title: 0-24h Embryo PolII ChIP-Seq extraction3_seq1 aliquote 1

description: channel ch1 is input DNA;

data_processing: Illumina_seq_maq_processing:DM:1 protocol. Using the MAQ command-line tool v.0.7.1, reads are converted from Illumina FASTQ to Sanger FASTQ to Binary FASTQ. The Drosophila genome v.5.1 is then converted into binary fasta format. Then the reads are mapped back to the Drosophila genome using maq 0.7.1 with a maximum of 3 mismatches per read and a mapview file is created which is then read into a local relational database.  Processed data are obtained using following parameters: genome version is 5.1   ChIPseq_analysis:DM:1 protocol. *  WIG Track Generation:          o Tracks are read into SPP and informative tags are selected using SPP's select.informative.tags function.          o Local sequencing anomalies are removed with SPP's remove.local.tag.anomalies function.          o Input subtracted ChIP density wiggle track is output with a step size of 100 and a bandwidth of 100 using SPP's get.smoothed.tag.density function. The tags are shifted 1/2 of the optimal shift size discovered with get.binding.characteristics.          o To combine replicates, all the reads were pooled together and the tag shift was estimated as the mean tag shift between the replicates.     * GFF3 Peak Call Generation:          o MAQ files were converted to ELAND using an in-house script.          o The PeakSeq preprocessing scripts were run by an in-house pipeline automation script.          o The PeakSeq v.1.01 C++ code was run with the default parameters and a maximum q-val of .05.          o To combine replicates, overlapping windows of enrichment between the two sets were combined, and the rest were discarded.

source_name: 0-24h Embryo PolII ChIP-Seq extraction3_seq1 channel_1


title: 0-24h Embryo PolII ChIP-Seq extraction1_seq1 aliquote 1

status: Public on Mar 23 2011

type: SRA

city: Toronto

first: DCC

last: modENCODE

state: Ontario

address: MaRS Centre, South Tower, 101 College Street, Suite 800

country: Canada

institute: Ontario Institute for Cancer Research

description: channel ch1 is ChIP DNA; Antibody information listed below: official name:Anti-RNA polymerase II, clone CTD4H8 ; aliases:Upstate 05-623 target name: RNA polymerase II; species:D. melanogaster;host: Mouse;purified: Protein A/G; clonal: Monoclonal;company:Upstate-Millipore;catalog:05-623 short description:   Anti-RNA polymerase II, clone CTD4H8. Peptide containing 10 repeats of YSPT[pS]PS corresponding to the carboxyl-terminal domain of RNA polymerase II. Purified mouse IgG1 in buffer containing 0.02 M phosphate buffer, pH 7.6, 0.25 M NaCl, and 0.1% Sodium Azide before the addition of glycerol to 30%.

library_source: genomic

data_processing: Illumina_seq_maq_processing:DM:1 protocol. Using the MAQ command-line tool v.0.7.1, reads are converted from Illumina FASTQ to Sanger FASTQ to Binary FASTQ. The Drosophila genome v.5.1 is then converted into binary fasta format. Then the reads are mapped back to the Drosophila genome using maq 0.7.1 with a maximum of 3 mismatches per read and a mapview file is created which is then read into a local relational database.  Processed data are obtained using following parameters: genome version is 5.1   ChIPseq_analysis:DM:1 protocol. *  BEDGRAPH Track Generation:          o Tracks are read into SPP and informative tags are selected using SPP's select.informative.tags function.          o Local sequencing anomalies are removed with SPP's remove.local.tag.anomalies function.          o Input subtracted ChIP density bedgraph track is output with a step size of 100 and a bandwidth of 100 using SPP's get.smoothed.tag.density function. The tags are shifted 1/2 of the optimal shift size discovered with get.binding.characteristics.          o To combine replicates, all the reads were pooled together and the tag shift was estimated as the mean tag shift between the replicates.     * GFF3 Peak Call Generation:          o MAQ files were converted to ELAND using an in-house script.          o The PeakSeq preprocessing scripts were run by an in-house pipeline automation script.          o The PeakSeq v.1.01 C++ code was run with the default parameters and a maximum q-val of .05.          o To combine replicates, overlapping windows of enrichment between the two sets were combined, and the rest were discarded.

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: 0-24h Embryo PolII ChIP-Seq extraction1_seq1 channel_1

growth_protocol: Embryo collection protocol

extract_protocol:
Cross linking and chromatin extraction protocol for Drosophila ChIP experiments.
Chromatin IP of a chromatin extract with an antibody.
Generation of a genomic library suitable for Illumina sequencing, using the standard Illumina protocol.  This includes a 150-200bp size selection step.
Load sample onto flow cell at a (usually 2-8 pM, variable) concentration and run on an Illumina Genome Analyzer II for single-end sequencing for 36 or 76 nt. Image data is then deconvoluted using the most current versions of Firecrest, Bustard, and Gerald (or equivalents).

tag: developmental stage

value: Mixed Embryos 0-24h


title: Reference Epigenome: ChIP-Seq Analysis of H3K36me3 in hESC H9 Cells; renlab.H3K36me3.hESC.H9.02.01

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: NTR_0000838
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K36me3 in hESC H9 Cells. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: SK278
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.5264
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.4286
****************
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: GSM667623_UCSD.H9.H3K36me3.SK278.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K36me3.hESC.H9.02.01.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of H9 Cell Line Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K36me3 ChIP-Seq on the H9 Cell Line, Library SK278 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.6295
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 3

QUALITY SCORES:
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 26
FINDPEAKS_SCORE: 0.1237
FINDPEAKS_PERCENTILE: 35
HOTSPOT_SCORE: 0.2786
HOTSPOT_PERCENTILE: 46
IROC_SCORE: 0.8764
IROC_PERCENTILE: 8
POISSON_SCORE: 0.3951
POISSON_PERCENTILE: 35

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

ANALYSIS FILE NAME: GSM667623_UCSD.H9.H3K36me3.SK278.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K36me3.hESC.H9.02.01.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of H9 Cell Line Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K36me3 ChIP-Seq read mappings from the H9 Cell Line, Library SK278 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.6637
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 3
BROWSER_TRACK_NAME: H9 H3K36me3 78
BROWSER_TRACK_DESCRIPTION: UCSD H9 Cell Line Histone H3K36me3 Library SK278 EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 26
FINDPEAKS_SCORE: 0.1237
FINDPEAKS_PERCENTILE: 35
HOTSPOT_SCORE: 0.2786
HOTSPOT_PERCENTILE: 46
IROC_SCORE: 0.8764
IROC_PERCENTILE: 8
POISSON_SCORE: 0.3951
POISSON_PERCENTILE: 35

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

organism: Homo sapiens

source_name: Human embryonic stem cells received from the James Thompson laboratory.  Cells are from the H9 line.; renlab.H3K36me3.hESC.H9.02.01

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

tag: sample alias

tag: sample common name

value: H9 Cell Line

tag: molecule

value: genomic DNA

tag: disease

value: James Thompson Laboratory

value: Cell Line

tag: line

tag: lineage

value: Embryonic Stem Cell

tag: passage

value: Between 30 and 50

tag: medium

value: mTeSER

tag: Sex

value: Female

tag: batch

value: Histone H3K36me3

value: Biorupter

value: 500 micrograms

value: magnetic anti-rabbit

value: 5 micrograms

value: Abcam


title: Reference Epigenome: ChIP-Seq Analysis of H3K4ac in hESC H1 Cells; renlab.H3K4ac.hESC.H1.02.01

description:
sample_term_id: EFO_0003042
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K4ac in hESC H1 Cells. Sequencing was done on the Illumina Genome Analyzer IIx and HiSeq 2000 platforms.
Library name: AK51
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.5972
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.5971
****************
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: GSM667624_UCSD.H1.H3K4ac.AK51.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4ac.hESC.H1.02.01.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of H1 Cell Line Histone H3K4ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4ac ChIP-Seq on the H1 Cell Line, Library AK51 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.6262
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 3

QUALITY SCORES:
NUMBER_OF_H3K4ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 2
FINDPEAKS_SCORE: 0.0046
FINDPEAKS_PERCENTILE: 50
HOTSPOT_SCORE: 0.0655
HOTSPOT_PERCENTILE: 50
IROC_SCORE: 0.769
IROC_PERCENTILE: 100
POISSON_SCORE: 0.1684
POISSON_PERCENTILE: 50

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

ANALYSIS FILE NAME: GSM667624_UCSD.H1.H3K4ac.AK51.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4ac.hESC.H1.02.01.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Cell Line Histone H3K4ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4ac ChIP-Seq read mappings from the H1 Cell Line, Library AK51 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.6604
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 3
BROWSER_TRACK_NAME: H1 H3K4ac 51
BROWSER_TRACK_DESCRIPTION: UCSD H1 Cell Line Histone H3K4ac Library AK51 EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K4ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 2
FINDPEAKS_SCORE: 0.0046
FINDPEAKS_PERCENTILE: 50
HOTSPOT_SCORE: 0.0655
HOTSPOT_PERCENTILE: 50
IROC_SCORE: 0.769
IROC_PERCENTILE: 100
POISSON_SCORE: 0.1684
POISSON_PERCENTILE: 50

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

source_name: Human embryonic stem cells received from the James Thompson laboratory.  Cells are from the H1 line.; renlab.H3K4ac.hESC.H1.02.01

value: H1 Cell Line

value: Male

value: Histone H3K4ac

value: Upstate


title: 0-24h Embryo PolII ChIP-Seq extraction4_seq1 aliquote 1

description: channel ch1 is input DNA;

source_name: 0-24h Embryo PolII ChIP-Seq extraction4_seq1 channel_1

value: Mixed Embryos 0-24h


title: Oct4 control

city: Singapore

first: Justin

middle: Jeyakani

last: Joseph Gnanakkan

state: Singapore

address: 60, Biopolis street

department: Computational and Systems Biology

country: Singapore

institute: Genome Institute of Singapore

description: ChIP was performed using commercial antibody

data_processing:
The raw images have been processed using the Solexa Pipeline and mapped to the reference genome (NCBI Build 36, hg18) using Eland software with maximal 2 mis-matches.
Peak detection was performed using MACS (Zhang, Y. et al 2008). The binding regions were ranked based on the enrichment of ChIP sequenced tags by comparing each ChIP library to an Input library as a control. Defined the binding peaks as those above the p-value cut-off of 1.00e-05.

source_name: embryonic stem cells, control ChIP-seq

growth_protocol: The hESC lines H1 (WA-01, passage 28) was used for this study. They were cultured feeder free on matri-gel (BD). Condition medium used for culturing human contained 20% KO serum replacement, 1 mM L-glutamine, 1% non-essential amino acids and 0.1 mM 2-mercaptoethanol and additional 8ng/ml of basic fibroblast growth factor (Invitrogen) supplemented to the hESCs unconditioned medium.

extract_protocol: 10ng of ChIP material, respectively, as per manufacturers protocol. Briefly, using the Solexa ChIP Seq DNA sample preparation kit universal linkers were added to the chromatin fragments and DNA was PCR amplified for 15 cycles. DNA was gel-purified and fragments between 200-300bp were selected for sequencing

treatment_protocol: The ES cells were fixed in 1 % formaldehyde for 10 minutes at room temperature. The formaldehyde was quenched using 0.1 M glycine before harvest for extract preparation

tag: antibody

tag: cell line

tag: cell type

value: embryonic stem cell

tag: passages


title: Nanog and CTCF control


title: Reference Epigenome: ChIP-Seq Analysis of H3K4ac in hESC H9 Cells; renlab.H3K4ac.hESC.H9.01.01

description:
sample_term_id: NTR_0000838
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K4ac in hESC H9 Cells. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: SK328
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.6064
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.6006
****************
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: GSM667625_UCSD.H9.H3K4ac.SK328.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4ac.hESC.H9.01.01.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of H9 Cell Line Histone H3K4ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4ac ChIP-Seq on the H9 Cell Line, Library SK328 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.6293
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 3

QUALITY SCORES:
NUMBER_OF_H3K4ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 2
FINDPEAKS_SCORE: 0.0076
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.0968
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.6244
IROC_PERCENTILE: 50
POISSON_SCORE: 0.2677
POISSON_PERCENTILE: 100

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

ANALYSIS FILE NAME: GSM667625_UCSD.H9.H3K4ac.SK328.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4ac.hESC.H9.01.01.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of H9 Cell Line Histone H3K4ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4ac ChIP-Seq read mappings from the H9 Cell Line, Library SK328 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.6635
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 3
BROWSER_TRACK_NAME: H9 H3K4ac 28
BROWSER_TRACK_DESCRIPTION: UCSD H9 Cell Line Histone H3K4ac Library SK328 EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K4ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 2
FINDPEAKS_SCORE: 0.0076
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.0968
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.6244
IROC_PERCENTILE: 50
POISSON_SCORE: 0.2677
POISSON_PERCENTILE: 100

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

source_name: Human embryonic stem cells received from the James Thompson laboratory.  Cells are from the H9 line.; renlab.H3K4ac.hESC.H9.01.01

value: H9 Cell Line

value: genomic DNA

value: James Thompson Laboratory

value: Cell Line


title: 24h Embryo Orc ChIP-Seq extraction4_seq1 aliquote 1

description: channel ch1 is input DNA;

data_processing: Illumina_seq_maq_processing:DM:1 protocol. Using the MAQ command-line tool v.0.7.1, reads are converted from Illumina FASTQ to Sanger FASTQ to Binary FASTQ. The Drosophila genome v.5.1 is then converted into binary fasta format. Then the reads are mapped back to the Drosophila genome using maq 0.7.1 with a maximum of 3 mismatches per read and a mapview file is created which is then read into a local relational database.  Processed data are obtained using following parameters: genome version is 5.1   ORC_ChIPseq_analysis:DM:1 protocol. *  WIG Track Generation:          o Tracks are read into SPP and informative tags are selected using SPP's select.informative.tags function.          o Local sequencing anomalies are removed with SPP's remove.local.tag.anomalies function.          o Input subtracted ChIP density wiggle track is output with a step size of 100 and a bandwidth of 100 using SPP's get.smoothed.tag.density function. The tags are shifted 1/2 of the optimal shift size discovered with get.binding.characteristics.          o To combine replicates, all the reads were pooled together and the tag shift was estimated as the mean tag shift between the replicates.     * GFF3 Peak Call Generation:          o MAQ files were converted to ELAND using an in-house script.          o The PeakSeq preprocessing scripts were run by an in-house pipeline automation script.          o The PeakSeq v.1.01 C++ code was run with the default parameters and a maximum q-val of .05.          o To combine replicates, overlapping windows of enrichment between the two sets were combined, and the rest were discarded.

source_name: 24h Embryo Orc ChIP-Seq extraction4_seq1 channel_1

growth_protocol: A copy of Embryo collection protocol with more generic DB fields


title: 24h Embryo Orc ChIP-Seq extraction3_seq1 aliquote 1

description: channel ch1 is input DNA;

source_name: 24h Embryo Orc ChIP-Seq extraction3_seq1 channel_1


title: Reference Epigenome: ChIP-Seq Analysis of H3K23ac in hESC H1 Cells; renlab.H3K23ac.hESC.H1.01.01

description:
sample_term_id: EFO_0003042
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K23ac in hESC H1 Cells. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AK53
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.6018
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.5971
****************
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: GSM667617_UCSD.H1.H3K23ac.AK53.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K23ac.hESC.H1.01.01.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of H1 Cell Line Histone H3K23ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K23ac ChIP-Seq on the H1 Cell Line, Library AK53 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.6284
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 3

QUALITY SCORES:
NUMBER_OF_H3K23ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 4
FINDPEAKS_SCORE: 0.0057
FINDPEAKS_PERCENTILE: 25
HOTSPOT_SCORE: 0.0938
HOTSPOT_PERCENTILE: 75
IROC_SCORE: 0.0
IROC_PERCENTILE: NA
POISSON_SCORE: 0.1979
POISSON_PERCENTILE: 75

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

ANALYSIS FILE NAME: GSM667617_UCSD.H1.H3K23ac.AK53.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K23ac.hESC.H1.01.01.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Cell Line Histone H3K23ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K23ac ChIP-Seq read mappings from the H1 Cell Line, Library AK53 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.6626
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 3
BROWSER_TRACK_NAME: H1 H3K23ac 53
BROWSER_TRACK_DESCRIPTION: UCSD H1 Cell Line Histone H3K23ac Library AK53 EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K23ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 4
FINDPEAKS_SCORE: 0.0057
FINDPEAKS_PERCENTILE: 25
HOTSPOT_SCORE: 0.0938
HOTSPOT_PERCENTILE: 75
IROC_SCORE: 0.0
IROC_PERCENTILE: NA
POISSON_SCORE: 0.1979
POISSON_PERCENTILE: 75

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

source_name: Human embryonic stem cells received from the James Thompson laboratory.  Cells are from the H1 line.; renlab.H3K23ac.hESC.H1.01.01

value: Embryonic Stem Cell

value: mTeSER

value: Histone H3K23ac


title: Reference Epigenome: ChIP-Seq Analysis of H3K23ac in hESC H1 Cells; renlab.H3K23ac.hESC.H1.02.01

description:
sample_term_id: EFO_0003042
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K23ac in hESC H1 Cells. Sequencing was done on the Illumina HiSeq 2000 and Genome Aanalyzer IIx  platforms.
Library name: AK59
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.6026
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.5258
****************
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: GSM667618_UCSD.H1.H3K23ac.AK59.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K23ac.hESC.H1.02.01.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of H1 Cell Line Histone H3K23ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K23ac ChIP-Seq on the H1 Cell Line, Library AK59 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.6300
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 3

QUALITY SCORES:
NUMBER_OF_H3K23ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 4
FINDPEAKS_SCORE: 0.0079
FINDPEAKS_PERCENTILE: 50
HOTSPOT_SCORE: 0.0796
HOTSPOT_PERCENTILE: 25
IROC_SCORE: 0.0
IROC_PERCENTILE: NA
POISSON_SCORE: 0.1922
POISSON_PERCENTILE: 50

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

ANALYSIS FILE NAME: GSM667618_UCSD.H1.H3K23ac.AK59.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K23ac.hESC.H1.02.01.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Cell Line Histone H3K23ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K23ac ChIP-Seq read mappings from the H1 Cell Line, Library AK59 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.6642
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 3
BROWSER_TRACK_NAME: H1 H3K23ac 59
BROWSER_TRACK_DESCRIPTION: UCSD H1 Cell Line Histone H3K23ac Library AK59 EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K23ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 4
FINDPEAKS_SCORE: 0.0079
FINDPEAKS_PERCENTILE: 50
HOTSPOT_SCORE: 0.0796
HOTSPOT_PERCENTILE: 25
IROC_SCORE: 0.0
IROC_PERCENTILE: NA
POISSON_SCORE: 0.1922
POISSON_PERCENTILE: 50

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

source_name: Human embryonic stem cells received from the James Thompson laboratory.  Cells are from the H1 line.; renlab.H3K23ac.hESC.H1.02.01

value: Biorupter

value: 500 micrograms


title: Reference Epigenome: ChIP-Seq Analysis of H3K23me2 in hESC H9 Cells; renlab.H3K23me2.hESC.H9.01.01

description:
sample_term_id: NTR_0000838
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K23me2 in hESC H9 Cells. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: SK277
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.6004
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.4286
****************
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: GSM667621_UCSD.H9.H3K23me2.SK277.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K23me2.hESC.H9.01.01.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of H9 Cell Line Histone H3K23me2 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K23me2 ChIP-Seq on the H9 Cell Line, Library SK277 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.6266
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 3

QUALITY SCORES:
NUMBER_OF_H3K23me2_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 1
FINDPEAKS_SCORE: 0.0632
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.2219
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.838
IROC_PERCENTILE: 100
POISSON_SCORE: 0.378
POISSON_PERCENTILE: 100

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

ANALYSIS FILE NAME: GSM667621_UCSD.H9.H3K23me2.SK277.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K23me2.hESC.H9.01.01.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of H9 Cell Line Histone H3K23me2 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K23me2 ChIP-Seq read mappings from the H9 Cell Line, Library SK277 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.6608
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 3
BROWSER_TRACK_NAME: H9 H3K23me2 77
BROWSER_TRACK_DESCRIPTION: UCSD H9 Cell Line Histone H3K23me2 Library SK277 EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K23me2_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 1
FINDPEAKS_SCORE: 0.0632
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.2219
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.838
IROC_PERCENTILE: 100
POISSON_SCORE: 0.378
POISSON_PERCENTILE: 100

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

source_name: Human embryonic stem cells received from the James Thompson laboratory.  Cells are from the H9 line.; renlab.H3K23me2.hESC.H9.01.01

value: Between 30 and 50

value: Female

value: Histone H3K23me2

value: magnetic anti-rabbit

value: 5 micrograms


title: Reference Epigenome: ChIP-Seq Analysis of H3K18ac in hESC H9 Cells; renlab.H3K18ac.hESC.H9.01.01

description:
sample_term_id: NTR_0000838
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K18ac in hESC H9 Cells. Sequencing was done on the Illumina Genome Analyzer IIx and HiSeq 2000 platforms.
Library name: SK276
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.5995
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.4286
****************
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: GSM667616_UCSD.H9.H3K18ac.SK276.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K18ac.hESC.H9.01.01.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of H9 Cell Line Histone H3K18ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K18ac ChIP-Seq on the H9 Cell Line, Library SK276 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.6285
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 3

QUALITY SCORES:
NUMBER_OF_H3K18ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 3
FINDPEAKS_SCORE: 0.0426
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.1918
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.768
IROC_PERCENTILE: 100
POISSON_SCORE: 0.3285
POISSON_PERCENTILE: 100

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

ANALYSIS FILE NAME: GSM667616_UCSD.H9.H3K18ac.SK276.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K18ac.hESC.H9.01.01.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of H9 Cell Line Histone H3K18ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K18ac ChIP-Seq read mappings from the H9 Cell Line, Library SK276 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.6627
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 3
BROWSER_TRACK_NAME: H9 H3K18ac 76
BROWSER_TRACK_DESCRIPTION: UCSD H9 Cell Line Histone H3K18ac Library SK276 EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K18ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 3
FINDPEAKS_SCORE: 0.0426
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.1918
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.768
IROC_PERCENTILE: 100
POISSON_SCORE: 0.3285
POISSON_PERCENTILE: 100

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

source_name: Human embryonic stem cells received from the James Thompson laboratory.  Cells are from the H9 line.; renlab.H3K18ac.hESC.H9.01.01

value: Histone H3K18ac

value: Abcam


title: Reference Epigenome: ChIP-Seq Analysis of H3K23ac in hESC H9 Cells; renlab.H3K23ac.hESC.H9.02.01

description:
sample_term_id: NTR_0000838
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K23ac in hESC H9 Cells. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: SK289
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.6015
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.4286
****************
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: GSM667620_UCSD.H9.H3K23ac.SK289.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K23ac.hESC.H9.02.01.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of H9 Cell Line Histone H3K23ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K23ac ChIP-Seq on the H9 Cell Line, Library SK289 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.6261
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 3

QUALITY SCORES:
NUMBER_OF_H3K23ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 4
FINDPEAKS_SCORE: 0.022
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.1619
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.6618
IROC_PERCENTILE: 100
POISSON_SCORE: 0.2651
POISSON_PERCENTILE: 100

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

ANALYSIS FILE NAME: GSM667620_UCSD.H9.H3K23ac.SK289.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K23ac.hESC.H9.02.01.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of H9 Cell Line Histone H3K23ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K23ac ChIP-Seq read mappings from the H9 Cell Line, Library SK289 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.6603
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 3
BROWSER_TRACK_NAME: H9 H3K23ac 89
BROWSER_TRACK_DESCRIPTION: UCSD H9 Cell Line Histone H3K23ac Library SK289 EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K23ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 4
FINDPEAKS_SCORE: 0.022
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.1619
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.6618
IROC_PERCENTILE: 100
POISSON_SCORE: 0.2651
POISSON_PERCENTILE: 100

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

source_name: Human embryonic stem cells received from the James Thompson laboratory.  Cells are from the H9 line.; renlab.H3K23ac.hESC.H9.02.01

value: Millipore


title: Reference Epigenome: ChIP-Seq Analysis of H3K14ac in hESC H1 Cells; renlab.H3K14ac.hESC.H1.02.01

description:
sample_term_id: EFO_0003042
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K14ac in hESC H1 Cells. Sequencing was done on the Illumina HiSeq 2000 and Genome Aanalyzer IIx  platforms.
Library name: AK58
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.6056
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.5258
****************
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: GSM667615_UCSD.H1.H3K14ac.AK58.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K14ac.hESC.H1.02.01.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of H1 Cell Line Histone H3K14ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K14ac ChIP-Seq on the H1 Cell Line, Library AK58 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.6263
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 3

QUALITY SCORES:
NUMBER_OF_H3K14ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 3
FINDPEAKS_SCORE: 0.0076
FINDPEAKS_PERCENTILE: 67
HOTSPOT_SCORE: 0.0893
HOTSPOT_PERCENTILE: 33
IROC_SCORE: 0.0
IROC_PERCENTILE: NA
POISSON_SCORE: 0.227
POISSON_PERCENTILE: 33

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

ANALYSIS FILE NAME: GSM667615_UCSD.H1.H3K14ac.AK58.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K14ac.hESC.H1.02.01.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Cell Line Histone H3K14ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K14ac ChIP-Seq read mappings from the H1 Cell Line, Library AK58 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.6605
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 3
BROWSER_TRACK_NAME: H1 H3K14ac 58
BROWSER_TRACK_DESCRIPTION: UCSD H1 Cell Line Histone H3K14ac Library AK58 EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K14ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 3
FINDPEAKS_SCORE: 0.0076
FINDPEAKS_PERCENTILE: 67
HOTSPOT_SCORE: 0.0893
HOTSPOT_PERCENTILE: 33
IROC_SCORE: 0.0
IROC_PERCENTILE: NA
POISSON_SCORE: 0.227
POISSON_PERCENTILE: 33

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

source_name: Human embryonic stem cells received from the James Thompson laboratory.  Cells are from the H1 line.; renlab.H3K14ac.hESC.H1.02.01

value: H1 Cell Line

value: Male

value: Histone H3K14ac


title: dgcr8_ko_cortex

city: San Francisco

first: Robert

last: Blelloch

address: 513 Parnassus Avenue, Campus Box #0525

institute: University of California, San Francisco

description: small RNA-Seq

library_source: transcriptomic

data_processing: Illumina Pipeline v1.3

molecule: total RNA

organism: Mus musculus

source_name: cortex

extract_protocol: Libraries were constructed with the Illumina small RNA kit version 1.5

treatment_protocol: The hippocampus and cortex were manually dissected.  Total RNA was prepared with Trizol Reagent

tag: strain

tag: age

tag: genotype/variation

value: dgcr8 ko


title: 24h Embryo Orc ChIP-Seq extraction2_seq1 aliquote 1

description: channel ch1 is ChIP DNA; Antibody information listed below:  official name: dORC2 target name: Drosophila ORC2p host: Rabbit antigen: purified full length protein clonal: Polyclonal purified: Crude company: Lab catalog: Stephen P.Bell MIT reference: Austin et al 1999

data_processing: Illumina_seq_maq_processing:DM:1 protocol. Using the MAQ command-line tool v.0.7.1, reads are converted from Illumina FASTQ to Sanger FASTQ to Binary FASTQ. The Drosophila genome v.5.1 is then converted into binary fasta format. Then the reads are mapped back to the Drosophila genome using maq 0.7.1 with a maximum of 3 mismatches per read and a mapview file is created which is then read into a local relational database.  Processed data are obtained using following parameters: genome version is 5.1   ORC_ChIPseq_analysis:DM:1 protocol. *  BEDGRAPH Track Generation:          o Tracks are read into SPP and informative tags are selected using SPP's select.informative.tags function.          o Local sequencing anomalies are removed with SPP's remove.local.tag.anomalies function.          o Input subtracted ChIP density bedgraph track is output with a step size of 100 and a bandwidth of 100 using SPP's get.smoothed.tag.density function. The tags are shifted 1/2 of the optimal shift size discovered with get.binding.characteristics.          o To combine replicates, all the reads were pooled together and the tag shift was estimated as the mean tag shift between the replicates.     * GFF3 Peak Call Generation:          o MAQ files were converted to ELAND using an in-house script.          o The PeakSeq preprocessing scripts were run by an in-house pipeline automation script.          o The PeakSeq v.1.01 C++ code was run with the default parameters and a maximum q-val of .05.          o To combine replicates, overlapping windows of enrichment between the two sets were combined, and the rest were discarded.

source_name: 24h Embryo Orc ChIP-Seq extraction2_seq1 channel_1

tag: developmental stage

value: Mixed Embryos 0-24h


title: 24h Embryo Orc ChIP-Seq extraction1_seq1 aliquote 1

description: channel ch1 is ChIP DNA; Antibody information listed below: official name: dORC2 target name: Drosophila ORC2p host: Rabbit antigen: purified full length protein clonal: Polyclonal purified: Crude company: Lab catalog: Stephen P. Bell MIT reference: Austin et al 1999

source_name: 24h Embryo Orc ChIP-Seq extraction1_seq1 channel_1


title: dicer_ko_hippocampus

description: small RNA-Seq

source_name: hippocampus

value: dicer ko


title: MCM S2 July 2010 extraction3_seq1 aliquote 1

description: channel ch1 is input DNA;

source_name: MCM S2 July 2010 extraction3_seq1 channel_1

growth_protocol: Growth of modENCODE cell lines for large scale chromatin extract preparation from asynchronous cultures.

tag: tissue

value: embryo-derived cell-line

value: late embryonic stage


title: Reference Epigenome: ChIP-Seq Analysis of H3K14ac in hESC H1 Cells; renlab.H3K14ac.hESC.H1.01.01

description:
sample_term_id: EFO_0003042
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K14ac in hESC H1 Cells. Sequencing was done on the Illumina HiSeq 2000 and Genome Aanalyzer IIx  platforms.
Library name: AK52
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.6068
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.5971
****************
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: GSM667614_UCSD.H1.H3K14ac.AK52.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K14ac.hESC.H1.01.01.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of H1 Cell Line Histone H3K14ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K14ac ChIP-Seq on the H1 Cell Line, Library AK52 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.6292
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 3

QUALITY SCORES:
NUMBER_OF_H3K14ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 3
FINDPEAKS_SCORE: 0.006
FINDPEAKS_PERCENTILE: 33
HOTSPOT_SCORE: 0.0988
HOTSPOT_PERCENTILE: 67
IROC_SCORE: 0.0
IROC_PERCENTILE: NA
POISSON_SCORE: 0.2303
POISSON_PERCENTILE: 67

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

ANALYSIS FILE NAME: GSM667614_UCSD.H1.H3K14ac.AK52.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K14ac.hESC.H1.01.01.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Cell Line Histone H3K14ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K14ac ChIP-Seq read mappings from the H1 Cell Line, Library AK52 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.6634
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 3
BROWSER_TRACK_NAME: H1 H3K14ac 52
BROWSER_TRACK_DESCRIPTION: UCSD H1 Cell Line Histone H3K14ac Library AK52 EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K14ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 3
FINDPEAKS_SCORE: 0.006
FINDPEAKS_PERCENTILE: 33
HOTSPOT_SCORE: 0.0988
HOTSPOT_PERCENTILE: 67
IROC_SCORE: 0.0
IROC_PERCENTILE: NA
POISSON_SCORE: 0.2303
POISSON_PERCENTILE: 67

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

source_name: Human embryonic stem cells received from the James Thompson laboratory.  Cells are from the H1 line.; renlab.H3K14ac.hESC.H1.01.01

tag: sample alias

tag: sample common name

tag: molecule

value: genomic DNA

value: James Thompson Laboratory

value: Cell Line

value: Embryonic Stem Cell

value: mTeSER

value: Biorupter

value: 500 micrograms


title: MCM S2 July 2010 extraction2_seq1 aliquote 1

description: channel ch1 is ChIP DNA; Antibody information listed below: official name: Pan MCM2-7 Antibody;target name: MCM2-7 complex;host: Mouse;antigen: MCM2-7 complex Walker B motif;clonal: Monoclonal;purified: Crude;company: Lab;catalog: Anthony Schwacha;reference: PMID: 12403810;short description: Monoclonal antibody against purified yeast MCM complex. Works cross species.;

source_name: MCM S2 July 2010 extraction2_seq1 channel_1


title: DGCR8_wt_cortex

description: small RNA-Seq

value: Dgcr8 het


title: DGCR8_wt_hippocampus

description: small RNA-Seq


title: MCM S2 July 2010 extraction1_seq1 aliquote 1

source_name: MCM S2 July 2010 extraction1_seq1 channel_1


title: Whole_Dpse_111.94_Female_Rep1

city: Bethesda

first: Brian

last: Oliver

state: MD

address: 50 South Drive

department: LBG

institute: NIDDK, NIH

data_processing:
Reads were trimmed to 75 bp due to low quality on the 3' end of the 101 bp reads. Trimmed 75 bp reads were used for subsequent analyses. Trimmed reads that passed the Illumina filter were mapped with Tophat 1.1.4. The species-specific reference sequence plus ERCC spike-in control sequences (see GEO entry GSE20555 for spike-in control sequences) was used to build a reference index for mapping. The reference index was created using the bowtie-build function with default parameters and reads were mapped to this reference using the Tophat parameters -g 1 -F 0 -r 150 -solexa1.3-quals.
supplementary_file_build: dp4+ERCC Spike-In Controls

molecule: polyA RNA

organism: Drosophila pseudoobscura

source_name: Whole tissue

growth_protocol: Adult flies were growth 5-7 days post eclosion. See GSE6640 for details.

extract_protocol: See GSE6640 for RNA extraction methods. We fragmented mRNA using alkaline hydrolysis. First, 9 µl of 100 ng of mRNA, 1 ng of ERCC spike-in controls, and 1 µl of 10X fragmentation buffer (Ambion, Austin, Texas.) was incubated at 70°C for 5 minutes to fragment mRNA. One microliter of Stop Buffer (Ambion, Austin, Texas) was added and samples were placed on ice. Fragments were precipitated with 1 µl 3 M NaOAC (pH 5.2), 2 µl glycogen (5 µg/µl , Ambion, Austin, Texas), and 30 µl 100% EtOH and then incubated for 30 minutes at -80 °C. Fragmented RNA was pelleted at 14000 rpm with a microcentrifuge at 4°C. The pellet was washed with 70% EtOH, air dried and resuspended with 10.5 µl RNase free H2O. Fragmented mRNA was reverse transcribed to create cDNA. One microliter of random hexamer primers (3µg/µl, Invitrogen, Carlsbad, California) was placed with 10.5 µl of fragmented mRNA, then samples were incubated at 65°C for 5 minutes and placed on ice. Four microliters 5X first strand buffer, 2 µl 100 mM DTT, 1 µl dNTP, and 0.5 µl RNaseOUT were added to the mRNA and samples were incubated at 25°C for 2 minutes. One microliter of SuperScript II (200 U/µl, Invitrogen, Carlsbad, California) was added and samples were incubated under the following conditions: 25°C-10 minutes, 42°C-50 minutes, 70°C-15 minutes. Samples were then placed on ice. Second strand cDNA was synthesized by adding 61µl H2O to the first strand mix, 10 µl 10X second strand buffer (500 mM Tris-HCl pH 7.8, 50 mM MgCl2, 10 mM DTT), and 3 µl dNTP (10 mM), mixed, incubated on ice for 5 minutes, then 1 µl RNaseH (2U/µl, Invitrogen, Carlsbad, California) and 5 µl DNA Pol I (10 U/µl, Invitrogen, Carlsbad, California) were added. Samples were incubated at 16°C for 2.5 hours and DNA products purified using a QIAquick spin column and following manufacture directions and eluted with 30 µl. cDNA fragment libraries were prepared for sequencing. The ends of cDNA fragments were repaired using 30 µl of DNA, 45 µl H2O, 10 µl T4 DNA ligase buffer with 10 mM ATP, 4 µl dNTP mix (10 mM), 5 µl T4 DNA polymerase (3 U/µl), 1 µl Klenow DNA polymerase (5U/µl), and 5 µl T4 PNK(10 U/µl). Samples were incubated for 30 minutes at 20°C, purified with QIAquick PCR spin columns, and eluted with 32 µl of Buffer EB. A single "A" base was added to the ends of cDNA by using 5 µl Klenow buffer, 10 µl dATP (1 mM) and 3 µl Klenow 3' to 5' exonuclease (5 U/µl). Samples were incubated at 37°C for 30 minutes, purified with a QIAquick MiniElute column, and eluted with 19µl of EB solution. Adaptor oligonucleotdies were ligated to A overhang fragments as follows. Overhang fragments were combined with 25 µl DNA ligase buffer, 1 µl adaptor olio mix, and 5 µl DNA ligase (1U/µl). Samples were incubated at room temperature for 15 minutes, purified with a QIAquick MiniElute column, and eluted with 10 µl of buffer EB. cDNA templates were sized selected by gel purification then amplified by PCR using oligo-specific primers. Samples were loaded into a 2% agarose gel with 1X TAE buffer and run for 50 minutes with a 100 bp ladder. The gel was stained with ethidium bromide and bands were visualized under UV fluorescence. For each sample, a gel slice was cut at the 300 (+/- 25) bp region, purified with a QIAquick gel extraction kit, and eluted with 30 µl buffer EB. Purified cDNA was amplified in a 50 µl reaction using 25 µl Phusion Mix (Phusion polymerase, dNTPs, and buffer), 1 µl primer 1.1, 1 µl primer 2.1, and 23 µl template along with the following cycling conditions: initial denaturation 98°C-30 sec, cycle denaturation 98°C-10 sec, anneal 65°C-30 sec, and extend 72°C -30 sec with 15X cycles and a final extension of 72°C for 5 minutes followed by a hold at 4°C. The amplified product was purified using a QIAquick column and eluted with 30 µl buffer EB.

treatment_protocol: Flies were raised in incubators with no photoperiod at 22 C and 60% humidity. See GSE6640 for details.

value: Drosophila Species Stock Center (DSSC) 14011-0121.94. See Drosophila 12 Genomes Consortium. 2007. Evolution of genes and genomes on the Drosophila phylogeny. Nature 450:203-218 for more details about strain origin.

value: Whole flies

value: Adult

tag: sex

value: Female

value: 5-7 days post eclosion


title: Reference Epigenome: ChIP-Seq Analysis of H2BK5ac in hESC H9 Cells; renlab.H2BK5ac.hESC.H9.02.01

description:
sample_term_id: NTR_0000838
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H2BK5ac in hESC H9 Cells. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AK29
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.5957
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.4286
****************
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: GSM667613_UCSD.H9.H2BK5ac.AK29.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H2BK5ac.hESC.H9.02.01.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of H9 Cell Line Histone H2BK5ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H2BK5ac ChIP-Seq on the H9 Cell Line, Library AK29 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.6287
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 3

QUALITY SCORES:
NUMBER_OF_H2BK5ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 2
FINDPEAKS_SCORE: 0.0072
FINDPEAKS_PERCENTILE: 50
HOTSPOT_SCORE: 0.0367
HOTSPOT_PERCENTILE: 50
IROC_SCORE: 0.0
IROC_PERCENTILE: 50
POISSON_SCORE: 0.1114
POISSON_PERCENTILE: 50

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

ANALYSIS FILE NAME: GSM667613_UCSD.H9.H2BK5ac.AK29.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H2BK5ac.hESC.H9.02.01.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of H9 Cell Line Histone H2BK5ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H2BK5ac ChIP-Seq read mappings from the H9 Cell Line, Library AK29 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.6629
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 3
BROWSER_TRACK_NAME: H9 H2BK5ac 29
BROWSER_TRACK_DESCRIPTION: UCSD H9 Cell Line Histone H2BK5ac Library AK29 EA Release 3

QUALITY SCORES:
NUMBER_OF_H2BK5ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 2
FINDPEAKS_SCORE: 0.0072
FINDPEAKS_PERCENTILE: 50
HOTSPOT_SCORE: 0.0367
HOTSPOT_PERCENTILE: 50
IROC_SCORE: 0.0
IROC_PERCENTILE: 50
POISSON_SCORE: 0.1114
POISSON_PERCENTILE: 50

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

source_name: Human embryonic stem cells received from the James Thompson laboratory.  Cells are from the H9 line.; renlab.H2BK5ac.hESC.H9.02.01

value: H9 Cell Line

tag: disease

tag: line

tag: lineage

tag: passage

value: Between 30 and 50

value: Histone H2BK5ac

value: magnetic anti-rabbit

value: 5 micrograms

value: Active Motif


title: Whole_Dmel_yw_Female_Rep2

data_processing:
Reads were trimmed to 75 bp due to low quality on the 3' end of the 101 bp reads. Trimmed 75 bp reads were used for subsequent analyses. Trimmed reads that passed the Illumina filter were mapped with Tophat 1.1.4. The species-specific reference sequence plus ERCC spike-in control sequences (see GEO entry GSE20555 for spike-in control sequences) was used to build a reference index for mapping. The reference index was created using the bowtie-build function with default parameters and reads were mapped to this reference using the Tophat parameters -g 1 -F 0 -r 150 -solexa1.3-quals.
supplementary_file_build: dm3 (no chrUextra)+ERCC Spike-In Controls


title: Whole_Dmel_yw_Male_Rep2

value: Male


title: dicer_ko_cortex

description: small RNA-Seq

value: dicer ko


title: PPARgamma ChIP-seq day 6

status: Public on Mar 22 2011

city: Odense M

first: Susanne

last: Mandrup

address: Campusvej 55

department: Biochemistry and Molecular Biology

country: Denmark

institute: University of Southern Denmark

description: PPARgamma ChIP-seq day 6

data_processing:
processed data file build: mm9
Bed: Areas of enrichment were identified using a newly developed hotspot algorithm.
Bedgraph: Tag density profiles were generated by the newly developed hotspot algorithm.

source_name: Preadipocyte cell line

growth_protocol: 3T3-L1 cells were maintained in DMEM supplemented with calf serum.

extract_protocol: ChIP-seq: Chromatin from various time points of 3T3-L1 differentiation was subjected to ChIP using different antibodies. Purified DNA was prepared for sequencing according to the manufacturer (Illumina). DHS-seq: Nuclei were isolated at various time points of 3T3-L1 differentiation and subjected to a limited DNase I digestion. Small DNA fragments where DNase I cut twice were isolated and prepared for sequencing according to the manufacturer (Illumina).

treatment_protocol: Two days post confluency (day 0), 3T3-L1 cells were  induced to differentiate using a standard cocktail of adipogenic inducers (dexamethasone, insulin, 3-isobutyl-1-methylxanthine, and fetal bovine serum). Two days post induction (day 2), medium was changed to DMEM supplemented with fetal bovine serum and insulin. Cells were  maintained in DMEM supplemented with fetal bovine serum for the remainder of the differentiation.

value: 3T3-L1 preadipocyte cell line

tag: differentiation stage

value: Mature adipocyte

tag: time

value: day 6

tag: chip antibody

value: PPARgamma


title: Reference Epigenome: ChIP-Seq Analysis of H3K27ac in hESC H9 Cells; renlab.H3K27ac.hESC.H9.02.01

description:
sample_term_id: NTR_0000838
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K27ac in hESC H9 Cells. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: SK265
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.5261
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.4286
****************
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: GSM665037_UCSD.H9.H3K27ac.SK265.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27ac.hESC.H9.02.01.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of H9 Cell Line Histone H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27ac ChIP-Seq on the H9 Cell Line, Library SK265 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.6268
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 3

QUALITY SCORES:
NUMBER_OF_H3K27ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 2
FINDPEAKS_SCORE: 0.0373
FINDPEAKS_PERCENTILE: 50
HOTSPOT_SCORE: 0.1614
HOTSPOT_PERCENTILE: 50
IROC_SCORE: 0.6925
IROC_PERCENTILE: 50
POISSON_SCORE: 0.258
POISSON_PERCENTILE: 50

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

ANALYSIS FILE NAME: GSM665037_UCSD.H9.H3K27ac.SK265.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27ac.hESC.H9.02.01.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of H9 Cell Line Histone H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27ac ChIP-Seq read mappings from the H9 Cell Line, Library SK265 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.6610
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 3
BROWSER_TRACK_NAME: H9 H3K27ac 65
BROWSER_TRACK_DESCRIPTION: UCSD H9 Cell Line Histone H3K27ac Library SK265 EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K27ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 2
FINDPEAKS_SCORE: 0.0373
FINDPEAKS_PERCENTILE: 50
HOTSPOT_SCORE: 0.1614
HOTSPOT_PERCENTILE: 50
IROC_SCORE: 0.6925
IROC_PERCENTILE: 50
POISSON_SCORE: 0.258
POISSON_PERCENTILE: 50

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

source_name: Human embryonic stem cells received from the James Thompson laboratory.  Cells are from the H9 line.; renlab.H3K27ac.hESC.H9.02.01

value: genomic DNA

value: James Thompson Laboratory

value: Cell Line

value: Embryonic Stem Cell

tag: medium

value: mTeSER

tag: Sex

tag: batch

value: Histone H3K27ac

value: Biorupter

value: 500 micrograms


title: Whole_Dpse_111.94_Male_Rep1

tag: strain

value: Drosophila Species Stock Center (DSSC) 14011-0121.94. See Drosophila 12 Genomes Consortium. 2007. Evolution of genes and genomes on the Drosophila phylogeny. Nature 450:203-218 for more details about strain origin.

value: Whole flies

value: Adult

tag: age

value: 5-7 days post eclosion


title: Input

description: Input

tag: cell line

tag: dnase treatment


title: RNA Pol II ChIP-seq 4 hours

description: RNA Pol II ChIP-seq 4 hours

value: Early stage

value: 4 hours

value: RNA Pol II


title: Reference Epigenome: ChIP-Seq Analysis of H3K4me3 in hESC H9 Cells; renlab.H3K4me3.hESC.H9.02.01

description:
sample_term_id: NTR_0000838
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K4me3 in hESC H9 Cells. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AK39
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.4289
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.4286
****************
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: GSM616128_UCSD.H9.H3K4me3.AK39.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4me3.hESC.H9.02.01.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of H9 Cell Line Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me3 ChIP-Seq on the H9 Cell Line, Library AK39 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.6290
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 3

QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 25
FINDPEAKS_SCORE: 0.3245
FINDPEAKS_PERCENTILE: 44
HOTSPOT_SCORE: 0.4015
HOTSPOT_PERCENTILE: 48
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.3959
POISSON_PERCENTILE: 40

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

ANALYSIS FILE NAME: GSM616128_UCSD.H9.H3K4me3.AK39.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4me3.hESC.H9.02.01.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of H9 Cell Line Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me3 ChIP-Seq read mappings from the H9 Cell Line, Library AK39 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.6632
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 3
BROWSER_TRACK_NAME: H9 H3K4me3 39
BROWSER_TRACK_DESCRIPTION: UCSD H9 Cell Line Histone H3K4me3 Library AK39 EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 25
FINDPEAKS_SCORE: 0.3245
FINDPEAKS_PERCENTILE: 44
HOTSPOT_SCORE: 0.4015
HOTSPOT_PERCENTILE: 48
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.3959
POISSON_PERCENTILE: 40

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

source_name: Human embryonic stem cells received from the James Thompson laboratory.  Cells are from the H9 line.; renlab.H3K4me3.hESC.H9.02.01

value: Between 30 and 50

value: Female

value: Histone H3K4me3

value: 250 micrograms

value: magnetic anti-rabbit

value: 5 micrograms

value: Millipore


title: RXR CHIP-seq 4 hours

description: RXR CHIP-seq 4 hours

value: 3T3-L1 preadipocyte cell line

value: RXR


title: Reference Epigenome: ChIP-Seq Analysis of H3K4me2 in hESC H9 Cells; renlab.H3K4me2.hESC.H9.02.01

description:
sample_term_id: NTR_0000838
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K4me2 in hESC H9 Cells. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AK38
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.4287
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.4286
****************
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: GSM616127_UCSD.H9.H3K4me2.AK38.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4me2.hESC.H9.02.01.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of H9 Cell Line Histone H3K4me2 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me2 ChIP-Seq on the H9 Cell Line, Library AK38 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.6265
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 3

QUALITY SCORES:
NUMBER_OF_H3K4me2_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 1
FINDPEAKS_SCORE: 0.244
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.333
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.3581
POISSON_PERCENTILE: 100

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

ANALYSIS FILE NAME: GSM616127_UCSD.H9.H3K4me2.AK38.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4me2.hESC.H9.02.01.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of H9 Cell Line Histone H3K4me2 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me2 ChIP-Seq read mappings from the H9 Cell Line, Library AK38 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.6607
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 3
BROWSER_TRACK_NAME: H9 H3K4me2 38
BROWSER_TRACK_DESCRIPTION: UCSD H9 Cell Line Histone H3K4me2 Library AK38 EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K4me2_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 1
FINDPEAKS_SCORE: 0.244
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.333
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.3581
POISSON_PERCENTILE: 100

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

source_name: Human embryonic stem cells received from the James Thompson laboratory.  Cells are from the H9 line.; renlab.H3K4me2.hESC.H9.02.01

value: genomic DNA

value: James Thompson Laboratory

value: Cell Line

value: Embryonic Stem Cell

value: mTeSER

value: Histone H3K4me2

value: Biorupter

value: Abcam


title: Reference Epigenome: ChIP-Seq Analysis of H3K27ac in hESC H1 Cells; renlab.H3K27ac.hESC.H1.03.01

description:
sample_term_id: EFO_0003042
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K27ac in hESC H1 Cells. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: SAK270
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.5256
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.5258
****************
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: GSM663427_UCSD.H1.H3K27ac.SAK270.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27ac.hESC.H1.03.01.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of H1 Cell Line Histone H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27ac ChIP-Seq on the H1 Cell Line, Library SAK270 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.6270
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 3

QUALITY SCORES:
NUMBER_OF_H3K27ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 2
FINDPEAKS_SCORE: 0.204
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.2837
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9864
IROC_PERCENTILE: 100
POISSON_SCORE: 0.3337
POISSON_PERCENTILE: 100

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

ANALYSIS FILE NAME: GSM663427_UCSD.H1.H3K27ac.SAK270.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27ac.hESC.H1.03.01.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Cell Line Histone H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27ac ChIP-Seq read mappings from the H1 Cell Line, Library SAK270 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.6612
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 3
BROWSER_TRACK_NAME: H1 H3K27ac 70
BROWSER_TRACK_DESCRIPTION: UCSD H1 Cell Line Histone H3K27ac Library SAK270 EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K27ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 2
FINDPEAKS_SCORE: 0.204
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.2837
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9864
IROC_PERCENTILE: 100
POISSON_SCORE: 0.3337
POISSON_PERCENTILE: 100

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

source_name: Human embryonic stem cells received from the James Thompson laboratory.  Cells are from the H1 line.; renlab.H3K27ac.hESC.H1.03.01

value: Male

value: Histone H3K27ac

value: Active Motif


title: DICER_wt_hippocampus

description: small RNA-Seq

tag: genotype/variation

value: Dicer het


title: Reference Epigenome: ChIP-Seq Analysis of H3K9ac in hESC H9 Cells; renlab.H3K9ac.hESC.H9.02.01

description:
sample_term_id: NTR_0000838
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K9ac in hESC H9 Cells. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AK35
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.4291
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.4286
****************
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: GSM616129_UCSD.H9.H3K9ac.AK35.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K9ac.hESC.H9.02.01.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of H9 Cell Line Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9ac ChIP-Seq on the H9 Cell Line, Library AK35 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.6291
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 3

QUALITY SCORES:
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 25
FINDPEAKS_SCORE: 0.0282
FINDPEAKS_PERCENTILE: 4
HOTSPOT_SCORE: 0.1388
HOTSPOT_PERCENTILE: 8
IROC_SCORE: 0.631
IROC_PERCENTILE: 4
POISSON_SCORE: 0.2166
POISSON_PERCENTILE: 16

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

ANALYSIS FILE NAME: GSM616129_UCSD.H9.H3K9ac.AK35.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K9ac.hESC.H9.02.01.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of H9 Cell Line Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9ac ChIP-Seq read mappings from the H9 Cell Line, Library AK35 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.6633
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 3
BROWSER_TRACK_NAME: H9 H3K9ac 35
BROWSER_TRACK_DESCRIPTION: UCSD H9 Cell Line Histone H3K9ac Library AK35 EA Release 3

QUALITY SCORES:
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 25
FINDPEAKS_SCORE: 0.0282
FINDPEAKS_PERCENTILE: 4
HOTSPOT_SCORE: 0.1388
HOTSPOT_PERCENTILE: 8
IROC_SCORE: 0.631
IROC_PERCENTILE: 4
POISSON_SCORE: 0.2166
POISSON_PERCENTILE: 16

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

source_name: Human embryonic stem cells received from the James Thompson laboratory.  Cells are from the H9 line.; renlab.H3K9ac.hESC.H9.02.01

tag: molecule

value: Between 30 and 50

value: Female

value: Histone H3K9ac

value: 250 micrograms

value: magnetic anti-rabbit


title: RNA Pol II ChIP-seq day 0

description: RNA Pol II ChIP-seq day 0

value: 3T3-L1 preadipocyte cell line

value: Preadipocyte

value: day 0

value: RNA Pol II


title: PPARgamma ChIP-seq day 2

description: PPARgamma ChIP-seq day 2

value: Intermediate stage

value: day 2

value: PPARgamma


title: C/EBPdelta ChIP-seq day 0

description: C/EBPdelta ChIP-seq day 0

value: C/EBPdelta


title: Stat5a ChIP-seq 4 hours

description: Stat5a ChIP-seq 4 hours

value: Early stage

value: 4 hours


title: BCV

city: Hangzhou

first: Xiaowei

last: Wang

address: 866 Yuhangtang Road

department: Insect Sciences

country: China

institute: Zhejiang University

description: obtain virus on infected tabocco plants

data_processing: The adapter-ligated tags are fixed on the Solexa Sequencing Chip to form single-molecule cluster, and then sequencing by synthesis is performed to generate millions of raw data with sequencing length of 35bp. Raw sequences were transformed into clean tags through removing adaptor sequence, low quality sequences. For annotation, all tags were mapped to the reference sequences and only allowed no more than 1 nucleotide mismatch. For gene expression analysis, the number of unambiguous clean tags for each gene was calculated and then normalized to TPM.

organism: Bemisia tabaci

source_name: Whitefly female adult

growth_protocol: Culture of B biotype whitefly was maintained on cotton plants.

extract_protocol: 1. mRNA is captured using the magnetic oligo(dT) beads from the extracted total RNA and first- and second-strand cDNA is synthesized. 2. Bead-bound cDNA is subsequently digested with restriction enzyme NlaIII (recognition sequence CATG). 3. The fragments apart from the 3’cDNA fragments connected to oligo(dT) beads are washed away and a special adapter containing a restriction site for MmeI is ligated to the sticky 5’end of the digested bead-bound cDNA fragments. 4. The MmeI cuts 17 bp downstream from the recognition site, then product the 21 bp tag starting with the recognition site of restriction enzyme NlaIII (CATG). 5. A second adapter is ligated at the site of MmeI cleavage. After enriched by polymerase chain reaction (PCR) amplification, the adapter-ligated tags are purified by 6% tris borate (TBE) buffer, polyacrylamide gel electrophoresis (PAGE).

treatment_protocol: Three thousands of newly emerged adults of whitefly on cotton were released onto the leaves of healthy and viruliferous tobacco plants. They were allowed to feed for 24 h. After that, non-viruliferous and viruliferous whiteflies were transferred respectively to cotton plants in different cages and allowed to feed for 120 h. Then approximately 1,000 non-viruliferous and viruliferous female adults of whitefly were collected, respectively.

tag: biotype

value: B biotype

tag: growth condition

value: maintained on cotton

tag: agent

value: with TYLCCNV


title: Reference Epigenome: ChIP-Seq Analysis of H2AK5ac in hESC H9 Cells; renlab.H2AK5ac.hESC.H9.02.01

description:
sample_term_id: NTR_0000838
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H2AK5ac in hESC H9 Cells. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AK28
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.5954
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.4286
****************
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: GSM667609_UCSD.H9.H2AK5ac.AK28.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H2AK5ac.hESC.H9.02.01.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of H9 Cell Line Histone H2AK5ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H2AK5ac ChIP-Seq on the H9 Cell Line, Library AK28 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.6288
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 3

QUALITY SCORES:
NUMBER_OF_H2AK5ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 2
FINDPEAKS_SCORE: 0.0049
FINDPEAKS_PERCENTILE: 50
HOTSPOT_SCORE: 0.0451
HOTSPOT_PERCENTILE: 50
IROC_SCORE: 0.0
IROC_PERCENTILE: 50
POISSON_SCORE: 0.1201
POISSON_PERCENTILE: 50

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

ANALYSIS FILE NAME: GSM667609_UCSD.H9.H2AK5ac.AK28.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H2AK5ac.hESC.H9.02.01.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of H9 Cell Line Histone H2AK5ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H2AK5ac ChIP-Seq read mappings from the H9 Cell Line, Library AK28 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.6630
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 3
BROWSER_TRACK_NAME: H9 H2AK5ac 28
BROWSER_TRACK_DESCRIPTION: UCSD H9 Cell Line Histone H2AK5ac Library AK28 EA Release 3

QUALITY SCORES:
NUMBER_OF_H2AK5ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 2
FINDPEAKS_SCORE: 0.0049
FINDPEAKS_PERCENTILE: 50
HOTSPOT_SCORE: 0.0451
HOTSPOT_PERCENTILE: 50
IROC_SCORE: 0.0
IROC_PERCENTILE: 50
POISSON_SCORE: 0.1201
POISSON_PERCENTILE: 50

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

source_name: Human embryonic stem cells received from the James Thompson laboratory.  Cells are from the H9 line.; renlab.H2AK5ac.hESC.H9.02.01

tag: sample alias

tag: sample common name

value: H9 Cell Line

value: genomic DNA

tag: disease

value: James Thompson Laboratory

value: Cell Line

tag: line

tag: lineage

value: Embryonic Stem Cell

value: Between 30 and 50

value: mTeSER

value: Female

value: Histone H2AK5ac

value: Biorupter

value: 500 micrograms

value: 5 micrograms

value: Abcam