title: E0-8_Fru_INPUT_1

city: Chicago

first: Kevin

middle: P.

last: White

state: IL

address: 900 E. 57th STR. 10th FL.

department: Institute for Genomics and Systems Biology

institute: University of Chicago

data_processing: Reads were aligned to the flybase BDGPv5 reference genome using Bowtie 0.12.5. Signal files were generated with the R 2.7.1 package SPP 2.7.1. Peaks were called with MACS 1.3.7.

organism: Drosophila melanogaster

growth_protocol: 1. the iso1 (y; bw cn sp) flies or the transgenic flies are cultivated in cages with apple juice agar plates covered with yeast powder. and the egg laying is performed for the desired amount of time to correspond to the proper stage. The biological material is collected using a filter mesh and a brush and rinsed extensively with Embryonic Wash Buffer (EWB). The material is then used freshly for cross-linking.

extract_protocol: After chromatin immuno-precipitation, the DNA is purified in 30ul of water.  Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3' end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: No Treatment

tag: developmental stage

tag: strain


title: ChIP-Seq analysis of H3K36me3 in human CD25- Th cells; DNA_Lib 361

status: Public on Dec 28 2011

type: SRA

city: Cambridge

first: BROAD

last: INSTITUTE

state: MA

country: USA

institute: Broad Institute

description:
sample_term_id: CL_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 361
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8556
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9442
****************
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: GSM772866_BI.CD4+_CD25-_Th_Primary_Cells.H3K36me3.Donor_62.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 361-DNA_Lib 361-DNA_Lib 361-DNA_Lib 361.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of CD4+ CD25- Th Primary Cells Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K36me3 ChIP-Seq on CD4+ CD25- Th Primary Cells, Donor Donor 62, 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.10641
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: 25,524,358
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.3909
FINDPEAKS_PERCENTILE: 84
HOTSPOT_SCORE: 0.334
HOTSPOT_PERCENTILE: 82
IROC_SCORE: 0.9935
IROC_PERCENTILE: 84
POISSON_SCORE: 0.546
POISSON_PERCENTILE: 84
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM772866_BI.CD4+_CD25-_Th_Primary_Cells.H3K36me3.Donor_62.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 361-DNA_Lib 361-DNA_Lib 361-DNA_Lib 361.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of CD4+ CD25- Th Primary Cells Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K36me3 ChIP-Seq read mappings from CD4+ CD25- Th Primary Cells, Donor Donor 62, 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.10905
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: CCT H3K36me3 62 61
BROWSER_TRACK_DESCRIPTION: BI CD4+ CD25- Th Primary Cells Histone H3K36me3 Donor 62 Library DNA_Lib 361 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 25,524,358
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.3909
FINDPEAKS_PERCENTILE: 84
HOTSPOT_SCORE: 0.334
HOTSPOT_PERCENTILE: 82
IROC_SCORE: 0.9935
IROC_PERCENTILE: 84
POISSON_SCORE: 0.546
POISSON_PERCENTILE: 84
MAXIMUM_REPLICATE_CORRELATION: NA

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

molecule: genomic DNA

organism: Homo sapiens

source_name: CD25- Th  is one of  CD4+  T cell subsets  that purified by microbeads, LS column and FACS ; DNA_Lib 361

extract_protocol: Library construction protocol: Single read - Illumina

tag: sample alias

value: BioSam 130

tag: sample common name

value: CD4+ CD25- Th Primary Cells

value: presumed normal

tag: molecule

value: genomic DNA

tag: disease

tag: markers

value: CD4+ T cell

value: CD25- Th

value: Unknown

value: Primary Cell

value: Donor 62

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 H3K36me3

value: Branson


title: ChIP-Seq analysis of H3K36me3 in human Mobilized CD34 cells; DNA_Lib 257

description:
sample_term_id: CL_0000837
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 257
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8555
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.2397
****************
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: GSM772865_BI.Mobilized_CD34_Primary_Cells.H3K36me3.RO_01536.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 257-DNA_Lib 257-DNA_Lib 257-DNA_Lib 257-DNA_Lib 257.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Mobilized CD34 Primary Cells Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K36me3 ChIP-Seq on Mobilized CD34 Primary Cells, Donor RO 01536, 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.10837
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: 21,987,269
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.6102
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.4966
HOTSPOT_PERCENTILE: 98
IROC_SCORE: 0.999
IROC_PERCENTILE: 96
POISSON_SCORE: 0.7111
POISSON_PERCENTILE: 98
MAXIMUM_REPLICATE_CORRELATION: 0.93

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

ANALYSIS FILE NAME: GSM772865_BI.Mobilized_CD34_Primary_Cells.H3K36me3.RO_01536.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 257-DNA_Lib 257-DNA_Lib 257-DNA_Lib 257-DNA_Lib 257.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Mobilized CD34 Primary Cells Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K36me3 ChIP-Seq read mappings from Mobilized CD34 Primary Cells, Donor RO 01536, 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.11101
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: MCD34 H3K36me3 36 57
BROWSER_TRACK_DESCRIPTION: BI Mobilized CD34 Primary Cells Histone H3K36me3 Donor RO 01536 Library DNA_Lib 257 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 21,987,269
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.6102
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.4966
HOTSPOT_PERCENTILE: 98
IROC_SCORE: 0.999
IROC_PERCENTILE: 96
POISSON_SCORE: 0.7111
POISSON_PERCENTILE: 98
MAXIMUM_REPLICATE_CORRELATION: 0.93

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

source_name: flow sorted CD34+ cells from cord blood; DNA_Lib 257

value: CD34 Primary Cells

value: FHCRC HEIMFELD

value: 27 years

value: Female

value: Hispanic


title: ChIP-Seq analysis of WCE in human substantia nigra cells; DNA_Lib 560

description:
sample_term_id: UBERON_0002038
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 560
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8554
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9444
****************
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: GSM772864_BI.Brain_Substantia_Nigra.Input.149.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 560-DNA_Lib 560-DNA_Lib 560.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Brain Substantia Nigra ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on Brain Substantia Nigra, Donor 149, 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.10808
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: 19,006,947
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 56
FINDPEAKS_SCORE: 0.0068
FINDPEAKS_PERCENTILE: 79
HOTSPOT_SCORE: 0.0343
HOTSPOT_PERCENTILE: 75
IROC_SCORE: 0.9668
IROC_PERCENTILE: 52
POISSON_SCORE: 0.0698
POISSON_PERCENTILE: 67
MAXIMUM_REPLICATE_CORRELATION: 0.92

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

ANALYSIS FILE NAME: GSM772864_BI.Brain_Substantia_Nigra.Input.149.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 560-DNA_Lib 560-DNA_Lib 560.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Brain Substantia Nigra ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from Brain Substantia Nigra, Donor 149, 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.11072
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: BSN Input 49 60
BROWSER_TRACK_DESCRIPTION: BI Brain Substantia Nigra ChIP-Seq Input Donor 149 Library DNA_Lib 560 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 19,006,947
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 56
FINDPEAKS_SCORE: 0.0068
FINDPEAKS_PERCENTILE: 79
HOTSPOT_SCORE: 0.0343
HOTSPOT_PERCENTILE: 75
IROC_SCORE: 0.9668
IROC_PERCENTILE: 52
POISSON_SCORE: 0.0698
POISSON_PERCENTILE: 67
MAXIMUM_REPLICATE_CORRELATION: 0.92

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

source_name: specified brain region obtained by post-mortem collection in a longitudinal study; DNA_Lib 560

value: Brain, Substantia Nigra

value: Post-Mortem

value: no AD evident at demise

value: genomic DNA

value: Substantia Nigra

value: Male

value: Primary Tissue

value: Brain

value: Rush University Medical Center

value: 81.0 Years

value: standard

value: ChIP-Seq Input

value: Input


title: ChIP-Seq analysis of H3K4me3 in human angular gyrus cells; Lib EpiLabSPL Row 1837

description:
sample_term_id: UBERON_0002686
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib EpiLabSPL Row 1837
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8030
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.8183
****************
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: GSM772769_BI.Brain_Angular_Gyrus.H3K4me3.112.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib EpiLabSPL Row 1837.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Brain Angular Gyrus Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me3 ChIP-Seq on Brain Angular Gyrus, Donor 112, 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.10647
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: 35,585,965
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.1408
FINDPEAKS_PERCENTILE: 22
HOTSPOT_SCORE: 0.1688
HOTSPOT_PERCENTILE: 17
IROC_SCORE: 0.9991
IROC_PERCENTILE: 52
POISSON_SCORE: 0.2025
POISSON_PERCENTILE: 11
MAXIMUM_REPLICATE_CORRELATION: 0.95

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

ANALYSIS FILE NAME: GSM772769_BI.Brain_Angular_Gyrus.H3K4me3.112.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib EpiLabSPL Row 1837.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Brain Angular Gyrus Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me3 ChIP-Seq read mappings from Brain Angular Gyrus, Donor 112, 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.10911
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: BAG H3K4me3 12 37
BROWSER_TRACK_DESCRIPTION: BI Brain Angular Gyrus Histone H3K4me3 Donor 112 Library Lib EpiLabSPL Row 1837 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 35,585,965
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.1408
FINDPEAKS_PERCENTILE: 22
HOTSPOT_SCORE: 0.1688
HOTSPOT_PERCENTILE: 17
IROC_SCORE: 0.9991
IROC_PERCENTILE: 52
POISSON_SCORE: 0.2025
POISSON_PERCENTILE: 11
MAXIMUM_REPLICATE_CORRELATION: 0.95

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

source_name: human post mortem brain region from a non Alzheimer's donor; Lib EpiLabSPL Row 1837

value: Brain, Angular Gyrus

value: post-mortem

value: Angular Gyrus

value: brain

value: Protein A-Sepharose 4B

value: 10 million cells

value: SDS lysis

value: 70 ul bed volume

value: Millipore

value: Histone H3K4me3

value: Bioruptor


title: ChIP-Seq analysis of WCE in human CD19 cells; DNA_Lib 440

description:
sample_term_id: CL_0000236
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 440
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8553
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.12577
****************
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: GSM772863_BI.iPS-20b.Input.DNA_Lib_440.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 440-DNA_Lib 440-DNA_Lib 440-DNA_Lib 440.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of iPS-20b Cell Line ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on the iPS-20b Cell Line, Library DNA_Lib 440, 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.10786
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: 34,337,278
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 56
FINDPEAKS_SCORE: 0.0053
FINDPEAKS_PERCENTILE: 52
HOTSPOT_SCORE: 0.0046
HOTSPOT_PERCENTILE: 25
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.0335
POISSON_PERCENTILE: 23
MAXIMUM_REPLICATE_CORRELATION: 0.9

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

ANALYSIS FILE NAME: GSM772863_BI.iPS-20b.Input.DNA_Lib_440.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 440-DNA_Lib 440-DNA_Lib 440-DNA_Lib 440.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of iPS-20b Cell Line ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from the iPS-20b Cell Line, Library DNA_Lib 440, 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.11050
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: iPS20b Input 40
BROWSER_TRACK_DESCRIPTION: BI iPS-20b Cell Line ChIP-Seq Input Library DNA_Lib 440 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 34,337,278
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 56
FINDPEAKS_SCORE: 0.0053
FINDPEAKS_PERCENTILE: 52
HOTSPOT_SCORE: 0.0046
HOTSPOT_PERCENTILE: 25
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.0335
POISSON_PERCENTILE: 23
MAXIMUM_REPLICATE_CORRELATION: 0.9

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

source_name: CD19 Primary Cells; DNA_Lib 440

value: CD19 Primary Cells

value: presumed normal

value: genomic DNA

value: Female

value: Cell Line

value: FHCRC

value: 0 years

value: cell/nuclei lysis

value: Branson


title: E0-8_sc_ChIPSeq_1 and 2

tag: antibody name

value: sc

tag: manufacturer

value: White Lab

tag: lot/batch#

tag: catalog


title: E0-8_Fru_ChIPSeq_1 and 2

value: Fru


title: sim_ChIPSeq_1 and 2

value: sim


title: Usp_INPUT_1

value: USP, transgenic


title: ChIP-Seq analysis of H3K36me3 in human angular gyrus cells; Lib EpiLabSPL Row 1838

description:
sample_term_id: UBERON_0002686
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib EpiLabSPL Row 1838
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8029
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.8183
****************
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: GSM772768_BI.Brain_Angular_Gyrus.H3K36me3.112.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib EpiLabSPL Row 1838.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Brain Angular Gyrus Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K36me3 ChIP-Seq on Brain Angular Gyrus, Donor 112, 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.10730
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: 35,845,035
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.0556
FINDPEAKS_PERCENTILE: 22
HOTSPOT_SCORE: 0.1508
HOTSPOT_PERCENTILE: 22
IROC_SCORE: 0.8925
IROC_PERCENTILE: 31
POISSON_SCORE: 0.2917
POISSON_PERCENTILE: 22
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

ANALYSIS FILE NAME: GSM772768_BI.Brain_Angular_Gyrus.H3K36me3.112.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib EpiLabSPL Row 1838.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Brain Angular Gyrus Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K36me3 ChIP-Seq read mappings from Brain Angular Gyrus, Donor 112, 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.10994
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: BAG H3K36me3 12 38
BROWSER_TRACK_DESCRIPTION: BI Brain Angular Gyrus Histone H3K36me3 Donor 112 Library Lib EpiLabSPL Row 1838 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 35,845,035
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.0556
FINDPEAKS_PERCENTILE: 22
HOTSPOT_SCORE: 0.1508
HOTSPOT_PERCENTILE: 22
IROC_SCORE: 0.8925
IROC_PERCENTILE: 31
POISSON_SCORE: 0.2917
POISSON_PERCENTILE: 22
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

source_name: human post mortem brain region from a non Alzheimer's donor; Lib EpiLabSPL Row 1838

value: Brain, Angular Gyrus

value: post-mortem

value: Angular Gyrus

value: Primary Tissue

value: brain

value: Rush University Medical Center

value: Protein A-Sepharose 4B

value: 10 million cells

value: SDS lysis

value: 70 ul bed volume

value: Abcam

value: Histone H3K36me3


title: ChIP-Seq analysis of H3K9ac in human HUES48 cells; Lib EpiLabSPL Row 1717

description:
sample_term_id: NTR_0000848
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib EpiLabSPL Row 1717
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8057
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.8177
****************
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: GSM772796_BI.HUES48.H3K9ac.Lib_EpiLabSPL_Row_1717.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib EpiLabSPL Row 1717.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of HUES48 Cell Line Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9ac ChIP-Seq on the HUES48 Cell Line, Library Lib EpiLabSPL Row 1717, 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.10637
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 26,778,248
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 19
FINDPEAKS_SCORE: 0.0733
FINDPEAKS_PERCENTILE: 21
HOTSPOT_SCORE: 0.1371
HOTSPOT_PERCENTILE: 21
IROC_SCORE: 0.9866
IROC_PERCENTILE: 32
POISSON_SCORE: 0.1847
POISSON_PERCENTILE: 21
MAXIMUM_REPLICATE_CORRELATION: 0.91

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

ANALYSIS FILE NAME: GSM772796_BI.HUES48.H3K9ac.Lib_EpiLabSPL_Row_1717.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib EpiLabSPL Row 1717.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of HUES48 Cell Line Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9ac ChIP-Seq read mappings from the HUES48 Cell Line, Library Lib EpiLabSPL Row 1717, 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.10901
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: HUES48 H3K9ac 17
BROWSER_TRACK_DESCRIPTION: BI HUES48 Cell Line Histone H3K9ac Library Lib EpiLabSPL Row 1717 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 26,778,248
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 19
FINDPEAKS_SCORE: 0.0733
FINDPEAKS_PERCENTILE: 21
HOTSPOT_SCORE: 0.1371
HOTSPOT_PERCENTILE: 21
IROC_SCORE: 0.9866
IROC_PERCENTILE: 32
POISSON_SCORE: 0.1847
POISSON_PERCENTILE: 21
MAXIMUM_REPLICATE_CORRELATION: 0.91

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

source_name: Harvard University Embryonic Stem Cells; Lib EpiLabSPL Row 1717

value: HUES48 stem cells

value: HUES48 Cell Line

tag: lineage

value: embrionic stem cell

tag: medium

value: KSR

value: genomic DNA

tag: passage

tag: line

tag: batch

value: ES cell HUES_48-2

value: Cell Line

value: undifferentiated

tag: Sex

value: Unknown

value: Harvard University

value: Histone H3K9ac

value: Bioruptor


title: ChIP-Seq analysis of H3K4me1 in human HUES48 cells; Lib EpiLabSPL Row 1713

description:
sample_term_id: NTR_0000848
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib EpiLabSPL Row 1713
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8054
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.8177
****************
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: GSM772793_BI.HUES48.H3K4me1.Lib_EpiLabSPL_Row_1713.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib EpiLabSPL Row 1713.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of HUES48 Cell Line Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me1 ChIP-Seq on the HUES48 Cell Line, Library Lib EpiLabSPL Row 1713, 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.10828
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: 34,297,929
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.2508
FINDPEAKS_PERCENTILE: 44
HOTSPOT_SCORE: 0.3374
HOTSPOT_PERCENTILE: 63
IROC_SCORE: 0.9615
IROC_PERCENTILE: 41
POISSON_SCORE: 0.5057
POISSON_PERCENTILE: 72
MAXIMUM_REPLICATE_CORRELATION: 0.95

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

ANALYSIS FILE NAME: GSM772793_BI.HUES48.H3K4me1.Lib_EpiLabSPL_Row_1713.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib EpiLabSPL Row 1713.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of HUES48 Cell Line Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me1 ChIP-Seq read mappings from the HUES48 Cell Line, Library Lib EpiLabSPL Row 1713, 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.11092
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: HUES48 H3K4me1 13
BROWSER_TRACK_DESCRIPTION: BI HUES48 Cell Line Histone H3K4me1 Library Lib EpiLabSPL Row 1713 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 34,297,929
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.2508
FINDPEAKS_PERCENTILE: 44
HOTSPOT_SCORE: 0.3374
HOTSPOT_PERCENTILE: 63
IROC_SCORE: 0.9615
IROC_PERCENTILE: 41
POISSON_SCORE: 0.5057
POISSON_PERCENTILE: 72
MAXIMUM_REPLICATE_CORRELATION: 0.95

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

source_name: Harvard University Embryonic Stem Cells; Lib EpiLabSPL Row 1713

value: Protein A-Sepharose 4B

value: 10 million cells

value: Histone H3K4me1


title: ChIP-Seq analysis of H3K9me3 in human HUES48 cells; Lib EpiLabSPL Row 1707

description:
sample_term_id: NTR_0000848
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib EpiLabSPL Row 1707
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8041
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5930
****************
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: GSM772780_BI.HUES48.H3K9me3.Lib_EpiLabSPL_Row_1707.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib EpiLabSPL Row 1707.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of HUES48 Cell Line Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9me3 ChIP-Seq on the HUES48 Cell Line, Library Lib EpiLabSPL Row 1707, 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.10682
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: 15,866,288
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.2537
FINDPEAKS_PERCENTILE: 94
HOTSPOT_SCORE: 0.2345
HOTSPOT_PERCENTILE: 90
IROC_SCORE: 0.9608
IROC_PERCENTILE: 98
POISSON_SCORE: 0.4439
POISSON_PERCENTILE: 96
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM772780_BI.HUES48.H3K9me3.Lib_EpiLabSPL_Row_1707.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib EpiLabSPL Row 1707.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of HUES48 Cell Line Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9me3 ChIP-Seq read mappings from the HUES48 Cell Line, Library Lib EpiLabSPL Row 1707, 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.10946
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: HUES48 H3K9me3 07
BROWSER_TRACK_DESCRIPTION: BI HUES48 Cell Line Histone H3K9me3 Library Lib EpiLabSPL Row 1707 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 15,866,288
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.2537
FINDPEAKS_PERCENTILE: 94
HOTSPOT_SCORE: 0.2345
HOTSPOT_PERCENTILE: 90
IROC_SCORE: 0.9608
IROC_PERCENTILE: 98
POISSON_SCORE: 0.4439
POISSON_PERCENTILE: 96
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

source_name: Harvard University Embryonic Stem Cells; Lib EpiLabSPL Row 1707

value: ES cell HUES_48-1

value: SDS lysis

value: 70 ul bed volume

value: Abcam

value: Histone H3K9me3


title: ChIP-Seq analysis of H3K4me1 in human hiPS-15b cells; Lib:MC:20100211:04--ChIP:MC:20100208:04:hiPS-15b:H3K4Me1

description:
sample_term_id: NTR_0001162
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:MC:20100211:04--ChIP:MC:20100208:04:hiPS-15b:H3K4Me1
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8028
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.2300
****************
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: GSM772767_BI.iPS-15b.H3K4me1.Lib_MC_20100211_04--ChIP_MC_20100208_04_hiPS-15b_H3K4Me1.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100211:04--ChIP:MC:20100208:04:hiPS-15b:H3K4Me1.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of iPS-15b Cell Line Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me1 ChIP-Seq on the iPS-15b Cell Line, Library Lib:MC:20100211:04--ChIP:MC:20100208:04:hiPS-15b:H3K4Me1, 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.10751
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: 28,150,257
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.2333
FINDPEAKS_PERCENTILE: 39
HOTSPOT_SCORE: 0.3174
HOTSPOT_PERCENTILE: 43
IROC_SCORE: 0.954
IROC_PERCENTILE: 33
POISSON_SCORE: 0.4717
POISSON_PERCENTILE: 56
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM772767_BI.iPS-15b.H3K4me1.Lib_MC_20100211_04--ChIP_MC_20100208_04_hiPS-15b_H3K4Me1.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100211:04--ChIP:MC:20100208:04:hiPS-15b:H3K4Me1.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of iPS-15b Cell Line Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me1 ChIP-Seq read mappings from the iPS-15b Cell Line, Library Lib:MC:20100211:04--ChIP:MC:20100208:04:hiPS-15b:H3K4Me1, 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.11015
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: iPS15b H3K4me1 e1
BROWSER_TRACK_DESCRIPTION: BI iPS-15b Cell Line Histone H3K4me1 Library Lib:MC:20100211:04--ChIP:MC:20100208:04:hiPS-15b:H3K4Me1 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 28,150,257
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.2333
FINDPEAKS_PERCENTILE: 39
HOTSPOT_SCORE: 0.3174
HOTSPOT_PERCENTILE: 43
IROC_SCORE: 0.954
IROC_PERCENTILE: 33
POISSON_SCORE: 0.4717
POISSON_PERCENTILE: 56
MAXIMUM_REPLICATE_CORRELATION: NA

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

value: iPS-15b Cell Line

value: induced pluripotent cells

value: KSR

value: Female


title: ChIP-Seq analysis of H3K27ac in human CD25- CD45RO+ mem cells; DNA_Lib 723

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 723
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8549
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9449
****************
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: GSM772859_BI.CD4+_CD25-_CD45RO+_Memory_Primary_Cells.H3K27ac.Donor_62.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 723-DNA_Lib 723-DNA_Lib 723-DNA_Lib 723.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of CD4+ CD25- CD45RO+ Memory Primary Cells Histone H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27ac ChIP-Seq on CD4+ CD25- CD45RO+ Memory Primary Cells, Donor Donor 62, 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.10665
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: 8,623,532
NUMBER_OF_H3K27ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 34
FINDPEAKS_SCORE: 0.3905
FINDPEAKS_PERCENTILE: 85
HOTSPOT_SCORE: 0.434
HOTSPOT_PERCENTILE: 85
IROC_SCORE: 0.9989
IROC_PERCENTILE: 85
POISSON_SCORE: 0.4534
POISSON_PERCENTILE: 82
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM772859_BI.CD4+_CD25-_CD45RO+_Memory_Primary_Cells.H3K27ac.Donor_62.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 723-DNA_Lib 723-DNA_Lib 723-DNA_Lib 723.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of CD4+ CD25- CD45RO+ Memory Primary Cells Histone H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27ac ChIP-Seq read mappings from CD4+ CD25- CD45RO+ Memory Primary Cells, Donor Donor 62, 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.10929
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: CCCM H3K27ac 62 23
BROWSER_TRACK_DESCRIPTION: BI CD4+ CD25- CD45RO+ Memory Primary Cells Histone H3K27ac Donor 62 Library DNA_Lib 723 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 8,623,532
NUMBER_OF_H3K27ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 34
FINDPEAKS_SCORE: 0.3905
FINDPEAKS_PERCENTILE: 85
HOTSPOT_SCORE: 0.434
HOTSPOT_PERCENTILE: 85
IROC_SCORE: 0.9989
IROC_PERCENTILE: 85
POISSON_SCORE: 0.4534
POISSON_PERCENTILE: 82
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: CD25- CD45RO+ mem is one of  CD4+  T cell subsets  that purified by microbeads, LS column and FACS ; DNA_Lib 723

value: BioSam 132

value: CD4+ CD25- CD45RO+ Memory Primary Cells

value: presumed normal

value: genomic DNA

value: CD4+ T cell

value: CD25- CD45RO+ mem

value: Primary Cell

value: Donor 62

value: Dana Farber

value: 0.5 to 3 million cells

value: cell/nuclei lysis

value: ~1 ug

value: 10 ul bed volume

value: Histone H3K27ac

value: Branson


title: ChIP-Seq analysis of H3K9me3 in human HUES64 derived CD184+ cells; DNA_Lib 248

description:
sample_term_id: CL_0000223
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 248
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8546
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9461
****************
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: GSM772856_BI.hESC_Derived_CD184+_Endoderm_Cultured_Cells.H3K9me3.DNA_Lib_248.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 248-DNA_Lib 248-DNA_Lib 248-DNA_Lib 248-DNA_Lib 248.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of hESC Derived CD184+ Endoderm Cultured Cells Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9me3 ChIP-Seq on hESC Derived CD184+ Endoderm Cultured Cells, Donor DNA_Lib 248, 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.10804
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: 19,033,512
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.2558
FINDPEAKS_PERCENTILE: 96
HOTSPOT_SCORE: 0.2827
HOTSPOT_PERCENTILE: 98
IROC_SCORE: 0.946
IROC_PERCENTILE: 94
POISSON_SCORE: 0.4833
POISSON_PERCENTILE: 98
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM772856_BI.hESC_Derived_CD184+_Endoderm_Cultured_Cells.H3K9me3.DNA_Lib_248.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 248-DNA_Lib 248-DNA_Lib 248-DNA_Lib 248-DNA_Lib 248.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of hESC Derived CD184+ Endoderm Cultured Cells Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9me3 ChIP-Seq read mappings from hESC Derived CD184+ Endoderm Cultured Cells, Donor DNA_Lib 248, 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.11068
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: hDCE H3K9me3 48
BROWSER_TRACK_DESCRIPTION: BI hESC Derived CD184+ Endoderm Cultured Cells Histone H3K9me3 Library DNA_Lib 248 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 19,033,512
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.2558
FINDPEAKS_PERCENTILE: 96
HOTSPOT_SCORE: 0.2827
HOTSPOT_PERCENTILE: 98
IROC_SCORE: 0.946
IROC_PERCENTILE: 94
POISSON_SCORE: 0.4833
POISSON_PERCENTILE: 98
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: CD184+ endoderm differentiated in vitro from stem cells; DNA_Lib 248

value: CD184+ endoderm cultured cells

value: RPMI 100ng/mL Activin A 50ng/mL Wnt3a

value: HUES64 derived CD184+

value: in vitro culture

value: BioSAli 136

value: Cell Line

value: differentiated

value: Male

value: Harvard University

value: Protein A-Sepharose 4B

value: Abcam

value: Histone H3K9me3


title: WPP_SuHw_ChIPSeq_1 and 2

source_name: WPP

tag: developmental stage

value: WPP

value: SuHw

value: White Lab


title: Usp_ChIPSeq_1 and 2

value: Usp

tag: strain

value: USP, transgenic


title: H3K4me3_ChIPSeq_1 and 2


title: ChIP-Seq analysis of H3K4me3 in human CD25- CD45RA+ naive cells; DNA_Lib 726

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 726
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8542
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9443
****************
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: GSM772852_BI.CD4+_CD25-_CD45RA+_Naive_Primary_Cells.H3K4me3.Donor_62.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 726-DNA_Lib 726-DNA_Lib 726-DNA_Lib 726.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of CD4+ CD25- CD45RA+ Naive Primary Cells Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me3 ChIP-Seq on CD4+ CD25- CD45RA+ Naive Primary Cells, Donor Donor 62, 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.10809
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 12,311,515
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.23
FINDPEAKS_PERCENTILE: 52
HOTSPOT_SCORE: 0.2919
HOTSPOT_PERCENTILE: 44
IROC_SCORE: 0.9997
IROC_PERCENTILE: 76
POISSON_SCORE: 0.2973
POISSON_PERCENTILE: 37
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM772852_BI.CD4+_CD25-_CD45RA+_Naive_Primary_Cells.H3K4me3.Donor_62.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 726-DNA_Lib 726-DNA_Lib 726-DNA_Lib 726.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of CD4+ CD25- CD45RA+ Naive Primary Cells Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me3 ChIP-Seq read mappings from CD4+ CD25- CD45RA+ Naive Primary Cells, Donor Donor 62, 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.11073
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: CCCN H3K4me3 62 26
BROWSER_TRACK_DESCRIPTION: BI CD4+ CD25- CD45RA+ Naive Primary Cells Histone H3K4me3 Donor 62 Library DNA_Lib 726 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 12,311,515
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.23
FINDPEAKS_PERCENTILE: 52
HOTSPOT_SCORE: 0.2919
HOTSPOT_PERCENTILE: 44
IROC_SCORE: 0.9997
IROC_PERCENTILE: 76
POISSON_SCORE: 0.2973
POISSON_PERCENTILE: 37
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: CD25- CD45RA+ naive is one of  CD4+  T cell subsets  that purified by microbeads, LS column and FACS ; DNA_Lib 726

tag: sample alias

value: BioSam 133

value: CD4+ CD25- CD45RA+ Naive Primary Cells

value: presumed normal

value: genomic DNA

value: CD4+ T cell

value: CD25- CD45RA+ naive

value: Unknown

value: Primary Cell

value: Donor 62

value: Dana Farber

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: H3K4me3_INPUT_1

value: WPP


title: WPP+12_USP_INPUT_1

value: USP, transgenic


title: ChIP-Seq analysis of H3K9me3 in human CD25- Th cells; DNA_Lib 359

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 359
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8540
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9442
****************
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: GSM772850_BI.CD4+_CD25-_Th_Primary_Cells.H3K9me3.Donor_62.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 359-DNA_Lib 359-DNA_Lib 359-DNA_Lib 359.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of CD4+ CD25- Th Primary Cells Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9me3 ChIP-Seq on CD4+ CD25- Th Primary Cells, Donor Donor 62, 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.10772
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: 20,903,555
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.0642
FINDPEAKS_PERCENTILE: 67
HOTSPOT_SCORE: 0.1347
HOTSPOT_PERCENTILE: 65
IROC_SCORE: 0.7491
IROC_PERCENTILE: 24
POISSON_SCORE: 0.3279
POISSON_PERCENTILE: 67
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM772850_BI.CD4+_CD25-_Th_Primary_Cells.H3K9me3.Donor_62.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 359-DNA_Lib 359-DNA_Lib 359-DNA_Lib 359.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of CD4+ CD25- Th Primary Cells Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9me3 ChIP-Seq read mappings from CD4+ CD25- Th Primary Cells, Donor Donor 62, 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.11036
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: CCT H3K9me3 62 59
BROWSER_TRACK_DESCRIPTION: BI CD4+ CD25- Th Primary Cells Histone H3K9me3 Donor 62 Library DNA_Lib 359 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 20,903,555
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.0642
FINDPEAKS_PERCENTILE: 67
HOTSPOT_SCORE: 0.1347
HOTSPOT_PERCENTILE: 65
IROC_SCORE: 0.7491
IROC_PERCENTILE: 24
POISSON_SCORE: 0.3279
POISSON_PERCENTILE: 67
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: CD25- Th  is one of  CD4+  T cell subsets  that purified by microbeads, LS column and FACS ; DNA_Lib 359

value: BioSam 130

tag: sample common name

value: CD4+ CD25- Th Primary Cells

value: presumed normal

value: CD25- Th

value: Protein A-Sepharose 4B

value: Abcam

value: Histone H3K9me3


title: ChIP-Seq analysis of H3K4me1 in human CD25- Th cells; DNA_Lib 358

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 358
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8539
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9442
****************
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: GSM772849_BI.CD4+_CD25-_Th_Primary_Cells.H3K4me1.Donor_62.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 358-DNA_Lib 358-DNA_Lib 358-DNA_Lib 358.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of CD4+ CD25- Th Primary Cells Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me1 ChIP-Seq on CD4+ CD25- Th Primary Cells, Donor Donor 62, 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.10770
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: 17,741,442
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.5069
FINDPEAKS_PERCENTILE: 91
HOTSPOT_SCORE: 0.4981
HOTSPOT_PERCENTILE: 89
IROC_SCORE: 0.9994
IROC_PERCENTILE: 98
POISSON_SCORE: 0.5963
POISSON_PERCENTILE: 91
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM772849_BI.CD4+_CD25-_Th_Primary_Cells.H3K4me1.Donor_62.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 358-DNA_Lib 358-DNA_Lib 358-DNA_Lib 358.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of CD4+ CD25- Th Primary Cells Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me1 ChIP-Seq read mappings from CD4+ CD25- Th Primary Cells, Donor Donor 62, 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.11034
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: CCT H3K4me1 62 58
BROWSER_TRACK_DESCRIPTION: BI CD4+ CD25- Th Primary Cells Histone H3K4me1 Donor 62 Library DNA_Lib 358 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 17,741,442
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.5069
FINDPEAKS_PERCENTILE: 91
HOTSPOT_SCORE: 0.4981
HOTSPOT_PERCENTILE: 89
IROC_SCORE: 0.9994
IROC_PERCENTILE: 98
POISSON_SCORE: 0.5963
POISSON_PERCENTILE: 91
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: CD25- Th  is one of  CD4+  T cell subsets  that purified by microbeads, LS column and FACS ; DNA_Lib 358

tag: molecule

value: genomic DNA

value: CD4+ T cell

value: Unknown

value: Primary Cell

value: Donor 62

value: Dana Farber

value: Histone H3K4me1


title: ChIP-Seq analysis of H3K27ac in human hiPS-20b cells; DNA_Lib 357

description:
sample_term_id: NTR_0001168
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 357
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8538
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9470
****************
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: GSM772848_BI.iPS-20b.H3K27ac.DNA_Lib_357.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 357-DNA_Lib 357-DNA_Lib 357-DNA_Lib 357.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of iPS-20b Cell Line Histone H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27ac ChIP-Seq on the iPS-20b Cell Line, Library DNA_Lib 357, 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.10806
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: 22,503,706
NUMBER_OF_H3K27ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 34
FINDPEAKS_SCORE: 0.0693
FINDPEAKS_PERCENTILE: 18
HOTSPOT_SCORE: 0.1514
HOTSPOT_PERCENTILE: 18
IROC_SCORE: 0.9421
IROC_PERCENTILE: 21
POISSON_SCORE: 0.2437
POISSON_PERCENTILE: 18
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM772848_BI.iPS-20b.H3K27ac.DNA_Lib_357.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 357-DNA_Lib 357-DNA_Lib 357-DNA_Lib 357.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of iPS-20b Cell Line Histone H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27ac ChIP-Seq read mappings from the iPS-20b Cell Line, Library DNA_Lib 357, 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.11070
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: iPS20b H3K27ac 57
BROWSER_TRACK_DESCRIPTION: BI iPS-20b Cell Line Histone H3K27ac Library DNA_Lib 357 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 22,503,706
NUMBER_OF_H3K27ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 34
FINDPEAKS_SCORE: 0.0693
FINDPEAKS_PERCENTILE: 18
HOTSPOT_SCORE: 0.1514
HOTSPOT_PERCENTILE: 18
IROC_SCORE: 0.9421
IROC_PERCENTILE: 21
POISSON_SCORE: 0.2437
POISSON_PERCENTILE: 18
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: induced pleuripotent 20b stem cell line; DNA_Lib 357

value: induced pluripotent stem cells 20b

value: BioSam 174

value: iPS-20b Cell Line

value: induced pluripotent cells

value: 10% KOSR (Invitrogen)

tag: disease

value: p14 and p15 mixed

value: BioSAli 177

value: Cell Line

value: undifferentiated

value: Harvard

value: 0.5 to 3 million cells

value: cell/nuclei lysis

value: ~1 ug

value: 10 ul bed volume

value: Histone H3K27ac

value: Branson


title: ChIP-Seq analysis of H3K4me1 in human angular gyrus cells; Lib EpiLabSPL Row 1836

description:
sample_term_id: UBERON_0002686
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib EpiLabSPL Row 1836
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8031
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.8183
****************
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: GSM772770_BI.Brain_Angular_Gyrus.H3K4me1.112.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib EpiLabSPL Row 1836.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Brain Angular Gyrus Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me1 ChIP-Seq on Brain Angular Gyrus, Donor 112, 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.10652
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: 36,479,020
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.0607
FINDPEAKS_PERCENTILE: 11
HOTSPOT_SCORE: 0.175
HOTSPOT_PERCENTILE: 9
IROC_SCORE: 0.8767
IROC_PERCENTILE: 13
POISSON_SCORE: 0.3502
POISSON_PERCENTILE: 13
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

ANALYSIS FILE NAME: GSM772770_BI.Brain_Angular_Gyrus.H3K4me1.112.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib EpiLabSPL Row 1836.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Brain Angular Gyrus Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me1 ChIP-Seq read mappings from Brain Angular Gyrus, Donor 112, 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.10916
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: BAG H3K4me1 12 36
BROWSER_TRACK_DESCRIPTION: BI Brain Angular Gyrus Histone H3K4me1 Donor 112 Library Lib EpiLabSPL Row 1836 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 36,479,020
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.0607
FINDPEAKS_PERCENTILE: 11
HOTSPOT_SCORE: 0.175
HOTSPOT_PERCENTILE: 9
IROC_SCORE: 0.8767
IROC_PERCENTILE: 13
POISSON_SCORE: 0.3502
POISSON_PERCENTILE: 13
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

source_name: human post mortem brain region from a non Alzheimer's donor; Lib EpiLabSPL Row 1836

value: Brain, Angular Gyrus

value: post-mortem

value: genomic DNA

value: Angular Gyrus

value: Female

value: Primary Tissue

value: brain

value: Rush University Medical Center

value: Protein A-Sepharose 4B

value: 10 million cells

value: SDS lysis

value: 70 ul bed volume

value: Abcam

value: Histone H3K4me1

value: Bioruptor


title: WPP+12_USP_ChIPSeq_1 and 2

data_processing: Reads were aligned to the flybase BDGPv5 reference genome using Bowtie 0.12.5. Signal files were generated with the R 2.7.1 package SPP 2.7.1. Peaks were called with MACS 1.3.7.

value: USP

value: White Lab

value: USP, transgenic


title: modmdg4_INPUT_1


title: ChIP-Seq analysis of H3K27me3 in human hiPS-20b cells; DNA_Lib 356

description:
sample_term_id: NTR_0001168
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 356
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8537
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9470
****************
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: GSM772847_BI.iPS-20b.H3K27me3.DNA_Lib_356.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 356-DNA_Lib 356-DNA_Lib 356-DNA_Lib 356.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of iPS-20b Cell Line Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27me3 ChIP-Seq on the iPS-20b Cell Line, Library DNA_Lib 356, 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.10812
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: 25,275,748
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.446
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.4558
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9969
IROC_PERCENTILE: 90
POISSON_SCORE: 0.5024
POISSON_PERCENTILE: 98
MAXIMUM_REPLICATE_CORRELATION: 0.95

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

ANALYSIS FILE NAME: GSM772847_BI.iPS-20b.H3K27me3.DNA_Lib_356.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 356-DNA_Lib 356-DNA_Lib 356-DNA_Lib 356.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of iPS-20b Cell Line Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27me3 ChIP-Seq read mappings from the iPS-20b Cell Line, Library DNA_Lib 356, 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.11076
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: iPS20b H3K27me3 56
BROWSER_TRACK_DESCRIPTION: BI iPS-20b Cell Line Histone H3K27me3 Library DNA_Lib 356 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 25,275,748
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.446
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.4558
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9969
IROC_PERCENTILE: 90
POISSON_SCORE: 0.5024
POISSON_PERCENTILE: 98
MAXIMUM_REPLICATE_CORRELATION: 0.95

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

source_name: induced pleuripotent 20b stem cell line; DNA_Lib 356

value: induced pluripotent stem cells 20b

value: BioSam 174

value: iPS-20b Cell Line

value: induced pluripotent cells

value: 10% KOSR (Invitrogen)

value: presumed normal

value: p14 and p15 mixed

value: BioSAli 177

value: Cell Line

value: undifferentiated

value: Unknown

value: Harvard

value: 0.5 to 3 million cells

value: cell/nuclei lysis

value: ~1 ug

value: 10 ul bed volume

value: Millipore

value: Histone H3K27me3

value: Branson


title: ChIP-Seq analysis of H3K36me3 in human hiPS-20b cells; DNA_Lib 355

description:
sample_term_id: NTR_0001168
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 355
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8536
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9470
****************
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: GSM772846_BI.iPS-20b.H3K36me3.DNA_Lib_355.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 355-DNA_Lib 355-DNA_Lib 355-DNA_Lib 355.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of iPS-20b Cell Line Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K36me3 ChIP-Seq on the iPS-20b Cell Line, Library DNA_Lib 355, 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.10587
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: 39,688,896
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.3012
FINDPEAKS_PERCENTILE: 76
HOTSPOT_SCORE: 0.2957
HOTSPOT_PERCENTILE: 71
IROC_SCORE: 0.9918
IROC_PERCENTILE: 82
POISSON_SCORE: 0.4787
POISSON_PERCENTILE: 73
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

ANALYSIS FILE NAME: GSM772846_BI.iPS-20b.H3K36me3.DNA_Lib_355.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 355-DNA_Lib 355-DNA_Lib 355-DNA_Lib 355.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of iPS-20b Cell Line Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K36me3 ChIP-Seq read mappings from the iPS-20b Cell Line, Library DNA_Lib 355, 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.10851
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: iPS20b H3K36me3 55
BROWSER_TRACK_DESCRIPTION: BI iPS-20b Cell Line Histone H3K36me3 Library DNA_Lib 355 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 39,688,896
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.3012
FINDPEAKS_PERCENTILE: 76
HOTSPOT_SCORE: 0.2957
HOTSPOT_PERCENTILE: 71
IROC_SCORE: 0.9918
IROC_PERCENTILE: 82
POISSON_SCORE: 0.4787
POISSON_PERCENTILE: 73
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

source_name: induced pleuripotent 20b stem cell line; DNA_Lib 355

value: induced pluripotent stem cells 20b

value: BioSam 174

value: iPS-20b Cell Line

value: genomic DNA

value: Protein A-Sepharose 4B

value: Abcam

value: Histone H3K36me3


title: ChIP-Seq analysis of H3K4me1 in human hiPS-20b cells; DNA_Lib 354

description:
sample_term_id: NTR_0001168
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 354
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8535
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9470
****************
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: GSM772845_BI.iPS-20b.H3K4me1.DNA_Lib_354.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 354-DNA_Lib 354-DNA_Lib 354-DNA_Lib 354.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of iPS-20b Cell Line Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me1 ChIP-Seq on the iPS-20b Cell Line, Library DNA_Lib 354, 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.10785
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: 29,197,428
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.3161
FINDPEAKS_PERCENTILE: 74
HOTSPOT_SCORE: 0.388
HOTSPOT_PERCENTILE: 72
IROC_SCORE: 0.9766
IROC_PERCENTILE: 54
POISSON_SCORE: 0.5405
POISSON_PERCENTILE: 78
MAXIMUM_REPLICATE_CORRELATION: 0.87

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

ANALYSIS FILE NAME: GSM772845_BI.iPS-20b.H3K4me1.DNA_Lib_354.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 354-DNA_Lib 354-DNA_Lib 354-DNA_Lib 354.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of iPS-20b Cell Line Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me1 ChIP-Seq read mappings from the iPS-20b Cell Line, Library DNA_Lib 354, 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.11049
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: iPS20b H3K4me1 54
BROWSER_TRACK_DESCRIPTION: BI iPS-20b Cell Line Histone H3K4me1 Library DNA_Lib 354 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 29,197,428
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.3161
FINDPEAKS_PERCENTILE: 74
HOTSPOT_SCORE: 0.388
HOTSPOT_PERCENTILE: 72
IROC_SCORE: 0.9766
IROC_PERCENTILE: 54
POISSON_SCORE: 0.5405
POISSON_PERCENTILE: 78
MAXIMUM_REPLICATE_CORRELATION: 0.87

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

source_name: induced pleuripotent 20b stem cell line; DNA_Lib 354

value: induced pluripotent cells

value: 10% KOSR (Invitrogen)

value: presumed normal

value: p14 and p15 mixed

value: BioSAli 177

value: Cell Line

value: undifferentiated

value: Histone H3K4me1


title: ChIP-Seq analysis of H3K9me3 in human hiPS-20b cells; DNA_Lib 351

description:
sample_term_id: NTR_0001168
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 351
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8532
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9470
****************
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: GSM772842_BI.iPS-20b.H3K9me3.DNA_Lib_351.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 351-DNA_Lib 351-DNA_Lib 351-DNA_Lib 351.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of iPS-20b Cell Line Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9me3 ChIP-Seq on the iPS-20b Cell Line, Library DNA_Lib 351, 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.10793
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: 18,059,881
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.2804
FINDPEAKS_PERCENTILE: 98
HOTSPOT_SCORE: 0.2562
HOTSPOT_PERCENTILE: 92
IROC_SCORE: 0.9693
IROC_PERCENTILE: 100
POISSON_SCORE: 0.439
POISSON_PERCENTILE: 94
MAXIMUM_REPLICATE_CORRELATION: 0.94

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

ANALYSIS FILE NAME: GSM772842_BI.iPS-20b.H3K9me3.DNA_Lib_351.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 351-DNA_Lib 351-DNA_Lib 351-DNA_Lib 351.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of iPS-20b Cell Line Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9me3 ChIP-Seq read mappings from the iPS-20b Cell Line, Library DNA_Lib 351, 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.11057
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: iPS20b H3K9me3 51
BROWSER_TRACK_DESCRIPTION: BI iPS-20b Cell Line Histone H3K9me3 Library DNA_Lib 351 EA Release 5

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 18,059,881
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 49
FINDPEAKS_SCORE: 0.2804
FINDPEAKS_PERCENTILE: 98
HOTSPOT_SCORE: 0.2562
HOTSPOT_PERCENTILE: 92
IROC_SCORE: 0.9693
IROC_PERCENTILE: 100
POISSON_SCORE: 0.439
POISSON_PERCENTILE: 94
MAXIMUM_REPLICATE_CORRELATION: 0.94

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

source_name: induced pleuripotent 20b stem cell line; DNA_Lib 351

value: Unknown

value: Harvard

value: 0.5 to 3 million cells

value: cell/nuclei lysis

value: ~1 ug

value: 10 ul bed volume

value: Histone H3K9me3


title: Zfh1_ChIPSeq_1 and 2

value: White Lab