title: Inf299

description: Validation Test Set

value: peripheral blood

value: Serratia marcescens


title: Inf075

status: Public on Aug 12 2014

type: RNA

city: Cardiff

first: Peter

last: Ghazal

address: Sir Geraint Evans Building, Academic Avenue

department: Systems Immunity University Research Institute

country: United Kingdom

institute: Cardiff University

description:
Corrected_gestational_age_(weeks+days):36+4
Birthweight_(g):890

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Raw scan data were background subtracted, VST transformed and subsequently robust spline normalised as performed by the lumi package of Bioconductor.  Array probe features that had a present count in one or more samples were retained.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: peripheral blood

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

extract_protocol: RNA was extracted from whole blood samples with PAXgene blood RNA reagent, followed by clean-up and DNase I treatment with QIAGEN PAXgene blood RNA kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: neonate

value: infected

tag: gender

value: Female

tag: tissue

tag: on antibiotics at time of sample

value: No

tag: bloodculture result

value: negative

tag: other positive results

value: CMV in blood and urine

tag: corrected gestational age (weeks+days)

tag: birthweight (g)


title: NEC253

description: Validation Test Set

hyb_protocol: Standard Affymetrix GeneTitan 3' IVT hybridisation and wash procedure.

scan_protocol: GeneChips were scanned using the Affymetrix GeneTitan Scanner using the GCOS software tool

data_processing: R/Bioconductor using RMA normalisation, non specific expression level filter of 50 applied and empirical Bayes statistical test with Benjamini-Hochberg FDR adjustment performed.

label_protocol: Biotinylated cRNA were prepared with the standard Affymetrix GeneChip GeneTitan 3' IVT labeling kit.

tag: corrected gestational age at sample (weeks+days)

value: Yes

value: Coagulase -ve Staph. aureus previous day


title: Inf047

description: set:Training Set

value: control

value: Male

value: candida

value: klebsiella in peritoneal fluid and ET secretions, NEC 1 week previously, candida in blood 4 days previously


title: Con207

description: set:Training Set


title: Inf297

description: Validation Test Set


title: Con206

description: set:Training Set


title: Inf275

description: Validation Test Set

value: Coagulase -ve Staph. aureus


title: Con200

description: set:Training Set


title: Inf287

description: Validation Test Set

value: E. coli


title: Con202

description: set:Training Set


title: Con181

description: set:Training Set


title: Inf009

description: set:Training Set

value: Coagulase negative staphylococcus

value: coag neg staph long line tip next day, previous ureaplasma,,no previous positive blood cultures


title: Inf262

description: Validation Test Set

value: peripheral blood

value: Group B Strep.


title: Inf239

description: Validation Test Set

value: Pseudomonas aeruginosa & Coagulase -ve Staph. aureus

value: Next day, peritoneal swab enterococcus, pseudomonas aeruginosa and klebsiella oxytoca


title: Con097

description: set:Training Set

value: No


title: Inf226

description: Validation Test Set

value: Enterococcus & Staph. warneri

value: BC next day grew Staphylococcus warneri


title: Con096

description: set:Training Set


title: Con165

description: set:Training Set

value: Female


title: Con081

description: set:Training Set


title: Con079

description: set:Training Set


title: Con077

description: set:Training Set


title: Con087

description: set:Training Set


title: Con260

description: Validation Test Set


title: Inf271

description: Validation Test Set

value: Yes

value: Staph. epidermidis

value: grew yeasts 2 days later


title: Inf216

description: Validation Test Set

value: Enterococcus


title: Con086

description: set:Training Set

value: control

value: Male


title: Con293

description: Validation Test Set


title: Con073

description: set:Training Set

value: well. 3 days later had Saureus in wound swab.


title: Con270

description: Validation Test Set


title: Con220

description: Validation Test Set


title: Con069

description: set:Training Set


title: Con213

description: Validation Test Set


title: Con071

description: set:Training Set


title: Con049

description: set:Training Set


title: Con072

description: set:Training Set


title: Con051

description: set:Training Set


title: Con058

description: set:Training Set


title: Con062

description: set:Training Set

value: no. blood culture 3 days previously negative


title: Con042

description: set:Training Set

value: umbilical swab grew anaerobes, coliforms, Saureus and gp B strep


title: Con040

description: set:Training Set

value: peripheral blood


title: Con063

description: set:Training Set


title: Con065

description: set:Training Set


title: Con029

description: set:Training Set


title: Con043

description: set:Training Set


title: Con022

description: set:Training Set


title: Con017

description: set:Training Set


title: Con021

description: set:Training Set


title: Con028

description: set:Training Set


title: Con046

description: set:Training Set


title: Con001

description: set:Training Set


title: Con209

description: Validation Test Set


title: ChIP-Seq analysis of H3K9me3 in human CD45RA CD8 cells; DNA_Lib 501

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 501
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8721
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9462
****************
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: GSM773031_BI.CD8_Naive_Primary_Cells.H3K9me3.Donor_101_8_pooled_leukopaks_Jan_20_2011.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 501-DNA_Lib 501-DNA_Lib 501.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of CD8 Naive Primary Cells Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9me3 ChIP-Seq on CD8 Naive Primary Cells, Donor Donor 101 8 pooled leukopaks Jan 20 2011, were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.10764
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: 27,558,685
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.0155
FINDPEAKS_PERCENTILE: 20
HOTSPOT_SCORE: 0.048
HOTSPOT_PERCENTILE: 8
IROC_SCORE: 0.919
IROC_PERCENTILE: 88
POISSON_SCORE: 0.1236
POISSON_PERCENTILE: 12
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

ANALYSIS FILE NAME: GSM773031_BI.CD8_Naive_Primary_Cells.H3K9me3.Donor_101_8_pooled_leukopaks_Jan_20_2011.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 501-DNA_Lib 501-DNA_Lib 501.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of CD8 Naive Primary Cells Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9me3 ChIP-Seq read mappings from CD8 Naive Primary Cells, Donor Donor 101 8 pooled leukopaks Jan 20 2011, were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.11028
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 H3K9me3 01 01
BROWSER_TRACK_DESCRIPTION: BI CD8 Naive Primary Cells Histone H3K9me3 Donor 101 8 pooled leukopaks Jan 20 2011 Library DNA_Lib 501 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 27,558,685
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.0155
FINDPEAKS_PERCENTILE: 20
HOTSPOT_SCORE: 0.048
HOTSPOT_PERCENTILE: 8
IROC_SCORE: 0.919
IROC_PERCENTILE: 88
POISSON_SCORE: 0.1236
POISSON_PERCENTILE: 12
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

molecule: genomic DNA

source_name: Naive CD8+ T cells; DNA_Lib 501

extract_protocol: Library construction protocol: Single read - Illumina

tag: sample alias

value: BioSam 188

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: Primary Cell

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: Abcam

value: Histone H3K9me3

value: Branson


title: ChIP-Seq analysis of H3K27ac in human CD45RA CD8 cells; DNA_Lib 496

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 496
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8666
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9462
****************
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: GSM772976_BI.CD8_Naive_Primary_Cells.H3K27ac.Donor_101_8_pooled_leukopaks_Jan_20_2011.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 496-DNA_Lib 496-DNA_Lib 496.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of CD8 Naive Primary Cells Histone H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27ac ChIP-Seq on CD8 Naive Primary Cells, Donor Donor 101 8 pooled leukopaks Jan 20 2011, were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.10778
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 18,506,258
NUMBER_OF_H3K27ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 34
FINDPEAKS_SCORE: 0.233
FINDPEAKS_PERCENTILE: 65
HOTSPOT_SCORE: 0.2736
HOTSPOT_PERCENTILE: 56
IROC_SCORE: 0.9993
IROC_PERCENTILE: 91
POISSON_SCORE: 0.2963
POISSON_PERCENTILE: 35
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

ANALYSIS FILE NAME: GSM772976_BI.CD8_Naive_Primary_Cells.H3K27ac.Donor_101_8_pooled_leukopaks_Jan_20_2011.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 496-DNA_Lib 496-DNA_Lib 496.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of CD8 Naive Primary Cells Histone H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27ac ChIP-Seq read mappings from CD8 Naive Primary Cells, Donor Donor 101 8 pooled leukopaks Jan 20 2011, were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.11042
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 H3K27ac 01 96
BROWSER_TRACK_DESCRIPTION: BI CD8 Naive Primary Cells Histone H3K27ac Donor 101 8 pooled leukopaks Jan 20 2011 Library DNA_Lib 496 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 18,506,258
NUMBER_OF_H3K27ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 34
FINDPEAKS_SCORE: 0.233
FINDPEAKS_PERCENTILE: 65
HOTSPOT_SCORE: 0.2736
HOTSPOT_PERCENTILE: 56
IROC_SCORE: 0.9993
IROC_PERCENTILE: 91
POISSON_SCORE: 0.2963
POISSON_PERCENTILE: 35
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

source_name: Naive CD8+ T cells; DNA_Lib 496

value: Histone H3K27ac


title: ChIP-Seq analysis of H3K27me3 in human CD45RA CD4 cells; DNA_Lib 659

description:
sample_term_id: CL_0000492
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 659
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8637
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9469
****************
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: GSM772947_BI.CD4_Naive_Primary_Cells.H3K27me3.Donor_100_7_pooled_leukopaks_Jan_7_2011.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 659-DNA_Lib 659-DNA_Lib 659.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of CD4 Naive Primary Cells Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27me3 ChIP-Seq on CD4 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.10814
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 18,689,875
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.0117
FINDPEAKS_PERCENTILE: 27
HOTSPOT_SCORE: 0.1001
HOTSPOT_PERCENTILE: 29
IROC_SCORE: 0.7063
IROC_PERCENTILE: 37
POISSON_SCORE: 0.1781
POISSON_PERCENTILE: 16
MAXIMUM_REPLICATE_CORRELATION: 0.88

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

ANALYSIS FILE NAME: GSM772947_BI.CD4_Naive_Primary_Cells.H3K27me3.Donor_100_7_pooled_leukopaks_Jan_7_2011.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 659-DNA_Lib 659-DNA_Lib 659.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of CD4 Naive Primary Cells Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27me3 ChIP-Seq read mappings from CD4 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.11078
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: CD4N H3K27me3 00 59
BROWSER_TRACK_DESCRIPTION: BI CD4 Naive Primary Cells Histone H3K27me3 Donor 100 7 pooled leukopaks Jan 7 2011 Library DNA_Lib 659 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 18,689,875
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.0117
FINDPEAKS_PERCENTILE: 27
HOTSPOT_SCORE: 0.1001
HOTSPOT_PERCENTILE: 29
IROC_SCORE: 0.7063
IROC_PERCENTILE: 37
POISSON_SCORE: 0.1781
POISSON_PERCENTILE: 16
MAXIMUM_REPLICATE_CORRELATION: 0.88

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

source_name: Naive CD4+ T cells; DNA_Lib 659

value: BioSam 183

value: CD4 Naive Primary Cells

value: CD4 Naive Primary Cell

value: Donor 100 7 pooled leukopaks Jan 7 2011

value: Millipore

value: Histone H3K27me3


title: Con048

description: set:Training Set

value: control

value: Male

value: peripheral blood

value: No


title: ChIP-Seq analysis of H3K36me3 in human CD45RA CD4 cells; DNA_Lib 660

description:
sample_term_id: CL_0000492
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 660
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8622
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9469
****************
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: GSM772932_BI.CD4_Naive_Primary_Cells.H3K36me3.Donor_100_7_pooled_leukopaks_Jan_7_2011.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 660-DNA_Lib 660-DNA_Lib 660.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of CD4 Naive Primary Cells Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K36me3 ChIP-Seq on CD4 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.10779
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: 19,772,778
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.0403
FINDPEAKS_PERCENTILE: 16
HOTSPOT_SCORE: 0.146
HOTSPOT_PERCENTILE: 16
IROC_SCORE: 0.8384
IROC_PERCENTILE: 14
POISSON_SCORE: 0.2825
POISSON_PERCENTILE: 16
MAXIMUM_REPLICATE_CORRELATION: 0.94

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

ANALYSIS FILE NAME: GSM772932_BI.CD4_Naive_Primary_Cells.H3K36me3.Donor_100_7_pooled_leukopaks_Jan_7_2011.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 660-DNA_Lib 660-DNA_Lib 660.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of CD4 Naive Primary Cells Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K36me3 ChIP-Seq read mappings from CD4 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.11043
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: CD4N H3K36me3 00 60
BROWSER_TRACK_DESCRIPTION: BI CD4 Naive Primary Cells Histone H3K36me3 Donor 100 7 pooled leukopaks Jan 7 2011 Library DNA_Lib 660 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 19,772,778
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.0403
FINDPEAKS_PERCENTILE: 16
HOTSPOT_SCORE: 0.146
HOTSPOT_PERCENTILE: 16
IROC_SCORE: 0.8384
IROC_PERCENTILE: 14
POISSON_SCORE: 0.2825
POISSON_PERCENTILE: 16
MAXIMUM_REPLICATE_CORRELATION: 0.94

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

source_name: Naive CD4+ T cells; DNA_Lib 660

value: presumed normal

value: genomic DNA

value: Unknown

value: Primary Cell

value: Dana Farber

value: Protein A-Sepharose 4B

value: 0.5 to 3 million cells

value: cell/nuclei lysis

value: Histone H3K36me3


title: CpG-activated for 2 hrs C57BL6 macrophages

status: Public on Sep 07 2013

city: Boston

first: Alexander

last: Poltorak

state: Massachusetts

address: 150 Harrison avenue

institute: Tufts University

description: thioglycollate-elicited macrophages

hyb_protocol: according to standard Affymetrix protocol

data_processing: The matrix table was generated using Expression Console (Affymetrix) software and RMA algorithm.

organism: Mus musculus

source_name: C57BL6 mice

growth_protocol: Cells were plated for 16 hrs in DMEM with 2% penn/strep and 10% FCS

extract_protocol: TRIZOL

treatment_protocol: Cell were  activated the following day with 200 nM CpG

tag: strain

tag: treatment

value: CpG-activated 2 hrs

tag: cell type

value: macrophages


title: ChIP-Seq analysis of H3K27ac in human CD45RA CD4 cells; DNA_Lib 661

description:
sample_term_id: CL_0000492
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 661
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8624
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9469
****************
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: GSM772934_BI.CD4_Naive_Primary_Cells.H3K27ac.Donor_100_7_pooled_leukopaks_Jan_7_2011.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 661-DNA_Lib 661-DNA_Lib 661.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of CD4 Naive Primary Cells Histone H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27ac ChIP-Seq on CD4 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.10691
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: 4,974,563
NUMBER_OF_H3K27ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 34
FINDPEAKS_SCORE: 0.3243
FINDPEAKS_PERCENTILE: 82
HOTSPOT_SCORE: 0.4112
HOTSPOT_PERCENTILE: 82
IROC_SCORE: 0.9979
IROC_PERCENTILE: 74
POISSON_SCORE: 0.4112
POISSON_PERCENTILE: 71
MAXIMUM_REPLICATE_CORRELATION: 0.9

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

ANALYSIS FILE NAME: GSM772934_BI.CD4_Naive_Primary_Cells.H3K27ac.Donor_100_7_pooled_leukopaks_Jan_7_2011.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 661-DNA_Lib 661-DNA_Lib 661.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of CD4 Naive Primary Cells Histone H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27ac ChIP-Seq read mappings from CD4 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.10955
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: CD4N H3K27ac 00 61
BROWSER_TRACK_DESCRIPTION: BI CD4 Naive Primary Cells Histone H3K27ac Donor 100 7 pooled leukopaks Jan 7 2011 Library DNA_Lib 661 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 4,974,563
NUMBER_OF_H3K27ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 34
FINDPEAKS_SCORE: 0.3243
FINDPEAKS_PERCENTILE: 82
HOTSPOT_SCORE: 0.4112
HOTSPOT_PERCENTILE: 82
IROC_SCORE: 0.9979
IROC_PERCENTILE: 74
POISSON_SCORE: 0.4112
POISSON_PERCENTILE: 71
MAXIMUM_REPLICATE_CORRELATION: 0.9

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

source_name: Naive CD4+ T cells; DNA_Lib 661

value: BioSam 183

value: CD4 Naive Primary Cells

value: CD4 Naive Primary Cell

value: Donor 100 7 pooled leukopaks Jan 7 2011

value: ~1 ug

value: 10 ul bed volume

value: Abcam

value: Histone H3K27ac

value: Branson


title: Non-activated F1 macrophages

description: thioglycollate-elicited macrophages

scan_protocol: according to standard Affymetrix protocol

source_name: F1 mice

value: F1 (C57BL6 x MOLF)

value: non-activated


title: Non-activated C57BL6 macrophages

description: thioglycollate-elicited macrophages

label_protocol: according to standard Affymetrix protocol


title: CpG-activated for 4 hrs F1 macrophages

description: thioglycollate-elicited macrophages

value: CpG-activated 4 hrs


title: CpG-activated for 2 hrs F1 macrophages

description: thioglycollate-elicited macrophages


title: human_colon.paired

status: Public on Jan 05 2012

first: Robert

middle: K

last: Bradley

address: 77 Massachusetts Avenue, 68-223A

department: Biology

institute: MIT

library_source: transcriptomic

data_processing:
Alignment: The files human.nagnag.junctions.gff and mouse.nagnag.junctions.gff (see Series supplementary files) give the intron-proximal and intron-distal splice junctions of all NAGNAG splicing events analyzed in this study. The 'start' field specifies the last base of the upstream exon and the 'end' field specifies the first base of the downstream exon (upstream and downstream defined with respect to the gene). For each NAGNAG, we extracted the transcript sequence flanking the proximal and distal 3' splice sites and used Bowtie version 0.12.7 to map reads to these two sequences. We required that short reads have at least 6 nt on either side of the splice junction (an "overhang" of 6 nt), and furthermore that there be no mismatches within the overhang region.
Human genome build: hg19
Mouse genome build: mm9

molecule: polyA RNA

source_name: colon

extract_protocol:
Human: RNA-Seq libraries are from the Body Map 2.0 dataset distributed by Illumina, available at the ENA archive with accession number ERP000546.
Mouse: Tissues from a 10-week-old male were extracted immediately after death and stored in RNAlater per the manufacturerâs instructions (Ambion). Tissue was lysed in Trizol and RNA was extracted with Qiagen miRNeasy mini columns. Using 5ug of total RNA, we performed polyA selection and prepared strand-specific libraries for Illumina sequencing following the dUTP protocol and the SPRIworks Fragment library system (Beckman Coulter). We obtained final insert sizes of approximately 160 bp. We sequenced these libraries using the Illumina HiSeq 2000 and the GAIIx machines.

tag: library type

value: paired-end

tag: read length

tag: insert size

tag: insert standard deviation


title: human_lymph_node.paired

source_name: lymph node


title: human_liver.paired

source_name: liver


title: human_adipose.paired

source_name: adipose


title: ChIP-Seq analysis of H3K27me3 in human CD45RA CD4 cells; DNA_Lib 524

description:
sample_term_id: CL_0000492
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 524
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8609
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9466
****************
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: GSM772919_BI.CD4_Naive_Primary_Cells.H3K27me3.Donor_101_8_pooled_leukopaks_Jan_20_2011.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 524-DNA_Lib 524-DNA_Lib 524.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of CD4 Naive Primary Cells Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27me3 ChIP-Seq on CD4 Naive Primary Cells, Donor Donor 101 8 pooled leukopaks Jan 20 2011, were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.10698
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: 15,936,173
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.0076
FINDPEAKS_PERCENTILE: 12
HOTSPOT_SCORE: 0.1056
HOTSPOT_PERCENTILE: 35
IROC_SCORE: 0.4416
IROC_PERCENTILE: 2
POISSON_SCORE: 0.1903
POISSON_PERCENTILE: 24
MAXIMUM_REPLICATE_CORRELATION: 0.88

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

ANALYSIS FILE NAME: GSM772919_BI.CD4_Naive_Primary_Cells.H3K27me3.Donor_101_8_pooled_leukopaks_Jan_20_2011.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 524-DNA_Lib 524-DNA_Lib 524.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of CD4 Naive Primary Cells Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27me3 ChIP-Seq read mappings from CD4 Naive Primary Cells, Donor Donor 101 8 pooled leukopaks Jan 20 2011, were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.10962
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: CD4N H3K27me3 01 24
BROWSER_TRACK_DESCRIPTION: BI CD4 Naive Primary Cells Histone H3K27me3 Donor 101 8 pooled leukopaks Jan 20 2011 Library DNA_Lib 524 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 15,936,173
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.0076
FINDPEAKS_PERCENTILE: 12
HOTSPOT_SCORE: 0.1056
HOTSPOT_PERCENTILE: 35
IROC_SCORE: 0.4416
IROC_PERCENTILE: 2
POISSON_SCORE: 0.1903
POISSON_PERCENTILE: 24
MAXIMUM_REPLICATE_CORRELATION: 0.88

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

source_name: Naive CD4+ T cells; DNA_Lib 524

value: BioSam 187

value: presumed normal

value: genomic DNA

value: Unknown

value: Primary Cell

value: Dana Farber

value: Protein A-Sepharose 4B

value: 0.5 to 3 million cells

value: cell/nuclei lysis

value: Millipore

value: Histone H3K27me3


title: ChIP-Seq analysis of H3K36me3 in human CD45RA CD4 cells; DNA_Lib 525

description:
sample_term_id: CL_0000492
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 525
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8608
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9466
****************
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: GSM772918_BI.CD4_Naive_Primary_Cells.H3K36me3.Donor_101_8_pooled_leukopaks_Jan_20_2011.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 525-DNA_Lib 525-DNA_Lib 525.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of CD4 Naive Primary Cells Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K36me3 ChIP-Seq on CD4 Naive Primary Cells, Donor Donor 101 8 pooled leukopaks Jan 20 2011, were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.10604
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 18,527,964
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.0597
FINDPEAKS_PERCENTILE: 27
HOTSPOT_SCORE: 0.161
HOTSPOT_PERCENTILE: 27
IROC_SCORE: 0.8584
IROC_PERCENTILE: 18
POISSON_SCORE: 0.2856
POISSON_PERCENTILE: 20
MAXIMUM_REPLICATE_CORRELATION: 0.94

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

ANALYSIS FILE NAME: GSM772918_BI.CD4_Naive_Primary_Cells.H3K36me3.Donor_101_8_pooled_leukopaks_Jan_20_2011.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 525-DNA_Lib 525-DNA_Lib 525.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of CD4 Naive Primary Cells Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K36me3 ChIP-Seq read mappings from CD4 Naive Primary Cells, Donor Donor 101 8 pooled leukopaks Jan 20 2011, were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.10868
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: CD4N H3K36me3 01 25
BROWSER_TRACK_DESCRIPTION: BI CD4 Naive Primary Cells Histone H3K36me3 Donor 101 8 pooled leukopaks Jan 20 2011 Library DNA_Lib 525 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 18,527,964
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.0597
FINDPEAKS_PERCENTILE: 27
HOTSPOT_SCORE: 0.161
HOTSPOT_PERCENTILE: 27
IROC_SCORE: 0.8584
IROC_PERCENTILE: 18
POISSON_SCORE: 0.2856
POISSON_PERCENTILE: 20
MAXIMUM_REPLICATE_CORRELATION: 0.94

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

source_name: Naive CD4+ T cells; DNA_Lib 525

value: CD4 Naive Primary Cells

value: CD4 Naive Primary Cell

value: ~1 ug

value: 10 ul bed volume

value: Abcam

value: Histone H3K36me3


title: ChIP-Seq analysis of H3K9me3 in human CD45RA CD4 cells; DNA_Lib 526

description:
sample_term_id: CL_0000492
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 526
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8607
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9466
****************
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: GSM772917_BI.CD4_Naive_Primary_Cells.H3K9me3.Donor_101_8_pooled_leukopaks_Jan_20_2011.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 526-DNA_Lib 526-DNA_Lib 526.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of CD4 Naive Primary Cells Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9me3 ChIP-Seq on CD4 Naive Primary Cells, Donor Donor 101 8 pooled leukopaks Jan 20 2011, were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.10776
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: 20,153,170
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.0149
FINDPEAKS_PERCENTILE: 16
HOTSPOT_SCORE: 0.0712
HOTSPOT_PERCENTILE: 20
IROC_SCORE: 0.9063
IROC_PERCENTILE: 76
POISSON_SCORE: 0.1458
POISSON_PERCENTILE: 16
MAXIMUM_REPLICATE_CORRELATION: 0.95

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

ANALYSIS FILE NAME: GSM772917_BI.CD4_Naive_Primary_Cells.H3K9me3.Donor_101_8_pooled_leukopaks_Jan_20_2011.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 526-DNA_Lib 526-DNA_Lib 526.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of CD4 Naive Primary Cells Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9me3 ChIP-Seq read mappings from CD4 Naive Primary Cells, Donor Donor 101 8 pooled leukopaks Jan 20 2011, were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.11040
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: CD4N H3K9me3 01 26
BROWSER_TRACK_DESCRIPTION: BI CD4 Naive Primary Cells Histone H3K9me3 Donor 101 8 pooled leukopaks Jan 20 2011 Library DNA_Lib 526 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 20,153,170
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.0149
FINDPEAKS_PERCENTILE: 16
HOTSPOT_SCORE: 0.0712
HOTSPOT_PERCENTILE: 20
IROC_SCORE: 0.9063
IROC_PERCENTILE: 76
POISSON_SCORE: 0.1458
POISSON_PERCENTILE: 16
MAXIMUM_REPLICATE_CORRELATION: 0.95

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

source_name: Naive CD4+ T cells; DNA_Lib 526

value: BioSam 187

value: Histone H3K9me3

value: Branson


title: ChIP-Seq analysis of WCE in human CD45RA CD4 cells; DNA_Lib 527

description:
sample_term_id: CL_0000492
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 527
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8606
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9466
****************
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: GSM772916_BI.CD4_Naive_Primary_Cells.Input.Donor_101_8_pooled_leukopaks_Jan_20_2011.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 527-DNA_Lib 527-DNA_Lib 527.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of CD4 Naive Primary Cells ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on CD4 Naive Primary Cells, Donor Donor 101 8 pooled leukopaks Jan 20 2011, were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.10829
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: 29,918,313
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 56
FINDPEAKS_SCORE: 0.0061
FINDPEAKS_PERCENTILE: 69
HOTSPOT_SCORE: 0.0162
HOTSPOT_PERCENTILE: 59
IROC_SCORE: 0.0
IROC_PERCENTILE: 33
POISSON_SCORE: 0.0683
POISSON_PERCENTILE: 64
MAXIMUM_REPLICATE_CORRELATION: 0.95

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

ANALYSIS FILE NAME: GSM772916_BI.CD4_Naive_Primary_Cells.Input.Donor_101_8_pooled_leukopaks_Jan_20_2011.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 527-DNA_Lib 527-DNA_Lib 527.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of CD4 Naive Primary Cells ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from CD4 Naive Primary Cells, Donor Donor 101 8 pooled leukopaks Jan 20 2011, were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.11093
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: CD4N Input 01 27
BROWSER_TRACK_DESCRIPTION: BI CD4 Naive Primary Cells ChIP-Seq Input Donor 101 8 pooled leukopaks Jan 20 2011 Library DNA_Lib 527 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 29,918,313
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 56
FINDPEAKS_SCORE: 0.0061
FINDPEAKS_PERCENTILE: 69
HOTSPOT_SCORE: 0.0162
HOTSPOT_PERCENTILE: 59
IROC_SCORE: 0.0
IROC_PERCENTILE: 33
POISSON_SCORE: 0.0683
POISSON_PERCENTILE: 64
MAXIMUM_REPLICATE_CORRELATION: 0.95

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

source_name: Naive CD4+ T cells; DNA_Lib 527

value: presumed normal

value: genomic DNA

value: Unknown

value: standard

value: ChIP-Seq Input

value: Input


title: ChIP-Seq analysis of H3K27me3 in human CD45RA CD8 cells; DNA_Lib 497

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 497
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8590
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9462
****************
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: GSM772900_BI.CD8_Naive_Primary_Cells.H3K27me3.Donor_101_8_pooled_leukopaks_Jan_20_2011.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 497-DNA_Lib 497-DNA_Lib 497-DNA_Lib 497.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of CD8 Naive Primary Cells Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27me3 ChIP-Seq on CD8 Naive Primary Cells, Donor Donor 101 8 pooled leukopaks Jan 20 2011, were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.10607
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: 14,301,410
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.011
FINDPEAKS_PERCENTILE: 22
HOTSPOT_SCORE: 0.1115
HOTSPOT_PERCENTILE: 47
IROC_SCORE: 0.5306
IROC_PERCENTILE: 10
POISSON_SCORE: 0.1883
POISSON_PERCENTILE: 20
MAXIMUM_REPLICATE_CORRELATION: 0.94

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

ANALYSIS FILE NAME: GSM772900_BI.CD8_Naive_Primary_Cells.H3K27me3.Donor_101_8_pooled_leukopaks_Jan_20_2011.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 497-DNA_Lib 497-DNA_Lib 497-DNA_Lib 497.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of CD8 Naive Primary Cells Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27me3 ChIP-Seq read mappings from CD8 Naive Primary Cells, Donor Donor 101 8 pooled leukopaks Jan 20 2011, were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.10871
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 H3K27me3 01 97
BROWSER_TRACK_DESCRIPTION: BI CD8 Naive Primary Cells Histone H3K27me3 Donor 101 8 pooled leukopaks Jan 20 2011 Library DNA_Lib 497 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 14,301,410
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.011
FINDPEAKS_PERCENTILE: 22
HOTSPOT_SCORE: 0.1115
HOTSPOT_PERCENTILE: 47
IROC_SCORE: 0.5306
IROC_PERCENTILE: 10
POISSON_SCORE: 0.1883
POISSON_PERCENTILE: 20
MAXIMUM_REPLICATE_CORRELATION: 0.94

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

source_name: Naive CD8+ T cells; DNA_Lib 497

value: BioSam 188

value: CD8 Naive Primary Cells

value: CD8 Naive Primary Cell

value: Primary Cell

value: Dana Farber

value: Protein A-Sepharose 4B

value: 0.5 to 3 million cells

value: cell/nuclei lysis

value: Millipore


title: ChIP-Seq analysis of H3K36me3 in human CD45RA CD8 cells; DNA_Lib 499

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 499
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8585
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9462
****************
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: GSM772895_BI.CD8_Naive_Primary_Cells.H3K36me3.Donor_101_8_pooled_leukopaks_Jan_20_2011.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 499-DNA_Lib 499-DNA_Lib 499-DNA_Lib 499.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of CD8 Naive Primary Cells Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K36me3 ChIP-Seq on CD8 Naive Primary Cells, Donor Donor 101 8 pooled leukopaks Jan 20 2011, were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.10608
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: 22,337,264
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.0485
FINDPEAKS_PERCENTILE: 20
HOTSPOT_SCORE: 0.1504
HOTSPOT_PERCENTILE: 18
IROC_SCORE: 0.8648
IROC_PERCENTILE: 22
POISSON_SCORE: 0.297
POISSON_PERCENTILE: 27
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

ANALYSIS FILE NAME: GSM772895_BI.CD8_Naive_Primary_Cells.H3K36me3.Donor_101_8_pooled_leukopaks_Jan_20_2011.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 499-DNA_Lib 499-DNA_Lib 499-DNA_Lib 499.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of CD8 Naive Primary Cells Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K36me3 ChIP-Seq read mappings from CD8 Naive Primary Cells, Donor Donor 101 8 pooled leukopaks Jan 20 2011, were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.10872
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 H3K36me3 01 99
BROWSER_TRACK_DESCRIPTION: BI CD8 Naive Primary Cells Histone H3K36me3 Donor 101 8 pooled leukopaks Jan 20 2011 Library DNA_Lib 499 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 22,337,264
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.0485
FINDPEAKS_PERCENTILE: 20
HOTSPOT_SCORE: 0.1504
HOTSPOT_PERCENTILE: 18
IROC_SCORE: 0.8648
IROC_PERCENTILE: 22
POISSON_SCORE: 0.297
POISSON_PERCENTILE: 27
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

source_name: Naive CD8+ T cells; DNA_Lib 499

value: ~1 ug

value: 10 ul bed volume

value: Abcam

value: Histone H3K36me3


title: ChIP-Seq analysis of H3K9me3 in human CD45RA CD8 cells; DNA_Lib 669

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 669
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8572
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
****************

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

ANALYSIS FILE NAME: GSM772882_BI.CD8_Naive_Primary_Cells.H3K9me3.Donor_100_7_pooled_leukopaks_Jan_7_2011.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 669-DNA_Lib 669-DNA_Lib 669.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of CD8 Naive Primary Cells Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9me3 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.10633
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: 15,210,235
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.0231
FINDPEAKS_PERCENTILE: 33
HOTSPOT_SCORE: 0.1026
HOTSPOT_PERCENTILE: 43
IROC_SCORE: 0.6273
IROC_PERCENTILE: 8
POISSON_SCORE: 0.176
POISSON_PERCENTILE: 27
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

ANALYSIS FILE NAME: GSM772882_BI.CD8_Naive_Primary_Cells.H3K9me3.Donor_100_7_pooled_leukopaks_Jan_7_2011.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 669-DNA_Lib 669-DNA_Lib 669.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of CD8 Naive Primary Cells Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9me3 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.10897
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 H3K9me3 00 69
BROWSER_TRACK_DESCRIPTION: BI CD8 Naive Primary Cells Histone H3K9me3 Donor 100 7 pooled leukopaks Jan 7 2011 Library DNA_Lib 669 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 15,210,235
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.0231
FINDPEAKS_PERCENTILE: 33
HOTSPOT_SCORE: 0.1026
HOTSPOT_PERCENTILE: 43
IROC_SCORE: 0.6273
IROC_PERCENTILE: 8
POISSON_SCORE: 0.176
POISSON_PERCENTILE: 27
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

source_name: Naive CD8+ T cells; DNA_Lib 669

value: BioSam 184

value: presumed normal

value: genomic DNA

value: Unknown

value: Donor 100 7 pooled leukopaks Jan 7 2011

value: Histone H3K9me3

value: Branson


title: ChIP-Seq analysis of H3K9me3 in human CD45RA CD4 cells; DNA_Lib 662

description:
sample_term_id: CL_0000492
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 662
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8565
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9469
****************
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: GSM772875_BI.CD4_Naive_Primary_Cells.H3K9me3.Donor_100_7_pooled_leukopaks_Jan_7_2011.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 662-DNA_Lib 662-DNA_Lib 662.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of CD4 Naive Primary Cells Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9me3 ChIP-Seq on CD4 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.10593
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: 21,675,849
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.0202
FINDPEAKS_PERCENTILE: 27
HOTSPOT_SCORE: 0.0748
HOTSPOT_PERCENTILE: 27
IROC_SCORE: 0.8763
IROC_PERCENTILE: 63
POISSON_SCORE: 0.1505
POISSON_PERCENTILE: 18
MAXIMUM_REPLICATE_CORRELATION: 0.95

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

ANALYSIS FILE NAME: GSM772875_BI.CD4_Naive_Primary_Cells.H3K9me3.Donor_100_7_pooled_leukopaks_Jan_7_2011.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 662-DNA_Lib 662-DNA_Lib 662.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of CD4 Naive Primary Cells Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9me3 ChIP-Seq read mappings from CD4 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.10857
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: CD4N H3K9me3 00 62
BROWSER_TRACK_DESCRIPTION: BI CD4 Naive Primary Cells Histone H3K9me3 Donor 100 7 pooled leukopaks Jan 7 2011 Library DNA_Lib 662 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 21,675,849
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.0202
FINDPEAKS_PERCENTILE: 27
HOTSPOT_SCORE: 0.0748
HOTSPOT_PERCENTILE: 27
IROC_SCORE: 0.8763
IROC_PERCENTILE: 63
POISSON_SCORE: 0.1505
POISSON_PERCENTILE: 18
MAXIMUM_REPLICATE_CORRELATION: 0.95

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

source_name: Naive CD4+ T cells; DNA_Lib 662

value: BioSam 183

value: CD4 Naive Primary Cells

value: CD4 Naive Primary Cell

value: Primary Cell


title: ChIP-Seq analysis of WCE in human CD45RA CD8 cells; DNA_Lib 502

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 502
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8724
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9462
****************
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: GSM773034_BI.CD8_Naive_Primary_Cells.Input.Donor_101_8_pooled_leukopaks_Jan_20_2011.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 502-DNA_Lib 502-DNA_Lib 502.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of CD8 Naive Primary Cells ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on CD8 Naive Primary Cells, Donor Donor 101 8 pooled leukopaks Jan 20 2011, were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.10723
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: 27,699,818
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 56
FINDPEAKS_SCORE: 0.0064
FINDPEAKS_PERCENTILE: 75
HOTSPOT_SCORE: 0.0217
HOTSPOT_PERCENTILE: 67
IROC_SCORE: 0.0
IROC_PERCENTILE: 33
POISSON_SCORE: 0.0726
POISSON_PERCENTILE: 70
MAXIMUM_REPLICATE_CORRELATION: 0.91

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

ANALYSIS FILE NAME: GSM773034_BI.CD8_Naive_Primary_Cells.Input.Donor_101_8_pooled_leukopaks_Jan_20_2011.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 502-DNA_Lib 502-DNA_Lib 502.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of CD8 Naive Primary Cells ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from CD8 Naive Primary Cells, Donor Donor 101 8 pooled leukopaks Jan 20 2011, were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.10987
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 Input 01 02
BROWSER_TRACK_DESCRIPTION: BI CD8 Naive Primary Cells ChIP-Seq Input Donor 101 8 pooled leukopaks Jan 20 2011 Library DNA_Lib 502 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 27,699,818
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 56
FINDPEAKS_SCORE: 0.0064
FINDPEAKS_PERCENTILE: 75
HOTSPOT_SCORE: 0.0217
HOTSPOT_PERCENTILE: 67
IROC_SCORE: 0.0
IROC_PERCENTILE: 33
POISSON_SCORE: 0.0726
POISSON_PERCENTILE: 70
MAXIMUM_REPLICATE_CORRELATION: 0.91

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

source_name: Naive CD8+ T cells; DNA_Lib 502

value: BioSam 188

value: CD8 Naive Primary Cells

value: CD8 Naive Primary Cell

value: Dana Farber

value: standard

value: cell/nuclei lysis

value: ChIP-Seq Input

value: Input


title: ChIP-Seq analysis of WCE in human CD45RA CD4 cells; DNA_Lib 663

description:
sample_term_id: CL_0000492
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 663
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8566
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9469
****************
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: GSM772876_BI.CD4_Naive_Primary_Cells.Input.Donor_100_7_pooled_leukopaks_Jan_7_2011.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 663-DNA_Lib 663-DNA_Lib 663.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of CD4 Naive Primary Cells ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on CD4 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.10597
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: 26,817,612
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 56
FINDPEAKS_SCORE: 0.0068
FINDPEAKS_PERCENTILE: 79
HOTSPOT_SCORE: 0.0228
HOTSPOT_PERCENTILE: 69
IROC_SCORE: 0.0
IROC_PERCENTILE: 33
POISSON_SCORE: 0.0714
POISSON_PERCENTILE: 69
MAXIMUM_REPLICATE_CORRELATION: 0.95

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

ANALYSIS FILE NAME: GSM772876_BI.CD4_Naive_Primary_Cells.Input.Donor_100_7_pooled_leukopaks_Jan_7_2011.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 663-DNA_Lib 663-DNA_Lib 663.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of CD4 Naive Primary Cells ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from CD4 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.10861
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: CD4N Input 00 63
BROWSER_TRACK_DESCRIPTION: BI CD4 Naive Primary Cells ChIP-Seq Input Donor 100 7 pooled leukopaks Jan 7 2011 Library DNA_Lib 663 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 26,817,612
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 56
FINDPEAKS_SCORE: 0.0068
FINDPEAKS_PERCENTILE: 79
HOTSPOT_SCORE: 0.0228
HOTSPOT_PERCENTILE: 69
IROC_SCORE: 0.0
IROC_PERCENTILE: 33
POISSON_SCORE: 0.0714
POISSON_PERCENTILE: 69
MAXIMUM_REPLICATE_CORRELATION: 0.95

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

source_name: Naive CD4+ T cells; DNA_Lib 663

value: presumed normal

value: genomic DNA


title: CpG-activated for 4 hrs C57BL6 macrophages

description: thioglycollate-elicited macrophages

source_name: C57BL6 mice

value: CpG-activated 4 hrs

value: macrophages


title: Inf132

description: set:Training Set

data_processing: Raw scan data were background subtracted, VST transformed and subsequently robust spline normalised as performed by the lumi package of Bioconductor.  Array probe features that had a present count in one or more samples were retained.

source_name: peripheral blood

tag: neonate

value: infected

tag: gender

value: Male

tag: tissue

value: peripheral blood

tag: on antibiotics at time of sample

value: Yes

tag: bloodculture result

value: Positive (E faecalis)

value: blood culture 2 and 4 days previously and next day also enterococcus


title: ChIP-Seq analysis of H3K27ac in human CD45RA CD8 cells; DNA_Lib 668

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 668
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8639
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
****************

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

ANALYSIS FILE NAME: GSM772949_BI.CD8_Naive_Primary_Cells.H3K27ac.Donor_100_7_pooled_leukopaks_Jan_7_2011.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 668-DNA_Lib 668-DNA_Lib 668.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of CD8 Naive Primary Cells Histone H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27ac 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.10737
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: 16,514,594
NUMBER_OF_H3K27ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 34
FINDPEAKS_SCORE: 0.1788
FINDPEAKS_PERCENTILE: 44
HOTSPOT_SCORE: 0.2393
HOTSPOT_PERCENTILE: 41
IROC_SCORE: 0.9987
IROC_PERCENTILE: 76
POISSON_SCORE: 0.2538
POISSON_PERCENTILE: 21
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

ANALYSIS FILE NAME: GSM772949_BI.CD8_Naive_Primary_Cells.H3K27ac.Donor_100_7_pooled_leukopaks_Jan_7_2011.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 668-DNA_Lib 668-DNA_Lib 668.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of CD8 Naive Primary Cells Histone H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27ac 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.11001
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 H3K27ac 00 68
BROWSER_TRACK_DESCRIPTION: BI CD8 Naive Primary Cells Histone H3K27ac Donor 100 7 pooled leukopaks Jan 7 2011 Library DNA_Lib 668 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 16,514,594
NUMBER_OF_H3K27ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 34
FINDPEAKS_SCORE: 0.1788
FINDPEAKS_PERCENTILE: 44
HOTSPOT_SCORE: 0.2393
HOTSPOT_PERCENTILE: 41
IROC_SCORE: 0.9987
IROC_PERCENTILE: 76
POISSON_SCORE: 0.2538
POISSON_PERCENTILE: 21
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

source_name: Naive CD8+ T cells; DNA_Lib 668

tag: sample alias

value: BioSam 184

value: CD8 Naive Primary Cells

value: Unknown

value: Primary Cell

value: Donor 100 7 pooled leukopaks Jan 7 2011

value: Protein A-Sepharose 4B

value: 0.5 to 3 million cells

value: ~1 ug

value: 10 ul bed volume

value: Abcam

value: Histone H3K27ac

value: Branson


title: ChIP-Seq analysis of WCE in human CD45RA CD8 cells; DNA_Lib 670

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 670
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8544
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
****************

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

ANALYSIS FILE NAME: GSM772854_BI.CD8_Naive_Primary_Cells.Input.Donor_100_7_pooled_leukopaks_Jan_7_2011.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 670-DNA_Lib 670-DNA_Lib 670.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of CD8 Naive Primary Cells ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input 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.10768
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: 21,863,698
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 56
FINDPEAKS_SCORE: 0.0078
FINDPEAKS_PERCENTILE: 85
HOTSPOT_SCORE: 0.062
HOTSPOT_PERCENTILE: 89
IROC_SCORE: 0.9302
IROC_PERCENTILE: 42
POISSON_SCORE: 0.1113
POISSON_PERCENTILE: 92
MAXIMUM_REPLICATE_CORRELATION: 0.91

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

ANALYSIS FILE NAME: GSM772854_BI.CD8_Naive_Primary_Cells.Input.Donor_100_7_pooled_leukopaks_Jan_7_2011.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 670-DNA_Lib 670-DNA_Lib 670.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of CD8 Naive Primary Cells ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input 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.11032
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 Input 00 70
BROWSER_TRACK_DESCRIPTION: BI CD8 Naive Primary Cells ChIP-Seq Input Donor 100 7 pooled leukopaks Jan 7 2011 Library DNA_Lib 670 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 21,863,698
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 56
FINDPEAKS_SCORE: 0.0078
FINDPEAKS_PERCENTILE: 85
HOTSPOT_SCORE: 0.062
HOTSPOT_PERCENTILE: 89
IROC_SCORE: 0.9302
IROC_PERCENTILE: 42
POISSON_SCORE: 0.1113
POISSON_PERCENTILE: 92
MAXIMUM_REPLICATE_CORRELATION: 0.91

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

source_name: Naive CD8+ T cells; DNA_Lib 670

tag: sample common name

value: presumed normal

value: genomic DNA

value: CD8 Naive Primary Cell

value: Dana Farber

value: standard

value: cell/nuclei lysis

value: ChIP-Seq Input

value: Input


title: ChIP-Seq analysis of H3K27ac in human CD45RA CD4 cells; DNA_Lib 523

description:
sample_term_id: CL_0000492
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 523
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8525
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9466
****************
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: GSM772835_BI.CD4_Naive_Primary_Cells.H3K27ac.Donor_101_8_pooled_leukopaks_Jan_20_2011.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 523-DNA_Lib 523-DNA_Lib 523.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of CD4 Naive Primary Cells Histone H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27ac ChIP-Seq on CD4 Naive Primary Cells, Donor Donor 101 8 pooled leukopaks Jan 20 2011, were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.10784
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: 6,749,825
NUMBER_OF_H3K27ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 34
FINDPEAKS_SCORE: 0.2746
FINDPEAKS_PERCENTILE: 71
HOTSPOT_SCORE: 0.3593
HOTSPOT_PERCENTILE: 76
IROC_SCORE: 0.9989
IROC_PERCENTILE: 85
POISSON_SCORE: 0.364
POISSON_PERCENTILE: 56
MAXIMUM_REPLICATE_CORRELATION: 0.9

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

ANALYSIS FILE NAME: GSM772835_BI.CD4_Naive_Primary_Cells.H3K27ac.Donor_101_8_pooled_leukopaks_Jan_20_2011.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 523-DNA_Lib 523-DNA_Lib 523.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of CD4 Naive Primary Cells Histone H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27ac ChIP-Seq read mappings from CD4 Naive Primary Cells, Donor Donor 101 8 pooled leukopaks Jan 20 2011, were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.11048
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: CD4N H3K27ac 01 23
BROWSER_TRACK_DESCRIPTION: BI CD4 Naive Primary Cells Histone H3K27ac Donor 101 8 pooled leukopaks Jan 20 2011 Library DNA_Lib 523 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 6,749,825
NUMBER_OF_H3K27ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 34
FINDPEAKS_SCORE: 0.2746
FINDPEAKS_PERCENTILE: 71
HOTSPOT_SCORE: 0.3593
HOTSPOT_PERCENTILE: 76
IROC_SCORE: 0.9989
IROC_PERCENTILE: 85
POISSON_SCORE: 0.364
POISSON_PERCENTILE: 56
MAXIMUM_REPLICATE_CORRELATION: 0.9

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

source_name: Naive CD4+ T cells; DNA_Lib 523

value: BioSam 187

value: CD4 Naive Primary Cells

tag: molecule

value: CD4 Naive Primary Cell

value: Unknown

value: Primary Cell


title: ChIP-Seq analysis of H3K36me3 in human CD45RA CD8 cells; DNA_Lib 667

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 667
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8562
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
****************

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

ANALYSIS FILE NAME: GSM772872_BI.CD8_Naive_Primary_Cells.H3K36me3.Donor_100_7_pooled_leukopaks_Jan_7_2011.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 667-DNA_Lib 667-DNA_Lib 667.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of CD8 Naive Primary Cells Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K36me3 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.10765
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: 19,248,586
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.034
FINDPEAKS_PERCENTILE: 14
HOTSPOT_SCORE: 0.1431
HOTSPOT_PERCENTILE: 14
IROC_SCORE: 0.8189
IROC_PERCENTILE: 12
POISSON_SCORE: 0.2713
POISSON_PERCENTILE: 14
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

ANALYSIS FILE NAME: GSM772872_BI.CD8_Naive_Primary_Cells.H3K36me3.Donor_100_7_pooled_leukopaks_Jan_7_2011.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 667-DNA_Lib 667-DNA_Lib 667.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of CD8 Naive Primary Cells Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K36me3 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.11029
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 H3K36me3 00 67
BROWSER_TRACK_DESCRIPTION: BI CD8 Naive Primary Cells Histone H3K36me3 Donor 100 7 pooled leukopaks Jan 7 2011 Library DNA_Lib 667 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 19,248,586
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.034
FINDPEAKS_PERCENTILE: 14
HOTSPOT_SCORE: 0.1431
HOTSPOT_PERCENTILE: 14
IROC_SCORE: 0.8189
IROC_PERCENTILE: 12
POISSON_SCORE: 0.2713
POISSON_PERCENTILE: 14
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

source_name: Naive CD8+ T cells; DNA_Lib 667

value: BioSam 184

value: CD8 Naive Primary Cells

tag: disease

value: Donor 100 7 pooled leukopaks Jan 7 2011

value: Protein A-Sepharose 4B

value: 0.5 to 3 million cells

value: ~1 ug

value: 10 ul bed volume

value: Histone H3K36me3


title: Donor 3, Ebola infected 1hr

status: Public on Sep 01 2011

city: Beaverton

first: Victor

last: DeFilippis

state: OR

address: 505 NW 185th Ave.

department: Vaccine and Gene Therapy Institute

institute: Oregon Health and Science University

description: Gene expression data from Ebola-infected macrophages

hyb_protocol: The arrays were hybridized in a GeneChip Hybridization Oven 640 (Affymetrix, Santa Clara, CA) for 16 hours at 45°C, followed by washing, staining with streptavidin-phycoerythrin (SAPE; Molecular Probes, Eugene, OR), signal amplification with biotinylated anti-streptavidin antibody (Vector Labs, Burlingame, CA), and a final staining with SAPE. The staining and washing were performed using two GeneChip Fluidic Station 400s (Affymetrix, Santa Clara, CA) running standard Affymetrix fluidics script.

scan_protocol: The distribution of fluorescent material on the processed array was determined using the Agilent G2500 GeneArray Scanner (Agilent Technologies, Santa Clara, CA). The array image scan was processed using Affymetrix Microarray Suite, version 5.0 (MAS 5.0), which resulted in the generation of raw, probe level data in the CEL file format.

data_processing: Affymetrix MAS5

source_name: Ebola-infected macrophages harvested at 1h post-treatment from donor 3

label_protocol: Using 5 µg of total RNA as input, messenger RNA was amplified and labeled in two steps. In the first step, mRNA was converted to double-stranded cDNA using Superscript Reverse Transcriptase (Invitrogen, Carlsbad, CA, USA) and an oligo-dT primer linked to a T7 RNA polymerase binding site sequence (IDT, Coralville, IA). Double-stranded cDNA was purified by phenol-chloroform-isoamyl alcohol extraction and a standard ethanol precipitation. In the second step, the cDNA was converted to labeled cRNA (the target) using T7 RNA polymerase in the presence of biotinylated UTP and CTP (Enzo, Farmingdale, NY). Unincorporated nucleotides were removed using the RNeasy Mini kit (Qiagen) and was followed by an ethanol precipitation of the labeled target. The target was fragmented to produce a uniform distribution of short cRNAs. 10µg each of fragmented target was combined with hybridization control oligomer (Affymetrix, Santa Clara, CA) and control cRNAs (1.5pM BioB, 5.0pM BioC, 25pM BioD, and 100pM Cre; Affymetrix, Santa Clara, CA), in hybridization buffer and applied to the array.

growth_protocol: Cells were cultivated in RPMI 1640 (Invitrogen, Carlsbad, CA) containing 20% heat-inactivated human AB serum (Sigma-Aldrich, St. Louis, MO), penicillin (100 U/ml), streptomycin (100 µg/ml), and L-glutamine (2 mM); cells were incubated at 37 ºC in a humidified 5% CO2 environment

extract_protocol: Cell supernatants were removed from the cells 1 h or 6 h post infection, and RNA from cells was purified using the RNeasy Mini Kit (QIAGEN, Valencia, CA) according to the manufacturer's instructions.

treatment_protocol: Cells were infected with either mock virus preparation or ZEBOV at a multiplicity of infection (MOI) of 10.

tag: cells

value: Differentiated macrophages

tag: disease state

value: Ebola infected

tag: post-treatment

tag: donor


title: Donor 1, mock infected 6hr

description: Gene expression data from mock-infected macrophages

source_name: Mock infected macrophages harvested at 6h post-treatment from donor 1

value: mock infected


title: Donor 2, mock infected 6hr

source_name: Mock infected macrophages harvested at 6h post-treatment from donor 2


title: Donor 3, mock infected 1hr

source_name: Mock infected macrophages harvested at 1h post-treatment from donor 3


title: Donor 2, mock infected 1hr

source_name: Mock infected macrophages harvested at 1h post-treatment from donor 2


title: Donor 3, Ebola infected 6hr

source_name: Ebola-infected macrophages harvested at 6h post-treatment from donor 3


title: Donor 1, mock infected 1hr

source_name: Mock infected macrophages harvested at 1h post-treatment from donor 1


title: Donor 2, Ebola infected 1hr

source_name: Ebola-infected macrophages harvested at 1h post-treatment from donor 2


title: Donor 2, Ebola infected 6hr

source_name: Ebola-infected macrophages harvested at 6h post-treatment from donor 2


title: Donor 1, Ebola infected 6hr

source_name: Ebola-infected macrophages harvested at 6h post-treatment from donor 1


title: Donor 3, mock infected 6hr

source_name: Mock infected macrophages harvested at 6h post-treatment from donor 3


title: Donor 1, Ebola infected 1hr

source_name: Ebola-infected macrophages harvested at 1h post-treatment from donor 1