title: ChIP-Seq analysis of H3K36me3 in human H1 cells; 42LR0AAXX091002-6-S

description:
sample_term_id: EFO_0003042
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Solexa-14961
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.2499
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.2509
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************
BED and WIG files were replaced on April 29, 2014

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

ANALYSIS FILE NAME: GSM537684_BI.H1.H3K36me3.Solexa-14961.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 42LR0AAXX091002-6-S.hg19.level.1
ANALYSIS TITLE: Mapping of H1 Cell Line Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K36me3 ChIP-Seq on the H1 Cell Line, Library Solexa-14961 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.4713
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED: 54
FINDPEAKS_SCORE: 0.1895
FINDPEAKS_PERCENTILE: 35
HOTSPOT_SCORE: 0.0
HOTSPOT_PERCENTILE: NA
IROC_SCORE: 0.9661
IROC_PERCENTILE: 52
POISSON_SCORE: 0.5049
POISSON_PERCENTILE: 52

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

ANALYSIS FILE NAME: GSM537684_BI.H1.H3K36me3.Solexa-14961.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 42LR0AAXX091002-6-S.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Cell Line Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K36me3 ChIP-Seq read mappings from the H1 Cell Line, Library Solexa-14961 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.4987
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: H1 H3K36me3 61
BROWSER_TRACK_DESCRIPTION: BI H1 Cell Line Histone H3K36me3 Library Solexa-14961 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED: 54
FINDPEAKS_SCORE: 0.1895
FINDPEAKS_PERCENTILE: 35
HOTSPOT_SCORE: 0.0
HOTSPOT_PERCENTILE: NA
IROC_SCORE: 0.9661
IROC_PERCENTILE: 52
POISSON_SCORE: 0.5049
POISSON_PERCENTILE: 52

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

source_name: H1 stem cells from Cellular Dynamics; 42LR0AAXX091002-6-S

value: Histone H3K36me3

value: Protein A-Sepharose 4B

value: 70 ul bed volume


title: A.thaliana_aerial-bolting_21days

status: Public on May 14 2010

type: SRA

city: Saint Louis

first: James

middle: C

last: Carrington

state: MO

address: 975 North Warson Road

country: USA

institute: Donald Danforth Plant Science Center

description:
Wild type A. thaliana aerial tissue small RNA.
AT01

library_source: transcriptomic

data_processing: Small RNA sequences were parsed from Illumina sequencing data files through identification of the 3' adaptor boundary (the first six nucleotides of the 3' adaptor: CTGTAG). Only sequences that mapped perfectly to the A. thaliana (TAIR8; http://www.arabidopsis.org) or A. lyrata (v1.0; http://genome.jgi-psf.org/Araly1/Araly1.info.html ; http://www.phytozome.net/alyrata) genomes were included in the analysis.

molecule: total RNA

organism: Arabidopsis thaliana

source_name: total aerial, bolting and flowering (21 days)

extract_protocol: Small RNA were extracted from total RNA by size fractionation and converted to DNA amplicons by serial adaptor ligation to both ends followed by RT-PCR.  DNA amplicons were sequenced using an Ilumina Genome Analyzer.

tag: strain

tag: tissue

value: total aerial, bolting and flowering

tag: age

value: 21 days


title: ChIP-Seq analysis of H3K9ac in human hiPS-20b cells; 61BWEAAXX100226-2-S

status: Public on Apr 28 2010

city: Cambridge

first: BROAD

last: INSTITUTE

state: MA

institute: Broad Institute

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: Solexa-20764
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.2513
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.2304
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************
BED and WIG files were replaced on April 29, 2014

library_source: genomic

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

ANALYSIS FILE NAME: GSM537689_BI.iPS-20b.H3K9ac.Solexa-20764.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 61BWEAAXX100226-2-S.hg19.level.1
ANALYSIS TITLE: Mapping of iPS-20b Cell Line Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9ac ChIP-Seq on the iPS-20b Cell Line, Library Solexa-20764 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.4734
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED: 35
FINDPEAKS_SCORE: 0.0556
FINDPEAKS_PERCENTILE: 3
HOTSPOT_SCORE: 0.1303
HOTSPOT_PERCENTILE: 6
IROC_SCORE: 0.9441
IROC_PERCENTILE: 23
POISSON_SCORE: 0.3077
POISSON_PERCENTILE: 17

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

ANALYSIS FILE NAME: GSM537689_BI.iPS-20b.H3K9ac.Solexa-20764.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 61BWEAAXX100226-2-S.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of iPS-20b Cell Line Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9ac ChIP-Seq read mappings from the iPS-20b Cell Line, Library Solexa-20764 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.5008
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: iPS20b H3K9ac 64
BROWSER_TRACK_DESCRIPTION: BI iPS-20b Cell Line Histone H3K9ac Library Solexa-20764 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED: 35
FINDPEAKS_SCORE: 0.0556
FINDPEAKS_PERCENTILE: 3
HOTSPOT_SCORE: 0.1303
HOTSPOT_PERCENTILE: 6
IROC_SCORE: 0.9441
IROC_PERCENTILE: 23
POISSON_SCORE: 0.3077
POISSON_PERCENTILE: 17

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

molecule: genomic DNA

organism: Homo sapiens

source_name: IPS cell line 20b; 61BWEAAXX100226-2-S

extract_protocol: Library construction protocol: Single read - Illumina

value: induced pluripotent stem cells 20b

tag: molecule

value: genomic DNA

tag: disease

value: Harvard University

value: Cell Line

tag: line

tag: lineage

value: induced pluripotent cells

value: undifferentiated

tag: passage

tag: medium

value: KSR

tag: Sex

value: Male

tag: batch

value: Histone H3K9ac

value: SDS lysis

value: Bioruptor

value: 10 million cells

value: Abcam


title: G613T

city: Piscataway

first: Sam

middle: Guoping

last: Gu

state: NJ

address: Nelson Labs A125, 604 Allison Road

department: Molecular Biology and Biochemistry

institute: Rutgers University

description:
5' monophosphate dependent small RNA cloning
ggg

data_processing: frequencies of  known and novel miRNAs expressed in human cervical cancer tissues and matched normal tissues calculated (see Series record)

source_name: cervical cancer

growth_protocol: not applicable

extract_protocol: Small RNA isolation was performed using mirVana miRNA isolation kit (Applied Biosystems/Ambion, Austin, TX). Purified small RNAs were ligated to the 3’-adaptor [“Linker-1”, IDT Inc., Coralville, IA] and 5’ adaptor [5’-ACGCTCTTCCGATCTv-3’ (uppercase, DNA; v=barcodes with triple RNA molecules: aaa, ggg, ccc or uuu; IDT Inc., Coralville, IA)] oligonucleotides. Products from the second ligation were gel-purified and reverse transcribed using the RT primer [5'-ATTGATGGTGCCTACAG-3’]. cDNA was amplified with 16-20 PCR cycles, using a forward primer 5'- GAT ACG GCG ACC ACC GAG ATC TAC ACT CTT TCC CTA CAC GAC GCT CTT CCG ATC T-3' and a reverse primer 5’-CAA GCA GAA GAC GGC ATA CGA GCT CTT CCG ATC TAT TGA TGG TGC CTA CAG-3', to produce sequencing libraries that were subjected to Solexa/Illumina sequencing platform.

treatment_protocol: not applicable

tag: diagnosis

value: squamous cell carcinoma

value: tumor


title: G613N

description:
5' monophosphate dependent small RNA cloning
aaa

source_name: normal cervix

value: normal

value: normal cervix


title: ChIP-Seq analysis of WCE in human H1 cells; 30H81AAXX090613-1-S

description:
sample_term_id: EFO_0003042
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Solexa-12532
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.2497
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.2353
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************
BED and WIG files were replaced on April 29, 2014

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

ANALYSIS FILE NAME: GSM537682_BI.H1.Input.Solexa-12532.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 30H81AAXX090613-1-S.hg19.level.1
ANALYSIS TITLE: Mapping of H1 Cell Line ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on the H1 Cell Line, Library Solexa-12532 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.4665
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED: 67
FINDPEAKS_SCORE: 0.0139
FINDPEAKS_PERCENTILE: 66
HOTSPOT_SCORE: 0.0809
HOTSPOT_PERCENTILE: 61
IROC_SCORE: 0.0
IROC_PERCENTILE: NA
POISSON_SCORE: 0.1225
POISSON_PERCENTILE: 1

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

ANALYSIS FILE NAME: GSM537682_BI.H1.Input.Solexa-12532.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 30H81AAXX090613-1-S.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Cell Line ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from the H1 Cell Line, Library Solexa-12532 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.4939
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: H1 Input 32
BROWSER_TRACK_DESCRIPTION: BI H1 Cell Line ChIP-Seq Input Library Solexa-12532 EA Release 2

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED: 67
FINDPEAKS_SCORE: 0.0139
FINDPEAKS_PERCENTILE: 66
HOTSPOT_SCORE: 0.0809
HOTSPOT_PERCENTILE: 61
IROC_SCORE: 0.0
IROC_PERCENTILE: NA
POISSON_SCORE: 0.1225
POISSON_PERCENTILE: 1

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

source_name: H1 stem cells from Cellular Dynamics; 30H81AAXX090613-1-S

value: Cellular Dynamics

value: TESR

tag: sex

value: ChIP-Seq Input

value: Input

value: standard


title: ChIP-Seq analysis of H3K4me3 in human H1 cells; 314G7AAXX090305-5-S

description:
sample_term_id: EFO_0003042
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Solexa-10398
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.2495
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.2508
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************
BED and WIG files were replaced on April 29, 2014

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

ANALYSIS FILE NAME: GSM537680_BI.H1.H3K4me3.Solexa-10398.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 314G7AAXX090305-5-S.hg19.level.1
ANALYSIS TITLE: Mapping of H1 Cell Line Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me3 ChIP-Seq on the H1 Cell Line, Library Solexa-10398 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.4763
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED: 62
FINDPEAKS_SCORE: 0.282
FINDPEAKS_PERCENTILE: 29
HOTSPOT_SCORE: 0.3314
HOTSPOT_PERCENTILE: 36
IROC_SCORE: 0.9985
IROC_PERCENTILE: 42
POISSON_SCORE: 0.3716
POISSON_PERCENTILE: 23

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

ANALYSIS FILE NAME: GSM537680_BI.H1.H3K4me3.Solexa-10398.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 314G7AAXX090305-5-S.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Cell Line Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me3 ChIP-Seq read mappings from the H1 Cell Line, Library Solexa-10398 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.5037
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: H1 H3K4me3 98
BROWSER_TRACK_DESCRIPTION: BI H1 Cell Line Histone H3K4me3 Library Solexa-10398 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED: 62
FINDPEAKS_SCORE: 0.282
FINDPEAKS_PERCENTILE: 29
HOTSPOT_SCORE: 0.3314
HOTSPOT_PERCENTILE: 36
IROC_SCORE: 0.9985
IROC_PERCENTILE: 42
POISSON_SCORE: 0.3716
POISSON_PERCENTILE: 23

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

source_name: H1 stem cells from Cellular Dynamics; 314G7AAXX090305-5-S

value: genomic DNA

value: Cell Line

value: undifferentiated

value: Histone H3K4me3

value: Protein A-Sepharose 4B

value: 70 ul bed volume

value: Millipore


title: G026T


title: G575T

description:
5' monophosphate dependent small RNA cloning
uuu


title: sRNA from grape berries

status: Public on Apr 29 2010

city: Norwich

first: Simon

last: Moxon

state: Norfolk

address: University of East Anglia

country: United Kingdom

institute: University of East Anglia

description: Total endogenous small RNAs from Vitis vinifera cv. Pinot noir, clone ENTAV115 1-5 mm berries

data_processing: Removed adaptors. Sequences without adaptor matches were discarded.

organism: Vitis vinifera

source_name: Vitis vinifera cv. Pinot noir, clone ENTAV115, small berries and bunch stems

growth_protocol: Samples were collected from plants grown in collection field during the vegetative start.

extract_protocol: Size fractionated small RNA from total RNA extracts was ligated to adaptors, purified again and reverse transcribed. After PCR amplification the sample was subjected to Illumina sequencing

value: RNA extracted from small berries and bunch stems


title: ChIP-Seq analysis of H3K9me3 in human hiPS-18c cells; 42TPLAAXX100219-6-S

description:
sample_term_id: NTR_0001167
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Solexa-19774
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.2155
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.2154
****************
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: GSM537678_BI.iPS-18c.H3K9me3.Solexa-19774.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 42TPLAAXX100219-6-S.hg19.level.1
ANALYSIS TITLE: Mapping of iPS-18c Cell Line Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9me3 ChIP-Seq on the iPS-18c Cell Line, Library Solexa-19774 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.4663
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED: 59
FINDPEAKS_SCORE: 0.1039
FINDPEAKS_PERCENTILE: 56
HOTSPOT_SCORE: 0.2451
HOTSPOT_PERCENTILE: 78
IROC_SCORE: 0.8124
IROC_PERCENTILE: 46
POISSON_SCORE: 0.353
POISSON_PERCENTILE: 44

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

ANALYSIS FILE NAME: GSM537678_BI.iPS-18c.H3K9me3.Solexa-19774.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 42TPLAAXX100219-6-S.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of iPS-18c Cell Line Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9me3 ChIP-Seq read mappings from the iPS-18c Cell Line, Library Solexa-19774 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.4937
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: iPS18c H3K9me3 74
BROWSER_TRACK_DESCRIPTION: BI iPS-18c Cell Line Histone H3K9me3 Library Solexa-19774 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED: 59
FINDPEAKS_SCORE: 0.1039
FINDPEAKS_PERCENTILE: 56
HOTSPOT_SCORE: 0.2451
HOTSPOT_PERCENTILE: 78
IROC_SCORE: 0.8124
IROC_PERCENTILE: 46
POISSON_SCORE: 0.353
POISSON_PERCENTILE: 44

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

source_name: IPS cell line 18c; 42TPLAAXX100219-6-S

value: induced pluripotent stem cells

value: Harvard University

value: induced pluripotent cells

value: KSR

value: Female

value: Histone H3K9me3

value: SDS lysis

value: Bioruptor

value: 10 million cells

value: Abcam


title: G575N

description:
5' monophosphate dependent small RNA cloning
ccc

value: normal

value: normal cervix


title: ChIP-Seq analysis of H3K4me3 in human hiPS-18c cells; 42TPLAAXX100219-3-S

description:
sample_term_id: NTR_0001167
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Solexa-19747
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.2233
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.2232
****************
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: GSM537676_BI.iPS-18c.H3K4me3.Solexa-19747.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 42TPLAAXX100219-3-S.hg19.level.1
ANALYSIS TITLE: Mapping of iPS-18c Cell Line Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me3 ChIP-Seq on the iPS-18c Cell Line, Library Solexa-19747 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.4573
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED: 62
FINDPEAKS_SCORE: 0.5631
FINDPEAKS_PERCENTILE: 81
HOTSPOT_SCORE: 0.5588
HOTSPOT_PERCENTILE: 80
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.6053
POISSON_PERCENTILE: 77

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

ANALYSIS FILE NAME: GSM537676_BI.iPS-18c.H3K4me3.Solexa-19747.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 42TPLAAXX100219-3-S.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of iPS-18c Cell Line Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me3 ChIP-Seq read mappings from the iPS-18c Cell Line, Library Solexa-19747 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.4847
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: iPS18c H3K4me3 47
BROWSER_TRACK_DESCRIPTION: BI iPS-18c Cell Line Histone H3K4me3 Library Solexa-19747 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED: 62
FINDPEAKS_SCORE: 0.5631
FINDPEAKS_PERCENTILE: 81
HOTSPOT_SCORE: 0.5588
HOTSPOT_PERCENTILE: 80
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.6053
POISSON_PERCENTILE: 77

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

source_name: IPS cell line 18c; 42TPLAAXX100219-3-S

value: genomic DNA

value: Cell Line

value: undifferentiated

value: Histone H3K4me3


title: G699N_2


title: ChIP-Seq analysis of H3K27me3 in human hiPS-18c cells; 42TPLAAXX100219-1-S

description:
sample_term_id: NTR_0001167
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Solexa-19791
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.2158
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.2157
****************
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: GSM537674_BI.iPS-18c.H3K27me3.Solexa-19791.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 42TPLAAXX100219-1-S.hg19.level.1
ANALYSIS TITLE: Mapping of iPS-18c Cell Line Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27me3 ChIP-Seq on the iPS-18c Cell Line, Library Solexa-19791 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.4635
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED: 52
FINDPEAKS_SCORE: 0.3215
FINDPEAKS_PERCENTILE: 88
HOTSPOT_SCORE: 0.4168
HOTSPOT_PERCENTILE: 98
IROC_SCORE: 0.9958
IROC_PERCENTILE: 98
POISSON_SCORE: 0.5043
POISSON_PERCENTILE: 63

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

ANALYSIS FILE NAME: GSM537674_BI.iPS-18c.H3K27me3.Solexa-19791.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 42TPLAAXX100219-1-S.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of iPS-18c Cell Line Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27me3 ChIP-Seq read mappings from the iPS-18c Cell Line, Library Solexa-19791 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.4909
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: iPS18c H3K27me3 91
BROWSER_TRACK_DESCRIPTION: BI iPS-18c Cell Line Histone H3K27me3 Library Solexa-19791 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED: 52
FINDPEAKS_SCORE: 0.3215
FINDPEAKS_PERCENTILE: 88
HOTSPOT_SCORE: 0.4168
HOTSPOT_PERCENTILE: 98
IROC_SCORE: 0.9958
IROC_PERCENTILE: 98
POISSON_SCORE: 0.5043
POISSON_PERCENTILE: 63

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

source_name: IPS cell line 18c; 42TPLAAXX100219-1-S

value: Histone H3K27me3

value: Protein A-Sepharose 4B

value: 70 ul bed volume

value: Millipore


title: ChIP-Seq analysis of H3K9ac in human hES-I3 cells; 42MNCAAXX100106-6-S

description:
sample_term_id: NTR_0000836
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Solexa-15383
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.2260
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.2259
****************
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: GSM537670_BI.ES-I3.H3K9ac.Solexa-15383.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 42MNCAAXX100106-6-S.hg19.level.1
ANALYSIS TITLE: Mapping of ES-I3 Cell Line Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9ac ChIP-Seq on the ES-I3 Cell Line, Library Solexa-15383 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.4694
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED: 35
FINDPEAKS_SCORE: 0.6889
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.6464
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9995
IROC_PERCENTILE: 100
POISSON_SCORE: 0.7083
POISSON_PERCENTILE: 89

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

ANALYSIS FILE NAME: GSM537670_BI.ES-I3.H3K9ac.Solexa-15383.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 42MNCAAXX100106-6-S.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of ES-I3 Cell Line Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9ac ChIP-Seq read mappings from the ES-I3 Cell Line, Library Solexa-15383 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.4968
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: ESI3 H3K9ac 83
BROWSER_TRACK_DESCRIPTION: BI ES-I3 Cell Line Histone H3K9ac Library Solexa-15383 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED: 35
FINDPEAKS_SCORE: 0.6889
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.6464
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9995
IROC_PERCENTILE: 100
POISSON_SCORE: 0.7083
POISSON_PERCENTILE: 89

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

source_name: I3(eye three) stem cells; 42MNCAAXX100106-6-S

value: Harvard University

value: embrionic stem cell

value: KSR

value: Histone H3K9ac


title: G701T

value: adenosquamous cell carcinoma

value: tumor


title: G701N


title: ChIP-Seq analysis of H3K36me3 in human hES I3 TESR cells; 42NF9AAXX091210-1-S

description:
sample_term_id: NTR_0000836
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Solexa-16493
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.2221
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.2220
****************
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: GSM537672_BI.ES-I3.H3K36me3.Solexa-16493.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 42NF9AAXX091210-1-S.hg19.level.1
ANALYSIS TITLE: Mapping of ES-I3 Cell Line Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K36me3 ChIP-Seq on the ES-I3 Cell Line, Library Solexa-16493 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.4668
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED: 54
FINDPEAKS_SCORE: 0.1987
FINDPEAKS_PERCENTILE: 39
HOTSPOT_SCORE: 0.2333
HOTSPOT_PERCENTILE: 38
IROC_SCORE: 0.8835
IROC_PERCENTILE: 20
POISSON_SCORE: 0.3975
POISSON_PERCENTILE: 20

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

ANALYSIS FILE NAME: GSM537672_BI.ES-I3.H3K36me3.Solexa-16493.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 42NF9AAXX091210-1-S.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of ES-I3 Cell Line Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K36me3 ChIP-Seq read mappings from the ES-I3 Cell Line, Library Solexa-16493 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.4942
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: ESI3 H3K36me3 93
BROWSER_TRACK_DESCRIPTION: BI ES-I3 Cell Line Histone H3K36me3 Library Solexa-16493 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED: 54
FINDPEAKS_SCORE: 0.1987
FINDPEAKS_PERCENTILE: 39
HOTSPOT_SCORE: 0.2333
HOTSPOT_PERCENTILE: 38
IROC_SCORE: 0.8835
IROC_PERCENTILE: 20
POISSON_SCORE: 0.3975
POISSON_PERCENTILE: 20

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

source_name: I3(eye three) stem cells; 42NF9AAXX091210-1-S

value: hES I3 TESR

value: TESR

value: Female

value: Histone H3K36me3

value: SDS lysis

value: Bioruptor

value: 10 million cells

value: Abcam


title: G645T

value: squamous cell carcinoma


title: ChIP-Seq analysis of H3K9ac in human hiPS-18c cells; 42TPLAAXX100219-5-S

description:
sample_term_id: NTR_0001167
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Solexa-19756
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.2251
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.2250
****************
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: GSM537677_BI.iPS-18c.H3K9ac.Solexa-19756.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 42TPLAAXX100219-5-S.hg19.level.1
ANALYSIS TITLE: Mapping of iPS-18c Cell Line Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9ac ChIP-Seq on the iPS-18c Cell Line, Library Solexa-19756 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.4685
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED: 35
FINDPEAKS_SCORE: 0.1148
FINDPEAKS_PERCENTILE: 31
HOTSPOT_SCORE: 0.2533
HOTSPOT_PERCENTILE: 57
IROC_SCORE: 0.9183
IROC_PERCENTILE: 17
POISSON_SCORE: 0.3311
POISSON_PERCENTILE: 31

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

ANALYSIS FILE NAME: GSM537677_BI.iPS-18c.H3K9ac.Solexa-19756.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 42TPLAAXX100219-5-S.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of iPS-18c Cell Line Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9ac ChIP-Seq read mappings from the iPS-18c Cell Line, Library Solexa-19756 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.4959
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: iPS18c H3K9ac 56
BROWSER_TRACK_DESCRIPTION: BI iPS-18c Cell Line Histone H3K9ac Library Solexa-19756 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED: 35
FINDPEAKS_SCORE: 0.1148
FINDPEAKS_PERCENTILE: 31
HOTSPOT_SCORE: 0.2533
HOTSPOT_PERCENTILE: 57
IROC_SCORE: 0.9183
IROC_PERCENTILE: 17
POISSON_SCORE: 0.3311
POISSON_PERCENTILE: 31

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

source_name: IPS cell line 18c; 42TPLAAXX100219-5-S

value: induced pluripotent stem cells

value: genomic DNA

value: Cell Line

value: induced pluripotent cells

value: undifferentiated

value: Protein A-Sepharose 4B

value: 70 ul bed volume


title: G761T_2

value: adenocarcinoma

value: tumor


title: ChIP-Seq analysis of H3K36me3 in human hiPS-18c cells; 42TPLAAXX100219-2-S

description:
sample_term_id: NTR_0001167
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Solexa-19808
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.2167
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.2166
****************
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: GSM537675_BI.iPS-18c.H3K36me3.Solexa-19808.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 42TPLAAXX100219-2-S.hg19.level.1
ANALYSIS TITLE: Mapping of iPS-18c Cell Line Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K36me3 ChIP-Seq on the iPS-18c Cell Line, Library Solexa-19808 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.4707
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED: 54
FINDPEAKS_SCORE: 0.2188
FINDPEAKS_PERCENTILE: 44
HOTSPOT_SCORE: 0.3174
HOTSPOT_PERCENTILE: 68
IROC_SCORE: 0.9401
IROC_PERCENTILE: 37
POISSON_SCORE: 0.4621
POISSON_PERCENTILE: 35

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

ANALYSIS FILE NAME: GSM537675_BI.iPS-18c.H3K36me3.Solexa-19808.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 42TPLAAXX100219-2-S.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of iPS-18c Cell Line Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K36me3 ChIP-Seq read mappings from the iPS-18c Cell Line, Library Solexa-19808 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.4981
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: iPS18c H3K36me3 08
BROWSER_TRACK_DESCRIPTION: BI iPS-18c Cell Line Histone H3K36me3 Library Solexa-19808 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED: 54
FINDPEAKS_SCORE: 0.2188
FINDPEAKS_PERCENTILE: 44
HOTSPOT_SCORE: 0.3174
HOTSPOT_PERCENTILE: 68
IROC_SCORE: 0.9401
IROC_PERCENTILE: 37
POISSON_SCORE: 0.4621
POISSON_PERCENTILE: 35

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

source_name: IPS cell line 18c; 42TPLAAXX100219-2-S

value: Harvard University

value: KSR


title: A.lyrata_vegetative-rosette-leaves

description:
Wild type A. lyrata leaf small RNA.
AL01

organism: Arabidopsis lyrata

source_name: vegetative rosette leaves

value: vegetative rosette leaves


title: ChIP-Seq analysis of H3K4me1 in human hES-I3 cells; 42MNCAAXX100106-3-S

description:
sample_term_id: NTR_0000836
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Solexa-15382
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.2275
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.2274
****************
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: GSM537668_BI.ES-I3.H3K4me1.Solexa-15382.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 42MNCAAXX100106-3-S.hg19.level.1
ANALYSIS TITLE: Mapping of ES-I3 Cell Line Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me1 ChIP-Seq on the ES-I3 Cell Line, Library Solexa-15382 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.4824
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED: 43
FINDPEAKS_SCORE: 0.5351
FINDPEAKS_PERCENTILE: 81
HOTSPOT_SCORE: 0.4313
HOTSPOT_PERCENTILE: 70
IROC_SCORE: 0.9831
IROC_PERCENTILE: 48
POISSON_SCORE: 0.6098
POISSON_PERCENTILE: 67

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

ANALYSIS FILE NAME: GSM537668_BI.ES-I3.H3K4me1.Solexa-15382.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 42MNCAAXX100106-3-S.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of ES-I3 Cell Line Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me1 ChIP-Seq read mappings from the ES-I3 Cell Line, Library Solexa-15382 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.5098
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: ESI3 H3K4me1 82
BROWSER_TRACK_DESCRIPTION: BI ES-I3 Cell Line Histone H3K4me1 Library Solexa-15382 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED: 43
FINDPEAKS_SCORE: 0.5351
FINDPEAKS_PERCENTILE: 81
HOTSPOT_SCORE: 0.4313
HOTSPOT_PERCENTILE: 70
IROC_SCORE: 0.9831
IROC_PERCENTILE: 48
POISSON_SCORE: 0.6098
POISSON_PERCENTILE: 67

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

source_name: I3(eye three) stem cells; 42MNCAAXX100106-3-S

value: embrionic stem cell

value: Female

value: Histone H3K4me1

value: SDS lysis


title: ChIP-Seq analysis of H3K9me3 in human hES-I3 cells; 42M0GAAXX091022-1-S

description:
sample_term_id: NTR_0000836
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Solexa-15475
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.2164
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.2163
****************
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: GSM537664_BI.ES-I3.H3K9me3.Solexa-15475.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 42M0GAAXX091022-1-S.hg19.level.1
ANALYSIS TITLE: Mapping of ES-I3 Cell Line Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9me3 ChIP-Seq on the ES-I3 Cell Line, Library Solexa-15475 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.4614
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED: 59
FINDPEAKS_SCORE: 0.1093
FINDPEAKS_PERCENTILE: 58
HOTSPOT_SCORE: 0.1778
HOTSPOT_PERCENTILE: 54
IROC_SCORE: 0.7762
IROC_PERCENTILE: 34
POISSON_SCORE: 0.3323
POISSON_PERCENTILE: 34

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

ANALYSIS FILE NAME: GSM537664_BI.ES-I3.H3K9me3.Solexa-15475.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 42M0GAAXX091022-1-S.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of ES-I3 Cell Line Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9me3 ChIP-Seq read mappings from the ES-I3 Cell Line, Library Solexa-15475 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.4888
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: ESI3 H3K9me3 75
BROWSER_TRACK_DESCRIPTION: BI ES-I3 Cell Line Histone H3K9me3 Library Solexa-15475 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED: 59
FINDPEAKS_SCORE: 0.1093
FINDPEAKS_PERCENTILE: 58
HOTSPOT_SCORE: 0.1778
HOTSPOT_PERCENTILE: 54
IROC_SCORE: 0.7762
IROC_PERCENTILE: 34
POISSON_SCORE: 0.3323
POISSON_PERCENTILE: 34

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

source_name: I3(eye three) stem cells; 42M0GAAXX091022-1-S

value: Histone H3K9me3

value: Bioruptor

value: 10 million cells

value: Abcam


title: G645N

value: normal

value: normal cervix


title: ChIP-Seq analysis of H3K9me3 in human Mobilized CD34 cells; 42M09AAXX090926-7-S

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: Solexa-14519
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.2194
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.2193
****************
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: GSM537663_BI.Mobilized_CD34_Primary_Cells.H3K9me3.Mobilized_CD34_5_28_09.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 42M09AAXX090926-7-S.hg19.level.1
ANALYSIS TITLE: Mapping of Mobilized CD34 Primary Cells Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9me3 ChIP-Seq on Mobilized CD34 Primary Cells, Donor RO 01508 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.4797
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED: 59
FINDPEAKS_SCORE: 0.2607
FINDPEAKS_PERCENTILE: 86
HOTSPOT_SCORE: 0.3479
HOTSPOT_PERCENTILE: 95
IROC_SCORE: 0.9239
IROC_PERCENTILE: 78
POISSON_SCORE: 0.4912
POISSON_PERCENTILE: 85

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

ANALYSIS FILE NAME: GSM537663_BI.Mobilized_CD34_Primary_Cells.H3K9me3.Mobilized_CD34_5_28_09.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 42M09AAXX090926-7-S.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Mobilized CD34 Primary Cells Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9me3 ChIP-Seq read mappings from Mobilized CD34 Primary Cells, Donor RO 01508 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.5071
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: MCD34 H3K9me3 28
BROWSER_TRACK_DESCRIPTION: BI Mobilized CD34 Primary Cells Histone H3K9me3 Donor RO 01508 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED: 59
FINDPEAKS_SCORE: 0.2607
FINDPEAKS_PERCENTILE: 86
HOTSPOT_SCORE: 0.3479
HOTSPOT_PERCENTILE: 95
IROC_SCORE: 0.9239
IROC_PERCENTILE: 78
POISSON_SCORE: 0.4912
POISSON_PERCENTILE: 85

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

source_name: CD34 cells mobilized into peripheral blood; 42M09AAXX090926-7-S

value: genomic DNA

value: FHCRC

value: Primary Cell

value: Mobilized CD34 Primary Cells

tag: markers

value: Unknown

value: not passaged

value: Protein A-Sepharose 4B


title: sRNA from grape tendrils

description: Total endogenous small RNAs from the tendrils of Vitis vinifera cv. Pinot noir, clone ENTAV115

source_name: Vitis vinifera cv. Pinot noir, clone ENTAV115, tendrils

value: RNA extracted from tendrils


title: ChIP-Seq analysis of WCE in human Mobilized CD34 cells; 42LWTAAXX091016-1-S

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: Solexa-15156
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.2236
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.2235
****************
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: GSM537662_BI.Mobilized_CD34_Primary_Cells.Input.Mobilized_CD34_5_28_09.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 42LWTAAXX091016-1-S.hg19.level.1
ANALYSIS TITLE: Mapping of Mobilized CD34 Primary Cells ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on Mobilized CD34 Primary Cells, Donor RO 01508 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.4755
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED: 67
FINDPEAKS_SCORE: 0.0184
FINDPEAKS_PERCENTILE: 73
HOTSPOT_SCORE: 0.082
HOTSPOT_PERCENTILE: 64
IROC_SCORE: 0.0
IROC_PERCENTILE: NA
POISSON_SCORE: 0.1853
POISSON_PERCENTILE: 18

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

ANALYSIS FILE NAME: GSM537662_BI.Mobilized_CD34_Primary_Cells.Input.Mobilized_CD34_5_28_09.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 42LWTAAXX091016-1-S.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Mobilized CD34 Primary Cells ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from Mobilized CD34 Primary Cells, Donor RO 01508 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.5029
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: MCD34 Input 28
BROWSER_TRACK_DESCRIPTION: BI Mobilized CD34 Primary Cells ChIP-Seq Input Donor RO 01508 EA Release 2

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED: 67
FINDPEAKS_SCORE: 0.0184
FINDPEAKS_PERCENTILE: 73
HOTSPOT_SCORE: 0.082
HOTSPOT_PERCENTILE: 64
IROC_SCORE: 0.0
IROC_PERCENTILE: NA
POISSON_SCORE: 0.1853
POISSON_PERCENTILE: 18

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

source_name: CD34 cells mobilized into peripheral blood; 42LWTAAXX091016-1-S

value: ChIP-Seq Input

value: Input

value: standard


title: ChIP-Seq analysis of H3K4me1 in human H1 cells; 30E62AAXX090709-5-S

description:
sample_term_id: EFO_0003042
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Solexa-13061
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.2494
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.2353
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************
BED and WIG files were replaced on April 29, 2014

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

ANALYSIS FILE NAME: GSM537679_BI.H1.H3K4me1.Solexa-13061.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 30E62AAXX090709-5-S.hg19.level.1
ANALYSIS TITLE: Mapping of H1 Cell Line Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me1 ChIP-Seq on the H1 Cell Line, Library Solexa-13061 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.4572
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED: 43
FINDPEAKS_SCORE: 0.2109
FINDPEAKS_PERCENTILE: 23
HOTSPOT_SCORE: 0.2723
HOTSPOT_PERCENTILE: 19
IROC_SCORE: 0.9498
IROC_PERCENTILE: 19
POISSON_SCORE: 0.4752
POISSON_PERCENTILE: 19

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

ANALYSIS FILE NAME: GSM537679_BI.H1.H3K4me1.Solexa-13061.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 30E62AAXX090709-5-S.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Cell Line Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me1 ChIP-Seq read mappings from the H1 Cell Line, Library Solexa-13061 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.4846
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: H1 H3K4me1 61
BROWSER_TRACK_DESCRIPTION: BI H1 Cell Line Histone H3K4me1 Library Solexa-13061 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED: 43
FINDPEAKS_SCORE: 0.2109
FINDPEAKS_PERCENTILE: 23
HOTSPOT_SCORE: 0.2723
HOTSPOT_PERCENTILE: 19
IROC_SCORE: 0.9498
IROC_PERCENTILE: 19
POISSON_SCORE: 0.4752
POISSON_PERCENTILE: 19

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

source_name: H1 stem cells from Cellular Dynamics; 30E62AAXX090709-5-S

value: Cellular Dynamics

value: Cell Line

value: undifferentiated

value: TESR

value: Male

value: Histone H3K4me1

value: SDS lysis

value: 70 ul bed volume


title: G623N

description:
5' monophosphate dependent small RNA cloning
aaa

source_name: normal cervix

value: normal

value: normal cervix


title: G623T

description:
5' monophosphate dependent small RNA cloning
ggg

source_name: cervical cancer

value: squamous cell carcinoma

value: tumor


title: sRNA from grape inflorescences

description: Total endogenous small RNAs from Vitis vinifera cv. Pinot noir, clone ENTAV115 inflorescences

source_name: Vitis vinifera cv. Pinot noir, clone ENTAV115, inflorescences

value: RNA extracted from inflorescences


title: G648N

description:
5' monophosphate dependent small RNA cloning
ccc


title: G648T

description:
5' monophosphate dependent small RNA cloning
uuu


title: ChIP-Seq analysis of H3K27me3 in human cultured CD34 cells; 42LP1AAXX090808-8-S

description:
sample_term_id: CL_0001059
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Solexa-12290
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.2176
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.2175
****************
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: GSM537656_BI.CD34_Cultured_Cells.H3K27me3.cultured_CD34_2_20_09.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 42LP1AAXX090808-8-S.hg19.level.1
ANALYSIS TITLE: Mapping of CD34 Cultured Cells Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27me3 ChIP-Seq on CD34 Cultured Cells, Donor cultured CD34_2/20/09 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.4564
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED: 52
FINDPEAKS_SCORE: 0.2916
FINDPEAKS_PERCENTILE: 85
HOTSPOT_SCORE: 0.3021
HOTSPOT_PERCENTILE: 79
IROC_SCORE: 0.9417
IROC_PERCENTILE: 67
POISSON_SCORE: 0.5315
POISSON_PERCENTILE: 75

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

ANALYSIS FILE NAME: GSM537656_BI.CD34_Cultured_Cells.H3K27me3.cultured_CD34_2_20_09.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 42LP1AAXX090808-8-S.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of CD34 Cultured Cells Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27me3 ChIP-Seq read mappings from CD34 Cultured Cells, Donor cultured CD34_2/20/09 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.4838
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: CD34 H3K27me3 20
BROWSER_TRACK_DESCRIPTION: BI CD34 Cultured Cells Histone H3K27me3 Donor cultured CD34_2/20/09 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED: 52
FINDPEAKS_SCORE: 0.2916
FINDPEAKS_PERCENTILE: 85
HOTSPOT_SCORE: 0.3021
HOTSPOT_PERCENTILE: 79
IROC_SCORE: 0.9417
IROC_PERCENTILE: 67
POISSON_SCORE: 0.5315
POISSON_PERCENTILE: 75

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

source_name: flow sorted CD34+ cells from cord blood expanded in short term culture; 42LP1AAXX090808-8-S

value: genomic DNA

value: FHCRC

value: Primary Cell

value: CD34 Cultured Cells

value: cultured CD34_2/20/09

value: Unknown

value: short term

value: Histone H3K27me3

value: Bioruptor

value: 10 million cells

value: Protein A-Sepharose 4B

value: Millipore


title: ChIP-Seq analysis of H3K9me3 in human cultured CD34 cells; 42LP1AAXX090808-5-S

description:
sample_term_id: CL_0001059
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Solexa-12458
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.2242
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.2241
****************
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: GSM537653_BI.CD34_Cultured_Cells.H3K9me3.cultured_CD34_2_20_09.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 42LP1AAXX090808-5-S.hg19.level.1
ANALYSIS TITLE: Mapping of CD34 Cultured Cells Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9me3 ChIP-Seq on CD34 Cultured Cells, Donor cultured CD34_2/20/09 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.4739
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED: 59
FINDPEAKS_SCORE: 0.1712
FINDPEAKS_PERCENTILE: 80
HOTSPOT_SCORE: 0.2666
HOTSPOT_PERCENTILE: 83
IROC_SCORE: 0.8751
IROC_PERCENTILE: 69
POISSON_SCORE: 0.4397
POISSON_PERCENTILE: 68

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

ANALYSIS FILE NAME: GSM537653_BI.CD34_Cultured_Cells.H3K9me3.cultured_CD34_2_20_09.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 42LP1AAXX090808-5-S.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of CD34 Cultured Cells Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9me3 ChIP-Seq read mappings from CD34 Cultured Cells, Donor cultured CD34_2/20/09 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.5013
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: CD34 H3K9me3 20
BROWSER_TRACK_DESCRIPTION: BI CD34 Cultured Cells Histone H3K9me3 Donor cultured CD34_2/20/09 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED: 59
FINDPEAKS_SCORE: 0.1712
FINDPEAKS_PERCENTILE: 80
HOTSPOT_SCORE: 0.2666
HOTSPOT_PERCENTILE: 83
IROC_SCORE: 0.8751
IROC_PERCENTILE: 69
POISSON_SCORE: 0.4397
POISSON_PERCENTILE: 68

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

source_name: flow sorted CD34+ cells from cord blood expanded in short term culture; 42LP1AAXX090808-5-S

value: Histone H3K9me3

value: SDS lysis

value: 70 ul bed volume

value: Abcam


title: ChIP-Seq analysis of H3K9me3 in human CD19 cells; 42LP1AAXX090808-6-S

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: Solexa-12292
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.2179
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.2178
****************
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: GSM537654_BI.CD19_Primary_Cells.H3K9me3.CD19_2_20_09.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 42LP1AAXX090808-6-S.hg19.level.1
ANALYSIS TITLE: Mapping of CD19 Primary Cells Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9me3 ChIP-Seq on CD19 Primary Cells, Donor CD19_2/20/09 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.4746
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED: 59
FINDPEAKS_SCORE: 0.1447
FINDPEAKS_PERCENTILE: 66
HOTSPOT_SCORE: 0.2524
HOTSPOT_PERCENTILE: 81
IROC_SCORE: 0.8631
IROC_PERCENTILE: 63
POISSON_SCORE: 0.3809
POISSON_PERCENTILE: 51

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

ANALYSIS FILE NAME: GSM537654_BI.CD19_Primary_Cells.H3K9me3.CD19_2_20_09.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 42LP1AAXX090808-6-S.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of CD19 Primary Cells Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9me3 ChIP-Seq read mappings from CD19 Primary Cells, Donor CD19_2/20/09 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.5020
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: CD19 H3K9me3 20
BROWSER_TRACK_DESCRIPTION: BI CD19 Primary Cells Histone H3K9me3 Donor CD19_2/20/09 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED: 59
FINDPEAKS_SCORE: 0.1447
FINDPEAKS_PERCENTILE: 66
HOTSPOT_SCORE: 0.2524
HOTSPOT_PERCENTILE: 81
IROC_SCORE: 0.8631
IROC_PERCENTILE: 63
POISSON_SCORE: 0.3809
POISSON_PERCENTILE: 51

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

source_name: flow sorted CD19+ cells from cord blood; 42LP1AAXX090808-6-S

value: CD19 Primary Cells

value: not passaged


title: ChIP-Seq analysis of H3K36me3 in human hES-I3 cells; 42MNCAAXX100106-5-S

description:
sample_term_id: NTR_0000836
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Solexa-15381
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.2230
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.2229
****************
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: GSM537669_BI.ES-I3.H3K36me3.Solexa-15381.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 42MNCAAXX100106-5-S.hg19.level.1
ANALYSIS TITLE: Mapping of ES-I3 Cell Line Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K36me3 ChIP-Seq on the ES-I3 Cell Line, Library Solexa-15381 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.4627
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED: 54
FINDPEAKS_SCORE: 0.0966
FINDPEAKS_PERCENTILE: 20
HOTSPOT_SCORE: 0.2282
HOTSPOT_PERCENTILE: 34
IROC_SCORE: 0.8556
IROC_PERCENTILE: 17
POISSON_SCORE: 0.3361
POISSON_PERCENTILE: 9

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

ANALYSIS FILE NAME: GSM537669_BI.ES-I3.H3K36me3.Solexa-15381.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 42MNCAAXX100106-5-S.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of ES-I3 Cell Line Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K36me3 ChIP-Seq read mappings from the ES-I3 Cell Line, Library Solexa-15381 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.4901
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: ESI3 H3K36me3 81
BROWSER_TRACK_DESCRIPTION: BI ES-I3 Cell Line Histone H3K36me3 Library Solexa-15381 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED: 54
FINDPEAKS_SCORE: 0.0966
FINDPEAKS_PERCENTILE: 20
HOTSPOT_SCORE: 0.2282
HOTSPOT_PERCENTILE: 34
IROC_SCORE: 0.8556
IROC_PERCENTILE: 17
POISSON_SCORE: 0.3361
POISSON_PERCENTILE: 9

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

source_name: I3(eye three) stem cells; 42MNCAAXX100106-5-S

value: genomic DNA

value: Harvard University

value: Cell Line

value: embrionic stem cell

value: undifferentiated

value: KSR

value: Female

value: Histone H3K36me3


title: G727N

data_processing: frequencies of  known and novel miRNAs expressed in human cervical cancer tissues and matched normal tissues calculated (see Series record)

value: normal

value: normal cervix


title: G727T

value: squamous cell carcinoma

value: tumor


title: G529N


title: ChIP-Seq analysis of H3K4me1 in human Mobilized CD34 cells; 42LNLAAXX090804-5-S

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: Solexa-13499
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.2272
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.2271
****************
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: GSM537650_BI.Mobilized_CD34_Primary_Cells.H3K4me1.Mobilized_CD34_5_28_09.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 42LNLAAXX090804-5-S.hg19.level.1
ANALYSIS TITLE: Mapping of Mobilized CD34 Primary Cells Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me1 ChIP-Seq on Mobilized CD34 Primary Cells, Donor RO 01508 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.4606
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED: 43
FINDPEAKS_SCORE: 0.5244
FINDPEAKS_PERCENTILE: 77
HOTSPOT_SCORE: 0.5335
HOTSPOT_PERCENTILE: 86
IROC_SCORE: 0.9922
IROC_PERCENTILE: 67
POISSON_SCORE: 0.622
POISSON_PERCENTILE: 74

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

ANALYSIS FILE NAME: GSM537650_BI.Mobilized_CD34_Primary_Cells.H3K4me1.Mobilized_CD34_5_28_09.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 42LNLAAXX090804-5-S.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Mobilized CD34 Primary Cells Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me1 ChIP-Seq read mappings from Mobilized CD34 Primary Cells, Donor RO 01508 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.4880
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: MCD34 H3K4me1 28
BROWSER_TRACK_DESCRIPTION: BI Mobilized CD34 Primary Cells Histone H3K4me1 Donor RO 01508 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED: 43
FINDPEAKS_SCORE: 0.5244
FINDPEAKS_PERCENTILE: 77
HOTSPOT_SCORE: 0.5335
HOTSPOT_PERCENTILE: 86
IROC_SCORE: 0.9922
IROC_PERCENTILE: 67
POISSON_SCORE: 0.622
POISSON_PERCENTILE: 74

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

source_name: CD34 cells mobilized into peripheral blood; 42LNLAAXX090804-5-S

value: FHCRC

value: Primary Cell

value: Mobilized CD34 Primary Cells

value: Unknown

value: Histone H3K4me1

value: SDS lysis

value: Bioruptor

value: 10 million cells

value: Protein A-Sepharose 4B


title: ChIP-Seq analysis of H3K36me3 in human Mobilized CD34 cells; 42LNLAAXX090804-6-S

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: Solexa-13498
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.2185
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.2184
****************
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: GSM537651_BI.Mobilized_CD34_Primary_Cells.H3K36me3.Mobilized_CD34_5_28_09.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 42LNLAAXX090804-6-S.hg19.level.1
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 01508 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.4703
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED: 54
FINDPEAKS_SCORE: 0.6274
FINDPEAKS_PERCENTILE: 96
HOTSPOT_SCORE: 0.4509
HOTSPOT_PERCENTILE: 96
IROC_SCORE: 0.9916
IROC_PERCENTILE: 87
POISSON_SCORE: 0.7107
POISSON_PERCENTILE: 96

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

ANALYSIS FILE NAME: GSM537651_BI.Mobilized_CD34_Primary_Cells.H3K36me3.Mobilized_CD34_5_28_09.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 42LNLAAXX090804-6-S.hg19.level.2
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 01508 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.4977
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: MCD34 H3K36me3 28
BROWSER_TRACK_DESCRIPTION: BI Mobilized CD34 Primary Cells Histone H3K36me3 Donor RO 01508 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED: 54
FINDPEAKS_SCORE: 0.6274
FINDPEAKS_PERCENTILE: 96
HOTSPOT_SCORE: 0.4509
HOTSPOT_PERCENTILE: 96
IROC_SCORE: 0.9916
IROC_PERCENTILE: 87
POISSON_SCORE: 0.7107
POISSON_PERCENTILE: 96

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

source_name: CD34 cells mobilized into peripheral blood; 42LNLAAXX090804-6-S

value: genomic DNA

value: not passaged

value: 70 ul bed volume

value: Abcam


title: ChIP-Seq analysis of H3K4me1 in human WA-7 cells; 30H88AAXX090617-5-S

description:
sample_term_id: NTR_0000837
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Solexa-12611
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.2257
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.2256
****************
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: GSM537641_BI.ES-WA7.H3K4me1.Solexa-12611.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 30H88AAXX090617-5-S.hg19.level.1
ANALYSIS TITLE: Mapping of ES-WA7 Cell Line Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me1 ChIP-Seq on the ES-WA7 Cell Line, Library Solexa-12611 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.4609
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED: 43
FINDPEAKS_SCORE: 0.3741
FINDPEAKS_PERCENTILE: 53
HOTSPOT_SCORE: 0.4247
HOTSPOT_PERCENTILE: 67
IROC_SCORE: 0.9788
IROC_PERCENTILE: 40
POISSON_SCORE: 0.5603
POISSON_PERCENTILE: 49

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

ANALYSIS FILE NAME: GSM537641_BI.ES-WA7.H3K4me1.Solexa-12611.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: 30H88AAXX090617-5-S.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of ES-WA7 Cell Line Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me1 ChIP-Seq read mappings from the ES-WA7 Cell Line, Library Solexa-12611 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.4883
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: ESWA7 H3K4me1 11
BROWSER_TRACK_DESCRIPTION: BI ES-WA7 Cell Line Histone H3K4me1 Library Solexa-12611 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED: 43
FINDPEAKS_SCORE: 0.3741
FINDPEAKS_PERCENTILE: 53
HOTSPOT_SCORE: 0.4247
HOTSPOT_PERCENTILE: 67
IROC_SCORE: 0.9788
IROC_PERCENTILE: 40
POISSON_SCORE: 0.5603
POISSON_PERCENTILE: 49

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

source_name: WA7 stem cells; 30H88AAXX090617-5-S

value: Harvard University

value: Cell Line

value: embrionic stem cell

value: undifferentiated

value: KSR

value: Female