title: Reference Epigenome: ChIP-Seq Analysis of H3K79me2 in BMP4 Trophoblast Cells; renlab.H3K79me2.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 H3K79me2 in BMP4 Trophoblast Cells. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AY230
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.12133
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.12116
****************
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: GSM908960_UCSD.H1_BMP4_Derived_Trophoblast_Cultured_Cells.H3K79me2.AY230.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K79me2.BMP4T.01.01.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of H1 BMP4 Derived Trophoblast Cultured Cells H3K79me2 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K79me2 ChIP-Seq on H1 BMP4 Derived Trophoblast Cultured Cells, Library AY230, 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.13446
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 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 28,881,792
NUMBER_OF_H3K79me2_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 2
FINDPEAKS_SCORE: 0.1323
FINDPEAKS_PERCENTILE: 50
HOTSPOT_SCORE: 0.2498
HOTSPOT_PERCENTILE: 50
IROC_SCORE: 0.9091
IROC_PERCENTILE: 50
POISSON_SCORE: 0.4226
POISSON_PERCENTILE: 50
MAXIMUM_REPLICATE_CORRELATION: 0.95

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

ANALYSIS FILE NAME: GSM908960_UCSD.H1_BMP4_Derived_Trophoblast_Cultured_Cells.H3K79me2.AY230.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K79me2.BMP4T.01.01.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of H1 BMP4 Derived Trophoblast Cultured Cells H3K79me2 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K79me2 ChIP-Seq read mappings from the H1 BMP4 Derived Trophoblast Cultured Cells, Library AY230, 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.13566
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 8
BROWSER_TRACK_NAME: HBDT H3K79me2 30
BROWSER_TRACK_DESCRIPTION: UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K79me2 Library AY230 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 28,881,792
NUMBER_OF_H3K79me2_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 2
FINDPEAKS_SCORE: 0.1323
FINDPEAKS_PERCENTILE: 50
HOTSPOT_SCORE: 0.2498
HOTSPOT_PERCENTILE: 50
IROC_SCORE: 0.9091
IROC_PERCENTILE: 50
POISSON_SCORE: 0.4226
POISSON_PERCENTILE: 50
MAXIMUM_REPLICATE_CORRELATION: 0.95

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

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.H3K79me2.BMP4T.01.01

value: James Thomson Laboratory

value: Cell Line

value: Embryonic Stem Cell

value: Histone H3K79me2

value: Active Motif


title: Reference Epigenome: ChIP-Seq Analysis of H3K4ac in BMP4 Trophoblast Cells; renlab.H3K4ac.BMP4T.01.01

status: Public on Apr 05 2012

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: UBERON_0000088
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K4ac in BMP4 Trophoblast Cells. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AY228
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.12129
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.12116
****************
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: GSM908954_UCSD.H1_BMP4_Derived_Trophoblast_Cultured_Cells.H3K4ac.AY228.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4ac.BMP4T.01.01.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of H1 BMP4 Derived Trophoblast Cultured Cells H3K4ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K4ac ChIP-Seq on H1 BMP4 Derived Trophoblast Cultured Cells, Library AY228, 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.13487
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 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 19,877,339
NUMBER_OF_H3K4ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 3
FINDPEAKS_SCORE: 0.2615
FINDPEAKS_PERCENTILE: 67
HOTSPOT_SCORE: 0.3074
HOTSPOT_PERCENTILE: 67
IROC_SCORE: 0.9883
IROC_PERCENTILE: 67
POISSON_SCORE: 0.4127
POISSON_PERCENTILE: 67
MAXIMUM_REPLICATE_CORRELATION: 0.95

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

ANALYSIS FILE NAME: GSM908954_UCSD.H1_BMP4_Derived_Trophoblast_Cultured_Cells.H3K4ac.AY228.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4ac.BMP4T.01.01.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of H1 BMP4 Derived Trophoblast Cultured Cells H3K4ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K4ac ChIP-Seq read mappings from the H1 BMP4 Derived Trophoblast Cultured Cells, Library AY228, 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.13607
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 8
BROWSER_TRACK_NAME: HBDT H3K4ac 28
BROWSER_TRACK_DESCRIPTION: UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K4ac Library AY228 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 19,877,339
NUMBER_OF_H3K4ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 3
FINDPEAKS_SCORE: 0.2615
FINDPEAKS_PERCENTILE: 67
HOTSPOT_SCORE: 0.3074
HOTSPOT_PERCENTILE: 67
IROC_SCORE: 0.9883
IROC_PERCENTILE: 67
POISSON_SCORE: 0.4127
POISSON_PERCENTILE: 67
MAXIMUM_REPLICATE_CORRELATION: 0.95

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

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 trophoblast by treatment with BMP4.; renlab.H3K4ac.BMP4T.01.01

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

tag: sample alias

tag: sample common name

tag: molecule

value: genomic DNA

tag: disease

tag: line

tag: lineage

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

tag: passage

tag: medium

tag: Sex

value: Male

tag: batch

value: Histone H3K4ac

value: Biorupter

value: 500 micrograms

value: magnetic anti-rabbit

value: 5 micrograms

value: Upstate


title: Reference Epigenome: ChIP-Seq Analysis of H3K4me2 in Neural Progenitor Cells; renlab.H3K4me2.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 H3K4me2 in Neural Progenitor Cells. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AK260
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.12160
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: GSM908957_UCSD.H1_Derived_Neuronal_Progenitor_Cultured_Cells.H3K4me2.AK260.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4me2.NPC.01.01.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of H1 Derived Neuronal Progenitor Cultured Cells H3K4me2 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K4me2 ChIP-Seq on H1 Derived Neuronal Progenitor Cultured Cells, Library AK260, 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.13465
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 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 6,730,783
NUMBER_OF_H3K4me2_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 1
FINDPEAKS_SCORE: 0.4235
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.5171
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.492
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM908957_UCSD.H1_Derived_Neuronal_Progenitor_Cultured_Cells.H3K4me2.AK260.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4me2.NPC.01.01.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Derived Neuronal Progenitor Cultured Cells H3K4me2 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K4me2 ChIP-Seq read mappings from the H1 Derived Neuronal Progenitor Cultured Cells, Library AK260, 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.13585
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 8
BROWSER_TRACK_NAME: HDNP H3K4me2 60
BROWSER_TRACK_DESCRIPTION: UCSD H1 Derived Neuronal Progenitor Cultured Cells Histone H3K4me2 Library AK260 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 6,730,783
NUMBER_OF_H3K4me2_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 1
FINDPEAKS_SCORE: 0.4235
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.5171
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.492
POISSON_PERCENTILE: 100
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.H3K4me2.NPC.01.01

value: Embryonic stem cell differentiated into neural progenitor cells

value: Publication in progress

value: Histone H3K4me2

value: Abcam


title: Reference Epigenome: ChIP-Seq Analysis of H3K4ac in Neural Progenitor Cells; renlab.H3K4ac.NPC.02.01

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: AK386
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.12077
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.11641
****************
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: GSM908956_UCSD.H1_Derived_Neuronal_Progenitor_Cultured_Cells.H3K4ac.AK386.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4ac.NPC.02.01.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of H1 Derived Neuronal Progenitor Cultured Cells H3K4ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K4ac ChIP-Seq on H1 Derived Neuronal Progenitor Cultured Cells, Library AK386, 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.13489
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 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 31,057,635
NUMBER_OF_H3K4ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 3
FINDPEAKS_SCORE: 0.0054
FINDPEAKS_PERCENTILE: 33
HOTSPOT_SCORE: 0.0308
HOTSPOT_PERCENTILE: 33
IROC_SCORE: 0.7377
IROC_PERCENTILE: 33
POISSON_SCORE: 0.1445
POISSON_PERCENTILE: 33
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM908956_UCSD.H1_Derived_Neuronal_Progenitor_Cultured_Cells.H3K4ac.AK386.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4ac.NPC.02.01.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Derived Neuronal Progenitor Cultured Cells H3K4ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K4ac ChIP-Seq read mappings from the H1 Derived Neuronal Progenitor Cultured Cells, Library AK386, 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.13609
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 8
BROWSER_TRACK_NAME: HDNP H3K4ac 86
BROWSER_TRACK_DESCRIPTION: UCSD H1 Derived Neuronal Progenitor Cultured Cells Histone H3K4ac Library AK386 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 31,057,635
NUMBER_OF_H3K4ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 3
FINDPEAKS_SCORE: 0.0054
FINDPEAKS_PERCENTILE: 33
HOTSPOT_SCORE: 0.0308
HOTSPOT_PERCENTILE: 33
IROC_SCORE: 0.7377
IROC_PERCENTILE: 33
POISSON_SCORE: 0.1445
POISSON_PERCENTILE: 33
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.H3K4ac.NPC.02.01

value: James Thomson Laboratory

value: Cell Line

value: Embryonic Stem Cell


title: Reference Epigenome: ChIP-Seq Analysis of H3K18ac in BMP4 Mesendoderm Cells; renlab.H3K18ac.BMP4M.01.01

description:
sample_term_id: NTR_0000856
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K18ac in BMP4 Mesendoderm Cells. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AK402
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.12073
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.11184
****************
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: GSM908948_UCSD.H1_BMP4_Derived_Mesendoderm_Cultured_Cells.H3K18ac.AK402.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K18ac.BMP4M.01.01.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of H1 BMP4 Derived Mesendoderm Cultured Cells H3K18ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K18ac ChIP-Seq on H1 BMP4 Derived Mesendoderm Cultured Cells, Library AK402, 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.13530
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 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 26,311,316
NUMBER_OF_H3K18ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 3
FINDPEAKS_SCORE: 0.0939
FINDPEAKS_PERCENTILE: 33
HOTSPOT_SCORE: 0.2047
HOTSPOT_PERCENTILE: 33
IROC_SCORE: 0.8987
IROC_PERCENTILE: 33
POISSON_SCORE: 0.3571
POISSON_PERCENTILE: 33
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM908948_UCSD.H1_BMP4_Derived_Mesendoderm_Cultured_Cells.H3K18ac.AK402.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K18ac.BMP4M.01.01.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of H1 BMP4 Derived Mesendoderm Cultured Cells H3K18ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K18ac ChIP-Seq read mappings from the H1 BMP4 Derived Mesendoderm Cultured Cells, Library AK402, 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.13650
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 8
BROWSER_TRACK_NAME: HBDM H3K18ac 02
BROWSER_TRACK_DESCRIPTION: UCSD H1 BMP4 Derived Mesendoderm Cultured Cells Histone H3K18ac Library AK402 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 26,311,316
NUMBER_OF_H3K18ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 3
FINDPEAKS_SCORE: 0.0939
FINDPEAKS_PERCENTILE: 33
HOTSPOT_SCORE: 0.2047
HOTSPOT_PERCENTILE: 33
IROC_SCORE: 0.8987
IROC_PERCENTILE: 33
POISSON_SCORE: 0.3571
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 mesendoderm by treatment with BMP4.; renlab.H3K18ac.BMP4M.01.01

value: genomic DNA

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: Histone H3K18ac


title: Reference Epigenome: ChIP-Seq Analysis of H3K18ac in BMP4 Trophoblast Cells; renlab.H3K18ac.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 H3K18ac in BMP4 Trophoblast Cells. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AY75
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.12110
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.11191
****************
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: GSM908949_UCSD.H1_BMP4_Derived_Trophoblast_Cultured_Cells.H3K18ac.AY75.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K18ac.BMP4T.01.01.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of H1 BMP4 Derived Trophoblast Cultured Cells H3K18ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K18ac ChIP-Seq on H1 BMP4 Derived Trophoblast Cultured Cells, Library AY75, 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.13466
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 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 24,593,226
NUMBER_OF_H3K18ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 3
FINDPEAKS_SCORE: 0.4312
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.4918
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9893
IROC_PERCENTILE: 100
POISSON_SCORE: 0.5837
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

ANALYSIS FILE NAME: GSM908949_UCSD.H1_BMP4_Derived_Trophoblast_Cultured_Cells.H3K18ac.AY75.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K18ac.BMP4T.01.01.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of H1 BMP4 Derived Trophoblast Cultured Cells H3K18ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K18ac ChIP-Seq read mappings from the H1 BMP4 Derived Trophoblast Cultured Cells, Library AY75, 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.13586
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 8
BROWSER_TRACK_NAME: HBDT H3K18ac 75
BROWSER_TRACK_DESCRIPTION: UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K18ac Library AY75 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 24,593,226
NUMBER_OF_H3K18ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 3
FINDPEAKS_SCORE: 0.4312
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.4918
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9893
IROC_PERCENTILE: 100
POISSON_SCORE: 0.5837
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 trophoblast by treatment with BMP4.; renlab.H3K18ac.BMP4T.01.01

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 H3K14ac in Mesenchymal Stem Cells; renlab.H3K14ac.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 H3K14ac in Mesenchymal Stem Cells. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AK378
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.12075
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: GSM908947_UCSD.H1_Derived_Mesenchymal_Stem_Cells.H3K14ac.AK378.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K14ac.MSC.02.01.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of H1 Derived Mesenchymal Stem Cells H3K14ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K14ac ChIP-Seq on H1 Derived Mesenchymal Stem Cells, Library AK378, 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.13554
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 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 23,407,045
NUMBER_OF_H3K14ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 4
FINDPEAKS_SCORE: 0.0039
FINDPEAKS_PERCENTILE: 25
HOTSPOT_SCORE: 0.0721
HOTSPOT_PERCENTILE: 25
IROC_SCORE: 0.8852
IROC_PERCENTILE: 25
POISSON_SCORE: 0.1511
POISSON_PERCENTILE: 25
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM908947_UCSD.H1_Derived_Mesenchymal_Stem_Cells.H3K14ac.AK378.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K14ac.MSC.02.01.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Derived Mesenchymal Stem Cells H3K14ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K14ac ChIP-Seq read mappings from the H1 Derived Mesenchymal Stem Cells, Library AK378, 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.13674
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 8
BROWSER_TRACK_NAME: HDMSC H3K14ac 78
BROWSER_TRACK_DESCRIPTION: UCSD H1 Derived Mesenchymal Stem Cells Histone H3K14ac Library AK378 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 23,407,045
NUMBER_OF_H3K14ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 4
FINDPEAKS_SCORE: 0.0039
FINDPEAKS_PERCENTILE: 25
HOTSPOT_SCORE: 0.0721
HOTSPOT_PERCENTILE: 25
IROC_SCORE: 0.8852
IROC_PERCENTILE: 25
POISSON_SCORE: 0.1511
POISSON_PERCENTILE: 25
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 mesenchymal stem cells.; renlab.H3K14ac.MSC.02.01

value: H1 Derived Mesenchymal Stem Cells

value: Embryonic stem cell differentiated into mesenchymal stem cells

value: Histone H3K14ac

value: Biorupter

value: 500 micrograms

value: magnetic anti-rabbit


title: Reference Epigenome: ChIP-Seq Analysis of H2BK12ac in BMP4 Trophoblast Cells; renlab.H2BK12ac.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 H2BK12ac in BMP4 Trophoblast Cells. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AY224
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.12123
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.12116
****************
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: GSM908943_UCSD.H1_BMP4_Derived_Trophoblast_Cultured_Cells.H2BK12ac.AY224.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H2BK12ac.BMP4T.02.01.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of H1 BMP4 Derived Trophoblast Cultured Cells H2BK12ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H2BK12ac ChIP-Seq on H1 BMP4 Derived Trophoblast Cultured Cells, Library AY224, 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.13558
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 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 24,949,754
NUMBER_OF_H2BK12ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 2
FINDPEAKS_SCORE: 0.2732
FINDPEAKS_PERCENTILE: 50
HOTSPOT_SCORE: 0.3724
HOTSPOT_PERCENTILE: 50
IROC_SCORE: 0.966
IROC_PERCENTILE: 100
POISSON_SCORE: 0.5056
POISSON_PERCENTILE: 50
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

ANALYSIS FILE NAME: GSM908943_UCSD.H1_BMP4_Derived_Trophoblast_Cultured_Cells.H2BK12ac.AY224.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H2BK12ac.BMP4T.02.01.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of H1 BMP4 Derived Trophoblast Cultured Cells H2BK12ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H2BK12ac ChIP-Seq read mappings from the H1 BMP4 Derived Trophoblast Cultured Cells, Library AY224, 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.13678
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 8
BROWSER_TRACK_NAME: HBDT H2BK12ac 24
BROWSER_TRACK_DESCRIPTION: UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H2BK12ac Library AY224 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 24,949,754
NUMBER_OF_H2BK12ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 2
FINDPEAKS_SCORE: 0.2732
FINDPEAKS_PERCENTILE: 50
HOTSPOT_SCORE: 0.3724
HOTSPOT_PERCENTILE: 50
IROC_SCORE: 0.966
IROC_PERCENTILE: 100
POISSON_SCORE: 0.5056
POISSON_PERCENTILE: 50
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 trophoblast by treatment with BMP4.; renlab.H2BK12ac.BMP4T.02.01

value: Histone H2BK12ac

value: 5 micrograms

value: Abcam


title: Reference Epigenome: ChIP-Seq Analysis of H3K14ac in BMP4 Trophoblast Cells; renlab.H3K14ac.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 H3K14ac in BMP4 Trophoblast Cells. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AY74
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.12112
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.11191
****************
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: GSM908945_UCSD.H1_BMP4_Derived_Trophoblast_Cultured_Cells.H3K14ac.AY74.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K14ac.BMP4T.01.01.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of H1 BMP4 Derived Trophoblast Cultured Cells H3K14ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K14ac ChIP-Seq on H1 BMP4 Derived Trophoblast Cultured Cells, Library AY74, 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.13494
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 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 24,784,949
NUMBER_OF_H3K14ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 4
FINDPEAKS_SCORE: 0.179
FINDPEAKS_PERCENTILE: 50
HOTSPOT_SCORE: 0.3363
HOTSPOT_PERCENTILE: 50
IROC_SCORE: 0.9198
IROC_PERCENTILE: 50
POISSON_SCORE: 0.5054
POISSON_PERCENTILE: 50
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

ANALYSIS FILE NAME: GSM908945_UCSD.H1_BMP4_Derived_Trophoblast_Cultured_Cells.H3K14ac.AY74.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K14ac.BMP4T.01.01.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of H1 BMP4 Derived Trophoblast Cultured Cells H3K14ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K14ac ChIP-Seq read mappings from the H1 BMP4 Derived Trophoblast Cultured Cells, Library AY74, 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.13614
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 8
BROWSER_TRACK_NAME: HBDT H3K14ac 74
BROWSER_TRACK_DESCRIPTION: UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K14ac Library AY74 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 24,784,949
NUMBER_OF_H3K14ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 4
FINDPEAKS_SCORE: 0.179
FINDPEAKS_PERCENTILE: 50
HOTSPOT_SCORE: 0.3363
HOTSPOT_PERCENTILE: 50
IROC_SCORE: 0.9198
IROC_PERCENTILE: 50
POISSON_SCORE: 0.5054
POISSON_PERCENTILE: 50
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 trophoblast by treatment with BMP4.; renlab.H3K14ac.BMP4T.01.01

value: James Thomson Laboratory

value: Cell Line

value: Embryonic Stem Cell


title: Reference Epigenome: ChIP-Seq Analysis of H4K8ac in BMP4 Trophoblast Cells; renlab.H4K8ac.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 H4K8ac in BMP4 Trophoblast Cells. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AY205
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.12166
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.11191
****************
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: GSM908965_UCSD.H1_BMP4_Derived_Trophoblast_Cultured_Cells.H4K8ac.AY205.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H4K8ac.BMP4T.02.01.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of H1 BMP4 Derived Trophoblast Cultured Cells H4K8ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H4K8ac ChIP-Seq on H1 BMP4 Derived Trophoblast Cultured Cells, Library AY205, 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.13470
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 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 13,187,938
NUMBER_OF_H4K8ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 4
FINDPEAKS_SCORE: 0.4154
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.5005
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9774
IROC_PERCENTILE: 100
POISSON_SCORE: 0.559
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

ANALYSIS FILE NAME: GSM908965_UCSD.H1_BMP4_Derived_Trophoblast_Cultured_Cells.H4K8ac.AY205.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H4K8ac.BMP4T.02.01.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of H1 BMP4 Derived Trophoblast Cultured Cells H4K8ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H4K8ac ChIP-Seq read mappings from the H1 BMP4 Derived Trophoblast Cultured Cells, Library AY205, 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.13590
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 8
BROWSER_TRACK_NAME: HBDT H4K8ac 05
BROWSER_TRACK_DESCRIPTION: UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H4K8ac Library AY205 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 13,187,938
NUMBER_OF_H4K8ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 4
FINDPEAKS_SCORE: 0.4154
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.5005
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9774
IROC_PERCENTILE: 100
POISSON_SCORE: 0.559
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 trophoblast by treatment with BMP4.; renlab.H4K8ac.BMP4T.02.01

value: genomic DNA

value: Histone H4K8ac

value: Millipore


title: Reference Epigenome: ChIP-Seq Analysis of H3K14ac in BMP4 Trophoblast Cells; renlab.H3K14ac.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 H3K14ac in BMP4 Trophoblast Cells. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AY226
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.12125
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.12116
****************
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: GSM908946_UCSD.H1_BMP4_Derived_Trophoblast_Cultured_Cells.H3K14ac.AY226.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K14ac.BMP4T.02.01.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of H1 BMP4 Derived Trophoblast Cultured Cells H3K14ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K14ac ChIP-Seq on H1 BMP4 Derived Trophoblast Cultured Cells, Library AY226, 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.13501
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 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 24,217,989
NUMBER_OF_H3K14ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 4
FINDPEAKS_SCORE: 0.3594
FINDPEAKS_PERCENTILE: 75
HOTSPOT_SCORE: 0.4285
HOTSPOT_PERCENTILE: 75
IROC_SCORE: 0.987
IROC_PERCENTILE: 100
POISSON_SCORE: 0.5333
POISSON_PERCENTILE: 75
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

ANALYSIS FILE NAME: GSM908946_UCSD.H1_BMP4_Derived_Trophoblast_Cultured_Cells.H3K14ac.AY226.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K14ac.BMP4T.02.01.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of H1 BMP4 Derived Trophoblast Cultured Cells H3K14ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K14ac ChIP-Seq read mappings from the H1 BMP4 Derived Trophoblast Cultured Cells, Library AY226, 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.13621
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 8
BROWSER_TRACK_NAME: HBDT H3K14ac 26
BROWSER_TRACK_DESCRIPTION: UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K14ac Library AY226 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 24,217,989
NUMBER_OF_H3K14ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 4
FINDPEAKS_SCORE: 0.3594
FINDPEAKS_PERCENTILE: 75
HOTSPOT_SCORE: 0.4285
HOTSPOT_PERCENTILE: 75
IROC_SCORE: 0.987
IROC_PERCENTILE: 100
POISSON_SCORE: 0.5333
POISSON_PERCENTILE: 75
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 trophoblast by treatment with BMP4.; renlab.H3K14ac.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


title: Reference Epigenome: ChIP-Seq Analysis of H3K79me2 in BMP4 Trophoblast Cells; renlab.H3K79me2.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 H3K79me2 in BMP4 Trophoblast Cells. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AY202
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.12154
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.11191
****************
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: GSM908961_UCSD.H1_BMP4_Derived_Trophoblast_Cultured_Cells.H3K79me2.AY202.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K79me2.BMP4T.02.01.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of H1 BMP4 Derived Trophoblast Cultured Cells H3K79me2 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K79me2 ChIP-Seq on H1 BMP4 Derived Trophoblast Cultured Cells, Library AY202, 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.13549
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 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 8,820,414
NUMBER_OF_H3K79me2_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 2
FINDPEAKS_SCORE: 0.3907
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.4615
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9852
IROC_PERCENTILE: 100
POISSON_SCORE: 0.5344
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.95

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

ANALYSIS FILE NAME: GSM908961_UCSD.H1_BMP4_Derived_Trophoblast_Cultured_Cells.H3K79me2.AY202.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K79me2.BMP4T.02.01.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of H1 BMP4 Derived Trophoblast Cultured Cells H3K79me2 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K79me2 ChIP-Seq read mappings from the H1 BMP4 Derived Trophoblast Cultured Cells, Library AY202, 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.13669
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 8
BROWSER_TRACK_NAME: HBDT H3K79me2 02
BROWSER_TRACK_DESCRIPTION: UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K79me2 Library AY202 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 8,820,414
NUMBER_OF_H3K79me2_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 2
FINDPEAKS_SCORE: 0.3907
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.4615
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9852
IROC_PERCENTILE: 100
POISSON_SCORE: 0.5344
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.95

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

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.H3K79me2.BMP4T.02.01

value: Male

value: Histone H3K79me2

value: Active Motif


title: Reference Epigenome: ChIP-Seq Analysis of H2BK120ac in Mesenchymal Stem Cells; renlab.H2BK120ac.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 H2BK120ac in Mesenchymal Stem Cells. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AK395
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.12114
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: GSM908942_UCSD.H1_Derived_Mesenchymal_Stem_Cells.H2BK120ac.AK395.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H2BK120ac.MSC.01.01.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of H1 Derived Mesenchymal Stem Cells H2BK120ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H2BK120ac ChIP-Seq on H1 Derived Mesenchymal Stem Cells, Library AK395, 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.13484
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 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 16,376,996
NUMBER_OF_H2BK120ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 4
FINDPEAKS_SCORE: 0.1442
FINDPEAKS_PERCENTILE: 50
HOTSPOT_SCORE: 0.2604
HOTSPOT_PERCENTILE: 50
IROC_SCORE: 0.9196
IROC_PERCENTILE: 75
POISSON_SCORE: 0.3601
POISSON_PERCENTILE: 50
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM908942_UCSD.H1_Derived_Mesenchymal_Stem_Cells.H2BK120ac.AK395.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H2BK120ac.MSC.01.01.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Derived Mesenchymal Stem Cells H2BK120ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H2BK120ac ChIP-Seq read mappings from the H1 Derived Mesenchymal Stem Cells, Library AK395, 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.13604
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 8
BROWSER_TRACK_NAME: HDMSC H2BK120ac 95
BROWSER_TRACK_DESCRIPTION: UCSD H1 Derived Mesenchymal Stem Cells Histone H2BK120ac Library AK395 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 16,376,996
NUMBER_OF_H2BK120ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 4
FINDPEAKS_SCORE: 0.1442
FINDPEAKS_PERCENTILE: 50
HOTSPOT_SCORE: 0.2604
HOTSPOT_PERCENTILE: 50
IROC_SCORE: 0.9196
IROC_PERCENTILE: 75
POISSON_SCORE: 0.3601
POISSON_PERCENTILE: 50
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 mesenchymal stem cells.; renlab.H2BK120ac.MSC.01.01

value: H1 Derived Mesenchymal Stem Cells

value: Embryonic stem cell differentiated into mesenchymal stem cells

value: Publication in progress

value: Histone H2BK120ac

value: Biorupter


title: Reference Epigenome: ChIP-Seq Analysis of H3K18ac in BMP4 Trophoblast Cells; renlab.H3K18ac.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 H3K18ac in BMP4 Trophoblast Cells. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AY227
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.12127
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.12116
****************
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: GSM908950_UCSD.H1_BMP4_Derived_Trophoblast_Cultured_Cells.H3K18ac.AY227.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K18ac.BMP4T.02.01.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of H1 BMP4 Derived Trophoblast Cultured Cells H3K18ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K18ac ChIP-Seq on H1 BMP4 Derived Trophoblast Cultured Cells, Library AY227, 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.13541
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 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 22,411,996
NUMBER_OF_H3K18ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 3
FINDPEAKS_SCORE: 0.2131
FINDPEAKS_PERCENTILE: 67
HOTSPOT_SCORE: 0.3121
HOTSPOT_PERCENTILE: 67
IROC_SCORE: 0.9472
IROC_PERCENTILE: 67
POISSON_SCORE: 0.4749
POISSON_PERCENTILE: 67
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

ANALYSIS FILE NAME: GSM908950_UCSD.H1_BMP4_Derived_Trophoblast_Cultured_Cells.H3K18ac.AY227.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K18ac.BMP4T.02.01.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of H1 BMP4 Derived Trophoblast Cultured Cells H3K18ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K18ac ChIP-Seq read mappings from the H1 BMP4 Derived Trophoblast Cultured Cells, Library AY227, 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.13661
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 8
BROWSER_TRACK_NAME: HBDT H3K18ac 27
BROWSER_TRACK_DESCRIPTION: UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K18ac Library AY227 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 22,411,996
NUMBER_OF_H3K18ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 3
FINDPEAKS_SCORE: 0.2131
FINDPEAKS_PERCENTILE: 67
HOTSPOT_SCORE: 0.3121
HOTSPOT_PERCENTILE: 67
IROC_SCORE: 0.9472
IROC_PERCENTILE: 67
POISSON_SCORE: 0.4749
POISSON_PERCENTILE: 67
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 trophoblast by treatment with BMP4.; renlab.H3K18ac.BMP4T.02.01

value: Histone H3K18ac

value: 500 micrograms

value: magnetic anti-rabbit

value: 5 micrograms

value: Abcam


title: Reference Epigenome: ChIP-Seq Analysis of H2BK120ac in BMP4 Mesendoderm Cells; renlab.H2BK120ac.BMP4M.01.01

description:
sample_term_id: NTR_0000856
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H2BK120ac in BMP4 Mesendoderm Cells. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AK401
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.12108
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.11184
****************
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: GSM908940_UCSD.H1_BMP4_Derived_Mesendoderm_Cultured_Cells.H2BK120ac.AK401.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H2BK120ac.BMP4M.01.01.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of H1 BMP4 Derived Mesendoderm Cultured Cells H2BK120ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H2BK120ac ChIP-Seq on H1 BMP4 Derived Mesendoderm Cultured Cells, Library AK401, 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.13482
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 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 14,106,661
NUMBER_OF_H2BK120ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 4
FINDPEAKS_SCORE: 0.1246
FINDPEAKS_PERCENTILE: 25
HOTSPOT_SCORE: 0.2566
HOTSPOT_PERCENTILE: 25
IROC_SCORE: 0.8803
IROC_PERCENTILE: 25
POISSON_SCORE: 0.3569
POISSON_PERCENTILE: 25
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM908940_UCSD.H1_BMP4_Derived_Mesendoderm_Cultured_Cells.H2BK120ac.AK401.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H2BK120ac.BMP4M.01.01.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of H1 BMP4 Derived Mesendoderm Cultured Cells H2BK120ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H2BK120ac ChIP-Seq read mappings from the H1 BMP4 Derived Mesendoderm Cultured Cells, Library AK401, 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.13602
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 8
BROWSER_TRACK_NAME: HBDM H2BK120ac 01
BROWSER_TRACK_DESCRIPTION: UCSD H1 BMP4 Derived Mesendoderm Cultured Cells Histone H2BK120ac Library AK401 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 14,106,661
NUMBER_OF_H2BK120ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 4
FINDPEAKS_SCORE: 0.1246
FINDPEAKS_PERCENTILE: 25
HOTSPOT_SCORE: 0.2566
HOTSPOT_PERCENTILE: 25
IROC_SCORE: 0.8803
IROC_PERCENTILE: 25
POISSON_SCORE: 0.3569
POISSON_PERCENTILE: 25
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 mesendoderm by treatment with BMP4.; renlab.H2BK120ac.BMP4M.01.01

value: genomic DNA

value: James Thomson Laboratory

value: Cell Line

value: Embryonic Stem Cell

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


title: Reference Epigenome: ChIP-Seq Analysis of H2AK5ac in BMP4 Trophoblast Cells; renlab.H2AK5ac.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 H2AK5ac in BMP4 Trophoblast Cells. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AY222
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.12119
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.12116
****************
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: GSM908939_UCSD.H1_BMP4_Derived_Trophoblast_Cultured_Cells.H2AK5ac.AY222.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H2AK5ac.BMP4T.02.01.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of H1 BMP4 Derived Trophoblast Cultured Cells H2AK5ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H2AK5ac ChIP-Seq on H1 BMP4 Derived Trophoblast Cultured Cells, Library AY222, 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.13533
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 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 29,743,389
NUMBER_OF_H2AK5ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 2
FINDPEAKS_SCORE: 0.2112
FINDPEAKS_PERCENTILE: 50
HOTSPOT_SCORE: 0.3008
HOTSPOT_PERCENTILE: 50
IROC_SCORE: 0.9472
IROC_PERCENTILE: 100
POISSON_SCORE: 0.4815
POISSON_PERCENTILE: 50
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM908939_UCSD.H1_BMP4_Derived_Trophoblast_Cultured_Cells.H2AK5ac.AY222.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H2AK5ac.BMP4T.02.01.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of H1 BMP4 Derived Trophoblast Cultured Cells H2AK5ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H2AK5ac ChIP-Seq read mappings from the H1 BMP4 Derived Trophoblast Cultured Cells, Library AY222, 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.13653
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 8
BROWSER_TRACK_NAME: HBDT H2AK5ac 22
BROWSER_TRACK_DESCRIPTION: UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H2AK5ac Library AY222 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 29,743,389
NUMBER_OF_H2AK5ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 2
FINDPEAKS_SCORE: 0.2112
FINDPEAKS_PERCENTILE: 50
HOTSPOT_SCORE: 0.3008
HOTSPOT_PERCENTILE: 50
IROC_SCORE: 0.9472
IROC_PERCENTILE: 100
POISSON_SCORE: 0.4815
POISSON_PERCENTILE: 50
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 trophoblast by treatment with BMP4.; renlab.H2AK5ac.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

value: Histone H2AK5ac


title: Reference Epigenome: ChIP-Seq Analysis of H2A.Z in hESC H1 Cells; renlab.H2A.Z.hESC.H1.02.01

description:
sample_term_id: EFO_0003042
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H2A.Z in hESC H1 Cells. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AY1
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.12164
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.5971
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM908938_UCSD.H1.H2A.Z.AY1.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H2A.Z.hESC.H1.02.01.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of H1 Cell Line H2A.Z ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H2A.Z ChIP-Seq on H1 Cell Line, Library AY1, 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.13444
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 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 8,680,395
NUMBER_OF_H2A.Z_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 3
FINDPEAKS_SCORE: 0.1378
FINDPEAKS_PERCENTILE: 33
HOTSPOT_SCORE: 0.3309
HOTSPOT_PERCENTILE: 33
IROC_SCORE: 0.8939
IROC_PERCENTILE: 33
POISSON_SCORE: 0.3777
POISSON_PERCENTILE: 33
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM908938_UCSD.H1.H2A.Z.AY1.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H2A.Z.hESC.H1.02.01.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Cell Line H2A.Z ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H2A.Z ChIP-Seq read mappings from the H1 Cell Line, Library AY1, 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.13564
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 8
BROWSER_TRACK_NAME: H1 H2A.Z Y1
BROWSER_TRACK_DESCRIPTION: UCSD H1 Cell Line Histone H2A.Z Library AY1 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 8,680,395
NUMBER_OF_H2A.Z_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 3
FINDPEAKS_SCORE: 0.1378
FINDPEAKS_PERCENTILE: 33
HOTSPOT_SCORE: 0.3309
HOTSPOT_PERCENTILE: 33
IROC_SCORE: 0.8939
IROC_PERCENTILE: 33
POISSON_SCORE: 0.3777
POISSON_PERCENTILE: 33
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: Human embryonic stem cells received from the James Thompson laboratory.  Cells are from the H1 line.; renlab.H2A.Z.hESC.H1.02.01

value: H1 Cell Line

value: James Thompson Laboratory

value: mTeSER

value: Histone H2A.Z


title: Reference Epigenome: ChIP-Seq Analysis of H2A.Z in BMP4 Trophoblast Cells; renlab.H2A.Z.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 H2A.Z in BMP4 Trophoblast Cells. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AY221
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.12117
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.12116
****************
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: GSM908937_UCSD.H1_BMP4_Derived_Trophoblast_Cultured_Cells.H2A.Z.AY221.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H2A.Z.BMP4T.02.01.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of H1 BMP4 Derived Trophoblast Cultured Cells H2A.Z ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H2A.Z ChIP-Seq on H1 BMP4 Derived Trophoblast Cultured Cells, Library AY221, 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.13492
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 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 10,267,529
NUMBER_OF_H2A.Z_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 3
FINDPEAKS_SCORE: 0.425
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.4962
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9789
IROC_PERCENTILE: 100
POISSON_SCORE: 0.5658
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.95

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

ANALYSIS FILE NAME: GSM908937_UCSD.H1_BMP4_Derived_Trophoblast_Cultured_Cells.H2A.Z.AY221.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H2A.Z.BMP4T.02.01.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of H1 BMP4 Derived Trophoblast Cultured Cells H2A.Z ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H2A.Z ChIP-Seq read mappings from the H1 BMP4 Derived Trophoblast Cultured Cells, Library AY221, 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.13612
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 8
BROWSER_TRACK_NAME: HBDT H2A.Z 21
BROWSER_TRACK_DESCRIPTION: UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H2A.Z Library AY221 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 10,267,529
NUMBER_OF_H2A.Z_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 3
FINDPEAKS_SCORE: 0.425
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.4962
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9789
IROC_PERCENTILE: 100
POISSON_SCORE: 0.5658
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: 0.95

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

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.H2A.Z.BMP4T.02.01

value: Biorupter

value: 500 micrograms

value: magnetic anti-rabbit


title: U87_RNA_POL2

city: Cambridge

first: Richard

middle: A

last: Young

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

description:
Chromatin IP against Total RNAPol2 in U87 Rep1
barcode (already removed): TTAGGC

data_processing:
Images analysis and base calling was done using the solexa pipeline.
For all samples reads were aligned to their indicated build using bowtie with parameters -e 70 -k 2 -m 2 -n 2 --best --concise. Seed length (-l) was set to read length for each dataset.
Genome_build: hg18
Supplementary_files_format_and_content: WIG files: For all samples aligned sequences were extended 150bp upstream and 0bp downstream (with respect to read strand) and allocated into 25bp bins. Counts were normalized to reads per million, and bins with at least 1 read per million are shown.
Supplementary_files_format_and_content: Alignment (ylf) files: The .ylf files are in [Y]oung [L]ab [F]ormat. It is a compact flat file representation of aligned read locations determined by bowtie. The file contains the locations of the bowtie aligned reads with the following format:
#BWT1 (read category BWT1)
>1 (chromomsome 1)
-12345 (minus strand read)
-9876 (minus strand read)
54321 (plus strand read)
>2 (chromomsome 2)
-67890 (minus strand read)
98765 (plus strand read)
132323 (plus strand read)
#BWT2 (read category BWT2)
etc..

source_name: Glioblastoma

growth_protocol: RPMI 1640 + FBS

extract_protocol: Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using different antibodies. Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.

tag: chip antibody

value: RNA Pol II (Rpb1 N-terminus)

tag: antibody details (vendor, catalog number)

value: Santa Cruz SC-899

tag: cell type


title: MM1S_WCE_DMSO_1

description:
Whole cell extract from MM.1S cells (DMSO)
barcode (already removed): TGACCA

source_name: Multiple myeloma

growth_protocol: RPMI 1640 supplemented with 10% FCS and 1% GlutaMAX

treatment_protocol: DMSO treatment for 24 hours

value: None WCE

value: Plasma cell

tag: duration

tag: drug

value: DMSO


title: MM1S_MYC_DMSO

description:
Chromatin IP against c-Myc in MM.1S (DMSO)
barcode (already removed): ACAGTG

value: c-Myc

value: Santa Cruz SC-764


title: MM1S_MED1_DMSO

description:
Chromatin IP against Med1 in MM.1S (DMSO)
barcode (already removed): CAGATC

value: Bethyl A300-793A


title: H2171_WCE_1

description:
WCE in SCLC H2171 Rep1
barcode (already removed): CAGATC

source_name: Small Cell Lung Carcinoma


title: H2171_RNA_POL2_1

description:
Chromatin IP against RNA Pol2 SCLC H2171 Rep1
barcode (already removed): TAGCTT


title: H2171_MYC_1

description:
Chromatin IP against cMyc H2171 SCLC Rep1
barcode (already removed): CGATGT

value: cMyc


title: H128_WCE_1

description:
WCE for SCLC H128 Rep1
barcode (already removed): ACTTGA


title: H128_RNA_POL2_1

description:
Chromatin IP against Total RNA Pol2 SCLC H128 Rep1
barcode (already removed): CTTGTA


title: H2171_MAX_1

description:
Chromatin IP against Max in SCLC H2171 Rep1
barcode (already removed): GGCTAC

value: Max

value: Santa Cruz SC-197


title: H128_MAX_1

description:
Chromatin IP against Max in H128_SCLC Rep1
barcode (already removed): ACAGTG


title: H128_WCE_CHROM

description:
WCE for H128 SCLC for chromatin marks rep1
barcode (already removed): ATCACG


title: H128_MYC_1

description:
Chromatin IP against cMyc SCLC H128 Rep1
barcode (already removed): ATCACG


title: P493-6_T0_WCE

description:
WCE P493-6 T=0 hour
barcode (already removed): ATCACG

source_name: B-cell lymphoma

growth_protocol: RPMI 1640 + FBS.  Tetracycline repressed cMyc transgene expression.  cMyc expression released for 0 hours.


title: Reference Epigenome: ChIP-Seq Analysis of H2BK120ac in BMP4 Trophoblast Cells; renlab.H2BK120ac.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 H2BK120ac in BMP4 Trophoblast Cells. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AY223
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.12121
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.12116
****************
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: GSM908941_UCSD.H1_BMP4_Derived_Trophoblast_Cultured_Cells.H2BK120ac.AY223.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H2BK120ac.BMP4T.02.01.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of H1 BMP4 Derived Trophoblast Cultured Cells H2BK120ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H2BK120ac ChIP-Seq on H1 BMP4 Derived Trophoblast Cultured Cells, Library AY223, 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.13491
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 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 22,231,603
NUMBER_OF_H2BK120ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 4
FINDPEAKS_SCORE: 0.3363
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.4068
HOTSPOT_PERCENTILE: 75
IROC_SCORE: 0.9867
IROC_PERCENTILE: 100
POISSON_SCORE: 0.5051
POISSON_PERCENTILE: 75
MAXIMUM_REPLICATE_CORRELATION: 0.94

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

ANALYSIS FILE NAME: GSM908941_UCSD.H1_BMP4_Derived_Trophoblast_Cultured_Cells.H2BK120ac.AY223.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H2BK120ac.BMP4T.02.01.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of H1 BMP4 Derived Trophoblast Cultured Cells H2BK120ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H2BK120ac ChIP-Seq read mappings from the H1 BMP4 Derived Trophoblast Cultured Cells, Library AY223, 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.13611
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 8
BROWSER_TRACK_NAME: HBDT H2BK120ac 23
BROWSER_TRACK_DESCRIPTION: UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H2BK120ac Library AY223 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 22,231,603
NUMBER_OF_H2BK120ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 4
FINDPEAKS_SCORE: 0.3363
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.4068
HOTSPOT_PERCENTILE: 75
IROC_SCORE: 0.9867
IROC_PERCENTILE: 100
POISSON_SCORE: 0.5051
POISSON_PERCENTILE: 75
MAXIMUM_REPLICATE_CORRELATION: 0.94

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

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.H2BK120ac.BMP4T.02.01

value: genomic DNA

value: James Thomson Laboratory

value: Cell Line

value: Embryonic Stem Cell

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

value: Histone H2BK120ac

value: 5 micrograms

value: Active Motif


title: P493-6_T1_WCE

description:
WCE P493-6 T=1 hour
barcode (already removed): CGATGT

growth_protocol: RPMI 1640 + FBS.  Tetracycline repressed cMyc transgene expression.  cMyc expression released for 1 hour.

value: None WCE


title: U87_WCE_1

description:
WCE from U87 with Upstate Conditions
barcode (already removed): CGATGT


title: P493-6_T24_RNA_POL2

description:
Chromatin IP against Pol2 N20 in P493-6 T=24 hour
barcode (already removed): CAGATC

growth_protocol: RPMI 1640 + FBS.  Tetracycline repressed cMyc transgene expression.  cMyc expression released for 24 hours.

value: RNA Pol II (Rpb1 N-terminus)

value: Santa Cruz SC-899


title: P493-6_T24_WCE

description:
WCE P493-6 T=24 hour
barcode (already removed): TTAGGC

treatment_protocol: Tetracycline repressed cMyc transgene expression.  cMyc expression released for 24 hours.


title: MM1S_H3K27AC_DMSO

description:
Chromatin IP against H3K27ac in MM.1S (DMSO) for 12022011_B0A1WABXX*
barcode (already removed): TGACCA

value: Abcam AB4729

value: Plasma cell

value: DMSO


title: MM1S_H3K4ME3_DMSO

description:
Chromatin IP against H3K4me3 in MM.1S (DMSO) for 12022011_B0A1WABXX*
barcode (already removed): GCCAAT

value: Millipore 07-473


title: MM1S_RNA_POL2_DMSO

description:
Chromatin IP against RNAPII in MM.1S (DMSO) for 12022011_B0A1WABXX*
barcode (already removed): TAGCTT


title: P493-6_T0_RNA_POL2

description:
Chromatin IP against Pol2 N20 in P493-6 T=0 hours
barcode (already removed): TTAGGC

treatment_protocol: Tetracycline repressed cMyc transgene expression.  cMyc expression released for 0 hours.


title: H2171_MED1_1

description:
Chromatin IP against Med1 in H2171 Rep1
barcode (already removed): ACTTGA

value: Bethyl A300-793A


title: U87_MED1

description:
Chromatin IP against Med1 in U87 Rep1
barcode (already removed): GCCAAT


title: U87_MAX

description:
Chromatin IP against Max in U87 Rep1
barcode (already removed): CGATGT

value: Max

value: Santa Cruz SC-197


title: Reference Epigenome: ChIP-Seq Analysis of H2BK5ac in BMP4 Trophoblast Cells; renlab.H2BK5ac.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 H2BK5ac in BMP4 Trophoblast Cells. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AY225
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.12148
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.12116
****************
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: GSM908944_UCSD.H1_BMP4_Derived_Trophoblast_Cultured_Cells.H2BK5ac.AY225.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H2BK5ac.BMP4T.02.01.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of H1 BMP4 Derived Trophoblast Cultured Cells H2BK5ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H2BK5ac ChIP-Seq on H1 BMP4 Derived Trophoblast Cultured Cells, Library AY225, 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.13452
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 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 19,065,808
NUMBER_OF_H2BK5ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 2
FINDPEAKS_SCORE: 0.2811
FINDPEAKS_PERCENTILE: 50
HOTSPOT_SCORE: 0.3814
HOTSPOT_PERCENTILE: 50
IROC_SCORE: 0.9772
IROC_PERCENTILE: 100
POISSON_SCORE: 0.4784
POISSON_PERCENTILE: 50
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

ANALYSIS FILE NAME: GSM908944_UCSD.H1_BMP4_Derived_Trophoblast_Cultured_Cells.H2BK5ac.AY225.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H2BK5ac.BMP4T.02.01.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of H1 BMP4 Derived Trophoblast Cultured Cells H2BK5ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H2BK5ac ChIP-Seq read mappings from the H1 BMP4 Derived Trophoblast Cultured Cells, Library AY225, 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.13572
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 8
BROWSER_TRACK_NAME: HBDT H2BK5ac 25
BROWSER_TRACK_DESCRIPTION: UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H2BK5ac Library AY225 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 19,065,808
NUMBER_OF_H2BK5ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 2
FINDPEAKS_SCORE: 0.2811
FINDPEAKS_PERCENTILE: 50
HOTSPOT_SCORE: 0.3814
HOTSPOT_PERCENTILE: 50
IROC_SCORE: 0.9772
IROC_PERCENTILE: 100
POISSON_SCORE: 0.4784
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 trophoblast by treatment with BMP4.; renlab.H2BK5ac.BMP4T.02.01

value: genomic DNA

value: James Thomson Laboratory

value: Cell Line

value: Embryonic Stem Cell

value: Histone H2BK5ac

value: Biorupter

value: 500 micrograms

value: magnetic anti-rabbit


title: P493-6_T0_MED1

description:
Chromatin IP against Med1 in P493-6 Time = 0 hr
barcode (already removed): CAGATC


title: H2171_WCE_3

description:
WCE for H2171 SCLC for Med1 ChIPs
barcode (already removed): CTTGTA

value: None WCE


title: P493-6_T1_MED1

description:
Chromatin IP against Med1 in P493-6 Time = 1 hr
barcode (already removed): TTAGGC

growth_protocol: RPMI 1640 + FBS.  Tetracycline repressed cMyc transgene expression.  cMyc expression released for 1 hours.


title: P493-6_T24_MED1

description:
Chromatin IP against Med1 in P493-6 Time = 24 hr
barcode (already removed): GGCTAC


title: U87_WCE_2

description:
WCE from U87 for SOP Conditions
barcode (already removed): ATCACG


title: P493-6_T24_MAX

description:
Chromatin IP against Max in P493-6 T=24 hours
barcode (already removed): GCCAAT


title: H2171_WCE_CHROM

description:
WCE for H2171 SCLC for chromatin marks rep1
barcode (already removed): CGATGT


title: H2171_H3K4ME3

description:
Chromatin IP against H3K4me3 in H2171 SCLC rep1
barcode (already removed): GATCAG