title: Reference Epigenome: ChIP-Seq Analysis of H3K27me3 in hESC H9 Cells; renlab.H3K27me3.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 H3K27me3 in hESC H9 Cells. Sequencing was done on the Illumina Genome Analyzer IIx platform.
Library name: AK142
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.6950
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.6947
****************
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: GSM706066_UCSD.H9.H3K27me3.AK142.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27me3.hESC.H9.02.01.hg19.level.1.release.4
ANALYSIS TITLE: Mapping of H9 Cell Line Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27me3 ChIP-Seq on the H9 Cell Line, Library AK142 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.8290
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 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 32,287,285
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 11
FINDPEAKS_SCORE: 0.0139
FINDPEAKS_PERCENTILE: 18
HOTSPOT_SCORE: 0.0398
HOTSPOT_PERCENTILE: 9
IROC_SCORE: 0.9104
IROC_PERCENTILE: 27
POISSON_SCORE: 0.098
POISSON_PERCENTILE: 9
MAXIMUM_REPLICATE_CORRELATION: 0.57

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

ANALYSIS FILE NAME: GSM706066_UCSD.H9.H3K27me3.AK142.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27me3.hESC.H9.02.01.hg19.level.2.release.4
ANALYSIS TITLE: Raw Signal Density Graphs of H9 Cell Line Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27me3 ChIP-Seq read mappings from the H9 Cell Line, Library AK142 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.8309
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 4
BROWSER_TRACK_NAME: H9 H3K27me3 42
BROWSER_TRACK_DESCRIPTION: UCSD H9 Cell Line Histone H3K27me3 Library AK142 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 32,287,285
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 11
FINDPEAKS_SCORE: 0.0139
FINDPEAKS_PERCENTILE: 18
HOTSPOT_SCORE: 0.0398
HOTSPOT_PERCENTILE: 9
IROC_SCORE: 0.9104
IROC_PERCENTILE: 27
POISSON_SCORE: 0.098
POISSON_PERCENTILE: 9
MAXIMUM_REPLICATE_CORRELATION: 0.57

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

source_name: Human embryonic stem cells received from the James Thompson laboratory.  Cells are from the H9 line.; renlab.H3K27me3.hESC.H9.02.01

value: H9 Cell Line

value: Embryonic Stem Cell

value: Between 30 and 50

value: mTeSER

value: Female


title: Reference Epigenome: ChIP-Seq Analysis of H3K27ac in iPS 19.11 Cells; renlab.H3K27ac.iPS-19.11_01.01

status: Public on Apr 13 2011

type: SRA

city: La Jolla

first: UCSD AND

last: SALK

state: CA

address: Health Sciences Drive

country: USA

institute: University of California, San Diego

description:
sample_term_id: NTR_0001173
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K27ac in iPS 19.11 Cells. Sequencing was done on the Illumina Genome Analyzer IIx platform.
Library name: SK402
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.6814
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.6813
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

library_source: genomic

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

ANALYSIS FILE NAME: GSM706065_UCSD.iPS_DF_19.11.H3K27ac.SK402.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27ac.iPS-19.11_01.01.hg19.level.1.release.4
ANALYSIS TITLE: Mapping of iPS DF 19.11 Cell Line Histone H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27ac ChIP-Seq on the iPS DF 19.11 Cell Line, Library SK402 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.8284
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 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 18,706,248
NUMBER_OF_H3K27ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 1
FINDPEAKS_SCORE: 0.0533
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.1728
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.8331
IROC_PERCENTILE: 100
POISSON_SCORE: 0.2904
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM706065_UCSD.iPS_DF_19.11.H3K27ac.SK402.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27ac.iPS-19.11_01.01.hg19.level.2.release.4
ANALYSIS TITLE: Raw Signal Density Graphs of iPS DF 19.11 Cell Line Histone H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27ac ChIP-Seq read mappings from the iPS DF 19.11 Cell Line, Library SK402 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.8303
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 4
BROWSER_TRACK_NAME: iD19.11 H3K27ac 02
BROWSER_TRACK_DESCRIPTION: UCSD iPS DF 19.11 Cell Line Histone H3K27ac Library SK402 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 18,706,248
NUMBER_OF_H3K27ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 1
FINDPEAKS_SCORE: 0.0533
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.1728
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.8331
IROC_PERCENTILE: 100
POISSON_SCORE: 0.2904
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: NA

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

molecule: genomic DNA

organism: Homo sapiens

source_name: Human induced pluripotent stem cell line derived from foreskin fibroblasts, isolated as described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009).; renlab.H3K27ac.iPS-19.11_01.01

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

tag: sample alias

tag: sample common name

value: iPS DF 19.11 Cell Line

tag: molecule

value: genomic DNA

tag: disease

value: James Thompson Laboratory

value: Cell Line

tag: line

tag: lineage

value: Induced pluripotent stem cell line derived from foreskin fibroblasts

value: Induced pluripotent stem cell

value: As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009).

tag: passage

value: Between 30 and 40

tag: medium

value: mTeSR

tag: Sex

value: Male

tag: batch

value: Histone H3K27ac

value: Biorupter

value: 500 micrograms

value: magnetic anti-rabbit

value: 5 micrograms

value: Active Motif


title: Reference Epigenome: ChIP-Seq Analysis of H2BK15ac in hESC H9 Cells; renlab.H2BK15ac.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 H2B1K5ac in hESC H9 Cells. Sequencing was done on the Illumina Genome Analyzer IIx platform.
Library name: AK113
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.6938
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: GSM706062_UCSD.H9.H2BK15ac.AK113.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H2BK15ac.hESC.H9.01.01.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of H9 Cell Line Histone H2BK15ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H2BK15ac ChIP-Seq on H9 Cell Line, Library AK113, 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.12376
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 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 33,614,560
NUMBER_OF_H2BK15ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 2
FINDPEAKS_SCORE: 0.0042
FINDPEAKS_PERCENTILE: 50
HOTSPOT_SCORE: 0.0585
HOTSPOT_PERCENTILE: 50
IROC_SCORE: 0.8511
IROC_PERCENTILE: 100
POISSON_SCORE: 0.1668
POISSON_PERCENTILE: 50
MAXIMUM_REPLICATE_CORRELATION: 0.88

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

ANALYSIS FILE NAME: GSM706062_UCSD.H9.H2BK15ac.AK113.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H2BK15ac.hESC.H9.01.01.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of H9 Cell Line Histone H2BK15ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H2BK15ac ChIP-Seq read mappings from the H9 Cell Line, Library AK113, 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.12449
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 6
BROWSER_TRACK_NAME: H9 H2BK15ac 13
BROWSER_TRACK_DESCRIPTION: UCSD H9 Cell Line Histone H2BK15ac Library AK113 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 33,614,560
NUMBER_OF_H2BK15ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 2
FINDPEAKS_SCORE: 0.0042
FINDPEAKS_PERCENTILE: 50
HOTSPOT_SCORE: 0.0585
HOTSPOT_PERCENTILE: 50
IROC_SCORE: 0.8511
IROC_PERCENTILE: 100
POISSON_SCORE: 0.1668
POISSON_PERCENTILE: 50
MAXIMUM_REPLICATE_CORRELATION: 0.88

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

source_name: Human embryonic stem cells received from the James Thompson laboratory.  Cells are from the H9 line.; renlab.H2BK15ac.hESC.H9.01.01

value: H9 Cell Line

value: Embryonic Stem Cell

value: Between 30 and 50

value: mTeSER

value: Female

value: Histone H2BK15ac

value: Abcam


title: Reference Epigenome: ChIP-Seq Analysis of H3K18ac in hESC H9 Cells; renlab.H3K18ac.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 H3K18ac in hESC H9 Cells. Sequencing was done on the Illumina Genome Analyzer IIx platform.
Library name: SK375
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.6943
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.6940
****************
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: GSM706064_UCSD.H9.H3K18ac.SK375.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K18ac.hESC.H9.02.01.hg19.level.1.release.4
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 SK375 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.8295
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 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 24,951,740
NUMBER_OF_H3K18ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 1
FINDPEAKS_SCORE: 0.1106
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.2141
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.894
IROC_PERCENTILE: 100
POISSON_SCORE: 0.3445
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.81

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

ANALYSIS FILE NAME: GSM706064_UCSD.H9.H3K18ac.SK375.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K18ac.hESC.H9.02.01.hg19.level.2.release.4
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 SK375 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.8314
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 4
BROWSER_TRACK_NAME: H9 H3K18ac 75
BROWSER_TRACK_DESCRIPTION: UCSD H9 Cell Line Histone H3K18ac Library SK375 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 24,951,740
NUMBER_OF_H3K18ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 1
FINDPEAKS_SCORE: 0.1106
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.2141
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.894
IROC_PERCENTILE: 100
POISSON_SCORE: 0.3445
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.81

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

source_name: Human embryonic stem cells received from the James Thompson laboratory.  Cells are from the H9 line.; renlab.H3K18ac.hESC.H9.02.01

value: genomic DNA

value: James Thompson Laboratory

value: Cell Line

value: Histone H3K18ac


title: Reference Epigenome: ChIP-Seq Analysis of H3K27me3 in iPS 19.11 Cells; renlab.H3K27me3.iPS-19.11_01.01

description:
sample_term_id: NTR_0001173
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K27me3 in iPS 19.11 Cells. Sequencing was done on the Illumina Genome Analyzer IIx platform.
Library name: SK230
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.6816
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.6813
****************
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: GSM706067_UCSD.iPS_DF_19.11.H3K27me3.SK230.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27me3.iPS-19.11_01.01.hg19.level.1.release.4
ANALYSIS TITLE: Mapping of iPS DF 19.11 Cell Line Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27me3 ChIP-Seq on the iPS DF 19.11 Cell Line, Library SK230 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.8289
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 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 22,508,749
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 11
FINDPEAKS_SCORE: 0.0214
FINDPEAKS_PERCENTILE: 27
HOTSPOT_SCORE: 0.0791
HOTSPOT_PERCENTILE: 27
IROC_SCORE: 0.9617
IROC_PERCENTILE: 55
POISSON_SCORE: 0.1158
POISSON_PERCENTILE: 18
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM706067_UCSD.iPS_DF_19.11.H3K27me3.SK230.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27me3.iPS-19.11_01.01.hg19.level.2.release.4
ANALYSIS TITLE: Raw Signal Density Graphs of iPS DF 19.11 Cell Line Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27me3 ChIP-Seq read mappings from the iPS DF 19.11 Cell Line, Library SK230 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.8308
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 4
BROWSER_TRACK_NAME: iD19.11 H3K27me3 30
BROWSER_TRACK_DESCRIPTION: UCSD iPS DF 19.11 Cell Line Histone H3K27me3 Library SK230 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 22,508,749
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 11
FINDPEAKS_SCORE: 0.0214
FINDPEAKS_PERCENTILE: 27
HOTSPOT_SCORE: 0.0791
HOTSPOT_PERCENTILE: 27
IROC_SCORE: 0.9617
IROC_PERCENTILE: 55
POISSON_SCORE: 0.1158
POISSON_PERCENTILE: 18
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: Human induced pluripotent stem cell line derived from foreskin fibroblasts, isolated as described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009).; renlab.H3K27me3.iPS-19.11_01.01

value: iPS DF 19.11 Cell Line

value: Induced pluripotent stem cell line derived from foreskin fibroblasts

value: Induced pluripotent stem cell

value: As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009).

value: Between 30 and 40

value: mTeSR

value: Male

value: Histone H3K27me3


title: Reference Epigenome: ChIP-Seq Analysis of H2BK15ac in hESC H9 Cells; renlab.H2BK15ac.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 H2B1K5ac in hESC H9 Cells. Sequencing was done on the Illumina Genome Analyzer IIx platform.
Library name: SK376
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.6945
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.6940
****************
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: GSM706063_UCSD.H9.H2BK15ac.SK376.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H2BK15ac.hESC.H9.02.01.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of H9 Cell Line Histone H2BK15ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H2BK15ac ChIP-Seq on H9 Cell Line, Library SK376, 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.12405
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 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 14,904,074
NUMBER_OF_H2BK15ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 2
FINDPEAKS_SCORE: 0.0107
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.1406
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.6418
IROC_PERCENTILE: 50
POISSON_SCORE: 0.2666
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.88

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

ANALYSIS FILE NAME: GSM706063_UCSD.H9.H2BK15ac.SK376.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H2BK15ac.hESC.H9.02.01.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of H9 Cell Line Histone H2BK15ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H2BK15ac ChIP-Seq read mappings from the H9 Cell Line, Library SK376, 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.12478
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 6
BROWSER_TRACK_NAME: H9 H2BK15ac 76
BROWSER_TRACK_DESCRIPTION: UCSD H9 Cell Line Histone H2BK15ac Library SK376 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 14,904,074
NUMBER_OF_H2BK15ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 2
FINDPEAKS_SCORE: 0.0107
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.1406
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.6418
IROC_PERCENTILE: 50
POISSON_SCORE: 0.2666
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.88

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

source_name: Human embryonic stem cells received from the James Thompson laboratory.  Cells are from the H9 line.; renlab.H2BK15ac.hESC.H9.02.01

value: H9 Cell Line

value: Embryonic Stem Cell

value: Biorupter

value: 500 micrograms

value: magnetic anti-rabbit

value: 5 micrograms


title: IgG_DnmtTKO

city: Copenhagen

first: Kristine

last: Williams

address: Ole Maaløes vej 5

department: BRIC

country: Denmark

institute: University of Copenhagen

data_processing: Preprocessing: Sequenced adapters and low quality reads were removed. Alignment: Tags were mapped to the mouse genome (assembly mm9) with the Bowtie alignment tool with parameters: -t --best -k 1 -y -p 4 --solexa1.3-quals --chunkmbs 512 -n 2 -l 28 -e 120 and the Solexa Analysis Pipeline. To avoid any PCR bias we allowed only one count (match) per chromosomal position thus eliminating spurious spikes. Peak detection, binding and gene annotation analysis were performed using the Cisgenome program.

organism: Mus musculus

source_name: embryonic stem cells

growth_protocol: Low passage (p17) E14TG2a.4 feeder independent ES cells were cultured on 0.1% gelatin-coated plates in Glasgow medium (Sigma) supplemented with glutamine (Gibco), nonessential amino acids (Gibco), sodium pyruvate (Gibco), 50 ìM ßmercaptoethanol, and 15% foetal bovine serum (HyClone) in the presence of LIF. Recombinant lentiviruses encoding TET1 shRNA were produced by standard methods employing co-transfection of PLKO.1 shRNA and packaging vectors in 293FT cells. shRNA transduced ES cells were selected 36 hours post transduction with 2 ìg per ml of puromycin for 72 hours.

extract_protocol:
Chromatin immunoprecipitation assays (ChIP) were performed and analysed as previously described {Pasini et al. (2010). Nature. 2010 Mar 11;464(7286):306-10. ES cell DNA was sonicated to an average size between 300-600 bp. Adaptor-ligated libraries for hmC or mC DNA immunoprecipitation assays (hm-DIP/me-DIP) were constructed using the NEBNext™ DNA Sample Prep Master Mix, NEB combined with Illumina adaptors. hme/me-DIP assays were performed as described by {Weber et al., Nat Genet. 2005 Aug;37(8):853-62} using one µg of denatured sonicated or adaptor-ligated DNA in 100 ul of binding buffer and 0.1-4 µg of affinity purified rabbit hmC antibody or monoclonal mC antibody (Eurogentec BI-MECY-0500). The samples were incubated for four hours at 4ºC before addition of 10 µl of anti-rabbit/mouse Dynabeads (InVitrogen). After two hours of incubation, the samples were washed four times and bound DNA was eluted by incubation for one hour at 55 ºC in 100 ml of 50 mM Tris-HCl, 10 mM EDTA, 0.5% SDS and 20 mg proteinase K. The DNA was purified using a Qiaquick PCR purification kit (Qiagen) and amplified by 16 cycles of PCR. For ChIP-seq analysis, the DNA obtained from the ChIP assays were adaptor-ligated and amplified using a kit from Illumina (IP-102-1001). The amplified DNA from hme/me-DIP or ChIP-seq experiments was analyzed by Solexa/Illumina high-throughput sequencing. The tags were mapped to the mouse genome (assembly mm9) with the Bowtie alignment tool and the Solexa Analysis Pipeline.
DNA was adaptor-ligated and amplified using a kit from Illumina (IP-102-1001). The amplified DNA from hme/me-DIP or ChIP-seq experiments was analyzed by Solexa/Illumina high-throughput sequencing. The tags were mapped to the mouse genome (assembly mm9) with the Bowtie alignment tool26 and the Solexa Analysis Pipeline. To avoid any PCR bias we allowed only one count (match) per chromosomal position thus eliminating spurious spikes. Peak detection, binding and gene annotation analysis were performed using the CisGenome program22 at an FDR cut-off value <0.1 or <0.01 as indicated in the text. IgG was used for normalization

treatment_protocol: Cells were either untransfected or transfected with a scrambled or Tet1 specific shRNA

tag: chip or dip

value: DIP

tag: cell type

value: embryonic stem cells

tag: genotype/variation

value: Dnmt tripple knock out

tag: chip/dip antibody

value: IgG ctrl


title: mC_shTet1

value: methycytosine


title: hmC_DnmtTKO

value: hydroxymethylcytosine


title: Reference Epigenome: ChIP-Seq Analysis of H3K56ac in hESC H9 Cells; renlab.H3K56ac.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 H3K56ac in hESC H9 Cells. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: SK279
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.6936
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: GSM706076_UCSD.H9.H3K56ac.SK279.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K56ac.hESC.H9.02.01.hg19.level.1.release.4
ANALYSIS TITLE: Mapping of H9 Cell Line Histone H3K56ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K56ac ChIP-Seq on the H9 Cell Line, Library SK279 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.8296
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 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 16,046,009
NUMBER_OF_H3K56ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 1
FINDPEAKS_SCORE: 0.0244
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.1777
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.7202
IROC_PERCENTILE: 100
POISSON_SCORE: 0.3316
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.92

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

ANALYSIS FILE NAME: GSM706076_UCSD.H9.H3K56ac.SK279.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K56ac.hESC.H9.02.01.hg19.level.2.release.4
ANALYSIS TITLE: Raw Signal Density Graphs of H9 Cell Line Histone H3K56ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K56ac ChIP-Seq read mappings from the H9 Cell Line, Library SK279 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.8315
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 4
BROWSER_TRACK_NAME: H9 H3K56ac 79
BROWSER_TRACK_DESCRIPTION: UCSD H9 Cell Line Histone H3K56ac Library SK279 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 16,046,009
NUMBER_OF_H3K56ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 1
FINDPEAKS_SCORE: 0.0244
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.1777
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.7202
IROC_PERCENTILE: 100
POISSON_SCORE: 0.3316
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.92

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

source_name: Human embryonic stem cells received from the James Thompson laboratory.  Cells are from the H9 line.; renlab.H3K56ac.hESC.H9.02.01

value: genomic DNA

value: James Thompson Laboratory

value: Cell Line

value: Between 30 and 50

value: mTeSER

value: Female

value: Histone H3K56ac

value: Millipore


title: mC_DnmtTKO


title: mC_shScr

value: shScr


title: mC

value: untransfected


title: Sin3A_SCruz

value: ChIP

value: Sin3A from Santa Cruz


title: hmC_shTet1

value: DIP

value: embryonic stem cells


title: IgG_ChIP

value: IgG ctrl


title: Shotgun sequencing of polyA+ RNA isolated from the iPS cell line clone 19.11; mRNA-Seq_ff_ips_19_11_r3

description:
sample_term_id: NTR_0001173
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: Shotgun sequencing of polyA+ RNA isolated from the iPS cell line clone 19.11 derived from reprogramming of foreskin fibroblasts
Library name: mRNA-Seq_ff_ips_19_11_r3
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.6934
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.6926
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

library_source: transcriptomic

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

ANALYSIS FILE NAME: GSM706051_UCSD.iPS_DF_19.11.mRNA-Seq.mRNA-Seq_ff_ips_19_11_r3.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: mRNA-Seq_ff_ips_19_11_r3.hg19.level.1.release.4
ANALYSIS TITLE: Mapping of iPS DF 19.11 Cell Line mRNA-Seq Data
ANALYSIS DESCRIPTION: SOLiD reads produced by mRNA-Seq on the iPS DF 19.11 Cell Line, Library mRNA-Seq_ff_ips_19_11_r3 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.9493
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 15,084,409
NUMBER_OF_MRNA-SEQ_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 8
PERCENT_READS_MAPPING_TO_UCSC_GENES: 92.74
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 75
MAXIMUM_REPLICATE_CORRELATION: 0.94

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

ANALYSIS FILE NAME: GSM706051_UCSD.iPS_DF_19.11.mRNA-Seq.mRNA-Seq_ff_ips_19_11_r3.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: mRNA-Seq_ff_ips_19_11_r3.hg19.level.2.release.4
ANALYSIS TITLE: Raw Signal Density Graphs of iPS DF 19.11 Cell Line mRNA-Seq Data
ANALYSIS DESCRIPTION: SOLiD mRNA-Seq read mappings from the iPS DF 19.11 Cell Line, Library mRNA-Seq_ff_ips_19_11_r3 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.9501
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 4
BROWSER_TRACK_NAME: iD19.11 mRNA r3
BROWSER_TRACK_DESCRIPTION: UCSD iPS DF 19.11 Cell Line mRNA-Seq Library mRNA-Seq_ff_ips_19_11_r3 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 15,084,409
NUMBER_OF_MRNA-SEQ_EXPERIMENTS_SCORED: 8
PERCENT_READS_MAPPING_TO_UCSC_GENES: 92.74
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 75
MAXIMUM_REPLICATE_CORRELATION: 0.94

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

molecule: total RNA

source_name: iPS cell line clone 19.11 derived from reprogramming of foreskin fibroblasts, biological replicate 3 (r3); mRNA-Seq_ff_ips_19_11_r3

extract_protocol: Library construction protocol: SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)

value: iPS DF 19.11 Cell Line

value: Thomson Laboratory

value: iPS DF 19.11

value: induced pluripotent stem cell

value: TeSR

value: Male

value: Replicate 3

value: mRNA-Seq

value: RNeasy Blood and Tissue Kit (Qiagen)

value: Poly(A)Purist MAG Kit (Ambion)


title: Shotgun sequencing of polyA+ RNA isolated from the iPS cell line clone 6.9; mRNA-Seq_ff_ips_6_9_r1

description:
sample_term_id: NTR_0001172
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: Shotgun sequencing of polyA+ RNA isolated from the iPS cell line clone 6.9 derived from reprogramming of foreskin fibroblasts
Library name: mRNA-Seq_ff_ips_6_9_r1
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.6935
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.6923
****************
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: GSM706052_UCSD.iPS_DF_6.9.mRNA-Seq.mRNA-Seq_ff_ips_6_9_r1.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: mRNA-Seq_ff_ips_6_9_r1.hg19.level.1.release.4
ANALYSIS TITLE: Mapping of iPS DF 6.9 Cell Line mRNA-Seq Data
ANALYSIS DESCRIPTION: SOLiD reads produced by mRNA-Seq on the iPS DF 6.9 Cell Line, Library mRNA-Seq_ff_ips_6_9_r1 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.9492
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 15,319,378
NUMBER_OF_MRNA-SEQ_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 8
PERCENT_READS_MAPPING_TO_UCSC_GENES: 89.84
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 38
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM706052_UCSD.iPS_DF_6.9.mRNA-Seq.mRNA-Seq_ff_ips_6_9_r1.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: mRNA-Seq_ff_ips_6_9_r1.hg19.level.2.release.4
ANALYSIS TITLE: Raw Signal Density Graphs of iPS DF 6.9 Cell Line mRNA-Seq Data
ANALYSIS DESCRIPTION: SOLiD mRNA-Seq read mappings from the iPS DF 6.9 Cell Line, Library mRNA-Seq_ff_ips_6_9_r1 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.9500
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 4
BROWSER_TRACK_NAME: iD6.9 mRNA r1
BROWSER_TRACK_DESCRIPTION: UCSD iPS DF 6.9 Cell Line mRNA-Seq Library mRNA-Seq_ff_ips_6_9_r1 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 15,319,378
NUMBER_OF_MRNA-SEQ_EXPERIMENTS_SCORED: 8
PERCENT_READS_MAPPING_TO_UCSC_GENES: 89.84
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 38
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: iPS cell line clone 6.9 derived from reprogramming of foreskin fibroblasts, biological replicate 1 (r1); mRNA-Seq_ff_ips_6_9_r1

value: iPS DF 6.9 Cell Line

value: genomic DNA

value: Cell Line

value: iPS DF 6.9

value: Replicate 1

value: SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)


title: Shotgun sequencing of polyA+ RNA from the H1 cell line differentiated into neural progenitor cells; mRNA-Seq_h1-npc_r2

description:
sample_term_id: CL_0000047
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: Shotgun sequencing of polyA+ RNA isolated from the H1 cell line differentiated into neural progenitor cells
Library name: mRNA-Seq_h1-npc_r2
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.6932
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.6200
****************
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: GSM706049_UCSD.H1_Derived_Neuronal_Progenitor_Cultured_Cells.mRNA-Seq.mRNA-Seq_h1-npc_r2.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: mRNA-Seq_h1-npc_r2.hg19.level.1.release.4
ANALYSIS TITLE: Mapping of H1 Derived Neuronal Progenitor Cultured Cells mRNA-Seq Data
ANALYSIS DESCRIPTION: SOLiD reads produced by mRNA-Seq on H1 Derived Neuronal Progenitor Cultured Cells, Donor mRNA-Seq_h1-npc_r2 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.9496
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 14,860,811
NUMBER_OF_MRNA-SEQ_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 8
PERCENT_READS_MAPPING_TO_UCSC_GENES: 92.03
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 63
MAXIMUM_REPLICATE_CORRELATION: 0.12

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

ANALYSIS FILE NAME: GSM706049_UCSD.H1_Derived_Neuronal_Progenitor_Cultured_Cells.mRNA-Seq.mRNA-Seq_h1-npc_r2.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: mRNA-Seq_h1-npc_r2.hg19.level.2.release.4
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Derived Neuronal Progenitor Cultured Cells mRNA-Seq Data
ANALYSIS DESCRIPTION: SOLiD mRNA-Seq read mappings from H1 Derived Neuronal Progenitor Cultured Cells, Donor mRNA-Seq_h1-npc_r2 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.9504
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 4
BROWSER_TRACK_NAME: HDNP mRNA r2
BROWSER_TRACK_DESCRIPTION: UCSD H1 Derived Neuronal Progenitor Cultured Cells mRNA-Seq Donor mRNA-Seq_h1-npc_r2 Library mRNA-Seq_h1-npc_r2 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 14,860,811
NUMBER_OF_MRNA-SEQ_EXPERIMENTS_SCORED: 8
PERCENT_READS_MAPPING_TO_UCSC_GENES: 92.03
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 63
MAXIMUM_REPLICATE_CORRELATION: 0.12

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

source_name: H1 cell line differentiated into neural progenitor cells, biological replicate 2 (r2); mRNA-Seq_h1-npc_r2

value: embryonic stem cell differentiated into neural progenitor cells

value: H1 cells were differentiated by culturing in insulin, SB, Noggin

value: Replicate 2


title: Sin3A_Abcam

value: ChIP

value: embryonic stem cells

value: untransfected

value: Sin3A from Abcam


title: IgG_DIP

value: DIP

value: IgG ctrl


title: Shotgun sequencing of polyA+ RNA from the H1 cell line differentiated into neural progenitor cells; mRNA-Seq_h1-npc_r1

description:
sample_term_id: CL_0000047
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: Shotgun sequencing of polyA+ RNA isolated from the H1 cell line differentiated into neural progenitor cells
Library name: mRNA-Seq_h1-npc_r1
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.6931
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.6199
****************
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: GSM706048_UCSD.H1_Derived_Neuronal_Progenitor_Cultured_Cells.mRNA-Seq.mRNA-Seq_h1-npc_r1.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: mRNA-Seq_h1-npc_r1.hg19.level.1.release.4
ANALYSIS TITLE: Mapping of H1 Derived Neuronal Progenitor Cultured Cells mRNA-Seq Data
ANALYSIS DESCRIPTION: SOLiD reads produced by mRNA-Seq on H1 Derived Neuronal Progenitor Cultured Cells, Donor mRNA-Seq_h1-npc_r1 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.9495
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 16,828,861
NUMBER_OF_MRNA-SEQ_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 8
PERCENT_READS_MAPPING_TO_UCSC_GENES: 89.61
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 13
MAXIMUM_REPLICATE_CORRELATION: 0.12

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

ANALYSIS FILE NAME: GSM706048_UCSD.H1_Derived_Neuronal_Progenitor_Cultured_Cells.mRNA-Seq.mRNA-Seq_h1-npc_r1.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: mRNA-Seq_h1-npc_r1.hg19.level.2.release.4
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Derived Neuronal Progenitor Cultured Cells mRNA-Seq Data
ANALYSIS DESCRIPTION: SOLiD mRNA-Seq read mappings from H1 Derived Neuronal Progenitor Cultured Cells, Donor mRNA-Seq_h1-npc_r1 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.9503
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 4
BROWSER_TRACK_NAME: HDNP mRNA r1
BROWSER_TRACK_DESCRIPTION: UCSD H1 Derived Neuronal Progenitor Cultured Cells mRNA-Seq Donor mRNA-Seq_h1-npc_r1 Library mRNA-Seq_h1-npc_r1 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 16,828,861
NUMBER_OF_MRNA-SEQ_EXPERIMENTS_SCORED: 8
PERCENT_READS_MAPPING_TO_UCSC_GENES: 89.61
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 13
MAXIMUM_REPLICATE_CORRELATION: 0.12

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

source_name: H1 cell line differentiated into neural progenitor cells, biological replicate 1 (r1); mRNA-Seq_h1-npc_r1

value: Thomson Laboratory

value: TeSR

value: Male

value: mRNA-Seq

value: RNeasy Blood and Tissue Kit (Qiagen)


title: Tet1-C_shScr

value: shScr


title: Shotgun sequencing of polyA+ RNA isolated from the H1+BMP4 trophoblast cell line; mRNA-Seq_h1+bmp4_r2

description:
sample_term_id: UBERON_0000088
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: Shotgun sequencing of polyA+ RNA isolated from the H1+BMP4 trophoblast cell line
Library name: mRNA-Seq_h1+bmp4_r2
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.6930
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.3378
****************
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: GSM706047_UCSD.H1-BMP4.mRNA-Seq.mRNA-Seq_h1+bmp4_r2.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: mRNA-Seq_h1+bmp4_r2.hg19.level.1.release.4
ANALYSIS TITLE: Mapping of H1-BMP4 Cell Line mRNA-Seq Data
ANALYSIS DESCRIPTION: SOLiD reads produced by mRNA-Seq on the H1-BMP4 Cell Line, Library mRNA-Seq_h1+bmp4_r2 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.9494
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 14,984,957
NUMBER_OF_MRNA-SEQ_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 8
PERCENT_READS_MAPPING_TO_UCSC_GENES: 93.34
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 88
MAXIMUM_REPLICATE_CORRELATION: 0.72

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

ANALYSIS FILE NAME: GSM706047_UCSD.H1-BMP4.mRNA-Seq.mRNA-Seq_h1+bmp4_r2.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: mRNA-Seq_h1+bmp4_r2.hg19.level.2.release.4
ANALYSIS TITLE: Raw Signal Density Graphs of H1-BMP4 Cell Line mRNA-Seq Data
ANALYSIS DESCRIPTION: SOLiD mRNA-Seq read mappings from the H1-BMP4 Cell Line, Library mRNA-Seq_h1+bmp4_r2 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.9502
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 4
BROWSER_TRACK_NAME: H1BMP4 mRNA r2
BROWSER_TRACK_DESCRIPTION: UCSD H1-BMP4 Cell Line mRNA-Seq Library mRNA-Seq_h1+bmp4_r2 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 14,984,957
NUMBER_OF_MRNA-SEQ_EXPERIMENTS_SCORED: 8
PERCENT_READS_MAPPING_TO_UCSC_GENES: 93.34
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 88
MAXIMUM_REPLICATE_CORRELATION: 0.72

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

source_name: H1 Cell Line treated with BMP4, biological replicate 2 (r2); mRNA-Seq_h1+bmp4_r2

value: H1-BMP4 Cell Line

value: Cell Line

value: embryonic stem cell differentiated by treatment with BMP4

value: H1 cells were cultured in TeSR containing 50 ng/ml BMP4 for 5 days

value: 25, including 10 passages in TeSR

value: Poly(A)Purist MAG Kit (Ambion)


title: Tet1-N_shTet1

value: ChIP

value: embryonic stem cells


title: Tet1-C_shTet1


title: Shotgun sequencing of polyA+ RNA isolated from the H1+BMP4 trophoblast cell line; mRNA-Seq_h1+bmp4_r1

description:
sample_term_id: UBERON_0000088
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: Shotgun sequencing of polyA+ RNA isolated from the H1+BMP4 trophoblast cell line
Library name: mRNA-Seq_h1+bmp4_r1
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.6929
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.3377
****************
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: GSM706046_UCSD.H1-BMP4.mRNA-Seq.mRNA-Seq_h1+bmp4_r1.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: mRNA-Seq_h1+bmp4_r1.hg19.level.1.release.4
ANALYSIS TITLE: Mapping of H1-BMP4 Cell Line mRNA-Seq Data
ANALYSIS DESCRIPTION: SOLiD reads produced by mRNA-Seq on the H1-BMP4 Cell Line, Library mRNA-Seq_h1+bmp4_r1 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.9491
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 17,059,655
NUMBER_OF_MRNA-SEQ_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 8
PERCENT_READS_MAPPING_TO_UCSC_GENES: 91.06
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 50
MAXIMUM_REPLICATE_CORRELATION: 0.72

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

ANALYSIS FILE NAME: GSM706046_UCSD.H1-BMP4.mRNA-Seq.mRNA-Seq_h1+bmp4_r1.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: mRNA-Seq_h1+bmp4_r1.hg19.level.2.release.4
ANALYSIS TITLE: Raw Signal Density Graphs of H1-BMP4 Cell Line mRNA-Seq Data
ANALYSIS DESCRIPTION: SOLiD mRNA-Seq read mappings from the H1-BMP4 Cell Line, Library mRNA-Seq_h1+bmp4_r1 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.9499
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 4
BROWSER_TRACK_NAME: H1BMP4 mRNA r1
BROWSER_TRACK_DESCRIPTION: UCSD H1-BMP4 Cell Line mRNA-Seq Library mRNA-Seq_h1+bmp4_r1 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 17,059,655
NUMBER_OF_MRNA-SEQ_EXPERIMENTS_SCORED: 8
PERCENT_READS_MAPPING_TO_UCSC_GENES: 91.06
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 50
MAXIMUM_REPLICATE_CORRELATION: 0.72

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

source_name: H1 Cell Line treated with BMP4, biological replicate 1 (r1); mRNA-Seq_h1+bmp4_r1

value: 27, including 16 passages in TeSR

value: Replicate 1

value: SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)


title: Tet1-N_shScr


title: Shotgun sequencing of polyA+ RNA isolated from the H9 cell line; mRNA-Seq_h9_r1

description:
sample_term_id: NTR_0000838
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: Shotgun sequencing of polyA+ RNA isolated from the H9 cell line
Library name: mRNA-Seq_h9_r1
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.6927
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.6860
****************
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: Various levels of processed data files will be made available as this project proceeds.

source_name: H9 cell line, biological replicate 1 (r1); mRNA-Seq_h9_r1

value: H9 Cell Line

value: Thomson Laboratory

value: embryonic stem cell

value: Female


title: hmC_shScr

value: DIP

value: hydroxymethylcytosine


title: hmC

value: untransfected


title: Shotgun sequencing of polyA+ RNA from the iPS cell line clone 19.11; mRNA-Seq_ff_ips_19_11_r1

description:
sample_term_id: NTR_0001173
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: Shotgun sequencing of polyA+ RNA isolated from the iPS cell line clone 19.11 derived from reprogramming of foreskin fibroblasts
Library name: mRNA-Seq_ff_ips_19_11_r1
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.6933
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.6900
****************
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: GSM706050_UCSD.iPS_DF_19.11.mRNA-Seq.mRNA-Seq_ff_ips_19_11_r1.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: mRNA-Seq_ff_ips_19_11_r1.hg19.level.1.release.4
ANALYSIS TITLE: Mapping of iPS DF 19.11 Cell Line mRNA-Seq Data
ANALYSIS DESCRIPTION: SOLiD reads produced by mRNA-Seq on the iPS DF 19.11 Cell Line, Library mRNA-Seq_ff_ips_19_11_r1 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.9490
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 13,133,143
NUMBER_OF_MRNA-SEQ_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 8
PERCENT_READS_MAPPING_TO_UCSC_GENES: 89.69
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 25
MAXIMUM_REPLICATE_CORRELATION: 0.94

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

ANALYSIS FILE NAME: GSM706050_UCSD.iPS_DF_19.11.mRNA-Seq.mRNA-Seq_ff_ips_19_11_r1.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: mRNA-Seq_ff_ips_19_11_r1.hg19.level.2.release.4
ANALYSIS TITLE: Raw Signal Density Graphs of iPS DF 19.11 Cell Line mRNA-Seq Data
ANALYSIS DESCRIPTION: SOLiD mRNA-Seq read mappings from the iPS DF 19.11 Cell Line, Library mRNA-Seq_ff_ips_19_11_r1 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.9498
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 4
BROWSER_TRACK_NAME: iD19.11 mRNA r1
BROWSER_TRACK_DESCRIPTION: UCSD iPS DF 19.11 Cell Line mRNA-Seq Library mRNA-Seq_ff_ips_19_11_r1 EA Release 4

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 13,133,143
NUMBER_OF_MRNA-SEQ_EXPERIMENTS_SCORED: 8
PERCENT_READS_MAPPING_TO_UCSC_GENES: 89.69
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 25
MAXIMUM_REPLICATE_CORRELATION: 0.94

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

source_name: iPS cell line clone 19.11 derived from reprogramming of foreskin fibroblasts, biological replicate 1 (r1); mRNA-Seq_ff_ips_19_11_r1

value: iPS DF 19.11 Cell Line

value: Cell Line

value: iPS DF 19.11

value: induced pluripotent stem cell

value: TeSR

value: Male

value: mRNA-Seq

value: RNeasy Blood and Tissue Kit (Qiagen)


title: LAU-Me235 melanoma cells patient LAU63 (454)

status: Public on Apr 07 2011

city: Lausanne

first: Armand

last: Valsesia

address: Bâtiment Génopode

country: Switzerland

institute: Ludwig Institute for Cancer Research

description:
cDNA was sequenced using single end read with the Roche 454 technology
hg18 used for NHM_7Mel_mRNA_cnt.txt

data_processing: All experiments produced about 1M single end reads, with a median length of 367 nucleotides (interquartile range 265-436). We derived transcript tag count using the Tromer pipeline described in Jongeneel et al. (PNAS 2003)

source_name: Low-passage culture of lymph node metastasis from cutaneous melanoma

growth_protocol: Melanoma cell lines were cultured in RPMI-1640 medium supplemented with 10% FCS. Normal human melanocytes were grown in HAM-F10 medium supplemented with 2% FCS, 5% MelanoMax supplement (Gentaur, Belgium) and 6 mM HEPES.

extract_protocol: mRNA isolation and cDNA preparation were performed following the protocol used by Bainbridge et al (BMC Genomics. 2006 ). Then 3-5 µg of cDNA were used for 454 libraries preparation, according to manufactures’ procedures.

tag: gender

value: male

tag: cell line

value: cell derived from metastatic melanoma

tag: source tissue

value: lymph node


title: LAU-Me275 melanoma cells patient LAU50 (454)


title: Wdr5_ChIP-seq

status: Public on Apr 08 2011

city: New York

first: Jonathan

last: Monk

state: NY

address: One Gustave L. Levy Place

department: Gene and Cell Medicine

institute: Mt. Sinai School of Medicine

description: Chromatin IP against Wdr5

data_processing:
Base-calling: Images acquired were processed through the bundled image extraction software which identified polony positions, performed base-calling and generated QC statistics.
Alignment: Sequence reads were aligned using the ELAND software and referenced to mouse genome NCBI Build 37 (UCSC,mm9). Only uniquely mapped coordinates were used for further analysis. Uniquely aligned 36 bp sequences were extended to 110 bp in the 3’ direction and allocated into 20 bp bins.
Peak finding: We used MACS for peak-finding. Binding regions were identified based on (1) 110bp bandwidth, (2) >10–fold change between total tag counts of each ChIP library versus the negative/input ChIP library and (3) p-value threshold of 10-5.

source_name: ES cell

growth_protocol: Mouse ES cell line CCE was cultured feeder-free on 0.1% gelatin-coated plates in ES cell medium (Dulbecco's modified Eagle's medium (DMEM; Hi-Glucose), 15% fetal bovine serum , non-essential amino acids, L-glutamine, β-mercaptoethanol, penicillin/streptomycin, sodium pyruvate and leukemia inhibitory factor (LIF; Millipore).

extract_protocol: 15 ng of ChIP DNA was end repaired with T4 DNA polymerase and polynucleotide kinase. An A-base was added to the end-repaired DNA fragments. Solexa adaptors were ligated to the ChIP DNA fragments and 175-250bp(representing shear fragments between 75 and 150nt in length and ~100bp of primer sequence) size fractions were excised from 2% agarose  gel stained with GelStar. Adapter-modified fragments were enriched by 18 cycles of PCR amplification. The DNA library prep was validated in Bioanalyzer for quantity and size.

tag: strain

value: CCE

tag: antibody

tag: antibody manufacturer

value: Bethyl

tag: antibody catalog number


title: Input DNA

description: input DNA library


title: Oct4_ChIP-seq

description: Chromatin IP against Oct4

value: Santa Cruz


title: Negative

description: negative library


title: WDR5-FL_ChIP-seq

description: Chromatin IP against WDR5-FL

value: Sigma


title: Rbbp5_ChIP-seq

description: Chromatin IP against Rbbp5

value: Allis Lab (RockefellerU)

value: not applicable


title: H3K4me3_ChIP-seq

description: Chromatin IP against H3K4me3

value: Millipore


title: LAU-Me246.M1melanoma cells patient LAU108 (454)

source_name: Low-passage culture of cutaneous metastasis from cutaneous melanoma

value: female

value: skin


title: LAU-T50B melanoma cells patient LAU50 (454)


title: LAU-T149D melanoma cells patient LAU149D (454)

source_name: Low-passage culture of visceral metastasis from cutaneous melanoma

value: visceral tissue


title: Normal melanocytes pool of 2 samples (454)

source_name: Cultures of epidermal melanocytes

value: cultured melanocyte


title: LAU-Me280.R.LN melanoma cells patient LAU165 (454)


title: cell line SKBR3

status: Public on Apr 06 2011

city: Cologne

first: Axel

last: HILLMER

address: Kerpener Str. 62

department: Institute of Pathology

country: Germany

institute: University of Cologne

description: genomic DNA hydrosheared in 8.3 kb fragments (std dev: 815 bp below median; 524 above median), 2x25bp paired-end (mate pair) sequences

data_processing: For the project, sequence tags were mapped to the human reference sequence (NCBI Build 36) allowing 2 color code mismatches and paired using SOLiD System Analysis Pipeline Tool, Corona Lite (Applied Biosystems). If sequence tags had multiple mapping locations and one of them was located in the expected distance and orientation to its mate, this location was chosen by a process termed ‘rescue’. Discordant paired-end tags (PETs) were defined and clustered to call structural variations as described by Hillmer et al.: Comprehensive Long Span Paired-End-Tag Mapping Reveals Characteristic Patterns of Structural Variations in Epithelial Cancer Genomes. The Readme file includes additional information about the supplementary cluster and gff files.

source_name: Cell line was established from a 43 year old Caucasian woman

growth_protocol: standard growth conditions for cell lines

extract_protocol: Genomic DNA was hydrosheared, EcoP15I recognition sites were methylated and EcoP15I CAP adaptors were ligated to the ends of DNA fragments. The methylated DNA constructs were separated on agarose gel and 10 Kb sized fragments were selected for ligation resulting in circularized products where 5’ and 3’ ends of 10 Kb fragments were connected by an internal biotinylated adaptor with two flanking non-methylated EcoP15I CAP adaptors. Constructs were digested by methylation sensitive EcoP15I to release 5’ and 3’ paired-end tag (PET) constructs. Sequencing adaptors were ligated to the PET constructs, which were then amplified by PCR and sequenced by the Applied Biosystems SOLiD system.

tag: tumor type

value: adenocarcinoma, pleural effusion

tag: tissue

value: mammary gland; breast


title: cell line MCF-7, 2

description: genomic DNA hydrosheared in 12 kb fragments (std dev: 2,779 bp below median; 1,624 above median), 2x25bp paired-end (mate pair) sequences

data_processing:
For the project, sequence tags were mapped to the human reference sequence (NCBI Build 36) allowing 2 color code mismatches and paired using SOLiD System Analysis Pipeline Tool, Corona Lite (Applied Biosystems). If sequence tags had multiple mapping locations and one of them was located in the expected distance and orientation to its mate, this location was chosen by a process termed ‘rescue’. Discordant paired-end tags (PETs) were defined and clustered to call structural variations as described by Hillmer et al.: Comprehensive Long Span Paired-End-Tag Mapping Reveals Characteristic Patterns of Structural Variations in Epithelial Cancer Genomes. The Readme file includes additional information about the supplementary cluster and gff files.
Processed data for cell line MCF-7 is available on Sample record GSM663572

source_name: Cell line was established from a 69-year-old Caucasian woman (after radio- and hormone therapy)

value: metastatic mammary carcinoma, pleural effusion


title: cell line MCF-7, 1

description: genomic DNA hydrosheared in 10.2 kb fragments (std dev: 2,515 bp below median; 1,314 above median), 2x25bp paired-end (mate pair) sequences


title: cell line TMk1

description: genomic DNA hydrosheared in 10.3 kb fragments (std dev: 653 bp below median; 562 above median), 2x25bp paired-end (mate pair) sequences

source_name: Cell line was established from gastric tumor of a male patient

value: poorly differentiated adenocarcinoma

value: gastric


title: cell line HCT116, library IHH020

description: genomic DNA hydrosheared in 9.3 kb fragments (std dev: 1,140 bp below median; 685 above median), 2x25bp paired-end (mate pair) sequences, library IHH020

source_name: Cell line was established from the primary colon carcinoma of an adult man

value: primary carcinoma

value: colon


title: LAU-T618A melanoma cells patient LAU618 (454)

value: cell derived from metastatic melanoma


title: cell line K562, SOLiD

description: genomic DNA hydrosheared in 8.3 kb fragments (std dev: 655 bp below median; 597 above median), 2x25bp paired-end (mate pair) sequences

data_processing:
For the project, sequence tags were mapped to the human reference sequence (NCBI Build 36) allowing 2 color code mismatches and paired using SOLiD System Analysis Pipeline Tool, Corona Lite (Applied Biosystems). If sequence tags had multiple mapping locations and one of them was located in the expected distance and orientation to its mate, this location was chosen by a process termed ‘rescue’. Discordant paired-end tags (PETs) were defined and clustered to call structural variations as described by Hillmer et al.: Comprehensive Long Span Paired-End-Tag Mapping Reveals Characteristic Patterns of Structural Variations in Epithelial Cancer Genomes. The Readme file includes additional information about the supplementary cluster and gff files.
Processed data for cell line K562 is available on Sample record GSM663570

source_name: Pleural effusion of a 53-year-old woman with chronic myeloid leukemia (CML) in blast crisis

value: chronic myeloid leukemia

value: myeloid blast cells


title: Mouse_Adipocytes_PPARg_rep2 (GAII)

city: RTP

first: Logan

middle: J

last: Everett

state: North Carolina

address: 109 T.W. Alexander Dr

department: Office of Research and Development

institute: U.S. Environmental Protection Agency

description:
The raw data for this sample was combined with previously published and uploaded data in record GSE21314 prior to GLITR analysis.
Chromatin IP against PPARgamma
processed data file:  Mouse_3T3L1_Ads_PPARg_GLITR_1p5_FDR.bed

data_processing:
Fastq Files: Sequencing output was analyzed using the Illumina Genome Analyzer Pipeline. Sequence tags that aligned uniquely to the reference genome with zero, one, or two mismatches, according to the ELAND alignment algorithm, were used for further analysis.
Bed Files: All ChIP-Seq data sets were analyzed using GLITR with default parameters and a 1.5% FDR cutoff. Pseudo-ChIP data sets that had the same number of tags as each filtered data set were sampled from the input sequence tag data available for MM8 and HG18 at http://web.me.com/kaestnerlab1/GLITR/, and the remaining input sequence tags in these sets were used as background for the GLITR sampling procedure. Data were further filtered to remove peaks that resulted from amplification bias.
processed data file build: mm8, hg18

source_name: Mouse 3T3-L1 Adipocyte Culture

growth_protocol: 3T3-L1 cells were maintained in Dulbecco’s modified Eagle’s medium supplemented with 10% fetal bovine serum, 100 units/ml penicillin, and 100 ug/ml streptomycin. Cells were grown to confluence and induced to differentiate 2 days after confluence with medium containing 1 uM dexamethasone, 10 ug/ml bovine insulin, and 0.5 mM 3-isobutyl-1-methylxanthine for 2 days and for an additional 2 days in insulin only.  Cells were harvested at day 10.

extract_protocol: Libraries for each ChIP experiment were prepared as per Illumina's instructions (http://www.illumina.com). Briefly, DNA fragments were blunted, phosphorylated, and ligated to Illumina library adapters. For input DNA preparation, 10 ng of starting material was used. Size selection was performed using gel electrophoresis by excising DNA fragments at 200 ± 25 base pairs. Following gel purification, PCR amplification was performed [30 s at 98°C; (10 s at 98°C, 30 s at 65°C, 30 s at 72°C) × 18 cycles; 5 min at 72°C]. Amplified material was evaluated on a Agilent 2100 bioanalyzer using the DNA 1000 Kit to ensure proper size selection, and was subsequently diluted to a concentration of 10 nM.

treatment_protocol: Cells were cross-linked in 1% Formaldehyde for 10 min, followed by quenching with 1/20 volume of 2.5 M glycine solution, and two washes with 1× PBS. Nuclear extracts were prepared by dounce homogenizing in nuclear lysis buffer (20 mM HEPES, 0.25 M sucrose, 3 mM MgCl2, 0.2% NP-40, 3 mM beta-mercaptoethanol, 0.4 mM PMSF, Complete protease inhibitor tablets from Roche). Chromatin fragmentation was performed by sonication in ChIP SDS lysis buffer (50 mM HEPES, 1% SDS, 10 mM EDTA), using Bioruptor (Diagenode). Proteins were immunoprecipitated in ChIP dilution buffer (50 mM Hepes/NaOH at ph 7.5, 155 mM NaCl, 1.1% Triton X-100, 0.11% Na-deoxy- cholate, 1 mM PMSF, Complete protease inhibitor tablet), using anti-PPARgamma antibodies. Cross-linking was reversed overnight at 65°C, and DNA isolated using phenol/chloroform/isoamyl alcohol.

value: Cultured Adipocytes

tag: chip antibody

value: PPARgamma

tag: antibody vendor

value: Santa Cruz Biotechnology

tag: antibody lot/batch number(s)


title: Human_Liver_Input_rep1 (GAI)

description:
Input DNA
processed data file:  Human_Liver_FOXA2_GLITR_1p5_FDR.bed

source_name: Homogenized Human Liver

treatment_protocol: Mouse and human livers were minced finely in cold PBS and cross-linked in 1% formaldehyde for 10 min while rotating. Cross-linking was quenched by adding glycine to a final concentration of 0.125 M for 5 min while rotating. The tissue was rinsed in cold PBS and homogenized with a Dounce homogenizer in cold cell lysis buffer (10 mM Tris–Cl, pH 8.0, 10 mM NaCl, 3 mM MgCl2, 0.5% NP-40) and protease inhibitors. Cells were incubated at 48C for 5 min to release nuclei. Nuclei were centrifuged at 13000 g for 5 min to form a pellet. The pellet was resuspended in nuclear lysis buffer (1% SDS, 5 mM EDTA, 50 mM Tris–Cl, pH 8.1) and protease inhibitors and sonicated using the Diagenode Bioruptor for 10 min on high, using 30 s intervals. Debris were removed by centrifugation at 13000 g for 10 min, and the supernatant was collected and snap frozen in liquid nitrogen. A 10 ml aliquot was reversed by the addition of NaCl to a final concentration of 192 mM, overnight incubation at 658C, and purification using a PCR urification kit (Qiagen). The chromatin concentration was determined using a NanoDrop 3.1.0 nucleic acid assay (Agilent Technologies). Ten micrograms of chromatin per sample was precleared by adding 90 ml of protein G-agarose in 1 ml of ChIP dilution buffer (0.01% SDS, 1.1% Triton X-100, 167 mM NaCl, 16.7 mM Tris–Cl, pH 8.1) and rotating the sample for 1 h at 48C. Protein G-agarose was sedimented by centrifugation at 3000 g for 30 s. Two micrograms of rabbit anti-Foxa2 serum (provided by J.A. Whitsett), was added to the supernatant and incubated overnight at 48C. Protein G-agarose was blocked overnight at 48C with 1mg/ml bovine serum albumin and 0.1mg/ml herring sperm DNA in ChIP dilution buffer, added to the chromatin, and rotated for 1 h at 48C. Following three consecutive washes of 5 min each with TSE I (0.1% SDS, 1% Triton X-100, 2mM EDTA, 20mM Tris–Cl, pH 8.1, 150mM NaCl), TSE II (0.1% SDS, 1% Triton X-100, 2mM EDTA, 20mM Tris–Cl, pH 8.1, 500mM NaCl) and ChIP buffer III (0.25 M LiCl, 1% NP-40, 1% deoxycholate, 1 mM EDTA, 10 mM Tris–Cl, pH 8.1), chromatin was eluted by adding 100 ml of freshly made ChIP elution buffer (1% SDS, 0.1 M NHCO3) to the pellet and rotating the sample for 10 min. Elution was repeated with an additional 100 ml of ChIP elution buffer, and the eluates were combined. Cross-linking was reversed by the addition of NaCl to a final concentration of 192mM and overnight incubation at 658C.

value: Liver tissue


title: Human_Liver_FOXA2_rep2 (GAI)

description:
Chromatin IP against FOXA2
processed data file:  Human_Liver_FOXA2_GLITR_1p5_FDR.bed

tag: antibody provider

value: Dr. Jeffrey Whitsett

tag: antibody reference

value: Gene Expr Patterns. 2004 Dec;5(2):193-208. Immunohistochemical localization of Foxa1 and Foxa2 in mouse embryos and adult tissues. Besnard V, Wert SE, Hull WM, Whitsett JA.


title: Human_Liver_Input_rep2 (GAI)

tag: cell type


title: gastric tumor 28

description: genomic DNA hydrosheared in 9.8 kb fragments (std dev: 2,396 bp below median; 1,111 above median), 2x25bp paired-end (mate pair) sequences

source_name: Primary gastric tumor of a Chinese male

value: TNM stage 3a

value: Lauren classification intestinal-type moderately-differentiated adenocarcinoma


title: Mouse_Liver_FOXA2_rep4 (GAII)

description:
Chromatin IP against FOXA2
processed data file:  Mouse_Liver_FOXA2_GLITR_1p5_FDR.bed

source_name: Homogenized Mouse Liver

growth_protocol: Adult mice were sacrificed and liver was dissected.


title: Yoruba (HapMap) NA19139 control

description: genomic DNA hydrosheared in 8.3 kb fragments (std dev: 2,697 bp below median; 1,281 above median), 2x25bp paired-end (mate pair) sequences

source_name: Lymphoblastoid cell line of a Yoruba male

value: normal control

value: lymphoblastoid cell line


title: gastric tumor 26

description: genomic DNA hydrosheared in 9.6 kb fragments (std dev: 1,997 bp below median; 899 above median), 2x25bp paired-end (mate pair) sequences

source_name: Primary gastric tumor of a Malay male

value: TNM stage 3b

value: Lauren classification diffuse-type, poorly differentiated signet ring cell carcinoma


title: gastric tumor 17

description: genomic DNA hydrosheared in 10 kb fragments (std dev: 848 bp below median; 505 above median), 2x50bp paired-end (mate pair) sequences

extract_protocol: LMP CAP adaptors with only a single 5’ phosphorylated end were ligated to the hydro-sheared DNA, thus creating a nick on each strand after circularization of the DNA. Both nicks were translated >50 bp into the circularized genomic DNA fragment by DNA polymerase I, and paired-end tags of >50 bp were released by T7 exonuclease and S1 nuclease. SOLiD sequencing adaptors P1 and P2 were ligated to the paired-end tag (PET) constructs, which were then amplified by PCR and sequenced by the Applied Biosystems SOLiD system.

value: TNM stage 4

value: Lauren classification mixed-type, poorly-differentiated signet ring cell carcinoma


title: gastric tumor 38

description: genomic DNA hydrosheared in 9.2 kb fragments (std dev: 1,726 bp below median; 867 above median), 2x25bp paired-end (mate pair) sequences

value: Lauren classification mixed-type, poorly-differentiated signet ring cell carcinomas


title: Human_Adipocytes_PPARg_rep2 (GAII)

description:
Chromatin IP against PPARgamma
processed data file:  Human_SGBS_Ads_PPARg_GLITR_1p5_FDR.bed

source_name: Human Adipocytes

growth_protocol: Preadipocytes were grown in growth medium containing Dulbecco’s modified Eagle’s medium (DMEM) F-12, 8 mg/liter biotin, 4 mg/liter pantothenic acid, 1% penicillin-streptomycin, and 10% bovine calf serum. Media were changed twice a week. On reaching confluence, differentiation into mature adipocytes was induced using medium containing DMEM F-12, biotin, pantothenic acid, penicillin-streptomycin, 500 uM isobutyl- methylxanthine, 20 nM dexamethasone, 10 uM cortisol, 0.2 nM triiodothyronine, 10 mg/liter apo-transferrin, 20 nM recombinant human insulin, and 2 uM rosiglitazone. The cells were maintained in the induction medium for 7 days and then maintained in adipogenic medium containing DMEM F-12, biotin, pantothenic acid, penicillin-streptomycin, cortisol, triiodothyronine, apo- transferrin, and insulin.  Cells were harvested at day 20.

value: Simpson Golabi Behmel Syndrome (SGBS) human adi- pocytes


title: Mouse_Liver_FOXA2_rep3 (GAII)


title: Human_Adipocytes_PPARg_rep1 (GAII)


title: cell line K562, Illumina

description: genomic DNA hydrosheared in 8.3 kb fragments (std dev: 643 bp below median; 594 above median), 2x36bp paired-end (mate pair) sequences, run GA1R68 lane 7 tag 1 and 2 sequence

extract_protocol: Illumina sequencing adaptors were ligated to the PET constructs, which were then amplified by PCR and sequenced by an Illumina Genome Analyzer II. For the above menioned study, 36 bp tags were trimmed to 27 bp tags for further analysis.

value: chronic myeloid leukemia

value: myeloid blast cells


title: Input rep2

city: Worcester

first: Lihua

middle: Julie

last: Zhu

state: MA

address: 364 Plantation St

department: Program in Gene Function and Expression

institute: Umass Medial School

description: Input DNA

data_processing:
Alignments: Sequence reads were obtained and mapped to the zebrafish (Zv7) genomes using the Illumina Genome Analyzer Pipeline. All reads uniquely mapped with two or fewer mismatches were retained for subsequent peak detection.
Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS 1.3.6) algorithm (http://liulab.dfci.harvard.edu/MACS/)  with default setting except for these parameters --shiftsize=150 --oldfdr  --gsize=1700000000 --tsize=36 --bw=150 --mfold=10

organism: Danio rerio

source_name: whole embryo at 24 hours post fertilization, input

extract_protocol: Histone-DNA complexes were isolated from sonicated chromtin using antibodies against H3K4me1 or H3K4me3. DNA was isolated and ends were polished using the END-IT DNA Repair Kit (Epicentre). Blunt ends were treated with exo-minus Klenow  and dATP to add a protruding 3' adenosine.  Standard Illumina adpators were ligated and the resulting library was PCR amplified with Illumina primers for 15 cycles followed by gel purification of approximately 250 bp library fragments. Cluster generation and subsequent sequencing was performed on a Genome Analyzer according to manufacturer's specifications.

value: whole embryo

tag: developmental stage

value: 24 hours post fertilization

tag: genotype

value: wild type


title: cell line T47D

description: genomic DNA hydrosheared in 9.6 kb fragments (std dev: 2,217 bp below median; 1,038 above median), 2x25bp paired-end (mate pair) sequences

source_name: Cell line was established from pleural effusion of a 54 year old woman

value: ductal carcinoma; pleural effusion

value: mammary gland; breast


title: Human_Adipocytes_Input_rep1 (GAII)

description:
Input DNA
processed data file:  Human_SGBS_Ads_PPARg_GLITR_1p5_FDR.bed


title: Human_Liver_FOXA2_rep1 (GAI)

value: Liver tissue

value: Dr. Jeffrey Whitsett

value: Gene Expr Patterns. 2004 Dec;5(2):193-208. Immunohistochemical localization of Foxa1 and Foxa2 in mouse embryos and adult tissues. Besnard V, Wert SE, Hull WM, Whitsett JA.


title: H3K4me3_ChIPSeq rep2

description: Chromatin IP against H3K4me3

source_name: whole embryo at 24 hours post fertilization, H3K4me3 ChIP


title: European control

description: genomic DNA hydrosheared in 9.1 kb fragments (std dev: 636 bp below median; 577 above median), 2x25bp paired-end (mate pair) sequences

source_name: Venous blood of a European male

value: normal control

value: Venous blood


title: breast tumor 14, slide 2

description: genomic DNA hydrosheared in 9.3 kb fragments (std dev: 3,318 bp below median; 2,046 above median), 2x25bp paired-end (mate pair) sequences, slide 2

data_processing:
For the project, sequence tags were mapped to the human reference sequence (NCBI Build 36) allowing 2 color code mismatches and paired using SOLiD System Analysis Pipeline Tool, Corona Lite (Applied Biosystems). If sequence tags had multiple mapping locations and one of them was located in the expected distance and orientation to its mate, this location was chosen by a process termed ‘rescue’. Discordant paired-end tags (PETs) were defined and clustered to call structural variations as described by Hillmer et al.: Comprehensive Long Span Paired-End-Tag Mapping Reveals Characteristic Patterns of Structural Variations in Epithelial Cancer Genomes. The Readme file includes additional information about the supplementary cluster and gff files.
Processed data for breast tumor 14 is available on Sample record GSM663560

source_name: Primary breast tumor

value: basal-like subgroup based on micro array expression data


title: Mouse_Liver_Input_rep3 (GAI)

description:
Input DNA
processed data file:  Mouse_Liver_FOXA2_GLITR_1p5_FDR.bed


title: Human_Liver_Input_rep1 (GAII)


title: Mouse_Liver_Input_rep2 (GAI)


title: breast tumor 13, slide 1

description: genomic DNA hydrosheared in 5 kb fragments (std dev: 974 bp below median; 548 above median), 2x25bp paired-end (mate pair) sequences, slide 1


title: breast tumor 14, slide 1

description: genomic DNA hydrosheared in 9.3 kb fragments (std dev: 3,318 bp below median; 2,046 above median), 2x25bp paired-end (mate pair) sequences, slide 1


title: breast tumor 5, slide 2

description: genomic DNA hydrosheared in 9.8 kb fragments (std dev: 2,931 bp below median; 1,590 above median), 2x25bp paired-end (mate pair) sequences, slide 2

data_processing:
For the project, sequence tags were mapped to the human reference sequence (NCBI Build 36) allowing 2 color code mismatches and paired using SOLiD System Analysis Pipeline Tool, Corona Lite (Applied Biosystems). If sequence tags had multiple mapping locations and one of them was located in the expected distance and orientation to its mate, this location was chosen by a process termed ‘rescue’. Discordant paired-end tags (PETs) were defined and clustered to call structural variations as described by Hillmer et al.: Comprehensive Long Span Paired-End-Tag Mapping Reveals Characteristic Patterns of Structural Variations in Epithelial Cancer Genomes. The Readme file includes additional information about the supplementary cluster and gff files.
Processed data for breast tumor 5 is available on Sample record GSM663556


title: Mouse_Liver_FOXA2_rep3 (GAI)


title: breast tumor 13, slide 2

description: genomic DNA hydrosheared in 5 kb fragments (std dev: 974 bp below median; 548 above median), 2x25bp paired-end (mate pair) sequences, slide 2

data_processing:
For the project, sequence tags were mapped to the human reference sequence (NCBI Build 36) allowing 2 color code mismatches and paired using SOLiD System Analysis Pipeline Tool, Corona Lite (Applied Biosystems). If sequence tags had multiple mapping locations and one of them was located in the expected distance and orientation to its mate, this location was chosen by a process termed ‘rescue’. Discordant paired-end tags (PETs) were defined and clustered to call structural variations as described by Hillmer et al.: Comprehensive Long Span Paired-End-Tag Mapping Reveals Characteristic Patterns of Structural Variations in Epithelial Cancer Genomes. The Readme file includes additional information about the supplementary cluster and gff files.
Processed data for breast tumor 13 is available on Sample record GSM663558


title: Human_Liver_FOXA2_rep1 (GAII)

description:
Chromatin IP against FOXA2
processed data file:  Human_Liver_FOXA2_GLITR_1p5_FDR.bed


title: Mouse_Liver_FOXA2_rep2 (GAI)

description:
Chromatin IP against FOXA2
processed data file:  Mouse_Liver_FOXA2_GLITR_1p5_FDR.bed


title: Human_Liver_FOXA2_rep2 (GAII)


title: Mouse_Liver_Input_rep1 (GAI)


title: Input_MCF7 stables_ChIP-seq_rep2

status: Public on Apr 04 2011

city: Palo Alto

first: Philip

last: Cayting

address: 1501 S California Ave

department: Genetics

institute: Stanford University

description: genomic DNA used as input for Chromatin IP

data_processing:
Alignment: Sequence reads were obtained and mapped to the human genome assembly hg18 (March, 2006) or hg19 (February, 2009) using the Illumina Genome Analyzer Pipeline. All reads mapping with two or fewer mismatches were retained and read starts were summed in sliding windows of 400 bp to create summary windows.
Peaks were called with Sole-Search (http://chipseq.genomecenter.ucdavis.edu/cgi-bin/chipseq.cgi)

source_name: breast adenocarcinoma cell line

growth_protocol: All cells were grown according to ENCODE standards (http://genomewiki.ucsc.edu/EncodeDCC/index.php/Cell_lines)

extract_protocol:
ChIP assay was performed following the ChIP protocol provided at: http://farnham.genomecenter.ucdavis.edu/pdf/FarnhamLabChIP%20Protocol.pdf
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.  Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (3 to 5 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3â end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

value: MCF7 cell line stably expressing HA ER E2F1 DNA binding domain mutant

tag: harvest date


title: Input_MCF7 stables_ChIP-seq_rep1b

value: MCF7 cell line stably expressing HA ER E2F1ÎC mutant


title: Mouse_Liver_FOXA2_rep4 (GAI)


title: HA ER E2F1ÎMB_MCF7 stables_ChIP-seq_rep1

description: Chromatin IP against HA ER E2F1 5'NLS ÎMB mutant

value: MCF7 cell line stably expressing HA ER E2F1 5'NLS ÎMB mutant

value: mouse anti-HA (Covance, catalog # MMS-101P)


title: H3K4me1_ChIPSeq rep2

description: Chromatin IP against H3K4me1

source_name: whole embryo at 24 hours post fertilization, H3K4me1 ChIP


title: Set P, Control for Set O

city: Bethesda

first: Ivan

last: Gregoretti

state: MD

address: 5 Memorial Dr, Building 5, Room 205.

department: National Institute of Diabetes and Digestive and Kidney Diseases

institute: National Institutes of Health

description: input DNA

data_processing:
Sequencing reads were aligned to the mm9 mouse genome annotation using ELAND and the Illumina Genome Analizer pipeline. The resulting export.txt files were converted to the BAM format with Samtools/Picard.
Peak finding was performed with MACS 1.3.7 (http://liulab.dfci.harvard.edu/MACS/) with a p-value threshold of 0.0001 and the. The resulting peaks were kept only if the MCAS-estimated FDR was 50% or less. In the case of Dmc1, the peaks were resized to 3.4kb.

source_name: liver

growth_protocol: Cells were extracted from testis (or liver) of euthanized mice and immediately subjected to immunoprecipitation.

extract_protocol: Lysates from mice testis cells were sonicated, clarified and DNA protein complexes were isolated with anti Dmc1 or anti Rad51 or H3K4Me3 antibodies. DNA purified from proteins and libraries were prepared according to Illumina's instructions accompanying the genomic DNA Sample preparing kit part number 1000181. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenowpolymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (3’ to 5’ exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 18 cycles and library fragments of 150~250 bp were isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

value: 13R/9R cross

tag: genotype/variation

value: input DNA


title: Set O, H3K4me3, liver

description: Chromatin IP against H3K4me3

tag: antibody lot

value: Millipore


title: breast tumor 5, slide 1

description: genomic DNA hydrosheared in 9.8 kb fragments (std dev: 2,931 bp below median; 1,590 above median), 2x25bp paired-end (mate pair) sequences, slide 1


title: breast tumor 2

description: genomic DNA hydrosheared in 9.4 kb fragments (std dev: 2,403 bp below median; 1,332 above median), 2x25bp paired-end (mate pair) sequences


title: HA ER E2F1ÎN/C_MCF7 stables_ChIP-seq_rep1

description: Chromatin IP against HA ER E2F1ÎN/C mutant

value: MCF7 cell line stably expressing HA ER E2F1ÎN/C mutant