title: ChIP-Seq analysis of H3K4me1 in human CD56+ ectoderm cells; DNA_Lib 1809

status: Public on Jun 24 2013

city: Cambridge

first: BROAD

last: INSTITUTE

state: MA

institute: Broad Institute

description:
sample_term_id: CL_0000221
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 1809
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.13167
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.13314
****************
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: GSM997254_BI.hESC_Derived_CD56+_Ectoderm_Cultured_Cells.H3K4me1.DNA_Lib_1809.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 1809.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of hESC Derived CD56+ Ectoderm Cultured Cells H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K4me1 ChIP-Seq on the hESC Derived CD56+ Ectoderm Cultured Cells, Library DNA_Lib 1809, 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.17210
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 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 13,896,320
FINDPEAKS_SCORE: 0.3706
FINDPEAKS_PERCENTILE: 72
HOTSPOT_SCORE: 0.4573
HOTSPOT_PERCENTILE: 78
IROC_SCORE: 0.9809
IROC_PERCENTILE: 59
POISSON_SCORE: 0.5743
POISSON_PERCENTILE: 83
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM997254_BI.hESC_Derived_CD56+_Ectoderm_Cultured_Cells.H3K4me1.DNA_Lib_1809.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 1809.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of hESC Derived CD56+ Ectoderm Cultured Cells H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K4me1 ChIP-Seq read mappings from the hESC Derived CD56+ Ectoderm Cultured Cells, Library DNA_Lib 1809, 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.17393
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 9
BROWSER_TRACK_NAME: hDCEcto H3K4me1 09
BROWSER_TRACK_DESCRIPTION: BI hESC Derived CD56+ Ectoderm Cultured Cells Histone H3K4me1 Library DNA_Lib 1809 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 13,896,320
FINDPEAKS_SCORE: 0.3706
FINDPEAKS_PERCENTILE: 72
HOTSPOT_SCORE: 0.4573
HOTSPOT_PERCENTILE: 78
IROC_SCORE: 0.9809
IROC_PERCENTILE: 59
POISSON_SCORE: 0.5743
POISSON_PERCENTILE: 83
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: CD56+ ectodermal germ layer cells derived in vitro from embrionic stem cells by culture in the presence of inhibitors of the BMP, TGFbeta, and WNT signaling pathways.; DNA_Lib 1809

extract_protocol: Library construction protocol: Single read - Illumina

tag: sample alias

value: BioSam 707

tag: sample common name

tag: lineage

value: ectoderm

tag: medium

value: Days 0-5:DMEM F12, 15% KSR, Dorsomorphin (2um), A83-01 (2um), PNU 74654 (2um)

tag: molecule

value: genomic DNA

tag: disease

value: presumed normal

tag: line

value: CD56+ ectoderm

value: adherence

tag: batch

value: BioSAli 877

value: Cell Line

tag: Sex

value: Male

value: Harvard

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 H3K4me1

value: Branson


title: ChIP-Seq analysis of H3K4me3 in human CD56+ ectoderm cells; DNA_Lib 2073

type: SRA

country: USA

description:
sample_term_id: CL_0000221
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 2073
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.13134
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.13310
****************
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: GSM997221_BI.hESC_Derived_CD56+_Ectoderm_Cultured_Cells.H3K4me3.DNA_Lib_2073.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 2073.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of hESC Derived CD56+ Ectoderm Cultured Cells H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K4me3 ChIP-Seq on the hESC Derived CD56+ Ectoderm Cultured Cells, Library DNA_Lib 2073, 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.17254
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 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 11,717,382
FINDPEAKS_SCORE: 0.4879
FINDPEAKS_PERCENTILE: 79
HOTSPOT_SCORE: 0.5065
HOTSPOT_PERCENTILE: 77
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.4931
POISSON_PERCENTILE: 75
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

ANALYSIS FILE NAME: GSM997221_BI.hESC_Derived_CD56+_Ectoderm_Cultured_Cells.H3K4me3.DNA_Lib_2073.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 2073.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of hESC Derived CD56+ Ectoderm Cultured Cells H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K4me3 ChIP-Seq read mappings from the hESC Derived CD56+ Ectoderm Cultured Cells, Library DNA_Lib 2073, 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.17437
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 9
BROWSER_TRACK_NAME: hDCEcto H3K4me3 73
BROWSER_TRACK_DESCRIPTION: BI hESC Derived CD56+ Ectoderm Cultured Cells Histone H3K4me3 Library DNA_Lib 2073 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 11,717,382
FINDPEAKS_SCORE: 0.4879
FINDPEAKS_PERCENTILE: 79
HOTSPOT_SCORE: 0.5065
HOTSPOT_PERCENTILE: 77
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.4931
POISSON_PERCENTILE: 75
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

molecule: genomic DNA

organism: Homo sapiens

source_name: CD56+ ectodermal germ layer cells derived in vitro from embrionic stem cells by culture in the presence of inhibitors of the BMP, TGFbeta, and WNT signaling pathways.; DNA_Lib 2073

value: BioSam 826

value: ectoderm

value: CD56 ectoderm - Days 0-5:DMEM F12, 15% KSR, Dorsomorphin (2um), A83-01 (2um), PNU 74654 (2um)

tag: passage

value: BioSAli 1031

value: Millipore

value: Histone H3K4me3


title: spheroids_rep1

status: Public on Jan 03 2014

type: RNA

city: indianapolis

first: salvatore

last: condello

address: 980 west walnut street

institute: iu school of medicine

hyb_protocol: Standar hybridization cocktail, hybed 17 hours at 45C.

scan_protocol: Standard wash and stain controlled by GCOS

data_processing: Cel Files generated by GCOS, imported into Partek (ver. 6.2) and RMA signals were generated for only the core probe sets (28,869).   RMA signals were generated for the core probe sets using the RMA background correction, quantile normalization and summarization by Median Polish.  Summarized signals for each probe set were log2 transformed.

label: biotin

molecule: total RNA

source_name: ovarian cancer cell line IGROV-1

label_protocol: Standard Affymetrix WT labeling and control kit.

extract_protocol: standard RNA extraction. Trizol

tag: cell type

value: ovarian cancer

tag: phenotype

value: spheroids


title: Replicate 1

status: Public on Oct 08 2014

city: Suzhou

first: Yiqiang

last: Wang

state: Jiangsu

address: 111 Renai Road

country: China

institute: Xi'an Jiaotong-Liverpool University

hyb_protocol: An Agilent SurePrint G3 Human Gene Expression 8x60K (Cat# G2543-60015. Agilent) was used

scan_protocol: G2505C was used to scan the arrys and images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).

data_processing: Normalized with GENESPRING12.0 (Silicon Genetics, Redwood City, CA)

label_protocol: Low Input Quick-Amp Labeling Kit of Agilent was used to amplify and label cRNA, the FlgE treated or control samples labeled with Cy3 and Cy5 fluorescence respectively.

growth_protocol: The SV40-immortalized human corneal epithelial cell line (HCEC, ATCC CRL-11135) were seeded in 24well plates at 1.5×104 in 500μL Dulbecco’s modified Eagle’s medium (DMEM)/F12 medium supplemented with 10% heat-inactivated fetal bovine serum (Invitrogen, Carlsbad, CA, USA) at 37℃.

extract_protocol: mirVana RNA Isolation Kit (ABS p/n AM1556) was used to extract RNA

treatment_protocol: When 80%-90% confluence was reached, the cells were starved for 4 hours in culture medium without bovine serum, and then FlgE was added to 20ug/mL for 4 hours in triplicates. Control wells were added with PBS instead.

tag: cell line

value: HCEC

value: SV40-immortalized human corneal epithelial cells

tag: treated with

value: 20ug/mL FlgE for 4hrs

value: PBS for 4hrs


title: Replicate 2


title: Retina of P9 WT C57BL/6J vs. RNV of P13 OIR C57BL/6J, replicate 2

status: Public on Dec 05 2012

description:
This Sample represents 2 dye-swap samples.
Retina_P9_RNV_P13_Rep2_1.gpr: Cy5=WT; Cy3=OIR
Retina_P9_RNV_P13_Rep2_2.gpr: Cy5=OIR; Cy3=WT
The non-averaged log2 normalized ratios (Cy5/Cy3) in the Sample data table are derived from Retina_P9_RNV_P13_Rep2_1.gpr and Retina_P9_RNV_P13_Rep2_2.gpr.

hyb_protocol: Phalanx Hybridization Protocol.

scan_protocol: Scanned on a GenePix 4000B [90708].

data_processing: Data extraction and filtering, LOWESS normalized (R language software was used), MA plot for each array, calculated average log2 ratios (treated vs. control sample).

label: Cy5, Cy3

organism: Mus musculus

source_name: normal retina of wild-type mice, postnatal 9 days (N9)

label_protocol: The sample preparation reagent used for this service is the Ambion MessageAmp aRNA kit (Cat. No. 1753) or the Ambion amino allyl cDNA kit (Cat. No. 1705). The reactive amino group of 5-(3-aminoallyl)-UTP/5-(3-aminoallyl)-dUTP was used to conjugate the purified aRNA/cDNA with the NHS-CyDye. Labeling efficiency can be calculated by the concentration of CyDye and aRNA/cDNA measured by NanoDrop ND-1000. For the sake of good microarray results, labeling efficiency should be above 10.

growth_protocol: OIR C57BL/6J model: newborn pups at postnatal day 7 were transferred to chambers supplied with 75%±2% oxygen for 5 days, returned to room air at P12, and remained in this condition until sacrifice; wild-type C57BL/6J pups were rasied in room air from birth to sacrifice.

extract_protocol: Total RNA was extracted using Trizol following the manufacturer's instructions.

treatment_protocol: RNV induction with 75%±2% oxygen.

tag: strain/background

tag: genotype

value: WT

tag: tissue

value: retina

tag: developmental stage

value: postnatal day 9

label: Cy3, Cy5

source_name: RNV of OIR mice, postnatal 13 days (P13)

value: OIR

value: postnatal day 13


title: P9 vs. P30 retina of WT C57BL/6J, replicate 2

description:
This Sample represents 2 dye-swap samples.
Retina_P9_P30_Rep2_1.gpr: Cy5=WT(N9); Cy3=WT(N30)
Retina_P9_P30_Rep2_2.gpr: Cy5=WT(N30); Cy3=WT(N9)
The non-averaged log2 normalized ratios (Cy5/Cy3) in the Sample data table are derived from Retina_P9_P30_Rep2_1.gpr and Retina_P9_P30_Rep2_2.gpr.

source_name: normal retina of wild-type mice, postnatal 30 days (N30)

value: postnatal day 30


title: ChIP-Seq analysis of H3K4me3 in human CD45RO CD4 cells; DNA_Lib 482

status: Public on Dec 28 2011

description:
sample_term_id: CL_0000897
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 482
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8615
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9464
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM772925_BI.CD4_Memory_Primary_Cells.H3K4me3.Donor_101_8_pooled_leukopaks_Jan_20_2011.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 482-DNA_Lib 482-DNA_Lib 482-DNA_Lib 482.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of CD4 Memory Primary Cells Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me3 ChIP-Seq on CD4 Memory Primary Cells, Donor Donor 101 8 pooled leukopaks Jan 20 2011, were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.10595
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: 20,986,541
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.2171
FINDPEAKS_PERCENTILE: 43
HOTSPOT_SCORE: 0.2395
HOTSPOT_PERCENTILE: 31
IROC_SCORE: 0.9998
IROC_PERCENTILE: 85
POISSON_SCORE: 0.2699
POISSON_PERCENTILE: 28
MAXIMUM_REPLICATE_CORRELATION: 0.87

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

ANALYSIS FILE NAME: GSM772925_BI.CD4_Memory_Primary_Cells.H3K4me3.Donor_101_8_pooled_leukopaks_Jan_20_2011.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 482-DNA_Lib 482-DNA_Lib 482-DNA_Lib 482.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of CD4 Memory Primary Cells Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me3 ChIP-Seq read mappings from CD4 Memory Primary Cells, Donor Donor 101 8 pooled leukopaks Jan 20 2011, were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.10859
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 5
BROWSER_TRACK_NAME: CD4M H3K4me3 01 82
BROWSER_TRACK_DESCRIPTION: BI CD4 Memory Primary Cells Histone H3K4me3 Donor 101 8 pooled leukopaks Jan 20 2011 Library DNA_Lib 482 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 20,986,541
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.2171
FINDPEAKS_PERCENTILE: 43
HOTSPOT_SCORE: 0.2395
HOTSPOT_PERCENTILE: 31
IROC_SCORE: 0.9998
IROC_PERCENTILE: 85
POISSON_SCORE: 0.2699
POISSON_PERCENTILE: 28
MAXIMUM_REPLICATE_CORRELATION: 0.87

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

source_name: Memory CD4+ T cells; DNA_Lib 482

tag: sample alias

value: BioSam 185

tag: sample common name

value: CD4 Memory Primary Cells

value: presumed normal

value: genomic DNA

tag: markers

value: CD45RO CD4

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: Branson


title: ChIP-Seq analysis of H3K4me1 in human CD45RA CD8 cells; DNA_Lib 500

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 500
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8722
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: GSM773032_BI.CD8_Naive_Primary_Cells.H3K4me1.Donor_101_8_pooled_leukopaks_Jan_20_2011.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 500-DNA_Lib 500-DNA_Lib 500-DNA_Lib 500.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of CD8 Naive Primary Cells Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me1 ChIP-Seq on CD8 Naive Primary Cells, Donor Donor 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.10631
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: 19,411,082
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.3044
FINDPEAKS_PERCENTILE: 69
HOTSPOT_SCORE: 0.3301
HOTSPOT_PERCENTILE: 56
IROC_SCORE: 0.9944
IROC_PERCENTILE: 80
POISSON_SCORE: 0.4214
POISSON_PERCENTILE: 35
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

ANALYSIS FILE NAME: GSM773032_BI.CD8_Naive_Primary_Cells.H3K4me1.Donor_101_8_pooled_leukopaks_Jan_20_2011.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 500-DNA_Lib 500-DNA_Lib 500-DNA_Lib 500.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of CD8 Naive Primary Cells Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me1 ChIP-Seq read mappings from CD8 Naive Primary Cells, Donor Donor 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.10895
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 5
BROWSER_TRACK_NAME: CD8N H3K4me1 01 00
BROWSER_TRACK_DESCRIPTION: BI CD8 Naive Primary Cells Histone H3K4me1 Donor 101 8 pooled leukopaks Jan 20 2011 Library DNA_Lib 500 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 19,411,082
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.3044
FINDPEAKS_PERCENTILE: 69
HOTSPOT_SCORE: 0.3301
HOTSPOT_PERCENTILE: 56
IROC_SCORE: 0.9944
IROC_PERCENTILE: 80
POISSON_SCORE: 0.4214
POISSON_PERCENTILE: 35
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

source_name: Naive CD8+ T cells; DNA_Lib 500

value: BioSam 188

value: CD8 Naive Primary Cells

tag: molecule

value: CD8 Naive Primary Cell

value: Abcam

value: Histone H3K4me1


title: ChIP-Seq analysis of H3K4me3 in human CD45RO CD4 cells; DNA_Lib 536

description:
sample_term_id: CL_0000897
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 536
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8644
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9467
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM772954_BI.CD4_Memory_Primary_Cells.H3K4me3.Donor_100_7_pooled_leukopaks_Jan_7_2011.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 536-DNA_Lib 536-DNA_Lib 536.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of CD4 Memory Primary Cells Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me3 ChIP-Seq on CD4 Memory Primary Cells, Donor Donor 100 7 pooled leukopaks Jan 7 2011, were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.10653
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: 28,213,970
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.0623
FINDPEAKS_PERCENTILE: 6
HOTSPOT_SCORE: 0.0994
HOTSPOT_PERCENTILE: 4
IROC_SCORE: 0.9791
IROC_PERCENTILE: 19
POISSON_SCORE: 0.1401
POISSON_PERCENTILE: 4
MAXIMUM_REPLICATE_CORRELATION: 0.87

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

ANALYSIS FILE NAME: GSM772954_BI.CD4_Memory_Primary_Cells.H3K4me3.Donor_100_7_pooled_leukopaks_Jan_7_2011.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 536-DNA_Lib 536-DNA_Lib 536.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of CD4 Memory Primary Cells Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me3 ChIP-Seq read mappings from CD4 Memory Primary Cells, Donor Donor 100 7 pooled leukopaks Jan 7 2011, were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.10917
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 5
BROWSER_TRACK_NAME: CD4M H3K4me3 00 36
BROWSER_TRACK_DESCRIPTION: BI CD4 Memory Primary Cells Histone H3K4me3 Donor 100 7 pooled leukopaks Jan 7 2011 Library DNA_Lib 536 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 28,213,970
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.0623
FINDPEAKS_PERCENTILE: 6
HOTSPOT_SCORE: 0.0994
HOTSPOT_PERCENTILE: 4
IROC_SCORE: 0.9791
IROC_PERCENTILE: 19
POISSON_SCORE: 0.1401
POISSON_PERCENTILE: 4
MAXIMUM_REPLICATE_CORRELATION: 0.87

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

source_name: Memory CD4+ T cells; DNA_Lib 536

value: BioSam 181

value: CD4 Memory Primary Cells

value: presumed normal

tag: disease

value: Donor 100 7 pooled leukopaks Jan 7 2011

value: Millipore

value: Histone H3K4me3


title: ChIP-Seq analysis of H3K4me3 in human CD45RA CD8 cells; DNA_Lib 665

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 665
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8612
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: GSM772922_BI.CD8_Naive_Primary_Cells.H3K4me3.Donor_100_7_pooled_leukopaks_Jan_7_2011.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 665-DNA_Lib 665-DNA_Lib 665.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of CD8 Naive Primary Cells Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me3 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.10761
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: 15,619,994
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.1362
FINDPEAKS_PERCENTILE: 20
HOTSPOT_SCORE: 0.2022
HOTSPOT_PERCENTILE: 28
IROC_SCORE: 0.9979
IROC_PERCENTILE: 41
POISSON_SCORE: 0.2287
POISSON_PERCENTILE: 19
MAXIMUM_REPLICATE_CORRELATION: 0.93

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

ANALYSIS FILE NAME: GSM772922_BI.CD8_Naive_Primary_Cells.H3K4me3.Donor_100_7_pooled_leukopaks_Jan_7_2011.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 665-DNA_Lib 665-DNA_Lib 665.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of CD8 Naive Primary Cells Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me3 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.11025
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 H3K4me3 00 65
BROWSER_TRACK_DESCRIPTION: BI CD8 Naive Primary Cells Histone H3K4me3 Donor 100 7 pooled leukopaks Jan 7 2011 Library DNA_Lib 665 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 15,619,994
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.1362
FINDPEAKS_PERCENTILE: 20
HOTSPOT_SCORE: 0.2022
HOTSPOT_PERCENTILE: 28
IROC_SCORE: 0.9979
IROC_PERCENTILE: 41
POISSON_SCORE: 0.2287
POISSON_PERCENTILE: 19
MAXIMUM_REPLICATE_CORRELATION: 0.93

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

source_name: Naive CD8+ T cells; DNA_Lib 665

value: BioSam 184

value: genomic DNA

value: Unknown

value: Primary Cell

value: Dana Farber

value: Protein A-Sepharose 4B


title: ChIP-Seq analysis of H3K4me3 in human CD45RO CD8 cells; DNA_Lib 543

description:
sample_term_id: CL_0000909
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 543
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8657
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9468
****************
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: GSM772967_BI.CD8_Memory_Primary_Cells.H3K4me3.Donor_100_7_pooled_leukopaks_Jan_7_2011.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 543-DNA_Lib 543-DNA_Lib 543.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of CD8 Memory Primary Cells Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me3 ChIP-Seq on CD8 Memory Primary Cells, Donor Donor 100 7 pooled leukopaks Jan 7 2011, were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.10672
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 31,454,341
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.1184
FINDPEAKS_PERCENTILE: 15
HOTSPOT_SCORE: 0.1454
HOTSPOT_PERCENTILE: 11
IROC_SCORE: 0.9983
IROC_PERCENTILE: 44
POISSON_SCORE: 0.1851
POISSON_PERCENTILE: 7
MAXIMUM_REPLICATE_CORRELATION: 0.94

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

ANALYSIS FILE NAME: GSM772967_BI.CD8_Memory_Primary_Cells.H3K4me3.Donor_100_7_pooled_leukopaks_Jan_7_2011.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 543-DNA_Lib 543-DNA_Lib 543.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of CD8 Memory Primary Cells Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me3 ChIP-Seq read mappings from CD8 Memory Primary Cells, Donor Donor 100 7 pooled leukopaks Jan 7 2011, were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.10936
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: CD8M H3K4me3 00 43
BROWSER_TRACK_DESCRIPTION: BI CD8 Memory Primary Cells Histone H3K4me3 Donor 100 7 pooled leukopaks Jan 7 2011 Library DNA_Lib 543 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 31,454,341
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.1184
FINDPEAKS_PERCENTILE: 15
HOTSPOT_SCORE: 0.1454
HOTSPOT_PERCENTILE: 11
IROC_SCORE: 0.9983
IROC_PERCENTILE: 44
POISSON_SCORE: 0.1851
POISSON_PERCENTILE: 7
MAXIMUM_REPLICATE_CORRELATION: 0.94

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

source_name: Memory CD8+ T cells; DNA_Lib 543

value: BioSam 182

value: CD8 Memory Primary Cells

value: CD45RO CD8

value: 0.5 to 3 million cells

value: cell/nuclei lysis

value: ~1 ug

value: 10 ul bed volume

value: Branson


title: RNA-Seq analysis of cDNA_Lib 4 derived from human liver cells; cDNA_Lib 4

status: Public on Sep 05 2012

description:
sample_term_id: UBERON_0002107
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: mRNA-Seq for REMC on Illumina
Library name: cDNA_Lib 4
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.12079
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.12085
****************
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: transcriptomic

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

ANALYSIS FILE NAME: GSM916093_BI.Adult_Liver.mRNA-Seq.Donor_177_REMC_27.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: cDNA_Lib 4.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of Adult Liver mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by mRNA-Seq on Adult Liver, Donor Donor 177 REMC 27 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.13717
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: mRNA-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: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 122,094,489
NUMBER_OF_MRNA-SEQ_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 22
PERCENT_READS_MAPPING_TO_UCSC_GENES: 87.29
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 36
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM916093_BI.Adult_Liver.mRNA-Seq.Donor_177_REMC_27.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: cDNA_Lib 4.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of Adult Liver mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina mRNA-Seq read mappings from Adult Liver, Donor Donor 177 REMC 27 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.13720
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 8
BROWSER_TRACK_NAME: AL mRNA 77
BROWSER_TRACK_DESCRIPTION: BI Adult Liver mRNA-Seq Donor 177 REMC 27 Library cDNA_Lib 4 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 122,094,489
NUMBER_OF_MRNA-SEQ_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 22
PERCENT_READS_MAPPING_TO_UCSC_GENES: 87.29
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 36
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: normal liver,resected from patient with metastatic carcinoid; cDNA_Lib 4

extract_protocol: Library construction protocol: Strand specific cDNA libraries were constructed for Illumina sequencing using the dUTP method essentially as described in S. Zhong et al, Cold Spring Harbor Protoc 8, 940 - 949 (2011).

value: BioSam 321 REMC 27

value: Adult Liver

value: Surgery

value: patient with metastatic carcinoid

value: Caucasian

value: Female

value: Primary Tissue

value: Liver

value: Donor 177 REMC 27

value: MGH

value: 45.0 Years

value: 1.8X SPRI cleanup (no size selection)

value: Dynabeads mRNA purification kit (Invitrogen)

value: 95C  2mins, 10 cycles of: 98C for 30 sec, 55C for 30 sec, 72C for 1 min, then 72C for 10 min, hold 4C

value: NNNNNN

value: Qiagen AllPrep DNA/RNA/Protein Mini Kit

value: Adapter ligated cDNA made by reverse transcription of RNA

value: PFU Ultra II

value: CAAGCAGAAGACGGCATACGAGAT

value: 98C for 40 min in 0.2 mM sodium citrate, pH 6.4 (Ambion), followed by concentrating it to 3.5 ul, mixing with 1 ul 2 uM SMART tagged random primer, incubating at 70deg C for 10 min and chilling on ice for 2 min.

value: mRNA-Seq

value: We synthesized first-strand cDNA with this RNA primer mix by adding 4 ul 5x first-strand buffer, 2 ul 100 mM DTT, 1 ul 10 mM dNTPs, 4 ug of actinomycin D, 200 U SuperScript III and 20 U SUPERase-In, incubating at room temperature for 10 min followed by 1 h at 55degC. We cleaned up first-strand cDNA by PCIA extraction twice, ethanol precipitation with 0.1 volumes 5 M ammonium acetate to remove dNTPs and resuspension in 104 ul H2O. We synthesized second-strand cDNA by adding 4 ul of 5x first-strand buffer, 2 ul of 100 mM DTT, 4 ul of 10 mM dNTPs with dTTP replaced by dUTP (Sigma), 30 ul of 5x second-strand buffer, 40 U of Escherichia coli DNA polymerase, 10 U of E. coli DNA ligase and 2 U of E. coli RNase H, and incubating at 16degC for 2 h.


title: Retina of WT C57BL/6J vs. RNV of OIR C57BL/6J, P8, replicate 2

description:
This Sample represents 2 dye-swap samples.
RNV_P8_Rep2_1.gpr: Cy5=WT; Cy3=OIR
RNV_P8_Rep2_2.gpr: Cy5=OIR; Cy3=WT
The non-averaged log2 normalized ratios (Cy5/Cy3) in the Sample data table are derived from RNV_P8_Rep2_1.gpr and RNV_P8_Rep2_2.gpr.

source_name: normal retina of wild-type mice, postnatal 8 days (N8)

value: WT

value: retina

value: postnatal day 8

source_name: RNV of OIR mice, postnatal 8 days (P8)

value: OIR


title: ChIP-Seq analysis of H3K4me3 in human CD45RA CD8 cells; DNA_Lib 498

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 498
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8586
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: GSM772896_BI.CD8_Naive_Primary_Cells.H3K4me3.Donor_101_8_pooled_leukopaks_Jan_20_2011.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 498-DNA_Lib 498-DNA_Lib 498-DNA_Lib 498.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of CD8 Naive Primary Cells Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me3 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.10689
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: 22,304,344
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.223
FINDPEAKS_PERCENTILE: 48
HOTSPOT_SCORE: 0.2473
HOTSPOT_PERCENTILE: 37
IROC_SCORE: 0.9998
IROC_PERCENTILE: 85
POISSON_SCORE: 0.2749
POISSON_PERCENTILE: 30
MAXIMUM_REPLICATE_CORRELATION: 0.93

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

ANALYSIS FILE NAME: GSM772896_BI.CD8_Naive_Primary_Cells.H3K4me3.Donor_101_8_pooled_leukopaks_Jan_20_2011.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 498-DNA_Lib 498-DNA_Lib 498-DNA_Lib 498.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of CD8 Naive Primary Cells Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me3 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.10953
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 H3K4me3 01 98
BROWSER_TRACK_DESCRIPTION: BI CD8 Naive Primary Cells Histone H3K4me3 Donor 101 8 pooled leukopaks Jan 20 2011 Library DNA_Lib 498 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 22,304,344
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.223
FINDPEAKS_PERCENTILE: 48
HOTSPOT_SCORE: 0.2473
HOTSPOT_PERCENTILE: 37
IROC_SCORE: 0.9998
IROC_PERCENTILE: 85
POISSON_SCORE: 0.2749
POISSON_PERCENTILE: 30
MAXIMUM_REPLICATE_CORRELATION: 0.93

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

source_name: Naive CD8+ T cells; DNA_Lib 498

value: BioSam 188

value: CD8 Naive Primary Cells

value: presumed normal

value: genomic DNA

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: Millipore

value: Histone H3K4me3

value: Branson


title: Retina of WT C57BL/6J vs. RNV of OIR C57BL/6J, P12, replicate 2

description:
This Sample represents 2 dye-swap samples.
RNV_P12_Rep2_1.gpr: Cy5=WT; Cy3=OIR
RNV_P12_Rep2_2.gpr: Cy5=OIR; Cy3=WT
The non-averaged log2 normalized ratios (Cy5/Cy3) in the Sample data table are derived from RNV_P12_Rep2_1.gpr and RNV_P12_Rep2_2.gpr.

source_name: normal retina of wild-type mice, postnatal 12 days (N12)

value: WT

value: retina

value: postnatal day 12

source_name: RNV of OIR mice, postnatal 12 days (P12)

value: OIR


title: ChIP-Seq analysis of H3K4me3 in human CD45RA CD4 cells; DNA_Lib 658

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 658
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8638
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: GSM772948_BI.CD4_Naive_Primary_Cells.H3K4me3.Donor_100_7_pooled_leukopaks_Jan_7_2011.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 658-DNA_Lib 658-DNA_Lib 658.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of CD4 Naive Primary Cells Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me3 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.10722
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: 25,332,708
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.2222
FINDPEAKS_PERCENTILE: 46
HOTSPOT_SCORE: 0.2442
HOTSPOT_PERCENTILE: 35
IROC_SCORE: 0.9998
IROC_PERCENTILE: 85
POISSON_SCORE: 0.2773
POISSON_PERCENTILE: 31
MAXIMUM_REPLICATE_CORRELATION: 0.91

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

ANALYSIS FILE NAME: GSM772948_BI.CD4_Naive_Primary_Cells.H3K4me3.Donor_100_7_pooled_leukopaks_Jan_7_2011.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 658-DNA_Lib 658-DNA_Lib 658.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of CD4 Naive Primary Cells Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me3 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.10986
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 H3K4me3 00 58
BROWSER_TRACK_DESCRIPTION: BI CD4 Naive Primary Cells Histone H3K4me3 Donor 100 7 pooled leukopaks Jan 7 2011 Library DNA_Lib 658 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 25,332,708
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.2222
FINDPEAKS_PERCENTILE: 46
HOTSPOT_SCORE: 0.2442
HOTSPOT_PERCENTILE: 35
IROC_SCORE: 0.9998
IROC_PERCENTILE: 85
POISSON_SCORE: 0.2773
POISSON_PERCENTILE: 31
MAXIMUM_REPLICATE_CORRELATION: 0.91

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

source_name: Naive CD4+ T cells; DNA_Lib 658

value: BioSam 183

value: CD4 Naive Primary Cells

value: presumed normal

value: genomic DNA

value: CD4 Naive Primary Cell

value: Donor 100 7 pooled leukopaks Jan 7 2011


title: Retina of P9 WT C57BL/6J vs. RNV of P13 OIR C57BL/6J, replicate 3

description:
This Sample represents 2 dye-swap samples.
Retina_P9_RNV_P13_Rep3_1.gpr: Cy5=WT; Cy3=OIR
Retina_P9_RNV_P13_Rep3_2.gpr: Cy5=OIR; Cy3=WT
The non-averaged log2 normalized ratios (Cy5/Cy3) in the Sample data table are derived from Retina_P9_RNV_P13_Rep3_1.gpr and Retina_P9_RNV_P13_Rep3_2.gpr.

value: postnatal day 9

value: postnatal day 13


title: Retina of WT C57BL/6J vs. RNV of OIR C57BL/6J, P13, replicate 2

description:
This Sample represents 2 dye-swap samples.
RNV_P13_Rep2_1.gpr: Cy5=WT; Cy3=OIR
RNV_P13_Rep2_2.gpr: Cy5=OIR; Cy3=WT
The non-averaged log2 normalized ratios (Cy5/Cy3) in the Sample data table are derived from RNV_P13_Rep2_1.gpr and RNV_P13_Rep2_2.gpr.

source_name: normal retina of wild-type mice, postnatal 13 days (N13)


title: Retina of WT C57BL/6J vs. RNV of OIR C57BL/6J, P8, replicate 1

description:
This Sample represents 2 dye-swap samples.
RNV_P8_Rep1_1.gpr: Cy5=WT; Cy3=OIR
RNV_P8_Rep1_2.gpr: Cy5=OIR; Cy3=WT
The non-averaged log2 normalized ratios (Cy5/Cy3) in the Sample data table are derived from RNV_P8_Rep1_1.gpr and RNV_P8_Rep1_2.gpr.

value: postnatal day 8


title: ChIP-Seq analysis of H3K4me1 in human CD45RO CD4 cells; DNA_Lib 481

description:
sample_term_id: CL_0000897
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 481
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8614
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9464
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM772924_BI.CD4_Memory_Primary_Cells.H3K4me1.Donor_101_8_pooled_leukopaks_Jan_20_2011.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 481-DNA_Lib 481-DNA_Lib 481-DNA_Lib 481.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of CD4 Memory Primary Cells Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me1 ChIP-Seq on CD4 Memory Primary Cells, Donor Donor 101 8 pooled leukopaks Jan 20 2011, were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.10836
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: 18,568,647
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.2533
FINDPEAKS_PERCENTILE: 46
HOTSPOT_SCORE: 0.297
HOTSPOT_PERCENTILE: 31
IROC_SCORE: 0.9914
IROC_PERCENTILE: 69
POISSON_SCORE: 0.3786
POISSON_PERCENTILE: 20
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

ANALYSIS FILE NAME: GSM772924_BI.CD4_Memory_Primary_Cells.H3K4me1.Donor_101_8_pooled_leukopaks_Jan_20_2011.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 481-DNA_Lib 481-DNA_Lib 481-DNA_Lib 481.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of CD4 Memory Primary Cells Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me1 ChIP-Seq read mappings from CD4 Memory Primary Cells, Donor Donor 101 8 pooled leukopaks Jan 20 2011, were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.11100
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 5
BROWSER_TRACK_NAME: CD4M H3K4me1 01 81
BROWSER_TRACK_DESCRIPTION: BI CD4 Memory Primary Cells Histone H3K4me1 Donor 101 8 pooled leukopaks Jan 20 2011 Library DNA_Lib 481 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 18,568,647
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.2533
FINDPEAKS_PERCENTILE: 46
HOTSPOT_SCORE: 0.297
HOTSPOT_PERCENTILE: 31
IROC_SCORE: 0.9914
IROC_PERCENTILE: 69
POISSON_SCORE: 0.3786
POISSON_PERCENTILE: 20
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

source_name: Memory CD4+ T cells; DNA_Lib 481

value: BioSam 185

value: CD4 Memory Primary Cells

value: CD45RO CD4

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 H3K4me1


title: ChIP-Seq analysis of H3K4me3 in human CD45RO CD8 cells; DNA_Lib 529

description:
sample_term_id: CL_0000909
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 529
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8619
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9465
****************
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: GSM772929_BI.CD8_Memory_Primary_Cells.H3K4me3.Donor_101_8_pooled_leukopaks_Jan_20_2011.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 529-DNA_Lib 529-DNA_Lib 529.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of CD8 Memory Primary Cells Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me3 ChIP-Seq on CD8 Memory Primary Cells, Donor Donor 101 8 pooled leukopaks Jan 20 2011, were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.10628
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: 29,715,165
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.1284
FINDPEAKS_PERCENTILE: 19
HOTSPOT_SCORE: 0.1597
HOTSPOT_PERCENTILE: 15
IROC_SCORE: 0.9968
IROC_PERCENTILE: 35
POISSON_SCORE: 0.2062
POISSON_PERCENTILE: 13
MAXIMUM_REPLICATE_CORRELATION: 0.94

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

ANALYSIS FILE NAME: GSM772929_BI.CD8_Memory_Primary_Cells.H3K4me3.Donor_101_8_pooled_leukopaks_Jan_20_2011.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 529-DNA_Lib 529-DNA_Lib 529.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of CD8 Memory Primary Cells Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me3 ChIP-Seq read mappings from CD8 Memory Primary Cells, Donor Donor 101 8 pooled leukopaks Jan 20 2011, were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.10892
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: CD8M H3K4me3 01 29
BROWSER_TRACK_DESCRIPTION: BI CD8 Memory Primary Cells Histone H3K4me3 Donor 101 8 pooled leukopaks Jan 20 2011 Library DNA_Lib 529 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 29,715,165
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.1284
FINDPEAKS_PERCENTILE: 19
HOTSPOT_SCORE: 0.1597
HOTSPOT_PERCENTILE: 15
IROC_SCORE: 0.9968
IROC_PERCENTILE: 35
POISSON_SCORE: 0.2062
POISSON_PERCENTILE: 13
MAXIMUM_REPLICATE_CORRELATION: 0.94

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

source_name: Memory CD8+ T cells; DNA_Lib 529

value: BioSam 186

value: CD8 Memory Primary Cells

value: presumed normal

value: genomic DNA

value: CD45RO CD8

value: Millipore

value: Histone H3K4me3

value: Branson


title: ChIP-Seq analysis of H3K4me1 in human CD45RO CD4 cells; DNA_Lib 542

description:
sample_term_id: CL_0000897
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 542
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8574
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9467
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM772884_BI.CD4_Memory_Primary_Cells.H3K4me1.Donor_100_7_pooled_leukopaks_Jan_7_2011.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 542-DNA_Lib 542-DNA_Lib 542.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of CD4 Memory Primary Cells Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me1 ChIP-Seq on CD4 Memory Primary Cells, Donor Donor 100 7 pooled leukopaks Jan 7 2011, were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.10792
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: 21,077,683
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.4457
FINDPEAKS_PERCENTILE: 87
HOTSPOT_SCORE: 0.4449
HOTSPOT_PERCENTILE: 83
IROC_SCORE: 0.9983
IROC_PERCENTILE: 94
POISSON_SCORE: 0.5562
POISSON_PERCENTILE: 81
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

ANALYSIS FILE NAME: GSM772884_BI.CD4_Memory_Primary_Cells.H3K4me1.Donor_100_7_pooled_leukopaks_Jan_7_2011.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 542-DNA_Lib 542-DNA_Lib 542.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of CD4 Memory Primary Cells Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me1 ChIP-Seq read mappings from CD4 Memory Primary Cells, Donor Donor 100 7 pooled leukopaks Jan 7 2011, were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.11056
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 5
BROWSER_TRACK_NAME: CD4M H3K4me1 00 42
BROWSER_TRACK_DESCRIPTION: BI CD4 Memory Primary Cells Histone H3K4me1 Donor 100 7 pooled leukopaks Jan 7 2011 Library DNA_Lib 542 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 21,077,683
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.4457
FINDPEAKS_PERCENTILE: 87
HOTSPOT_SCORE: 0.4449
HOTSPOT_PERCENTILE: 83
IROC_SCORE: 0.9983
IROC_PERCENTILE: 94
POISSON_SCORE: 0.5562
POISSON_PERCENTILE: 81
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

source_name: Memory CD4+ T cells; DNA_Lib 542

value: BioSam 181

value: CD4 Memory Primary Cells

value: CD45RO CD4

value: Unknown

value: Primary Cell

value: Donor 100 7 pooled leukopaks Jan 7 2011


title: Retina of P9 WT C57BL/6J vs. RNV of P13 OIR C57BL/6J, replicate 1

description:
This Sample represents 2 dye-swap samples.
Retina_P9_RNV_P13_Rep1_1.gpr: Cy5=WT; Cy3=OIR
Retina_P9_RNV_P13_Rep1_2.gpr: Cy5=OIR; Cy3=WT
The non-averaged log2 normalized ratios (Cy5/Cy3) in the Sample data table are derived from Retina_P9_RNV_P13_Rep1_1.gpr and Retina_P9_RNV_P13_Rep1_2.gpr.

source_name: normal retina of wild-type mice, postnatal 9 days (N9)

value: WT

value: retina

value: postnatal day 9

source_name: RNV of OIR mice, postnatal 13 days (P13)

value: OIR

value: postnatal day 13


title: Retina of WT C57BL/6J vs. RNV of OIR C57BL/6J, P13, replicate 1

description:
This Sample represents 2 dye-swap samples.
RNV_P13_Rep1_1.gpr: Cy5=WT; Cy3=OIR
RNV_P13_Rep1_2.gpr: Cy5=OIR; Cy3=WT
The non-averaged log2 normalized ratios (Cy5/Cy3) in the Sample data table are derived from RNV_P13_Rep1_1.gpr and RNV_P13_Rep1_2.gpr.


title: Retina of WT C57BL/6J vs. RNV of OIR C57BL/6J, P12, replicate 1

description:
This Sample represents 2 dye-swap samples.
RNV_P12_Rep1_1.gpr: Cy5=WT; Cy3=OIR
RNV_P12_Rep1_2.gpr: Cy5=OIR; Cy3=WT
The non-averaged log2 normalized ratios (Cy5/Cy3) in the Sample data table are derived from RNV_P12_Rep1_1.gpr and RNV_P12_Rep1_2.gpr.

value: postnatal day 12


title: P9 vs. P30 retina of WT C57BL/6J, replicate 1

description:
This Sample represents 2 dye-swap samples.
Retina_P9_P30_Rep1_1.gpr: Cy5=WT(N9); Cy3=WT(N30)
Retina_P9_P30_Rep1_2.gpr: Cy5=WT(N30); Cy3=WT(N9)
The non-averaged log2 normalized ratios (Cy5/Cy3) in the Sample data table are derived from Retina_P9_P30_Rep1_1.gpr and Retina_P9_P30_Rep1_2.gpr.

source_name: normal retina of wild-type mice, postnatal 30 days (N30)

value: postnatal day 30


title: Retina of WT C57BL/6J vs. RNV of OIR C57BL/6J, P8, replicate 3

description:
This Sample represents 2 dye-swap samples.
RNV_P8_Rep3_1.gpr: Cy5=WT; Cy3=OIR
RNV_P8_Rep3_2.gpr: Cy5=OIR; Cy3=WT
The non-averaged log2 normalized ratios (Cy5/Cy3) in the Sample data table are derived from RNV_P8_Rep3_1.gpr and RNV_P8_Rep3_2.gpr.

value: postnatal day 8


title: Retina of WT C57BL/6J vs. RNV of OIR C57BL/6J, P13, replicate 3

description:
This Sample represents 2 dye-swap samples.
RNV_P13_Rep3_1.gpr: Cy5=WT; Cy3=OIR
RNV_P13_Rep3_2.gpr: Cy5=OIR; Cy3=WT
The non-averaged log2 normalized ratios (Cy5/Cy3) in the Sample data table are derived from RNV_P13_Rep3_1.gpr and RNV_P13_Rep3_2.gpr.


title: ChIP-Seq analysis of H3K4me1 in human CD45RO CD8 cells; DNA_Lib 549

description:
sample_term_id: CL_0000909
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 549
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8563
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9468
****************
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: GSM772873_BI.CD8_Memory_Primary_Cells.H3K4me1.Donor_100_7_pooled_leukopaks_Jan_7_2011.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 549-DNA_Lib 549-DNA_Lib 549.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of CD8 Memory Primary Cells Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me1 ChIP-Seq on CD8 Memory Primary Cells, Donor Donor 100 7 pooled leukopaks Jan 7 2011, were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.10662
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: 18,085,765
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.2832
FINDPEAKS_PERCENTILE: 63
HOTSPOT_SCORE: 0.3231
HOTSPOT_PERCENTILE: 46
IROC_SCORE: 0.9906
IROC_PERCENTILE: 65
POISSON_SCORE: 0.4158
POISSON_PERCENTILE: 30
MAXIMUM_REPLICATE_CORRELATION: 0.88

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

ANALYSIS FILE NAME: GSM772873_BI.CD8_Memory_Primary_Cells.H3K4me1.Donor_100_7_pooled_leukopaks_Jan_7_2011.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 549-DNA_Lib 549-DNA_Lib 549.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of CD8 Memory Primary Cells Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me1 ChIP-Seq read mappings from CD8 Memory Primary Cells, Donor Donor 100 7 pooled leukopaks Jan 7 2011, were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.10926
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: CD8M H3K4me1 00 49
BROWSER_TRACK_DESCRIPTION: BI CD8 Memory Primary Cells Histone H3K4me1 Donor 100 7 pooled leukopaks Jan 7 2011 Library DNA_Lib 549 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 18,085,765
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.2832
FINDPEAKS_PERCENTILE: 63
HOTSPOT_SCORE: 0.3231
HOTSPOT_PERCENTILE: 46
IROC_SCORE: 0.9906
IROC_PERCENTILE: 65
POISSON_SCORE: 0.4158
POISSON_PERCENTILE: 30
MAXIMUM_REPLICATE_CORRELATION: 0.88

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

source_name: Memory CD8+ T cells; DNA_Lib 549

value: BioSam 182

value: CD8 Memory Primary Cells

value: presumed normal

value: genomic DNA

value: CD45RO CD8

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 H3K4me1


title: ChIP-Seq analysis of H3K4me3 in human Memory CD4 cells; Lib:RI:20100324:07--ChIP:MA:20100319:07:Memory CD4:H3K4Me3

description:
sample_term_id: CL_0000897
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:RI:20100324:07--ChIP:MA:20100319:07:Memory CD4:H3K4Me3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8051
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3884
****************
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: GSM772790_BI.CD4_Memory_Primary_Cells.H3K4me3.20.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:RI:20100324:07--ChIP:MA:20100319:07:Memory CD4:H3K4Me3.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of CD4 Memory Primary Cells Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me3 ChIP-Seq on CD4 Memory Primary Cells, Donor 20, 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.10611
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: 5,750,447
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.1923
FINDPEAKS_PERCENTILE: 35
HOTSPOT_SCORE: 0.3634
HOTSPOT_PERCENTILE: 63
IROC_SCORE: 0.9994
IROC_PERCENTILE: 59
POISSON_SCORE: 0.3824
POISSON_PERCENTILE: 56
MAXIMUM_REPLICATE_CORRELATION: 0.87

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

ANALYSIS FILE NAME: GSM772790_BI.CD4_Memory_Primary_Cells.H3K4me3.20.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:RI:20100324:07--ChIP:MA:20100319:07:Memory CD4:H3K4Me3.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of CD4 Memory Primary Cells Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me3 ChIP-Seq read mappings from CD4 Memory Primary Cells, Donor 20, 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.10875
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 5
BROWSER_TRACK_NAME: CD4M H3K4me3 20
BROWSER_TRACK_DESCRIPTION: BI CD4 Memory Primary Cells Histone H3K4me3 Donor 20 Library Lib:RI:20100324:07--ChIP:MA:20100319:07:Memory CD4:H3K4Me3 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 5,750,447
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.1923
FINDPEAKS_PERCENTILE: 35
HOTSPOT_SCORE: 0.3634
HOTSPOT_PERCENTILE: 63
IROC_SCORE: 0.9994
IROC_PERCENTILE: 59
POISSON_SCORE: 0.3824
POISSON_PERCENTILE: 56
MAXIMUM_REPLICATE_CORRELATION: 0.87

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

source_name: "Memory CD4 cells derived from fom pooled leukopacks by Ficoll sedimentation, magnetic bead purification, and FACS"; Lib:RI:20100324:07--ChIP:MA:20100319:07:Memory CD4:H3K4Me3

value: CD4 Memory Primary Cells

value: CD45RO CD4

value: Unknown

value: Primary Cell

value: Whitehead Institute

value: 10 million cells

value: SDS lysis

value: 70 ul bed volume

value: Millipore

value: Histone H3K4me3

value: Bioruptor


title: Retina of WT C57BL/6J vs. RNV of OIR C57BL/6J, P12, replicate 3

description:
This Sample represents 2 dye-swap samples.
RNV_P12_Rep3_1.gpr: Cy5=WT; Cy3=OIR
RNV_P12_Rep3_2.gpr: Cy5=OIR; Cy3=WT
The non-averaged log2 normalized ratios (Cy5/Cy3) in the Sample data table are derived from RNV_P12_Rep3_1.gpr and RNV_P12_Rep3_2.gpr.

value: WT

value: retina

value: postnatal day 12

value: OIR


title: ChIP-Seq analysis of H3K4me1 in human CD45RA CD4 cells; DNA_Lib 664

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 664
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8559
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: GSM772869_BI.CD4_Naive_Primary_Cells.H3K4me1.Donor_100_7_pooled_leukopaks_Jan_7_2011.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 664-DNA_Lib 664-DNA_Lib 664.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of CD4 Naive Primary Cells Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me1 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.10734
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: 20,958,536
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.3117
FINDPEAKS_PERCENTILE: 72
HOTSPOT_SCORE: 0.3304
HOTSPOT_PERCENTILE: 57
IROC_SCORE: 0.9944
IROC_PERCENTILE: 80
POISSON_SCORE: 0.4274
POISSON_PERCENTILE: 37
MAXIMUM_REPLICATE_CORRELATION: 0.88

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

ANALYSIS FILE NAME: GSM772869_BI.CD4_Naive_Primary_Cells.H3K4me1.Donor_100_7_pooled_leukopaks_Jan_7_2011.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 664-DNA_Lib 664-DNA_Lib 664.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of CD4 Naive Primary Cells Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me1 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.10998
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 H3K4me1 00 64
BROWSER_TRACK_DESCRIPTION: BI CD4 Naive Primary Cells Histone H3K4me1 Donor 100 7 pooled leukopaks Jan 7 2011 Library DNA_Lib 664 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 20,958,536
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.3117
FINDPEAKS_PERCENTILE: 72
HOTSPOT_SCORE: 0.3304
HOTSPOT_PERCENTILE: 57
IROC_SCORE: 0.9944
IROC_PERCENTILE: 80
POISSON_SCORE: 0.4274
POISSON_PERCENTILE: 37
MAXIMUM_REPLICATE_CORRELATION: 0.88

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

source_name: Naive CD4+ T cells; DNA_Lib 664

value: BioSam 183

value: CD4 Naive Primary Cells

value: presumed normal

value: genomic DNA

value: CD4 Naive Primary Cell

value: Donor 100 7 pooled leukopaks Jan 7 2011

value: Dana Farber

value: Protein A-Sepharose 4B

value: 0.5 to 3 million cells

value: cell/nuclei lysis

value: ~1 ug

value: 10 ul bed volume

value: Abcam

value: Branson


title: ChIP-Seq analysis of H3K4me1 in human CD45RO CD8 cells; DNA_Lib 535

description:
sample_term_id: CL_0000909
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 535
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8623
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9465
****************
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: GSM772933_BI.CD8_Memory_Primary_Cells.H3K4me1.Donor_101_8_pooled_leukopaks_Jan_20_2011.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 535-DNA_Lib 535-DNA_Lib 535.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of CD8 Memory Primary Cells Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me1 ChIP-Seq on CD8 Memory Primary Cells, Donor Donor 101 8 pooled leukopaks Jan 20 2011, were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.10747
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 24,862,825
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.2117
FINDPEAKS_PERCENTILE: 30
HOTSPOT_SCORE: 0.2544
HOTSPOT_PERCENTILE: 20
IROC_SCORE: 0.9858
IROC_PERCENTILE: 61
POISSON_SCORE: 0.3502
POISSON_PERCENTILE: 13
MAXIMUM_REPLICATE_CORRELATION: 0.88

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

ANALYSIS FILE NAME: GSM772933_BI.CD8_Memory_Primary_Cells.H3K4me1.Donor_101_8_pooled_leukopaks_Jan_20_2011.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 535-DNA_Lib 535-DNA_Lib 535.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of CD8 Memory Primary Cells Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me1 ChIP-Seq read mappings from CD8 Memory Primary Cells, Donor Donor 101 8 pooled leukopaks Jan 20 2011, were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.11011
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: CD8M H3K4me1 01 35
BROWSER_TRACK_DESCRIPTION: BI CD8 Memory Primary Cells Histone H3K4me1 Donor 101 8 pooled leukopaks Jan 20 2011 Library DNA_Lib 535 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 24,862,825
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.2117
FINDPEAKS_PERCENTILE: 30
HOTSPOT_SCORE: 0.2544
HOTSPOT_PERCENTILE: 20
IROC_SCORE: 0.9858
IROC_PERCENTILE: 61
POISSON_SCORE: 0.3502
POISSON_PERCENTILE: 13
MAXIMUM_REPLICATE_CORRELATION: 0.88

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

source_name: Memory CD8+ T cells; DNA_Lib 535

value: BioSam 186

value: CD8 Memory Primary Cells

value: CD45RO CD8

value: Unknown

value: Primary Cell

value: Histone H3K4me1


title: ChIP-Seq analysis of H3K4me1 in human CD45RA CD4 cells; DNA_Lib 528

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 528
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8550
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: GSM772860_BI.CD4_Naive_Primary_Cells.H3K4me1.Donor_101_8_pooled_leukopaks_Jan_20_2011.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 528-DNA_Lib 528-DNA_Lib 528.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of CD4 Naive Primary Cells Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me1 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.10645
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: 15,494,536
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.2828
FINDPEAKS_PERCENTILE: 59
HOTSPOT_SCORE: 0.3245
HOTSPOT_PERCENTILE: 48
IROC_SCORE: 0.9926
IROC_PERCENTILE: 74
POISSON_SCORE: 0.3983
POISSON_PERCENTILE: 26
MAXIMUM_REPLICATE_CORRELATION: 0.88

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

ANALYSIS FILE NAME: GSM772860_BI.CD4_Naive_Primary_Cells.H3K4me1.Donor_101_8_pooled_leukopaks_Jan_20_2011.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 528-DNA_Lib 528-DNA_Lib 528.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of CD4 Naive Primary Cells Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me1 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.10909
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 H3K4me1 01 28
BROWSER_TRACK_DESCRIPTION: BI CD4 Naive Primary Cells Histone H3K4me1 Donor 101 8 pooled leukopaks Jan 20 2011 Library DNA_Lib 528 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 15,494,536
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.2828
FINDPEAKS_PERCENTILE: 59
HOTSPOT_SCORE: 0.3245
HOTSPOT_PERCENTILE: 48
IROC_SCORE: 0.9926
IROC_PERCENTILE: 74
POISSON_SCORE: 0.3983
POISSON_PERCENTILE: 26
MAXIMUM_REPLICATE_CORRELATION: 0.88

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

source_name: Naive CD4+ T cells; DNA_Lib 528

value: BioSam 187

value: CD4 Naive Primary Cells

value: presumed normal

value: genomic DNA


title: P9 vs. P30 retina of WT C57BL/6J, replicate 3

description:
This Sample represents 2 dye-swap samples.
Retina_P9_P30_Rep3_1.gpr: Cy5=WT(N9); Cy3=WT(N30)
Retina_P9_P30_Rep3_2.gpr: Cy5=WT(N30); Cy3=WT(N9)
The non-averaged log2 normalized ratios (Cy5/Cy3) in the Sample data table are derived from Retina_P9_P30_Rep3_1.gpr and Retina_P9_P30_Rep3_2.gpr.

data_processing: Data extraction and filtering, LOWESS normalized (R language software was used), MA plot for each array, calculated average log2 ratios (treated vs. control sample).

value: WT

value: retina

value: postnatal day 9

value: postnatal day 30


title: ChIP-Seq analysis of H3K4me3 in human CD45RA CD4 cells; DNA_Lib 522

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 522
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8526
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: GSM772836_BI.CD4_Naive_Primary_Cells.H3K4me3.Donor_101_8_pooled_leukopaks_Jan_20_2011.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 522-DNA_Lib 522-DNA_Lib 522.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of CD4 Naive Primary Cells Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me3 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.10692
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: 25,281,281
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.1179
FINDPEAKS_PERCENTILE: 13
HOTSPOT_SCORE: 0.1556
HOTSPOT_PERCENTILE: 13
IROC_SCORE: 0.9972
IROC_PERCENTILE: 37
POISSON_SCORE: 0.1948
POISSON_PERCENTILE: 9
MAXIMUM_REPLICATE_CORRELATION: 0.91

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

ANALYSIS FILE NAME: GSM772836_BI.CD4_Naive_Primary_Cells.H3K4me3.Donor_101_8_pooled_leukopaks_Jan_20_2011.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 522-DNA_Lib 522-DNA_Lib 522.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of CD4 Naive Primary Cells Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me3 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.10956
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 H3K4me3 01 22
BROWSER_TRACK_DESCRIPTION: BI CD4 Naive Primary Cells Histone H3K4me3 Donor 101 8 pooled leukopaks Jan 20 2011 Library DNA_Lib 522 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 25,281,281
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.1179
FINDPEAKS_PERCENTILE: 13
HOTSPOT_SCORE: 0.1556
HOTSPOT_PERCENTILE: 13
IROC_SCORE: 0.9972
IROC_PERCENTILE: 37
POISSON_SCORE: 0.1948
POISSON_PERCENTILE: 9
MAXIMUM_REPLICATE_CORRELATION: 0.91

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

source_name: Naive CD4+ T cells; DNA_Lib 522

value: CD4 Naive 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: Millipore

value: Histone H3K4me3