title: Reference Epigenome: ChIP-Seq Analysis of H3K9ac in BMP4 Trophoblast Cells; renlab.H3K9ac.BMP4T.02.01

description:
sample_term_id: UBERON_0000088
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K9ac in BMP4 Trophoblast Cells. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: SK496
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.10133
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.7847
****************
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: GSM818049_UCSD.H1_BMP4_Derived_Trophoblast_Cultured_Cells.H3K9ac.SK496.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K9ac.BMP4T.02.01.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9ac ChIP-Seq on H1 BMP4 Derived Trophoblast Cultured Cells, Library SK496, 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.12418
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: 108,700,066
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 9
FINDPEAKS_SCORE: 0.0217
FINDPEAKS_PERCENTILE: 11
HOTSPOT_SCORE: 0.0428
HOTSPOT_PERCENTILE: 11
IROC_SCORE: 0.8891
IROC_PERCENTILE: 22
POISSON_SCORE: 0.2091
POISSON_PERCENTILE: 33
MAXIMUM_REPLICATE_CORRELATION: 1.0

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

ANALYSIS FILE NAME: GSM818049_UCSD.H1_BMP4_Derived_Trophoblast_Cultured_Cells.H3K9ac.SK496.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K9ac.BMP4T.02.01.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9ac ChIP-Seq read mappings from the H1 BMP4 Derived Trophoblast Cultured Cells, Library SK496, 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.12491
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: HBDT H3K9ac 96
BROWSER_TRACK_DESCRIPTION: UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K9ac Library SK496 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 108,700,066
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 9
FINDPEAKS_SCORE: 0.0217
FINDPEAKS_PERCENTILE: 11
HOTSPOT_SCORE: 0.0428
HOTSPOT_PERCENTILE: 11
IROC_SCORE: 0.8891
IROC_PERCENTILE: 22
POISSON_SCORE: 0.2091
POISSON_PERCENTILE: 33
MAXIMUM_REPLICATE_CORRELATION: 1.0

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

source_name: Human embryonic stem cells received from the James Thomson laboratory.  Cells are from the H1 line and are differentiated into trophoblast by treatment with BMP4.; renlab.H3K9ac.BMP4T.02.01

value: Embryonic stem cell differentiated into trophoblast by treatment with BMP4

value: H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days

value: Male


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

status: Public on Oct 15 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: EFO_0000586
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K9ac in Mesenchymal Stem Cells. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: SK518
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.10174
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.7874
****************
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: GSM818050_UCSD.H1_Derived_Mesenchymal_Stem_Cells.H3K9ac.SK518.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K9ac.MSC.01.01.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of H1 Derived Mesenchymal Stem Cells Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9ac ChIP-Seq on H1 Derived Mesenchymal Stem Cells, Library SK518, 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.12390
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: 98,899,340
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 9
FINDPEAKS_SCORE: 0.0872
FINDPEAKS_PERCENTILE: 44
HOTSPOT_SCORE: 0.1765
HOTSPOT_PERCENTILE: 44
IROC_SCORE: 0.8284
IROC_PERCENTILE: 11
POISSON_SCORE: 0.324
POISSON_PERCENTILE: 44
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM818050_UCSD.H1_Derived_Mesenchymal_Stem_Cells.H3K9ac.SK518.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K9ac.MSC.01.01.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Derived Mesenchymal Stem Cells Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9ac ChIP-Seq read mappings from the H1 Derived Mesenchymal Stem Cells, Library SK518, 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.12463
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: HDMSC H3K9ac 18
BROWSER_TRACK_DESCRIPTION: UCSD H1 Derived Mesenchymal Stem Cells Histone H3K9ac Library SK518 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 98,899,340
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 9
FINDPEAKS_SCORE: 0.0872
FINDPEAKS_PERCENTILE: 44
HOTSPOT_SCORE: 0.1765
HOTSPOT_PERCENTILE: 44
IROC_SCORE: 0.8284
IROC_PERCENTILE: 11
POISSON_SCORE: 0.324
POISSON_PERCENTILE: 44
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

molecule: genomic DNA

organism: Homo sapiens

source_name: Human embryonic stem cells received from the James Thomson laboratory.  Cells are from the H1 line and are differentiated into mesenchymal stem cells.; renlab.H3K9ac.MSC.01.01

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

tag: sample alias

tag: sample common name

value: H1 Derived Mesenchymal Stem Cells

tag: molecule

value: genomic DNA

tag: disease

value: James Thomson Laboratory

value: Cell Line

tag: line

tag: lineage

value: Embryonic Stem Cell

value: Embryonic stem cell differentiated into mesenchymal stem cells

value: Publication in progress

tag: passage

tag: medium

tag: Sex

tag: batch

value: Histone H3K9ac

value: Biorupter

value: 500 micrograms

value: magnetic anti-rabbit

value: 5 micrograms

value: Active Motif


title: Reference Epigenome: ChIP-Seq Analysis of H3K9ac in BMP4 Trophoblast Cells; renlab.H3K9ac.BMP4T.01.01

description:
sample_term_id: UBERON_0000088
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K9ac in BMP4 Trophoblast Cells. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: SK495
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.10096
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.7840
****************
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: GSM818048_UCSD.H1_BMP4_Derived_Trophoblast_Cultured_Cells.H3K9ac.SK495.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K9ac.BMP4T.01.01.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9ac ChIP-Seq on H1 BMP4 Derived Trophoblast Cultured Cells, Library SK495, 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.12417
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: 96,504,081
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 9
FINDPEAKS_SCORE: 0.039
FINDPEAKS_PERCENTILE: 22
HOTSPOT_SCORE: 0.0557
HOTSPOT_PERCENTILE: 22
IROC_SCORE: 0.9664
IROC_PERCENTILE: 44
POISSON_SCORE: 0.1799
POISSON_PERCENTILE: 22
MAXIMUM_REPLICATE_CORRELATION: 1.0

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

ANALYSIS FILE NAME: GSM818048_UCSD.H1_BMP4_Derived_Trophoblast_Cultured_Cells.H3K9ac.SK495.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K9ac.BMP4T.01.01.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9ac ChIP-Seq read mappings from the H1 BMP4 Derived Trophoblast Cultured Cells, Library SK495, 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.12490
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: HBDT H3K9ac 95
BROWSER_TRACK_DESCRIPTION: UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K9ac Library SK495 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 96,504,081
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 9
FINDPEAKS_SCORE: 0.039
FINDPEAKS_PERCENTILE: 22
HOTSPOT_SCORE: 0.0557
HOTSPOT_PERCENTILE: 22
IROC_SCORE: 0.9664
IROC_PERCENTILE: 44
POISSON_SCORE: 0.1799
POISSON_PERCENTILE: 22
MAXIMUM_REPLICATE_CORRELATION: 1.0

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

source_name: Human embryonic stem cells received from the James Thomson laboratory.  Cells are from the H1 line and are differentiated into trophoblast by treatment with BMP4.; renlab.H3K9ac.BMP4T.01.01


title: Medicago truncatula Root

status: Public on Oct 24 2011

city: St. Louis

first: Blake

middle: C.

last: Meyers

state: MO

address: 975 N Warson Road

institute: Donald Danforth Plant Science Center

description:
MYR1
Processed data contain distinct smallRNAs with their raw abundance after removing the adapter sequences

library_source: transcriptomic

data_processing: Adapter sequences were removed using a Perl script, generating small RNA sequences plus abundances . Twenty-one small RNA libraries were made the materials described above, representing four legume species, including eight libraries from M. truncatula, seven from Glycine max (soybean), two from Arachis hypogaea (peanut), and four from Phaseolus vulgaris (common bean); one PARE library was made from Medicago flower.These libraries were sequenced on an Illumina GAII, generating ~62 million small RNA sequences after removing adapters and low-quality reads, with trimmed lengths between 18 and 34 nucleotides. After excluding small RNAs matching structural RNAs (t/rRNA loci), 12.1 million and 12.6 million reads were mapped to the M. truncatula genome (Mt3.5) (http://www.medicago.org) and the Glycine max genome (Gmax101) (Schmutz et al., 2010), respectively.

molecule: total RNA

organism: Medicago truncatula

source_name: Root

extract_protocol: Medicago small RNA libraries (except MTR01) were constructed and sequenced at Illumina; all other legume libraries plus MTR01 were constructed as previously described (Lu et al. 2007) and sequenced on an Illumina Genome Analyzer II instrument at the Delaware Biotechnology Institute. PARE library was constructed as previously described (German et al. 2008)

tag: accession/ecotype

tag: tissue

value: Root


title: Reference Epigenome: ChIP-Seq Analysis of H3K9ac in BMP4 Mesendoderm Cells; renlab.H3K9ac.BMP4M.02.01

description:
sample_term_id: NTR_0000856
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K9ac in BMP4 Mesendoderm Cells. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AK172
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.9780
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.7808
****************
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: GSM818047_UCSD.H1_BMP4_Derived_Mesendoderm_Cultured_Cells.H3K9ac.AK172.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K9ac.BMP4M.02.01.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of H1 BMP4 Derived Mesendoderm Cultured Cells Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9ac ChIP-Seq on H1 BMP4 Derived Mesendoderm Cultured Cells, Library AK172, 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.12433
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: 76,158,885
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 9
FINDPEAKS_SCORE: 0.2643
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.275
HOTSPOT_PERCENTILE: 56
IROC_SCORE: 0.9981
IROC_PERCENTILE: 100
POISSON_SCORE: 0.3553
POISSON_PERCENTILE: 78
MAXIMUM_REPLICATE_CORRELATION: 0.82

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

ANALYSIS FILE NAME: GSM818047_UCSD.H1_BMP4_Derived_Mesendoderm_Cultured_Cells.H3K9ac.AK172.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K9ac.BMP4M.02.01.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of H1 BMP4 Derived Mesendoderm Cultured Cells Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9ac ChIP-Seq read mappings from the H1 BMP4 Derived Mesendoderm Cultured Cells, Library AK172, 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.12506
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: HBDM H3K9ac 72
BROWSER_TRACK_DESCRIPTION: UCSD H1 BMP4 Derived Mesendoderm Cultured Cells Histone H3K9ac Library AK172 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 76,158,885
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 9
FINDPEAKS_SCORE: 0.2643
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.275
HOTSPOT_PERCENTILE: 56
IROC_SCORE: 0.9981
IROC_PERCENTILE: 100
POISSON_SCORE: 0.3553
POISSON_PERCENTILE: 78
MAXIMUM_REPLICATE_CORRELATION: 0.82

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

source_name: Human embryonic stem cells received from the James Thomson laboratory.  Cells are from the H1 line and are differentiated into mesendoderm by treatment with BMP4.; renlab.H3K9ac.BMP4M.02.01

value: Embryonic stem cell differentiated into mesendoderm by treatment with BMP4

value: H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days

value: Between 20 and 30


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

description:
sample_term_id: EFO_0000586
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K79me1 in Mesenchymal Stem Cells. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: SK514
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.10194
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.7874
****************
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: GSM818044_UCSD.H1_Derived_Mesenchymal_Stem_Cells.H3K79me1.SK514.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K79me1.MSC.01.01.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of H1 Derived Mesenchymal Stem Cells Histone H3K79me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K79me1 ChIP-Seq on H1 Derived Mesenchymal Stem Cells, Library SK514, 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.12439
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: 112,453,902
NUMBER_OF_H3K79me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 5
FINDPEAKS_SCORE: 0.1058
FINDPEAKS_PERCENTILE: 80
HOTSPOT_SCORE: 0.1674
HOTSPOT_PERCENTILE: 60
IROC_SCORE: 0.9279
IROC_PERCENTILE: 20
POISSON_SCORE: 0.4392
POISSON_PERCENTILE: 80
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

ANALYSIS FILE NAME: GSM818044_UCSD.H1_Derived_Mesenchymal_Stem_Cells.H3K79me1.SK514.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K79me1.MSC.01.01.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Derived Mesenchymal Stem Cells Histone H3K79me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K79me1 ChIP-Seq read mappings from the H1 Derived Mesenchymal Stem Cells, Library SK514, 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.12512
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: HDMSC H3K79me1 14
BROWSER_TRACK_DESCRIPTION: UCSD H1 Derived Mesenchymal Stem Cells Histone H3K79me1 Library SK514 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 112,453,902
NUMBER_OF_H3K79me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 5
FINDPEAKS_SCORE: 0.1058
FINDPEAKS_PERCENTILE: 80
HOTSPOT_SCORE: 0.1674
HOTSPOT_PERCENTILE: 60
IROC_SCORE: 0.9279
IROC_PERCENTILE: 20
POISSON_SCORE: 0.4392
POISSON_PERCENTILE: 80
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

source_name: Human embryonic stem cells received from the James Thomson laboratory.  Cells are from the H1 line and are differentiated into mesenchymal stem cells.; renlab.H3K79me1.MSC.01.01

value: H1 Derived Mesenchymal Stem Cells

value: Male

value: Histone H3K79me1

value: Abcam


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

description:
sample_term_id: CL_0000047
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K79me1 in Neural Progenitor Cells. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AK261
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.10182
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.10100
****************
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: GSM818046_UCSD.H1_Derived_Neuronal_Progenitor_Cultured_Cells.H3K79me1.AK261.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K79me1.NPC.01.01.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of H1 Derived Neuronal Progenitor Cultured Cells Histone H3K79me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K79me1 ChIP-Seq on H1 Derived Neuronal Progenitor Cultured Cells, Library AK261, 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.12392
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: 37,206,996
NUMBER_OF_H3K79me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 5
FINDPEAKS_SCORE: 0.064
FINDPEAKS_PERCENTILE: 40
HOTSPOT_SCORE: 0.3139
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9397
IROC_PERCENTILE: 60
POISSON_SCORE: 0.3837
POISSON_PERCENTILE: 40
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM818046_UCSD.H1_Derived_Neuronal_Progenitor_Cultured_Cells.H3K79me1.AK261.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K79me1.NPC.01.01.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Derived Neuronal Progenitor Cultured Cells Histone H3K79me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K79me1 ChIP-Seq read mappings from the H1 Derived Neuronal Progenitor Cultured Cells, Library AK261, 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.12465
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: HDNP H3K79me1 61
BROWSER_TRACK_DESCRIPTION: UCSD H1 Derived Neuronal Progenitor Cultured Cells Histone H3K79me1 Library AK261 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 37,206,996
NUMBER_OF_H3K79me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 5
FINDPEAKS_SCORE: 0.064
FINDPEAKS_PERCENTILE: 40
HOTSPOT_SCORE: 0.3139
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9397
IROC_PERCENTILE: 60
POISSON_SCORE: 0.3837
POISSON_PERCENTILE: 40
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: Human embryonic stem cells received from the James Thomson laboratory.  Cells are from the H1 line and are differentiated into neural progenitor cells.; renlab.H3K79me1.NPC.01.01

value: genomic DNA

value: James Thomson Laboratory

value: Cell Line

value: Embryonic Stem Cell

value: Embryonic stem cell differentiated into neural progenitor cells


title: Reference Epigenome: ChIP-Seq Analysis of H3K79me1 in Mesenchymal Stem Cells; renlab.H3K79me1.MSC.02.01

description:
sample_term_id: EFO_0000586
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K79me1 in Mesenchymal Stem Cells. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: SK515
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.10201
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.7914
****************
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: GSM818045_UCSD.H1_Derived_Mesenchymal_Stem_Cells.H3K79me1.SK515.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K79me1.MSC.02.01.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of H1 Derived Mesenchymal Stem Cells Histone H3K79me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K79me1 ChIP-Seq on H1 Derived Mesenchymal Stem Cells, Library SK515, 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.12440
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: 107,951,488
NUMBER_OF_H3K79me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 5
FINDPEAKS_SCORE: 0.2471
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.2355
HOTSPOT_PERCENTILE: 80
IROC_SCORE: 0.9637
IROC_PERCENTILE: 80
POISSON_SCORE: 0.5129
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

ANALYSIS FILE NAME: GSM818045_UCSD.H1_Derived_Mesenchymal_Stem_Cells.H3K79me1.SK515.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K79me1.MSC.02.01.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Derived Mesenchymal Stem Cells Histone H3K79me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K79me1 ChIP-Seq read mappings from the H1 Derived Mesenchymal Stem Cells, Library SK515, 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.12513
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: HDMSC H3K79me1 15
BROWSER_TRACK_DESCRIPTION: UCSD H1 Derived Mesenchymal Stem Cells Histone H3K79me1 Library SK515 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 107,951,488
NUMBER_OF_H3K79me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 5
FINDPEAKS_SCORE: 0.2471
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.2355
HOTSPOT_PERCENTILE: 80
IROC_SCORE: 0.9637
IROC_PERCENTILE: 80
POISSON_SCORE: 0.5129
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

source_name: Human embryonic stem cells received from the James Thomson laboratory.  Cells are from the H1 line and are differentiated into mesenchymal stem cells.; renlab.H3K79me1.MSC.02.01

value: Embryonic stem cell differentiated into mesenchymal stem cells

value: Publication in progress

value: Biorupter

value: 500 micrograms


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

description:
sample_term_id: EFO_0000586
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K4me2 in Mesenchymal Stem Cells. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: SK521
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.10190
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.7914
****************
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: GSM818042_UCSD.H1_Derived_Mesenchymal_Stem_Cells.H3K4me2.SK521.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4me2.MSC.02.01.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of H1 Derived Mesenchymal Stem Cells Histone H3K4me2 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me2 ChIP-Seq on H1 Derived Mesenchymal Stem Cells, Library SK521, 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.12444
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: 105,922,599
NUMBER_OF_H3K4me2_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 2
FINDPEAKS_SCORE: 0.097
FINDPEAKS_PERCENTILE: 50
HOTSPOT_SCORE: 0.1561
HOTSPOT_PERCENTILE: 50
IROC_SCORE: 0.8668
IROC_PERCENTILE: 50
POISSON_SCORE: 0.2765
POISSON_PERCENTILE: 50
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

ANALYSIS FILE NAME: GSM818042_UCSD.H1_Derived_Mesenchymal_Stem_Cells.H3K4me2.SK521.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4me2.MSC.02.01.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Derived Mesenchymal Stem Cells Histone H3K4me2 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me2 ChIP-Seq read mappings from the H1 Derived Mesenchymal Stem Cells, Library SK521, 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.12517
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: HDMSC H3K4me2 21
BROWSER_TRACK_DESCRIPTION: UCSD H1 Derived Mesenchymal Stem Cells Histone H3K4me2 Library SK521 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 105,922,599
NUMBER_OF_H3K4me2_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 2
FINDPEAKS_SCORE: 0.097
FINDPEAKS_PERCENTILE: 50
HOTSPOT_SCORE: 0.1561
HOTSPOT_PERCENTILE: 50
IROC_SCORE: 0.8668
IROC_PERCENTILE: 50
POISSON_SCORE: 0.2765
POISSON_PERCENTILE: 50
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

source_name: Human embryonic stem cells received from the James Thomson laboratory.  Cells are from the H1 line and are differentiated into mesenchymal stem cells.; renlab.H3K4me2.MSC.02.01

value: Histone H3K4me2

value: magnetic anti-rabbit

value: 5 micrograms


title: FB0167P_cMYC_REP2

status: Public on Oct 18 2011

city: Austin

first: Vishy

last: Iyer

state: TX

address: 2500 Speedway Dr. MBB 3.212

department: Molecular Biosciences

institute: University of Texas at Austin

description: Chromatin IP against c-Myc

data_processing: peaks were identified using a Parzen window based algorithm as described previously with minor modifications (Shivaswamy et al. 2008. PLoS Biol 6: e65. )

source_name: Progeria fibroblast

growth_protocol: Cells were grown according to the approved ENCODE cell culture protocols.Specific protocol descriptions can be found at http://genome.ucsc.edu/ENCODE/cellTypes.html.

extract_protocol:
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 (32 to 52 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, library fragments of ~230 bp (insert plus adaptor and PCR primer sequences) were selected from an agarose gel.  The final size-selected lib. was amplified by 15 cycle of PCR followed by column purification of amplified DNA. 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.
ChIP was performed by cross-linking proteins to DNA using 1% formaldehyde solution (Bhinge et al. 2007; Birney et al. 2007). Immunoprecipitated DNA were sequenced using Illumina sequencers, (ChIP-seq). Input sequencing data were generated for GM12878, K562, HeLa-S3, HepG2, and HUVEC by cross-linking chromatin, shearing and reversing cross-links without immunoprecipitating.

tag: cell type

value: Progeria fibroblast

tag: cell line

tag: antibody

value: cMYC

tag: antibody (vender, cat#, lot#)

value: Santa Cruz, sc-764X, C1309


title: Medicago truncatula Root Knot

description:
MRMI1
Processed data contain distinct smallRNAs with their raw abundance after removing the adapter sequences

source_name: Root Knot

value: Root Knot


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

description:
sample_term_id: EFO_0000586
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K4ac in Mesenchymal Stem Cells. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AK274
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.10230
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.10198
****************
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: GSM818036_UCSD.H1_Derived_Mesenchymal_Stem_Cells.H3K4ac.AK274.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4ac.MSC.01.01.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of H1 Derived Mesenchymal Stem Cells Histone H3K4ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4ac ChIP-Seq on H1 Derived Mesenchymal Stem Cells, Library AK274, 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.12438
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: 35,784,780
NUMBER_OF_H3K4ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 3
FINDPEAKS_SCORE: 0.1241
FINDPEAKS_PERCENTILE: 67
HOTSPOT_SCORE: 0.3316
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9614
IROC_PERCENTILE: 100
POISSON_SCORE: 0.3714
POISSON_PERCENTILE: 67
MAXIMUM_REPLICATE_CORRELATION: 0.93

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

ANALYSIS FILE NAME: GSM818036_UCSD.H1_Derived_Mesenchymal_Stem_Cells.H3K4ac.AK274.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4ac.MSC.01.01.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Derived Mesenchymal Stem Cells Histone H3K4ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4ac ChIP-Seq read mappings from the H1 Derived Mesenchymal Stem Cells, Library AK274, 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.12511
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: HDMSC H3K4ac 74
BROWSER_TRACK_DESCRIPTION: UCSD H1 Derived Mesenchymal Stem Cells Histone H3K4ac Library AK274 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 35,784,780
NUMBER_OF_H3K4ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 3
FINDPEAKS_SCORE: 0.1241
FINDPEAKS_PERCENTILE: 67
HOTSPOT_SCORE: 0.3316
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9614
IROC_PERCENTILE: 100
POISSON_SCORE: 0.3714
POISSON_PERCENTILE: 67
MAXIMUM_REPLICATE_CORRELATION: 0.93

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

source_name: Human embryonic stem cells received from the James Thomson laboratory.  Cells are from the H1 line and are differentiated into mesenchymal stem cells.; renlab.H3K4ac.MSC.01.01

value: H1 Derived Mesenchymal Stem Cells

value: Male

value: Histone H3K4ac

value: Upstate


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

description:
sample_term_id: CL_0000047
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K4ac in Neural Progenitor Cells. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AK259
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.10180
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.10100
****************
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: GSM818038_UCSD.H1_Derived_Neuronal_Progenitor_Cultured_Cells.H3K4ac.AK259.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4ac.NPC.01.01.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of H1 Derived Neuronal Progenitor Cultured Cells Histone H3K4ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4ac ChIP-Seq on H1 Derived Neuronal Progenitor Cultured Cells, Library AK259, 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.12430
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: 38,138,079
NUMBER_OF_H3K4ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 3
FINDPEAKS_SCORE: 0.0415
FINDPEAKS_PERCENTILE: 33
HOTSPOT_SCORE: 0.2164
HOTSPOT_PERCENTILE: 33
IROC_SCORE: 0.8143
IROC_PERCENTILE: 33
POISSON_SCORE: 0.3162
POISSON_PERCENTILE: 33
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM818038_UCSD.H1_Derived_Neuronal_Progenitor_Cultured_Cells.H3K4ac.AK259.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4ac.NPC.01.01.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Derived Neuronal Progenitor Cultured Cells Histone H3K4ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4ac ChIP-Seq read mappings from the H1 Derived Neuronal Progenitor Cultured Cells, Library AK259, 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.12503
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: HDNP H3K4ac 59
BROWSER_TRACK_DESCRIPTION: UCSD H1 Derived Neuronal Progenitor Cultured Cells Histone H3K4ac Library AK259 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 38,138,079
NUMBER_OF_H3K4ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 3
FINDPEAKS_SCORE: 0.0415
FINDPEAKS_PERCENTILE: 33
HOTSPOT_SCORE: 0.2164
HOTSPOT_PERCENTILE: 33
IROC_SCORE: 0.8143
IROC_PERCENTILE: 33
POISSON_SCORE: 0.3162
POISSON_PERCENTILE: 33
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: Human embryonic stem cells received from the James Thomson laboratory.  Cells are from the H1 line and are differentiated into neural progenitor cells.; renlab.H3K4ac.NPC.01.01

value: genomic DNA

value: James Thomson Laboratory

value: Cell Line

value: Embryonic Stem Cell


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

description:
sample_term_id: CL_0000047
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K4me1 in Neural Progenitor Cells. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AK198
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.9788
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.7903
****************
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: GSM818039_UCSD.H1_Derived_Neuronal_Progenitor_Cultured_Cells.H3K4me1.AK198.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4me1.NPC.01.01.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of H1 Derived Neuronal Progenitor Cultured Cells Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me1 ChIP-Seq on H1 Derived Neuronal Progenitor Cultured Cells, Library AK198, 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.12432
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: 106,377,049
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 14
FINDPEAKS_SCORE: 0.0342
FINDPEAKS_PERCENTILE: 14
HOTSPOT_SCORE: 0.1161
HOTSPOT_PERCENTILE: 14
IROC_SCORE: 0.8498
IROC_PERCENTILE: 14
POISSON_SCORE: 0.3033
POISSON_PERCENTILE: 21
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

ANALYSIS FILE NAME: GSM818039_UCSD.H1_Derived_Neuronal_Progenitor_Cultured_Cells.H3K4me1.AK198.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4me1.NPC.01.01.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Derived Neuronal Progenitor Cultured Cells Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me1 ChIP-Seq read mappings from the H1 Derived Neuronal Progenitor Cultured Cells, Library AK198, 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.12505
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: HDNP H3K4me1 98
BROWSER_TRACK_DESCRIPTION: UCSD H1 Derived Neuronal Progenitor Cultured Cells Histone H3K4me1 Library AK198 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 106,377,049
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 14
FINDPEAKS_SCORE: 0.0342
FINDPEAKS_PERCENTILE: 14
HOTSPOT_SCORE: 0.1161
HOTSPOT_PERCENTILE: 14
IROC_SCORE: 0.8498
IROC_PERCENTILE: 14
POISSON_SCORE: 0.3033
POISSON_PERCENTILE: 21
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

source_name: Human embryonic stem cells received from the James Thomson laboratory.  Cells are from the H1 line and are differentiated into neural progenitor cells.; renlab.H3K4me1.NPC.01.01

value: Embryonic stem cell differentiated into neural progenitor cells

value: Publication in progress

value: Between 20 and 30

value: Histone H3K4me1

value: Biorupter

value: Abcam


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

description:
sample_term_id: EFO_0000586
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K4me2 in Mesenchymal Stem Cells. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: SK520
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.10172
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.7874
****************
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: GSM818041_UCSD.H1_Derived_Mesenchymal_Stem_Cells.H3K4me2.SK520.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4me2.MSC.01.01.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of H1 Derived Mesenchymal Stem Cells Histone H3K4me2 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me2 ChIP-Seq on H1 Derived Mesenchymal Stem Cells, Library SK520, 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.12442
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: 102,723,280
NUMBER_OF_H3K4me2_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 2
FINDPEAKS_SCORE: 0.2188
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.2653
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9963
IROC_PERCENTILE: 100
POISSON_SCORE: 0.3239
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

ANALYSIS FILE NAME: GSM818041_UCSD.H1_Derived_Mesenchymal_Stem_Cells.H3K4me2.SK520.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4me2.MSC.01.01.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Derived Mesenchymal Stem Cells Histone H3K4me2 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me2 ChIP-Seq read mappings from the H1 Derived Mesenchymal Stem Cells, Library SK520, 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.12515
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: HDMSC H3K4me2 20
BROWSER_TRACK_DESCRIPTION: UCSD H1 Derived Mesenchymal Stem Cells Histone H3K4me2 Library SK520 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 102,723,280
NUMBER_OF_H3K4me2_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 2
FINDPEAKS_SCORE: 0.2188
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.2653
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9963
IROC_PERCENTILE: 100
POISSON_SCORE: 0.3239
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

source_name: Human embryonic stem cells received from the James Thomson laboratory.  Cells are from the H1 line and are differentiated into mesenchymal stem cells.; renlab.H3K4me2.MSC.01.01

value: Embryonic stem cell differentiated into mesenchymal stem cells

value: Histone H3K4me2

value: 500 micrograms

value: magnetic anti-rabbit

value: 5 micrograms


title: Medicago truncatula Flower

description:
MINF
Processed data contain distinct smallRNAs with their raw abundance after removing the adapter sequences

source_name: Flower

value: Flower


title: Arachis hypogaea Nodule

description:
AHY01
Processed data contain distinct smallRNAs with their raw abundance after removing the adapter sequences

organism: Arachis hypogaea

source_name: Nodule

value: Nodule


title: Medicago truncatula Nodule

description:
MND1
Processed data contain distinct smallRNAs with their raw abundance after removing the adapter sequences


title: Reference Epigenome: ChIP-Seq Analysis of H3K27me3 in Neural Progenitor Cells; renlab.H3K27me3.NPC.01.01

description:
sample_term_id: CL_0000047
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K27me3 in Neural Progenitor Cells. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AK203
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.9786
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.7903
****************
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: Human embryonic stem cells received from the James Thomson laboratory.  Cells are from the H1 line and are differentiated into neural progenitor cells.; renlab.H3K27me3.NPC.01.01

value: H1 Derived Neuronal Progenitor Cultured Cells

value: genomic DNA

value: Male

value: Histone H3K27me3

value: Millipore


title: Whole genome shotgun bisulfite sequencing of the H1 mesendoderm cell line; methylC-seq_h1-mesendoderm_r1a

description:
Design description: Whole genome shotgun bisulfite sequencing of the H1 cell line treated with BMP4 and Activin A
Library name: methylC-seq_h1_mesendoderm_r1a
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.10254
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.10252
****************
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: GSM818003_UCSD.H1_BMP4_Derived_Mesendoderm_Cultured_Cells.Bisulfite-Seq.methylC-seq_h1_mesendoderm_r1a.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: methylC-seq_h1-mesendoderm_r1a.hg19.level.2.release.7
ANALYSIS TITLE: Methylation Proportion Graphs of H1 BMP4 Derived Mesendoderm Cultured Cells Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from the H1 BMP4 Derived Mesendoderm Cultured Cells, Library methylC-seq_h1_mesendoderm_r1a were processed into graphs of methylation proportions. Methylation proportions were calculated as (methylated calls / (methylated calls + unmethylated calls)) for all CpGs covered by at least 4 reads. Reads from the + and - strands were combined for methylation proportion calculations.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.12973
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
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: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 7
BROWSER_TRACK_NAME: HBDM BS 1a
BROWSER_TRACK_DESCRIPTION: UCSD H1 BMP4 Derived Mesendoderm Cultured Cells Bisulfite-Seq Library methylC-seq_h1_mesendoderm_r1a EA Release 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 232,256,182
NUMBER_OF_Bisulfite-Seq_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 6
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 98.38
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE: 17

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

ANALYSIS FILE NAME: GSM818003_UCSD.H1_BMP4_Derived_Mesendoderm_Cultured_Cells.Bisulfite-Seq.combined.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: methylC-seq_h1-mesendoderm_r1a-methylC-seq_h1-mesendoderm_r1b-methylC-seq_h1_mesendoderm_r2a-methylC-seq_h1_mesendoderm_r2b.hg19.level.2.release.7
ANALYSIS TITLE: Methylation Proportion Graphs of H1 BMP4 Derived Mesendoderm Cultured Cells Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from the H1 BMP4 Derived Mesendoderm Cultured Cells combined libraries were processed into graphs of methylation proportions. Methylation proportions were calculated as (methylated calls / (methylated calls + unmethylated calls)) for all CpGs covered by at least 4 reads. Reads from the + and - strands were combined for methylation proportion calculations.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.12976
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
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: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 7
BROWSER_TRACK_NAME: HBDM BS Combined
BROWSER_TRACK_DESCRIPTION: UCSD H1 BMP4 Derived Mesendoderm Cultured Cells Bisulfite-Seq Combined Libraries EA Release 7

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 898,944,318
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 98.44

SPECIAL NOTE: generated from combined data in GSM818003, GSM818004, GSM818005, GSM818006 (thus .wig files on these records are identical)

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

source_name: H1 cell line treated with BMP4 and Activin A biological replicate 1 (r1); methylC-seq_h1-mesendoderm_r1a

extract_protocol: Library construction protocol: Five µg of genomic DNA was extracted from frozen cell pellets using the DNeasy Mini Kit (Qiagen, Valencia, CA) and spiked with 25 ng unmethylated cl857 Sam7 Lambda DNA (Promega, Madison, WI). The DNA was fragmented with a Covaris S2 (Covaris, Woburn, MA) to 100-150 bp, followed by end repair and addition of a 3' A base. Cytosine-methylated adapters provided by Illumina (Illumina, San Diego, CA) were ligated to the sonicated DNA at 16C for 16 hours with T4 DNA ligase (New England Biolabs). Adapter-ligated DNA was isolated by two rounds of purification with AMPure XP beads (Beckman Coulter Genomics, Danvers, MA). Adapter-ligated DNA (450 ng) was subjected to sodium bisulfite conversion using the MethylCode kit (Life Technologies, Carlsbad, CA) as per manufacturer's instructions. The bisulfite-converted, adapter-ligated DNA molecules were enriched by 4 cycles of PCR with the following reaction composition: 2.5 U of uracil-insensitive PfuTurboCx Hotstart DNA polymerase (Stratagene), 5 µl 10X PfuTurbo reaction buffer, 31 µM dNTPs, 1 µl Primer 1, 1 µl Primer 2 (50 µl final). The thermocycling parameters were: 95C 2 min, 98C 30 sec, then 4-8 cycles of 98C 15 sec, 60C 30 sec and 72C 4 min, ending with one 72C 10 min step. The reaction products were purified using AMPure XP beads (two rounds). Up to three separate PCR reactions were performed on subsets of the adapter-ligated, bisulfite-converted DNA, yielding up to three independent libraries from the same biological sample.

value: Thomson Laboratory

value: Cell Line

value: embryonic stem cell differentiated into mesendoderm cells

value: H1 cells differentiated in +5ng/mL BMP4 +25ng/mL Activin A medium

value: TeSR

value: Replicate 1

value: DNA Methylation

value: Qiagen DNeasy mini kit, performed as per manufacturer's instructions

value: Covaris S2

value: Standard fragment express, 6 cycles

value: 5 µg

value: A:5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, B:5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT

value: 16ËšC for 16 hours with T4 DNA ligase (New England Biolabs)

value: Two rounds of purification with AMPure XP beads (Agencourt)

value: Invitrogen MethylCode

value: 99.5% of cytosines converted based on shotgun sequencing of unmethylated lambda phage control spiked into original genomic DNA sample

value: One third of the adapter-ligated, bisulfite converted DNA was used in each of three 50 µl PCR reaction

value: Stratagene Pfu Turbo Cx

value: 95C 2 min; 98C 30 sec, 4 cycles of 98C 15 sec, 60C 30 sec, 72C 4 min; 72C 10 min

value: 5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT

value: 25 µM


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

description:
sample_term_id: CL_0000047
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K36me3 in Neural Progenitor Cells. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AK202
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.10103
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.7903
****************
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: GSM818034_UCSD.H1_Derived_Neuronal_Progenitor_Cultured_Cells.H3K36me3.AK202.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K36me3.NPC.01.01.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of H1 Derived Neuronal Progenitor Cultured Cells Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K36me3 ChIP-Seq on H1 Derived Neuronal Progenitor Cultured Cells, Library AK202, 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.12399
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: 104,490,249
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 13
FINDPEAKS_SCORE: 0.0218
FINDPEAKS_PERCENTILE: 15
HOTSPOT_SCORE: 0.055
HOTSPOT_PERCENTILE: 8
IROC_SCORE: 0.7575
IROC_PERCENTILE: 15
POISSON_SCORE: 0.1753
POISSON_PERCENTILE: 8
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM818034_UCSD.H1_Derived_Neuronal_Progenitor_Cultured_Cells.H3K36me3.AK202.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K36me3.NPC.01.01.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Derived Neuronal Progenitor Cultured Cells Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K36me3 ChIP-Seq read mappings from the H1 Derived Neuronal Progenitor Cultured Cells, Library AK202, 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.12472
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: HDNP H3K36me3 02
BROWSER_TRACK_DESCRIPTION: UCSD H1 Derived Neuronal Progenitor Cultured Cells Histone H3K36me3 Library AK202 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 104,490,249
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 13
FINDPEAKS_SCORE: 0.0218
FINDPEAKS_PERCENTILE: 15
HOTSPOT_SCORE: 0.055
HOTSPOT_PERCENTILE: 8
IROC_SCORE: 0.7575
IROC_PERCENTILE: 15
POISSON_SCORE: 0.1753
POISSON_PERCENTILE: 8
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

source_name: Human embryonic stem cells received from the James Thomson laboratory.  Cells are from the H1 line and are differentiated into neural progenitor cells.; renlab.H3K36me3.NPC.01.01

value: genomic DNA

value: James Thomson Laboratory

value: Cell Line

value: Embryonic Stem Cell

value: Embryonic stem cell differentiated into neural progenitor cells

value: Publication in progress

value: Between 20 and 30

value: Male

value: Histone H3K36me3

value: Biorupter

value: 500 micrograms

value: magnetic anti-rabbit

value: 5 micrograms

value: Abcam


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

description:
sample_term_id: CL_0000047
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K23ac in Neural Progenitor Cells. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AK255
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.10147
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.10100
****************
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: GSM818030_UCSD.H1_Derived_Neuronal_Progenitor_Cultured_Cells.H3K23ac.AK255.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K23ac.NPC.01.01.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of H1 Derived Neuronal Progenitor Cultured Cells Histone H3K23ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K23ac ChIP-Seq on H1 Derived Neuronal Progenitor Cultured Cells, Library AK255, 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.12372
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: 32,709,398
NUMBER_OF_H3K23ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 6
FINDPEAKS_SCORE: 0.0253
FINDPEAKS_PERCENTILE: 83
HOTSPOT_SCORE: 0.1094
HOTSPOT_PERCENTILE: 67
IROC_SCORE: 0.8096
IROC_PERCENTILE: 50
POISSON_SCORE: 0.3742
POISSON_PERCENTILE: 83
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM818030_UCSD.H1_Derived_Neuronal_Progenitor_Cultured_Cells.H3K23ac.AK255.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K23ac.NPC.01.01.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Derived Neuronal Progenitor Cultured Cells Histone H3K23ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K23ac ChIP-Seq read mappings from the H1 Derived Neuronal Progenitor Cultured Cells, Library AK255, 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.12445
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: HDNP H3K23ac 55
BROWSER_TRACK_DESCRIPTION: UCSD H1 Derived Neuronal Progenitor Cultured Cells Histone H3K23ac Library AK255 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 32,709,398
NUMBER_OF_H3K23ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 6
FINDPEAKS_SCORE: 0.0253
FINDPEAKS_PERCENTILE: 83
HOTSPOT_SCORE: 0.1094
HOTSPOT_PERCENTILE: 67
IROC_SCORE: 0.8096
IROC_PERCENTILE: 50
POISSON_SCORE: 0.3742
POISSON_PERCENTILE: 83
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: Human embryonic stem cells received from the James Thomson laboratory.  Cells are from the H1 line and are differentiated into neural progenitor cells.; renlab.H3K23ac.NPC.01.01

value: Histone H3K23ac

value: Upstate


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

description:
sample_term_id: EFO_0000586
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K23ac in Mesenchymal Stem Cells. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AK284
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.10222
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.10206
****************
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: GSM818029_UCSD.H1_Derived_Mesenchymal_Stem_Cells.H3K23ac.AK284.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K23ac.MSC.02.01.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of H1 Derived Mesenchymal Stem Cells Histone H3K23ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K23ac ChIP-Seq on H1 Derived Mesenchymal Stem Cells, Library AK284, 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.12408
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: 48,188,211
NUMBER_OF_H3K23ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 6
FINDPEAKS_SCORE: 0.1024
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.3289
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9448
IROC_PERCENTILE: 83
POISSON_SCORE: 0.4274
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.7

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

ANALYSIS FILE NAME: GSM818029_UCSD.H1_Derived_Mesenchymal_Stem_Cells.H3K23ac.AK284.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K23ac.MSC.02.01.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Derived Mesenchymal Stem Cells Histone H3K23ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K23ac ChIP-Seq read mappings from the H1 Derived Mesenchymal Stem Cells, Library AK284, 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.12481
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: HDMSC H3K23ac 84
BROWSER_TRACK_DESCRIPTION: UCSD H1 Derived Mesenchymal Stem Cells Histone H3K23ac Library AK284 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 48,188,211
NUMBER_OF_H3K23ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 6
FINDPEAKS_SCORE: 0.1024
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.3289
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9448
IROC_PERCENTILE: 83
POISSON_SCORE: 0.4274
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.7

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

source_name: Human embryonic stem cells received from the James Thomson laboratory.  Cells are from the H1 line and are differentiated into mesenchymal stem cells.; renlab.H3K23ac.MSC.02.01

value: H1 Derived Mesenchymal Stem Cells

value: Embryonic stem cell differentiated into mesenchymal stem cells


title: Reference Epigenome: ChIP-Seq Analysis of H3K23ac in BMP4 Trophoblast Cells; renlab.H3K23ac.BMP4T.02.01

description:
sample_term_id: UBERON_0000088
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K23ac in BMP4 Trophoblast Cells. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: SK513
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.10131
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.7847
****************
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: GSM818027_UCSD.H1_BMP4_Derived_Trophoblast_Cultured_Cells.H3K23ac.SK513.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K23ac.BMP4T.02.01.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K23ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K23ac ChIP-Seq on H1 BMP4 Derived Trophoblast Cultured Cells, Library SK513, 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.12397
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: 113,049,273
NUMBER_OF_H3K23ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 6
FINDPEAKS_SCORE: 0.0181
FINDPEAKS_PERCENTILE: 67
HOTSPOT_SCORE: 0.0181
HOTSPOT_PERCENTILE: 17
IROC_SCORE: 0.9789
IROC_PERCENTILE: 100
POISSON_SCORE: 0.1104
POISSON_PERCENTILE: 17
MAXIMUM_REPLICATE_CORRELATION: 1.0

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

ANALYSIS FILE NAME: GSM818027_UCSD.H1_BMP4_Derived_Trophoblast_Cultured_Cells.H3K23ac.SK513.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K23ac.BMP4T.02.01.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K23ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K23ac ChIP-Seq read mappings from the H1 BMP4 Derived Trophoblast Cultured Cells, Library SK513, 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.12470
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: HBDT H3K23ac 13
BROWSER_TRACK_DESCRIPTION: UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K23ac Library SK513 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 113,049,273
NUMBER_OF_H3K23ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 6
FINDPEAKS_SCORE: 0.0181
FINDPEAKS_PERCENTILE: 67
HOTSPOT_SCORE: 0.0181
HOTSPOT_PERCENTILE: 17
IROC_SCORE: 0.9789
IROC_PERCENTILE: 100
POISSON_SCORE: 0.1104
POISSON_PERCENTILE: 17
MAXIMUM_REPLICATE_CORRELATION: 1.0

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

source_name: Human embryonic stem cells received from the James Thomson laboratory.  Cells are from the H1 line and are differentiated into trophoblast by treatment with BMP4.; renlab.H3K23ac.BMP4T.02.01

value: genomic DNA

value: James Thomson Laboratory

value: Embryonic stem cell differentiated into trophoblast by treatment with BMP4

value: H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days

value: Millipore


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

description:
sample_term_id: EFO_0000586
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K23ac in Mesenchymal Stem Cells. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AK273
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.10228
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.10198
****************
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: GSM818028_UCSD.H1_Derived_Mesenchymal_Stem_Cells.H3K23ac.AK273.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K23ac.MSC.01.01.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of H1 Derived Mesenchymal Stem Cells Histone H3K23ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K23ac ChIP-Seq on H1 Derived Mesenchymal Stem Cells, Library AK273, 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.12379
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: 32,812,318
NUMBER_OF_H3K23ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 6
FINDPEAKS_SCORE: 0.0156
FINDPEAKS_PERCENTILE: 33
HOTSPOT_SCORE: 0.1324
HOTSPOT_PERCENTILE: 83
IROC_SCORE: 0.7632
IROC_PERCENTILE: 33
POISSON_SCORE: 0.2755
POISSON_PERCENTILE: 67
MAXIMUM_REPLICATE_CORRELATION: 0.7

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

ANALYSIS FILE NAME: GSM818028_UCSD.H1_Derived_Mesenchymal_Stem_Cells.H3K23ac.AK273.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K23ac.MSC.01.01.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Derived Mesenchymal Stem Cells Histone H3K23ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K23ac ChIP-Seq read mappings from the H1 Derived Mesenchymal Stem Cells, Library AK273, 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.12452
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: HDMSC H3K23ac 73
BROWSER_TRACK_DESCRIPTION: UCSD H1 Derived Mesenchymal Stem Cells Histone H3K23ac Library AK273 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 32,812,318
NUMBER_OF_H3K23ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 6
FINDPEAKS_SCORE: 0.0156
FINDPEAKS_PERCENTILE: 33
HOTSPOT_SCORE: 0.1324
HOTSPOT_PERCENTILE: 83
IROC_SCORE: 0.7632
IROC_PERCENTILE: 33
POISSON_SCORE: 0.2755
POISSON_PERCENTILE: 67
MAXIMUM_REPLICATE_CORRELATION: 0.7

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

source_name: Human embryonic stem cells received from the James Thomson laboratory.  Cells are from the H1 line and are differentiated into mesenchymal stem cells.; renlab.H3K23ac.MSC.01.01

value: Cell Line

value: Embryonic Stem Cell

value: Publication in progress


title: Reference Epigenome: ChIP-Seq Analysis of H3K23ac in BMP4 Trophoblast Cells; renlab.H3K23ac.BMP4T.01.01

description:
sample_term_id: UBERON_0000088
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K23ac in BMP4 Trophoblast Cells. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: SK512
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.10098
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.7840
****************
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: GSM818026_UCSD.H1_BMP4_Derived_Trophoblast_Cultured_Cells.H3K23ac.SK512.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K23ac.BMP4T.01.01.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K23ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K23ac ChIP-Seq on H1 BMP4 Derived Trophoblast Cultured Cells, Library SK512, 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.12396
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: 109,360,280
NUMBER_OF_H3K23ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 6
FINDPEAKS_SCORE: 0.0164
FINDPEAKS_PERCENTILE: 50
HOTSPOT_SCORE: 0.0236
HOTSPOT_PERCENTILE: 33
IROC_SCORE: 0.9309
IROC_PERCENTILE: 67
POISSON_SCORE: 0.15
POISSON_PERCENTILE: 33
MAXIMUM_REPLICATE_CORRELATION: 1.0

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

ANALYSIS FILE NAME: GSM818026_UCSD.H1_BMP4_Derived_Trophoblast_Cultured_Cells.H3K23ac.SK512.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K23ac.BMP4T.01.01.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K23ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K23ac ChIP-Seq read mappings from the H1 BMP4 Derived Trophoblast Cultured Cells, Library SK512, 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.12469
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: HBDT H3K23ac 12
BROWSER_TRACK_DESCRIPTION: UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K23ac Library SK512 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 109,360,280
NUMBER_OF_H3K23ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 6
FINDPEAKS_SCORE: 0.0164
FINDPEAKS_PERCENTILE: 50
HOTSPOT_SCORE: 0.0236
HOTSPOT_PERCENTILE: 33
IROC_SCORE: 0.9309
IROC_PERCENTILE: 67
POISSON_SCORE: 0.15
POISSON_PERCENTILE: 33
MAXIMUM_REPLICATE_CORRELATION: 1.0

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

source_name: Human embryonic stem cells received from the James Thomson laboratory.  Cells are from the H1 line and are differentiated into trophoblast by treatment with BMP4.; renlab.H3K23ac.BMP4T.01.01

value: Male

value: Biorupter