title: RNA-Seq (Total RNA) Fetal Renal Cortex; RNA.RS20084

description:
sample_term_id: UBERON_0001225
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: RNA-Seq (Total RNA) Fetal Renal Cortex
Library name: lib-RNA.RS20084
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15206
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.7080
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: Fetal primary tissue, day 91; RNA.RS20084

value: UW

value: Random Primers(hexamers)


title: RNA-Seq (Total RNA) Fetal Intestine, Large; RNA.RS18146

status: Public on Jan 10 2013

type: SRA

city: Seattle

first: Northwest

last: REMC

state: WA

country: USA

institute: University of Washington

description:
sample_term_id: UBERON_0000059
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: RNA-Seq (Total RNA) Fetal Intestine, Large
Library name: lib-RNA.RS18146
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15246
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.7045
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

library_source: transcriptomic

data_processing: Various levels of processed data files will be made available as this project proceeds.

molecule: total RNA

organism: Homo sapiens

source_name: Fetal primary tissue, day 85; RNA.RS18146

extract_protocol: Library construction protocol: Illumina TruSeq RNA PART# 15008136 REVISION A

tag: sample alias

tag: sample common name

value: Fetal Intestine, Large

tag: disease

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

value: Primary Tissue

value: fetal

value: day 85

value: Female

value: mRNA-Seq

value: Qiagen TissueLyser and RNeasy Lipid Tx Mini kit

value: Part of Library Prep, Truseq RNA-Seq Sample Prep Kit

value: TruSeq RNA

value: cDNA

value: Proprietary

value: 98C 30 sec, 15 cycles of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold


title: RNA-Seq (Total RNA) Fetal Renal Pelvis, Left; RNA.RS19665

description:
sample_term_id: UBERON_0001224
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: RNA-Seq (Total RNA) Fetal Renal Pelvis, Left
Library name: lib-RNA.RS19665
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15199
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.9979
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: Fetal Kidney, renal, pelvis, Left primary tissue, day 105; RNA.RS19665

value: Fetal Renal Pelvis, Left

value: day 105

value: Male

value: Ambion mirVana miRNA isolation kit


title: RNA-Seq (Total RNA) Fetal Renal Pelvis; RNA.RS20011

description:
sample_term_id: UBERON_0001224
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: RNA-Seq (Total RNA) Fetal Renal Pelvis
Library name: lib-RNA.RS20011
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15177
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.9984
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: Fetal Kidney, renal, pelvis primary tissue, day 97; RNA.RS20011

value: Fetal Renal Pelvis

value: UW

value: day 97

value: Random Primers(hexamers)


title: RNA-Seq (Total RNA) Fetal Renal Cortex, Left; RNA.RS20010

description:
sample_term_id: UBERON_0001225
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: RNA-Seq (Total RNA) Fetal Renal Cortex, Left
Library name: lib-RNA.RS20010
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15216
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
****************

source_name: Fetal Kidney, renal, cortex, Left primary tissue, day 105; RNA.RS20010

value: Fetal Renal Cortex, Left

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

value: Primary Tissue

value: fetal


title: RNA-Seq (Total RNA) Fetal Renal Cortex, Right; RNA.RS19454

description:
sample_term_id: UBERON_0001225
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: RNA-Seq (Total RNA) Fetal Renal Cortex, Right
Library name: lib-RNA.RS19454
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15214
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.10003
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: Fetal Kidney, renal, cortex, Right primary tissue, day 120; RNA.RS19454

value: Fetal Renal Cortex, Right

value: day 120

value: mRNA-Seq

value: Part of Library Prep, Truseq RNA-Seq Sample Prep Kit


title: RNA-Seq (Total RNA) Fetal Renal Cortex, Left; RNA.RS19455

description:
sample_term_id: UBERON_0001225
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: RNA-Seq (Total RNA) Fetal Renal Cortex, Left
Library name: lib-RNA.RS19455
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15218
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.10017
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: Fetal Kidney, renal, cortex, Left primary tissue, day 120; RNA.RS19455

value: TruSeq RNA

value: cDNA

value: Proprietary

value: 98C 30 sec, 15 cycles of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold


title: RNA-Seq (Total RNA) Fetal Renal Pelvis, Right; RNA.RS19664

description:
sample_term_id: UBERON_0001224
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: RNA-Seq (Total RNA) Fetal Renal Pelvis, Right
Library name: lib-RNA.RS19664
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15192
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.9959
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: Fetal Kidney, renal, pelvis, Right primary tissue, day 105; RNA.RS19664

value: Fetal Renal Pelvis, Right

value: day 105

value: Male

value: Ambion mirVana miRNA isolation kit


title: RNA-Seq (Total RNA) Fetal Intestine, Small; RNA.RS17915

description:
sample_term_id: UBERON_0002108
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: RNA-Seq (Total RNA) Fetal Intestine, Small
Library name: lib-RNA.RS17915
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15167
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.7055
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: Fetal primary tissue, day 108; RNA.RS17915

value: Fetal Intestine, Small

value: UW

value: day 108

value: Qiagen TissueLyser and RNeasy Lipid Tx Mini kit

value: Random Primers(hexamers)


title: Digital Genomic Footprinting assay of CD8 Primary Cells; DGF.DS17885

description:
sample_term_id: CL_0000625
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Digital Genomic Footprinting determination via DNase-seq
Library name: DGF.DS17885
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.14981
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.7035
****************
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

molecule: genomic DNA

source_name: flow sorted CD8+ Cells, year 37; DGF.DS17885

extract_protocol: Library construction protocol: Single read - Illumina

value: CD8 Primary Cells

tag: molecule

value: genomic DNA

value: FHCRC HEIMFELD

value: Primary Cell

tag: markers

value: year 37

value: Hispanic

value: Digital Genomic Footprinting

value: Qiagen minElut


title: RNA-Seq (Total RNA) Fetal Intestine, Large; RNA.RS17914

description:
sample_term_id: UBERON_0000059
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: RNA-Seq (Total RNA) Fetal Intestine, Large
Library name: lib-RNA.RS17914
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15115
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.7041
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: Fetal primary tissue, day 108; RNA.RS17914

value: Fetal Intestine, Large

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

value: Primary Tissue

value: fetal

value: mRNA-Seq

value: Part of Library Prep, Truseq RNA-Seq Sample Prep Kit

value: TruSeq RNA

value: cDNA

value: Proprietary

value: 98C 30 sec, 15 cycles of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold


title: ChIP-Seq Input of Fetal Muscle, Leg; Histone.DS21509

description:
sample_term_id: UBERON_0001383
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Input
Library name: Histone.DS21509
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.14972
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.14904
****************
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: GSM1058788_UW.Fetal_Muscle_Leg.Input.H-24644.Histone.DS21509.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS21509.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Fetal Muscle Leg Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Input ChIP-Seq on Fetal Muscle Leg, Donor H-24644, 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.16876
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 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 23,511,773
FINDPEAKS_SCORE: 0.0035
FINDPEAKS_PERCENTILE: 17
HOTSPOT_SCORE: 0.0112
HOTSPOT_PERCENTILE: 49
IROC_SCORE: 0.0
IROC_PERCENTILE: 25
POISSON_SCORE: 0.0426
POISSON_PERCENTILE: 38
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1058788_UW.Fetal_Muscle_Leg.Input.H-24644.Histone.DS21509.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS21509.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Muscle Leg Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Input ChIP-Seq read mappings from Fetal Muscle Leg, Donor H-24644, 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.16972
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 9
BROWSER_TRACK_NAME: FML Input 44 09
BROWSER_TRACK_DESCRIPTION: UW Fetal Muscle Leg ChIP-Seq Input Donor H-24644 Library Histone.DS21509 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 23,511,773
FINDPEAKS_SCORE: 0.0035
FINDPEAKS_PERCENTILE: 17
HOTSPOT_SCORE: 0.0112
HOTSPOT_PERCENTILE: 49
IROC_SCORE: 0.0
IROC_PERCENTILE: 25
POISSON_SCORE: 0.0426
POISSON_PERCENTILE: 38
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: Fetal Muscle, Leg primary tissue, day 110; Histone.DS21509

value: Fetal Muscle, Leg

value: genomic DNA

value: UW

value: day 110

value: Female

value: ChIP-Seq Input

value: Diagenode Bioruptor

value: 20-40 cycles of 0.5 minute on and 0.5 minute off

value: Input


title: ChIP-Seq Input of CD3 Primary Cells; Histone.DS21626

description:
sample_term_id: CL_0000084
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Input
Library name: Histone.DS21626
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.14901
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.6984
****************
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: GSM1058789_UW.CD3_Primary_Cells.Input.RO_01701.Histone.DS21626.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS21626-Histone.DS21626.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of CD3 Primary Cells Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Input ChIP-Seq on CD3 Primary Cells, Donor RO 01701, 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.16863
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 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 36,315,122
FINDPEAKS_SCORE: 0.0054
FINDPEAKS_PERCENTILE: 37
HOTSPOT_SCORE: 0.0035
HOTSPOT_PERCENTILE: 20
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.0247
POISSON_PERCENTILE: 14
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

ANALYSIS FILE NAME: GSM1058789_UW.CD3_Primary_Cells.Input.RO_01701.Histone.DS21626.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS21626-Histone.DS21626.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of CD3 Primary Cells Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Input ChIP-Seq read mappings from CD3 Primary Cells, Donor RO 01701, 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.16959
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 9
BROWSER_TRACK_NAME: CD3 Input 01 26
BROWSER_TRACK_DESCRIPTION: UW CD3 Primary Cells ChIP-Seq Input Donor RO 01701 Library Histone.DS21626 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 36,315,122
FINDPEAKS_SCORE: 0.0054
FINDPEAKS_PERCENTILE: 37
HOTSPOT_SCORE: 0.0035
HOTSPOT_PERCENTILE: 20
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.0247
POISSON_PERCENTILE: 14
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

source_name: flow sorted CD3+ Cells, year 37; Histone.DS21626

value: CD3 Primary Cells

value: FHCRC HEIMFELD

value: Primary Cell

value: year 37

value: Male

value: Hispanic


title: ChIP-Seq Input of Fetal Intestine, Small; Histone.DS21507

description:
sample_term_id: UBERON_0002108
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Input
Library name: Histone.DS21507
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.14938
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.14909
****************
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: GSM1058787_UW.Fetal_Intestine_Small.Input.H-24595.Histone.DS21507.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS21507-Histone.DS21507.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Fetal Intestine Small Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Input ChIP-Seq on Fetal Intestine Small, Donor H-24595, 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.16814
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 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 32,564,030
FINDPEAKS_SCORE: 0.0019
FINDPEAKS_PERCENTILE: 5
HOTSPOT_SCORE: 0.007
HOTSPOT_PERCENTILE: 38
IROC_SCORE: 0.0
IROC_PERCENTILE: 25
POISSON_SCORE: 0.0506
POISSON_PERCENTILE: 46
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1058787_UW.Fetal_Intestine_Small.Input.H-24595.Histone.DS21507.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS21507-Histone.DS21507.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Intestine Small Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Input ChIP-Seq read mappings from Fetal Intestine Small, Donor H-24595, 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.16910
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 9
BROWSER_TRACK_NAME: FIS Input 95 07
BROWSER_TRACK_DESCRIPTION: UW Fetal Intestine Small ChIP-Seq Input Donor H-24595 Library Histone.DS21507 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 32,564,030
FINDPEAKS_SCORE: 0.0019
FINDPEAKS_PERCENTILE: 5
HOTSPOT_SCORE: 0.007
HOTSPOT_PERCENTILE: 38
IROC_SCORE: 0.0
IROC_PERCENTILE: 25
POISSON_SCORE: 0.0506
POISSON_PERCENTILE: 46
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: Fetal Intestine, Small primary tissue, day 108; Histone.DS21507

value: Fetal Intestine, Small

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

value: Primary Tissue

value: fetal

value: day 108


title: ChIP-Seq Input of Fetal Intestine, Large; Histone.DS21506

description:
sample_term_id: UBERON_0000059
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Input
Library name: Histone.DS21506
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.14953
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.14913
****************
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: GSM1058786_UW.Fetal_Intestine_Large.Input.H-24595.Histone.DS21506.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS21506-Histone.DS21506.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Fetal Intestine Large Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Input ChIP-Seq on Fetal Intestine Large, Donor H-24595, 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.16857
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 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 33,012,427
FINDPEAKS_SCORE: 0.0022
FINDPEAKS_PERCENTILE: 6
HOTSPOT_SCORE: 0.0159
HOTSPOT_PERCENTILE: 54
IROC_SCORE: 0.0
IROC_PERCENTILE: 25
POISSON_SCORE: 0.0771
POISSON_PERCENTILE: 58
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1058786_UW.Fetal_Intestine_Large.Input.H-24595.Histone.DS21506.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS21506-Histone.DS21506.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Intestine Large Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Input ChIP-Seq read mappings from Fetal Intestine Large, Donor H-24595, 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.16953
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 9
BROWSER_TRACK_NAME: FIL Input 95 06
BROWSER_TRACK_DESCRIPTION: UW Fetal Intestine Large ChIP-Seq Input Donor H-24595 Library Histone.DS21506 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 33,012,427
FINDPEAKS_SCORE: 0.0022
FINDPEAKS_PERCENTILE: 6
HOTSPOT_SCORE: 0.0159
HOTSPOT_PERCENTILE: 54
IROC_SCORE: 0.0
IROC_PERCENTILE: 25
POISSON_SCORE: 0.0771
POISSON_PERCENTILE: 58
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: Fetal Intestine, Large primary tissue, day 108; Histone.DS21506

value: Fetal Intestine, Large

value: genomic DNA

value: UW


title: Histone H3K9me3 ChIP-Seq of Fetal Muscle, Leg; Histone.DS22903

description:
sample_term_id: UBERON_0001383
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Histone H3K9me3 ChIP-Seq
Library name: Histone.DS22903
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.14956
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.14904
****************
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: GSM1058785_UW.Fetal_Muscle_Leg.H3K9me3.H-24644.Histone.DS22903.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS22903-Histone.DS22903.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Fetal Muscle Leg H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K9me3 ChIP-Seq on Fetal Muscle Leg, Donor H-24644, 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.16816
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 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 25,833,032
FINDPEAKS_SCORE: 0.0627
FINDPEAKS_PERCENTILE: 56
HOTSPOT_SCORE: 0.1471
HOTSPOT_PERCENTILE: 58
IROC_SCORE: 0.8554
IROC_PERCENTILE: 66
POISSON_SCORE: 0.3206
POISSON_PERCENTILE: 56
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM1058785_UW.Fetal_Muscle_Leg.H3K9me3.H-24644.Histone.DS22903.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS22903-Histone.DS22903.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Muscle Leg H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K9me3 ChIP-Seq read mappings from Fetal Muscle Leg, Donor H-24644, 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.16912
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 9
BROWSER_TRACK_NAME: FML H3K9me3 44 03
BROWSER_TRACK_DESCRIPTION: UW Fetal Muscle Leg Histone H3K9me3 Donor H-24644 Library Histone.DS22903 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 25,833,032
FINDPEAKS_SCORE: 0.0627
FINDPEAKS_PERCENTILE: 56
HOTSPOT_SCORE: 0.1471
HOTSPOT_PERCENTILE: 58
IROC_SCORE: 0.8554
IROC_PERCENTILE: 66
POISSON_SCORE: 0.3206
POISSON_PERCENTILE: 56
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

source_name: Fetal Muscle, Leg primary tissue, day 110; Histone.DS22903

value: Fetal Muscle, Leg

value: day 110

value: Female

value: Histone H3K9me3

value: Diagenode Bioruptor

value: Millipore A/G agarose beads

value: 30ul A/G bead slurry

value: Active Motif


title: Histone H3K9me3 ChIP-Seq of CD3 Primary Cells; Histone.DS22898

description:
sample_term_id: CL_0000084
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Histone H3K9me3 ChIP-Seq
Library name: Histone.DS22898
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.14882
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.5322
****************
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: GSM1058783_UW.CD3_Primary_Cells.H3K9me3.RO_01679.Histone.DS22898.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS22898-Histone.DS22898-Histone.DS22898-Histone.DS22898.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of CD3 Primary Cells H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K9me3 ChIP-Seq on CD3 Primary Cells, Donor RO 01679, 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.16877
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 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 15,969,471
FINDPEAKS_SCORE: 0.1213
FINDPEAKS_PERCENTILE: 74
HOTSPOT_SCORE: 0.1833
HOTSPOT_PERCENTILE: 66
IROC_SCORE: 0.7938
IROC_PERCENTILE: 46
POISSON_SCORE: 0.3605
POISSON_PERCENTILE: 78
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

ANALYSIS FILE NAME: GSM1058783_UW.CD3_Primary_Cells.H3K9me3.RO_01679.Histone.DS22898.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS22898-Histone.DS22898-Histone.DS22898-Histone.DS22898.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of CD3 Primary Cells H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K9me3 ChIP-Seq read mappings from CD3 Primary Cells, Donor RO 01679, 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.16973
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 9
BROWSER_TRACK_NAME: CD3 H3K9me3 79 98
BROWSER_TRACK_DESCRIPTION: UW CD3 Primary Cells Histone H3K9me3 Donor RO 01679 Library Histone.DS22898 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 15,969,471
FINDPEAKS_SCORE: 0.1213
FINDPEAKS_PERCENTILE: 74
HOTSPOT_SCORE: 0.1833
HOTSPOT_PERCENTILE: 66
IROC_SCORE: 0.7938
IROC_PERCENTILE: 46
POISSON_SCORE: 0.3605
POISSON_PERCENTILE: 78
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

source_name: flow sorted CD3+ Cells,year 21; Histone.DS22898

value: CD3 Primary Cells

value: FHCRC HEIMFELD

value: Primary Cell

value: year 21

value: Male

value: Caucasian

value: 20-40 cycles of 0.5 minute on and 0.5 minute off


title: Histone H3K9me3 ChIP-Seq of CD19 Primary Cells; Histone.DS22899

description:
sample_term_id: CL_0000236
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Histone H3K9me3 ChIP-Seq
Library name: Histone.DS22899
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.14878
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.6965
****************
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: GSM1058784_UW.CD19_Primary_Cells.H3K9me3.RO_01679.Histone.DS22899.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS22899-Histone.DS22899-Histone.DS22899.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of CD19 Primary Cells H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K9me3 ChIP-Seq on CD19 Primary Cells, Donor RO 01679, 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.16860
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 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 33,190,795
FINDPEAKS_SCORE: 0.0653
FINDPEAKS_PERCENTILE: 58
HOTSPOT_SCORE: 0.1201
HOTSPOT_PERCENTILE: 44
IROC_SCORE: 0.908
IROC_PERCENTILE: 82
POISSON_SCORE: 0.2874
POISSON_PERCENTILE: 46
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

ANALYSIS FILE NAME: GSM1058784_UW.CD19_Primary_Cells.H3K9me3.RO_01679.Histone.DS22899.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS22899-Histone.DS22899-Histone.DS22899.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of CD19 Primary Cells H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K9me3 ChIP-Seq read mappings from CD19 Primary Cells, Donor RO 01679, 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.16956
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 9
BROWSER_TRACK_NAME: CD19 H3K9me3 79 99
BROWSER_TRACK_DESCRIPTION: UW CD19 Primary Cells Histone H3K9me3 Donor RO 01679 Library Histone.DS22899 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 33,190,795
FINDPEAKS_SCORE: 0.0653
FINDPEAKS_PERCENTILE: 58
HOTSPOT_SCORE: 0.1201
HOTSPOT_PERCENTILE: 44
IROC_SCORE: 0.908
IROC_PERCENTILE: 82
POISSON_SCORE: 0.2874
POISSON_PERCENTILE: 46
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

source_name: flow sorted CD19+ Cells, year 21; Histone.DS22899

value: CD19 Primary Cells

value: genomic DNA


title: Histone H3K4me3 ChIP-Seq of Fetal Muscle, Leg; Histone.DS21536

description:
sample_term_id: UBERON_0001383
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Histone H3K4me3 ChIP-Seq
Library name: Histone.DS21536
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.14969
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.14904
****************
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: GSM1058781_UW.Fetal_Muscle_Leg.H3K4me3.H-24644.Histone.DS21536.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS21536-Histone.DS21536.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Fetal Muscle Leg H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K4me3 ChIP-Seq on Fetal Muscle Leg, Donor H-24644, 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.16803
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 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 29,878,006
FINDPEAKS_SCORE: 0.4062
FINDPEAKS_PERCENTILE: 55
HOTSPOT_SCORE: 0.4066
HOTSPOT_PERCENTILE: 45
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.4071
POISSON_PERCENTILE: 48
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1058781_UW.Fetal_Muscle_Leg.H3K4me3.H-24644.Histone.DS21536.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS21536-Histone.DS21536.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Muscle Leg H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K4me3 ChIP-Seq read mappings from Fetal Muscle Leg, Donor H-24644, 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.16899
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 9
BROWSER_TRACK_NAME: FML H3K4me3 44 36
BROWSER_TRACK_DESCRIPTION: UW Fetal Muscle Leg Histone H3K4me3 Donor H-24644 Library Histone.DS21536 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 29,878,006
FINDPEAKS_SCORE: 0.4062
FINDPEAKS_PERCENTILE: 55
HOTSPOT_SCORE: 0.4066
HOTSPOT_PERCENTILE: 45
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.4071
POISSON_PERCENTILE: 48
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: Fetal Muscle, Leg primary tissue, day 110; Histone.DS21536

value: Fetal Muscle, Leg

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

value: Primary Tissue

value: UW

value: fetal

value: Histone H3K4me3

value: Invitrogen Dynabeads

value: Cell Signaling

value: lot 2


title: Histone H3K4me3 ChIP-Seq of CD3 Primary Cells; Histone.DS21703

description:
sample_term_id: CL_0000084
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Histone H3K4me3 ChIP-Seq
Library name: Histone.DS21703
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.14898
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.6984
****************
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: GSM1058782_UW.CD3_Primary_Cells.H3K4me3.RO_01701.Histone.DS21703.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS21703-Histone.DS21703.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of CD3 Primary Cells H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K4me3 ChIP-Seq on CD3 Primary Cells, Donor RO 01701, 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.16852
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 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 29,416,278
FINDPEAKS_SCORE: 0.4227
FINDPEAKS_PERCENTILE: 61
HOTSPOT_SCORE: 0.4231
HOTSPOT_PERCENTILE: 54
IROC_SCORE: 0.9999
IROC_PERCENTILE: 47
POISSON_SCORE: 0.4236
POISSON_PERCENTILE: 59
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

ANALYSIS FILE NAME: GSM1058782_UW.CD3_Primary_Cells.H3K4me3.RO_01701.Histone.DS21703.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS21703-Histone.DS21703.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of CD3 Primary Cells H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K4me3 ChIP-Seq read mappings from CD3 Primary Cells, Donor RO 01701, 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.16948
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 9
BROWSER_TRACK_NAME: CD3 H3K4me3 01 03
BROWSER_TRACK_DESCRIPTION: UW CD3 Primary Cells Histone H3K4me3 Donor RO 01701 Library Histone.DS21703 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 29,416,278
FINDPEAKS_SCORE: 0.4227
FINDPEAKS_PERCENTILE: 61
HOTSPOT_SCORE: 0.4231
HOTSPOT_PERCENTILE: 54
IROC_SCORE: 0.9999
IROC_PERCENTILE: 47
POISSON_SCORE: 0.4236
POISSON_PERCENTILE: 59
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

source_name: flow sorted CD3+ Cells, year 37; Histone.DS21703

value: CD3 Primary Cells

value: FHCRC HEIMFELD

value: year 37

value: Hispanic

value: Diagenode Bioruptor


title: Histone H3K4me3 ChIP-Seq of Fetal Intestine, Small; Histone.DS21533

description:
sample_term_id: UBERON_0002108
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Histone H3K4me3 ChIP-Seq
Library name: Histone.DS21533
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.14935
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.14909
****************
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: GSM1058780_UW.Fetal_Intestine_Small.H3K4me3.H-24595.Histone.DS21533.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS21533-Histone.DS21533.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Fetal Intestine Small H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K4me3 ChIP-Seq on Fetal Intestine Small, Donor H-24595, 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.16815
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 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 26,501,611
FINDPEAKS_SCORE: 0.4321
FINDPEAKS_PERCENTILE: 63
HOTSPOT_SCORE: 0.4378
HOTSPOT_PERCENTILE: 59
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.437
POISSON_PERCENTILE: 63
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1058780_UW.Fetal_Intestine_Small.H3K4me3.H-24595.Histone.DS21533.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS21533-Histone.DS21533.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Intestine Small H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K4me3 ChIP-Seq read mappings from Fetal Intestine Small, Donor H-24595, 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.16911
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 9
BROWSER_TRACK_NAME: FIS H3K4me3 95 33
BROWSER_TRACK_DESCRIPTION: UW Fetal Intestine Small Histone H3K4me3 Donor H-24595 Library Histone.DS21533 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 26,501,611
FINDPEAKS_SCORE: 0.4321
FINDPEAKS_PERCENTILE: 63
HOTSPOT_SCORE: 0.4378
HOTSPOT_PERCENTILE: 59
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.437
POISSON_PERCENTILE: 63
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: Fetal Intestine, Small primary tissue, day 108; Histone.DS21533

value: Fetal Intestine, Small

value: day 108

value: Male

value: 20-40 cycles of 0.5 minute on and 0.5 minute off


title: Histone H3K4me3 ChIP-Seq of Fetal Intestine, Large; Histone.DS21530

description:
sample_term_id: UBERON_0000059
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Histone H3K4me3 ChIP-Seq
Library name: Histone.DS21530
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.14950
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.14913
****************
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: GSM1058779_UW.Fetal_Intestine_Large.H3K4me3.H-24595.Histone.DS21530.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS21530-Histone.DS21530.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Fetal Intestine Large H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K4me3 ChIP-Seq on Fetal Intestine Large, Donor H-24595, 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.16835
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 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 20,655,791
FINDPEAKS_SCORE: 0.5016
FINDPEAKS_PERCENTILE: 82
HOTSPOT_SCORE: 0.5043
HOTSPOT_PERCENTILE: 75
IROC_SCORE: 0.9999
IROC_PERCENTILE: 47
POISSON_SCORE: 0.5017
POISSON_PERCENTILE: 77
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1058779_UW.Fetal_Intestine_Large.H3K4me3.H-24595.Histone.DS21530.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS21530-Histone.DS21530.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Intestine Large H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K4me3 ChIP-Seq read mappings from Fetal Intestine Large, Donor H-24595, 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.16931
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 9
BROWSER_TRACK_NAME: FIL H3K4me3 95 30
BROWSER_TRACK_DESCRIPTION: UW Fetal Intestine Large Histone H3K4me3 Donor H-24595 Library Histone.DS21530 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 20,655,791
FINDPEAKS_SCORE: 0.5016
FINDPEAKS_PERCENTILE: 82
HOTSPOT_SCORE: 0.5043
HOTSPOT_PERCENTILE: 75
IROC_SCORE: 0.9999
IROC_PERCENTILE: 47
POISSON_SCORE: 0.5017
POISSON_PERCENTILE: 77
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: Fetal Intestine, Large primary tissue, day 108; Histone.DS21530

value: Fetal Intestine, Large

value: genomic DNA

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


title: Histone H3K4me1 ChIP-Seq of Fetal Muscle, Leg; Histone.DS22558

description:
sample_term_id: UBERON_0001383
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Histone H3K4me1 ChIP-Seq
Library name: Histone.DS22558
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.14905
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.14904
****************
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: GSM1058777_UW.Fetal_Muscle_Leg.H3K4me1.H-24644.Histone.DS22558.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS22558-Histone.DS22558-Histone.DS22558.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Fetal Muscle Leg H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K4me1 ChIP-Seq on Fetal Muscle Leg, Donor H-24644, 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.16799
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 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 31,443,531
FINDPEAKS_SCORE: 0.4467
FINDPEAKS_PERCENTILE: 86
HOTSPOT_SCORE: 0.4952
HOTSPOT_PERCENTILE: 86
IROC_SCORE: 0.9946
IROC_PERCENTILE: 80
POISSON_SCORE: 0.5996
POISSON_PERCENTILE: 88
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1058777_UW.Fetal_Muscle_Leg.H3K4me1.H-24644.Histone.DS22558.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS22558-Histone.DS22558-Histone.DS22558.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Muscle Leg H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K4me1 ChIP-Seq read mappings from Fetal Muscle Leg, Donor H-24644, 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.16895
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 9
BROWSER_TRACK_NAME: FML H3K4me1 44 58
BROWSER_TRACK_DESCRIPTION: UW Fetal Muscle Leg Histone H3K4me1 Donor H-24644 Library Histone.DS22558 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 31,443,531
FINDPEAKS_SCORE: 0.4467
FINDPEAKS_PERCENTILE: 86
HOTSPOT_SCORE: 0.4952
HOTSPOT_PERCENTILE: 86
IROC_SCORE: 0.9946
IROC_PERCENTILE: 80
POISSON_SCORE: 0.5996
POISSON_PERCENTILE: 88
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: Fetal Muscle, Leg primary tissue, day 110; Histone.DS22558

value: Fetal Muscle, Leg

value: Primary Tissue

value: UW

value: fetal

value: day 110

value: Female

value: Histone H3K4me1

value: Millipore A/G agarose beads

value: 30ul A/G bead slurry

value: Active Motif


title: Histone H3K4me1 ChIP-Seq of CD3 Primary Cells; Histone.DS22561

description:
sample_term_id: CL_0000084
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Histone H3K4me1 ChIP-Seq
Library name: Histone.DS22561
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.14890
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.5322
****************
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: GSM1058778_UW.CD3_Primary_Cells.H3K4me1.RO_01679.Histone.DS22561.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS22561-Histone.DS22561-Histone.DS22561-Histone.DS22561.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of CD3 Primary Cells H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K4me1 ChIP-Seq on CD3 Primary Cells, Donor RO 01679, 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.16830
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 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 23,350,056
FINDPEAKS_SCORE: 0.6046
FINDPEAKS_PERCENTILE: 96
HOTSPOT_SCORE: 0.5861
HOTSPOT_PERCENTILE: 95
IROC_SCORE: 0.9994
IROC_PERCENTILE: 95
POISSON_SCORE: 0.6607
POISSON_PERCENTILE: 95
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

ANALYSIS FILE NAME: GSM1058778_UW.CD3_Primary_Cells.H3K4me1.RO_01679.Histone.DS22561.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS22561-Histone.DS22561-Histone.DS22561-Histone.DS22561.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of CD3 Primary Cells H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K4me1 ChIP-Seq read mappings from CD3 Primary Cells, Donor RO 01679, 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.16926
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 9
BROWSER_TRACK_NAME: CD3 H3K4me1 79 61
BROWSER_TRACK_DESCRIPTION: UW CD3 Primary Cells Histone H3K4me1 Donor RO 01679 Library Histone.DS22561 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 23,350,056
FINDPEAKS_SCORE: 0.6046
FINDPEAKS_PERCENTILE: 96
HOTSPOT_SCORE: 0.5861
HOTSPOT_PERCENTILE: 95
IROC_SCORE: 0.9994
IROC_PERCENTILE: 95
POISSON_SCORE: 0.6607
POISSON_PERCENTILE: 95
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

source_name: flow sorted CD3+ Cells,year 21; Histone.DS22561

value: CD3 Primary Cells

value: FHCRC HEIMFELD

value: Primary Cell

value: year 21

value: Caucasian

value: Diagenode Bioruptor


title: Histone H3K4me1 ChIP-Seq of Fetal Intestine, Large; Histone.DS22552

description:
sample_term_id: UBERON_0000059
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Histone H3K4me1 ChIP-Seq
Library name: Histone.DS22552
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.14914
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.14913
****************
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: GSM1058775_UW.Fetal_Intestine_Large.H3K4me1.H-24595.Histone.DS22552.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS22552-Histone.DS22552.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Fetal Intestine Large H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K4me1 ChIP-Seq on Fetal Intestine Large, Donor H-24595, 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.16865
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 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 26,727,023
FINDPEAKS_SCORE: 0.3648
FINDPEAKS_PERCENTILE: 70
HOTSPOT_SCORE: 0.4064
HOTSPOT_PERCENTILE: 68
IROC_SCORE: 0.9903
IROC_PERCENTILE: 73
POISSON_SCORE: 0.5219
POISSON_PERCENTILE: 68
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1058775_UW.Fetal_Intestine_Large.H3K4me1.H-24595.Histone.DS22552.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS22552-Histone.DS22552.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Intestine Large H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K4me1 ChIP-Seq read mappings from Fetal Intestine Large, Donor H-24595, 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.16961
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 9
BROWSER_TRACK_NAME: FIL H3K4me1 95 52
BROWSER_TRACK_DESCRIPTION: UW Fetal Intestine Large Histone H3K4me1 Donor H-24595 Library Histone.DS22552 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 26,727,023
FINDPEAKS_SCORE: 0.3648
FINDPEAKS_PERCENTILE: 70
HOTSPOT_SCORE: 0.4064
HOTSPOT_PERCENTILE: 68
IROC_SCORE: 0.9903
IROC_PERCENTILE: 73
POISSON_SCORE: 0.5219
POISSON_PERCENTILE: 68
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: Fetal Intestine, Large primary tissue, day 108; Histone.DS22552

value: Fetal Intestine, Large

value: genomic DNA

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

value: day 108

value: Male

value: 20-40 cycles of 0.5 minute on and 0.5 minute off


title: Histone H3K36me3 ChIP-Seq of CD3 Primary Cells; Histone.DS22563

description:
sample_term_id: CL_0000084
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Histone H3K36me3 ChIP-Seq
Library name: Histone.DS22563
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.14887
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.5322
****************
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: GSM1058774_UW.CD3_Primary_Cells.H3K36me3.RO_01679.Histone.DS22563.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS22563-Histone.DS22563.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of CD3 Primary Cells H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K36me3 ChIP-Seq on CD3 Primary Cells, Donor RO 01679, 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.16858
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 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 22,840,894
FINDPEAKS_SCORE: 0.4471
FINDPEAKS_PERCENTILE: 86
HOTSPOT_SCORE: 0.3826
HOTSPOT_PERCENTILE: 86
IROC_SCORE: 0.9955
IROC_PERCENTILE: 88
POISSON_SCORE: 0.613
POISSON_PERCENTILE: 88
MAXIMUM_REPLICATE_CORRELATION: 0.93

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

ANALYSIS FILE NAME: GSM1058774_UW.CD3_Primary_Cells.H3K36me3.RO_01679.Histone.DS22563.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS22563-Histone.DS22563.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of CD3 Primary Cells H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K36me3 ChIP-Seq read mappings from CD3 Primary Cells, Donor RO 01679, 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.16954
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 9
BROWSER_TRACK_NAME: CD3 H3K36me3 79 63
BROWSER_TRACK_DESCRIPTION: UW CD3 Primary Cells Histone H3K36me3 Donor RO 01679 Library Histone.DS22563 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 22,840,894
FINDPEAKS_SCORE: 0.4471
FINDPEAKS_PERCENTILE: 86
HOTSPOT_SCORE: 0.3826
HOTSPOT_PERCENTILE: 86
IROC_SCORE: 0.9955
IROC_PERCENTILE: 88
POISSON_SCORE: 0.613
POISSON_PERCENTILE: 88
MAXIMUM_REPLICATE_CORRELATION: 0.93

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

source_name: flow sorted CD3+ Cells,year 21; Histone.DS22563

value: Histone H3K36me3


title: Histone H3K36me3 ChIP-Seq of Fetal Intestine, Small; Histone.DS22557

description:
sample_term_id: UBERON_0002108
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Histone H3K36me3 ChIP-Seq
Library name: Histone.DS22557
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.14924
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.14909
****************
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: GSM1058772_UW.Fetal_Intestine_Small.H3K36me3.H-24595.Histone.DS22557.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS22557-Histone.DS22557-Histone.DS22557-Histone.DS22557.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Fetal Intestine Small H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K36me3 ChIP-Seq on Fetal Intestine Small, Donor H-24595, 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.16821
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 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 36,230,212
FINDPEAKS_SCORE: 0.4789
FINDPEAKS_PERCENTILE: 90
HOTSPOT_SCORE: 0.4412
HOTSPOT_PERCENTILE: 91
IROC_SCORE: 0.9962
IROC_PERCENTILE: 90
POISSON_SCORE: 0.6092
POISSON_PERCENTILE: 84
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1058772_UW.Fetal_Intestine_Small.H3K36me3.H-24595.Histone.DS22557.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS22557-Histone.DS22557-Histone.DS22557-Histone.DS22557.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Intestine Small H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K36me3 ChIP-Seq read mappings from Fetal Intestine Small, Donor H-24595, 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.16917
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 9
BROWSER_TRACK_NAME: FIS H3K36me3 95 57
BROWSER_TRACK_DESCRIPTION: UW Fetal Intestine Small Histone H3K36me3 Donor H-24595 Library Histone.DS22557 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 36,230,212
FINDPEAKS_SCORE: 0.4789
FINDPEAKS_PERCENTILE: 90
HOTSPOT_SCORE: 0.4412
HOTSPOT_PERCENTILE: 91
IROC_SCORE: 0.9962
IROC_PERCENTILE: 90
POISSON_SCORE: 0.6092
POISSON_PERCENTILE: 84
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: Fetal Intestine, Small primary tissue, day 108; Histone.DS22557

value: Fetal Intestine, Small

value: Primary Tissue

value: UW

value: fetal


title: RNA-Seq (Total RNA) Fetal Heart; RNA.RS20082

description:
sample_term_id: UBERON_0000948
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: RNA-Seq (Total RNA) Fetal Heart
Library name: lib-RNA.RS20082
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15251
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.11599
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing: Various levels of processed data files will be made available as this project proceeds.

source_name: Fetal Heart primary tissue, day 120; RNA.RS20082

value: Fetal Heart

value: day 120

value: mRNA-Seq

value: Ambion mirVana miRNA isolation kit

value: Part of Library Prep, Truseq RNA-Seq Sample Prep Kit

value: Random Primers(hexamers)

value: TruSeq RNA

value: cDNA

value: Proprietary

value: 98C 30 sec, 15 cycles of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold


title: Histone H3K36me3 ChIP-Seq of Fetal Intestine, Large; Histone.DS22554

description:
sample_term_id: UBERON_0000059
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Histone H3K36me3 ChIP-Seq
Library name: Histone.DS22554
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.14941
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.14913
****************
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: GSM1058771_UW.Fetal_Intestine_Large.H3K36me3.H-24595.Histone.DS22554.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS22554-Histone.DS22554.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Fetal Intestine Large H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K36me3 ChIP-Seq on Fetal Intestine Large, Donor H-24595, 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.16810
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 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 24,228,739
FINDPEAKS_SCORE: 0.2889
FINDPEAKS_PERCENTILE: 55
HOTSPOT_SCORE: 0.3036
HOTSPOT_PERCENTILE: 53
IROC_SCORE: 0.975
IROC_PERCENTILE: 45
POISSON_SCORE: 0.5186
POISSON_PERCENTILE: 60
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM1058771_UW.Fetal_Intestine_Large.H3K36me3.H-24595.Histone.DS22554.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS22554-Histone.DS22554.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Intestine Large H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K36me3 ChIP-Seq read mappings from Fetal Intestine Large, Donor H-24595, 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.16906
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 9
BROWSER_TRACK_NAME: FIL H3K36me3 95 54
BROWSER_TRACK_DESCRIPTION: UW Fetal Intestine Large Histone H3K36me3 Donor H-24595 Library Histone.DS22554 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 24,228,739
FINDPEAKS_SCORE: 0.2889
FINDPEAKS_PERCENTILE: 55
HOTSPOT_SCORE: 0.3036
HOTSPOT_PERCENTILE: 53
IROC_SCORE: 0.975
IROC_PERCENTILE: 45
POISSON_SCORE: 0.5186
POISSON_PERCENTILE: 60
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

source_name: Fetal Intestine, Large primary tissue, day 108; Histone.DS22554

value: Fetal Intestine, Large

value: genomic DNA

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

value: day 108

value: Male

value: Diagenode Bioruptor

value: Millipore A/G agarose beads

value: 30ul A/G bead slurry

value: Active Motif


title: RNA-Seq (Total RNA) CD4 Primary Cells; RNA.RS19106

description:
sample_term_id: CL_0000492
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: RNA-Seq (Total RNA) CD4 Primary Cells
Library name: lib-RNA.RS19106
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15119
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.5345
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

source_name: flow sorted CD4+ Cells,year 21; RNA.RS19106

value: CD4 Primary Cells

value: FHCRC HEIMFELD

value: Primary Cell

value: year 21

value: Caucasian

value: mRNA-Seq

value: Ambion Ribopure


title: Histone H3K27me3 ChIP-Seq of Fetal Intestine, Small; Histone.DS22556

description:
sample_term_id: UBERON_0002108
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Histone H3K27me3 ChIP-Seq
Library name: Histone.DS22556
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.14929
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.14909
****************
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: GSM1058769_UW.Fetal_Intestine_Small.H3K27me3.H-24595.Histone.DS22556.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS22556-Histone.DS22556.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Fetal Intestine Small H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27me3 ChIP-Seq on Fetal Intestine Small, Donor H-24595, 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.16805
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 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 21,198,238
FINDPEAKS_SCORE: 0.1244
FINDPEAKS_PERCENTILE: 73
HOTSPOT_SCORE: 0.219
HOTSPOT_PERCENTILE: 66
IROC_SCORE: 0.94
IROC_PERCENTILE: 69
POISSON_SCORE: 0.3349
POISSON_PERCENTILE: 46
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1058769_UW.Fetal_Intestine_Small.H3K27me3.H-24595.Histone.DS22556.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS22556-Histone.DS22556.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Intestine Small H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27me3 ChIP-Seq read mappings from Fetal Intestine Small, Donor H-24595, 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.16901
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 9
BROWSER_TRACK_NAME: FIS H3K27me3 95 56
BROWSER_TRACK_DESCRIPTION: UW Fetal Intestine Small Histone H3K27me3 Donor H-24595 Library Histone.DS22556 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 21,198,238
FINDPEAKS_SCORE: 0.1244
FINDPEAKS_PERCENTILE: 73
HOTSPOT_SCORE: 0.219
HOTSPOT_PERCENTILE: 66
IROC_SCORE: 0.94
IROC_PERCENTILE: 69
POISSON_SCORE: 0.3349
POISSON_PERCENTILE: 46
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: Fetal Intestine, Small primary tissue, day 108; Histone.DS22556

value: Fetal Intestine, Small

value: Primary Tissue

value: UW

value: fetal

value: Histone H3K27me3

value: 20-40 cycles of 0.5 minute on and 0.5 minute off

value: Millipore


title: Histone H3K27ac ChIP-Seq of Fetal Muscle, Leg; Histone.DS21782

description:
sample_term_id: UBERON_0001383
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Histone H3K27ac ChIP-Seq
Library name: Histone.DS21782
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.14966
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.14904
****************
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: GSM1058767_UW.Fetal_Muscle_Leg.H3K27ac.H-24644.Histone.DS21782.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS21782-Histone.DS21782.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Fetal Muscle Leg H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27ac ChIP-Seq on Fetal Muscle Leg, Donor H-24644, 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.16850
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 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 26,118,255
FINDPEAKS_SCORE: 0.4844
FINDPEAKS_PERCENTILE: 73
HOTSPOT_SCORE: 0.5044
HOTSPOT_PERCENTILE: 73
IROC_SCORE: 0.9976
IROC_PERCENTILE: 68
POISSON_SCORE: 0.5578
POISSON_PERCENTILE: 72
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1058767_UW.Fetal_Muscle_Leg.H3K27ac.H-24644.Histone.DS21782.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS21782-Histone.DS21782.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Muscle Leg H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27ac ChIP-Seq read mappings from Fetal Muscle Leg, Donor H-24644, 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.16946
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 9
BROWSER_TRACK_NAME: FML H3K27ac 44 82
BROWSER_TRACK_DESCRIPTION: UW Fetal Muscle Leg Histone H3K27ac Donor H-24644 Library Histone.DS21782 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 26,118,255
FINDPEAKS_SCORE: 0.4844
FINDPEAKS_PERCENTILE: 73
HOTSPOT_SCORE: 0.5044
HOTSPOT_PERCENTILE: 73
IROC_SCORE: 0.9976
IROC_PERCENTILE: 68
POISSON_SCORE: 0.5578
POISSON_PERCENTILE: 72
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: Fetal Muscle, Leg primary tissue, day 110; Histone.DS21782

value: Fetal Muscle, Leg

value: genomic DNA

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

value: day 110

value: Female

value: Histone H3K27ac

value: Diagenode Bioruptor

value: Invitrogen Dynabeads


title: Histone H3K27ac ChIP-Seq of Fetal Intestine, Small; Histone.DS21781

description:
sample_term_id: UBERON_0002108
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Histone H3K27ac ChIP-Seq
Library name: Histone.DS21781
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.14932
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.14909
****************
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: GSM1058766_UW.Fetal_Intestine_Small.H3K27ac.H-24595.Histone.DS21781.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS21781-Histone.DS21781.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Fetal Intestine Small H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27ac ChIP-Seq on Fetal Intestine Small, Donor H-24595, 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.16801
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 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 29,713,085
FINDPEAKS_SCORE: 0.5628
FINDPEAKS_PERCENTILE: 84
HOTSPOT_SCORE: 0.5681
HOTSPOT_PERCENTILE: 82
IROC_SCORE: 0.9992
IROC_PERCENTILE: 86
POISSON_SCORE: 0.6114
POISSON_PERCENTILE: 81
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1058766_UW.Fetal_Intestine_Small.H3K27ac.H-24595.Histone.DS21781.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS21781-Histone.DS21781.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Intestine Small H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27ac ChIP-Seq read mappings from Fetal Intestine Small, Donor H-24595, 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.16897
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 9
BROWSER_TRACK_NAME: FIS H3K27ac 95 81
BROWSER_TRACK_DESCRIPTION: UW Fetal Intestine Small Histone H3K27ac Donor H-24595 Library Histone.DS21781 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 29,713,085
FINDPEAKS_SCORE: 0.5628
FINDPEAKS_PERCENTILE: 84
HOTSPOT_SCORE: 0.5681
HOTSPOT_PERCENTILE: 82
IROC_SCORE: 0.9992
IROC_PERCENTILE: 86
POISSON_SCORE: 0.6114
POISSON_PERCENTILE: 81
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: Fetal Intestine, Small primary tissue, day 108; Histone.DS21781

value: day 108

value: Male

value: Active Motif