title: Chromatin accessibility assay of Fetal Muscle, Arm; DS19380

description:
sample_term_id: UBERON_0001499
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS19380
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.9884
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.9883
****************
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: GSM817216_UW.Fetal_Muscle_Arm.ChromatinAccessibility.H-24272.DS19380.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS19380.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of Fetal Muscle Arm Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Muscle Arm, Donor H-24272, Library DS19380 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.12636
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 35,817,248
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.4659
FINDPEAKS_PERCENTILE: 76
HOTSPOT_SCORE: 0.4494
HOTSPOT_PERCENTILE: 73
IROC_SCORE: 0.9941
IROC_PERCENTILE: 67
POISSON_SCORE: 0.5179
POISSON_PERCENTILE: 71
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM817216_UW.Fetal_Muscle_Arm.ChromatinAccessibility.H-24272.DS19380.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS19380.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Muscle Arm Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Muscle Arm, Donor H-24272, Library DS19380 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.12699
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 150bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 6
BROWSER_TRACK_NAME: FMA DNase 72 80
BROWSER_TRACK_DESCRIPTION: UW Fetal Muscle Arm DNase Hypersensitivity Donor H-24272 Library DS19380 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 35,817,248
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.4659
FINDPEAKS_PERCENTILE: 76
HOTSPOT_SCORE: 0.4494
HOTSPOT_PERCENTILE: 73
IROC_SCORE: 0.9941
IROC_PERCENTILE: 67
POISSON_SCORE: 0.5179
POISSON_PERCENTILE: 71
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

source_name: Fetal Muscle, Arm primary tissue, day 85; DS19380

value: Fetal Muscle, Arm


title: Chromatin accessibility assay of Fetal Muscle, Back; DS19384

status: Public on Oct 15 2011

type: SRA

city: Seattle

first: Northwest

last: REMC

state: WA

country: USA

institute: University of Washington

description:
sample_term_id: UBERON_0002324
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS19384
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.9851
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.9850
****************
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: GSM817217_UW.Fetal_Muscle_Back.ChromatinAccessibility.H-24272.DS19384.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS19384.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of Fetal Muscle Back Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Muscle Back, Donor H-24272, Library DS19384 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.12637
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 35,914,094
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.5089
FINDPEAKS_PERCENTILE: 90
HOTSPOT_SCORE: 0.4911
HOTSPOT_PERCENTILE: 86
IROC_SCORE: 0.9959
IROC_PERCENTILE: 87
POISSON_SCORE: 0.5542
POISSON_PERCENTILE: 90
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

ANALYSIS FILE NAME: GSM817217_UW.Fetal_Muscle_Back.ChromatinAccessibility.H-24272.DS19384.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS19384.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Muscle Back Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Muscle Back, Donor H-24272, Library DS19384 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.12700
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 150bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 6
BROWSER_TRACK_NAME: FMB DNase 72 84
BROWSER_TRACK_DESCRIPTION: UW Fetal Muscle Back DNase Hypersensitivity Donor H-24272 Library DS19384 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 35,914,094
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.5089
FINDPEAKS_PERCENTILE: 90
HOTSPOT_SCORE: 0.4911
HOTSPOT_PERCENTILE: 86
IROC_SCORE: 0.9959
IROC_PERCENTILE: 87
POISSON_SCORE: 0.5542
POISSON_PERCENTILE: 90
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

molecule: genomic DNA

organism: Homo sapiens

source_name: Fetal Muscle, Back primary tissue, day 85; DS19384

extract_protocol: Library construction protocol: Single read - Illumina

tag: sample alias

tag: sample common name

value: Fetal Muscle, Back

tag: molecule

value: genomic DNA

tag: disease

value: University of Washington, Congenital Defects Lab. Ian Glass

value: Primary Tissue

value: UW

value: fetal

value: day 85

value: Female

value: Chromatin Accessibility

value: Qiagen minElut

value: Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)


title: Chromatin accessibility assay of Fetal Muscle, Upper Back; DS19283

description:
sample_term_id: UBERON_0002324
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS19283
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.10156
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.10155
****************
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: GSM817212_UW.Fetal_Muscle_Back.ChromatinAccessibility.H-24244.DS19283.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS19283.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of Fetal Muscle Back Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Muscle Back, Donor H-24244, Library DS19283 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.12632
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 26,255,104
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.3755
FINDPEAKS_PERCENTILE: 51
HOTSPOT_SCORE: 0.3631
HOTSPOT_PERCENTILE: 48
IROC_SCORE: 0.9937
IROC_PERCENTILE: 59
POISSON_SCORE: 0.4458
POISSON_PERCENTILE: 52
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

ANALYSIS FILE NAME: GSM817212_UW.Fetal_Muscle_Back.ChromatinAccessibility.H-24244.DS19283.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS19283.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Muscle Back Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Muscle Back, Donor H-24244, Library DS19283 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.12695
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 150bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 6
BROWSER_TRACK_NAME: FMB DNase 44 83
BROWSER_TRACK_DESCRIPTION: UW Fetal Muscle Back DNase Hypersensitivity Donor H-24244 Library DS19283 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 26,255,104
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.3755
FINDPEAKS_PERCENTILE: 51
HOTSPOT_SCORE: 0.3631
HOTSPOT_PERCENTILE: 48
IROC_SCORE: 0.9937
IROC_PERCENTILE: 59
POISSON_SCORE: 0.4458
POISSON_PERCENTILE: 52
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

source_name: Fetal Muscle, Upper, back primary tissue, day 96; DS19283

value: day 96

value: Male


title: Chromatin accessibility assay of Fetal Muscle, Arm; DS19295

description:
sample_term_id: UBERON_0001499
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS19295
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.9890
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.9889
****************
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: GSM817214_UW.Fetal_Muscle_Arm.ChromatinAccessibility.H-24259.DS19295.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS19295.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of Fetal Muscle Arm Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Muscle Arm, Donor H-24259, Library DS19295 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.12634
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 28,052,040
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.4724
FINDPEAKS_PERCENTILE: 84
HOTSPOT_SCORE: 0.4624
HOTSPOT_PERCENTILE: 79
IROC_SCORE: 0.9949
IROC_PERCENTILE: 78
POISSON_SCORE: 0.528
POISSON_PERCENTILE: 76
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

ANALYSIS FILE NAME: GSM817214_UW.Fetal_Muscle_Arm.ChromatinAccessibility.H-24259.DS19295.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS19295.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Muscle Arm Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Muscle Arm, Donor H-24259, Library DS19295 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.12697
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 150bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 6
BROWSER_TRACK_NAME: FMA DNase 59 95
BROWSER_TRACK_DESCRIPTION: UW Fetal Muscle Arm DNase Hypersensitivity Donor H-24259 Library DS19295 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 28,052,040
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.4724
FINDPEAKS_PERCENTILE: 84
HOTSPOT_SCORE: 0.4624
HOTSPOT_PERCENTILE: 79
IROC_SCORE: 0.9949
IROC_PERCENTILE: 78
POISSON_SCORE: 0.528
POISSON_PERCENTILE: 76
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

source_name: Fetal Muscle, Arm primary tissue, day 97; DS19295

value: day 97


title: Chromatin accessibility assay of Fetal Muscle, Leg; DS19291

description:
sample_term_id: UBERON_0001383
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS19291
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.9828
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.9827
****************
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: GSM817213_UW.Fetal_Muscle_Leg.ChromatinAccessibility.H-24259.DS19291.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS19291.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of Fetal Muscle Leg Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Muscle Leg, Donor H-24259, Library DS19291 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.12633
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 29,214,405
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.4702
FINDPEAKS_PERCENTILE: 81
HOTSPOT_SCORE: 0.4634
HOTSPOT_PERCENTILE: 81
IROC_SCORE: 0.994
IROC_PERCENTILE: 65
POISSON_SCORE: 0.5167
POISSON_PERCENTILE: 70
MAXIMUM_REPLICATE_CORRELATION: 0.89

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

ANALYSIS FILE NAME: GSM817213_UW.Fetal_Muscle_Leg.ChromatinAccessibility.H-24259.DS19291.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS19291.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Muscle Leg Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Muscle Leg, Donor H-24259, Library DS19291 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.12696
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 150bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 6
BROWSER_TRACK_NAME: FML DNase 59 91
BROWSER_TRACK_DESCRIPTION: UW Fetal Muscle Leg DNase Hypersensitivity Donor H-24259 Library DS19291 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 29,214,405
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.4702
FINDPEAKS_PERCENTILE: 81
HOTSPOT_SCORE: 0.4634
HOTSPOT_PERCENTILE: 81
IROC_SCORE: 0.994
IROC_PERCENTILE: 65
POISSON_SCORE: 0.5167
POISSON_PERCENTILE: 70
MAXIMUM_REPLICATE_CORRELATION: 0.89

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

source_name: Fetal Muscle, Leg primary tissue, day 97; DS19291

value: Fetal Muscle, Leg


title: Reference Epigenome: ChIP-Seq Input from Neural Progenitor Cells; renlab.Input.NPC.03.01

city: La Jolla

first: UCSD AND

last: SALK

state: CA

address: Health Sciences Drive

institute: University of California, San Diego

description:
sample_term_id: CL_0000047
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Input from Neural Progenitor Cells. Sequencing was done on the Illumina Genome Analyzer IIx platform.
Library name: AK222
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.10168
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: GSM818063_UCSD.H1_Derived_Neuronal_Progenitor_Cultured_Cells.Input.AK222.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.Input.NPC.03.01.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of H1 Derived Neuronal Progenitor Cultured Cells ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on H1 Derived Neuronal Progenitor Cultured Cells, Library AK222, 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.12425
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 38,921,154
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 15
FINDPEAKS_SCORE: 0.0248
FINDPEAKS_PERCENTILE: 93
HOTSPOT_SCORE: 0.0215
HOTSPOT_PERCENTILE: 67
IROC_SCORE: 0.9865
IROC_PERCENTILE: 47
POISSON_SCORE: 0.0609
POISSON_PERCENTILE: 67
MAXIMUM_REPLICATE_CORRELATION: 0.47

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

ANALYSIS FILE NAME: GSM818063_UCSD.H1_Derived_Neuronal_Progenitor_Cultured_Cells.Input.AK222.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.Input.NPC.03.01.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Derived Neuronal Progenitor Cultured Cells ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from the H1 Derived Neuronal Progenitor Cultured Cells, Library AK222, 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.12498
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 6
BROWSER_TRACK_NAME: HDNP Input 22
BROWSER_TRACK_DESCRIPTION: UCSD H1 Derived Neuronal Progenitor Cultured Cells ChIP-Seq Input Library AK222 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 38,921,154
NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 15
FINDPEAKS_SCORE: 0.0248
FINDPEAKS_PERCENTILE: 93
HOTSPOT_SCORE: 0.0215
HOTSPOT_PERCENTILE: 67
IROC_SCORE: 0.9865
IROC_PERCENTILE: 47
POISSON_SCORE: 0.0609
POISSON_PERCENTILE: 67
MAXIMUM_REPLICATE_CORRELATION: 0.47

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

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.Input.NPC.03.01

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

value: James Thomson Laboratory

value: Cell Line

tag: line

tag: lineage

value: Embryonic Stem Cell

value: Embryonic stem cell differentiated into neural progenitor cells

value: Publication in progress

tag: passage

tag: medium

tag: Sex

tag: batch

value: ChIP-Seq Input

value: Biorupter

value: Input

value: 500 micrograms


title: Chromatin accessibility assay of Fetal Renal Cortex, Right; DS19254

description:
sample_term_id: UBERON_0001225
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS19254
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.9995
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.9994
****************
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: GSM817210_UW.Fetal_Renal_Cortex_Right.ChromatinAccessibility.H-24232.DS19254.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS19254.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of Fetal Renal Cortex Right Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Renal Cortex Right, Donor H-24232, Library DS19254 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.12630
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 28,788,816
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.476
FINDPEAKS_PERCENTILE: 87
HOTSPOT_SCORE: 0.4643
HOTSPOT_PERCENTILE: 83
IROC_SCORE: 0.9954
IROC_PERCENTILE: 81
POISSON_SCORE: 0.5349
POISSON_PERCENTILE: 78
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

ANALYSIS FILE NAME: GSM817210_UW.Fetal_Renal_Cortex_Right.ChromatinAccessibility.H-24232.DS19254.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS19254.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Renal Cortex Right Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Renal Cortex Right, Donor H-24232, Library DS19254 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.12693
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 150bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 6
BROWSER_TRACK_NAME: FRCR DNase 32 54
BROWSER_TRACK_DESCRIPTION: UW Fetal Renal Cortex Right DNase Hypersensitivity Donor H-24232 Library DS19254 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 28,788,816
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.476
FINDPEAKS_PERCENTILE: 87
HOTSPOT_SCORE: 0.4643
HOTSPOT_PERCENTILE: 83
IROC_SCORE: 0.9954
IROC_PERCENTILE: 81
POISSON_SCORE: 0.5349
POISSON_PERCENTILE: 78
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

source_name: Fetal Kidney, renal, cortex, Right primary tissue, day 105; DS19254

value: Fetal Renal Cortex, Right

value: genomic DNA

value: University of Washington, Congenital Defects Lab. Ian Glass

value: Primary Tissue

value: UW

value: fetal

value: day 105


title: Chromatin accessibility assay of Fetal Renal Cortex, Left; DS19257

description:
sample_term_id: UBERON_0001225
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS19257
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.10008
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.10007
****************
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: GSM817211_UW.Fetal_Renal_Cortex_Left.ChromatinAccessibility.H-24232.DS19257.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS19257.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of Fetal Renal Cortex Left Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Renal Cortex Left, Donor H-24232, Library DS19257 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.12631
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 34,013,742
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.4785
FINDPEAKS_PERCENTILE: 89
HOTSPOT_SCORE: 0.4644
HOTSPOT_PERCENTILE: 84
IROC_SCORE: 0.9945
IROC_PERCENTILE: 71
POISSON_SCORE: 0.538
POISSON_PERCENTILE: 81
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM817211_UW.Fetal_Renal_Cortex_Left.ChromatinAccessibility.H-24232.DS19257.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS19257.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Renal Cortex Left Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Renal Cortex Left, Donor H-24232, Library DS19257 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.12694
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 150bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 6
BROWSER_TRACK_NAME: FRCL DNase 32 57
BROWSER_TRACK_DESCRIPTION: UW Fetal Renal Cortex Left DNase Hypersensitivity Donor H-24232 Library DS19257 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 34,013,742
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.4785
FINDPEAKS_PERCENTILE: 89
HOTSPOT_SCORE: 0.4644
HOTSPOT_PERCENTILE: 84
IROC_SCORE: 0.9945
IROC_PERCENTILE: 71
POISSON_SCORE: 0.538
POISSON_PERCENTILE: 81
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

source_name: Fetal Kidney, renal, cortex, Left primary tissue, day 105; DS19257

value: Fetal Renal Cortex, Left

value: Male

value: Chromatin Accessibility

value: Qiagen minElut

value: Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)


title: Reference Epigenome: ChIP-Seq Analysis of H3K9me3 in Neural Progenitor Cells; renlab.H3K9me3.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 H3K9me3 in Neural Progenitor Cells. Sequencing was done on the Illumina Genome Analyzer IIx platform.
Library name: AK244
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.10153
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: GSM818056_UCSD.H1_Derived_Neuronal_Progenitor_Cultured_Cells.H3K9me3.AK244.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K9me3.NPC.02.01.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of H1 Derived Neuronal Progenitor Cultured Cells Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9me3 ChIP-Seq on H1 Derived Neuronal Progenitor Cultured Cells, Library AK244, 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.12443
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 35,880,551
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 13
FINDPEAKS_SCORE: 0.047
FINDPEAKS_PERCENTILE: 46
HOTSPOT_SCORE: 0.0702
HOTSPOT_PERCENTILE: 8
IROC_SCORE: 0.8037
IROC_PERCENTILE: 46
POISSON_SCORE: 0.1458
POISSON_PERCENTILE: 8
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

ANALYSIS FILE NAME: GSM818056_UCSD.H1_Derived_Neuronal_Progenitor_Cultured_Cells.H3K9me3.AK244.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K9me3.NPC.02.01.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Derived Neuronal Progenitor Cultured Cells Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9me3 ChIP-Seq read mappings from the H1 Derived Neuronal Progenitor Cultured Cells, Library AK244, 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.12516
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 6
BROWSER_TRACK_NAME: HDNP H3K9me3 44
BROWSER_TRACK_DESCRIPTION: UCSD H1 Derived Neuronal Progenitor Cultured Cells Histone H3K9me3 Library AK244 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 35,880,551
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 13
FINDPEAKS_SCORE: 0.047
FINDPEAKS_PERCENTILE: 46
HOTSPOT_SCORE: 0.0702
HOTSPOT_PERCENTILE: 8
IROC_SCORE: 0.8037
IROC_PERCENTILE: 46
POISSON_SCORE: 0.1458
POISSON_PERCENTILE: 8
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

source_name: Human embryonic stem cells received from the James Thomson laboratory.  Cells are from the H1 line and are differentiated into neural progenitor cells.; renlab.H3K9me3.NPC.02.01

value: James Thomson Laboratory

value: Cell Line

value: Embryonic Stem Cell

value: Embryonic stem cell differentiated into neural progenitor cells

value: Publication in progress

value: Histone H3K9me3

value: magnetic anti-rabbit

value: 5 micrograms

value: Abcam


title: Reference Epigenome: ChIP-Seq Analysis of H2BK12ac in Neural Progenitor Cells; renlab.H2BK12ac.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 H2BK12ac in Neural Progenitor Cells. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AK249
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.10141
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: GSM818016_UCSD.H1_Derived_Neuronal_Progenitor_Cultured_Cells.H2BK12ac.AK249.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H2BK12ac.NPC.01.01.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of H1 Derived Neuronal Progenitor Cultured Cells Histone H2BK12ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H2BK12ac ChIP-Seq on H1 Derived Neuronal Progenitor Cultured Cells, Library AK249, 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.12409
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 36,672,918
NUMBER_OF_H2BK12ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 3
FINDPEAKS_SCORE: 0.0193
FINDPEAKS_PERCENTILE: 33
HOTSPOT_SCORE: 0.0786
HOTSPOT_PERCENTILE: 33
IROC_SCORE: 0.7014
IROC_PERCENTILE: 33
POISSON_SCORE: 0.2982
POISSON_PERCENTILE: 33
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM818016_UCSD.H1_Derived_Neuronal_Progenitor_Cultured_Cells.H2BK12ac.AK249.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H2BK12ac.NPC.01.01.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Derived Neuronal Progenitor Cultured Cells Histone H2BK12ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H2BK12ac ChIP-Seq read mappings from the H1 Derived Neuronal Progenitor Cultured Cells, Library AK249, 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.12482
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 6
BROWSER_TRACK_NAME: HDNP H2BK12ac 49
BROWSER_TRACK_DESCRIPTION: UCSD H1 Derived Neuronal Progenitor Cultured Cells Histone H2BK12ac Library AK249 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 36,672,918
NUMBER_OF_H2BK12ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 3
FINDPEAKS_SCORE: 0.0193
FINDPEAKS_PERCENTILE: 33
HOTSPOT_SCORE: 0.0786
HOTSPOT_PERCENTILE: 33
IROC_SCORE: 0.7014
IROC_PERCENTILE: 33
POISSON_SCORE: 0.2982
POISSON_PERCENTILE: 33
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: Human embryonic stem cells received from the James Thomson laboratory.  Cells are from the H1 line and are differentiated into neural progenitor cells.; renlab.H2BK12ac.NPC.01.01

value: genomic DNA

value: Histone H2BK12ac

value: Biorupter

value: 500 micrograms


title: Reference Epigenome: ChIP-Seq Analysis of H3K9me3 in BMP4 Trophoblast Cells; renlab.H3K9me3.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 H3K9me3 in BMP4 Trophoblast Cells. Sequencing was done on the Illumina Genome Analyzer IIx platform.
Library name: LH8
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.9784
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.7847
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM818054_UCSD.H1_BMP4_Derived_Trophoblast_Cultured_Cells.H3K9me3.LH8.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K9me3.BMP4T.02.01.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9me3 ChIP-Seq on H1 BMP4 Derived Trophoblast Cultured Cells, Library LH8, 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.12406
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 25,841,511
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 13
FINDPEAKS_SCORE: 0.0904
FINDPEAKS_PERCENTILE: 62
HOTSPOT_SCORE: 0.1842
HOTSPOT_PERCENTILE: 85
IROC_SCORE: 0.8899
IROC_PERCENTILE: 77
POISSON_SCORE: 0.3954
POISSON_PERCENTILE: 85
MAXIMUM_REPLICATE_CORRELATION: 0.92

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

ANALYSIS FILE NAME: GSM818054_UCSD.H1_BMP4_Derived_Trophoblast_Cultured_Cells.H3K9me3.LH8.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K9me3.BMP4T.02.01.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9me3 ChIP-Seq read mappings from the H1 BMP4 Derived Trophoblast Cultured Cells, Library LH8, 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.12479
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 6
BROWSER_TRACK_NAME: HBDT H3K9me3 H8
BROWSER_TRACK_DESCRIPTION: UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K9me3 Library LH8 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 25,841,511
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 13
FINDPEAKS_SCORE: 0.0904
FINDPEAKS_PERCENTILE: 62
HOTSPOT_SCORE: 0.1842
HOTSPOT_PERCENTILE: 85
IROC_SCORE: 0.8899
IROC_PERCENTILE: 77
POISSON_SCORE: 0.3954
POISSON_PERCENTILE: 85
MAXIMUM_REPLICATE_CORRELATION: 0.92

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

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.H3K9me3.BMP4T.02.01

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

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

value: Male


title: Chromatin accessibility assay of Fetal Renal Pelvis, Left; DS19238

description:
sample_term_id: UBERON_0001224
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS19238
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.9965
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.9964
****************
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: GSM817209_UW.Fetal_Renal_Pelvis_Left.ChromatinAccessibility.H-24232.DS19238.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS19238.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of Fetal Renal Pelvis Left Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Renal Pelvis Left, Donor H-24232, Library DS19238 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.12629
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 30,445,610
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.4116
FINDPEAKS_PERCENTILE: 62
HOTSPOT_SCORE: 0.41
HOTSPOT_PERCENTILE: 60
IROC_SCORE: 0.9928
IROC_PERCENTILE: 43
POISSON_SCORE: 0.4764
POISSON_PERCENTILE: 60
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

ANALYSIS FILE NAME: GSM817209_UW.Fetal_Renal_Pelvis_Left.ChromatinAccessibility.H-24232.DS19238.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS19238.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Renal Pelvis Left Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Renal Pelvis Left, Donor H-24232, Library DS19238 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.12692
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 150bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 6
BROWSER_TRACK_NAME: FRPL DNase 32 38
BROWSER_TRACK_DESCRIPTION: UW Fetal Renal Pelvis Left DNase Hypersensitivity Donor H-24232 Library DS19238 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 30,445,610
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.4116
FINDPEAKS_PERCENTILE: 62
HOTSPOT_SCORE: 0.41
HOTSPOT_PERCENTILE: 60
IROC_SCORE: 0.9928
IROC_PERCENTILE: 43
POISSON_SCORE: 0.4764
POISSON_PERCENTILE: 60
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

source_name: Fetal Kidney, renal, pelvis, Left primary tissue, day 105; DS19238

value: Fetal Renal Pelvis, Left

value: University of Washington, Congenital Defects Lab. Ian Glass

value: Primary Tissue

value: UW

value: fetal

value: day 105

value: Chromatin Accessibility

value: Qiagen minElut

value: Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)


title: Reference Epigenome: ChIP-Seq Analysis of H3K9me3 in BMP4 Trophoblast Cells; renlab.H3K9me3.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 H3K9me3 in BMP4 Trophoblast Cells. Sequencing was done on the Illumina Genome Analyzer IIx platform.
Library name: LH4
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.9782
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.7840
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM818053_UCSD.H1_BMP4_Derived_Trophoblast_Cultured_Cells.H3K9me3.LH4.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K9me3.BMP4T.01.01.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9me3 ChIP-Seq on H1 BMP4 Derived Trophoblast Cultured Cells, Library LH4, 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.12403
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 26,722,940
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 13
FINDPEAKS_SCORE: 0.1012
FINDPEAKS_PERCENTILE: 85
HOTSPOT_SCORE: 0.1684
HOTSPOT_PERCENTILE: 69
IROC_SCORE: 0.8466
IROC_PERCENTILE: 54
POISSON_SCORE: 0.3653
POISSON_PERCENTILE: 69
MAXIMUM_REPLICATE_CORRELATION: 0.92

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

ANALYSIS FILE NAME: GSM818053_UCSD.H1_BMP4_Derived_Trophoblast_Cultured_Cells.H3K9me3.LH4.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K9me3.BMP4T.01.01.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9me3 ChIP-Seq read mappings from the H1 BMP4 Derived Trophoblast Cultured Cells, Library LH4, 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.12476
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 6
BROWSER_TRACK_NAME: HBDT H3K9me3 H4
BROWSER_TRACK_DESCRIPTION: UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K9me3 Library LH4 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 26,722,940
NUMBER_OF_H3K9me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 13
FINDPEAKS_SCORE: 0.1012
FINDPEAKS_PERCENTILE: 85
HOTSPOT_SCORE: 0.1684
HOTSPOT_PERCENTILE: 69
IROC_SCORE: 0.8466
IROC_PERCENTILE: 54
POISSON_SCORE: 0.3653
POISSON_PERCENTILE: 69
MAXIMUM_REPLICATE_CORRELATION: 0.92

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

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.H3K9me3.BMP4T.01.01

value: James Thomson Laboratory

value: Cell Line

value: Embryonic Stem Cell

value: Histone H3K9me3

value: magnetic anti-rabbit

value: 5 micrograms

value: Abcam


title: Chromatin accessibility assay of Fetal Renal Pelvis, Right; DS19235

description:
sample_term_id: UBERON_0001224
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS19235
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.9946
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.9945
****************
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: GSM817208_UW.Fetal_Renal_Pelvis_Right.ChromatinAccessibility.H-24232.DS19235.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS19235.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of Fetal Renal Pelvis Right Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Renal Pelvis Right, Donor H-24232, Library DS19235 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.12628
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 31,338,934
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.3362
FINDPEAKS_PERCENTILE: 37
HOTSPOT_SCORE: 0.3274
HOTSPOT_PERCENTILE: 37
IROC_SCORE: 0.9918
IROC_PERCENTILE: 33
POISSON_SCORE: 0.3936
POISSON_PERCENTILE: 24
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

ANALYSIS FILE NAME: GSM817208_UW.Fetal_Renal_Pelvis_Right.ChromatinAccessibility.H-24232.DS19235.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS19235.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Renal Pelvis Right Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Renal Pelvis Right, Donor H-24232, Library DS19235 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.12691
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 150bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 6
BROWSER_TRACK_NAME: FRPR DNase 32 35
BROWSER_TRACK_DESCRIPTION: UW Fetal Renal Pelvis Right DNase Hypersensitivity Donor H-24232 Library DS19235 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 31,338,934
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.3362
FINDPEAKS_PERCENTILE: 37
HOTSPOT_SCORE: 0.3274
HOTSPOT_PERCENTILE: 37
IROC_SCORE: 0.9918
IROC_PERCENTILE: 33
POISSON_SCORE: 0.3936
POISSON_PERCENTILE: 24
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

source_name: Fetal Kidney, renal, pelvis, Right primary tissue, day 105; DS19235

value: Fetal Renal Pelvis, Right

value: genomic DNA

value: Male


title: Reference Epigenome: ChIP-Seq Analysis of H3K4me3 in Neural Progenitor Cells; renlab.H3K4me3.NPC.03.01

description:
sample_term_id: CL_0000047
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K4me3 in Neural Progenitor Cells. Sequencing was done on the Illumina Genome Analyzer IIx platform.
Library name: AK243
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.10151
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: GSM818043_UCSD.H1_Derived_Neuronal_Progenitor_Cultured_Cells.H3K4me3.AK243.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4me3.NPC.03.01.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of H1 Derived Neuronal Progenitor Cultured Cells Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me3 ChIP-Seq on H1 Derived Neuronal Progenitor Cultured Cells, Library AK243, 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.12414
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 37,698,637
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 11
FINDPEAKS_SCORE: 0.2078
FINDPEAKS_PERCENTILE: 36
HOTSPOT_SCORE: 0.21
HOTSPOT_PERCENTILE: 27
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.2264
POISSON_PERCENTILE: 27
MAXIMUM_REPLICATE_CORRELATION: 0.55

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

ANALYSIS FILE NAME: GSM818043_UCSD.H1_Derived_Neuronal_Progenitor_Cultured_Cells.H3K4me3.AK243.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4me3.NPC.03.01.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Derived Neuronal Progenitor Cultured Cells Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me3 ChIP-Seq read mappings from the H1 Derived Neuronal Progenitor Cultured Cells, Library AK243, 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.12487
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 6
BROWSER_TRACK_NAME: HDNP H3K4me3 43
BROWSER_TRACK_DESCRIPTION: UCSD H1 Derived Neuronal Progenitor Cultured Cells Histone H3K4me3 Library AK243 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 37,698,637
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 11
FINDPEAKS_SCORE: 0.2078
FINDPEAKS_PERCENTILE: 36
HOTSPOT_SCORE: 0.21
HOTSPOT_PERCENTILE: 27
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.2264
POISSON_PERCENTILE: 27
MAXIMUM_REPLICATE_CORRELATION: 0.55

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

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.H3K4me3.NPC.03.01

value: Embryonic stem cell differentiated into neural progenitor cells

value: Publication in progress

value: Histone H3K4me3

value: Biorupter

value: 500 micrograms

value: Active Motif


title: Chromatin accessibility assay of Fetal Muscle, Back; DS19117

description:
sample_term_id: UBERON_0002324
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS19117
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.9867
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.9866
****************
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: GSM817207_UW.Fetal_Muscle_Back.ChromatinAccessibility.H-24218.DS19117.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS19117.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of Fetal Muscle Back Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Muscle Back, Donor H-24218, Library DS19117 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.12627
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 27,981,297
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.3343
FINDPEAKS_PERCENTILE: 35
HOTSPOT_SCORE: 0.3226
HOTSPOT_PERCENTILE: 33
IROC_SCORE: 0.9932
IROC_PERCENTILE: 49
POISSON_SCORE: 0.4069
POISSON_PERCENTILE: 30
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM817207_UW.Fetal_Muscle_Back.ChromatinAccessibility.H-24218.DS19117.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS19117.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Muscle Back Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Muscle Back, Donor H-24218, Library DS19117 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.12690
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 150bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 6
BROWSER_TRACK_NAME: FMB DNase 18 17
BROWSER_TRACK_DESCRIPTION: UW Fetal Muscle Back DNase Hypersensitivity Donor H-24218 Library DS19117 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 27,981,297
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.3343
FINDPEAKS_PERCENTILE: 35
HOTSPOT_SCORE: 0.3226
HOTSPOT_PERCENTILE: 33
IROC_SCORE: 0.9932
IROC_PERCENTILE: 49
POISSON_SCORE: 0.4069
POISSON_PERCENTILE: 30
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

source_name: Fetal Muscle, Back primary tissue, day 96; DS19117

value: Fetal Muscle, Back

value: University of Washington, Congenital Defects Lab. Ian Glass

value: Primary Tissue

value: UW

value: fetal

value: day 96

value: Chromatin Accessibility

value: Qiagen minElut

value: Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)


title: LmjF_WT_anti_JBP1

city: SEATTLE

first: Gowthaman

last: Ramasamy

state: WASHINGTON

address: 307 WESTLAKE AVE N

department: GHBC

institute: SEATTLE BIOMEDICAL RESEARCH INSTITUTE

data_processing: Small RNA reads were trimmed to remove any Illumina adapter sequence present in the tail of the reads. All read data were aligned using the Burrow Wheeler Aligner (BWA) using the default parameters. ChIP-seq data were filtered to remove all reads with a mapping quality equal or less than 21. The small RNA data were filtered to remove the reads with a mapping quality value less than 37 or reads that aligned with mismatches. For all datasets, multimappers were discarded. SL RNA-seq reads were trimmed to remove the first three 5’ bases specific to the SL sequencing primer and subsequently mapped to their respective reference genomes using the BOWTIE (v0.12.1) short read aligner.  Mapping was set to M = -1 which assigns a multi-mapping read randomly to one of the sites within the genome. Samtools (v 0.1.8) was used to convert SAM output into BAM files. bamTobed command from BEDtools(v2.13.3) were used to create bed files from BAM files.

organism: Leishmania major

source_name: mixed

growth_protocol: Leishmania were grown in SDM-79 medium until the culture reached a density of 108 cells/ml.

extract_protocol:
Production of the antibodies used were described in the following paper published in 1997. Van Leeuwen et al, Genes Dev. (1997) 11, 3232-3241.  Very briefly "Synthetically synthesized J nucleotides (JMP) were coupled to carrier proteins (keyhole limpet haemocyanin) and injected into rabbits".
ChIP-seq libraries were prepared with the Illumina sample preparation kit (IP-102-1001, Illumina Inc.); modified in the use of Covaris DNA Shearing (Covaris, Massachusetts, USA) instead of shearing by nebulization. Genomic DNA (30 μg) was sheared in 5μg aliquots in Covaris MicroTubes into fragments of 100 - 1500 bp and used for IP experiments. After the IP and cleanup of the DNA, the fragments were end-repaired, made to have an A-overhang and ligated to ten-fold diluted Illumina adapters (see above). The mixture was size selected for fragments ~ 200 bp in length either by agarose gel or by E-gel (Invitrogen)  and PCR-amplified for 18 cycles before sequencing on the Genome Analyzer IIx identical to a genomic DNA seq library (60 bp, SR).

treatment_protocol: L. tarentolae JBP2 KO in 0.6 μM BrdU containing medium were grown for 5 days before harvesting.

tag: strain

value: Friedlin

tag: developmental stage

value: mixed

tag: genotype/variation

value: WT

tag: chip antibody


title: LtaP_antiJBP1_JBP2KO_BrdU

organism: Leishmania tarentolae

source_name: Procyclic Promastigotes

value: Parrot

value: Procyclic Promastigotes

tag: treatment

value: BrdU


title: LmjF_WT_anti_baseJ


title: Reference Epigenome: ChIP-Seq Analysis of H3K36me3 in Neural Progenitor Cells; renlab.H3K36me3.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 H3K36me3 in Neural Progenitor Cells. Sequencing was done on the Illumina Genome Analyzer IIx platform.
Library name: AK241
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.10135
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: GSM818035_UCSD.H1_Derived_Neuronal_Progenitor_Cultured_Cells.H3K36me3.AK241.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K36me3.NPC.02.01.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of H1 Derived Neuronal Progenitor Cultured Cells Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K36me3 ChIP-Seq on H1 Derived Neuronal Progenitor Cultured Cells, Library AK241, 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.12441
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 35,117,712
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 13
FINDPEAKS_SCORE: 0.0488
FINDPEAKS_PERCENTILE: 31
HOTSPOT_SCORE: 0.1125
HOTSPOT_PERCENTILE: 15
IROC_SCORE: 0.8661
IROC_PERCENTILE: 38
POISSON_SCORE: 0.254
POISSON_PERCENTILE: 23
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM818035_UCSD.H1_Derived_Neuronal_Progenitor_Cultured_Cells.H3K36me3.AK241.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K36me3.NPC.02.01.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Derived Neuronal Progenitor Cultured Cells Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K36me3 ChIP-Seq read mappings from the H1 Derived Neuronal Progenitor Cultured Cells, Library AK241, 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.12514
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 6
BROWSER_TRACK_NAME: HDNP H3K36me3 41
BROWSER_TRACK_DESCRIPTION: UCSD H1 Derived Neuronal Progenitor Cultured Cells Histone H3K36me3 Library AK241 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 35,117,712
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 13
FINDPEAKS_SCORE: 0.0488
FINDPEAKS_PERCENTILE: 31
HOTSPOT_SCORE: 0.1125
HOTSPOT_PERCENTILE: 15
IROC_SCORE: 0.8661
IROC_PERCENTILE: 38
POISSON_SCORE: 0.254
POISSON_PERCENTILE: 23
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

source_name: Human embryonic stem cells received from the James Thomson laboratory.  Cells are from the H1 line and are differentiated into neural progenitor cells.; renlab.H3K36me3.NPC.02.01

value: genomic DNA

value: James Thomson Laboratory

value: Cell Line

value: Embryonic Stem Cell

value: Embryonic stem cell differentiated into neural progenitor cells

value: Publication in progress

value: Male

value: Histone H3K36me3

value: Biorupter

value: 500 micrograms

value: magnetic anti-rabbit

value: 5 micrograms

value: Abcam


title: LtaP_antiJBP1_JBP2KO


title: Reference Epigenome: ChIP-Seq Analysis of H3K4me1 in Neural Progenitor Cells; renlab.H3K4me1.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 H3K4me1 in Neural Progenitor Cells. Sequencing was done on the Illumina Genome Analyzer IIx platform.
Library name: AK242
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.10149
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: GSM818040_UCSD.H1_Derived_Neuronal_Progenitor_Cultured_Cells.H3K4me1.AK242.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4me1.NPC.02.01.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of H1 Derived Neuronal Progenitor Cultured Cells Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me1 ChIP-Seq on H1 Derived Neuronal Progenitor Cultured Cells, Library AK242, 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.12402
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 41,353,559
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 14
FINDPEAKS_SCORE: 0.0274
FINDPEAKS_PERCENTILE: 7
HOTSPOT_SCORE: 0.1016
HOTSPOT_PERCENTILE: 7
IROC_SCORE: 0.7631
IROC_PERCENTILE: 7
POISSON_SCORE: 0.2862
POISSON_PERCENTILE: 14
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

ANALYSIS FILE NAME: GSM818040_UCSD.H1_Derived_Neuronal_Progenitor_Cultured_Cells.H3K4me1.AK242.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4me1.NPC.02.01.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Derived Neuronal Progenitor Cultured Cells Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me1 ChIP-Seq read mappings from the H1 Derived Neuronal Progenitor Cultured Cells, Library AK242, 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.12475
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 6
BROWSER_TRACK_NAME: HDNP H3K4me1 42
BROWSER_TRACK_DESCRIPTION: UCSD H1 Derived Neuronal Progenitor Cultured Cells Histone H3K4me1 Library AK242 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 41,353,559
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 14
FINDPEAKS_SCORE: 0.0274
FINDPEAKS_PERCENTILE: 7
HOTSPOT_SCORE: 0.1016
HOTSPOT_PERCENTILE: 7
IROC_SCORE: 0.7631
IROC_PERCENTILE: 7
POISSON_SCORE: 0.2862
POISSON_PERCENTILE: 14
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

source_name: Human embryonic stem cells received from the James Thomson laboratory.  Cells are from the H1 line and are differentiated into neural progenitor cells.; renlab.H3K4me1.NPC.02.01

value: Histone H3K4me1


title: Chromatin accessibility assay of Fetal Renal Pelvis, Left; DS18964

description:
sample_term_id: UBERON_0001224
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS18964
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.9974
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.9973
****************
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: GSM817205_UW.Fetal_Renal_Pelvis_Left.ChromatinAccessibility.H-24169.DS18964.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS18964.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of Fetal Renal Pelvis Left Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Renal Pelvis Left, Donor H-24169, Library DS18964 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.12625
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 31,231,851
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.3375
FINDPEAKS_PERCENTILE: 38
HOTSPOT_SCORE: 0.3285
HOTSPOT_PERCENTILE: 38
IROC_SCORE: 0.9904
IROC_PERCENTILE: 24
POISSON_SCORE: 0.4037
POISSON_PERCENTILE: 29
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

ANALYSIS FILE NAME: GSM817205_UW.Fetal_Renal_Pelvis_Left.ChromatinAccessibility.H-24169.DS18964.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS18964.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Renal Pelvis Left Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Renal Pelvis Left, Donor H-24169, Library DS18964 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.12688
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 150bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 6
BROWSER_TRACK_NAME: FRPL DNase 69 64
BROWSER_TRACK_DESCRIPTION: UW Fetal Renal Pelvis Left DNase Hypersensitivity Donor H-24169 Library DS18964 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 31,231,851
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.3375
FINDPEAKS_PERCENTILE: 38
HOTSPOT_SCORE: 0.3285
HOTSPOT_PERCENTILE: 38
IROC_SCORE: 0.9904
IROC_PERCENTILE: 24
POISSON_SCORE: 0.4037
POISSON_PERCENTILE: 29
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

source_name: Fetal Kidney, renal, pelvis, Left primary tissue, day 120; DS18964

value: Fetal Renal Pelvis, Left

value: University of Washington, Congenital Defects Lab. Ian Glass

value: Primary Tissue

value: UW

value: fetal

value: day 120

value: Chromatin Accessibility

value: Qiagen minElut

value: Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)


title: Chromatin accessibility assay of Fetal Muscle, Leg; DS19115

description:
sample_term_id: UBERON_0001383
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS19115
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.9834
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.9833
****************
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: GSM817206_UW.Fetal_Muscle_Leg.ChromatinAccessibility.H-24218.DS19115.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS19115.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of Fetal Muscle Leg Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Muscle Leg, Donor H-24218, Library DS19115 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.12626
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 31,826,985
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.3873
FINDPEAKS_PERCENTILE: 54
HOTSPOT_SCORE: 0.3711
HOTSPOT_PERCENTILE: 51
IROC_SCORE: 0.9929
IROC_PERCENTILE: 44
POISSON_SCORE: 0.4497
POISSON_PERCENTILE: 54
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM817206_UW.Fetal_Muscle_Leg.ChromatinAccessibility.H-24218.DS19115.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS19115.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Muscle Leg Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Muscle Leg, Donor H-24218, Library DS19115 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.12689
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 150bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 6
BROWSER_TRACK_NAME: FML DNase 18 15
BROWSER_TRACK_DESCRIPTION: UW Fetal Muscle Leg DNase Hypersensitivity Donor H-24218 Library DS19115 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 31,826,985
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.3873
FINDPEAKS_PERCENTILE: 54
HOTSPOT_SCORE: 0.3711
HOTSPOT_PERCENTILE: 51
IROC_SCORE: 0.9929
IROC_PERCENTILE: 44
POISSON_SCORE: 0.4497
POISSON_PERCENTILE: 54
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

source_name: Fetal Muscle, Leg primary tissue, day 96; DS19115

value: Fetal Muscle, Leg

value: genomic DNA

value: day 96

value: Male


title: Chromatin accessibility assay of H1 BMP4 Derived Mesendoderm Cultured Cells; DS19310

description:
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS19310
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.10108
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.7805
****************
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: GSM817215_UW.H1_BMP4_Derived_Mesendoderm_Cultured_Cells.ChromatinAccessibility.DS19310.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS19310.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of H1 BMP4 Derived Mesendoderm Cultured Cells Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on the H1 BMP4 Derived Mesendoderm Cultured Cells, Library DS19310 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.12635
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 30,822,811
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.399
FINDPEAKS_PERCENTILE: 59
HOTSPOT_SCORE: 0.4537
HOTSPOT_PERCENTILE: 75
IROC_SCORE: 0.9946
IROC_PERCENTILE: 73
POISSON_SCORE: 0.4899
POISSON_PERCENTILE: 63
MAXIMUM_REPLICATE_CORRELATION: 1.0

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

ANALYSIS FILE NAME: GSM817215_UW.H1_BMP4_Derived_Mesendoderm_Cultured_Cells.ChromatinAccessibility.DS19310.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS19310.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of H1 BMP4 Derived Mesendoderm Cultured Cells Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  the H1 BMP4 Derived Mesendoderm Cultured Cells, Library DS19310 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.12698
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 150bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 6
BROWSER_TRACK_NAME: HBDM DNase 10
BROWSER_TRACK_DESCRIPTION: UW H1 BMP4 Derived Mesendoderm Cultured Cells DNase Hypersensitivity Donor  Library DS19310 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 30,822,811
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.399
FINDPEAKS_PERCENTILE: 59
HOTSPOT_SCORE: 0.4537
HOTSPOT_PERCENTILE: 75
IROC_SCORE: 0.9946
IROC_PERCENTILE: 73
POISSON_SCORE: 0.4899
POISSON_PERCENTILE: 63
MAXIMUM_REPLICATE_CORRELATION: 1.0

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

source_name: Human embryonic stem cells received from the James Thomson laboratory.  Cells are from the H1 line and are differentiated into mesendoderm by treatment with BMP4.; DS19310

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

value: Between 20 and 30


title: Reference Epigenome: ChIP-Seq Analysis of H3K27me3 in Neural Progenitor Cells; renlab.H3K27me3.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 H3K27me3 in Neural Progenitor Cells. Sequencing was done on the Illumina Genome Analyzer IIx platform.
Library name: AK221
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.10129
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: GSM818033_UCSD.H1_Derived_Neuronal_Progenitor_Cultured_Cells.H3K27me3.AK221.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27me3.NPC.02.01.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of H1 Derived Neuronal Progenitor Cultured Cells Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27me3 ChIP-Seq on H1 Derived Neuronal Progenitor Cultured Cells, Library AK221, 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.12373
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 31,270,318
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 10
FINDPEAKS_SCORE: 0.0467
FINDPEAKS_PERCENTILE: 70
HOTSPOT_SCORE: 0.0716
HOTSPOT_PERCENTILE: 10
IROC_SCORE: 0.9573
IROC_PERCENTILE: 80
POISSON_SCORE: 0.1414
POISSON_PERCENTILE: 10
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM818033_UCSD.H1_Derived_Neuronal_Progenitor_Cultured_Cells.H3K27me3.AK221.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27me3.NPC.02.01.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Derived Neuronal Progenitor Cultured Cells Histone H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27me3 ChIP-Seq read mappings from the H1 Derived Neuronal Progenitor Cultured Cells, Library AK221, 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.12446
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 6
BROWSER_TRACK_NAME: HDNP H3K27me3 21
BROWSER_TRACK_DESCRIPTION: UCSD H1 Derived Neuronal Progenitor Cultured Cells Histone H3K27me3 Library AK221 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 31,270,318
NUMBER_OF_H3K27me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 10
FINDPEAKS_SCORE: 0.0467
FINDPEAKS_PERCENTILE: 70
HOTSPOT_SCORE: 0.0716
HOTSPOT_PERCENTILE: 10
IROC_SCORE: 0.9573
IROC_PERCENTILE: 80
POISSON_SCORE: 0.1414
POISSON_PERCENTILE: 10
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.H3K27me3.NPC.02.01

value: Embryonic stem cell differentiated into neural progenitor cells

value: Publication in progress

value: Histone H3K27me3

value: Biorupter

value: 500 micrograms

value: magnetic anti-rabbit

value: 5 micrograms

value: Active Motif


title: LtaP_antiJBP1_WT

value: Parrot

value: Procyclic Promastigotes

value: WT