title: Reference Epigenome: ChIP-Seq Analysis of H3K36me3 in hESC H1 (hESC-01) Cells; renlab.H3K36me3.hESC-01.01

description:
sample_term_id: EFO_0003042
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Library name: LL160
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.1607
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.1595

****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM466737_UCSD.H1.H3K36me3.UCSD_30KBHAAXX_5.bam
ANALYSIS ALIAS: UCSD.H3K36me3.Level1.2.1
ANALYSIS TITLE: Mapping of H1 H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq for H3K36me3 in the H1 cell line 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.1784
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
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: GSM466737_UCSD.H1.H3K36me3.UCSD_30PFKAAXX_5.bam
ANALYSIS ALIAS: UCSD.H3K36me3.Level1.2.2
ANALYSIS TITLE: Mapping of H1 H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq for H3K36me3 in the H1 cell line 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.1786
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
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: GSM466737_UCSD.H1.H3K36me3.UCSD_30RKDAAXX_6.bam
ANALYSIS ALIAS: UCSD.H3K36me3.Level1.2.3
ANALYSIS TITLE: Mapping of H1 H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq for H3K36me3 in the H1 cell line 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.1788
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
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: GSM466737_UCSD.H1.H3K36me3.UCSD_42B3BAAXX_6.bam
ANALYSIS ALIAS: UCSD.H3K36me3.Level1.2.4
ANALYSIS TITLE: Mapping of H1 H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq for H3K36me3 in the H1 cell line 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.1790
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
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: GSM466737_UCSD.H1.H3K36me3.UCSD_313BFAAXX_6.bam
ANALYSIS ALIAS: UCSD.H3K36me3.Level1.2.5
ANALYSIS TITLE: Mapping of H1 H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq for H3K36me3 in the H1 cell line 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.1792
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
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: GSM466737_UCSD.H1.H3K36me3.wig
ANALYSIS ALIAS: UCSD.H3K36me3.Level2.2.3
ANALYSIS TITLE: Raw Signal Density Graphs of H1 H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq read mappings for H3K36me3 in the H1 cell line 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.1789
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
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: GSM466737_UCSD.H1.H3K36me3.LL160.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K36me3.hESC-01.01-renlab.H3K36me3.hESC-01.02.hg19.level.1
ANALYSIS TITLE: Mapping of H1 Cell Line Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K36me3 ChIP-Seq on the H1 Cell Line, Library LL160 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.4412
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED: 54
FINDPEAKS_SCORE: 0.4029
FINDPEAKS_PERCENTILE: 80
HOTSPOT_SCORE: 0.4284
HOTSPOT_PERCENTILE: 91
IROC_SCORE: 0.9768
IROC_PERCENTILE: 67
POISSON_SCORE: 0.6274
POISSON_PERCENTILE: 78

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

ANALYSIS FILE NAME: GSM466737_UCSD.H1.H3K36me3.LL160.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K36me3.hESC-01.01-renlab.H3K36me3.hESC-01.02.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Cell Line Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K36me3 ChIP-Seq read mappings from the H1 Cell Line, Library LL160 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.4550
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: H1 H3K36me3 60
BROWSER_TRACK_DESCRIPTION: UCSD H1 Cell Line Histone H3K36me3 Library LL160 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED: 54
FINDPEAKS_SCORE: 0.4029
FINDPEAKS_PERCENTILE: 80
HOTSPOT_SCORE: 0.4284
HOTSPOT_PERCENTILE: 91
IROC_SCORE: 0.9768
IROC_PERCENTILE: 67
POISSON_SCORE: 0.6274
POISSON_PERCENTILE: 78

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

source_name: hESC-01; renlab.H3K36me3.hESC-01.01

value: James Thompson Laboratory

value: Cell Line

value: Embryonic Stem Cell

value: Between 25 and 45

value: mTeSER

value: Male

value: Histone H3K36me3


status: Public on Jan 07 2010

type: SRA

city: San Francisco

first: UCSF-UBC

last: CENTER

state: CA

address: UCSF-UBC

country: USA

institute: UCSF-UBC

description:
design description: MRE-Seq analysis of H1 embryonic stem cell line (HS1153) using Illumina Genome Analyzer IIx
library name: HS1153
EXPERIMENT_TYPE: DNA Methylation
MRE_PROTOCOL: Refer to document 'Triple-MRE-seq library construction protocol v5' from the Costello Lab at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
MRE_PROTOCOL_CHROMATIN_AMOUNT: 3 ug
MRE_PROTOCOL_RESTRICTION_ENZYME: HpaII, Hin6I, AciI
MRE_PROTOCOL_SIZE_FRACTION: 150-400 bp
****************
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: GSM450236_UCSF-UBC.mre-seq.Run101596Lane3.bam
ANALYSIS ALIAS: UCSF-UBC.H1.MRE-Seq.Level1.5
ANALYSIS TITLE: Mapping of H1 MRE-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by MRE-Seq for DNA methylation assessment in the H1 cell line 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.1824
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: MRE-Seq
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: GSM450236_UCSF-UBC.mre-seq.Run104065Lane1.bam
ANALYSIS ALIAS: UCSF-UBC.H1.MRE-Seq.Level1.6
ANALYSIS TITLE: Mapping of H1 MRE-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by MRE-Seq for DNA methylation assessment in the H1 cell line 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.1826
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: MRE-Seq
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: GSM450236_UCSF-UBC.mre-seq.Run104066Lane2.bam
ANALYSIS ALIAS: UCSF-UBC.H1.MRE-Seq.Level1.7
ANALYSIS TITLE: Mapping of H1 MRE-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by MRE-Seq for DNA methylation assessment in the H1 cell line 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.1828
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: MRE-Seq
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: GSM450236_UCSF-UBC.mre-seq.Run104205Lane1.bam
ANALYSIS ALIAS: UCSF-UBC.H1.MRE-Seq.Level1.8
ANALYSIS TITLE: Mapping of H1 MRE-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by MRE-Seq for DNA methylation assessment in the H1 cell line 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.1830
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: MRE-Seq
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: GSM450236_UCSF-UBC.H1.mre-seq.wig
ANALYSIS ALIAS: UCSF-UBC.H1.MRE-Seq.Level2.combined.3
ANALYSIS TITLE: Raw Signal Density Graphs of H1 MRE-Seq Data
ANALYSIS DESCRIPTION: Illumina MRE-Seq read mappings for DNA methylation assessment in the H1 cell line 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.1861
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: MRE-Seq
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None

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

ANALYSIS FILE NAME: GSM450236_UCSF-UBC.H1.MRE-Seq.HS1153.bed
ANALYSIS ALIAS: HS1153-1_42F2TAAXX-HS1153-1_313MYAAXX-HS1153-1_42EMFAAXX.hg19.level.1
ANALYSIS TITLE: Mapping of H1 Cell Line MRE-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by MRE-Seq on the H1 Cell Line, Library HS1153 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.4214
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: MRE-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: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_MRE-SEQ_EXPERIMENTS_SCORED: 28
PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS: 89.07
PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS_PERCENTILE: 7

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

ANALYSIS FILE NAME: GSM450236_UCSF-UBC.H1.MRE-Seq.HS1153.wig
ANALYSIS ALIAS: HS1153-1_42F2TAAXX-HS1153-1_313MYAAXX-HS1153-1_42EMFAAXX.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Cell Line MRE-Seq Data
ANALYSIS DESCRIPTION: Illumina MRE-Seq read mappings from the H1 Cell Line, Library HS1153 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.4186
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: MRE-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: H1 MRE 53
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-UCD H1 Cell Line MRE-Seq Library HS1153 EA Release 2

QUALITY SCORES:
NUMBER_OF_MRE-SEQ_EXPERIMENTS_SCORED: 28
PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS: 89.07
PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS_PERCENTILE: 7

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

molecule: genomic DNA

organism: Homo sapiens

extract_protocol: library construction protocol: Refer to document 'Triple-MRE-seq library construction protocol v5' from the Costello Lab at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)

tag: submitted sample id

value: cell line

tag: line

tag: Sex

value: male

tag: body site

value: Embryo ICM

tag: histological type

value: Embryonic stem cell

tag: is tumor

value: No


title: IgG bound post IL21 dup

status: Public on Jan 08 2010

city: Duarte

first: Dustin

middle: E

last: Schones

address: 1500 E Duarte Rd.

institute: City of Hope

description: Chromatin IP against IgG

data_processing: To align sequence tags, analyze their clustering, identify binding motifs, and display results, new code was developed in C language as extensions of the AceView project (Thierry-Mieg and Thierry-Mieg, 2006). Each Solexa 25-mer tag was mapped on the mouse reference genome (version 37), allowing up to 2 mismatches (single base insertion, deletion, or substitution), and retained only if it had a single best position genome-wide. Each tag was shifted downstream by half the effective length of the sonicated sequenced fragments, measured as the maximum of the genome-wide correlation function between hits to the sense and antisense strands of the chromosomes, and represented by an elementary Gaussian with an area of 1 and s of 100 bp, which dampens the sampling fluctuations and introduces a controlled level of fuzziness and “smoothness”. Summing these elementary Gaussians yields a smoothed tag density. Regions where the density locally exceeds a given threshold are analyzed. The number of tags was measured after subtracting the local tags from the matched IgG experiment. If the tag number exceeded a second threshold, it was scored as a peak. Regions with an IgG peak were considered non-specific and eliminated. The peak height indicates the strength of protein binding. The position of the maximum of the peak (i.e., the maximum of the probability of binding the protein) is expected to coincide with the binding motif. The width covered by the peak (typically 200-600 bp) is the region protected by the protein or protein complex. Often, in large peaks, one can distinguish sub-peaks that are expected to correspond to the binding of multiple proteins. When multiple proteins bind to overlapping sequences, their peaks are clustered to generate a broader composite binding site.

organism: Mus musculus

source_name: murine CD4+ T

growth_protocol: CD4+ T cells were isolated from mouse spleen using anti-CD4-magnetic beads (Miltenyi). For pre-activation of CD4+ T cells, cells were stimulated with 3 μg/ml plate-bound anti-CD3 and 1 μg/ml soluble anti-CD28 for 3 days, and rested for 24 h in fresh RPMI medium.

extract_protocol: Chromatin from approximately 2x10^7 cells were used for each ChIP experiment. End repair for ChIP fragments was performed using PNK and Klenow enzyme, followed by treatment with Taq polymerase.  Sequencing adaptors were ligated to the repaired ends and ChIP DNA was amplified using adaptor primers for 17 cycles.  Fragments around 200bp were isolated from agarose gel and purified DNA was used directly for cluster generation and sequencing following the manufacturer protocols.

treatment_protocol: CD4+ T cells were treated with IL-21 (100ng/ml) for 1 hour.

tag: genotype/variation

value: wildtype

tag: antibody

value: IgG

tag: stimulation

value: post IL21


title: Chromatin accessibility assay of IMR90 Cell Line; DS11759

status: Public on Jan 06 2010

city: Seattle

first: Northwest

last: REMC

state: WA

institute: University of Washington

description:
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS11759
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.1632
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.1633
****************
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: GSM468792_IMR90-DS11759.UWStam_090902_SOLEXA-1GA-1_0021_FC42KVW_2.bam
ANALYSIS ALIAS: UW.IMR90.ChromatinAccessibility.Level1.1
ANALYSIS TITLE: Mapping of IMR90 Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on the IMR90 cell line 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.1844
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: GSM468792_IMR90-DS11759.UWStam_090921_SOLEXA-1GA-1_0028_FC42YD0_4.bam
ANALYSIS ALIAS: UW.IMR90.ChromatinAccessibility.Level1.2
ANALYSIS TITLE: Mapping of IMR90 Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on the IMR90 cell line 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.1846
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: GSM468792_UW.IMR90.rep1.ChromatinAccessibility.IMR90-DS11759.wig
ANALYSIS ALIAS: UW.IMR90.ChromatinAccessibility.Level2.combined.1
ANALYSIS TITLE: Raw Signal Density Graphs of IMR90 Chromatin Accessibility Replicate 1 Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from the IMR90 cell line 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.1857
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: GSM468792_UW.IMR90.ChromatinAccessibility.DS11759.bed
ANALYSIS ALIAS: DS11759.hg19.level.1
ANALYSIS TITLE: Mapping of IMR90 Cell Line Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on the IMR90 Cell Line, Library DS11759 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.4126
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: 0.3846
FINDPEAKS_PERCENTILE: 5
HOTSPOT_SCORE: 0.2914
HOTSPOT_PERCENTILE: 5
IROC_SCORE: 0.9966
IROC_PERCENTILE: 37
POISSON_SCORE: 0.3873
POISSON_PERCENTILE: 10

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

ANALYSIS FILE NAME: GSM468792_UW.IMR90.ChromatinAccessibility.DS11759.wig
ANALYSIS ALIAS: DS11759.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of IMR90 Cell Line Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from the IMR90 Cell Line, Library DS11759 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.4086
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: IMR90 DNase 59 59
BROWSER_TRACK_DESCRIPTION: UW IMR90 Cell Line DNase Hypersensitivity Library DS11759 EA Release 2

QUALITY SCORES:
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED: 40
FINDPEAKS_SCORE: 0.3846
FINDPEAKS_PERCENTILE: 5
HOTSPOT_SCORE: 0.2914
HOTSPOT_PERCENTILE: 5
IROC_SCORE: 0.9966
IROC_PERCENTILE: 37
POISSON_SCORE: 0.3873
POISSON_PERCENTILE: 10

source_name: IMR90 Cell Line; DS11759

extract_protocol: Library construction protocol: Single read - Illumina

tag: molecule

value: genomic DNA

tag: disease

value: ATCC

tag: lineage

value: Fetal lung fibroblast

tag: passage

tag: medium

value: Eagle's Minimum Essential Medium, Catalog No. 30-2003.

value: Female

tag: batch

value: Chromatin Accessibility

value: Qiagen minElut

value: Stamlab DNase Protocol


title: CMV delta2b in Arabidopsis thaliana (col)

status: Public on Jan 20 2010

city: Riverside

first: Qingfa

last: Wu

address: 900 University Ave

institute: UC Riverside

description:
total small RNAs in systemically infected leaves of A. thaliana
barcode: ATC

library_source: viral RNA

data_processing: All sequences containing perfect match 5' barcode (ATC/CGT/TAC) and at least 6 sucessive perfect-matched nucleotides of  the 3' linker ( CTGTAGGCACCATCAAT / CACTCGGGCACCAAGGA) were kept for later analysis. The barcode and linker sequences were computationally removed by in-house perl script. All trimmed sequences in length of 17~30nt were aligned with CMV genome and the perfect matched reads were used for all further analysis.

molecule: total RNA

organism:
Arabidopsis thaliana
Cucumber mosaic virus (strain FNY)

source_name: leaves of wt Arabidopsis thaliana infected with CMVf-Δ2b

extract_protocol: Small RNAs of 18- to 28-nt extracted by Trizol from the systemically infected leaves 14 days after inoculation with CMVf-Δ2b were purified from 15% denatured polyacrylamide gel. Purified small RNAs were directly ligated to the 3′-linker used for miRNA cloning (Integrated DNA Technology) by T4 RNA ligase 2Tr (New England Biolabs). The ligation products were purified and ligated to the 5′ Solexa linker (GUU CAG AGU UCU ACA GUC CGA CGA UC) by T4 RNA ligase I (New England Biolabs). The final ligation products were reverse transcribed using a primer targeting the 3′-linker (CTGTAGGCACCATCAAT OR CACTCGGGCACCAAGGA ) and the cDNA pool was amplified by PCR and sent for sequencing by the Solexa technology (Illumina). Duplicate libraries were constructed from two independent RNA samples from WT, rdr1, and rdr1 rdr2 rdr6 plants and sequenced by the Solexa platform in Illumina, Inc, and the University of California–Riverside Core Facility, respectively.

tag: a.thaliana genotype

value: wild type (col)

tag: a.thaliana tissue

value: leaves

tag: cmv genotype/variation

tag: cmv strain

value: FNY

tag: collected time

value: 14 days after inoculation


title: DsigB_replicate2

status: Public on Jan 05 2010

city: Ithaca

first: Lalit

last: Ponnala

state: NY

address: 616 Rhodes Hall

institute: Cornell University

description: 10403S lacking sigB

library_source: transcriptomic

data_processing: Processed data files (eland) contain alignment of short-reads against the 10403S supercontigs.

organism: Listeria monocytogenes

source_name: 10403S isogenic mutant

growth_protocol: Bacteria were grown in 5 ml Brain Heart Infusion (BHI) broth (BD Difco, Franklin Lakes, NJ) at 37ºC with shaking (230 rpm) for 15 h, followed by transfer of a 1% inoculum to 5 ml pre-warmed BHI.  After growth to OD600 ~ 0.4, a 1% inoculum was transferred to a 300 ml nephelo flask (Bellco, Vineland, NJ) containing 50 ml pre-warmed BHI.  This culture was incubated at 37ºC with shaking until cells reached stationary phase (defined as growth to OD600 = 1.0, followed by incubation for an additional 3 h).  Two independent growth replicates and RNA isolations were performed for each strain.

extract_protocol: Bacterial cells were treated with lysozyme followed by 6 sonication cycles at 18W on ice for 30s.  Total RNA was isolated and purified using the RNeasy Midi kit (Qiagen) according to the manufacturer’s protocol; RNA molecules <200 nt in length are not recovered well with this procedure, according to the manufacturer.  RNA was eluted from the column using RNase-free water.  Total RNA was incubated with RQ1 DNase (Promega, Madison, WI) in the presence of RNasin (Promega) to remove remaining DNA.  Subsequently, RNA was purified using two phenol-chloroform extractions and one chloroform extraction, followed by RNA precipitation and resuspension of the RNA in RNAse free TE (10 mM Tris, 1 mM EDTA; pH 8.0; Ambion, Austin, TX).  UV spectrophotometry (Nanodrop, Wilmington, DE) was used to quantify and assess purity of the RNA.

treatment_protocol: RNAProtect bacterial reagent (Qiagen, Valencia, CA) was added according to the manufacturer’s instructions to the cultures grown to stationary phase; treated cells were stored at -80ºC (for no longer than 24 h) until RNA isolation was performed.

tag: strain

value: 10403S lacking sigB


title: Reference Epigenome: ChIP-Seq Analysis of H3K4me1 in hESC H1 (hESC-01) Cells; renlab.H3K4me1.hESC-01.01

city: La Jolla

first: UCSD AND

last: SALK

address: Health Sciences Drive

institute: University of California, San Diego

description:
sample_term_id: EFO_0003042
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Library name: LL311
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.1614
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.1595

****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM466739_UCSD.H1.H3K4me1.UCSD_2008_09_25_2.bam
ANALYSIS ALIAS: UCSD.H3K4me1.Level1.2.2
ANALYSIS TITLE: Mapping of H1 H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq for H3K4me1 in the H1 cell line 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.1772
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
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: GSM466739_UCSD.H1.H3K4me1.UCSD_312C6AAXX_4.bam
ANALYSIS ALIAS: UCSD.H3K4me1.Level1.2.1
ANALYSIS TITLE: Mapping of H1 H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq for H3K4me1 in the H1 cell line 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.1770
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
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: GSM466739_UCSD.H1.H3K4me1.UCSD_3021CAAXX_7.bam
ANALYSIS ALIAS: UCSD.H3K4me1.Level1.2.3
ANALYSIS TITLE: Mapping of H1 H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq for H3K4me1 in the H1 cell line 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.1774
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
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: GSM466739_UCSD.H1.H3K4me1.wig
ANALYSIS ALIAS: UCSD.H3K4me1.Level2.2.2
ANALYSIS TITLE: Raw Signal Density Graphs of H1 H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq read mappings for H3K4me1 in the H1 cell line 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.1773
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
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: GSM466739_UCSD.H1.H3K4me1.LL311.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4me1.hESC-01.01-renlab.H3K4me1.hESC-01.02.hg19.level.1
ANALYSIS TITLE: Mapping of H1 Cell Line Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me1 ChIP-Seq on the H1 Cell Line, Library LL311 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.4395
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED: 43
FINDPEAKS_SCORE: 0.0663
FINDPEAKS_PERCENTILE: 9
HOTSPOT_SCORE: 0.34
HOTSPOT_PERCENTILE: 33
IROC_SCORE: 0.0
IROC_PERCENTILE: NA
POISSON_SCORE: 0.5253
POISSON_PERCENTILE: 42

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

ANALYSIS FILE NAME: GSM466739_UCSD.H1.H3K4me1.LL311.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4me1.hESC-01.01-renlab.H3K4me1.hESC-01.02.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Cell Line Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me1 ChIP-Seq read mappings from the H1 Cell Line, Library LL311 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.4545
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: H1 H3K4me1 11
BROWSER_TRACK_DESCRIPTION: UCSD H1 Cell Line Histone H3K4me1 Library LL311 EA Release 2

QUALITY SCORES:
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED: 43
FINDPEAKS_SCORE: 0.0663
FINDPEAKS_PERCENTILE: 9
HOTSPOT_SCORE: 0.34
HOTSPOT_PERCENTILE: 33
IROC_SCORE: 0.0
IROC_PERCENTILE: NA
POISSON_SCORE: 0.5253
POISSON_PERCENTILE: 42

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

source_name: hESC-01; renlab.H3K4me1.hESC-01.01

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

value: James Thompson Laboratory

value: Cell Line

tag: line

value: Embryonic Stem Cell

value: Between 25 and 45

value: mTeSER

tag: Sex

value: Male

value: Histone H3K4me1

value: Branson Tip Sonicator

value: 500 micrograms

value: magnetic anti-rabbit

value: 5 micrograms

value: Upstate


title: 10403S_replicate2

description: 10403S stationary phase

source_name: laboratory strain

value: 10403S wild type


title: 10403S_replicate1

description: 10403S stationary phase


description:
design description: miRNA-Seq analysis of H1 embryonic stem cell line (HS1295) using Illumina Genome Analyzer IIx
library name: HS1295
EXPERIMENT_TYPE: smRNA-Seq
EXTRACTION_PROTOCOL: Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instructions.
LIBRARY_GENERATION_PCR_POLYMERASE_TYPE: Phusion DNA Polymerase (Hot Start), 2U/ul (from NEB)
LIBRARY_GENERATION_PCR_THERMOCYCLING_PROGRAM: step1: 98C for 30sec, step2: 98C for 10sec, step3: 60C for 30sec, step4: 72C for 15sec.  Repeat step2-4 for 15 cycles, 72C for 5min.
LIBRARY_GENERATION_PCR_NUMBER_CYCLES: 15
LIBRARY_GENERATION_PCR_F_PRIMER_SEQUENCE: 5' AATGATACGGCGACCACCGACAGNNNNNNGTTCAGAGTTCTACAGTCCGA 3'
LIBRARY_GENERATION_PCR_R_PRIMER_SEQUENCE: 5' CAAGCAGAAGACGGCATACGAGAT 3'
LIBRARY_GENERATION_PCR_PRIMER_CONC: 25 uM
LIBRARY_GENERATION_PCR_PRODUCT_ISOLATION_PROTOCOL: 28uL of PCR products containing unique index sequences are pooled together and the 115bp miRNA containing fraction is isolated for each pool either manually:  12% PAGE gel 200V 6hours followed by gel elution, or robotically using Baraccuda size selection robot.  Fractions are Et0H preciptated, QCed on Agilent, and submitted for indexing single end (ISE) Illumina sequencing.
EXTRACTION_PROTOCOL_SMRNA_ENRICHMENT: Flowthrough of polyA+ MultiMACS 96 Separation Unit
SMRNA_PREPARATION_INITIAL_SMRNA_QLTY: RIN 9.7
SMRNA_PREPARATION_INITIAL_SMRNA_QNTY: 10000 ng
RNA_PREPARATION_5'_RNA_ADAPTER_SEQUENCE: 5' GTTCAGAGTTCTACAGTCCGACGATCTGGTCAA 3'
RNA_PREPARATION_3'_RNA_ADAPTER_SEQUENCE: 5' ATCTCGTATGCCGTCTTCTGCTTGT 3'
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PRIMER_SEQUENCE: 5' CAAGCAGAAGACGGCATACGAGAT 3'
RNA_PREPARATION_3'_RNA_ADAPTER_LIGATION_PROTOCOL: 1ug of total RNA (RN => 7.0) in a 4uL volume and 2uL of 3' Adenylated Adapter was heat denatured at 70C for 2min then snap chilled on ice for 1min.  Then 1uL of 10X T4 RNL2 truncated buffer, 0.8uL 100mM MgCl2, 0.2uL DEPC water, 0.5uL Rnase Out, and 1.5uL T4 RNA Ligase 2 trancated was added.  Ligation incubated at 22C in a Tetrad thermocycler for 60min.
RNA_PREPARATION_5'_RNA_ADAPTER_LIGATION_PROTOCOL: 5' RNA adapter was heat denatured at 70C for 2min then snap chilled on ice.  2uL of denatured 5' RNA Adapter was added to the 3' DNA Adapter Ligation reaction product from previous step and mixed.   Then 1uL of 10mM ATP and 1uL of Ambion T4 RNA Ligase were added and ligation reaction was incubated at 37C in a Tetrad thermocycler for 60min.
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PROTOCOL: To the 14uL of double adaptered miRNA product from previous step 2ul of RT-Primer was added and the mixture was heat denatured at 65C for 10 mins then quenched on ice.  The following reagents were added immediately to the sample (6ul of 5X First Strand Buffer, 2ul of 10mM dNTPs , 3ul of 100mM DTT, 1ul of RNaseOUT, and 2uL of SuperScript II RT.  Reaction was heated at 44C in a Thetrad thermocycler for 60 minutes.
LIBRARY_GENERATION_PCR_TEMPLATE: 15ul of the first strand cDNA product was used in the PCR
****************
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: GSM450239_UCSF-UBC.H1.smRNA.Run104536Lane5.bam
ANALYSIS ALIAS: UCSF-UBC.smRNA-seq.Level1.1
ANALYSIS TITLE: Mapping of H1 smRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by smRNA-Seq in the H1 cell line 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.1852
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: smRNA-Seq
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 10
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 10 positions it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None

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

ANALYSIS FILE NAME: GSM450239_UCSF-UBC.H1.smRNA.Run104536Lane5.wig
ANALYSIS ALIAS: UCSF-UBC.smRNA-seq.Level2.1
ANALYSIS TITLE: Raw Signal Density Graphs of H1 smRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina smRNA-Seq read mappings from the H1 cell line 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.1854
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: smRNA-Seq
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None

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

ANALYSIS FILE NAME: GSM450239_UCSF-UBC.H1.smRNA.Run104536Lane5.tag.tab
ANALYSIS ALIAS: UCSF-UBC.smRNA-seq.Level1.tag.1
ANALYSIS TITLE: Sequence Tag Counts of H1 smRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by smRNA-Seq in the H1 cell line had the sequence trimmed for adapters and the count of unique sequences calculated.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.1853
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: smRNA-Seq
SOFTWARE: In house scripts
SOFTWARE_VERSION: NA

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

ANALYSIS FILE NAME: GSM450239_UCSF-UBC.H1.smRNA-Seq.H1EScd1_batch2_vial1.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: HS1295-1_42ERCAAXX.hg19.level.1
ANALYSIS TITLE: Mapping of H1 Cell Line smRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by smRNA-Seq on the H1 Cell Line, Library H1EScd1 batch2 vial1 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.5204
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: smRNA-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: 100
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 100 positions it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 2
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA: 24.4
PERCENT_READS_MAPPING_TO_REPEATMASKER_RNA_REPEATS: 34.9

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

ANALYSIS FILE NAME: GSM450239_UCSF-UBC.H1.smRNA-Seq.H1EScd1_batch2_vial1.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: HS1295-1_42ERCAAXX.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Cell Line smRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina smRNA-Seq read mappings from the H1 Cell Line, Library H1EScd1 batch2 vial1 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.5206
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: smRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: H1 smRNA l1
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-UCD H1 Cell Line smRNA-Seq Library H1EScd1 batch2 vial1 EA Release 2
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA: 24.4
PERCENT_READS_MAPPING_TO_REPEATMASKER_RNA_REPEATS: 34.9

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

ANALYSIS FILE NAME: GSM450239_UCSF-UBC.H1.smRNA-Seq.H1EScd1_batch2_vial1.tag.tab
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: HS1295-1_42ERCAAXX.hg19.level.2.tag
ANALYSIS TITLE: Sequence Tag Counts of H1 Cell Line smRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by smRNA-Seq on the H1 Cell Line, Library H1EScd1 batch2 vial1 had the sequence trimmed for adapters and the count of unique sequences calculated.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.5208
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: smRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
RELEASE_NUMBER: Human Epigenome Atlas 2
PERCENT_READS_MAPPING_TO_miRBase_v16_miRNA: 24.4
PERCENT_READS_MAPPING_TO_REPEATMASKER_RNA_REPEATS: 34.9

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

extract_protocol: library construction protocol: Refer to document 'miRNA3 - Plate Format miRNA Library Construction' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)

tag: submitted sample id

value: cell line

value: male

tag: body site

value: Embryo ICM

tag: histological type

value: Embryonic stem cell

tag: is tumor

value: No


title: Chromatin accessibility assay of IMR90 Cell Line; DS11764

description:
sample_term_id: EFO_0001196
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS11764
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.1632
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.1642
****************
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: GSM468801_IMR90-DS11764.UWStam_090902_SOLEXA-1GA-1_0021_FC42KVW_3.bam
ANALYSIS ALIAS: UW.IMR90.ChromatinAccessibility.Level1.3
ANALYSIS TITLE: Mapping of IMR90 Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on the IMR90 cell line 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.1848
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: GSM468801_IMR90-DS11764.UWStam_090921_SOLEXA-1GA-1_0028_FC42YD0_5.bam
ANALYSIS ALIAS: UW.IMR90.ChromatinAccessibility.Level1.4
ANALYSIS TITLE: Mapping of IMR90 Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on the IMR90 cell line 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.1850
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: GSM468801_UW.IMR90.rep2.ChromatinAccessibility.IMR90-DS11764.wig
ANALYSIS ALIAS: UW.IMR90.ChromatinAccessibility.Level2.combined.2
ANALYSIS TITLE: Raw Signal Density Graphs of IMR90 Chromatin Accessibility Replicate 2 Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from the IMR90 cell line 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.1858
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: GSM468801_UW.IMR90.ChromatinAccessibility.DS11764.bed
ANALYSIS ALIAS: DS11764.hg19.level.1
ANALYSIS TITLE: Mapping of IMR90 Cell Line Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on the IMR90 Cell Line, Library DS11764 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.4127
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: 0.3825
FINDPEAKS_PERCENTILE: 2
HOTSPOT_SCORE: 0.2892
HOTSPOT_PERCENTILE: 2
IROC_SCORE: 0.9961
IROC_PERCENTILE: 32
POISSON_SCORE: 0.3911
POISSON_PERCENTILE: 15

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

ANALYSIS FILE NAME: GSM468801_UW.IMR90.ChromatinAccessibility.DS11764.wig
ANALYSIS ALIAS: DS11764.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of IMR90 Cell Line Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from the IMR90 Cell Line, Library DS11764 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.4087
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: IMR90 DNase 64 64
BROWSER_TRACK_DESCRIPTION: UW IMR90 Cell Line DNase Hypersensitivity Library DS11764 EA Release 2

QUALITY SCORES:
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED: 40
FINDPEAKS_SCORE: 0.3825
FINDPEAKS_PERCENTILE: 2
HOTSPOT_SCORE: 0.2892
HOTSPOT_PERCENTILE: 2
IROC_SCORE: 0.9961
IROC_PERCENTILE: 32
POISSON_SCORE: 0.3911
POISSON_PERCENTILE: 15

source_name: IMR90 Cell Line; DS11764

tag: molecule

value: genomic DNA

tag: disease

value: ATCC

value: Cell Line

value: Fetal lung fibroblast

value: Eagle's Minimum Essential Medium, Catalog No. 30-2003.

value: Female

value: Chromatin Accessibility

value: Qiagen minElut

value: Stamlab DNase Protocol


description:
design description: MRE-Seq analysis of H1 embryonic stem cell line (HS1052) using Illumina Genome Analyzer II
library name: HS1052
EXPERIMENT_TYPE: DNA Methylation
MRE_PROTOCOL: Refer to document 'Triple-MRE-seq library construction protocol v5' from the Costello Lab at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
MRE_PROTOCOL_CHROMATIN_AMOUNT: 6 ug
MRE_PROTOCOL_RESTRICTION_ENZYME: HpaII, Hin6I, AciI
MRE_PROTOCOL_SIZE_FRACTION: 150-400 bp
****************
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: GSM428286_UCSF-UBC.mre-seq.Run99923Lane5.bam
ANALYSIS ALIAS: UCSF-UBC.H1.MRE-Seq.Level1.1
ANALYSIS TITLE: Mapping of H1 MRE-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by MRE-Seq for DNA methylation assessment in the H1 cell line 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.1816
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: MRE-Seq
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: GSM428286_UCSF-UBC.mre-seq.Run101316Lane1.bam
ANALYSIS ALIAS: UCSF-UBC.H1.MRE-Seq.Level1.2
ANALYSIS TITLE: Mapping of H1 MRE-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by MRE-Seq for DNA methylation assessment in the H1 cell line 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.1818
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: MRE-Seq
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: GSM428286_UCSF-UBC.mre-seq.Run101317Lane2.bam
ANALYSIS ALIAS: UCSF-UBC.H1.MRE-Seq.Level1.3
ANALYSIS TITLE: Mapping of H1 MRE-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by MRE-Seq for DNA methylation assessment in the H1 cell line 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.1820
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: MRE-Seq
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: GSM428286_UCSF-UBC.mre-seq.Run101318Lane3.bam
ANALYSIS ALIAS: UCSF-UBC.H1.MRE-Seq.Level1.4
ANALYSIS TITLE: Mapping of H1 MRE-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by MRE-Seq for DNA methylation assessment in the H1 cell line 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.1822
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: MRE-Seq
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: GSM428286_UCSF-UBC.H1.mre-seq.wig
ANALYSIS ALIAS: UCSF-UBC.H1.MRE-Seq.Level2.combined.1
ANALYSIS TITLE: Raw Signal Density Graphs of H1 MRE-Seq Data
ANALYSIS DESCRIPTION: Illumina MRE-Seq read mappings for DNA methylation assessment in the H1 cell line 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.1859
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: MRE-Seq
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None

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

ANALYSIS FILE NAME: GSM428286_UCSF-UBC.H1.MRE-Seq.HS1052.bed
ANALYSIS ALIAS: HS1052-1_313MWAAXX-HS1052-1_30WLJAAXX.hg19.level.1
ANALYSIS TITLE: Mapping of H1 Cell Line MRE-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by MRE-Seq on the H1 Cell Line, Library HS1052 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.4210
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: MRE-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: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_MRE-SEQ_EXPERIMENTS_SCORED: 28
PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS: 82.85
PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS_PERCENTILE: 3

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

ANALYSIS FILE NAME: GSM428286_UCSF-UBC.H1.MRE-Seq.HS1052.wig
ANALYSIS ALIAS: HS1052-1_313MWAAXX-HS1052-1_30WLJAAXX.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Cell Line MRE-Seq Data
ANALYSIS DESCRIPTION: Illumina MRE-Seq read mappings from the H1 Cell Line, Library HS1052 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.4182
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: MRE-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: H1 MRE 52
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-UCD H1 Cell Line MRE-Seq Library HS1052 EA Release 2

QUALITY SCORES:
NUMBER_OF_MRE-SEQ_EXPERIMENTS_SCORED: 28
PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS: 82.85
PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS_PERCENTILE: 3

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


title: DsigB_replicate1

description: 10403S lacking sigB

value: 10403S lacking sigB


title: Liver

status: Public on Jan 01 2010

city: Cambridge

first: Pouya

last: Kheradpour

state: MA

address: 32 Vassar St 32-G822

institute: Massachusetts Institute of Technology

data_processing: read counts: number of reads for each unique sequence computed after removing linker

organism: Sarcophilus harrisii

source_name: Liver

growth_protocol: Tissues were harvested from wild Tasmanian devils

extract_protocol: RNA was extracted using Trizol. Total RNA was size fractionated on a PAGE gel, and the 18-24 nt fraction selected. Adaptors were ligated, and the libraries were reverse transcribed and PCR amplified (22 cycles) prior to sequencing.

treatment_protocol: Tissues were stored in RNAlater prior to RNA extraction

tag: animal

tag: tissue

value: Liver


title: Jarid2_ChIPSeq

city: boston

first: Manching

last: Ku

address: 185 Cambridge St. CPZN-8400

institute: MGH

description: Chromatin IP against Jarid2

data_processing:
For BED files: reads (of 36bps) produced by the Illumina platform were aligned by MAQ. Sequences with more than a single best matche in the reference genome were discarded. We also created a map of ?unalignable? genomic positions to which no unique 36 base read could be uniquely aligned due inherent sequence redundancy for consideration in downstream processing.
For WIG files: The short sequence reads correspond to the end of the DNA fragments in the library. Since the average size of the ChIP fragments is in the range of 200 bp, we extended the aligned reads in silico to a total length of 200 bases. The entire genome was divided to non-overlapping windows of 25bps. The signal in a given window was calculated as the number of extended reads that it fall within that window.

source_name: Embryonic Stem cells

growth_protocol: ES cell was cultured in 15% FCS/DMEM, supplemented with Pen/Strep, Glutamax, MEM non-essential amino acids, ESGRO and 2-mercaptoethanol. ES cells were passaged off feeder cells for ~2-3 passages before harvesting for ChIP experiments.

extract_protocol: Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.  Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired and 5' phosphorylated using END-It DNA End Repair Kit (Epicenter). Then, DNA was treated with Klenow fragment (3' to 5', exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp to 70bp (insert plus adaptor and PCR primer sequences) were isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

value: 129SvJae x C57BL/6

tag: cell type

value: embryonic stem cells

tag: passages

tag: chip antibody


title: DFTD2,met

source_name: Facial tumor (mammary metastasis)

value: Facial tumor (mammary metastasis)


title: Pancreas

source_name: Pancreas

value: Pancreas


title: MTF2_ChIPSeq

description: Chromatin IP against MTF2


title: Kidney

source_name: Kidney

value: Kidney


title: Heart

source_name: Heart

value: Heart


title: Lymph node

source_name: Lymph node

value: Lymph node


title: DFTD20

source_name: Facial tumor

value: Facial tumor


title: Bone marrow

source_name: Bone marrow

value: Bone marrow


title: Brain

source_name: Brain

value: Brain


title: Spleen

source_name: Spleen

value: Spleen


title: Skin

source_name: Skin

value: Skin


title: DFTD2


title: K562_PolIII_ChIPSeq

status: Public on Dec 31 2009

city: New Haven

first: Flora

last: Vaccarino

state: CT

address: 230 South Frontage Road

department: Child Study Center

institute: Yale University

description: ChIP against Pol III

data_processing: Enriched peak regions corresponding to transcription factor binding sites were identified by first extending all the uniquely mapped tags reads (mapped against hg18) to the averaged sequenced DNA fragment size ~200bps and then accumulated into fragment density signal maps. Peaks in these maps are identified by comparison to a computer simulated null model for each Mb of each chromosome (accounting for the variability in mappability of sequence tags across the human genome. For potential target regions the number of sequenced tags is compared against the normalized number of sequence tags overlapping the region from the matching Input DNA reference sample (GSM325934). Fold enrichment ratios are computed from the ratio of these two sets of counts for each regions as well as p-value using the cumulative distribution function for the binomial distribution. P-value are corrected for multiple hypothesis testing using a Benjamini-Hochberg correction factor and a false discovery rate threshold of 0.05 is imposed. (Rozowsky et al. Nature Biotechnology 27, 66 - 75, 2009)

growth_protocol: K562 cells were grown in RPMI media containing 10% FBS

extract_protocol: Nuclei were isolated from cross-linked (1% formaldehyde for 10 minutes at room temperature) K562 cells. Nuclei were lysed in RIPA buffer and extracted chromatin was sonicated using Branson Sonifier 250. ChIP DNA was prepared using Pol III antibody. Libraries were prepared according to Illumina's protocols using reagents purchased from different vendors. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase (Epicenter). The blunt, phosphorylated ends were treated with Klenow fragment (exo minus) (New England Biolab, NEB) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation (LigaFast, Promega) DNA was PCR amplified (Phusion polymerase, NEB) with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

tag: growth properties

value: Suspension Morphology

tag: lymphoblast antibody

value: RNA Pol III


title: K562_Myc_ChIPSeq

description: ChIP against Myc

extract_protocol: Nuclei were isolated from cross-linked (1% formaldehyde for 10 minutes at room temperature) K562 cells. Nuclei were lysed in RIPA buffer and extracted chromatin was sonicated using Branson Sonifier 250. ChIP DNA was prepared using Myc antibody. Libraries were prepared according to Illumina's protocols using reagents purchased from different vendors. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase (Epicenter). The blunt, phosphorylated ends were treated with Klenow fragment (exo minus) (New England Biolab, NEB) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation (LigaFast, Promega) DNA was PCR amplified (Phusion polymerase, NEB) with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

value: Myc


description:
design description: RNA-Seq analysis of H1 embryonic stem cell line (HS1272) using Illumina Genome Analyzer IIx
library name: HS1272
EXPERIMENT_TYPE: mRNA-Seq
EXTRACTION_PROTOCOL: Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instructions.
LIBRARY_GENERATION_PCR_POLYMERASE_TYPE: Phusion
LIBRARY_GENERATION_PCR_THERMOCYCLING_PROGRAM: 98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold
LIBRARY_GENERATION_PCR_NUMBER_CYCLES: 10
LIBRARY_GENERATION_PCR_F_PRIMER_SEQUENCE: AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT
LIBRARY_GENERATION_PCR_R_PRIMER_SEQUENCE: CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT
LIBRARY_GENERATION_PCR_PRIMER_CONC: 0.5 uM
LIBRARY_GENERATION_PCR_PRODUCT_ISOLATION_PROTOCOL: 8% Novex TBE PAGE gel purification
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PRIMER_SEQUENCE: NNNNNN
RNA_PREPARATION_REVERSE_TRANSCRIPTION_PROTOCOL: Invitrogen Superscript II RT
LIBRARY_GENERATION_PCR_TEMPLATE: cDNA
EXTRACTION_PROTOCOL_MRNA_ENRICHMENT: Purification of polyA+ mRNA using MultiMACS 96 Separation Unit
RNA_PREPARATION_INITIAL_RNA_QLTY: RIN 9.9
RNA_PREPARATION_INITIAL_RNA_QNTY: 20000 ng
LIBRARY_FRAGMENTATION: COVARIS E210
LIBRARY_FRAGMENT_SIZE_RANGE: 270-500 bp
****************
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: GSM484408_UCSF-UBC.H1.mRNA-seq.Run105124Lane7.bam
ANALYSIS ALIAS: UCSF-UBC.H1.mRNA-seq.Level1.7
ANALYSIS TITLE: Mapping of H1 mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by mRNA-Seq in the H1 cell line 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.1892
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: mRNA-Seq
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: GSM484408_UCSF-UBC.H1.mRNA-seq.Run106055Lane2.bam
ANALYSIS ALIAS: UCSF-UBC.H1.mRNA-seq.Level1.1
ANALYSIS TITLE: Mapping of H1 mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by mRNA-Seq in the H1 cell line 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.1893
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: mRNA-Seq
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: GSM484408_UCSF-UBC.H1.mRNA-seq.Run106056Lane3.bam
ANALYSIS ALIAS: UCSF-UBC.H1.mRNA-seq.Level1.2
ANALYSIS TITLE: Mapping of H1 mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by mRNA-Seq in the H1 cell line 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.1894
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: mRNA-Seq
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: GSM484408_UCSF-UBC.H1.mRNA-seq.Run106057Lane4.bam
ANALYSIS ALIAS: UCSF-UBC.H1.mRNA-seq.Level1.3
ANALYSIS TITLE: Mapping of H1 mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by mRNA-Seq in the H1 cell line 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.1895
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: mRNA-Seq
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: GSM484408_UCSF-UBC.H1.mRNA-seq.Run106058Lane5.bam
ANALYSIS ALIAS: UCSF-UBC.H1.mRNA-seq.Level1.4
ANALYSIS TITLE: Mapping of H1 mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by mRNA-Seq in the H1 cell line 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.1896
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: mRNA-Seq
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: GSM484408_UCSF-UBC.H1.mRNA-seq.Run106059Lane6.bam
ANALYSIS ALIAS: UCSF-UBC.H1.mRNA-seq.Level1.5
ANALYSIS TITLE: Mapping of H1 mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by mRNA-Seq in the H1 cell line 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.1897
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: mRNA-Seq
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: GSM484408_UCSF-UBC.H1.mRNA-seq.Run106060Lane7.bam
ANALYSIS ALIAS: UCSF-UBC.H1.mRNA-seq.Level1.6
ANALYSIS TITLE: Mapping of H1 mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by mRNA-Seq in the H1 cell line 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.1898
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: mRNA-Seq
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: GSM484408_UCSF-UBC.H1.mRNA-seq.wig
ANALYSIS ALIAS: UCSF-UBC.H1.mRNA-seq.Level2.1
ANALYSIS TITLE: Raw Signal Density Graphs of H1 mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina mRNA-Seq read mappings from the H1 cell line 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.1890
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: mRNA-Seq
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None

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

ANALYSIS FILE NAME: GSM484408_UCSF-UBC.H1.mRNA-Seq.H1EScd1_batch2_vial2.bed
ANALYSIS ALIAS: HS1272-1_612FTAAXX-HS1272-1_42VR1AAXX.hg19.level.1
ANALYSIS TITLE: Mapping of H1 Cell Line mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by mRNA-Seq on the H1 Cell Line, Library H1EScd1 batch2 vial2 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.4273
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: mRNA-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: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 2

QUALITY SCORES:
NUMBER_OF_MRNA-SEQ_EXPERIMENTS_SCORED: 4
PERCENT_READS_MAPPING_TO_UCSC_GENES: 89.50
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 25

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

ANALYSIS FILE NAME: GSM484408_UCSF-UBC.H1.mRNA-Seq.H1EScd1_batch2_vial2.wig
ANALYSIS ALIAS: HS1272-1_612FTAAXX-HS1272-1_42VR1AAXX.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Cell Line mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina mRNA-Seq read mappings from the H1 Cell Line, Library H1EScd1 batch2 vial2 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.4268
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: H1 mRNA l2
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-UCD H1 Cell Line mRNA-Seq Library H1EScd1 batch2 vial2 EA Release 2

QUALITY SCORES:
NUMBER_OF_MRNA-SEQ_EXPERIMENTS_SCORED: 4
PERCENT_READS_MAPPING_TO_UCSC_GENES: 89.50
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 25

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

extract_protocol: library construction protocol: Refer to document 'Strand Specific 96-well Library Construction for Illumina Sequencing' from BC at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)

value: cell line

value: male

value: Embryo ICM

value: Embryonic stem cell

value: No


title: K562_Fos_ChIPSeq

description: ChIP against Fos

extract_protocol: Nuclei were isolated from cross-linked (1% formaldehyde for 10 minutes at room temperature) K562 cells. Nuclei were lysed in RIPA buffer and extracted chromatin was sonicated using Branson Sonifier 250. ChIP DNA was prepared using Fos antibody. Libraries were prepared according to Illumina's protocols using reagents purchased from different vendors. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase (Epicenter). The blunt, phosphorylated ends were treated with Klenow fragment (exo minus) (New England Biolab, NEB) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation (LigaFast, Promega) DNA was PCR amplified (Phusion polymerase, NEB) with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

value: Fos


title: Testis

source_name: Testis

value: Testis


title: GM12878_PolIII_DNA

description: ChIP against Pol III

data_processing: Enriched peak regions corresponding to transcription factor binding sites were identified by first extending all the uniquely mapped tags reads (mapped against hg18) to the averaged sequenced DNA fragment size ~200bps and then accumulated into fragment density signal maps. Peaks in these maps are identified by comparison to a computer simulated null model for each Mb of each chromosome (accounting for the variability in mappability of sequence tags across the human genome. For potential target regions the number of sequenced tags is compared against the normalized number of sequence tags overlapping the region from the matching Input DNA reference sample (GSM487430). Fold enrichment ratios are computed from the ratio of these two sets of counts for each regions as well as p-value using the cumulative distribution function for the binomial distribution. P-value are corrected for multiple hypothesis testing using a Benjamini-Hochberg correction factor and a false discovery rate threshold of 0.05 is imposed. (Rozowsky et al. Nature Biotechnology 27, 66 - 75, 2009)

growth_protocol: GM12878 cells were grown in RPMI media containing 15% FBS

extract_protocol: Nuclei were isolated from cross-linked (1% formaldehyde for 10 minutes at room temperature) GM12878 cells. Nuclei were lysed in RIPA buffer and extracted chromatin was sonicated using Branson Sonifier 250. ChIP DNA was prepared using Pol III antibody. Libraries were prepared according to Illumina's protocols using reagents purchased from different vendors. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase (Epicenter). The blunt, phosphorylated ends were treated with Klenow fragment (exo minus) (New England Biolab, NEB) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation (LigaFast, Promega) DNA was PCR amplified (Phusion polymerase, NEB) with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

tag: lymphoblast cellular condition

value: IP


title: CMV delta2b in rdr1 mutant of Arabidopsis thaliana, replicate

description:
total small RNAs in systemically infected leaves of A. thaliana
barcode: TAC

source_name: leaves of mutant Arabidopsis thaliana infected with CMVf-Δ2b

tag: a.thaliana genotype

value: rdr1 mutant

tag: a.thaliana tissue

value: leaves

tag: cmv genotype/variation

tag: cmv strain

value: FNY

tag: collected time

value: 14 days after inoculation


title: DFTD3

value: Facial tumor


title: GM12878_Input_DNA

description: Input DNA

value: normal


title: K562_Jun_ChIPSeq

description: ChIP against Jun

extract_protocol: Nuclei were isolated from cross-linked (1% formaldehyde for 10 minutes at room temperature) K562 cells. Nuclei were lysed in RIPA buffer and extracted chromatin was sonicated using Branson Sonifier 250. ChIP DNA was prepared using Jun antibody. Libraries were prepared according to Illumina's protocols using reagents purchased from different vendors. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase (Epicenter). The blunt, phosphorylated ends were treated with Klenow fragment (exo minus) (New England Biolab, NEB) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation (LigaFast, Promega) DNA was PCR amplified (Phusion polymerase, NEB) with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

value: Suspension Morphology

value: Jun


title: Fibroblasts derived from human embryonic stem cells: Bisulfite sequencing

status: Public on Dec 29 2009

city: Singapore

first: Chia-Lin

last: Wei

address: 60 Biopolis Street #02-01

department: Genome Technology & Biology

country: Singapore

institute: Genome Institute of Singapore

description: hESC-Fibro DNA methylation mapping data

data_processing:
Alignment: Sequence reads were first processed by Illumina Genome Analyzer pipeline for base calling and quality filtering. Reads that passed filtering were aligned to human reference genome, Hg18, via SOAP2 alignment program with less than 2 mismatches. To accommodate the conversion of unmethylated cytosines to thymines by bisulfite conversion, we used a "reduced", three-letter alphabet comprising A, G and {C or T} to represent the genome.
Methylation levels of a C within an aligned read were gauged by the ratio of reads that contained a methylated C at that location vs. all the reads that covered the location.

source_name: Fibroblast

growth_protocol: WA09 hESC line was cultured feeder-free on MatrigelTM (Becton-Dickinson) in StemPro TM medium (Lifetech, Inc.), and passaged with Accutase (Lifetech, Inc.).  They were harvested at passage 41.  hESC-derived fibroblasts (hESC-Fibro) were derived as a stable proliferating population from spontaneously differentiating passage 40 WA09 hESC cells (Gonzalez et al., 2008); after their differentiation they were expanded in two batches, to passage 11 and passage 13 before harvesting. The neonatal fibroblast line (Fibro) cell line was obtained from GlobalStem, Inc (catalog number GSC-3002, Newborn Human Foreskin Fibroblasts, untreated) and was harvested for analysis at passage 13.  All cell lines were cultured at 37°C, ambient oxygen, and 5% CO2.  The hESC-Fibro and Fibro cell lines were cultured in DMEM+10%FBS and passaged with trypsin.

extract_protocol: Genomic DNA were extracted from the individual cell lines and fragmented via nebulization to sizes between 300 bp to 500 bp.  The fragmented DNA was end polished and ligated with Illumina methylated PE adaptors followed by two consecutive bisulfite treatments using the EpiTect Bisulfite Kit (Qiagen) to ensure maximal conversion rate.  The bisulfite treated DNA was enriched by 10 cycles of PCR with primers complementary to the adaptor sequences by uracil-insensitive Taq polymerase (Pfu Turbo Cx Hotstart DNA Polymerase; Stratagene). Sizes between 250 bp to 300 bp (including the adaptors) were selected and sequenced with the Illumina Genome Analyzer using the PE sequencing method at 75bp read length