title: Reference Epigenome: ChIP-Seq Input from hESC H1 Cells; renlab.Input.hESC-01.01

description:
sample_term_id: EFO_0003042
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Input from hESC H1 Cells. Sequencing was done on the Illumina GAII platform.
Library name: LL-H1-I1
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.3712
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.1595
****************
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: GSM605333_UCSD.H1.Input.LL-H1-I1.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.Input.hESC-01.01.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 LL-H1-I1 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.4400
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: 0.0103
FINDPEAKS_PERCENTILE: 57
HOTSPOT_SCORE: 0.1133
HOTSPOT_PERCENTILE: 77
IROC_SCORE: 0.6106
IROC_PERCENTILE: 39
POISSON_SCORE: 0.1977
POISSON_PERCENTILE: 27

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

ANALYSIS FILE NAME: GSM605333_UCSD.H1.Input.LL-H1-I1.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.Input.hESC-01.01.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 LL-H1-I1 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.4534
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 I1
BROWSER_TRACK_DESCRIPTION: UCSD H1 Cell Line ChIP-Seq Input Library LL-H1-I1 EA Release 2

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED: 67
FINDPEAKS_SCORE: 0.0103
FINDPEAKS_PERCENTILE: 57
HOTSPOT_SCORE: 0.1133
HOTSPOT_PERCENTILE: 77
IROC_SCORE: 0.6106
IROC_PERCENTILE: 39
POISSON_SCORE: 0.1977
POISSON_PERCENTILE: 27

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

source_name: Human embryonic stem cells; H1 cell line; renlab.Input.hESC-01.01

tag: lineage

value: Between 25 and 45

value: ChIP-Seq Input

value: Branson Tip Sonicator

value: Input


title: CSHL_RnaSeq_GM12878_cell_TAP-Only_shortTotal

status: Public on Oct 08 2010

type: SRA

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

country: USA

institute: ENCODE DCC

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

extract_protocol:
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeCshlShortRnaSeq
hg19: For extraction protocol details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeCshlShortRnaSeq

value: immortalized cell line

tag: line

tag: datatype

value: RnaSeq

tag: datatype description

value: Sequencing analysis of RNA expression

tag: cell description

value: B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus

tag: rnaextract

value: shortTotal

tag: rnaextract description

value: Rna shorter than 200 nt that has not been seperated based on Poly Adenalyation

tag: biorep

tag: labexpid

tag: labversion

value: Produced by Hannon Lab,iIDR

tag: readtype

tag: readtype description

value: Single 36 nt reads

tag: replicate

tag: localization description

value: Whole cell

tag: protocol

value: TAP-Only

tag: protocol description

value: This kind of library was made from RNA < 200 nucleotides that were pre-treated with Tobacco Acid Pyrophosphatase to remove any 5' caps that would preclude cloning. Hence, both capped and 5' monophosphate RNAs will be cloned.


title: CSHL_RnaSeq_K562_nucleolus_TAP-Only_shortTotal

molecule: nuclear RNA

tag: localization

value: nucleolus

value: The part of the nucleus where ribosomal RNA is actively transcribed


title: CSHL_RnaSeq_K562_nucleoplasm_TAP-Only_shortTotal

value: nucleoplasm

value: That part of the nuclear content other than the chromosomes or the nucleolus


title: Reference Epigenome: ChIP-Seq Analysis of H3K9me3 in hESC Cells; renlab.H3K9me3.hESC-02.01

status: Public on Oct 07 2010

city: La Jolla

first: UCSD AND

last: SALK

address: Health Sciences Drive

institute: University of California, San Diego

description:
sample_term_id: EFO_0003042
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K9me3 in hESC Cells. Sequencing was done on the Illumina GAII platform.
Library name: LL218
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.3709
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.1595
****************
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: GSM605325_UCSD.H1.H3K9me3.LL218.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K9me3.hESC-02.01-renlab.H3K9me3.hESC-02.02-renlab.H3K9me3.CDI-01.01.hg19.level.1
ANALYSIS TITLE: Mapping of H1 Cell Line Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9me3 ChIP-Seq on the H1 Cell Line, Library LL218 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.4416
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: 0.4171
FINDPEAKS_PERCENTILE:
HOTSPOT_SCORE: 0.4557
HOTSPOT_PERCENTILE:
IROC_SCORE: 0.977
IROC_PERCENTILE:
POISSON_SCORE: 0.5872
POISSON_PERCENTILE:

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

ANALYSIS FILE NAME: GSM605325_UCSD.H1.H3K9me3.LL218.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K9me3.hESC-02.01-renlab.H3K9me3.hESC-02.02-renlab.H3K9me3.CDI-01.01.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Cell Line Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9me3 ChIP-Seq read mappings from the H1 Cell Line, Library LL218 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.4472
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 H3K9me3 18
BROWSER_TRACK_DESCRIPTION: UCSD H1 Cell Line Histone H3K9me3 Library LL218 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED: 59
FINDPEAKS_SCORE: 0.4171
FINDPEAKS_PERCENTILE:
HOTSPOT_SCORE: 0.4557
HOTSPOT_PERCENTILE:
IROC_SCORE: 0.977
IROC_PERCENTILE:
POISSON_SCORE: 0.5872
POISSON_PERCENTILE:

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

molecule: genomic DNA

source_name: Human embryonic stem cells received from the James Thompson laboratory.  Cells are from the H1 line.; renlab.H3K9me3.hESC-02.01

extract_protocol: Library construction protocol: See http://bioinformatics-renlab.ucsd.edu/RenLabLibraryProtocolV1.pdf

tag: molecule

value: genomic DNA

tag: disease

value: James Thompson Laboratory

value: Cell Line

tag: lineage

value: Embryonic Stem Cell

tag: passage

value: Between 25 and 45

tag: medium

value: mTeSER

tag: Sex

value: Male

tag: batch

value: Histone H3K9me3

value: Biorupter

value: 500 micrograms

value: magnetic anti-rabbit

value: 5 micrograms

value: Abcam


title: Reference Epigenome: ChIP-Seq Analysis of H3K9ac in hESC H9 Cells; renlab.H3K9ac.hESC.H9.01.01

description:
sample_term_id: NTR_0000838
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K9ac in hESC H9 Cells. Sequencing was done on the Illumina GAII platform.
Library name: SK199
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.3700
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.3693
****************
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: GSM605324_UCSD.H9.H3K9ac.SK199.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K9ac.hESC.H9.01.01.hg19.level.1
ANALYSIS TITLE: Mapping of H9 Cell Line Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9ac ChIP-Seq on the H9 Cell Line, Library SK199 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.4392
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: 0.2841
FINDPEAKS_PERCENTILE: 66
HOTSPOT_SCORE: 0.229
HOTSPOT_PERCENTILE: 46
IROC_SCORE: 0.8644
IROC_PERCENTILE: 11
POISSON_SCORE: 0.3741
POISSON_PERCENTILE: 54

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

ANALYSIS FILE NAME: GSM605324_UCSD.H9.H3K9ac.SK199.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K9ac.hESC.H9.01.01.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of H9 Cell Line Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9ac ChIP-Seq read mappings from the H9 Cell Line, Library SK199 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.4546
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: H9 H3K9ac 99
BROWSER_TRACK_DESCRIPTION: UCSD H9 Cell Line Histone H3K9ac Library SK199 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED: 35
FINDPEAKS_SCORE: 0.2841
FINDPEAKS_PERCENTILE: 66
HOTSPOT_SCORE: 0.229
HOTSPOT_PERCENTILE: 46
IROC_SCORE: 0.8644
IROC_PERCENTILE: 11
POISSON_SCORE: 0.3741
POISSON_PERCENTILE: 54

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

source_name: Human embryonic stem cells received from the James Thompson laboratory.  Cells are from the H9 line.; renlab.H3K9ac.hESC.H9.01.01

tag: line

value: Between 30 and 50

value: Female

value: Histone H3K9ac

value: Active Motif


title: Reference Epigenome: ChIP-Seq Analysis of H3K79me1 in hESC Cells; renlab.H3K79me1.hESC-02.01

description:
sample_term_id: EFO_0003042
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K79me1 in hESC Cells. Sequencing was done on the Illumina GAII platform.
Library name: SAK73
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.3527
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.3524
****************
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: GSM605319_UCSD.H1.H3K79me1.SAK73.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K79me1.hESC-02.01.hg19.level.1
ANALYSIS TITLE: Mapping of H1 Cell Line Histone H3K79me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K79me1 ChIP-Seq on the H1 Cell Line, Library SAK73 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.5194
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_H3K79me1_EXPERIMENTS_SCORED: 7
FINDPEAKS_SCORE: 0.0989
FINDPEAKS_PERCENTILE: 14
HOTSPOT_SCORE: 0.1751
HOTSPOT_PERCENTILE: 29
IROC_SCORE: 0.8497
IROC_PERCENTILE: 29
POISSON_SCORE: 0.3789
POISSON_PERCENTILE: 29

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

ANALYSIS FILE NAME: GSM605319_UCSD.H1.H3K79me1.SAK73.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K79me1.hESC-02.01.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Cell Line Histone H3K79me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K79me1 ChIP-Seq read mappings from the H1 Cell Line, Library SAK73 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.4552
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 H3K79me1 73
BROWSER_TRACK_DESCRIPTION: UCSD H1 Cell Line Histone H3K79me1 Library SAK73 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K79me1_EXPERIMENTS_SCORED: 7
FINDPEAKS_SCORE: 0.0989
FINDPEAKS_PERCENTILE: 14
HOTSPOT_SCORE: 0.1751
HOTSPOT_PERCENTILE: 29
IROC_SCORE: 0.8497
IROC_PERCENTILE: 29
POISSON_SCORE: 0.3789
POISSON_PERCENTILE: 29

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

source_name: Human embryonic stem cells received from the James Thompson laboratory.  Cells are from the H1 line.; renlab.H3K79me1.hESC-02.01

value: genomic DNA

value: Between 20 and 40

value: Histone H3K79me1


title: Reference Epigenome: ChIP-Seq Analysis of H3K79me2 in hESC Cells; renlab.H3K79me2.hESC-01.01

description:
sample_term_id: EFO_0003042
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K79me2 in hESC Cells. Sequencing was done on the Illumina GAII platform.
Library name: SAK80
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.3674
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.3425
****************
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: GSM605321_UCSD.H1.H3K79me2.SAK80.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K79me2.hESC-01.01.hg19.level.1
ANALYSIS TITLE: Mapping of H1 Cell Line Histone H3K79me2 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K79me2 ChIP-Seq on the H1 Cell Line, Library SAK80 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.5151
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_H3K79me2_EXPERIMENTS_SCORED: 4
FINDPEAKS_SCORE: 0.161
FINDPEAKS_PERCENTILE: 25
HOTSPOT_SCORE: 0.1512
HOTSPOT_PERCENTILE: 25
IROC_SCORE: 0.8619
IROC_PERCENTILE: 50
POISSON_SCORE: 0.3034
POISSON_PERCENTILE: 25

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

ANALYSIS FILE NAME: GSM605321_UCSD.H1.H3K79me2.SAK80.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K79me2.hESC-01.01.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Cell Line Histone H3K79me2 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K79me2 ChIP-Seq read mappings from the H1 Cell Line, Library SAK80 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.4475
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 H3K79me2 80
BROWSER_TRACK_DESCRIPTION: UCSD H1 Cell Line Histone H3K79me2 Library SAK80 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K79me2_EXPERIMENTS_SCORED: 4
FINDPEAKS_SCORE: 0.161
FINDPEAKS_PERCENTILE: 25
HOTSPOT_SCORE: 0.1512
HOTSPOT_PERCENTILE: 25
IROC_SCORE: 0.8619
IROC_PERCENTILE: 50
POISSON_SCORE: 0.3034
POISSON_PERCENTILE: 25

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

source_name: Human embryonic stem cells received from the James Thompson laboratory.  Cells are from the H1 line.; renlab.H3K79me2.hESC-01.01

value: James Thompson Laboratory

value: Cell Line

value: Embryonic Stem Cell

value: Histone H3K79me2


title: Reference Epigenome: ChIP-Seq Analysis of H3K79me1 in hESC Cells; renlab.H3K79me1.hESC-03.01

description:
sample_term_id: EFO_0003042
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K79me1 in hESC Cells. Sequencing was done on the Illumina GAII platform.
Library name: YL192
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.3529
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.3510
****************
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: GSM605320_UCSD.H1.H3K79me1.YL192.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K79me1.hESC-03.01.hg19.level.1
ANALYSIS TITLE: Mapping of H1 Cell Line Histone H3K79me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K79me1 ChIP-Seq on the H1 Cell Line, Library YL192 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.5141
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_H3K79me1_EXPERIMENTS_SCORED: 7
FINDPEAKS_SCORE: 0.1239
FINDPEAKS_PERCENTILE: 29
HOTSPOT_SCORE: 0.123
HOTSPOT_PERCENTILE: 14
IROC_SCORE: 0.7418
IROC_PERCENTILE: 14
POISSON_SCORE: 0.3381
POISSON_PERCENTILE: 14

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

ANALYSIS FILE NAME: GSM605320_UCSD.H1.H3K79me1.YL192.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K79me1.hESC-03.01.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Cell Line Histone H3K79me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K79me1 ChIP-Seq read mappings from the H1 Cell Line, Library YL192 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.4508
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 H3K79me1 92
BROWSER_TRACK_DESCRIPTION: UCSD H1 Cell Line Histone H3K79me1 Library YL192 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K79me1_EXPERIMENTS_SCORED: 7
FINDPEAKS_SCORE: 0.1239
FINDPEAKS_PERCENTILE: 29
HOTSPOT_SCORE: 0.123
HOTSPOT_PERCENTILE: 14
IROC_SCORE: 0.7418
IROC_PERCENTILE: 14
POISSON_SCORE: 0.3381
POISSON_PERCENTILE: 14

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

source_name: Human embryonic stem cells received from the James Thompson laboratory.  Cells are from the H1 line.; renlab.H3K79me1.hESC-03.01

value: mTeSER

value: Male


title: Reference Epigenome: ChIP-Seq Analysis of H3K9ac in hESC Cells; renlab.H3K9ac.hESC-01.01

description:
sample_term_id: EFO_0003042
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K9ac in hESC Cells. Sequencing was done on the Illumina GAII platform.
Library name: SAK68
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.3531
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.3425
****************
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: GSM605323_UCSD.H1.H3K9ac.SAK68.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K9ac.hESC-01.01.hg19.level.1
ANALYSIS TITLE: Mapping of H1 Cell Line Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9ac ChIP-Seq on the H1 Cell Line, Library SAK68 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.4419
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: 0.2141
FINDPEAKS_PERCENTILE: 60
HOTSPOT_SCORE: 0.241
HOTSPOT_PERCENTILE: 49
IROC_SCORE: 0.8961
IROC_PERCENTILE: 14
POISSON_SCORE: 0.3581
POISSON_PERCENTILE: 46

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

ANALYSIS FILE NAME: GSM605323_UCSD.H1.H3K9ac.SAK68.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K9ac.hESC-01.01.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Cell Line Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9ac ChIP-Seq read mappings from the H1 Cell Line, Library SAK68 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.4453
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 H3K9ac 68
BROWSER_TRACK_DESCRIPTION: UCSD H1 Cell Line Histone H3K9ac Library SAK68 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED: 35
FINDPEAKS_SCORE: 0.2141
FINDPEAKS_PERCENTILE: 60
HOTSPOT_SCORE: 0.241
HOTSPOT_PERCENTILE: 49
IROC_SCORE: 0.8961
IROC_PERCENTILE: 14
POISSON_SCORE: 0.3581
POISSON_PERCENTILE: 46

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

source_name: Human embryonic stem cells received from the James Thompson laboratory.  Cells are from the H1 line.; renlab.H3K9ac.hESC-01.01

value: Biorupter

value: 500 micrograms


title: Reference Epigenome: ChIP-Seq Analysis of H3K79me1 in hESC Cells; renlab.H3K79me1.hESC-01.01

description:
Design description: ChIP-Seq Analysis of H3K79me1 in hESC Cells. Sequencing was done on the Illumina GAII platform.
Library name: YL82
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.3525
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.3524
****************
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: GSM605318_UCSD.H1.H3K79me1.YL82.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K79me1.hESC-01.01.hg19.level.1
ANALYSIS TITLE: Mapping of H1 Cell Line Histone H3K79me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K79me1 ChIP-Seq on the H1 Cell Line, Library YL82 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.5135
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_H3K79me1_EXPERIMENTS_SCORED: 7
FINDPEAKS_SCORE: 0.1696
FINDPEAKS_PERCENTILE: 43
HOTSPOT_SCORE: 0.1822
HOTSPOT_PERCENTILE: 43
IROC_SCORE: 0.8691
IROC_PERCENTILE: 43
POISSON_SCORE: 0.4249
POISSON_PERCENTILE: 43

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

ANALYSIS FILE NAME: GSM605318_UCSD.H1.H3K79me1.YL82.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K79me1.hESC-01.01.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Cell Line Histone H3K79me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K79me1 ChIP-Seq read mappings from the H1 Cell Line, Library YL82 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.4509
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 H3K79me1 82
BROWSER_TRACK_DESCRIPTION: UCSD H1 Cell Line Histone H3K79me1 Library YL82 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K79me1_EXPERIMENTS_SCORED: 7
FINDPEAKS_SCORE: 0.1696
FINDPEAKS_PERCENTILE: 43
HOTSPOT_SCORE: 0.1822
HOTSPOT_PERCENTILE: 43
IROC_SCORE: 0.8691
IROC_PERCENTILE: 43
POISSON_SCORE: 0.4249
POISSON_PERCENTILE: 43

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

source_name: Human embryonic stem cells received from the James Thompson laboratory.  Cells are from the H1 line.; renlab.H3K79me1.hESC-01.01

value: magnetic anti-rabbit

value: 5 micrograms


title: Reference Epigenome: ChIP-Seq Analysis of H3K56ac in hESC Cells; renlab.H3K56ac.hESC-01.01

description:
sample_term_id: EFO_0003042
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K56ac in hESC Cells. Sequencing was done on the Illumina GAII platform.
Library name: SAK211
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.3547
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.3456
****************
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: GSM605317_UCSD.H1.H3K56ac.SAK211.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K56ac.hESC-01.01.hg19.level.1
ANALYSIS TITLE: Mapping of H1 Cell Line Histone H3K56ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K56ac ChIP-Seq on the H1 Cell Line, Library SAK211 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.5138
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_H3K56ac_EXPERIMENTS_SCORED: 3
FINDPEAKS_SCORE: 0.1591
FINDPEAKS_PERCENTILE: 33
HOTSPOT_SCORE: 0.231
HOTSPOT_PERCENTILE: 33
IROC_SCORE: 0.8486
IROC_PERCENTILE: 33
POISSON_SCORE: 0.275
POISSON_PERCENTILE: 33

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

ANALYSIS FILE NAME: GSM605317_UCSD.H1.H3K56ac.SAK211.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K56ac.hESC-01.01.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Cell Line Histone H3K56ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K56ac ChIP-Seq read mappings from the H1 Cell Line, Library SAK211 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.4470
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 H3K56ac 11
BROWSER_TRACK_DESCRIPTION: UCSD H1 Cell Line Histone H3K56ac Library SAK211 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K56ac_EXPERIMENTS_SCORED: 3
FINDPEAKS_SCORE: 0.1591
FINDPEAKS_PERCENTILE: 33
HOTSPOT_SCORE: 0.231
HOTSPOT_PERCENTILE: 33
IROC_SCORE: 0.8486
IROC_PERCENTILE: 33
POISSON_SCORE: 0.275
POISSON_PERCENTILE: 33

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

source_name: Human embryonic stem cells received from the James Thompson laboratory.  Cells are from the H1 line.; renlab.H3K56ac.hESC-01.01

value: Histone H3K56ac

value: Upstate

value: Upstate 07-677


title: Reference Epigenome: ChIP-Seq Analysis of H3K4me3 in hESC H9 Cells; renlab.H3K4me3.hESC.H9.01.01

description:
sample_term_id: NTR_0000838
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K4me3 in hESC H9 Cells. Sequencing was done on the Illumina GAII platform.
Library name: SK101
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.3698
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.3693
****************
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: GSM605316_UCSD.H9.H3K4me3.SK101.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4me3.hESC.H9.01.01.hg19.level.1
ANALYSIS TITLE: Mapping of H9 Cell Line Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me3 ChIP-Seq on the H9 Cell Line, Library SK101 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.4425
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: 0.7016
FINDPEAKS_PERCENTILE: 89
HOTSPOT_SCORE: 0.6546
HOTSPOT_PERCENTILE: 89
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.6823
POISSON_PERCENTILE: 84

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

ANALYSIS FILE NAME: GSM605316_UCSD.H9.H3K4me3.SK101.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4me3.hESC.H9.01.01.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of H9 Cell Line Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me3 ChIP-Seq read mappings from the H9 Cell Line, Library SK101 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.4500
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: H9 H3K4me3 01
BROWSER_TRACK_DESCRIPTION: UCSD H9 Cell Line Histone H3K4me3 Library SK101 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED: 62
FINDPEAKS_SCORE: 0.7016
FINDPEAKS_PERCENTILE: 89
HOTSPOT_SCORE: 0.6546
HOTSPOT_PERCENTILE: 89
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.6823
POISSON_PERCENTILE: 84

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

source_name: Human embryonic stem cells received from the James Thompson laboratory.  Cells are from the H9 line.; renlab.H3K4me3.hESC.H9.01.01

value: Between 30 and 50

value: Female

value: Histone H3K4me3

value: Millipore


title: Reference Epigenome: ChIP-Seq Analysis of H3K4me2 in hESC H9 Cells; renlab.H3K4me2.hESC.H9.01.01

description:
sample_term_id: NTR_0000838
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K4me2 in hESC H9 Cells. Sequencing was done on the Illumina GAII platform.
Library name: SK198
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.3694
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.3693
****************
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: GSM605314_UCSD.H9.H3K4me2.SK198.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4me2.hESC.H9.01.01.hg19.level.1
ANALYSIS TITLE: Mapping of H9 Cell Line Histone H3K4me2 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me2 ChIP-Seq on the H9 Cell Line, Library SK198 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.5136
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_H3K4me2_EXPERIMENTS_SCORED: 8
FINDPEAKS_SCORE: 0.4087
FINDPEAKS_PERCENTILE: 13
HOTSPOT_SCORE: 0.3454
HOTSPOT_PERCENTILE: 13
IROC_SCORE: 0.998
IROC_PERCENTILE: 13
POISSON_SCORE: 0.4462
POISSON_PERCENTILE: 13

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

ANALYSIS FILE NAME: GSM605314_UCSD.H9.H3K4me2.SK198.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4me2.hESC.H9.01.01.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of H9 Cell Line Histone H3K4me2 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me2 ChIP-Seq read mappings from the H9 Cell Line, Library SK198 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.4526
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: H9 H3K4me2 98
BROWSER_TRACK_DESCRIPTION: UCSD H9 Cell Line Histone H3K4me2 Library SK198 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K4me2_EXPERIMENTS_SCORED: 8
FINDPEAKS_SCORE: 0.4087
FINDPEAKS_PERCENTILE: 13
HOTSPOT_SCORE: 0.3454
HOTSPOT_PERCENTILE: 13
IROC_SCORE: 0.998
IROC_PERCENTILE: 13
POISSON_SCORE: 0.4462
POISSON_PERCENTILE: 13

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

source_name: Human embryonic stem cells received from the James Thompson laboratory.  Cells are from the H9 line.; renlab.H3K4me2.hESC.H9.01.01

value: genomic DNA

value: James Thompson Laboratory

value: Histone H3K4me2

value: Abcam


title: Reference Epigenome: ChIP-Seq Analysis of H3K4ac in hESC Cells; renlab.H3K4ac.hESC-01.01

description:
sample_term_id: EFO_0003042
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K4ac in hESC Cells. Sequencing was done on the Illumina GAII platform.
Library name: SAK207
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.3549
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.3459
****************
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: GSM605311_UCSD.H1.H3K4ac.SAK207.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4ac.hESC-01.01.hg19.level.1
ANALYSIS TITLE: Mapping of H1 Cell Line Histone H3K4ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4ac ChIP-Seq on the H1 Cell Line, Library SAK207 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.5139
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_H3K4ac_EXPERIMENTS_SCORED: 3
FINDPEAKS_SCORE: 0.1789
FINDPEAKS_PERCENTILE: 33
HOTSPOT_SCORE: 0.1755
HOTSPOT_PERCENTILE: 33
IROC_SCORE: 0.8148
IROC_PERCENTILE: 33
POISSON_SCORE: 0.4009
POISSON_PERCENTILE: 33

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

ANALYSIS FILE NAME: GSM605311_UCSD.H1.H3K4ac.SAK207.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4ac.hESC-01.01.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Cell Line Histone H3K4ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4ac ChIP-Seq read mappings from the H1 Cell Line, Library SAK207 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.4448
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 H3K4ac 07
BROWSER_TRACK_DESCRIPTION: UCSD H1 Cell Line Histone H3K4ac Library SAK207 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K4ac_EXPERIMENTS_SCORED: 3
FINDPEAKS_SCORE: 0.1789
FINDPEAKS_PERCENTILE: 33
HOTSPOT_SCORE: 0.1755
HOTSPOT_PERCENTILE: 33
IROC_SCORE: 0.8148
IROC_PERCENTILE: 33
POISSON_SCORE: 0.4009
POISSON_PERCENTILE: 33

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

source_name: Human embryonic stem cells received from the James Thompson laboratory.  Cells are from the H1 line.; renlab.H3K4ac.hESC-01.01

value: Cell Line

value: Embryonic Stem Cell

value: mTeSER

value: Histone H3K4ac

value: Upstate 07-539


title: Reference Epigenome: ChIP-Seq Analysis of H3K36me3 in hESC Cells; renlab.H3K36me3.hESC-03.01

description:
sample_term_id: EFO_0003042
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K36me3 in hESC Cells. Sequencing was done on the Illumina GAII platform.
Library name: SAK70
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.3553
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.3425
****************
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: GSM605309_UCSD.H1.H3K36me3.SAK70.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K36me3.hESC-03.01.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 SAK70 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.4417
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: 0.2963
FINDPEAKS_PERCENTILE: 67
HOTSPOT_SCORE: 0.2825
HOTSPOT_PERCENTILE: 58
IROC_SCORE: 0.9624
IROC_PERCENTILE: 48
POISSON_SCORE: 0.4339
POISSON_PERCENTILE: 28

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

ANALYSIS FILE NAME: GSM605309_UCSD.H1.H3K36me3.SAK70.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K36me3.hESC-03.01.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 SAK70 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.4506
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 70
BROWSER_TRACK_DESCRIPTION: UCSD H1 Cell Line Histone H3K36me3 Library SAK70 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED: 54
FINDPEAKS_SCORE: 0.2963
FINDPEAKS_PERCENTILE: 67
HOTSPOT_SCORE: 0.2825
HOTSPOT_PERCENTILE: 58
IROC_SCORE: 0.9624
IROC_PERCENTILE: 48
POISSON_SCORE: 0.4339
POISSON_PERCENTILE: 28

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

source_name: Human embryonic stem cells received from the James Thompson laboratory.  Cells are from the H1 line.; renlab.H3K36me3.hESC-03.01

value: Between 20 and 40

value: Male

value: Histone H3K36me3

value: Biorupter

value: 500 micrograms

value: magnetic anti-rabbit

value: 5 micrograms


title: Reference Epigenome: ChIP-Seq Analysis of H3K36me3 in hESC H9 Cells; renlab.H3K36me3.hESC.H9.01.01

description:
sample_term_id: NTR_0000838
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K36me3 in hESC H9 Cells. Sequencing was done on the Illumina GAII platform.
Library name: SK102
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.3702
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.3693
****************
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: GSM605310_UCSD.H9.H3K36me3.SK102.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K36me3.hESC.H9.01.01.hg19.level.1
ANALYSIS TITLE: Mapping of H9 Cell Line Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K36me3 ChIP-Seq on the H9 Cell Line, Library SK102 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.4435
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: 0.3733
FINDPEAKS_PERCENTILE: 76
HOTSPOT_SCORE: 0.3335
HOTSPOT_PERCENTILE: 77
IROC_SCORE: 0.9915
IROC_PERCENTILE: 85
POISSON_SCORE: 0.4816
POISSON_PERCENTILE: 43

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

ANALYSIS FILE NAME: GSM605310_UCSD.H9.H3K36me3.SK102.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K36me3.hESC.H9.01.01.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of H9 Cell Line Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K36me3 ChIP-Seq read mappings from the H9 Cell Line, Library SK102 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.4521
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: H9 H3K36me3 02
BROWSER_TRACK_DESCRIPTION: UCSD H9 Cell Line Histone H3K36me3 Library SK102 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED: 54
FINDPEAKS_SCORE: 0.3733
FINDPEAKS_PERCENTILE: 76
HOTSPOT_SCORE: 0.3335
HOTSPOT_PERCENTILE: 77
IROC_SCORE: 0.9915
IROC_PERCENTILE: 85
POISSON_SCORE: 0.4816
POISSON_PERCENTILE: 43

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

source_name: Human embryonic stem cells received from the James Thompson laboratory.  Cells are from the H9 line.; renlab.H3K36me3.hESC.H9.01.01

value: Between 30 and 50

value: Female


title: Reference Epigenome: ChIP-Seq Analysis of H3K27ac in hESC H9 Cells; renlab.H3K27ac.hESC.H9.01.01

description:
sample_term_id: NTR_0000838
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K27ac in hESC H9 Cells. Sequencing was done on the Illumina GAII platform.
Library name: YL237
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.3704
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.3693
****************
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: GSM605307_UCSD.H9.H3K27ac.YL237.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27ac.hESC.H9.01.01.hg19.level.1
ANALYSIS TITLE: Mapping of H9 Cell Line Histone H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27ac ChIP-Seq on the H9 Cell Line, Library YL237 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.5185
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_H3K27ac_EXPERIMENTS_SCORED: 6
FINDPEAKS_SCORE: 0.2138
FINDPEAKS_PERCENTILE: 33
HOTSPOT_SCORE: 0.1947
HOTSPOT_PERCENTILE: 33
IROC_SCORE: 0.8392
IROC_PERCENTILE: 33
POISSON_SCORE: 0.3687
POISSON_PERCENTILE: 33

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

ANALYSIS FILE NAME: GSM605307_UCSD.H9.H3K27ac.YL237.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27ac.hESC.H9.01.01.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of H9 Cell Line Histone H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27ac ChIP-Seq read mappings from the H9 Cell Line, Library YL237 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.4539
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: H9 H3K27ac 37
BROWSER_TRACK_DESCRIPTION: UCSD H9 Cell Line Histone H3K27ac Library YL237 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K27ac_EXPERIMENTS_SCORED: 6
FINDPEAKS_SCORE: 0.2138
FINDPEAKS_PERCENTILE: 33
HOTSPOT_SCORE: 0.1947
HOTSPOT_PERCENTILE: 33
IROC_SCORE: 0.8392
IROC_PERCENTILE: 33
POISSON_SCORE: 0.3687
POISSON_PERCENTILE: 33

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

source_name: Human embryonic stem cells received from the James Thompson laboratory.  Cells are from the H9 line.; renlab.H3K27ac.hESC.H9.01.01

value: genomic DNA

value: James Thompson Laboratory

value: Histone H3K27ac

value: 300 micrograms

value: Active Motif


title: Reference Epigenome: ChIP-Seq Input from hESC H1 Cells; renlab.Input.hESC-02.01

description:
sample_term_id: EFO_0003042
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Input from hESC H1 Cells. Sequencing was done on the Illumina GAII platform.
Library name: LL-H1-I2
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.3714
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.890
****************
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: GSM605334_UCSD.H1.Input.LL-H1-I2.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.Input.hESC-02.01.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 LL-H1-I2 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.4404
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: 0.0557
FINDPEAKS_PERCENTILE: 84
HOTSPOT_SCORE: 0.1532
HOTSPOT_PERCENTILE: 82
IROC_SCORE: 0.753
IROC_PERCENTILE: 45
POISSON_SCORE: 0.2046
POISSON_PERCENTILE: 33

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

ANALYSIS FILE NAME: GSM605334_UCSD.H1.Input.LL-H1-I2.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.Input.hESC-02.01.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 LL-H1-I2 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.4541
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 I2
BROWSER_TRACK_DESCRIPTION: UCSD H1 Cell Line ChIP-Seq Input Library LL-H1-I2 EA Release 2

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED: 67
FINDPEAKS_SCORE: 0.0557
FINDPEAKS_PERCENTILE: 84
HOTSPOT_SCORE: 0.1532
HOTSPOT_PERCENTILE: 82
IROC_SCORE: 0.753
IROC_PERCENTILE: 45
POISSON_SCORE: 0.2046
POISSON_PERCENTILE: 33

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

source_name: Human embryonic stem cells; H1 cell line; renlab.Input.hESC-02.01

value: Cellular Dynamics International

value: Cell Line

value: Embryonic Stem Cell

value: mTeSER

value: ChIP-Seq Input

value: Branson Tip Sonicator

value: Input


title: Reference Epigenome: ChIP-Seq Analysis of H3K18ac in hESC Cells; renlab.H3K18ac.hESC-01.01

description:
sample_term_id: EFO_0003042
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K18ac in hESC Cells. Sequencing was done on the Illumina GAII platform.
Library name: LL321
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.3551
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.1595
****************
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: GSM605304_UCSD.H1.H3K18ac.LL321.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K18ac.hESC-01.01.hg19.level.1
ANALYSIS TITLE: Mapping of H1 Cell Line Histone H3K18ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K18ac ChIP-Seq on the H1 Cell Line, Library LL321 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.5201
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_H3K18ac_EXPERIMENTS_SCORED: 4
FINDPEAKS_SCORE: 0.2534
FINDPEAKS_PERCENTILE: 50
HOTSPOT_SCORE: 0.3196
HOTSPOT_PERCENTILE: 50
IROC_SCORE: 0.9651
IROC_PERCENTILE: 50
POISSON_SCORE: 0.5043
POISSON_PERCENTILE: 50

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

ANALYSIS FILE NAME: GSM605304_UCSD.H1.H3K18ac.LL321.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K18ac.hESC-01.01.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Cell Line Histone H3K18ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K18ac ChIP-Seq read mappings from the H1 Cell Line, Library LL321 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.4493
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 H3K18ac 21
BROWSER_TRACK_DESCRIPTION: UCSD H1 Cell Line Histone H3K18ac Library LL321 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K18ac_EXPERIMENTS_SCORED: 4
FINDPEAKS_SCORE: 0.2534
FINDPEAKS_PERCENTILE: 50
HOTSPOT_SCORE: 0.3196
HOTSPOT_PERCENTILE: 50
IROC_SCORE: 0.9651
IROC_PERCENTILE: 50
POISSON_SCORE: 0.5043
POISSON_PERCENTILE: 50

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

source_name: Human embryonic stem cells received from the James Thompson laboratory.  Cells are from the H1 line.; renlab.H3K18ac.hESC-01.01

value: Between 25 and 45

value: Male

value: Histone H3K18ac

value: Biorupter

value: 500 micrograms

value: Abcam


title: Reference Epigenome: ChIP-Seq Analysis of H3K23me2 in hESC Cells; renlab.H3K23me2.hESC-01.01

description:
sample_term_id: EFO_0003042
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K23me2 in hESC Cells. Sequencing was done on the Illumina GAII platform.
Library name: YL198
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.3520
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.3519
****************
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: GSM605305_UCSD.H1.H3K23me2.YL198.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K23me2.hESC-01.01.hg19.level.1
ANALYSIS TITLE: Mapping of H1 Cell Line Histone H3K23me2 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K23me2 ChIP-Seq on the H1 Cell Line, Library YL198 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.5146
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_H3K23me2_EXPERIMENTS_SCORED: 2
FINDPEAKS_SCORE: 0.1029
FINDPEAKS_PERCENTILE: 50
HOTSPOT_SCORE: 0.091
HOTSPOT_PERCENTILE: 50
IROC_SCORE: 0.6003
IROC_PERCENTILE: 50
POISSON_SCORE: 0.2705
POISSON_PERCENTILE: 50

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

ANALYSIS FILE NAME: GSM605305_UCSD.H1.H3K23me2.YL198.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K23me2.hESC-01.01.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Cell Line Histone H3K23me2 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K23me2 ChIP-Seq read mappings from the H1 Cell Line, Library YL198 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.4556
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 H3K23me2 98
BROWSER_TRACK_DESCRIPTION: UCSD H1 Cell Line Histone H3K23me2 Library YL198 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K23me2_EXPERIMENTS_SCORED: 2
FINDPEAKS_SCORE: 0.1029
FINDPEAKS_PERCENTILE: 50
HOTSPOT_SCORE: 0.091
HOTSPOT_PERCENTILE: 50
IROC_SCORE: 0.6003
IROC_PERCENTILE: 50
POISSON_SCORE: 0.2705
POISSON_PERCENTILE: 50

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

source_name: Human embryonic stem cells received from the James Thompson laboratory.  Cells are from the H1 line.; renlab.H3K23me2.hESC-01.01

value: genomic DNA

value: James Thompson Laboratory

value: Histone H3K23me2

value: magnetic anti-rabbit

value: 5 micrograms


title: Reference Epigenome: ChIP-Seq Analysis of H3K23me2 in hESC Cells; renlab.H3K23me2.hESC-02.01

description:
sample_term_id: EFO_0003042
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K23me2 in hESC Cells. Sequencing was done on the Illumina GAII platform.
Library name: SAK210
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.3522
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.3459
****************
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: GSM605306_UCSD.H1.H3K23me2.SAK210.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K23me2.hESC-02.01.hg19.level.1
ANALYSIS TITLE: Mapping of H1 Cell Line Histone H3K23me2 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K23me2 ChIP-Seq on the H1 Cell Line, Library SAK210 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.5193
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_H3K23me2_EXPERIMENTS_SCORED: 2
FINDPEAKS_SCORE: 0.2725
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.3013
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9431
IROC_PERCENTILE: 100
POISSON_SCORE: 0.3179
POISSON_PERCENTILE: 100

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

ANALYSIS FILE NAME: GSM605306_UCSD.H1.H3K23me2.SAK210.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K23me2.hESC-02.01.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Cell Line Histone H3K23me2 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K23me2 ChIP-Seq read mappings from the H1 Cell Line, Library SAK210 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.4440
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 H3K23me2 10
BROWSER_TRACK_DESCRIPTION: UCSD H1 Cell Line Histone H3K23me2 Library SAK210 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K23me2_EXPERIMENTS_SCORED: 2
FINDPEAKS_SCORE: 0.2725
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.3013
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9431
IROC_PERCENTILE: 100
POISSON_SCORE: 0.3179
POISSON_PERCENTILE: 100

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

source_name: Human embryonic stem cells received from the James Thompson laboratory.  Cells are from the H1 line.; renlab.H3K23me2.hESC-02.01

value: Cell Line


title: Reference Epigenome: ChIP-Seq Analysis of H2BK5ac in hESC Cells; renlab.H2BK5ac.hESC-01.01

description:
sample_term_id: EFO_0003042
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H2BK5ac in hESC Cells. Sequencing was done on the Illumina GAII platform.
Library name: YL98
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.3498
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.3425
****************
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: GSM605302_UCSD.H1.H2BK5ac.YL98.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H2BK5ac.hESC-01.01.hg19.level.1
ANALYSIS TITLE: Mapping of H1 Cell Line Histone H2BK5ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H2BK5ac ChIP-Seq on the H1 Cell Line, Library YL98 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.5200
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_H2BK5ac_EXPERIMENTS_SCORED: 2
FINDPEAKS_SCORE: 0.1719
FINDPEAKS_PERCENTILE: 50
HOTSPOT_SCORE: 0.2022
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.8514
IROC_PERCENTILE: 50
POISSON_SCORE: 0.4422
POISSON_PERCENTILE: 50

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

ANALYSIS FILE NAME: GSM605302_UCSD.H1.H2BK5ac.YL98.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H2BK5ac.hESC-01.01.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Cell Line Histone H2BK5ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H2BK5ac ChIP-Seq read mappings from the H1 Cell Line, Library YL98 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.4458
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 H2BK5ac 98
BROWSER_TRACK_DESCRIPTION: UCSD H1 Cell Line Histone H2BK5ac Library YL98 EA Release 2

QUALITY SCORES:
NUMBER_OF_H2BK5ac_EXPERIMENTS_SCORED: 2
FINDPEAKS_SCORE: 0.1719
FINDPEAKS_PERCENTILE: 50
HOTSPOT_SCORE: 0.2022
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.8514
IROC_PERCENTILE: 50
POISSON_SCORE: 0.4422
POISSON_PERCENTILE: 50

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

source_name: Human embryonic stem cells received from the James Thompson laboratory.  Cells are from the H1 line.; renlab.H2BK5ac.hESC-01.01

value: Embryonic Stem Cell

value: Between 20 and 40

value: Histone H2BK5ac


title: Reference Epigenome: ChIP-Seq Analysis of H2BK20ac in hESC Cells; renlab.H2BK20ac.hESC-01.01

description:
sample_term_id: EFO_0003042
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H2BK20ac in hESC Cells. Sequencing was done on the Illumina GAII platform.
Library name: YL207
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.3515
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.3510
****************
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: GSM605300_UCSD.H1.H2BK20ac.YL207.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H2BK20ac.hESC-01.01.hg19.level.1
ANALYSIS TITLE: Mapping of H1 Cell Line Histone H2BK20ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H2BK20ac ChIP-Seq on the H1 Cell Line, Library YL207 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.5162
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_H2BK20ac_EXPERIMENTS_SCORED: 4
FINDPEAKS_SCORE: 0.2035
FINDPEAKS_PERCENTILE: 25
HOTSPOT_SCORE: 0.121
HOTSPOT_PERCENTILE: 25
IROC_SCORE: 0.7237
IROC_PERCENTILE: 25
POISSON_SCORE: 0.391
POISSON_PERCENTILE: 25

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

ANALYSIS FILE NAME: GSM605300_UCSD.H1.H2BK20ac.YL207.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H2BK20ac.hESC-01.01.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Cell Line Histone H2BK20ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H2BK20ac ChIP-Seq read mappings from the H1 Cell Line, Library YL207 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.4449
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 H2BK20ac 07
BROWSER_TRACK_DESCRIPTION: UCSD H1 Cell Line Histone H2BK20ac Library YL207 EA Release 2

QUALITY SCORES:
NUMBER_OF_H2BK20ac_EXPERIMENTS_SCORED: 4
FINDPEAKS_SCORE: 0.2035
FINDPEAKS_PERCENTILE: 25
HOTSPOT_SCORE: 0.121
HOTSPOT_PERCENTILE: 25
IROC_SCORE: 0.7237
IROC_PERCENTILE: 25
POISSON_SCORE: 0.391
POISSON_PERCENTILE: 25

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

source_name: Human embryonic stem cells received from the James Thompson laboratory.  Cells are from the H1 line.; renlab.H2BK20ac.hESC-01.01

value: mTeSER

value: Histone H2BK20ac

value: Upstate

value: upstate 07-347


title: Reference Epigenome: ChIP-Seq Analysis of H2BK15ac in hESC Cells; renlab.H2BK15ac.hESC-01.01

description:
sample_term_id: EFO_0003042
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H2BK15ac in hESC Cells. Sequencing was done on the Illumina GAII platform.
Library name: YL206
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.3511
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.3510
****************
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: GSM605298_UCSD.H1.H2BK15ac.YL206.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H2BK15ac.hESC-01.01.hg19.level.1
ANALYSIS TITLE: Mapping of H1 Cell Line Histone H2BK15ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H2BK15ac ChIP-Seq on the H1 Cell Line, Library YL206 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.5178
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_H2BK15ac_EXPERIMENTS_SCORED: 5
FINDPEAKS_SCORE: 0.2214
FINDPEAKS_PERCENTILE: 20
HOTSPOT_SCORE: 0.1067
HOTSPOT_PERCENTILE: 20
IROC_SCORE: 0.6843
IROC_PERCENTILE: 20
POISSON_SCORE: 0.394
POISSON_PERCENTILE: 20

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

ANALYSIS FILE NAME: GSM605298_UCSD.H1.H2BK15ac.YL206.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H2BK15ac.hESC-01.01.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Cell Line Histone H2BK15ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H2BK15ac ChIP-Seq read mappings from the H1 Cell Line, Library YL206 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.4528
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 H2BK15ac 06
BROWSER_TRACK_DESCRIPTION: UCSD H1 Cell Line Histone H2BK15ac Library YL206 EA Release 2

QUALITY SCORES:
NUMBER_OF_H2BK15ac_EXPERIMENTS_SCORED: 5
FINDPEAKS_SCORE: 0.2214
FINDPEAKS_PERCENTILE: 20
HOTSPOT_SCORE: 0.1067
HOTSPOT_PERCENTILE: 20
IROC_SCORE: 0.6843
IROC_PERCENTILE: 20
POISSON_SCORE: 0.394
POISSON_PERCENTILE: 20

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

source_name: Human embryonic stem cells received from the James Thompson laboratory.  Cells are from the H1 line.; renlab.H2BK15ac.hESC-01.01

value: Male

value: Histone H2BK15ac


title: Reference Epigenome: ChIP-Seq Analysis of H2BK12ac in hESC Cells; renlab.H2BK12ac.hESC-01.01

description:
sample_term_id: EFO_0003042
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H2BK12ac in hESC Cells. Sequencing was done on the Illumina GAII platform.
Library name: YL93
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.3506
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.3425
****************
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: GSM605296_UCSD.H1.H2BK12ac.YL93.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H2BK12ac.hESC-01.01.hg19.level.1
ANALYSIS TITLE: Mapping of H1 Cell Line Histone H2BK12ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H2BK12ac ChIP-Seq on the H1 Cell Line, Library YL93 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.5160
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_H2BK12ac_EXPERIMENTS_SCORED: 4
FINDPEAKS_SCORE: 0.1519
FINDPEAKS_PERCENTILE: 25
HOTSPOT_SCORE: 0.1846
HOTSPOT_PERCENTILE: 25
IROC_SCORE: 0.8544
IROC_PERCENTILE: 25
POISSON_SCORE: 0.3609
POISSON_PERCENTILE: 25

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

ANALYSIS FILE NAME: GSM605296_UCSD.H1.H2BK12ac.YL93.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H2BK12ac.hESC-01.01.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Cell Line Histone H2BK12ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H2BK12ac ChIP-Seq read mappings from the H1 Cell Line, Library YL93 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.4455
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 H2BK12ac 93
BROWSER_TRACK_DESCRIPTION: UCSD H1 Cell Line Histone H2BK12ac Library YL93 EA Release 2

QUALITY SCORES:
NUMBER_OF_H2BK12ac_EXPERIMENTS_SCORED: 4
FINDPEAKS_SCORE: 0.1519
FINDPEAKS_PERCENTILE: 25
HOTSPOT_SCORE: 0.1846
HOTSPOT_PERCENTILE: 25
IROC_SCORE: 0.8544
IROC_PERCENTILE: 25
POISSON_SCORE: 0.3609
POISSON_PERCENTILE: 25

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

source_name: Human embryonic stem cells received from the James Thompson laboratory.  Cells are from the H1 line.; renlab.H2BK12ac.hESC-01.01

value: Histone H2BK12ac

value: Biorupter

value: 500 micrograms


title: Reference Epigenome: ChIP-Seq Analysis of H2BK120ac in hESC Cells; renlab.H2BK120ac.hESC-01.01

description:
sample_term_id: EFO_0003042
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H2BK120ac in hESC Cells. Sequencing was done on the Illumina GAII platform.
Library name: SAK206
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.3557
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.3459
****************
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: GSM605295_UCSD.H1.H2BK120ac.SAK206.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H2BK120ac.hESC-01.01.hg19.level.1
ANALYSIS TITLE: Mapping of H1 Cell Line Histone H2BK120ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H2BK120ac ChIP-Seq on the H1 Cell Line, Library SAK206 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.5155
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_H2BK120ac_EXPERIMENTS_SCORED: 3
FINDPEAKS_SCORE: 0.1851
FINDPEAKS_PERCENTILE: 33
HOTSPOT_SCORE: 0.148
HOTSPOT_PERCENTILE: 33
IROC_SCORE: 0.8085
IROC_PERCENTILE: 33
POISSON_SCORE: 0.3804
POISSON_PERCENTILE: 33

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

ANALYSIS FILE NAME: GSM605295_UCSD.H1.H2BK120ac.SAK206.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H2BK120ac.hESC-01.01.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Cell Line Histone H2BK120ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H2BK120ac ChIP-Seq read mappings from the H1 Cell Line, Library SAK206 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.4543
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 H2BK120ac 06
BROWSER_TRACK_DESCRIPTION: UCSD H1 Cell Line Histone H2BK120ac Library SAK206 EA Release 2

QUALITY SCORES:
NUMBER_OF_H2BK120ac_EXPERIMENTS_SCORED: 3
FINDPEAKS_SCORE: 0.1851
FINDPEAKS_PERCENTILE: 33
HOTSPOT_SCORE: 0.148
HOTSPOT_PERCENTILE: 33
IROC_SCORE: 0.8085
IROC_PERCENTILE: 33
POISSON_SCORE: 0.3804
POISSON_PERCENTILE: 33

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

source_name: Human embryonic stem cells received from the James Thompson laboratory.  Cells are from the H1 line.; renlab.H2BK120ac.hESC-01.01

value: genomic DNA

value: James Thompson Laboratory

value: Histone H2BK120ac

value: Active Motif