title: Reference Epigenome: ChIP-Seq Analysis of H3K79me1 in IMR90 Cells; renlab.H3K79me1.IMR90-03.01

description:
sample_term_id: EFO_0001196
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K79me1 in IMR90 cells. Sequencing was done on the Illumina GAII platform.
Library name: YL103
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.2079
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.2009
****************
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: GSM521907_UCSD.IMR90.H3K79me1.YL103.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K79me1.IMR90-03.01.hg19.level.1
ANALYSIS TITLE: Mapping of IMR90 Cell Line Histone H3K79me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K79me1 ChIP-Seq on the IMR90 Cell Line, Library YL103 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.5150
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: 0.6203
FINDPEAKS_PERCENTILE: 71
HOTSPOT_SCORE: 0.3893
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9855
IROC_PERCENTILE: 100
POISSON_SCORE: 0.7034
POISSON_PERCENTILE: 100

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

ANALYSIS FILE NAME: GSM521907_UCSD.IMR90.H3K79me1.YL103.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K79me1.IMR90-03.01.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of IMR90 Cell Line Histone H3K79me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K79me1 ChIP-Seq read mappings from the IMR90 Cell Line, Library YL103 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.4514
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: IMR90 H3K79me1 03
BROWSER_TRACK_DESCRIPTION: UCSD IMR90 Cell Line Histone H3K79me1 Library YL103 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K79me1_EXPERIMENTS_SCORED: 7
FINDPEAKS_SCORE: 0.6203
FINDPEAKS_PERCENTILE: 71
HOTSPOT_SCORE: 0.3893
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9855
IROC_PERCENTILE: 100
POISSON_SCORE: 0.7034
POISSON_PERCENTILE: 100

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

source_name: IMR90 Cell Line, biological replicate 2; renlab.H3K79me1.IMR90-03.01

value: genomic DNA

value: ATCC


title: Reference Epigenome: ChIP-Seq Analysis of H3K56ac in IMR90 Cells; renlab.H3K56ac.IMR90-02.01

status: Public on Mar 22 2010

type: SRA

city: La Jolla

first: UCSD AND

last: SALK

state: CA

address: Health Sciences Drive

country: USA

institute: University of California, San Diego

description:
sample_term_id: EFO_0001196
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K56ac in IMR90 cells. Sequencing was done on the Illumina GAII platform.
Library name: YL61
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.2044
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.1961
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

library_source: genomic

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

ANALYSIS FILE NAME: GSM521903_UCSD.IMR90.H3K56ac.YL61.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K56ac.IMR90-02.01.hg19.level.1
ANALYSIS TITLE: Mapping of IMR90 Cell Line Histone H3K56ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K56ac ChIP-Seq on the IMR90 Cell Line, Library YL61 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.5175
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: 0.2285
FINDPEAKS_PERCENTILE: 67
HOTSPOT_SCORE: 0.3096
HOTSPOT_PERCENTILE: 67
IROC_SCORE: 0.9793
IROC_PERCENTILE: 67
POISSON_SCORE: 0.4125
POISSON_PERCENTILE: 67

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

ANALYSIS FILE NAME: GSM521903_UCSD.IMR90.H3K56ac.YL61.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K56ac.IMR90-02.01.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of IMR90 Cell Line Histone H3K56ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K56ac ChIP-Seq read mappings from the IMR90 Cell Line, Library YL61 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.4473
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: IMR90 H3K56ac 61
BROWSER_TRACK_DESCRIPTION: UCSD IMR90 Cell Line Histone H3K56ac Library YL61 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K56ac_EXPERIMENTS_SCORED: 3
FINDPEAKS_SCORE: 0.2285
FINDPEAKS_PERCENTILE: 67
HOTSPOT_SCORE: 0.3096
HOTSPOT_PERCENTILE: 67
IROC_SCORE: 0.9793
IROC_PERCENTILE: 67
POISSON_SCORE: 0.4125
POISSON_PERCENTILE: 67

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

molecule: genomic DNA

organism: Homo sapiens

source_name: IMR90 Cell Line, biological replicate 2; renlab.H3K56ac.IMR90-02.01

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

tag: molecule

tag: disease

value: Cell Line

tag: line

tag: lineage

tag: batch

value: Fetal lung fibroblast

tag: passage

tag: medium

value: Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)

tag: Sex

value: Female

value: Histone H3K56ac

value: Biorupter

value: 500 micrograms

value: magnetic anti-rabbit

value: 5 micrograms

value: Upstate


title: Reference Epigenome: ChIP-Seq Analysis of H3K4me3 in IMR90 Cells; renlab.H3K4me3.IMR90-02.01

description:
sample_term_id: EFO_0001196
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K4me3 in IMR90 cells. Sequencing was done on the Illumina GAII platform.
Library name: SK03
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.1990
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.1957
****************
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: GSM521901_UCSD.IMR90.H3K4me3.SK03.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4me3.IMR90-02.01.hg19.level.1
ANALYSIS TITLE: Mapping of IMR90 Cell Line Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me3 ChIP-Seq on the IMR90 Cell Line, Library SK03 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.4405
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: 0.8457
FINDPEAKS_PERCENTILE: 98
HOTSPOT_SCORE: 0.7673
HOTSPOT_PERCENTILE: 98
IROC_SCORE: 0.9967
IROC_PERCENTILE: 23
POISSON_SCORE: 0.838
POISSON_PERCENTILE: 98

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

ANALYSIS FILE NAME: GSM521901_UCSD.IMR90.H3K4me3.SK03.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4me3.IMR90-02.01.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of IMR90 Cell Line Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me3 ChIP-Seq read mappings from the IMR90 Cell Line, Library SK03 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.4531
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: IMR90 H3K4me3 03
BROWSER_TRACK_DESCRIPTION: UCSD IMR90 Cell Line Histone H3K4me3 Library SK03 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED: 62
FINDPEAKS_SCORE: 0.8457
FINDPEAKS_PERCENTILE: 98
HOTSPOT_SCORE: 0.7673
HOTSPOT_PERCENTILE: 98
IROC_SCORE: 0.9967
IROC_PERCENTILE: 23
POISSON_SCORE: 0.838
POISSON_PERCENTILE: 98

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

source_name: IMR90 Cell Line, biological replicate 2; renlab.H3K4me3.IMR90-02.01

value: IMR90 cells

value: Histone H3K4me3

value: Bioruptor

value: Active Motif


title: Reference Epigenome: ChIP-Seq Analysis of H3K79me1 in IMR90 Cells; renlab.H3K79me1.IMR90-01.01

description:
sample_term_id: EFO_0001196
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K79me1 in IMR90 cells. Sequencing was done on the Illumina GAII platform.
Library name: YL16
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.2071
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.1987
****************
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: GSM521904_UCSD.IMR90.H3K79me1.YL16.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K79me1.IMR90-01.01-renlab.H3K79me1.IMR90-01.02.hg19.level.1
ANALYSIS TITLE: Mapping of IMR90 Cell Line Histone H3K79me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K79me1 ChIP-Seq on the IMR90 Cell Line, Library YL16 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.5148
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: 0.7391
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.3182
HOTSPOT_PERCENTILE: 71
IROC_SCORE: 0.9849
IROC_PERCENTILE: 86
POISSON_SCORE: 0.6968
POISSON_PERCENTILE: 86

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

ANALYSIS FILE NAME: GSM521904_UCSD.IMR90.H3K79me1.YL16.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K79me1.IMR90-01.01-renlab.H3K79me1.IMR90-01.02.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of IMR90 Cell Line Histone H3K79me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K79me1 ChIP-Seq read mappings from the IMR90 Cell Line, Library YL16 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.4559
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: IMR90 H3K79me1 16
BROWSER_TRACK_DESCRIPTION: UCSD IMR90 Cell Line Histone H3K79me1 Library YL16 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K79me1_EXPERIMENTS_SCORED: 7
FINDPEAKS_SCORE: 0.7391
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.3182
HOTSPOT_PERCENTILE: 71
IROC_SCORE: 0.9849
IROC_PERCENTILE: 86
POISSON_SCORE: 0.6968
POISSON_PERCENTILE: 86

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

source_name: IMR90 Cell Line, biological replicate 2; renlab.H3K79me1.IMR90-01.01

value: Histone H3K79me1

value: Abcam


title: Reference Epigenome: ChIP-Seq Input from IMR90 Cells; renlab.Input.IMR90-06.01

description:
sample_term_id: EFO_0001196
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Input from IMR90 Cells. Sequencing was done on the Illumina GAII platform.
Library name: IMR90-06-I1
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.2124
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.2009
****************
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: GSM521931_UCSD.IMR90.Input.IMR90-06-I1.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.Input.IMR90-06.01.hg19.level.1
ANALYSIS TITLE: Mapping of IMR90 Cell Line ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on the IMR90 Cell Line, Library IMR90-06-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.4434
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: 0.2076
FINDPEAKS_PERCENTILE: 99
HOTSPOT_SCORE: 0.2126
HOTSPOT_PERCENTILE: 91
IROC_SCORE: 0.9047
IROC_PERCENTILE: 65
POISSON_SCORE: 0.4096
POISSON_PERCENTILE: 96

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

ANALYSIS FILE NAME: GSM521931_UCSD.IMR90.Input.IMR90-06-I1.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.Input.IMR90-06.01.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of IMR90 Cell Line ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from the IMR90 Cell Line, Library IMR90-06-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.4561
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: IMR90 Input 06I1
BROWSER_TRACK_DESCRIPTION: UCSD IMR90 Cell Line ChIP-Seq Input Library IMR90-06-I1 EA Release 2

QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED: 67
FINDPEAKS_SCORE: 0.2076
FINDPEAKS_PERCENTILE: 99
HOTSPOT_SCORE: 0.2126
HOTSPOT_PERCENTILE: 91
IROC_SCORE: 0.9047
IROC_PERCENTILE: 65
POISSON_SCORE: 0.4096
POISSON_PERCENTILE: 96

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

source_name: IMR90 Cell Line, biological replicate 2; renlab.Input.IMR90-06.01

value: genomic DNA

value: ATCC

value: ChIP-Seq Input

value: Input


title: Reference Epigenome: ChIP-Seq Analysis of H3K4me2 in IMR90 Cells; renlab.H3K4me2.IMR90-02.01

description:
sample_term_id: EFO_0001196
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K4me2 in IMR90 cells. Sequencing was done on the Illumina GAII platform.
Library name: SK07
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.1984
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.1957
****************
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: GSM521900_UCSD.IMR90.H3K4me2.SK07.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4me2.IMR90-02.01.hg19.level.1
ANALYSIS TITLE: Mapping of IMR90 Cell Line Histone H3K4me2 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me2 ChIP-Seq on the IMR90 Cell Line, Library SK07 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.5144
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: 0.7805
FINDPEAKS_PERCENTILE: 88
HOTSPOT_SCORE: 0.6402
HOTSPOT_PERCENTILE: 88
IROC_SCORE: 0.9993
IROC_PERCENTILE: 88
POISSON_SCORE: 0.7571
POISSON_PERCENTILE: 88

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

ANALYSIS FILE NAME: GSM521900_UCSD.IMR90.H3K4me2.SK07.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4me2.IMR90-02.01.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of IMR90 Cell Line Histone H3K4me2 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me2 ChIP-Seq read mappings from the IMR90 Cell Line, Library SK07 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.4456
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: IMR90 H3K4me2 07
BROWSER_TRACK_DESCRIPTION: UCSD IMR90 Cell Line Histone H3K4me2 Library SK07 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K4me2_EXPERIMENTS_SCORED: 8
FINDPEAKS_SCORE: 0.7805
FINDPEAKS_PERCENTILE: 88
HOTSPOT_SCORE: 0.6402
HOTSPOT_PERCENTILE: 88
IROC_SCORE: 0.9993
IROC_PERCENTILE: 88
POISSON_SCORE: 0.7571
POISSON_PERCENTILE: 88

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

source_name: IMR90 Cell Line, biological replicate 2; renlab.H3K4me2.IMR90-02.01

value: Cell Line

value: Fetal lung fibroblast

value: Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)

value: Female

value: Histone H3K4me2


title: Reference Epigenome: ChIP-Seq Analysis of H3K4me2 in IMR90 Cells; renlab.H3K4me2.IMR90-01.01

description:
sample_term_id: EFO_0001196
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K4me2 in IMR90 cells. Sequencing was done on the Illumina GAII platform.
Library name: LL232
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.1981
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.1121
****************
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: GSM521899_UCSD.IMR90.H3K4me2.LL232.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4me2.IMR90-01.01.hg19.level.1
ANALYSIS TITLE: Mapping of IMR90 Cell Line Histone H3K4me2 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me2 ChIP-Seq on the IMR90 Cell Line, Library LL232 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.5156
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: 0.7828
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.6838
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9993
IROC_PERCENTILE: 88
POISSON_SCORE: 0.784
POISSON_PERCENTILE: 100

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

ANALYSIS FILE NAME: GSM521899_UCSD.IMR90.H3K4me2.LL232.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4me2.IMR90-01.01.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of IMR90 Cell Line Histone H3K4me2 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me2 ChIP-Seq read mappings from the IMR90 Cell Line, Library LL232 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.4523
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: IMR90 H3K4me2 32
BROWSER_TRACK_DESCRIPTION: UCSD IMR90 Cell Line Histone H3K4me2 Library LL232 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K4me2_EXPERIMENTS_SCORED: 8
FINDPEAKS_SCORE: 0.7828
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.6838
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9993
IROC_PERCENTILE: 88
POISSON_SCORE: 0.784
POISSON_PERCENTILE: 100

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

source_name: IMR90 Cell Line, biological replicate 1 (r1); renlab.H3K4me2.IMR90-01.01

value: Branson Tip Sonicator

value: 500 micrograms

value: magnetic anti-rabbit

value: 5 micrograms


title: Reference Epigenome: ChIP-Seq Analysis of H3K4me1 in IMR90 Cells; renlab.H3K4me1.IMR90-03.01

description:
sample_term_id: EFO_0001196
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K4me1 in IMR90 cells. Sequencing was done on the Illumina GAII platform.
Library name: SYL133
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.2049
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.2046
****************
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: GSM521898_UCSD.IMR90.H3K4me1.SYL133.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4me1.IMR90-03.01.hg19.level.1
ANALYSIS TITLE: Mapping of IMR90 Cell Line Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me1 ChIP-Seq on the IMR90 Cell Line, Library SYL133 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.4438
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED: 43
FINDPEAKS_SCORE: 0.6658
FINDPEAKS_PERCENTILE: 93
HOTSPOT_SCORE: 0.6392
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9976
IROC_PERCENTILE: 79
POISSON_SCORE: 0.7358
POISSON_PERCENTILE: 91

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

ANALYSIS FILE NAME: GSM521898_UCSD.IMR90.H3K4me1.SYL133.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4me1.IMR90-03.01.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of IMR90 Cell Line Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me1 ChIP-Seq read mappings from the IMR90 Cell Line, Library SYL133 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.4463
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: IMR90 H3K4me1 33
BROWSER_TRACK_DESCRIPTION: UCSD IMR90 Cell Line Histone H3K4me1 Library SYL133 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED: 43
FINDPEAKS_SCORE: 0.6658
FINDPEAKS_PERCENTILE: 93
HOTSPOT_SCORE: 0.6392
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9976
IROC_PERCENTILE: 79
POISSON_SCORE: 0.7358
POISSON_PERCENTILE: 91

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

source_name: IMR90 Cell Line, biological replicate 2; renlab.H3K4me1.IMR90-03.01

value: IMR90 cells

value: Histone H3K4me1

value: Biorupter


title: Reference Epigenome: ChIP-Seq Analysis of H3K4me1 in IMR90 Cells; renlab.H3K4me1.IMR90-02.01

description:
sample_term_id: EFO_0001196
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K4me1 in IMR90 cells. Sequencing was done on the Illumina GAII platform.
Library name: SK04
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.1978
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.1957
****************
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: GSM521897_UCSD.IMR90.H3K4me1.SK04.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4me1.IMR90-02.01.hg19.level.1
ANALYSIS TITLE: Mapping of IMR90 Cell Line Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me1 ChIP-Seq on the IMR90 Cell Line, Library SK04 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.4410
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED: 43
FINDPEAKS_SCORE: 0.7758
FINDPEAKS_PERCENTILE: 98
HOTSPOT_SCORE: 0.5718
HOTSPOT_PERCENTILE: 93
IROC_SCORE: 0.9979
IROC_PERCENTILE: 83
POISSON_SCORE: 0.7552
POISSON_PERCENTILE: 93

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

ANALYSIS FILE NAME: GSM521897_UCSD.IMR90.H3K4me1.SK04.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4me1.IMR90-02.01.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of IMR90 Cell Line Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me1 ChIP-Seq read mappings from the IMR90 Cell Line, Library SK04 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.4481
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: IMR90 H3K4me1 04
BROWSER_TRACK_DESCRIPTION: UCSD IMR90 Cell Line Histone H3K4me1 Library SK04 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED: 43
FINDPEAKS_SCORE: 0.7758
FINDPEAKS_PERCENTILE: 98
HOTSPOT_SCORE: 0.5718
HOTSPOT_PERCENTILE: 93
IROC_SCORE: 0.9979
IROC_PERCENTILE: 83
POISSON_SCORE: 0.7552
POISSON_PERCENTILE: 93

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

source_name: IMR90 Cell Line, biological replicate 2; renlab.H3K4me1.IMR90-02.01

value: Abcam


title: Reference Epigenome: ChIP-Seq Analysis of H3K56ac in IMR90 Cells; renlab.H3K56ac.IMR90-01.01

description:
sample_term_id: EFO_0001196
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K56ac in IMR90 cells. Sequencing was done on the Illumina GAII platform.
Library name: YL05
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.2040
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.1987
****************
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: GSM521902_UCSD.IMR90.H3K56ac.YL05.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K56ac.IMR90-01.01.hg19.level.1
ANALYSIS TITLE: Mapping of IMR90 Cell Line Histone H3K56ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K56ac ChIP-Seq on the IMR90 Cell Line, Library YL05 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.5133
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: 0.3219
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.3288
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9899
IROC_PERCENTILE: 100
POISSON_SCORE: 0.4147
POISSON_PERCENTILE: 100

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

ANALYSIS FILE NAME: GSM521902_UCSD.IMR90.H3K56ac.YL05.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K56ac.IMR90-01.01.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of IMR90 Cell Line Histone H3K56ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K56ac ChIP-Seq read mappings from the IMR90 Cell Line, Library YL05 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.4482
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: IMR90 H3K56ac 05
BROWSER_TRACK_DESCRIPTION: UCSD IMR90 Cell Line Histone H3K56ac Library YL05 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K56ac_EXPERIMENTS_SCORED: 3
FINDPEAKS_SCORE: 0.3219
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.3288
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9899
IROC_PERCENTILE: 100
POISSON_SCORE: 0.4147
POISSON_PERCENTILE: 100

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

source_name: IMR90 Cell Line, biological replicate 2; renlab.H3K56ac.IMR90-01.01

value: genomic DNA

value: Histone H3K56ac

value: Upstate


title: Reference Epigenome: ChIP-Seq Analysis of H3K36me3 in IMR90 Cells; renlab.H3K36me3.IMR90-02.01

description:
sample_term_id: EFO_0001196
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K36me3 in IMR90 cells. Sequencing was done on the Illumina GAII platform.
Library name: YL67
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.1971
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.1961
****************
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: GSM521892_UCSD.IMR90.H3K36me3.YL67.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K36me3.IMR90-02.01.hg19.level.1
ANALYSIS TITLE: Mapping of IMR90 Cell Line Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K36me3 ChIP-Seq on the IMR90 Cell Line, Library YL67 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.4398
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: 0.5781
FINDPEAKS_PERCENTILE: 93
HOTSPOT_SCORE: 0.4485
HOTSPOT_PERCENTILE: 94
IROC_SCORE: 0.9934
IROC_PERCENTILE: 89
POISSON_SCORE: 0.642
POISSON_PERCENTILE: 80

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

ANALYSIS FILE NAME: GSM521892_UCSD.IMR90.H3K36me3.YL67.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K36me3.IMR90-02.01.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of IMR90 Cell Line Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K36me3 ChIP-Seq read mappings from the IMR90 Cell Line, Library YL67 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.4491
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: IMR90 H3K36me3 67
BROWSER_TRACK_DESCRIPTION: UCSD IMR90 Cell Line Histone H3K36me3 Library YL67 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED: 54
FINDPEAKS_SCORE: 0.5781
FINDPEAKS_PERCENTILE: 93
HOTSPOT_SCORE: 0.4485
HOTSPOT_PERCENTILE: 94
IROC_SCORE: 0.9934
IROC_PERCENTILE: 89
POISSON_SCORE: 0.642
POISSON_PERCENTILE: 80

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

source_name: IMR90 Cell Line, biological replicate 2; renlab.H3K36me3.IMR90-02.01

value: ATCC

value: Histone H3K36me3


title: Reference Epigenome: ChIP-Seq Analysis of H3K4ac in IMR90 Cells; renlab.H3K4ac.IMR90-02.01

description:
sample_term_id: EFO_0001196
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K4ac in IMR90 cells. Sequencing was done on the Illumina GAII platform.
Library name: SK16
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.2026
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.2019
****************
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: GSM521894_UCSD.IMR90.H3K4ac.SK16.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4ac.IMR90-02.01.hg19.level.1
ANALYSIS TITLE: Mapping of IMR90 Cell Line Histone H3K4ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4ac ChIP-Seq on the IMR90 Cell Line, Library SK16 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.5167
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: 0.7559
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.4939
HOTSPOT_PERCENTILE: 67
IROC_SCORE: 0.9967
IROC_PERCENTILE: 67
POISSON_SCORE: 0.7229
POISSON_PERCENTILE: 100

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

ANALYSIS FILE NAME: GSM521894_UCSD.IMR90.H3K4ac.SK16.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4ac.IMR90-02.01.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of IMR90 Cell Line Histone H3K4ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4ac ChIP-Seq read mappings from the IMR90 Cell Line, Library SK16 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.4529
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: IMR90 H3K4ac 16
BROWSER_TRACK_DESCRIPTION: UCSD IMR90 Cell Line Histone H3K4ac Library SK16 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K4ac_EXPERIMENTS_SCORED: 3
FINDPEAKS_SCORE: 0.7559
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.4939
HOTSPOT_PERCENTILE: 67
IROC_SCORE: 0.9967
IROC_PERCENTILE: 67
POISSON_SCORE: 0.7229
POISSON_PERCENTILE: 100

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

source_name: IMR90 Cell Line, biological replicate 2; renlab.H3K4ac.IMR90-02.01

value: Cell Line

value: Fetal lung fibroblast

value: Histone H3K4ac


title: Reference Epigenome: ChIP-Seq Analysis of H3K36me3 in IMR90 Cells; renlab.H3K36me3.IMR90-01.01

description:
sample_term_id: EFO_0001196
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K36me3 in IMR90 cells. Sequencing was done on the Illumina GAII platform.
Library name: LL225
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.2065
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.1121
****************
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: GSM521890_UCSD.IMR90.H3K36me3.LL225.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K36me3.IMR90-01.01-renlab.H3K36me3.IMR90-01.02.hg19.level.1
ANALYSIS TITLE: Mapping of IMR90 Cell Line Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K36me3 ChIP-Seq on the IMR90 Cell Line, Library LL225 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.4394
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: 0.6972
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.4615
HOTSPOT_PERCENTILE: 98
IROC_SCORE: 0.9982
IROC_PERCENTILE: 96
POISSON_SCORE: 0.7053
POISSON_PERCENTILE: 91

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

ANALYSIS FILE NAME: GSM521890_UCSD.IMR90.H3K36me3.LL225.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K36me3.IMR90-01.01-renlab.H3K36me3.IMR90-01.02.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of IMR90 Cell Line Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K36me3 ChIP-Seq read mappings from the IMR90 Cell Line, Library LL225 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.4511
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: IMR90 H3K36me3 25
BROWSER_TRACK_DESCRIPTION: UCSD IMR90 Cell Line Histone H3K36me3 Library LL225 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED: 54
FINDPEAKS_SCORE: 0.6972
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.4615
HOTSPOT_PERCENTILE: 98
IROC_SCORE: 0.9982
IROC_PERCENTILE: 96
POISSON_SCORE: 0.7053
POISSON_PERCENTILE: 91

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

source_name: IMR90 Cell Line, biological replicate 1 (r1); renlab.H3K36me3.IMR90-01.01

value: Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)

value: Female


title: Reference Epigenome: ChIP-Seq Analysis of H3K27me3 in IMR90 Cells; renlab.H3K27me3.IMR90-02.01

description:
sample_term_id: EFO_0001196
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K27me3 in IMR90 cells. Sequencing was done on the Illumina GAII platform.
Library name: SK05
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.1964
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.1957
****************
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: GSM521889_UCSD.IMR90.H3K27me3.SK05.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27me3.IMR90-02.01.hg19.level.1
ANALYSIS TITLE: Mapping of IMR90 Cell Line Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27me3 ChIP-Seq on the IMR90 Cell Line, Library SK05 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.4421
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED: 52
FINDPEAKS_SCORE: 0.6056
FINDPEAKS_PERCENTILE: 98
HOTSPOT_SCORE: 0.2404
HOTSPOT_PERCENTILE: 54
IROC_SCORE: 0.9425
IROC_PERCENTILE: 69
POISSON_SCORE: 0.6219
POISSON_PERCENTILE: 92

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

ANALYSIS FILE NAME: GSM521889_UCSD.IMR90.H3K27me3.SK05.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27me3.IMR90-02.01.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of IMR90 Cell Line Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27me3 ChIP-Seq read mappings from the IMR90 Cell Line, Library SK05 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.4483
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: IMR90 H3K27me3 05
BROWSER_TRACK_DESCRIPTION: UCSD IMR90 Cell Line Histone H3K27me3 Library SK05 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED: 52
FINDPEAKS_SCORE: 0.6056
FINDPEAKS_PERCENTILE: 98
HOTSPOT_SCORE: 0.2404
HOTSPOT_PERCENTILE: 54
IROC_SCORE: 0.9425
IROC_PERCENTILE: 69
POISSON_SCORE: 0.6219
POISSON_PERCENTILE: 92

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

source_name: IMR90 Cell Line, biological replicate 2; renlab.H3K27me3.IMR90-02.01

value: Histone H3K27me3

value: 500 micrograms

value: Millipore


title: Reference Epigenome: ChIP-Seq Analysis of H3K27ac in IMR90 Cells; renlab.H3K27ac.IMR90-03.01

description:
sample_term_id: EFO_0001196
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K27ac in IMR90 cells. Sequencing was done on the Illumina GAII platform.
Library name: YL58
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.1962
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.1961
****************
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: GSM521887_UCSD.IMR90.H3K27ac.YL58.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27ac.IMR90-03.01.hg19.level.1
ANALYSIS TITLE: Mapping of IMR90 Cell Line Histone H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27ac ChIP-Seq on the IMR90 Cell Line, Library YL58 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.5174
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: 0.7728
FINDPEAKS_PERCENTILE: 83
HOTSPOT_SCORE: 0.7
HOTSPOT_PERCENTILE: 83
IROC_SCORE: 0.9984
IROC_PERCENTILE: 67
POISSON_SCORE: 0.7914
POISSON_PERCENTILE: 83

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

ANALYSIS FILE NAME: GSM521887_UCSD.IMR90.H3K27ac.YL58.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27ac.IMR90-03.01.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of IMR90 Cell Line Histone H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27ac ChIP-Seq read mappings from the IMR90 Cell Line, Library YL58 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.4516
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: IMR90 H3K27ac 58
BROWSER_TRACK_DESCRIPTION: UCSD IMR90 Cell Line Histone H3K27ac Library YL58 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K27ac_EXPERIMENTS_SCORED: 6
FINDPEAKS_SCORE: 0.7728
FINDPEAKS_PERCENTILE: 83
HOTSPOT_SCORE: 0.7
HOTSPOT_PERCENTILE: 83
IROC_SCORE: 0.9984
IROC_PERCENTILE: 67
POISSON_SCORE: 0.7914
POISSON_PERCENTILE: 83

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

source_name: IMR90 Cell Line, biological replicate 2; renlab.H3K27ac.IMR90-03.01

value: IMR90 cells

value: Histone H3K27ac

value: Bioruptor

value: magnetic anti-rabbit

value: 5 micrograms


title: Reference Epigenome: ChIP-Seq Analysis of H3K23ac in IMR90 Cells; renlab.H3K23ac.IMR90-02.01

description:
sample_term_id: EFO_0001196
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K23ac in IMR90 cells. Sequencing was done on the Illumina GAII platform.
Library name: SK18
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.2037
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.2019
****************
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: GSM521886_UCSD.IMR90.H3K23ac.SK18.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K23ac.IMR90-02.01.hg19.level.1
ANALYSIS TITLE: Mapping of IMR90 Cell Line Histone H3K23ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K23ac ChIP-Seq on the IMR90 Cell Line, Library SK18 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.5181
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_H3K23ac_EXPERIMENTS_SCORED: 2
FINDPEAKS_SCORE: 0.6602
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.3105
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9761
IROC_PERCENTILE: 100
POISSON_SCORE: 0.6276
POISSON_PERCENTILE: 100

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

ANALYSIS FILE NAME: GSM521886_UCSD.IMR90.H3K23ac.SK18.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K23ac.IMR90-02.01.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of IMR90 Cell Line Histone H3K23ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K23ac ChIP-Seq read mappings from the IMR90 Cell Line, Library SK18 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.4441
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: IMR90 H3K23ac 18
BROWSER_TRACK_DESCRIPTION: UCSD IMR90 Cell Line Histone H3K23ac Library SK18 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K23ac_EXPERIMENTS_SCORED: 2
FINDPEAKS_SCORE: 0.6602
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.3105
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9761
IROC_PERCENTILE: 100
POISSON_SCORE: 0.6276
POISSON_PERCENTILE: 100

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

source_name: IMR90 Cell Line, biological replicate 2; renlab.H3K23ac.IMR90-02.01

value: genomic DNA

value: Histone H3K23ac

value: Biorupter


title: dms4-1_sRNA

status: Public on Mar 31 2010

city: St. Louis

first: Blake

middle: C.

last: Meyers

state: MO

address: 975 N Warson Road

institute: Donald Danforth Plant Science Center

description: quantitative data on primary and secondary siRNAs

library_source: transcriptomic

data_processing:
Adapter sequences were removed using a Perl script, generating small RNA sequences plus abundances. Alignment: The data were matched to the Arabidopsis genome as well as the transgenes described in Kanno et al. (2008). Of the 6,670,921 total reads from transgenic wild type and 5,809,235 from the dms4-1 mutant, 5,155,187 (wt) and 4,069,752 (dms4-1) reads matched the genome excluding 275,681 (wt) and 522,229 (dms4-1) that matched tRNA, rRNA, snRNA or snoRNAs
Genome wide comparison: For the genome-wide comparison of the two libraries (dms4-1 versus wildtype T+S), we used a simplified analysis in which we arbitrarily defined 500 bp bins that cover the entire genome; in some cases, the repeat elements might be split into two clusters (although manual inspection showed this was relatively rare). We then filtered the set to identify those clusters which show greater than 10X difference in each comparison and for which the sum of abundance in each individual library was >10 TP2M. Loci encoding structural RNAs (tRNAs, rRNAs, snRNAs, snoRNAs) were removed from consideration.

molecule: total RNA

organism: Arabidopsis thaliana

source_name: Mixed stage inflorescense tissue

growth_protocol: Seeds were germinated on soil and grown for approximately 5 weeks at 22-23°C under a light cycle of 8 hours dark, 16 hours light. Mixed stage floral inflorescences (inflorescence meristem and floral buds to stage 12) were harvested between 9 and 12 AM and stored in 50 ml Falcom tubes at -80°C.

extract_protocol: Total RNA was isolated from mixed stage inflorescence tissues of the transgenic wild type and the dms4-1 mutant using TRIzol reagent (Invitrogen). Total RNA (300 ug) for each sample was used to construct the small RNA libraries as described previously (Lu et al., 2007) but with different adapters. The RNA oligos (Dharmacon) used for small RNA ligations were as follows: 5' RNA Adapter (5'OH-GUUCAGAGUUCUACAGUCCGACGAUC-OH 3’) and 3' RNA Adapter: (5'pUCGUAUGCCGUCUUCUGCUUGUidt 3’; p, phosphate; idT, inverted deoxythymidine). Libraries were sequenced on an Illumina GAII following the manufacturer's protocols at the Delaware Biotechnology Institute.

tag: genotype

value: IWR1-type transcription factor mutant, dms4

tag: ecotype

value: Columbia


title: Reference Epigenome: ChIP-Seq Analysis of H3K18ac in IMR90 Cells; renlab.H3K18ac.IMR90-02.01

description:
sample_term_id: EFO_0001196
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K18ac in IMR90 cells. Sequencing was done on the Illumina GAII platform.
Library name: SK09
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.1958
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.1957
****************
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: GSM521884_UCSD.IMR90.H3K18ac.SK09.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K18ac.IMR90-02.01.hg19.level.1
ANALYSIS TITLE: Mapping of IMR90 Cell Line Histone H3K18ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K18ac ChIP-Seq on the IMR90 Cell Line, Library SK09 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.5169
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: 0.8146
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.5626
HOTSPOT_PERCENTILE: 75
IROC_SCORE: 0.9982
IROC_PERCENTILE: 100
POISSON_SCORE: 0.7741
POISSON_PERCENTILE: 100

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

ANALYSIS FILE NAME: GSM521884_UCSD.IMR90.H3K18ac.SK09.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K18ac.IMR90-02.01.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of IMR90 Cell Line Histone H3K18ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K18ac ChIP-Seq read mappings from the IMR90 Cell Line, Library SK09 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.4442
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: IMR90 H3K18ac 09
BROWSER_TRACK_DESCRIPTION: UCSD IMR90 Cell Line Histone H3K18ac Library SK09 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K18ac_EXPERIMENTS_SCORED: 4
FINDPEAKS_SCORE: 0.8146
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.5626
HOTSPOT_PERCENTILE: 75
IROC_SCORE: 0.9982
IROC_PERCENTILE: 100
POISSON_SCORE: 0.7741
POISSON_PERCENTILE: 100

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

source_name: IMR90 Cell Line, biological replicate 2; renlab.H3K18ac.IMR90-02.01

value: ATCC

value: Cell Line

value: Fetal lung fibroblast

value: Histone H3K18ac

value: Abcam


title: Reference Epigenome: ChIP-Seq Analysis of H2BK15ac in IMR90 Cells; renlab.H2BK15ac.IMR90-03.01

description:
sample_term_id: EFO_0001196
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H2BK15ac in IMR90 cells. Sequencing was done on the Illumina GAII platform.
Library name: SK42
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.2014
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.2009
****************
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: GSM521878_UCSD.IMR90.H2BK15ac.SK42.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H2BK15ac.IMR90-03.01.hg19.level.1
ANALYSIS TITLE: Mapping of IMR90 Cell Line Histone H2BK15ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H2BK15ac ChIP-Seq on the IMR90 Cell Line, Library SK42 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.5198
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: 0.466
FINDPEAKS_PERCENTILE: 80
HOTSPOT_SCORE: 0.4116
HOTSPOT_PERCENTILE: 80
IROC_SCORE: 0.9839
IROC_PERCENTILE: 80
POISSON_SCORE: 0.5851
POISSON_PERCENTILE: 80

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

ANALYSIS FILE NAME: GSM521878_UCSD.IMR90.H2BK15ac.SK42.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H2BK15ac.IMR90-03.01.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of IMR90 Cell Line Histone H2BK15ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H2BK15ac ChIP-Seq read mappings from the IMR90 Cell Line, Library SK42 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.4452
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: IMR90 H2BK15ac 42
BROWSER_TRACK_DESCRIPTION: UCSD IMR90 Cell Line Histone H2BK15ac Library SK42 EA Release 2

QUALITY SCORES:
NUMBER_OF_H2BK15ac_EXPERIMENTS_SCORED: 5
FINDPEAKS_SCORE: 0.466
FINDPEAKS_PERCENTILE: 80
HOTSPOT_SCORE: 0.4116
HOTSPOT_PERCENTILE: 80
IROC_SCORE: 0.9839
IROC_PERCENTILE: 80
POISSON_SCORE: 0.5851
POISSON_PERCENTILE: 80

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

source_name: IMR90 Cell Line, biological replicate 2; renlab.H2BK15ac.IMR90-03.01

value: Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)

value: Female

value: Histone H2BK15ac

value: 500 micrograms


title: Reference Epigenome: ChIP-Seq Analysis of H3K23ac in IMR90 Cells; renlab.H3K23ac.IMR90-01.01

description:
sample_term_id: EFO_0001196
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K23ac in IMR90 cells. Sequencing was done on the Illumina GAII platform.
Library name: YL09
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.2034
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.1987
****************
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: GSM521885_UCSD.IMR90.H3K23ac.YL09.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K23ac.IMR90-01.01.hg19.level.1
ANALYSIS TITLE: Mapping of IMR90 Cell Line Histone H3K23ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K23ac ChIP-Seq on the IMR90 Cell Line, Library YL09 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.5179
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_H3K23ac_EXPERIMENTS_SCORED: 2
FINDPEAKS_SCORE: 0.3954
FINDPEAKS_PERCENTILE: 50
HOTSPOT_SCORE: 0.2996
HOTSPOT_PERCENTILE: 50
IROC_SCORE: 0.9576
IROC_PERCENTILE: 50
POISSON_SCORE: 0.5078
POISSON_PERCENTILE: 50

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

ANALYSIS FILE NAME: GSM521885_UCSD.IMR90.H3K23ac.YL09.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K23ac.IMR90-01.01.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of IMR90 Cell Line Histone H3K23ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K23ac ChIP-Seq read mappings from the IMR90 Cell Line, Library YL09 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.4540
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: IMR90 H3K23ac 09
BROWSER_TRACK_DESCRIPTION: UCSD IMR90 Cell Line Histone H3K23ac Library YL09 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K23ac_EXPERIMENTS_SCORED: 2
FINDPEAKS_SCORE: 0.3954
FINDPEAKS_PERCENTILE: 50
HOTSPOT_SCORE: 0.2996
HOTSPOT_PERCENTILE: 50
IROC_SCORE: 0.9576
IROC_PERCENTILE: 50
POISSON_SCORE: 0.5078
POISSON_PERCENTILE: 50

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

source_name: IMR90 Cell Line, biological replicate 2; renlab.H3K23ac.IMR90-01.01

value: Upstate


title: Reference Epigenome: ChIP-Seq Analysis of H3K4me1 in IMR90 Cells; renlab.H3K4me1.IMR90-01.01

description:
sample_term_id: EFO_0001196
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K4me1 in IMR90 cells. Sequencing was done on the Illumina GAII platform.
Library name: LL222
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.2067
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.1121
****************
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: GSM521895_UCSD.IMR90.H3K4me1.LL222.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4me1.IMR90-01.01-renlab.H3K4me1.IMR90-01.02.hg19.level.1
ANALYSIS TITLE: Mapping of IMR90 Cell Line Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me1 ChIP-Seq on the IMR90 Cell Line, Library LL222 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.4439
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED: 43
FINDPEAKS_SCORE: 0.788
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.5529
HOTSPOT_PERCENTILE: 88
IROC_SCORE: 0.9965
IROC_PERCENTILE: 76
POISSON_SCORE: 0.7632
POISSON_PERCENTILE: 95

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

ANALYSIS FILE NAME: GSM521895_UCSD.IMR90.H3K4me1.LL222.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4me1.IMR90-01.01-renlab.H3K4me1.IMR90-01.02.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of IMR90 Cell Line Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me1 ChIP-Seq read mappings from the IMR90 Cell Line, Library LL222 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.4522
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: IMR90 H3K4me1 22
BROWSER_TRACK_DESCRIPTION: UCSD IMR90 Cell Line Histone H3K4me1 Library LL222 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED: 43
FINDPEAKS_SCORE: 0.788
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.5529
HOTSPOT_PERCENTILE: 88
IROC_SCORE: 0.9965
IROC_PERCENTILE: 76
POISSON_SCORE: 0.7632
POISSON_PERCENTILE: 95

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

source_name: IMR90 Cell Line, biological replicate 1 (r1); renlab.H3K4me1.IMR90-01.01

value: IMR90 cells

value: Histone H3K4me1

value: Branson Tip Sonicator

value: magnetic anti-rabbit


title: Reference Epigenome: ChIP-Seq Analysis of H3K4ac in IMR90 Cells; renlab.H3K4ac.IMR90-01.01

description:
sample_term_id: EFO_0001196
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K4ac in IMR90 cells. Sequencing was done on the Illumina GAII platform.
Library name: LL239
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.2023
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.1987
****************
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: GSM521893_UCSD.IMR90.H3K4ac.LL239.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4ac.IMR90-01.01.hg19.level.1
ANALYSIS TITLE: Mapping of IMR90 Cell Line Histone H3K4ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4ac ChIP-Seq on the IMR90 Cell Line, Library LL239 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.5189
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: 0.6577
FINDPEAKS_PERCENTILE: 67
HOTSPOT_SCORE: 0.5219
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9968
IROC_PERCENTILE: 100
POISSON_SCORE: 0.6703
POISSON_PERCENTILE: 67

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

ANALYSIS FILE NAME: GSM521893_UCSD.IMR90.H3K4ac.LL239.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4ac.IMR90-01.01.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of IMR90 Cell Line Histone H3K4ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4ac ChIP-Seq read mappings from the IMR90 Cell Line, Library LL239 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.4553
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: IMR90 H3K4ac 39
BROWSER_TRACK_DESCRIPTION: UCSD IMR90 Cell Line Histone H3K4ac Library LL239 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K4ac_EXPERIMENTS_SCORED: 3
FINDPEAKS_SCORE: 0.6577
FINDPEAKS_PERCENTILE: 67
HOTSPOT_SCORE: 0.5219
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9968
IROC_PERCENTILE: 100
POISSON_SCORE: 0.6703
POISSON_PERCENTILE: 67

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

source_name: IMR90 Cell Line, biological replicate 2; renlab.H3K4ac.IMR90-01.01

value: genomic DNA

value: Histone H3K4ac

value: Biorupter

value: 5 micrograms


title: Reference Epigenome: ChIP-Seq Analysis of H2BK20ac in IMR90 Cells; renlab.H2BK20ac.IMR90-01.01

description:
sample_term_id: EFO_0001196
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H2BK20ac in IMR90 cells. Sequencing was done on the Illumina GAII platform.
Library name: YL07
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.2016
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.1987
****************
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: GSM521879_UCSD.IMR90.H2BK20ac.YL07.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H2BK20ac.IMR90-01.01.hg19.level.1
ANALYSIS TITLE: Mapping of IMR90 Cell Line Histone H2BK20ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H2BK20ac ChIP-Seq on the IMR90 Cell Line, Library YL07 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.5157
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: 0.4669
FINDPEAKS_PERCENTILE: 75
HOTSPOT_SCORE: 0.3776
HOTSPOT_PERCENTILE: 75
IROC_SCORE: 0.9858
IROC_PERCENTILE: 75
POISSON_SCORE: 0.555
POISSON_PERCENTILE: 75

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

ANALYSIS FILE NAME: GSM521879_UCSD.IMR90.H2BK20ac.YL07.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H2BK20ac.IMR90-01.01.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of IMR90 Cell Line Histone H2BK20ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H2BK20ac ChIP-Seq read mappings from the IMR90 Cell Line, Library YL07 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.4517
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: IMR90 H2BK20ac 07
BROWSER_TRACK_DESCRIPTION: UCSD IMR90 Cell Line Histone H2BK20ac Library YL07 EA Release 2

QUALITY SCORES:
NUMBER_OF_H2BK20ac_EXPERIMENTS_SCORED: 4
FINDPEAKS_SCORE: 0.4669
FINDPEAKS_PERCENTILE: 75
HOTSPOT_SCORE: 0.3776
HOTSPOT_PERCENTILE: 75
IROC_SCORE: 0.9858
IROC_PERCENTILE: 75
POISSON_SCORE: 0.555
POISSON_PERCENTILE: 75

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

source_name: IMR90 Cell Line, biological replicate 2; renlab.H2BK20ac.IMR90-01.01

value: ATCC

value: Cell Line

value: Histone H2BK20ac


title: Reference Epigenome: ChIP-Seq Analysis of H2BK20ac in IMR90 Cells; renlab.H2BK20ac.IMR90-02.01

description:
sample_term_id: EFO_0001196
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H2BK20ac in IMR90 cells. Sequencing was done on the Illumina GAII platform.
Library name: SK14
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.2020
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.2019
****************
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: GSM521880_UCSD.IMR90.H2BK20ac.SK14.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H2BK20ac.IMR90-02.01.hg19.level.1
ANALYSIS TITLE: Mapping of IMR90 Cell Line Histone H2BK20ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H2BK20ac ChIP-Seq on the IMR90 Cell Line, Library SK14 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.5154
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: 0.6624
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.4474
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9937
IROC_PERCENTILE: 100
POISSON_SCORE: 0.6586
POISSON_PERCENTILE: 100

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

ANALYSIS FILE NAME: GSM521880_UCSD.IMR90.H2BK20ac.SK14.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H2BK20ac.IMR90-02.01.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of IMR90 Cell Line Histone H2BK20ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H2BK20ac ChIP-Seq read mappings from the IMR90 Cell Line, Library SK14 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.4513
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: IMR90 H2BK20ac 14
BROWSER_TRACK_DESCRIPTION: UCSD IMR90 Cell Line Histone H2BK20ac Library SK14 EA Release 2

QUALITY SCORES:
NUMBER_OF_H2BK20ac_EXPERIMENTS_SCORED: 4
FINDPEAKS_SCORE: 0.6624
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.4474
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9937
IROC_PERCENTILE: 100
POISSON_SCORE: 0.6586
POISSON_PERCENTILE: 100

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

source_name: IMR90 Cell Line, biological replicate 2; renlab.H2BK20ac.IMR90-02.01

value: Fetal lung fibroblast