liver.H3K9ac.3.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 61GKJAAXX100226-2-S.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Adult Liver Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9ac ChIP-Seq read mappings from Adult Liver, Donor 3.0 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.5033
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: AL H3K9ac 3.0
BROWSER_TRACK_DESCRIPTION: BI Adult Liver Histone H3K9ac Donor 3.0 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED: 35
FINDPEAKS_SCORE: 0.1017
FINDPEAKS_PERCENTILE: 20
HOTSPOT_SCORE: 0.1628
HOTSPOT_PERCENTILE: 29
IROC_SCORE: 0.9853
IROC_PERCENTILE: 54
POISSON_SCORE: 0.3224
POISSON_PERCENTILE: 23

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

source_name: normal adult liver; 61GKJAAXX100226-2-S

value: genomic DNA

value: MGH Pathology

value: Histone H3K9ac


title: 3_CR

description: cerebellum

value: brain

value: N

value: M

value: LNV


title: 2_CR

description: cerebellum

value: A

value: F


title: 5_CR

description: cerebellum


title: ChIP-Seq analysis of WCE in hLiver cells; Lib:RI:20100105:11--ChIP:MK:20100104:11:hLiver:WCE

description:
sample_term_id: UBERON_0002107
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:RI:20100105:11--ChIP:MK:20100104:11:hLiver:WCE
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5651
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3350
****************
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: GSM669910_BI.Adult_Liver.Input.5.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:RI:20100105:11--ChIP:MK:20100104:11:hLiver:WCE.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Adult Liver ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on Adult Liver, Donor 5 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.6451
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 3

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 61
FINDPEAKS_SCORE: 0.0073
FINDPEAKS_PERCENTILE: 80
HOTSPOT_SCORE: 0.0242
HOTSPOT_PERCENTILE: 73
IROC_SCORE: 0.0
IROC_PERCENTILE: 38
POISSON_SCORE: 0.0655
POISSON_PERCENTILE: 70

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

ANALYSIS FILE NAME: GSM669910_BI.Adult_Liver.Input.5.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:RI:20100105:11--ChIP:MK:20100104:11:hLiver:WCE.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of Adult Liver ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from Adult Liver, Donor 5 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.6661
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 3
BROWSER_TRACK_NAME: AL Input 5
BROWSER_TRACK_DESCRIPTION: BI Adult Liver ChIP-Seq Input Donor 5 Library Lib:RI:20100105:11--ChIP:MK:20100104:11:hLiver:WCE EA Release 3

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 61
FINDPEAKS_SCORE: 0.0073
FINDPEAKS_PERCENTILE: 80
HOTSPOT_SCORE: 0.0242
HOTSPOT_PERCENTILE: 73
IROC_SCORE: 0.0
IROC_PERCENTILE: 38
POISSON_SCORE: 0.0655
POISSON_PERCENTILE: 70

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

source_name: normal adult liver; Lib:RI:20100105:11--ChIP:MK:20100104:11:hLiver:WCE

value: Adult Liver

value: surgery

value: Unknown

value: Primary Tissue

value: liver

value: standard

value: SDS lysis

value: ChIP-Seq Input

value: Input

value: Bioruptor


title: ChIP-Seq analysis of WCE in hLiver cells; Lib:RI:20091217:05--ChIP:MK:20091202:05:hLiver:WCE

description:
sample_term_id: UBERON_0002107
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:RI:20091217:05--ChIP:MK:20091202:05:hLiver:WCE
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5749
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5941
****************
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: GSM670008_BI.Adult_Liver.Input.3.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:RI:20091217:05--ChIP:MK:20091202:05:hLiver:WCE.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Adult Liver ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on Adult Liver, Donor 3 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.6447
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 3

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 61
FINDPEAKS_SCORE: 0.0067
FINDPEAKS_PERCENTILE: 53
HOTSPOT_SCORE: 0.0183
HOTSPOT_PERCENTILE: 67
IROC_SCORE: 0.0
IROC_PERCENTILE: 38
POISSON_SCORE: 0.0553
POISSON_PERCENTILE: 53

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

ANALYSIS FILE NAME: GSM670008_BI.Adult_Liver.Input.3.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:RI:20091217:05--ChIP:MK:20091202:05:hLiver:WCE.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of Adult Liver ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from Adult Liver, Donor 3 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.6657
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 3
BROWSER_TRACK_NAME: AL Input 3
BROWSER_TRACK_DESCRIPTION: BI Adult Liver ChIP-Seq Input Donor 3 Library Lib:RI:20091217:05--ChIP:MK:20091202:05:hLiver:WCE EA Release 3

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 61
FINDPEAKS_SCORE: 0.0067
FINDPEAKS_PERCENTILE: 53
HOTSPOT_SCORE: 0.0183
HOTSPOT_PERCENTILE: 67
IROC_SCORE: 0.0
IROC_PERCENTILE: 38
POISSON_SCORE: 0.0553
POISSON_PERCENTILE: 53

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

source_name: normal adult liver; Lib:RI:20091217:05--ChIP:MK:20091202:05:hLiver:WCE

value: genomic DNA

value: MGH Pathology


title: 4_CR

description: cerebellum

value: brain

value: N


title: human primary osteoblast passage 8 6 hours treated (1,25D3) Set1

value: femur

value: primary osteoblast


title: St.Clair_1-67_282_Kin-0_0.30mM-SA-in-0.02%-silwet_Rep1_ATH1

status: Public on Jan 08 2007

city: Loughborough

last: Nottingham Arabidopsis Stock Centre (NASC)

address: Sutton Bonington Campus

department: School of Biosciences, University of Nottingham

country: United Kingdom

description: Biological replicate 1

data_processing: The data were analysed using Affymetrix Microarray Suite 5.0 (MAS5)

label: biotin

organism: Arabidopsis thaliana

source_name: Kin-0, 0.30 mM SA in 0.02% silwet, 28hr

tag: ecotype

value: 0.30 mM SA in 0.02% silwet

tag: time point

value: 28 hr post-treatment


title: 1_CR

description: cerebellum

tag: age

tag: tissue

value: A

value: M

value: LNV