title: Reference Epigenome: ChIP-Seq Analysis of H2BK12ac in IMR90 Cells; renlab.H2BK12ac.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 H2BK12ac in IMR90 cells. Sequencing was done on the Illumina GAII platform.
Library name: YL138
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.2055
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: GSM521874_UCSD.IMR90.H2BK12ac.YL138.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H2BK12ac.IMR90-03.01.hg19.level.1
ANALYSIS TITLE: Mapping of IMR90 Cell Line Histone H2BK12ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H2BK12ac ChIP-Seq on the IMR90 Cell Line, Library YL138 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.5166
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H2BK12ac_EXPERIMENTS_SCORED: 4
FINDPEAKS_SCORE: 0.6307
FINDPEAKS_PERCENTILE: 75
HOTSPOT_SCORE: 0.5271
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9952
IROC_PERCENTILE: 75
POISSON_SCORE: 0.6983
POISSON_PERCENTILE: 100

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

ANALYSIS FILE NAME: GSM521874_UCSD.IMR90.H2BK12ac.YL138.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H2BK12ac.IMR90-03.01.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of IMR90 Cell Line Histone H2BK12ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H2BK12ac ChIP-Seq read mappings from the IMR90 Cell Line, Library YL138 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.4535
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 H2BK12ac 38
BROWSER_TRACK_DESCRIPTION: UCSD IMR90 Cell Line Histone H2BK12ac Library YL138 EA Release 2

QUALITY SCORES:
NUMBER_OF_H2BK12ac_EXPERIMENTS_SCORED: 4
FINDPEAKS_SCORE: 0.6307
FINDPEAKS_PERCENTILE: 75
HOTSPOT_SCORE: 0.5271
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9952
IROC_PERCENTILE: 75
POISSON_SCORE: 0.6983
POISSON_PERCENTILE: 100

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

source_name: IMR90 Cell Line, biological replicate 2; renlab.H2BK12ac.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: Histone H2BK12ac

value: Abcam


title: Reference Epigenome: ChIP-Seq Analysis of H2BK12ac in IMR90 Cells; renlab.H2BK12ac.IMR90-01.01

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 H2BK12ac in IMR90 cells. Sequencing was done on the Illumina GAII platform.
Library name: YL18
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.2053
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
****************

library_source: genomic

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

ANALYSIS FILE NAME: GSM521871_UCSD.IMR90.H2BK12ac.YL18.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H2BK12ac.IMR90-01.01-renlab.H2BK12ac.IMR90-01.02.hg19.level.1
ANALYSIS TITLE: Mapping of IMR90 Cell Line Histone H2BK12ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H2BK12ac ChIP-Seq on the IMR90 Cell Line, Library YL18 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.5142
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H2BK12ac_EXPERIMENTS_SCORED: 4
FINDPEAKS_SCORE: 0.6869
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.502
HOTSPOT_PERCENTILE: 75
IROC_SCORE: 0.9958
IROC_PERCENTILE: 100
POISSON_SCORE: 0.6945
POISSON_PERCENTILE: 75

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

ANALYSIS FILE NAME: GSM521871_UCSD.IMR90.H2BK12ac.YL18.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H2BK12ac.IMR90-01.01-renlab.H2BK12ac.IMR90-01.02.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of IMR90 Cell Line Histone H2BK12ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H2BK12ac ChIP-Seq read mappings from the IMR90 Cell Line, Library YL18 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.4480
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 H2BK12ac 18
BROWSER_TRACK_DESCRIPTION: UCSD IMR90 Cell Line Histone H2BK12ac Library YL18 EA Release 2

QUALITY SCORES:
NUMBER_OF_H2BK12ac_EXPERIMENTS_SCORED: 4
FINDPEAKS_SCORE: 0.6869
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.502
HOTSPOT_PERCENTILE: 75
IROC_SCORE: 0.9958
IROC_PERCENTILE: 100
POISSON_SCORE: 0.6945
POISSON_PERCENTILE: 75

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

molecule: genomic DNA

organism: Homo sapiens

source_name: IMR90 Cell Line, biological replicate 2; renlab.H2BK12ac.IMR90-01.01

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

tag: molecule

value: genomic DNA

tag: disease

value: ATCC

value: Cell Line

tag: line

tag: lineage

tag: batch

value: Fetal lung fibroblast

tag: passage

tag: medium

tag: Sex

value: Female

value: Biorupter

value: 500 micrograms

value: magnetic anti-rabbit

value: 5 micrograms


title: Col-dcl2,3,4/Col-dcl2,3,4 rep1

status: Public on Mar 24 2010

city: Cambridge

first: Krys

last: Kelly

address: Downing Street

department: Plant Sciences

country: United Kingdom

institute: University of Cambridge

description: Grafted plants are described using “shoot/root” notation

library_source: transcriptomic

data_processing: Small RNA adapters were removed using an exact match to the sequence of the appropriate adapter.   Reads were aligned to the Arabidopsis thaliana genome (TAIR v8) using SSAHA v3.1.

molecule: total RNA

organism: Arabidopsis thaliana

source_name: root total RNA

growth_protocol: standard growth conditions (10hr light, 20 C)

extract_protocol: Total nucleic acid (TNA) extracts were prepared from pooled shoot and root samples derived from 3-4 individual grafts according to White and Kaper, 1989. To clone small RNAs, sRNAfractions were enriched from 12.5-25 µg of TNA using MirVana columns (Ambion) according to the manufacturer’s instruction. SRNAs were cloned by the Illumina sRNAcloning kit.

tag: ecotype

tag: sample time

value: five weeks after grafting


title: Reference Epigenome: ChIP-Seq Analysis of H2BK12ac in IMR90 Cells; renlab.H2BK12ac.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 H2BK12ac in IMR90 cells. Sequencing was done on the Illumina GAII platform.
Library name: YL68
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.2002
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: GSM521873_UCSD.IMR90.H2BK12ac.YL68.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H2BK12ac.IMR90-02.01.hg19.level.1
ANALYSIS TITLE: Mapping of IMR90 Cell Line Histone H2BK12ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H2BK12ac ChIP-Seq on the IMR90 Cell Line, Library YL68 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.5171
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H2BK12ac_EXPERIMENTS_SCORED: 4
FINDPEAKS_SCORE: 0.5457
FINDPEAKS_PERCENTILE: 83
HOTSPOT_SCORE: 0.523
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.995
IROC_PERCENTILE: 100
POISSON_SCORE: 0.6469
POISSON_PERCENTILE: 83

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

ANALYSIS FILE NAME: GSM521873_UCSD.IMR90.H2BK12ac.YL68.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H2BK12ac.IMR90-02.01.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of IMR90 Cell Line Histone H2BK12ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H2BK12ac ChIP-Seq read mappings from the IMR90 Cell Line, Library YL68 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.4446
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 H2BK12ac 68
BROWSER_TRACK_DESCRIPTION: UCSD IMR90 Cell Line Histone H2BK12ac Library YL68 EA Release 2

QUALITY SCORES:
NUMBER_OF_H2BK12ac_EXPERIMENTS_SCORED: 4
FINDPEAKS_SCORE: 0.5457
FINDPEAKS_PERCENTILE: 83
HOTSPOT_SCORE: 0.523
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.995
IROC_PERCENTILE: 100
POISSON_SCORE: 0.6469
POISSON_PERCENTILE: 83

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

source_name: IMR90 Cell Line, biological replicate 2; renlab.H2BK12ac.IMR90-02.01


title: Reference Epigenome: ChIP-Seq Analysis of H2BK15ac in IMR90 Cells; renlab.H2BK15ac.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 H2BK15ac in IMR90 cells. Sequencing was done on the Illumina GAII platform.
Library name: YL19
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.2069
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: GSM521875_UCSD.IMR90.H2BK15ac.YL19.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H2BK15ac.IMR90-01.01-renlab.H2BK15ac.IMR90-01.02.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 YL19 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.5164
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: 0.6322
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.4578
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9929
IROC_PERCENTILE: 100
POISSON_SCORE: 0.6637
POISSON_PERCENTILE: 100

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

ANALYSIS FILE NAME: GSM521875_UCSD.IMR90.H2BK15ac.YL19.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H2BK15ac.IMR90-01.01-renlab.H2BK15ac.IMR90-01.02.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 YL19 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.4525
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 19
BROWSER_TRACK_DESCRIPTION: UCSD IMR90 Cell Line Histone H2BK15ac Library YL19 EA Release 2

QUALITY SCORES:
NUMBER_OF_H2BK15ac_EXPERIMENTS_SCORED: 5
FINDPEAKS_SCORE: 0.6322
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.4578
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9929
IROC_PERCENTILE: 100
POISSON_SCORE: 0.6637
POISSON_PERCENTILE: 100

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

source_name: IMR90 Cell Line, biological replicate 2; renlab.H2BK15ac.IMR90-01.01

value: Histone H2BK15ac


title: Reference Epigenome: ChIP-Seq Analysis of H2BK120ac in IMR90 Cells; renlab.H2BK120ac.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 H2BK120ac in IMR90 cells. Sequencing was done on the Illumina GAII platform.
Library name: SK15
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.2060
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: GSM521870_UCSD.IMR90.H2BK120ac.SK15.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H2BK120ac.IMR90-02.01.hg19.level.1
ANALYSIS TITLE: Mapping of IMR90 Cell Line Histone H2BK120ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H2BK120ac ChIP-Seq on the IMR90 Cell Line, Library SK15 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.5176
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H2BK120ac_EXPERIMENTS_SCORED: 3
FINDPEAKS_SCORE: 0.7541
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.5479
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9977
IROC_PERCENTILE: 100
POISSON_SCORE: 0.7411
POISSON_PERCENTILE: 100

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

ANALYSIS FILE NAME: GSM521870_UCSD.IMR90.H2BK120ac.SK15.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H2BK120ac.IMR90-02.01.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of IMR90 Cell Line Histone H2BK120ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H2BK120ac ChIP-Seq read mappings from the IMR90 Cell Line, Library SK15 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.4542
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 H2BK120ac 15
BROWSER_TRACK_DESCRIPTION: UCSD IMR90 Cell Line Histone H2BK120ac Library SK15 EA Release 2

QUALITY SCORES:
NUMBER_OF_H2BK120ac_EXPERIMENTS_SCORED: 3
FINDPEAKS_SCORE: 0.7541
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.5479
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9977
IROC_PERCENTILE: 100
POISSON_SCORE: 0.7411
POISSON_PERCENTILE: 100

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

source_name: IMR90 Cell Line, biological replicate 2; renlab.H2BK120ac.IMR90-02.01

value: Histone H2BK120ac

value: Upstate


title: Reference Epigenome: ChIP-Seq Analysis of H2AK5ac in IMR90 Cells; renlab.H2AK5ac.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 H2AK5ac in IMR90 cells. Sequencing was done on the Illumina GAII platform.
Library name: YL60
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.1993
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: GSM521868_UCSD.IMR90.H2AK5ac.YL60.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H2AK5ac.IMR90-02.01.hg19.level.1
ANALYSIS TITLE: Mapping of IMR90 Cell Line Histone H2AK5ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H2AK5ac ChIP-Seq on the IMR90 Cell Line, Library YL60 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.5159
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_H2AK5ac_EXPERIMENTS_SCORED: 6
FINDPEAKS_SCORE: 0.5136
FINDPEAKS_PERCENTILE: 67
HOTSPOT_SCORE: 0.4598
HOTSPOT_PERCENTILE: 50
IROC_SCORE: 0.9865
IROC_PERCENTILE: 50
POISSON_SCORE: 0.6385
POISSON_PERCENTILE: 50

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

ANALYSIS FILE NAME: GSM521868_UCSD.IMR90.H2AK5ac.YL60.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H2AK5ac.IMR90-02.01.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of IMR90 Cell Line Histone H2AK5ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H2AK5ac ChIP-Seq read mappings from the IMR90 Cell Line, Library YL60 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.4512
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 H2AK5ac 60
BROWSER_TRACK_DESCRIPTION: UCSD IMR90 Cell Line Histone H2AK5ac Library YL60 EA Release 2

QUALITY SCORES:
NUMBER_OF_H2AK5ac_EXPERIMENTS_SCORED: 6
FINDPEAKS_SCORE: 0.5136
FINDPEAKS_PERCENTILE: 67
HOTSPOT_SCORE: 0.4598
HOTSPOT_PERCENTILE: 50
IROC_SCORE: 0.9865
IROC_PERCENTILE: 50
POISSON_SCORE: 0.6385
POISSON_PERCENTILE: 50

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

source_name: IMR90 Cell Line, biological replicate 2; renlab.H2AK5ac.IMR90-02.01

value: Histone H2AK5ac


title: Reference Epigenome: ChIP-Seq Analysis of H2BK120ac in IMR90 Cells; renlab.H2BK120ac.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 H2BK120ac in IMR90 cells. Sequencing was done on the Illumina GAII platform.
Library name: YL06
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.2057
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: GSM521869_UCSD.IMR90.H2BK120ac.YL06.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H2BK120ac.IMR90-01.01.hg19.level.1
ANALYSIS TITLE: Mapping of IMR90 Cell Line Histone H2BK120ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H2BK120ac ChIP-Seq on the IMR90 Cell Line, Library YL06 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.5202
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H2BK120ac_EXPERIMENTS_SCORED: 3
FINDPEAKS_SCORE: 0.5964
FINDPEAKS_PERCENTILE: 67
HOTSPOT_SCORE: 0.492
HOTSPOT_PERCENTILE: 67
IROC_SCORE: 0.9957
IROC_PERCENTILE: 67
POISSON_SCORE: 0.6352
POISSON_PERCENTILE: 67

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

ANALYSIS FILE NAME: GSM521869_UCSD.IMR90.H2BK120ac.YL06.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H2BK120ac.IMR90-01.01.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of IMR90 Cell Line Histone H2BK120ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H2BK120ac ChIP-Seq read mappings from the IMR90 Cell Line, Library YL06 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.4445
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 H2BK120ac 06
BROWSER_TRACK_DESCRIPTION: UCSD IMR90 Cell Line Histone H2BK120ac Library YL06 EA Release 2

QUALITY SCORES:
NUMBER_OF_H2BK120ac_EXPERIMENTS_SCORED: 3
FINDPEAKS_SCORE: 0.5964
FINDPEAKS_PERCENTILE: 67
HOTSPOT_SCORE: 0.492
HOTSPOT_PERCENTILE: 67
IROC_SCORE: 0.9957
IROC_PERCENTILE: 67
POISSON_SCORE: 0.6352
POISSON_PERCENTILE: 67

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

source_name: IMR90 Cell Line, biological replicate 2; renlab.H2BK120ac.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)


title: Col/Col rep1


title: Reference Epigenome: ChIP-Seq Analysis of H3K14ac in IMR90 Cells; renlab.H3K14ac.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 H3K14ac in IMR90 cells. Sequencing was done on the Illumina GAII platform.
Library name: SK17
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.2031
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: GSM521883_UCSD.IMR90.H3K14ac.SK17.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K14ac.IMR90-02.01.hg19.level.1
ANALYSIS TITLE: Mapping of IMR90 Cell Line Histone H3K14ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K14ac ChIP-Seq on the IMR90 Cell Line, Library SK17 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.5143
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_H3K14ac_EXPERIMENTS_SCORED: 2
FINDPEAKS_SCORE: 0.6594
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.3307
HOTSPOT_PERCENTILE: 50
IROC_SCORE: 0.9803
IROC_PERCENTILE: 50
POISSON_SCORE: 0.6283
POISSON_PERCENTILE: 100

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

ANALYSIS FILE NAME: GSM521883_UCSD.IMR90.H3K14ac.SK17.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K14ac.IMR90-02.01.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of IMR90 Cell Line Histone H3K14ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K14ac ChIP-Seq read mappings from the IMR90 Cell Line, Library SK17 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.4497
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 H3K14ac 17
BROWSER_TRACK_DESCRIPTION: UCSD IMR90 Cell Line Histone H3K14ac Library SK17 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K14ac_EXPERIMENTS_SCORED: 2
FINDPEAKS_SCORE: 0.6594
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.3307
HOTSPOT_PERCENTILE: 50
IROC_SCORE: 0.9803
IROC_PERCENTILE: 50
POISSON_SCORE: 0.6283
POISSON_PERCENTILE: 100

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

source_name: IMR90 Cell Line, biological replicate 2; renlab.H3K14ac.IMR90-02.01

value: Histone H3K14ac


title: Reference Epigenome: ChIP-Seq Analysis of H3K14ac in IMR90 Cells; renlab.H3K14ac.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 H3K14ac in IMR90 cells. Sequencing was done on the Illumina GAII platform.
Library name: YL15
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.2063
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: GSM521881_UCSD.IMR90.H3K14ac.YL15.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K14ac.IMR90-01.01-renlab.H3K14ac.IMR90-01.02.hg19.level.1
ANALYSIS TITLE: Mapping of IMR90 Cell Line Histone H3K14ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K14ac ChIP-Seq on the IMR90 Cell Line, Library YL15 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.5180
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_H3K14ac_EXPERIMENTS_SCORED: 2
FINDPEAKS_SCORE: 0.559
FINDPEAKS_PERCENTILE: 50
HOTSPOT_SCORE: 0.367
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9822
IROC_PERCENTILE: 100
POISSON_SCORE: 0.611
POISSON_PERCENTILE: 50

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

ANALYSIS FILE NAME: GSM521881_UCSD.IMR90.H3K14ac.YL15.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K14ac.IMR90-01.01-renlab.H3K14ac.IMR90-01.02.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of IMR90 Cell Line Histone H3K14ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K14ac ChIP-Seq read mappings from the IMR90 Cell Line, Library YL15 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.4533
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 H3K14ac 15
BROWSER_TRACK_DESCRIPTION: UCSD IMR90 Cell Line Histone H3K14ac Library YL15 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K14ac_EXPERIMENTS_SCORED: 2
FINDPEAKS_SCORE: 0.559
FINDPEAKS_PERCENTILE: 50
HOTSPOT_SCORE: 0.367
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9822
IROC_PERCENTILE: 100
POISSON_SCORE: 0.611
POISSON_PERCENTILE: 50

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

source_name: IMR90 Cell Line, biological replicate 2; renlab.H3K14ac.IMR90-01.01


title: Chromatin accessibility assay of Fetal Kidney Primary Tissue; DS10986

city: Seattle

first: Northwest

last: REMC

state: WA

institute: University of Washington

description:
sample_term_id: UBERON_0002113
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS10986
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.1675
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.1676
****************
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: GSM493385_DS10986.UWStam_090616_SOLEXA-1GA-1_0007_FC427K6_4.bam
ANALYSIS ALIAS: UW.FetalKidney.ChromatinAccessibility.Level1.1
ANALYSIS TITLE: Mapping of Fetal Kidney Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Kidney primary tissue were mapped to the human genome (NCBI Build 36.1) using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.1864
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None

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

ANALYSIS FILE NAME: GSM493385_DS10986.UWStam_090629_SOLEXA-1GA-1_0011_FC42AT0_7.bam
ANALYSIS ALIAS: UW.FetalKidney.ChromatinAccessibility.Level1.2
ANALYSIS TITLE: Mapping of Fetal Kidney Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Kidney primary tissue were mapped to the human genome (NCBI Build 36.1) using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.1865
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None

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

ANALYSIS FILE NAME: GSM493385_DS10986.UWStam_090804_SOLEXA-1GA-2_0009_FC42ALL_3.bam
ANALYSIS ALIAS: UW.FetalKidney.ChromatinAccessibility.Level1.3
ANALYSIS TITLE: Mapping of Fetal Kidney Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Kidney primary tissue were mapped to the human genome (NCBI Build 36.1) using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.1866
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None

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

ANALYSIS FILE NAME: GSM493385_UW.FetalKidney.ChromatinAccessibility.fKidney-DS10986.wig
ANALYSIS ALIAS: UW.FetalKidney.ChromatinAccessibility.DS10986
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Kidney Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from Fetal Kidney 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%2FUniversity%20of%20Washington%2FANALYSIS%2FEDACC.2645
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None

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

ANALYSIS FILE NAME: GSM493385_UW.Fetal_Kidney.ChromatinAccessibility.H-22337.DS10986.bed
ANALYSIS ALIAS: DS10986.hg19.level.1
ANALYSIS TITLE: Mapping of Fetal Kidney Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Kidney, Donor H-22337, Library DS10986 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.4104
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED: 40
FINDPEAKS_SCORE: 0.526
FINDPEAKS_PERCENTILE: 40
HOTSPOT_SCORE: 0.397
HOTSPOT_PERCENTILE: 40
IROC_SCORE: 0.9941
IROC_PERCENTILE: 15
POISSON_SCORE: 0.5375
POISSON_PERCENTILE: 62

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

ANALYSIS FILE NAME: GSM493385_UW.Fetal_Kidney.ChromatinAccessibility.H-22337.DS10986.wig
ANALYSIS ALIAS: DS10986.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Kidney Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from Fetal Kidney, Donor H-22337, Library DS10986 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.4064
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 150bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: FK DNase 37 86
BROWSER_TRACK_DESCRIPTION: UW Fetal Kidney DNase Hypersensitivity Donor H-22337 Library DS10986 EA Release 2

QUALITY SCORES:
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED: 40
FINDPEAKS_SCORE: 0.526
FINDPEAKS_PERCENTILE: 40
HOTSPOT_SCORE: 0.397
HOTSPOT_PERCENTILE: 40
IROC_SCORE: 0.9941
IROC_PERCENTILE: 15
POISSON_SCORE: 0.5375
POISSON_PERCENTILE: 62

source_name: Fetal Kidney primary tissue, day 82; DS10986

extract_protocol: Library construction protocol: Single read - Illumina

value: University of Washington, Congenital Defects Lab. Ian Glass

value: Primary Tissue

value: fetal kidney

value: UW

value: fetal

value: 82 days

value: Caucasian

value: Chromatin Accessibility

value: Qiagen minElut

value: Stamlab DNase Protocol


title: Reference Epigenome: ChIP-Seq Analysis of H2AK5ac in IMR90 Cells; renlab.H2AK5ac.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 H2AK5ac in IMR90 cells. Sequencing was done on the Illumina GAII platform.
Library name: YL20
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.2051
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: GSM521866_UCSD.IMR90.H2AK5ac.YL20.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H2AK5ac.IMR90-01.01-renlab.H2AK5ac.IMR90-01.02.hg19.level.1
ANALYSIS TITLE: Mapping of IMR90 Cell Line Histone H2AK5ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H2AK5ac ChIP-Seq on the IMR90 Cell Line, Library YL20 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.5165
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_H2AK5ac_EXPERIMENTS_SCORED: 6
FINDPEAKS_SCORE: 0.4988
FINDPEAKS_PERCENTILE:
HOTSPOT_SCORE: 0.4734
HOTSPOT_PERCENTILE:
IROC_SCORE: 0.992
IROC_PERCENTILE:
POISSON_SCORE: 0.6422
POISSON_PERCENTILE:

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

ANALYSIS FILE NAME: GSM521866_UCSD.IMR90.H2AK5ac.YL20.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H2AK5ac.IMR90-01.01-renlab.H2AK5ac.IMR90-01.02.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of IMR90 Cell Line Histone H2AK5ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H2AK5ac ChIP-Seq read mappings from the IMR90 Cell Line, Library YL20 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.4462
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 H2AK5ac 20
BROWSER_TRACK_DESCRIPTION: UCSD IMR90 Cell Line Histone H2AK5ac Library YL20 EA Release 2

QUALITY SCORES:
NUMBER_OF_H2AK5ac_EXPERIMENTS_SCORED: 6
FINDPEAKS_SCORE: 0.4988
FINDPEAKS_PERCENTILE:
HOTSPOT_SCORE: 0.4734
HOTSPOT_PERCENTILE:
IROC_SCORE: 0.992
IROC_PERCENTILE:
POISSON_SCORE: 0.6422
POISSON_PERCENTILE:

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

source_name: IMR90 Cell Line, biological replicate 2; renlab.H2AK5ac.IMR90-01.01

value: genomic DNA

value: ATCC

value: Cell Line

value: Fetal lung fibroblast

value: Female

value: Biorupter

value: 500 micrograms

value: magnetic anti-rabbit

value: 5 micrograms

value: Abcam


title: WT (T+S)_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

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.

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: trasngenic wild type plant (contains trigger and silencer transgenes)

value: Columbia


title: Reference Epigenome: ChIP-Seq Analysis of H2BK15ac in IMR90 Cells; renlab.H2BK15ac.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 H2BK15ac in IMR90 cells. Sequencing was done on the Illumina GAII platform.
Library name: YL69
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.2012
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: GSM521877_UCSD.IMR90.H2BK15ac.YL69.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H2BK15ac.IMR90-02.01.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 YL69 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.5199
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: 0.2792
FINDPEAKS_PERCENTILE: 40
HOTSPOT_SCORE: 0.2964
HOTSPOT_PERCENTILE: 60
IROC_SCORE: 0.9433
IROC_PERCENTILE: 60
POISSON_SCORE: 0.4964
POISSON_PERCENTILE: 60

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

ANALYSIS FILE NAME: GSM521877_UCSD.IMR90.H2BK15ac.YL69.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H2BK15ac.IMR90-02.01.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 YL69 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.4504
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 69
BROWSER_TRACK_DESCRIPTION: UCSD IMR90 Cell Line Histone H2BK15ac Library YL69 EA Release 2

QUALITY SCORES:
NUMBER_OF_H2BK15ac_EXPERIMENTS_SCORED: 5
FINDPEAKS_SCORE: 0.2792
FINDPEAKS_PERCENTILE: 40
HOTSPOT_SCORE: 0.2964
HOTSPOT_PERCENTILE: 60
IROC_SCORE: 0.9433
IROC_PERCENTILE: 60
POISSON_SCORE: 0.4964
POISSON_PERCENTILE: 60

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

source_name: IMR90 Cell Line, biological replicate 2; renlab.H2BK15ac.IMR90-02.01

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: Histone H2BK15ac


title: GM12878_Pol_II_ChIPSeq_IgG_Rep2

city: New Haven

first: Flora

last: Vaccarino

state: CT

address: 230 South Frontage Road

department: Child Study Center

institute: Yale University

description: Chromatin IP against normal mouse IgG

data_processing: FASTQ files are either the sequence.txt files from the Illumnia pipeline (which exclude low quality reads) or, when available, are generated from the Illumina export.txt files which include all reads. Both types of alignment files, eland_result.txt and eland_multi.txt, are directly out of the Illumnia pipeline and unmodified. The narrowPeak files are the scored results generated from the PeakSeq pipeline (http://www.ncbi.nlm.nih.gov/pubmed/19122651?dopt=Abstract) and formatted in the UCSC narrowPeak format.

source_name: Lymphoblastoid Cells

growth_protocol: Lymphoblastoid cell lines were grown in RPMI-1640 Medium, supplemented with glutamine, 15% FBS, and antibiotics (penicillin-streptomycin) at 37C in 5% CO2, to a density of 6-8 x10^5 cells/ml.

extract_protocol: Chomatin immunoprecipitation was performed as previously described (Euskirchen et al. 2007; Rozowsky et al. 2009). 2 x 10^8 cells were cross-linked in 1% formaldehyde for 10 minutes at room temperature. The cross-linking reaction was quenched by adding glycine to a final concentration of 125 mM. Nuclear lysates were sonicated using a Branson 250 Sonifier (power setting 2, 100% duty cycle for 7 × 30-s intervals), such that the chromatin fragments ranged from 50-2000kb. Clarified lysates were divided in half and treated overnight at four degrees Celsius with 24μg of either mouse monoclonal 8WG16 antibody (Covance MMS-126R) or normal mouse IgG (Millipore #12-371). Protein-DNA complexes were captured on Protein A agarose beads (Upstate #16-156) and eluted in 1% SDS TE buffer at 65°C. Following cross-link reversal and purification, the ChIP DNA sequencing libraries were generated according to Illumina DNA Sample Kit Instructions (Illumina Part # 0801– 0303). The protocol was modified such that enzymes were obtained from other suppliers, as described in Auerbach et al. 2009.

treatment_protocol: For Pol II ChIP-Seq, cells were not treated prior to cross-linking.

tag: cell line

tag: cell type

value: Lymphoblastoid cell

tag: chip antibody

value: normal mouse IgG


title: GM12891_Pol_II_ChIPSeq_IgG_Rep1

description: Chromatin IP against normal mouse IgG


title: GM12891_Pol_II_ChIPSeq_IgG_Rep2

description: Chromatin IP against normal mouse IgG


title: GM12891_Pol_II_ChIPSeq_Rep6

description: Chromatin IP against Pol II

value: Pol II (8WG16)


title: GM12878_Pol_II_ChIPSeq_IgG_Rep1

description: Chromatin IP against normal mouse IgG


title: GM12891_Pol_II_ChIPSeq_Rep1

description: Chromatin IP against Pol II


title: GM12891_Pol_II_ChIPSeq_Rep2

description: Chromatin IP against Pol II


title: GM12878_Pol_II_ChIPSeq_Rep7

description: Chromatin IP against Pol II


title: GM12891_Pol_II_ChIPSeq_Rep5

description: Chromatin IP against Pol II


title: GM12891_Pol_II_ChIPSeq_Rep4

description: Chromatin IP against Pol II


title: GM12891_Pol_II_ChIPSeq_Rep3

description: Chromatin IP against Pol II


title: GM12878_Pol_II_ChIPSeq_Rep6

description: Chromatin IP against Pol II


title: GM12878_Pol_II_ChIPSeq_Rep3

description: Chromatin IP against Pol II


title: GM12878_Pol_II_ChIPSeq_Rep5

description: Chromatin IP against Pol II


title: GM12878_Pol_II_ChIPSeq_Rep4

description: Chromatin IP against Pol II


title: GM12878_Pol_II_ChIPSeq_Rep2

description: Chromatin IP against Pol II


title: GM18526_Pol_II_ChIPSeq_IgG_Rep3

description: Chromatin IP against normal mouse IgG


title: GM12878_Pol_II_ChIPSeq_Rep1

description: Chromatin IP against Pol II


title: GM18526_Pol_II_ChIPSeq_IgG_Rep2

description: Chromatin IP against normal mouse IgG


title: GM18526_Pol_II_ChIPSeq_Rep1

description: Chromatin IP against Pol II


title: GM18951_Pol_II_ChIPSeq_IgG_Rep1

description: Chromatin IP against normal mouse IgG


title: GM18951_Pol_II_ChIPSeq_Rep4

description: Chromatin IP against Pol II


title: GM18951_Pol_II_ChIPSeq_IgG_Rep2

description: Chromatin IP against normal mouse IgG


title: GM18526_Pol_II_ChIPSeq_Rep2

description: Chromatin IP against Pol II


title: GM18951_Pol_II_ChIPSeq_Rep3

description: Chromatin IP against Pol II


title: GM18951_Pol_II_ChIPSeq_Rep2

description: Chromatin IP against Pol II


title: GM18951_Pol_II_ChIPSeq_Rep1

description: Chromatin IP against Pol II


title: GM18526_Pol_II_ChIPSeq_IgG_Rep1

description: Chromatin IP against normal mouse IgG


title: GM10847_Pol_II_ChIPSeq_IgG_Rep1

description: Chromatin IP against normal mouse IgG


title: GM18526_Pol_II_ChIPSeq_Rep3

description: Chromatin IP against Pol II


title: GM10847_Pol_II_ChIPSeq_IgG_Rep2

description: Chromatin IP against normal mouse IgG


title: GM10847_Pol_II_ChIPSeq_Rep4

description: Chromatin IP against Pol II


title: GM15510_Pol_II_ChIPSeq_IgG_Rep2

description: Chromatin IP against normal mouse IgG


title: GM10847_Pol_II_ChIPSeq_Rep1

description: Chromatin IP against Pol II


title: GM10847_Pol_II_ChIPSeq_Rep3

description: Chromatin IP against Pol II


title: GM10847_Pol_II_ChIPSeq_Rep2

description: Chromatin IP against Pol II


title: GM12892_Pol_II_ChIPSeq_IgG_Rep1

description: Chromatin IP against normal mouse IgG


title: GM12892_Pol_II_ChIPSeq_Rep3

description: Chromatin IP against Pol II


title: GM15510_Pol_II_ChIPSeq_Rep2

description: Chromatin IP against Pol II


title: GM15510_Pol_II_ChIPSeq_IgG_Rep1

description: Chromatin IP against normal mouse IgG


title: GM12892_Pol_II_ChIPSeq_Rep2

description: Chromatin IP against Pol II


title: GM15510_Pol_II_ChIPSeq_Rep3

description: Chromatin IP against Pol II


title: GM12892_Pol_II_ChIPSeq_Rep1

description: Chromatin IP against Pol II


title: GM19099_Pol_II_ChIPSeq_Rep3

description: Chromatin IP against Pol II


title: GM19099_Pol_II_ChIPSeq_IgG_Rep2

description: Chromatin IP against normal mouse IgG


title: GM15510_Pol_II_ChIPSeq_Rep1

description: Chromatin IP against Pol II


title: GM12892_Pol_II_ChIPSeq_IgG_Rep2

description: Chromatin IP against normal mouse IgG


title: GM18505_Pol_II_ChIPSeq_IgG_Rep2

description: Chromatin IP against normal mouse IgG


title: GM19099_Pol_II_ChIPSeq_IgG_Rep1

description: Chromatin IP against normal mouse IgG


title: GM19099_Pol_II_ChIPSeq_Rep2

description: Chromatin IP against Pol II


title: GM18505_Pol_II_ChIPSeq_IgG_Rep1

description: Chromatin IP against normal mouse IgG


title: GM19099_Pol_II_ChIPSeq_Rep1

description: Chromatin IP against Pol II


title: GM18505_Pol_II_ChIPSeq_Rep4

description: Chromatin IP against Pol II


title: GM18505_Pol_II_ChIPSeq_Rep1

description: Chromatin IP against Pol II


title: GM18505_Pol_II_ChIPSeq_Rep3

description: Chromatin IP against Pol II


title: GM18505_Pol_II_ChIPSeq_Rep2

description: Chromatin IP against Pol II


title: GM19193_Pol_II_ChIPSeq_IgG_Rep2

description: Chromatin IP against normal mouse IgG


title: GM19193_Pol_II_ChIPSeq_IgG_Rep1

description: Chromatin IP against normal mouse IgG


title: GM19193_Pol_II_ChIPSeq_Rep4

description: Chromatin IP against Pol II


title: GM12878_NFkB_II_ChIPSeq_Rep2

description: Chromatin IP against NFκB p65 (C-20) rabbit polyclonal antibody

extract_protocol: Chomatin immunoprecipitation was performed as previously described (Euskirchen et al. 2007; Rozowsky et al. 2009). 2 x 10^8 cells were cross-linked in 1% formaldehyde for 10 minutes at room temperature. The cross-linking reaction was quenched by adding glycine to a final concentration of 125 mM. Nuclear lysates were sonicated using a Branson 250 Sonifier (power setting 2, 100% duty cycle for 7 × 30-s intervals), such that the chromatin fragments ranged from 50-2000kb. Clarified lysates were divided in half and treated overnight at four degrees Celsius with 8μg of either anti-NFκB p65 (C-20) rabbit polyclonal antibody (Santa Cruz sc-372) or normal rabbit IgG (Santa Cruz Sc-2027). Protein-DNA complexes were captured on Protein A agarose beads (Upstate #16-156) and eluted in 1% SDS TE buffer at 65°C. Following cross-link reversal and purification, the ChIP DNA sequencing libraries were generated according to Illumina DNA Sample Kit Instructions (Illumina Part # 0801– 0303). The protocol was modified such that enzymes were obtained from other suppliers, as described in Auerbach et al. 2009.

treatment_protocol: Prior to cross-linking, cells were treated with 25 ng/mL human recombinant TNF-alpha (eBioscience #14-8329) for six hours at 37°C, 5% CO2.

tag: treatment

value: TNF-alpha induced (6h)


title: GM19193_Pol_II_ChIPSeq_Rep3

description: Chromatin IP against Pol II


title: GM12891_NFkB_II_ChIPSeq_Rep2

value: NFκB p65 (C-20) rabbit polyclonal antibody


title: GM12891_NFkB_II_ChIPSeq_IgG_Rep2

description: Chromatin IP against normal rabbit IgG

value: normal rabbit IgG


title: GM19193_Pol_II_ChIPSeq_Rep2

description: Chromatin IP against Pol II


title: GM12891_NFkB_II_ChIPSeq_IgG_Rep1

description: Chromatin IP against normal rabbit IgG


title: GM19193_Pol_II_ChIPSeq_Rep1

description: Chromatin IP against Pol II


title: GM12878_NFkB_II_ChIPSeq_Rep3


title: GM12878_NFkB_II_ChIPSeq_Rep4


title: GM12891_NFkB_II_ChIPSeq_Rep1


title: GM12878_NFkB_II_ChIPSeq_IgG_Rep1

description: Chromatin IP against normal rabbit IgG


title: GM12891_NFkB_II_ChIPSeq_Rep3


title: GM12878_NFkB_II_ChIPSeq_Rep1


title: GM18526_NFkB_II_ChIPSeq_IgG_Rep1

description: Chromatin IP against normal rabbit IgG


title: GM18526_NFkB_II_ChIPSeq_IgG_Rep2

description: Chromatin IP against normal rabbit IgG


title: GM18526_NFkB_II_ChIPSeq_Rep3


title: GM18951_NFkB_II_ChIPSeq_IgG_Rep2

description: Chromatin IP against normal rabbit IgG


title: GM18951_NFkB_II_ChIPSeq_IgG_Rep1

description: Chromatin IP against normal rabbit IgG


title: GM18526_NFkB_II_ChIPSeq_Rep1


title: GM18951_NFkB_II_ChIPSeq_Rep2


title: GM18951_NFkB_II_ChIPSeq_Rep1


title: GM18526_NFkB_II_ChIPSeq_Rep2


title: GM10847_NFkB_II_ChIPSeq_IgG_Rep2

description: Chromatin IP against normal rabbit IgG


title: GM10847_NFkB_II_ChIPSeq_Rep5


title: GM18951_NFkB_II_ChIPSeq_Rep4


title: Reference Epigenome: ChIP-Seq Analysis of H3K79me1 in IMR90 Cells; renlab.H3K79me1.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 H3K79me1 in IMR90 cells. Sequencing was done on the Illumina GAII platform.
Library name: SK11
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.2076
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: GSM521906_UCSD.IMR90.H3K79me1.SK11.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K79me1.IMR90-02.01.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 SK11 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.5170
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: 0.6824
FINDPEAKS_PERCENTILE: 86
HOTSPOT_SCORE: 0.2999
HOTSPOT_PERCENTILE: 57
IROC_SCORE: 0.9815
IROC_PERCENTILE: 71
POISSON_SCORE: 0.6796
POISSON_PERCENTILE: 71

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

ANALYSIS FILE NAME: GSM521906_UCSD.IMR90.H3K79me1.SK11.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K79me1.IMR90-02.01.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 SK11 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.4519
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 11
BROWSER_TRACK_DESCRIPTION: UCSD IMR90 Cell Line Histone H3K79me1 Library SK11 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K79me1_EXPERIMENTS_SCORED: 7
FINDPEAKS_SCORE: 0.6824
FINDPEAKS_PERCENTILE: 86
HOTSPOT_SCORE: 0.2999
HOTSPOT_PERCENTILE: 57
IROC_SCORE: 0.9815
IROC_PERCENTILE: 71
POISSON_SCORE: 0.6796
POISSON_PERCENTILE: 71

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

source_name: IMR90 Cell Line, biological replicate 2; renlab.H3K79me1.IMR90-02.01

value: genomic DNA

value: ATCC

value: Cell Line

value: Fetal lung fibroblast

value: Histone H3K79me1


title: GM10847_NFkB_II_ChIPSeq_IgG_Rep1

description: Chromatin IP against normal rabbit IgG


title: GM10847_NFkB_II_ChIPSeq_Rep4


title: GM12878_NFkB_II_ChIPSeq_IgG_Rep2

description: Chromatin IP against normal rabbit IgG


title: GM10847_NFkB_II_ChIPSeq_Rep3


title: GM12892_NFkB_II_ChIPSeq_Rep2


title: GM12892_NFkB_II_ChIPSeq_IgG_Rep2

description: Chromatin IP against normal rabbit IgG


title: GM10847_NFkB_II_ChIPSeq_Rep2


title: GM12892_NFkB_II_ChIPSeq_Rep3


title: GM12892_NFkB_II_ChIPSeq_IgG_Rep1

description: Chromatin IP against normal rabbit IgG


title: GM15510_NFkB_II_ChIPSeq_IgG_Rep2

description: Chromatin IP against normal rabbit IgG


title: GM15510_NFkB_II_ChIPSeq_Rep5


title: GM15510_NFkB_II_ChIPSeq_IgG_Rep1

description: Chromatin IP against normal rabbit IgG


title: GM12892_NFkB_II_ChIPSeq_Rep1


title: GM18951_NFkB_II_ChIPSeq_Rep3


title: GM10847_NFkB_II_ChIPSeq_Rep1


title: GM19099_NFkB_II_ChIPSeq_Rep3


title: GM15510_NFkB_II_ChIPSeq_Rep2


title: GM19099_NFkB_II_ChIPSeq_IgG_Rep2

description: Chromatin IP against normal rabbit IgG


title: GM19099_NFkB_II_ChIPSeq_IgG_Rep1

description: Chromatin IP against normal rabbit IgG


title: GM15510_NFkB_II_ChIPSeq_Rep1


title: GM18505_NFkB_II_ChIPSeq_IgG_Rep1

description: Chromatin IP against normal rabbit IgG


title: GM18505_NFkB_II_ChIPSeq_IgG_Rep2

description: Chromatin IP against normal rabbit IgG


title: GM19099_NFkB_II_ChIPSeq_Rep1


title: GM18505_NFkB_II_ChIPSeq_Rep3


title: GM18505_NFkB_II_ChIPSeq_Rep5


title: GM19099_NFkB_II_ChIPSeq_Rep2


title: GM18505_NFkB_II_ChIPSeq_Rep4


title: GM19193_NFkB_II_ChIPSeq_IgG_Rep2

description: Chromatin IP against normal rabbit IgG


title: GM19193_NFkB_II_ChIPSeq_IgG_Rep1

description: Chromatin IP against normal rabbit IgG


title: GM18505_NFkB_II_ChIPSeq_Rep2


title: GM18505_NFkB_II_ChIPSeq_Rep1


title: GM15510_NFkB_II_ChIPSeq_Rep4


title: GM19193_NFkB_II_ChIPSeq_Rep3


title: GM15510_NFkB_II_ChIPSeq_Rep3


title: GM19193_NFkB_II_ChIPSeq_Rep2


title: GM19193_NFkB_II_ChIPSeq_Rep1


title: GM19193_RNA-SEQ_induced_Rep1

description: RNA-Seq of PolyA RNA

molecule: polyA RNA

extract_protocol: Total RNA was extracted from lymphoblastoid cell lines, purified and then poly(A)-enriched using two cycles of selection with oligo(dT) cellulose. The Poly(A)-RNA was fragmented and subsequently converted into doublestranded cDNA priming with random hexamers.  For construction of sequencing libraries cDNA was purified, size-seledcted on 2% agarose gel, end-repaired and phosphorylated with the End-It kit from. After treatment with Klenow fragment (NEB, Cat# M0212s) and dATP, Illumina adapters were ligated to the protruding 3_-‘A’ base (LigaFast, Promega Cat#M8221). DNA was amplified with Illumina genomic DNA primers 1.1 and 2.1 for 15 cycles by using the following program: 1. 30 s at 98 °C, 2. 15 cycles of 10 s at 98 °C, 30 s at 65 °C, 30 s at 72 °C, and 3. a 5-min extension at 72 °C. The product was run on 2% agarose E-gels (Invitrogen) to isolate the libraries from residual primers and adapters. Purified library DNA was captured on an Illumina flowcell for cluster generation and sequenced on an Illumina Genome Analyzer II following the manufacturer’s protocols.

treatment_protocol: Cells were treated with 25 ng/mL human recombinant TNF-alpha (eBioscience #14-8329) for six hours at 37°C, 5% CO2.


title: GM18951_RNA-SEQ_induced_Rep1

description: RNA-Seq of PolyA RNA


title: GM18505_RNA-SEQ_induced_Rep1

description: RNA-Seq of PolyA RNA


title: GM12892_RNA-SEQ_induced_Rep1

description: RNA-Seq of PolyA RNA


title: GM12891_RNA-SEQ_induced_Rep1

description: RNA-Seq of PolyA RNA


title: GM18526_RNA-SEQ_induced_Rep1

description: RNA-Seq of PolyA RNA


title: GM15510_RNA-SEQ_induced_Rep1

description: RNA-Seq of PolyA RNA


title: GM19193_RNA-SEQ_Rep1

description: RNA-Seq of PolyA RNA

value: Lymphoblastoid Cell


title: GM18526_RNA-SEQ_Rep1

description: RNA-Seq of PolyA RNA


title: GM18951_RNA-SEQ_Rep1

description: RNA-Seq of PolyA RNA


title: GM18505_RNA-SEQ_Rep2

description: RNA-Seq of PolyA RNA


title: GM18526_RNA-SEQ_Rep2

description: RNA-Seq of PolyA RNA


title: GM12891_RNA-SEQ_Rep1

description: RNA-Seq of PolyA RNA


title: GM10847_RNA-SEQ_induced_Rep1

description: RNA-Seq of PolyA RNA


title: GM12878_RNA-SEQ_induced_Rep1

description: RNA-Seq of PolyA RNA


title: GM12892_RNA-SEQ_Rep1

description: RNA-Seq of PolyA RNA


title: GM10847_RNA-SEQ_Rep2

description: RNA-Seq of PolyA RNA


title: GM10847_RNA-SEQ_Rep1

description: RNA-Seq of PolyA RNA


title: GM19099_RNA-SEQ_Rep1

description: RNA-Seq of PolyA RNA


title: GM18505_RNA-SEQ_Rep1

description: RNA-Seq of PolyA RNA


title: GM12878_RNA-SEQ_Rep2

description: RNA-Seq of PolyA RNA


title: GM12878_RNA-SEQ_Rep1

description: RNA-Seq of PolyA RNA


title: GM15510_RNA-SEQ_Rep1

description: RNA-Seq of PolyA RNA


title: GM19099_RNA-SEQ_induced_Rep1

description: RNA-Seq of PolyA RNA


title: Reference Epigenome: ChIP-Seq Analysis of H3K9ac in IMR90 Cells; renlab.H3K9ac.IMR90-01.01

description:
sample_term_id: EFO_0001196
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Library name: LL233
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.1728
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: GSM469973_UCSD.IMR90.H3K9ac.LL233.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K9ac.IMR90-01.01.hg19.level.1
ANALYSIS TITLE: Mapping of IMR90 Cell Line Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9ac ChIP-Seq on the IMR90 Cell Line, Library LL233 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.4407
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED: 35
FINDPEAKS_SCORE: 0.5609
FINDPEAKS_PERCENTILE: 91
HOTSPOT_SCORE: 0.5371
HOTSPOT_PERCENTILE: 91
IROC_SCORE: 0.9889
IROC_PERCENTILE: 63
POISSON_SCORE: 0.6152
POISSON_PERCENTILE: 83

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

ANALYSIS FILE NAME: GSM469973_UCSD.IMR90.H3K9ac.LL233.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K9ac.IMR90-01.01.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of IMR90 Cell Line Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9ac ChIP-Seq read mappings from the IMR90 Cell Line, Library LL233 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.4485
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 H3K9ac 33
BROWSER_TRACK_DESCRIPTION: UCSD IMR90 Cell Line Histone H3K9ac Library LL233 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED: 35
FINDPEAKS_SCORE: 0.5609
FINDPEAKS_PERCENTILE: 91
HOTSPOT_SCORE: 0.5371
HOTSPOT_PERCENTILE: 91
IROC_SCORE: 0.9889
IROC_PERCENTILE: 63
POISSON_SCORE: 0.6152
POISSON_PERCENTILE: 83

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

source_name: IMR90; renlab.H3K9ac.IMR90-01.01

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

value: IMR90 cells

value: Female

value: Histone H3K9ac

value: Branson Tip Sonicator

value: 500 micrograms

value: magnetic anti-rabbit

value: 5 micrograms

value: Abcam


title: Reference Epigenome: ChIP-Seq Analysis of H4K5ac in IMR90 Cells; renlab.H4K5ac.IMR90-01.01

description:
sample_term_id: EFO_0001196
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Library name: LL234
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.1664
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: GSM469975_UCSD.IMR90.H4K5ac.LL234.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H4K5ac.IMR90-01.01.hg19.level.1
ANALYSIS TITLE: Mapping of IMR90 Cell Line Histone H4K5ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H4K5ac ChIP-Seq on the IMR90 Cell Line, Library LL234 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.5132
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_H4K5ac_EXPERIMENTS_SCORED: 4
FINDPEAKS_SCORE: 0.6655
FINDPEAKS_PERCENTILE: 75
HOTSPOT_SCORE: 0.5581
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9966
IROC_PERCENTILE: 100
POISSON_SCORE: 0.7102
POISSON_PERCENTILE: 75

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

ANALYSIS FILE NAME: GSM469975_UCSD.IMR90.H4K5ac.LL234.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H4K5ac.IMR90-01.01.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of IMR90 Cell Line Histone H4K5ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H4K5ac ChIP-Seq read mappings from the IMR90 Cell Line, Library LL234 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.4560
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 H4K5ac 34
BROWSER_TRACK_DESCRIPTION: UCSD IMR90 Cell Line Histone H4K5ac Library LL234 EA Release 2

QUALITY SCORES:
NUMBER_OF_H4K5ac_EXPERIMENTS_SCORED: 4
FINDPEAKS_SCORE: 0.6655
FINDPEAKS_PERCENTILE: 75
HOTSPOT_SCORE: 0.5581
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9966
IROC_PERCENTILE: 100
POISSON_SCORE: 0.7102
POISSON_PERCENTILE: 75

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

source_name: IMR90; renlab.H4K5ac.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: Histone H4K5ac

value: Upstate


title: Reference Epigenome: ChIP-Seq Analysis of H3K27ac in IMR90 Cells; renlab.H3K27ac.IMR90-01.02

description:
sample_term_id: EFO_0001196
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Library name: LL235
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.1717
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: GSM469967_UCSD.IMR90.H3K27ac.LL235.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27ac.IMR90-01.02.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 LL235 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.5145
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: 0.8536
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.7232
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9994
IROC_PERCENTILE: 100
POISSON_SCORE: 0.8374
POISSON_PERCENTILE: 100

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

ANALYSIS FILE NAME: GSM469967_UCSD.IMR90.H3K27ac.LL235.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27ac.IMR90-01.02.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 LL235 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.4507
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 35
BROWSER_TRACK_DESCRIPTION: UCSD IMR90 Cell Line Histone H3K27ac Library LL235 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K27ac_EXPERIMENTS_SCORED: 6
FINDPEAKS_SCORE: 0.8536
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.7232
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9994
IROC_PERCENTILE: 100
POISSON_SCORE: 0.8374
POISSON_PERCENTILE: 100

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

source_name: IMR90; renlab.H3K27ac.IMR90-01.02

value: genomic DNA

value: Histone H3K27ac


title: Reference Epigenome: ChIP-Seq Analysis of H3K27ac in IMR90 Cells; renlab.H3K27ac.IMR90-01.01

description:
sample_term_id: EFO_0001196
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Library name: LL231
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.1672
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: GSM469966_UCSD.IMR90.H3K27ac.LL231.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27ac.IMR90-01.01.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 LL231 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.5131
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: 0.733
FINDPEAKS_PERCENTILE: 67
HOTSPOT_SCORE: 0.6371
HOTSPOT_PERCENTILE: 67
IROC_SCORE: 0.9988
IROC_PERCENTILE: 83
POISSON_SCORE: 0.7625
POISSON_PERCENTILE: 67

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

ANALYSIS FILE NAME: GSM469966_UCSD.IMR90.H3K27ac.LL231.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27ac.IMR90-01.01.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 LL231 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.4498
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 31
BROWSER_TRACK_DESCRIPTION: UCSD IMR90 Cell Line Histone H3K27ac Library LL231 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K27ac_EXPERIMENTS_SCORED: 6
FINDPEAKS_SCORE: 0.733
FINDPEAKS_PERCENTILE: 67
HOTSPOT_SCORE: 0.6371
HOTSPOT_PERCENTILE: 67
IROC_SCORE: 0.9988
IROC_PERCENTILE: 83
POISSON_SCORE: 0.7625
POISSON_PERCENTILE: 67

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

source_name: IMR90; renlab.H3K27ac.IMR90-01.01

value: ATCC

value: Cell Line


title: Reference Epigenome: ChIP-Seq Analysis of H3K18ac in IMR90 Cells; renlab.H3K18ac.IMR90-01.01

description:
sample_term_id: EFO_0001196
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Library name: LL230
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.1720
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: GSM469965_UCSD.IMR90.H3K18ac.LL230.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K18ac.IMR90-01.01.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 LL230 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.5197
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: 0.6566
FINDPEAKS_PERCENTILE: 75
HOTSPOT_SCORE: 0.6076
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9976
IROC_PERCENTILE: 75
POISSON_SCORE: 0.7287
POISSON_PERCENTILE: 75

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

ANALYSIS FILE NAME: GSM469965_UCSD.IMR90.H3K18ac.LL230.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K18ac.IMR90-01.01.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 LL230 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.4459
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 30
BROWSER_TRACK_DESCRIPTION: UCSD IMR90 Cell Line Histone H3K18ac Library LL230 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K18ac_EXPERIMENTS_SCORED: 4
FINDPEAKS_SCORE: 0.6566
FINDPEAKS_PERCENTILE: 75
HOTSPOT_SCORE: 0.6076
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9976
IROC_PERCENTILE: 75
POISSON_SCORE: 0.7287
POISSON_PERCENTILE: 75

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

source_name: IMR90; renlab.H3K18ac.IMR90-01.01

value: Fetal lung fibroblast

value: Histone H3K18ac


title: AG18359_Pol_II_ChIPSeq_IgG_Rep1

description: Chromatin IP against normal mouse IgG

organism: Pan troglodytes

value: Lymphoblastoid cell

value: normal mouse IgG


title: AG18359_Pol_II_ChIPSeq_Rep3

description: Chromatin IP against Pol II

value: Pol II (8WG16)


title: AG18359_Pol_II_ChIPSeq_Rep2

description: Chromatin IP against Pol II


title: AG18359_Pol_II_ChIPSeq_Rep1

description: Chromatin IP against Pol II


title: fibroblasts_cell_culture

status: Public on Mar 17 2010

city: New York

first: Thomas

last: Templin

state: NY

address: 630 West 168th Street

institute: Columbia University Medical Center

description: deep-sequencing of small RNA fraction, small RNA fraction (20-200 bp)

data_processing: The data was processed by the program ACGT101-miR-v2. This program was used to clean up the Solexa data, to map the sequenced RNAs to selected mir sequences in mirRbase, to map the mir sequences and other sequences to the genome and to cluster mapped mir sequences and other sequences according to genome position.

source_name: AG01522 normal human fibroblasts

growth_protocol: Human fibroblasts (AG01522) were received as cell cultures from Coriell at passage (PDL) 16 and expanded until PDL 20 by culturing in EEMEM (Invitrogen) supplemented with 15% FBS (ATCC).

extract_protocol: ~ 10 μg of RNA was size-fractionated on a 15% tris-borate-EDTA (TBE) urea polyacrylamide gel and the 15-50 base-pair fraction was purified followed by ligation of 5’ and 3’ primers. Ligated RNA was size-fractionated one more time on a 15% TBE urea polyacrylamide gel, and the 65-100 base-pair fraction was excised, eluted and precipitated. This RNA was converted to single-stranded cDNA using M-MLV (Invitrogen) with Illumina/Solexa’s RT-primers followed by cDNA amplification for 20 cycles by PCR, using Illumina/Solexa’s small RNA primers set. PCR products were purified on a 12% TBE polyacrylamide gel and the 80-120 base pair fraction was excised, eluted and precipitated. The purified PCR products were diluted to 10 nM and sequenced on the Illumina/Solexa G1 sequencer.

value: cultured fibroblasts

tag: coriell id