title: ChIP-Seq analysis of H3K4me1 in human Mobilized CD34 cells; DNA_Lib 251

status: Public on Dec 05 2011

description:
sample_term_id: CL_0000837
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 251
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.7085
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.2407
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM706845_BI.Mobilized_CD34_Primary_Cells.H3K4me1.RO_01480.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 251.hg19.level.1.release.4
ANALYSIS TITLE: Mapping of Mobilized CD34 Primary Cells Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me1 ChIP-Seq on Mobilized CD34 Primary Cells, Donor RO 01480 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.8242
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 18,630,364
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 12
FINDPEAKS_SCORE: 0.6282
FINDPEAKS_PERCENTILE: 85
HOTSPOT_SCORE: 0.6132
HOTSPOT_PERCENTILE: 85
IROC_SCORE: 0.9997
IROC_PERCENTILE: 92
POISSON_SCORE: 0.6828
POISSON_PERCENTILE: 85
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM706845_BI.Mobilized_CD34_Primary_Cells.H3K4me1.RO_01480.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 251.hg19.level.2.release.4
ANALYSIS TITLE: Raw Signal Density Graphs of Mobilized CD34 Primary Cells Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me1 ChIP-Seq read mappings from Mobilized CD34 Primary Cells, Donor RO 01480 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.8269
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 4
BROWSER_TRACK_NAME: MCD34 H3K4me1 80 51
BROWSER_TRACK_DESCRIPTION: BI Mobilized CD34 Primary Cells Histone H3K4me1 Donor RO 01480 Library DNA_Lib 251 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 18,630,364
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 12
FINDPEAKS_SCORE: 0.6282
FINDPEAKS_PERCENTILE: 85
HOTSPOT_SCORE: 0.6132
HOTSPOT_PERCENTILE: 85
IROC_SCORE: 0.9997
IROC_PERCENTILE: 92
POISSON_SCORE: 0.6828
POISSON_PERCENTILE: 85
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

source_name: flow sorted CD34+ cells from cord blood; DNA_Lib 251

value: CD34 Primary Cells

value: FHCRC HEIMFELD

value: Primary Cell

value: 27 years

value: Female

value: Caucasian

value: 10 million cells

value: SDS lysis

value: 70 ul bed volume

value: Abcam

value: Histone H3K4me1

value: Bioruptor


title: ChIP-Seq analysis of H3K4me1 in human CD45RA CD8 cells; DNA_Lib 671

status: Public on Dec 28 2011

type: SRA

city: Cambridge

first: BROAD

last: INSTITUTE

state: MA

country: USA

institute: Broad Institute

description:
sample_term_id: CL_0000625
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 671
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8543
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9463
****************
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: GSM772853_BI.CD8_Naive_Primary_Cells.H3K4me1.Donor_100_7_pooled_leukopaks_Jan_7_2011.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 671-DNA_Lib 671-DNA_Lib 671.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of CD8 Naive Primary Cells Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me1 ChIP-Seq on CD8 Naive 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.10617
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: 21,232,424
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.2652
FINDPEAKS_PERCENTILE: 54
HOTSPOT_SCORE: 0.3017
HOTSPOT_PERCENTILE: 35
IROC_SCORE: 0.9919
IROC_PERCENTILE: 72
POISSON_SCORE: 0.3915
POISSON_PERCENTILE: 24
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

ANALYSIS FILE NAME: GSM772853_BI.CD8_Naive_Primary_Cells.H3K4me1.Donor_100_7_pooled_leukopaks_Jan_7_2011.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 671-DNA_Lib 671-DNA_Lib 671.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of CD8 Naive Primary Cells Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me1 ChIP-Seq read mappings from CD8 Naive 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.10881
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: CD8N H3K4me1 00 71
BROWSER_TRACK_DESCRIPTION: BI CD8 Naive Primary Cells Histone H3K4me1 Donor 100 7 pooled leukopaks Jan 7 2011 Library DNA_Lib 671 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 21,232,424
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.2652
FINDPEAKS_PERCENTILE: 54
HOTSPOT_SCORE: 0.3017
HOTSPOT_PERCENTILE: 35
IROC_SCORE: 0.9919
IROC_PERCENTILE: 72
POISSON_SCORE: 0.3915
POISSON_PERCENTILE: 24
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

molecule: genomic DNA

organism: Homo sapiens

source_name: Naive CD8+ T cells; DNA_Lib 671

extract_protocol: Library construction protocol: Single read - Illumina

tag: sample alias

value: BioSam 184

tag: sample common name

value: CD8 Naive Primary Cells

value: presumed normal

tag: molecule

value: genomic DNA

tag: disease

tag: markers

value: CD8 Naive Primary Cell

value: Unknown

value: Donor 100 7 pooled leukopaks Jan 7 2011

value: Dana Farber

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: Branson


title: Embryo-injected-EXP1-rep6

status: Public on Dec 01 2011

type: RNA

city: San Francisco

first: Marcus

last: Breese

state: CA

address: 1550 Fourth St, 382

institute: UCSF

description: Gene expression data from whole embryo

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 17 hr at 45C on Xenopus Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station.

scan_protocol: GeneChips were scanned using the standard Affymetrix protocol.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 1000.

label: biotin

molecule: total RNA

organism: Xenopus laevis

source_name: Nkx2-5/GFP injected_EXP1

label_protocol: Biotinylated cRNA were prepared according to the standard 2-cycle Affymetrix protocol from 100ng of total RNA (Expression Analysis Technical Manual, Affymetrix).

extract_protocol: Total RNA was collected by homogenization in Invitrogen TRIzol reagent and further purified using an Qiagen RNeasy micro kit.

tag: development stage

tag: tissue

value: whole embryo

tag: sample origin/type

value: single embryo


title: Embryo-injected-EXP1-rep5

description: Gene expression data from whole embryo


title: Embryo-head-EXP2-rep4-pooled

description: Gene expression data from pooled heads

source_name: no treatment_EXP2

value: head section

value: pooled embryos


title: Embryo-injected-EXP1-rep4

description: Gene expression data from whole embryo


title: Embryo-injected-EXP1-rep1

description: Gene expression data from whole embryo


title: Embryo-control-EXP1-rep5

description: Gene expression data from whole embryo

source_name: GFP injected_EXP1


title: Embryo-head-EXP2-rep2

description: Gene expression data from head


title: Embryo-control-EXP1-rep6

description: Gene expression data from whole embryo


title: Embryo-tail-EXP2-rep3

description: Gene expression data from tail

value: tail section


title: Embryo-tail-EXP2-rep4-pooled

description: Gene expression data from pooled tails


title: Embryo-control-EXP1-rep2

description: Gene expression data from whole embryo


title: Embryo-tail-EXP2-rep2

description: Gene expression data from tail


title: Embryo-control-EXP1-rep1

description: Gene expression data from whole embryo


title: Embryo-injected-EXP1-rep3

description: Gene expression data from whole embryo


title: Embryo-head-EXP2-rep1

description: Gene expression data from head


title: Embryo-control-EXP1-rep4

description: Gene expression data from whole embryo


title: Embryo-head-EXP2-rep3

description: Gene expression data from head


title: Embryo-control-EXP1-rep3

description: Gene expression data from whole embryo


title: ChIP-Seq analysis of H3K4me1 in hLiver cells; Lib:XZ:20100827:04--ChIP:XZ:20100824:04:hLiver:H3K4Me1

status: Public on Mar 31 2011

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:20100827:04--ChIP:XZ:20100824:04:hLiver:H3K4Me1
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5713
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: GSM669972_BI.Adult_Liver.H3K4me1.4.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100827:04--ChIP:XZ:20100824:04:hLiver:H3K4Me1.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Adult Liver Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me1 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.6491
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 3

QUALITY SCORES:
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 50
FINDPEAKS_SCORE: 0.4242
FINDPEAKS_PERCENTILE: 68
HOTSPOT_SCORE: 0.4334
HOTSPOT_PERCENTILE: 64
IROC_SCORE: 0.9962
IROC_PERCENTILE: 75
POISSON_SCORE: 0.5533
POISSON_PERCENTILE: 61

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

ANALYSIS FILE NAME: GSM669972_BI.Adult_Liver.H3K4me1.4.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100827:04--ChIP:XZ:20100824:04:hLiver:H3K4Me1.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of Adult Liver Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me1 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.6701
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 H3K4me1 4
BROWSER_TRACK_DESCRIPTION: BI Adult Liver Histone H3K4me1 Donor 4 Library Lib:XZ:20100827:04--ChIP:XZ:20100824:04:hLiver:H3K4Me1 EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 50
FINDPEAKS_SCORE: 0.4242
FINDPEAKS_PERCENTILE: 68
HOTSPOT_SCORE: 0.4334
HOTSPOT_PERCENTILE: 64
IROC_SCORE: 0.9962
IROC_PERCENTILE: 75
POISSON_SCORE: 0.5533
POISSON_PERCENTILE: 61

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

source_name: normal adult liver; Lib:XZ:20100827:04--ChIP:XZ:20100824:04:hLiver:H3K4Me1

value: Adult Liver

value: surgery

value: Primary Tissue

value: liver

value: MGH Pathology

value: 10 million cells

value: SDS lysis

value: 70 ul bed volume

value: Abcam

value: Histone H3K4me1

value: Bioruptor


title: S100A8/control, 4hr, replicate 1

status: Public on Nov 20 2011

city: Suzhou

first: Yiqiang

last: Wang

state: Jiangsu

address: 111 Renai Road

country: China

institute: Xi'an Jiaotong-Liverpool University

description:
4 hour,_replicate 1
Agilent Feature Extraction file:
251485060959_S01_GE2_107_Sep09_1_1.txt
Processed data file: 4hr_rep1.txt

hyb_protocol: Each Slide was hybridized with 825ng Cy3-labeled cRNA and 825ng Cy-5 labeled cRNA using Gene Expression Hybridization Kit (Cat#5188-5242, Agilent technologies, Santa Clara, CA, US)in Hybridization Oven (Cat#G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US)with Gene Expression Wash Buffer Kit (Cat#5188-5327, Agilent technologies, Santa Clara, CA, US), Stabilization and Drying Solution (Cat#5185-5979, Agilent technologies, Santa Clara, CA, US) followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565BA, Agilent technologies, Santa Clara, CA, US)

data_processing: The scanned images were analyzed with Feature Extraction software10.7 (Agilent technologies, Santa Clara, CA, US)with default settings.

source_name: S100A8 treated HUVEC

label_protocol: Total RNA were amplified and labeled by Low RNA Input Linear Amplification kit (Cat#5184-3523, Agilent technologies, Santa Clara, CA, US), 5-(3-aminoallyl)-UTP (Cat#AM8436, Ambion, Austin, TX, US), Cy3 NHS ester (Cat#PA13105, GE healthcare Biosciences, Pittsburgh, PA, US) ，Cy5 NHS ester (Cat#PA15100, GE healthcare Biosciences, Pittsburgh, PA, US)followed the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany).

growth_protocol: Human vascular endothelial cells (HUVECs) were maintained in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% heat-inactivated fetal bovine serum (FBS)

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy micro kit (Cat#74004, QIAGEN, GmBH, Germany)and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: S100A8 was added to 10ug/mL

tag: cell line

value: HUVEC

tag: agent

tag: time

value: 4 hour

source_name: control HUVEC

value: control


title: S100A8/control, 24hr, replicate 3

description:
24 hour,_replicate 3
Agilent Feature Extraction file:
251485060960_S01_GE2_107_Sep09_1_2.txt
Processed data file: 24hr_rep3.txt

value: 24 hour


title: S100A8/control, 4hr, replicate 3

description:
4 hour,_replicate 3
Agilent Feature Extraction file:
251485060959_S01_GE2_107_Sep09_1_3.txt
Processed data file: 4hr_rep3.txt


title: S100A8/control, 24hr, replicate 1

description:
24 hour,_replicate 1
Agilent Feature Extraction file:
251485060959_S01_GE2_107_Sep09_1_4.txt
Processed data file: 24hr_rep1.txt


title: Dual, normal-Cys3, degenerative-Cy5

status: Public on Aug 29 2011

hyb_protocol: standard CapitalBio Methods

scan_protocol: Luxscan 10KA(CapitalBio)

data_processing: Using Luxscan 3.0 Image Analysis Software(CapitalBio) analysis Microarray images,convert image signal to digital signal,then normalizated based on LOWESS program.

organism: Mus musculus

source_name: degenarative cornea

label_protocol: Using CapitalBio cRNA Amplification and Labeling Kit(Cat.No.360060,CapitalBio,Beijing)

extract_protocol: Total RNA extracted using Trizol reagent (Invitrogen, Gaithersburg, MD, USA),concentrated using ethanol precipitation and purified using NucleoSpin® RNA clean-up Kit (MACHEREY-NAGEL,Germany).

tag: strain

value: Balb/c

source_name: normal cornea


title: S100A8/control, 4hr, replicate 2

description:
4 hour,_replicate 2
Agilent Feature Extraction file:
251485060959_S01_GE2_107_Sep09_1_2.txt
Processed data file: 4hr_rep2.txt


title: dye swap, normal-Cy5, degenerative-Cy3


title: ChIP-Seq analysis of H3K4me3 in human hLiver cells; Lib:XZ:20100104:04--ChIP:XZ:20091228:04:hLiver:H3K4Me3

status: Public on Nov 12 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: Lib:XZ:20100104:04--ChIP:XZ:20091228:04:hLiver:H3K4Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3259
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: GSM621675_BI.Adult_Liver.H3K4me3.4.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100104:04--ChIP:XZ:20091228:04:hLiver:H3K4Me3.hg19.level.1
ANALYSIS TITLE: Mapping of Adult Liver Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me3 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.4826
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED: 62
FINDPEAKS_SCORE: 0.2345
FINDPEAKS_PERCENTILE: 21
HOTSPOT_SCORE: 0.2413
HOTSPOT_PERCENTILE: 15
IROC_SCORE: 0.9999
IROC_PERCENTILE: 74
POISSON_SCORE: 0.3574
POISSON_PERCENTILE: 19

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

ANALYSIS FILE NAME: GSM621675_BI.Adult_Liver.H3K4me3.4.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100104:04--ChIP:XZ:20091228:04:hLiver:H3K4Me3.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Adult Liver Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me3 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.5100
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 H3K4me3 4
BROWSER_TRACK_DESCRIPTION: BI Adult Liver Histone H3K4me3 Donor 4 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED: 62
FINDPEAKS_SCORE: 0.2345
FINDPEAKS_PERCENTILE: 21
HOTSPOT_SCORE: 0.2413
HOTSPOT_PERCENTILE: 15
IROC_SCORE: 0.9999
IROC_PERCENTILE: 74
POISSON_SCORE: 0.3574
POISSON_PERCENTILE: 19

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

source_name: normal adult liver; Lib:XZ:20100104:04--ChIP:XZ:20091228:04:hLiver:H3K4Me3

value: genomic DNA

value: Unknown

value: Protein A-Sepharose 4B

value: Millipore

value: Histone H3K4me3


title: ChIP-Seq analysis of H3K4me1 in human hLiver cells; Lib:XZ:20100423:09--ChIP:XZ:20100331:09:hLiver:H3K4Me1

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:20100423:09--ChIP:XZ:20100331:09:hLiver:H3K4Me1
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3238
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
****************
BED and WIG files were replaced on April 29, 2014

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

ANALYSIS FILE NAME: GSM621654_BI.Adult_Liver.H3K4me1.5.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100423:09--ChIP:XZ:20100331:09:hLiver:H3K4Me1.hg19.level.1
ANALYSIS TITLE: Mapping of Adult Liver Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me1 ChIP-Seq 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.4623
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED: 43
FINDPEAKS_SCORE: 0.4076
FINDPEAKS_PERCENTILE: 67
HOTSPOT_SCORE: 0.3989
HOTSPOT_PERCENTILE: 60
IROC_SCORE: 0.9951
IROC_PERCENTILE: 71
POISSON_SCORE: 0.5749
POISSON_PERCENTILE: 58

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

ANALYSIS FILE NAME: GSM621654_BI.Adult_Liver.H3K4me1.5.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:XZ:20100423:09--ChIP:XZ:20100331:09:hLiver:H3K4Me1.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Adult Liver Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me1 ChIP-Seq 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.4897
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 H3K4me1 5
BROWSER_TRACK_DESCRIPTION: BI Adult Liver Histone H3K4me1 Donor 5 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED: 43
FINDPEAKS_SCORE: 0.4076
FINDPEAKS_PERCENTILE: 67
HOTSPOT_SCORE: 0.3989
HOTSPOT_PERCENTILE: 60
IROC_SCORE: 0.9951
IROC_PERCENTILE: 71
POISSON_SCORE: 0.5749
POISSON_PERCENTILE: 58

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

source_name: normal adult liver; Lib:XZ:20100423:09--ChIP:XZ:20100331:09:hLiver:H3K4Me1

value: surgery

value: Adult Liver

value: Primary Tissue

value: liver

value: MGH Pathology


title: ChIP-Seq analysis of H3K4me3 in human hLiver cells; 61C9RAAXX100224-5-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-20744
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.2521
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: GSM537697_BI.Adult_Liver.H3K4me3.3.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 61C9RAAXX100224-5-S.hg19.level.1
ANALYSIS TITLE: Mapping of Adult Liver Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me3 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.4602
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED: 62
FINDPEAKS_SCORE: 0.1941
FINDPEAKS_PERCENTILE: 10
HOTSPOT_SCORE: 0.2193
HOTSPOT_PERCENTILE: 11
IROC_SCORE: 0.9973
IROC_PERCENTILE: 27
POISSON_SCORE: 0.3758
POISSON_PERCENTILE: 26

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

ANALYSIS FILE NAME: GSM537697_BI.Adult_Liver.H3K4me3.3.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 61C9RAAXX100224-5-S.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Adult Liver Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me3 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.4876
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 H3K4me3 3.0
BROWSER_TRACK_DESCRIPTION: BI Adult Liver Histone H3K4me3 Donor 3.0 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED: 62
FINDPEAKS_SCORE: 0.1941
FINDPEAKS_PERCENTILE: 10
HOTSPOT_SCORE: 0.2193
HOTSPOT_PERCENTILE: 11
IROC_SCORE: 0.9973
IROC_PERCENTILE: 27
POISSON_SCORE: 0.3758
POISSON_PERCENTILE: 26

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

source_name: normal adult liver; 61C9RAAXX100224-5-S

value: Female

value: SDS lysis

value: 10 million cells

value: 70 ul bed volume


title: ChIP-Seq analysis of H3K4me1 in human hLiver cells; 61GKJAAXX100226-1-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-20736
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.2530
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: GSM537706_BI.Adult_Liver.H3K4me1.3.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 61GKJAAXX100226-1-S.hg19.level.1
ANALYSIS TITLE: Mapping of Adult Liver Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me1 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.4576
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED: 43
FINDPEAKS_SCORE: 0.4625
FINDPEAKS_PERCENTILE: 70
HOTSPOT_SCORE: 0.4319
HOTSPOT_PERCENTILE: 72
IROC_SCORE: 0.9979
IROC_PERCENTILE: 83
POISSON_SCORE: 0.6339
POISSON_PERCENTILE: 81

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

ANALYSIS FILE NAME: GSM537706_BI.Adult_Liver.H3K4me1.3.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 61GKJAAXX100226-1-S.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Adult Liver Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me1 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.4850
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 H3K4me1 3.0
BROWSER_TRACK_DESCRIPTION: BI Adult Liver Histone H3K4me1 Donor 3.0 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED: 43
FINDPEAKS_SCORE: 0.4625
FINDPEAKS_PERCENTILE: 70
HOTSPOT_SCORE: 0.4319
HOTSPOT_PERCENTILE: 72
IROC_SCORE: 0.9979
IROC_PERCENTILE: 83
POISSON_SCORE: 0.6339
POISSON_PERCENTILE: 81

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

source_name: normal adult liver; 61GKJAAXX100226-1-S

value: Histone H3K4me1

value: Bioruptor

value: Abcam


title: ChIP-Seq analysis of H3K4me3 in human hLiver cells; 61GKJAAXX100226-4-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-20738
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.2533
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.2563
****************
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: GSM537709_BI.Adult_Liver.H3K4me3.5.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 61GKJAAXX100226-4-S.hg19.level.1
ANALYSIS TITLE: Mapping of Adult Liver Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me3 ChIP-Seq on Adult Liver, Donor 5.0 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.4811
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED: 62
FINDPEAKS_SCORE: 0.3716
FINDPEAKS_PERCENTILE: 52
HOTSPOT_SCORE: 0.0
HOTSPOT_PERCENTILE: NA
IROC_SCORE: 0.9961
IROC_PERCENTILE: 19
POISSON_SCORE: 0.5711
POISSON_PERCENTILE: 71

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

ANALYSIS FILE NAME: GSM537709_BI.Adult_Liver.H3K4me3.5.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 61GKJAAXX100226-4-S.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Adult Liver Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me3 ChIP-Seq read mappings from Adult Liver, Donor 5.0 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.5085
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 H3K4me3 5.0
BROWSER_TRACK_DESCRIPTION: BI Adult Liver Histone H3K4me3 Donor 5.0 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED: 62
FINDPEAKS_SCORE: 0.3716
FINDPEAKS_PERCENTILE: 52
HOTSPOT_SCORE: 0.0
HOTSPOT_PERCENTILE: NA
IROC_SCORE: 0.9961
IROC_PERCENTILE: 19
POISSON_SCORE: 0.5711
POISSON_PERCENTILE: 71

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

source_name: normal adult liver; 61GKJAAXX100226-4-S

value: genomic DNA

value: Male


title: S100A8/control, 24hr, replicate 2

description:
24 hour,_replicate 2
Agilent Feature Extraction file:
251485060960_S01_GE2_107_Sep09_1_1.txt
Processed data file: 24hr_rep2.txt

value: HUVEC

value: 24 hour

value: control


title: ChIP-Seq analysis of H3K4me3 in human CD3 cells; 30BN3AAXX080918-1-S

status: Public on May 03 2010

description:
sample_term_id: CL_0000084
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Solexa-7458/Solexa-7463
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.1923
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.1922
****************
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: GSM537615_BI.CD3_Primary_Cells.H3K4me3.CD3_39661.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 30BN3AAXX080918-1-S-30BN3AAXX080918-6-S.hg19.level.1
ANALYSIS TITLE: Mapping of CD3 Primary Cells Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me3 ChIP-Seq on CD3 Primary Cells, Donor CD3_39661 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.4616
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED: 62
FINDPEAKS_SCORE: 0.4662
FINDPEAKS_PERCENTILE: 65
HOTSPOT_SCORE: 0.4738
HOTSPOT_PERCENTILE: 66
IROC_SCORE: 0.9981
IROC_PERCENTILE: 37
POISSON_SCORE: 0.5664
POISSON_PERCENTILE: 69

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

ANALYSIS FILE NAME: GSM537615_BI.CD3_Primary_Cells.H3K4me3.CD3_39661.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 30BN3AAXX080918-1-S-30BN3AAXX080918-6-S.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of CD3 Primary Cells Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me3 ChIP-Seq read mappings from CD3 Primary Cells, Donor CD3_39661 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.4890
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: CD3 H3K4me3 61
BROWSER_TRACK_DESCRIPTION: BI CD3 Primary Cells Histone H3K4me3 Donor CD3_39661 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED: 62
FINDPEAKS_SCORE: 0.4662
FINDPEAKS_PERCENTILE: 65
HOTSPOT_SCORE: 0.4738
HOTSPOT_PERCENTILE: 66
IROC_SCORE: 0.9981
IROC_PERCENTILE: 37
POISSON_SCORE: 0.5664
POISSON_PERCENTILE: 69

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

source_name: flow sorted CD3+ cells from cord blood; 30BN3AAXX080918-1-S

value: FHCRC

value: Primary Cell

value: CD3 Primary Cells

value: Unknown

value: Histone H3K4me3

value: Protein A-Sepharose 4B


title: Embryo-injected-EXP1-rep2

description: Gene expression data from whole embryo

value: whole embryo

value: single embryo


title: Embryo-tail-EXP2-rep1

description: Gene expression data from tail

value: tail section


title: ChIP-Seq analysis of H3K4me1 in human CD3 cells; 314MFAAXX090227-2-S

description:
sample_term_id: CL_0000084
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Solexa-10224
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.1944
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.1943
****************
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: GSM537646_BI.CD3_Primary_Cells.H3K4me1.CD3_39840.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 314MFAAXX090227-2-S.hg19.level.1
ANALYSIS TITLE: Mapping of CD3 Primary Cells Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me1 ChIP-Seq on CD3 Primary Cells, Donor CD3_39840 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.4832
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED: 43
FINDPEAKS_SCORE: 0.5186
FINDPEAKS_PERCENTILE: 74
HOTSPOT_SCORE: 0.4907
HOTSPOT_PERCENTILE: 77
IROC_SCORE: 0.9992
IROC_PERCENTILE: 100
POISSON_SCORE: 0.599
POISSON_PERCENTILE: 65

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

ANALYSIS FILE NAME: GSM537646_BI.CD3_Primary_Cells.H3K4me1.CD3_39840.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 314MFAAXX090227-2-S.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of CD3 Primary Cells Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me1 ChIP-Seq read mappings from CD3 Primary Cells, Donor CD3_39840 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.5106
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: CD3 H3K4me1 40
BROWSER_TRACK_DESCRIPTION: BI CD3 Primary Cells Histone H3K4me1 Donor CD3_39840 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED: 43
FINDPEAKS_SCORE: 0.5186
FINDPEAKS_PERCENTILE: 74
HOTSPOT_SCORE: 0.4907
HOTSPOT_PERCENTILE: 77
IROC_SCORE: 0.9992
IROC_PERCENTILE: 100
POISSON_SCORE: 0.599
POISSON_PERCENTILE: 65

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

source_name: flow sorted CD3+ cells from cord blood; 314MFAAXX090227-2-S

value: Histone H3K4me1

value: SDS lysis

value: 10 million cells

value: 70 ul bed volume


title: ChIP-Seq analysis of H3K4me1 in human pancreatic islets normal cells; 30J03AAXX090718-1-S

description:
sample_term_id: UBERON_0000016
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Solexa-13146
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.2263
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.2262
****************
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: GSM537642_BI.Pancreatic_Islets.H3K4me1.pancreatic_islets_normal_3_27_09.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 30J03AAXX090718-1-S.hg19.level.1
ANALYSIS TITLE: Mapping of Pancreatic Islets Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me1 ChIP-Seq on Pancreatic Islets, Donor pancreatic islets normal_3/27/09 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.4752
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED: 43
FINDPEAKS_SCORE: 0.3111
FINDPEAKS_PERCENTILE: 37
HOTSPOT_SCORE: 0.3816
HOTSPOT_PERCENTILE: 56
IROC_SCORE: 0.9707
IROC_PERCENTILE: 36
POISSON_SCORE: 0.503
POISSON_PERCENTILE: 33

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

ANALYSIS FILE NAME: GSM537642_BI.Pancreatic_Islets.H3K4me1.pancreatic_islets_normal_3_27_09.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 30J03AAXX090718-1-S.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Pancreatic Islets Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me1 ChIP-Seq read mappings from Pancreatic Islets, Donor pancreatic islets normal_3/27/09 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.5026
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: PI H3K4me1 27
BROWSER_TRACK_DESCRIPTION: BI Pancreatic Islets Histone H3K4me1 Donor pancreatic islets normal_3/27/09 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED: 43
FINDPEAKS_SCORE: 0.3111
FINDPEAKS_PERCENTILE: 37
HOTSPOT_SCORE: 0.3816
HOTSPOT_PERCENTILE: 56
IROC_SCORE: 0.9707
IROC_PERCENTILE: 36
POISSON_SCORE: 0.503
POISSON_PERCENTILE: 33

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

source_name: pancreatic islets from a normal donor; 30J03AAXX090718-1-S

value: genomic DNA

value: Islet Cell Resource Center

value: Pancreatic Islets

value: pancreatic islets normal_3/27/09

value: Male

value: not passaged

value: Bioruptor

value: Abcam


title: ChIP-Seq analysis of H3K4me1 in human CD3 cells; 30EDEAAXX090127-6-S

description:
sample_term_id: CL_0000084
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Solexa-9767
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.1929
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.1928
****************
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: GSM537636_BI.CD3_Primary_Cells.H3K4me1.CD3_39811.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 30EDEAAXX090127-6-S.hg19.level.1
ANALYSIS TITLE: Mapping of CD3 Primary Cells Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me1 ChIP-Seq on CD3 Primary Cells, Donor CD3_39811 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.4821
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED: 43
FINDPEAKS_SCORE: 0.3429
FINDPEAKS_PERCENTILE: 47
HOTSPOT_SCORE: 0.3765
HOTSPOT_PERCENTILE: 49
IROC_SCORE: 0.9935
IROC_PERCENTILE: 69
POISSON_SCORE: 0.489
POISSON_PERCENTILE: 28

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

ANALYSIS FILE NAME: GSM537636_BI.CD3_Primary_Cells.H3K4me1.CD3_39811.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 30EDEAAXX090127-6-S.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of CD3 Primary Cells Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me1 ChIP-Seq read mappings from CD3 Primary Cells, Donor CD3_39811 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.5095
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: CD3 H3K4me1 11
BROWSER_TRACK_DESCRIPTION: BI CD3 Primary Cells Histone H3K4me1 Donor CD3_39811 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED: 43
FINDPEAKS_SCORE: 0.3429
FINDPEAKS_PERCENTILE: 47
HOTSPOT_SCORE: 0.3765
HOTSPOT_PERCENTILE: 49
IROC_SCORE: 0.9935
IROC_PERCENTILE: 69
POISSON_SCORE: 0.489
POISSON_PERCENTILE: 28

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

source_name: flow sorted CD3+ cells from cord blood; 30EDEAAXX090127-6-S

value: FHCRC

value: Primary Cell

value: CD3 Primary Cells

value: Unknown


title: ChIP-Seq analysis of H3K4me3 in human CD3 cells; 30EBYAAXX090127-5-S

description:
sample_term_id: CL_0000084
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Solexa-9761
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.1953
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.1952
****************
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: GSM537633_BI.CD3_Primary_Cells.H3K4me3.CD3_39804.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 30EBYAAXX090127-5-S.hg19.level.1
ANALYSIS TITLE: Mapping of CD3 Primary Cells Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me3 ChIP-Seq on CD3 Primary Cells, Donor CD3_39804 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.4813
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED: 62
FINDPEAKS_SCORE: 0.3307
FINDPEAKS_PERCENTILE: 40
HOTSPOT_SCORE: 0.3808
HOTSPOT_PERCENTILE: 49
IROC_SCORE: 0.998
IROC_PERCENTILE: 34
POISSON_SCORE: 0.4101
POISSON_PERCENTILE: 32

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

ANALYSIS FILE NAME: GSM537633_BI.CD3_Primary_Cells.H3K4me3.CD3_39804.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 30EBYAAXX090127-5-S.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of CD3 Primary Cells Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me3 ChIP-Seq read mappings from CD3 Primary Cells, Donor CD3_39804 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.5087
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: CD3 H3K4me3 04
BROWSER_TRACK_DESCRIPTION: BI CD3 Primary Cells Histone H3K4me3 Donor CD3_39804 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED: 62
FINDPEAKS_SCORE: 0.3307
FINDPEAKS_PERCENTILE: 40
HOTSPOT_SCORE: 0.3808
HOTSPOT_PERCENTILE: 49
IROC_SCORE: 0.998
IROC_PERCENTILE: 34
POISSON_SCORE: 0.4101
POISSON_PERCENTILE: 32

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

source_name: flow sorted CD3+ cells from cord blood; 30EBYAAXX090127-5-S

value: Histone H3K4me3

value: Protein A-Sepharose 4B


title: Chemical burn-induced CNV After Injury 14 Day, Replication 2

status: Public on Feb 08 2011

hyb_protocol: Standard CapitalBio methods.

scan_protocol: Luxscan 10KA (CapitalBio).

data_processing: Using Luxscan 3.0 Image Analysis Software (CapitalBio), analyzed microarray images, converted image signal to digital signal, then normalized based on LOWESS  program.

source_name: Chemical burn-induced CNV cornea, Balb/c, 14D

label_protocol: Labeled using CapitalBio cRNA Amplification and Labeling Kit (Cat.No.360060,CapitalBio,Beijing).

extract_protocol: Total RNA extracted using Trizol reagent (Invitrogen, Gaithersburg, MD, USA), concentrated using ethanol precipitation and purified using NucleoSpin® RNA clean-up Kit (MACHEREY-NAGEL,Germany).

treatment_protocol: CNV induction with suture or chemical burn (NaOH).

value: cornea

value: Balb/c

tag: developmental stage

value: young adult

tag: treatment

value: chemical burn-induced corneal neovascularization

tag: time after treatment

value: 14 days

source_name: Normal cornea without any treatment


title: Chemical burn-induced CNV After Injury 6 Day, Replication 2

source_name: Chemical burn-induced CNV cornea, Balb/c, 6D

value: 6 days


title: Suture-induced CNV After Injury 5 Day, Replication 1

source_name: Suture-induced CNV cornea, Balb/c, 5D

value: 5 days


title: Suture-induced CNV After Injury 5 Day, Replication 2


title: Suture-induced CNV After Injury 10 Day, Replication 2

source_name: Suture-induced CNV cornea, Balb/c, 10D

value: 10 days


title: Chemical burn-induced CNV After Injury 6 Day, Replication 3


title: Chemical burn-induced CNV After Injury 6 Day, Replication 1 (C57BL/6)

source_name: Chemical burn-induced CNV cornea, C57BL/6, 6D


title: Chemical burn-induced CNV After Injury 6 Day, Replication 2 (C57BL/6)


title: Suture-induced CNV After Injury 5 Day, Replication 3


title: Chemical burn-induced CNV After Injury 14 Day, Replication 1


title: Chemical burn-induced CNV After Injury 6 Day, Replication 1


title: ChIP-Seq analysis of H3K4me3 in human pancreatic islets normal cells; 30J03AAXX090718-5-S

description:
sample_term_id: UBERON_0000016
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Solexa-13147
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.2173
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.2172
****************
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: GSM537643_BI.Pancreatic_Islets.H3K4me3.pancreatic_islets_normal_3_27_09.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 30J03AAXX090718-5-S.hg19.level.1
ANALYSIS TITLE: Mapping of Pancreatic Islets Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me3 ChIP-Seq on Pancreatic Islets, Donor pancreatic islets normal_3/27/09 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.4688
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED: 62
FINDPEAKS_SCORE: 0.4858
FINDPEAKS_PERCENTILE: 68
HOTSPOT_SCORE: 0.5002
HOTSPOT_PERCENTILE: 70
IROC_SCORE: 0.9966
IROC_PERCENTILE: 21
POISSON_SCORE: 0.5515
POISSON_PERCENTILE: 65

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

ANALYSIS FILE NAME: GSM537643_BI.Pancreatic_Islets.H3K4me3.pancreatic_islets_normal_3_27_09.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 30J03AAXX090718-5-S.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Pancreatic Islets Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me3 ChIP-Seq read mappings from Pancreatic Islets, Donor pancreatic islets normal_3/27/09 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.4962
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: PI H3K4me3 27
BROWSER_TRACK_DESCRIPTION: BI Pancreatic Islets Histone H3K4me3 Donor pancreatic islets normal_3/27/09 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED: 62
FINDPEAKS_SCORE: 0.4858
FINDPEAKS_PERCENTILE: 68
HOTSPOT_SCORE: 0.5002
HOTSPOT_PERCENTILE: 70
IROC_SCORE: 0.9966
IROC_PERCENTILE: 21
POISSON_SCORE: 0.5515
POISSON_PERCENTILE: 65

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

source_name: pancreatic islets from a normal donor; 30J03AAXX090718-5-S

value: genomic DNA

value: Islet Cell Resource Center

value: Pancreatic Islets

value: pancreatic islets normal_3/27/09

value: Male

value: not passaged

value: SDS lysis

value: 10 million cells

value: 70 ul bed volume


title: GIST_KIT_12

status: Public on Aug 21 2009

city: Warszawa

first: Krzysztof

last: Goryca

address: Banacha 2c

department: CeNT

country: Poland

institute: Uniwersytet Warszawski

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed (Fluidics Scripts FS450_001) and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray Scanner.

data_processing: The just.gcRMA normalization with normalize.ExpressionSet.lvs function from FLUSH.LVS.bundle package of the Bioconductor project was used. Low signal probesets were filtered out according to expression of probesets assigned to Y chromosome in female samples (expression lower than 95 percentile of Y-chromosome probesets in at least 20 samples), differential probesets were selected with Kruskal-Wallis test.

source_name: gastrointestinal stromal tumor

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual With Specific Protocols for Using the GeneChip® Hybridization, Wash, and Stain Kit, 2005-2009, Affymetrix).

extract_protocol: Extraction of total RNA was performed using the RNeasy Plus Mini Kit (cat. 74134) according to Qiagen's instructions.

tag: gender

tag: genome/variation

value: KIT mutation detected

tag: kit expression

value: HIGH

tag: mutation

tag: tumor histology

value: Spindle cell

tag: tumor size

value: 70 mm

tag: mitotic activity

tag: group

tag: tumor grade

value: Benign

tag: cd117 status

value: gastrointestinal stromal tumor


title: GIST_PDGFRA_8

value: PDGFRA mutation detected

value: LOW

value: Mixed

value: 65 mm

tag: tissue


title: GIST_PDGFRA_11

value: Female

value: MEDIUM

value: 90 mm


title: GIST_KIT_13

value: Male

value: 28 mm


title: GIST_KIT_14

value: 30 mm


title: GIST_KIT_15

value: 40 mm

value: Borderline


title: GIST_KIT_11

value: KIT mutation detected

value: 15 mm


title: GIST_PDGFRA_4

value: Spindle cell

value: 35 mm


title: GIST_PDGFRA_9

value: Benign

value: gastrointestinal stromal tumor


title: GIST_KIT_9

value: HIGH

value: Malignant


title: GIST_PDGFRA_7

value: PDGFRA mutation detected

value: LOW

value: Epithelioid

value: 25 mm


title: GIST_PDGFRA_10

value: Male

value: Mixed

value: 80 mm


title: GIST_PDGFRA_6

value: 50 mm


title: GIST_WT_3

value: no mutation detected

value: No mutation found

value: 90 mm


title: GIST_PDGFRA_5

value: Spindle cell

value: 60 mm


title: Suture-induced CNV After Injury 10 Day, Replication 1

value: cornea

value: Balb/c

value: young adult

value: 10 days


title: GIST_PDGFRA_2

value: PDGFRA mutation detected

value: 70 mm

value: Malignant

value: gastrointestinal stromal tumor


title: GIST_WT_1

value: Male

value: LOW

value: 55 mm


title: GIST_KIT_7

value: KIT mutation detected

value: HIGH

value: Benign


title: GIST_PDGFRA_1

value: Mixed

value: 35 mm


title: GIST_KIT_5

value: Spindle cell

value: 30 mm


title: GIST_KIT_6


title: GIST_KIT_3

value: Female

value: Borderline


title: GIST_KIT_4

value: 18 mm


title: GIST_PDGFRA_3

value: PDGFRA mutation detected

value: 95 mm


title: GIST_KIT_8

value: 20 mm


title: GIST_KIT_1

value: 40 mm

value: gastrointestinal stromal tumor


title: GIST_KIT_10

value: Male

value: LOW

value: 65 mm


title: GIST_WT_2

value: no mutation detected

value: HIGH

value: No mutation found

value: Epithelioid


title: GIST_KIT_2

data_processing: The just.gcRMA normalization with normalize.ExpressionSet.lvs function from FLUSH.LVS.bundle package of the Bioconductor project was used. Low signal probesets were filtered out according to expression of probesets assigned to Y chromosome in female samples (expression lower than 95 percentile of Y-chromosome probesets in at least 20 samples), differential probesets were selected with Kruskal-Wallis test..

value: KIT mutation detected

value: Spindle cell

value: 53 mm

value: Benign