title: ChIP-Seq Input of CD8 Primary Cells; Histone.DS21542

description:
sample_term_id: CL_0000625
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Input
Library name: Histone.DS21542
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15762
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.5352
****************
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: GSM1102806_UW.CD8_Primary_Cells.Input.RO_01679.Histone.DS21542.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS21542-Histone.DS21542-Histone.DS21542.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of CD8 Primary Cells Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Input ChIP-Seq on CD8 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.16866
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: 41,601,419
FINDPEAKS_SCORE: 0.0045
FINDPEAKS_PERCENTILE: 23
HOTSPOT_SCORE: 0.0029
HOTSPOT_PERCENTILE: 9
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.0248
POISSON_PERCENTILE: 15
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1102806_UW.CD8_Primary_Cells.Input.RO_01679.Histone.DS21542.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS21542-Histone.DS21542-Histone.DS21542.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of CD8 Primary Cells Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Input ChIP-Seq read mappings from CD8 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.16962
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: CD8 Input 79 42
BROWSER_TRACK_DESCRIPTION: UW CD8 Primary Cells ChIP-Seq Input Donor RO 01679 Library Histone.DS21542 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 41,601,419
FINDPEAKS_SCORE: 0.0045
FINDPEAKS_PERCENTILE: 23
HOTSPOT_SCORE: 0.0029
HOTSPOT_PERCENTILE: 9
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.0248
POISSON_PERCENTILE: 15
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: flow sorted CD8+ Cells,year 21; Histone.DS21542

value: ChIP-Seq Input

value: Input


title: CX137_SSRP1_ChIPSeq 3

status: Public on Mar 22 2013

type: SRA

city: Buffalo

first: Robert

middle: William

last: Leach

state: NY

address: 701 Ellicott Street

department: Center for Computational Research

country: USA

institute: Center of Excellence in Bioinformatics

library_source: genomic

data_processing:
Basecalls performed using CASAVA version 1.8.2
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using bowtie v0.12.7 with parameters -n 1 -m 1 -e 70 -l 28 -k 1 -t -p 8 -q -S —best
Control bam files were merged using bamtools merge, version 1.0.2 using default parameters
Peaks were called using PeakRanger, version 1.16, with parameters ccat --format bam -l 300
Genome_build: hg19
Supplementary_files_format_and_content: The *summit.bed files are tab delimited text files containing coordinates of peak summits of androgen receptor binding sites in the absence/presence of curaxin
Supplementary_files_format_and_content: The *region.bed files are tab delimited text files containing coordinates of peak regions of androgen receptor binding sites in the absence/presence of curaxin

molecule: genomic DNA

organism: Homo sapiens

source_name: HT1080 human fibrosarcoma cells

growth_protocol: HT1080 cells were maintaned in DMEM with 10% FBS, 1% pen-strep, used at a confluency 80%

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with SSRP1 antibody.
ChIP isolated DNA was treated using the standard ChIP-seq protocol from Illumina with the following modification.  After adaptor ligation the library was separated on a 2% agarose gel and the 150 to 500 bp region was excised and purified.  This larger excision region allows successfully sequencing libraries from low quality (< 10 ng) ChIP samples.

treatment_protocol: HT1080 cells were treated with 3 uM CX 137 for 1 hour

tag: tissue origin

value: derived from biopsy of fibrosarcoma of Human male

tag: treatment

value: curaxin

tag: antibody

value: SSRP1 (Biolegend, cat#609702, clone:10D1)


title: input DNA 2

value: none, input


title: Histone H3K4me3 ChIP-Seq of Fetal Stomach; Histone.DS22598

city: Seattle

first: Northwest

last: REMC

state: WA

institute: University of Washington

description:
sample_term_id: UBERON_0000945
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Histone H3K4me3 ChIP-Seq
Library name: Histone.DS22598
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15716
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.15694
****************
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: GSM1102800_UW.Fetal_Stomach.H3K4me3.H-24639.Histone.DS22598.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS22598-Histone.DS22598.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Fetal Stomach H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K4me3 ChIP-Seq on Fetal Stomach, Donor H-24639, 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.16846
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: 27,913,248
FINDPEAKS_SCORE: 0.3889
FINDPEAKS_PERCENTILE: 48
HOTSPOT_SCORE: 0.3901
HOTSPOT_PERCENTILE: 41
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.3898
POISSON_PERCENTILE: 43
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1102800_UW.Fetal_Stomach.H3K4me3.H-24639.Histone.DS22598.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS22598-Histone.DS22598.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Stomach H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K4me3 ChIP-Seq read mappings from Fetal Stomach, Donor H-24639, 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.16942
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: FS H3K4me3 39 98
BROWSER_TRACK_DESCRIPTION: UW Fetal Stomach Histone H3K4me3 Donor H-24639 Library Histone.DS22598 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 27,913,248
FINDPEAKS_SCORE: 0.3889
FINDPEAKS_PERCENTILE: 48
HOTSPOT_SCORE: 0.3901
HOTSPOT_PERCENTILE: 41
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.3898
POISSON_PERCENTILE: 43
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: Fetal Stomach primary tissue, day 98; Histone.DS22598

extract_protocol: Library construction protocol: Single read - Illumina

tag: sample alias

tag: sample common name

value: Fetal Stomach

tag: molecule

value: genomic DNA

tag: disease

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

value: Primary Tissue

value: UW

value: fetal

value: day 98

value: Female

value: Histone H3K4me3

value: Diagenode Bioruptor

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

value: Invitrogen Dynabeads

value: Cell Signaling

value: lot 2


title: Histone H3K4me1 ChIP-Seq of Fetal Adrenal Gland; Histone.DS23065

description:
sample_term_id: UBERON_0002369
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Histone H3K4me1 ChIP-Seq
Library name: Histone.DS23065
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15683
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.15682
****************
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: GSM1102796_UW.Fetal_Adrenal_Gland.H3K4me1.H-24800.Histone.DS23065.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS23065-Histone.DS23065.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Fetal Adrenal Gland H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K4me1 ChIP-Seq on Fetal Adrenal Gland, Donor H-24800, 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.16802
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: 27,556,533
FINDPEAKS_SCORE: 0.4625
FINDPEAKS_PERCENTILE: 88
HOTSPOT_SCORE: 0.4978
HOTSPOT_PERCENTILE: 88
IROC_SCORE: 0.9945
IROC_PERCENTILE: 79
POISSON_SCORE: 0.6108
POISSON_PERCENTILE: 91
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1102796_UW.Fetal_Adrenal_Gland.H3K4me1.H-24800.Histone.DS23065.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS23065-Histone.DS23065.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Adrenal Gland H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K4me1 ChIP-Seq read mappings from Fetal Adrenal Gland, Donor H-24800, 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.16898
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: FAG H3K4me1 00 65
BROWSER_TRACK_DESCRIPTION: UW Fetal Adrenal Gland Histone H3K4me1 Donor H-24800 Library Histone.DS23065 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 27,556,533
FINDPEAKS_SCORE: 0.4625
FINDPEAKS_PERCENTILE: 88
HOTSPOT_SCORE: 0.4978
HOTSPOT_PERCENTILE: 88
IROC_SCORE: 0.9945
IROC_PERCENTILE: 79
POISSON_SCORE: 0.6108
POISSON_PERCENTILE: 91
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: Fetal Adrenal Gland primary tissue, day 97; Histone.DS23065

value: Fetal Adrenal Gland

value: day 97

value: Male

value: Histone H3K4me1

value: Millipore A/G agarose beads

value: 30ul A/G bead slurry

value: Active Motif


title: Histone H3K36me3 ChIP-Seq of Fetal Placenta; Histone.DS23030

description:
sample_term_id: UBERON_0001987
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Histone H3K36me3 ChIP-Seq
Library name: Histone.DS23030
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15719
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.15690
****************
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: GSM1102792_UW.Fetal_Placenta.H3K36me3.H-24996.Histone.DS23030.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS23030-Histone.DS23030.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Fetal Placenta H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K36me3 ChIP-Seq on Fetal Placenta, Donor H-24996, 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.16871
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: 22,191,908
FINDPEAKS_SCORE: 0.3908
FINDPEAKS_PERCENTILE: 79
HOTSPOT_SCORE: 0.3475
HOTSPOT_PERCENTILE: 71
IROC_SCORE: 0.9929
IROC_PERCENTILE: 79
POISSON_SCORE: 0.5685
POISSON_PERCENTILE: 76
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1102792_UW.Fetal_Placenta.H3K36me3.H-24996.Histone.DS23030.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS23030-Histone.DS23030.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Placenta H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K36me3 ChIP-Seq read mappings from Fetal Placenta, Donor H-24996, 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.16967
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: FP H3K36me3 96 30
BROWSER_TRACK_DESCRIPTION: UW Fetal Placenta Histone H3K36me3 Donor H-24996 Library Histone.DS23030 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 22,191,908
FINDPEAKS_SCORE: 0.3908
FINDPEAKS_PERCENTILE: 79
HOTSPOT_SCORE: 0.3475
HOTSPOT_PERCENTILE: 71
IROC_SCORE: 0.9929
IROC_PERCENTILE: 79
POISSON_SCORE: 0.5685
POISSON_PERCENTILE: 76
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: Fetal Placenta primary tissue, day 113; Histone.DS23030

value: Fetal Placenta

value: genomic DNA

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

value: Primary Tissue

value: UW

value: day 113

value: Histone H3K36me3


title: Histone H3K4me1 ChIP-Seq of Fetal Stomach; Histone.DS22597

description:
sample_term_id: UBERON_0000945
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Histone H3K4me1 ChIP-Seq
Library name: Histone.DS22597
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15706
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.15709
****************
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: GSM1102794_UW.Fetal_Stomach.H3K4me1.H-24776.Histone.DS22597.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS22597-Histone.DS22597.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Fetal Stomach H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K4me1 ChIP-Seq on Fetal Stomach, Donor H-24776, 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.16864
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: 26,676,841
FINDPEAKS_SCORE: 0.2751
FINDPEAKS_PERCENTILE: 54
HOTSPOT_SCORE: 0.3362
HOTSPOT_PERCENTILE: 54
IROC_SCORE: 0.9777
IROC_PERCENTILE: 55
POISSON_SCORE: 0.4668
POISSON_PERCENTILE: 54
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1102794_UW.Fetal_Stomach.H3K4me1.H-24776.Histone.DS22597.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS22597-Histone.DS22597.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Stomach H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K4me1 ChIP-Seq read mappings from Fetal Stomach, Donor H-24776, 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.16960
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: FS H3K4me1 76 97
BROWSER_TRACK_DESCRIPTION: UW Fetal Stomach Histone H3K4me1 Donor H-24776 Library Histone.DS22597 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 26,676,841
FINDPEAKS_SCORE: 0.2751
FINDPEAKS_PERCENTILE: 54
HOTSPOT_SCORE: 0.3362
HOTSPOT_PERCENTILE: 54
IROC_SCORE: 0.9777
IROC_PERCENTILE: 55
POISSON_SCORE: 0.4668
POISSON_PERCENTILE: 54
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: Fetal Stomach primary tissue, day 96; Histone.DS22597

value: Fetal Stomach

value: fetal

value: day 96

value: Female

value: Diagenode Bioruptor

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


title: Histone H3K4me1 ChIP-Seq of CD14 Primary Cells; Histone.DS22403

description:
sample_term_id: CL_0001054
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Histone H3K4me1 ChIP-Seq
Library name: Histone.DS22403
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15722
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.5355
****************
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: GSM1102793_UW.CD14_Primary_Cells.H3K4me1.RO_01721.Histone.DS22403.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS22403-Histone.DS22403-Histone.DS22403.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of CD14 Primary Cells H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K4me1 ChIP-Seq on CD14 Primary Cells, Donor RO 01721, 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.16824
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: 30,987,045
FINDPEAKS_SCORE: 0.7488
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.7147
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9999
IROC_PERCENTILE: 100
POISSON_SCORE: 0.778
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1102793_UW.CD14_Primary_Cells.H3K4me1.RO_01721.Histone.DS22403.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS22403-Histone.DS22403-Histone.DS22403.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of CD14 Primary Cells H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K4me1 ChIP-Seq read mappings from CD14 Primary Cells, Donor RO 01721, 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.16920
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: CD14 H3K4me1 21 03
BROWSER_TRACK_DESCRIPTION: UW CD14 Primary Cells Histone H3K4me1 Donor RO 01721 Library Histone.DS22403 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 30,987,045
FINDPEAKS_SCORE: 0.7488
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.7147
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9999
IROC_PERCENTILE: 100
POISSON_SCORE: 0.778
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: flow sorted CD14+ Cells,year 21; Histone.DS22403

value: CD14 Primary Cells

value: FHCRC HEIMFELD

value: Primary Cell

tag: markers

value: year 21

value: Male

value: Caucasian

value: Histone H3K4me1


title: Histone H3K4me1 ChIP-Seq of Fetal Placenta; Histone.DS23027

description:
sample_term_id: UBERON_0001987
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Histone H3K4me1 ChIP-Seq
Library name: Histone.DS23027
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15691
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.15690
****************
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: GSM1102795_UW.Fetal_Placenta.H3K4me1.H-24996.Histone.DS23027.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS23027-Histone.DS23027.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Fetal Placenta H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K4me1 ChIP-Seq on Fetal Placenta, Donor H-24996, 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.16797
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: 26,600,392
FINDPEAKS_SCORE: 0.3656
FINDPEAKS_PERCENTILE: 71
HOTSPOT_SCORE: 0.4161
HOTSPOT_PERCENTILE: 71
IROC_SCORE: 0.9903
IROC_PERCENTILE: 73
POISSON_SCORE: 0.534
POISSON_PERCENTILE: 71
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1102795_UW.Fetal_Placenta.H3K4me1.H-24996.Histone.DS23027.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS23027-Histone.DS23027.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Placenta H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K4me1 ChIP-Seq read mappings from Fetal Placenta, Donor H-24996, 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.16893
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: FP H3K4me1 96 27
BROWSER_TRACK_DESCRIPTION: UW Fetal Placenta Histone H3K4me1 Donor H-24996 Library Histone.DS23027 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 26,600,392
FINDPEAKS_SCORE: 0.3656
FINDPEAKS_PERCENTILE: 71
HOTSPOT_SCORE: 0.4161
HOTSPOT_PERCENTILE: 71
IROC_SCORE: 0.9903
IROC_PERCENTILE: 73
POISSON_SCORE: 0.534
POISSON_PERCENTILE: 71
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: Fetal Placenta primary tissue, day 113; Histone.DS23027

value: Fetal Placenta

value: genomic DNA

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

value: Primary Tissue

value: Millipore A/G agarose beads

value: 30ul A/G bead slurry

value: Active Motif


title: Histone H3K36me3 ChIP-Seq of Fetal Stomach; Histone.DS22600

description:
sample_term_id: UBERON_0000945
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Histone H3K36me3 ChIP-Seq
Library name: Histone.DS22600
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15713
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.15694
****************
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: GSM1102789_UW.Fetal_Stomach.H3K36me3.H-24639.Histone.DS22600.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS22600-Histone.DS22600.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Fetal Stomach H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K36me3 ChIP-Seq on Fetal Stomach, Donor H-24639, 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.16813
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: 32,293,579
FINDPEAKS_SCORE: 0.4972
FINDPEAKS_PERCENTILE: 91
HOTSPOT_SCORE: 0.4558
HOTSPOT_PERCENTILE: 93
IROC_SCORE: 0.9976
IROC_PERCENTILE: 95
POISSON_SCORE: 0.6204
POISSON_PERCENTILE: 91
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1102789_UW.Fetal_Stomach.H3K36me3.H-24639.Histone.DS22600.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS22600-Histone.DS22600.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Stomach H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K36me3 ChIP-Seq read mappings from Fetal Stomach, Donor H-24639, 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.16909
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: FS H3K36me3 39 00
BROWSER_TRACK_DESCRIPTION: UW Fetal Stomach Histone H3K36me3 Donor H-24639 Library Histone.DS22600 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 32,293,579
FINDPEAKS_SCORE: 0.4972
FINDPEAKS_PERCENTILE: 91
HOTSPOT_SCORE: 0.4558
HOTSPOT_PERCENTILE: 93
IROC_SCORE: 0.9976
IROC_PERCENTILE: 95
POISSON_SCORE: 0.6204
POISSON_PERCENTILE: 91
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: Fetal Stomach primary tissue, day 98; Histone.DS22600

value: Fetal Stomach

value: UW

value: fetal

value: day 98

value: Female

value: Histone H3K36me3


title: Histone H3K36me3 ChIP-Seq of CD8 Primary Cells; Histone.DS22910

description:
sample_term_id: CL_0000625
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Histone H3K36me3 ChIP-Seq
Library name: Histone.DS22910
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15749
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
****************

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

ANALYSIS FILE NAME: GSM1102791_UW.CD8_Primary_Cells.H3K36me3.RO_01701.Histone.DS22910.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS22910-Histone.DS22910-Histone.DS22910.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of CD8 Primary Cells H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K36me3 ChIP-Seq on CD8 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.16886
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: 30,152,543
FINDPEAKS_SCORE: 0.1905
FINDPEAKS_PERCENTILE: 33
HOTSPOT_SCORE: 0.2082
HOTSPOT_PERCENTILE: 16
IROC_SCORE: 0.9668
IROC_PERCENTILE: 41
POISSON_SCORE: 0.4273
POISSON_PERCENTILE: 31
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1102791_UW.CD8_Primary_Cells.H3K36me3.RO_01701.Histone.DS22910.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS22910-Histone.DS22910-Histone.DS22910.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of CD8 Primary Cells H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K36me3 ChIP-Seq read mappings from CD8 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.16982
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: CD8 H3K36me3 01 10
BROWSER_TRACK_DESCRIPTION: UW CD8 Primary Cells Histone H3K36me3 Donor RO 01701 Library Histone.DS22910 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 30,152,543
FINDPEAKS_SCORE: 0.1905
FINDPEAKS_PERCENTILE: 33
HOTSPOT_SCORE: 0.2082
HOTSPOT_PERCENTILE: 16
IROC_SCORE: 0.9668
IROC_PERCENTILE: 41
POISSON_SCORE: 0.4273
POISSON_PERCENTILE: 31
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: flow sorted CD8+ Cells, year 37; Histone.DS22910

value: CD8 Primary Cells

value: FHCRC HEIMFELD

value: Primary Cell

value: year 37

value: Hispanic

value: Diagenode Bioruptor

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


title: Histone H3K27me3 ChIP-Seq of Fetal Stomach; Histone.DS22599

description:
sample_term_id: UBERON_0000945
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Histone H3K27me3 ChIP-Seq
Library name: Histone.DS22599
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15710
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.15709
****************
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: GSM1102786_UW.Fetal_Stomach.H3K27me3.H-24776.Histone.DS22599.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS22599-Histone.DS22599.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Fetal Stomach H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27me3 ChIP-Seq on Fetal Stomach, Donor H-24776, 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.16838
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: 21,373,139
FINDPEAKS_SCORE: 0.4357
FINDPEAKS_PERCENTILE: 96
HOTSPOT_SCORE: 0.4767
HOTSPOT_PERCENTILE: 96
IROC_SCORE: 0.9717
IROC_PERCENTILE: 83
POISSON_SCORE: 0.5769
POISSON_PERCENTILE: 95
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1102786_UW.Fetal_Stomach.H3K27me3.H-24776.Histone.DS22599.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS22599-Histone.DS22599.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Stomach H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27me3 ChIP-Seq read mappings from Fetal Stomach, Donor H-24776, 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.16934
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: FS H3K27me3 76 99
BROWSER_TRACK_DESCRIPTION: UW Fetal Stomach Histone H3K27me3 Donor H-24776 Library Histone.DS22599 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 21,373,139
FINDPEAKS_SCORE: 0.4357
FINDPEAKS_PERCENTILE: 96
HOTSPOT_SCORE: 0.4767
HOTSPOT_PERCENTILE: 96
IROC_SCORE: 0.9717
IROC_PERCENTILE: 83
POISSON_SCORE: 0.5769
POISSON_PERCENTILE: 95
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: Fetal Stomach primary tissue, day 96; Histone.DS22599

value: genomic DNA

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

value: Primary Tissue

value: day 96

value: Histone H3K27me3

value: Millipore


title: Histone H3K36me3 ChIP-Seq of CD14 Primary Cells; Histone.DS22406

description:
sample_term_id: CL_0001054
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Histone H3K36me3 ChIP-Seq
Library name: Histone.DS22406
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15735
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.5355
****************
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: GSM1102788_UW.CD14_Primary_Cells.H3K36me3.RO_01721.Histone.DS22406.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS22406.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of CD14 Primary Cells H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K36me3 ChIP-Seq on CD14 Primary Cells, Donor RO 01721, 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.16879
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: 20,547,010
FINDPEAKS_SCORE: 0.6281
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.5053
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9995
IROC_PERCENTILE: 100
POISSON_SCORE: 0.7198
POISSON_PERCENTILE: 98
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1102788_UW.CD14_Primary_Cells.H3K36me3.RO_01721.Histone.DS22406.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS22406.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of CD14 Primary Cells H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K36me3 ChIP-Seq read mappings from CD14 Primary Cells, Donor RO 01721, 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.16975
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: CD14 H3K36me3 21 06
BROWSER_TRACK_DESCRIPTION: UW CD14 Primary Cells Histone H3K36me3 Donor RO 01721 Library Histone.DS22406 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 20,547,010
FINDPEAKS_SCORE: 0.6281
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.5053
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9995
IROC_PERCENTILE: 100
POISSON_SCORE: 0.7198
POISSON_PERCENTILE: 98
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: flow sorted CD14+ Cells,year 21; Histone.DS22406

value: CD14 Primary Cells

value: year 21

value: Male

value: Caucasian

value: Millipore A/G agarose beads

value: 30ul A/G bead slurry

value: Active Motif


title: Histone H3K36me3 ChIP-Seq of CD4 Primary Cells; Histone.DS22906

description:
sample_term_id: CL_0000492
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Histone H3K36me3 ChIP-Seq
Library name: Histone.DS22906
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15766
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.7018
****************
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: GSM1102790_UW.CD4_Primary_Cells.H3K36me3.RO_01701.Histone.DS22906.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS22906-Histone.DS22906-Histone.DS22906.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of CD4 Primary Cells H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K36me3 ChIP-Seq on CD4 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.16818
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: 30,262,568
FINDPEAKS_SCORE: 0.4348
FINDPEAKS_PERCENTILE: 83
HOTSPOT_SCORE: 0.333
HOTSPOT_PERCENTILE: 66
IROC_SCORE: 0.9947
IROC_PERCENTILE: 86
POISSON_SCORE: 0.6127
POISSON_PERCENTILE: 86
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1102790_UW.CD4_Primary_Cells.H3K36me3.RO_01701.Histone.DS22906.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS22906-Histone.DS22906-Histone.DS22906.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of CD4 Primary Cells H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K36me3 ChIP-Seq read mappings from CD4 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.16914
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: CD4 H3K36me3 01 06
BROWSER_TRACK_DESCRIPTION: UW CD4 Primary Cells Histone H3K36me3 Donor RO 01701 Library Histone.DS22906 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 30,262,568
FINDPEAKS_SCORE: 0.4348
FINDPEAKS_PERCENTILE: 83
HOTSPOT_SCORE: 0.333
HOTSPOT_PERCENTILE: 66
IROC_SCORE: 0.9947
IROC_PERCENTILE: 86
POISSON_SCORE: 0.6127
POISSON_PERCENTILE: 86
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: flow sorted CD4+ Cells, year 37; Histone.DS22906

value: CD4 Primary Cells

value: FHCRC HEIMFELD

value: Primary Cell

value: year 37

value: Histone H3K36me3


title: Histone H3K27ac ChIP-Seq of Fetal Placenta; Histone.DS23301

description:
sample_term_id: UBERON_0001987
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Histone H3K27ac ChIP-Seq
Library name: Histone.DS23301
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15726
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.15690
****************
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: GSM1102784_UW.Fetal_Placenta.H3K27ac.H-24996.Histone.DS23301.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS23301-Histone.DS23301.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Fetal Placenta H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27ac ChIP-Seq on Fetal Placenta, Donor H-24996, 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.16884
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: 21,653,271
FINDPEAKS_SCORE: 0.4258
FINDPEAKS_PERCENTILE: 65
HOTSPOT_SCORE: 0.4398
HOTSPOT_PERCENTILE: 60
IROC_SCORE: 0.9984
IROC_PERCENTILE: 78
POISSON_SCORE: 0.5013
POISSON_PERCENTILE: 60
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1102784_UW.Fetal_Placenta.H3K27ac.H-24996.Histone.DS23301.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS23301-Histone.DS23301.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Placenta H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27ac ChIP-Seq read mappings from Fetal Placenta, Donor H-24996, 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.16980
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: FP H3K27ac 96 01
BROWSER_TRACK_DESCRIPTION: UW Fetal Placenta Histone H3K27ac Donor H-24996 Library Histone.DS23301 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 21,653,271
FINDPEAKS_SCORE: 0.4258
FINDPEAKS_PERCENTILE: 65
HOTSPOT_SCORE: 0.4398
HOTSPOT_PERCENTILE: 60
IROC_SCORE: 0.9984
IROC_PERCENTILE: 78
POISSON_SCORE: 0.5013
POISSON_PERCENTILE: 60
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: Fetal Placenta primary tissue, day 113; Histone.DS23301

value: Fetal Placenta

value: genomic DNA

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

value: UW

value: fetal

value: day 113

value: Female

value: Histone H3K27ac

value: Diagenode Bioruptor

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

value: Invitrogen Dynabeads


title: Histone H3K27me3 ChIP-Seq of CD14 Primary Cells; Histone.DS22405

description:
sample_term_id: CL_0001054
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Histone H3K27me3 ChIP-Seq
Library name: Histone.DS22405
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15733
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.5355
****************
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: GSM1102785_UW.CD14_Primary_Cells.H3K27me3.RO_01721.Histone.DS22405.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS22405.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of CD14 Primary Cells H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27me3 ChIP-Seq on CD14 Primary Cells, Donor RO 01721, 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.16883
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: 22,770,773
FINDPEAKS_SCORE: 0.264
FINDPEAKS_PERCENTILE: 91
HOTSPOT_SCORE: 0.3106
HOTSPOT_PERCENTILE: 80
IROC_SCORE: 0.9867
IROC_PERCENTILE: 93
POISSON_SCORE: 0.4382
POISSON_PERCENTILE: 79
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1102785_UW.CD14_Primary_Cells.H3K27me3.RO_01721.Histone.DS22405.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS22405.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of CD14 Primary Cells H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27me3 ChIP-Seq read mappings from CD14 Primary Cells, Donor RO 01721, 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.16979
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: CD14 H3K27me3 21 05
BROWSER_TRACK_DESCRIPTION: UW CD14 Primary Cells Histone H3K27me3 Donor RO 01721 Library Histone.DS22405 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 22,770,773
FINDPEAKS_SCORE: 0.264
FINDPEAKS_PERCENTILE: 91
HOTSPOT_SCORE: 0.3106
HOTSPOT_PERCENTILE: 80
IROC_SCORE: 0.9867
IROC_PERCENTILE: 93
POISSON_SCORE: 0.4382
POISSON_PERCENTILE: 79
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: flow sorted CD14+ Cells,year 21; Histone.DS22405

value: CD14 Primary Cells

value: year 21

value: Male

value: Caucasian

value: Histone H3K27me3

value: Millipore A/G agarose beads

value: 30ul A/G bead slurry

value: Millipore


title: Histone H3K27me3 ChIP-Seq of CD3 Primary Cells; Histone.DS22927

description:
sample_term_id: CL_0000084
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Histone H3K27me3 ChIP-Seq
Library name: Histone.DS22927
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15776
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: GSM1102787_UW.CD3_Primary_Cells.H3K27me3.RO_01679.Histone.DS22927.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS22927-Histone.DS22927.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of CD3 Primary Cells H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27me3 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.16794
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: 26,435,832
FINDPEAKS_SCORE: 0.2387
FINDPEAKS_PERCENTILE: 88
HOTSPOT_SCORE: 0.3563
HOTSPOT_PERCENTILE: 91
IROC_SCORE: 0.9589
IROC_PERCENTILE: 80
POISSON_SCORE: 0.5132
POISSON_PERCENTILE: 91
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

ANALYSIS FILE NAME: GSM1102787_UW.CD3_Primary_Cells.H3K27me3.RO_01679.Histone.DS22927.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS22927-Histone.DS22927.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of CD3 Primary Cells H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27me3 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.16890
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 H3K27me3 79 27
BROWSER_TRACK_DESCRIPTION: UW CD3 Primary Cells Histone H3K27me3 Donor RO 01679 Library Histone.DS22927 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 26,435,832
FINDPEAKS_SCORE: 0.2387
FINDPEAKS_PERCENTILE: 88
HOTSPOT_SCORE: 0.3563
HOTSPOT_PERCENTILE: 91
IROC_SCORE: 0.9589
IROC_PERCENTILE: 80
POISSON_SCORE: 0.5132
POISSON_PERCENTILE: 91
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

source_name: flow sorted CD3+ Cells,year 21; Histone.DS22927

value: CD3 Primary Cells

value: genomic DNA

value: FHCRC HEIMFELD

value: Primary Cell


title: Histone H3K27ac ChIP-Seq of Fetal Stomach; Histone.DS22929

description:
sample_term_id: UBERON_0000945
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Histone H3K27ac ChIP-Seq
Library name: Histone.DS22929
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15702
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.15705
****************
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: GSM1102783_UW.Fetal_Stomach.H3K27ac.H-24683.Histone.DS22929.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS22929-Histone.DS22929.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Fetal Stomach H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27ac ChIP-Seq on Fetal Stomach, Donor H-24683, 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.16880
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: 31,135,567
FINDPEAKS_SCORE: 0.5455
FINDPEAKS_PERCENTILE: 81
HOTSPOT_SCORE: 0.56
HOTSPOT_PERCENTILE: 81
IROC_SCORE: 0.9987
IROC_PERCENTILE: 82
POISSON_SCORE: 0.599
POISSON_PERCENTILE: 79
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1102783_UW.Fetal_Stomach.H3K27ac.H-24683.Histone.DS22929.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS22929-Histone.DS22929.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Stomach H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27ac ChIP-Seq read mappings from Fetal Stomach, Donor H-24683, 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.16976
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: FS H3K27ac 83 29
BROWSER_TRACK_DESCRIPTION: UW Fetal Stomach Histone H3K27ac Donor H-24683 Library Histone.DS22929 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 31,135,567
FINDPEAKS_SCORE: 0.5455
FINDPEAKS_PERCENTILE: 81
HOTSPOT_SCORE: 0.56
HOTSPOT_PERCENTILE: 81
IROC_SCORE: 0.9987
IROC_PERCENTILE: 82
POISSON_SCORE: 0.599
POISSON_PERCENTILE: 79
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: Fetal Stomach primary tissue, day 96; Histone.DS22929

value: Fetal Stomach

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

value: Primary Tissue

value: UW

value: fetal

value: day 96

value: Female

value: Active Motif


title: Digital Genomic Footprinting assay of Fetal Kidney; DGF.DS20786

description:
sample_term_id: UBERON_0002113
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Digital Genomic Footprinting determination via DNase-seq
Library name: DGF.DS20786
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15568
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.14462
****************
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 Kidney primary tissue, day 105; DGF.DS20786

value: Fetal Kidney

value: day 105

value: Male

value: Digital Genomic Footprinting

value: Qiagen minElut


title: Digital Genomic Footprinting assay of CD14 Primary Cells; DGF.DS17215

description:
sample_term_id: CL_0001054
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Digital Genomic Footprinting determination via DNase-seq
Library name: DGF.DS17215
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15523
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.5355
****************
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 CD14+ Cells,year 21; DGF.DS17215

value: CD14 Primary Cells

value: year 21

value: Caucasian


title: Digital Genomic Footprinting assay of CD3 Primary Cells, cord blood; DGF.DS17706

description:
sample_term_id: CL_0000084
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Digital Genomic Footprinting determination via DNase-seq
Library name: DGF.DS17706
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15519
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.7021
****************
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 CD3  Primary Cells, from cord blood; DGF.DS17706

value: CD3 Cord Blood Primary Cells

value: genomic DNA

value: FHCRC HEIMFELD

value: Primary Cell

value: CD3 Primary Cells

value: Unknown


title: RNA-Seq (Total RNA) Fetal Muscle, Arm; RNA.RS19415

description:
sample_term_id: UBERON_0001499
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: RNA-Seq (Total RNA) Fetal Muscle, Arm
Library name: lib-RNA.RS19415
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15664
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.9895
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

library_source: transcriptomic

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

ANALYSIS FILE NAME: GSM1101710_UW.Fetal_Muscle_Arm.mRNA-Seq.H-24125.lib-RNA.RS19415.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RNA.RS19415.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Fetal Muscle Arm mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by mRNA-Seq on Fetal Muscle Arm, Donor H-24125 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.16674
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 38,400,588
PERCENT_READS_MAPPING_TO_UCSC_GENES: 93.36
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 51
MAXIMUM_REPLICATE_CORRELATION: 0.64

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

ANALYSIS FILE NAME: GSM1101710_UW.Fetal_Muscle_Arm.mRNA-Seq.H-24125.lib-RNA.RS19415.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RNA.RS19415.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Muscle Arm mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina mRNA-Seq read mappings from Fetal Muscle Arm, Donor H-24125 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.17137
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: FMA mRNA 25 15
BROWSER_TRACK_DESCRIPTION: UW Fetal Muscle Arm mRNA-Seq Donor H-24125 Library lib-RNA.RS19415 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 38,400,588
PERCENT_READS_MAPPING_TO_UCSC_GENES: 93.36
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 51
MAXIMUM_REPLICATE_CORRELATION: 0.64

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

molecule: total RNA

source_name: Fetal Muscle, Arm primary tissue, day 101; RNA.RS19415

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

value: Fetal Muscle, Arm

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

value: Primary Tissue

value: UW

value: fetal

value: day 101

value: mRNA-Seq

value: Qiagen TissueLyser and RNeasy Lipid Tx Mini 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 H3K27ac ChIP-Seq of CD14 Primary Cells; Histone.DS22926

description:
sample_term_id: CL_0001054
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Histone H3K27ac ChIP-Seq
Library name: Histone.DS22926
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15737
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.5355
****************
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: GSM1102782_UW.CD14_Primary_Cells.H3K27ac.RO_01721.Histone.DS22926.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS22926-Histone.DS22926.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of CD14 Primary Cells H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27ac ChIP-Seq on CD14 Primary Cells, Donor RO 01721, 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.16843
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: 21,342,029
FINDPEAKS_SCORE: 0.48
FINDPEAKS_PERCENTILE: 71
HOTSPOT_SCORE: 0.4933
HOTSPOT_PERCENTILE: 69
IROC_SCORE: 0.9987
IROC_PERCENTILE: 82
POISSON_SCORE: 0.5159
POISSON_PERCENTILE: 66
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1102782_UW.CD14_Primary_Cells.H3K27ac.RO_01721.Histone.DS22926.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS22926-Histone.DS22926.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of CD14 Primary Cells H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27ac ChIP-Seq read mappings from CD14 Primary Cells, Donor RO 01721, 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.16939
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: CD14 H3K27ac 21 26
BROWSER_TRACK_DESCRIPTION: UW CD14 Primary Cells Histone H3K27ac Donor RO 01721 Library Histone.DS22926 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 21,342,029
FINDPEAKS_SCORE: 0.48
FINDPEAKS_PERCENTILE: 71
HOTSPOT_SCORE: 0.4933
HOTSPOT_PERCENTILE: 69
IROC_SCORE: 0.9987
IROC_PERCENTILE: 82
POISSON_SCORE: 0.5159
POISSON_PERCENTILE: 66
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: flow sorted CD14+ Cells,year 21; Histone.DS22926

value: CD14 Primary Cells

value: genomic DNA

value: FHCRC HEIMFELD

value: Primary Cell

value: year 21

value: Male

value: Caucasian

value: Histone H3K27ac

value: Diagenode Bioruptor

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

value: Invitrogen Dynabeads

value: Active Motif


title: RNA-Seq (Total RNA) Fetal Spinal Cord; RNA.RS19418

description:
sample_term_id: UBERON_0002240
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: RNA-Seq (Total RNA) Fetal Spinal Cord
Library name: lib-RNA.RS19418
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15576
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.10164
****************
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: GSM1101711_UW.Fetal_Spinal_Cord.mRNA-Seq.H-24111.lib-RNA.RS19418.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RNA.RS19418.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Fetal Spinal Cord mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by mRNA-Seq on Fetal Spinal Cord, Donor H-24111 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.16706
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 55,331,289
PERCENT_READS_MAPPING_TO_UCSC_GENES: 93.92
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 54
MAXIMUM_REPLICATE_CORRELATION: 0.58

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

ANALYSIS FILE NAME: GSM1101711_UW.Fetal_Spinal_Cord.mRNA-Seq.H-24111.lib-RNA.RS19418.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RNA.RS19418.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Spinal Cord mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina mRNA-Seq read mappings from Fetal Spinal Cord, Donor H-24111 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.17169
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: FSC mRNA 11 18
BROWSER_TRACK_DESCRIPTION: UW Fetal Spinal Cord mRNA-Seq Donor H-24111 Library lib-RNA.RS19418 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 55,331,289
PERCENT_READS_MAPPING_TO_UCSC_GENES: 93.92
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 54
MAXIMUM_REPLICATE_CORRELATION: 0.58

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

source_name: Fetal Spinal, Cord primary tissue, day 105; RNA.RS19418

value: Fetal Spinal Cord

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

value: Primary Tissue

value: UW

value: fetal

value: day 105

value: mRNA-Seq

value: Qiagen TissueLyser and RNeasy Lipid Tx Mini kit

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

value: Random Primers(hexamers)


title: RNA-Seq (Total RNA) Fetal Lung, Left; RNA.RS19413

description:
sample_term_id: UBERON_0002168
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: RNA-Seq (Total RNA) Fetal Lung, Left
Library name: lib-RNA.RS19413
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15643
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.9925
****************
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: GSM1101708_UW.Fetal_Lung_Left.mRNA-Seq.H-24111.lib-RNA.RS19413.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RNA.RS19413.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Fetal Lung Left mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by mRNA-Seq on Fetal Lung Left, Donor H-24111 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.16680
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 39,418,222
PERCENT_READS_MAPPING_TO_UCSC_GENES: 94.57
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 69
MAXIMUM_REPLICATE_CORRELATION: 0.62

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

ANALYSIS FILE NAME: GSM1101708_UW.Fetal_Lung_Left.mRNA-Seq.H-24111.lib-RNA.RS19413.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RNA.RS19413.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Lung Left mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina mRNA-Seq read mappings from Fetal Lung Left, Donor H-24111 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.17143
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: FLL mRNA 11 13
BROWSER_TRACK_DESCRIPTION: UW Fetal Lung Left mRNA-Seq Donor H-24111 Library lib-RNA.RS19413 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 39,418,222
PERCENT_READS_MAPPING_TO_UCSC_GENES: 94.57
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 69
MAXIMUM_REPLICATE_CORRELATION: 0.62

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

source_name: Fetal Lung, Left primary tissue, day 105; RNA.RS19413

value: Fetal Lung, Left

value: Male

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 Muscle, Leg; RNA.RS19035

description:
sample_term_id: UBERON_0001383
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: RNA-Seq (Total RNA) Fetal Muscle, Leg
Library name: lib-RNA.RS19035
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15606
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.9842
****************
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: GSM1101706_UW.Fetal_Muscle_Leg.mRNA-Seq.H-24111.lib-RNA.RS19035.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RNA.RS19035.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Fetal Muscle Leg mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by mRNA-Seq on Fetal Muscle Leg, Donor H-24111 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.16672
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 58,100,616
PERCENT_READS_MAPPING_TO_UCSC_GENES: 89.35
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 24
MAXIMUM_REPLICATE_CORRELATION: 0.57

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

ANALYSIS FILE NAME: GSM1101706_UW.Fetal_Muscle_Leg.mRNA-Seq.H-24111.lib-RNA.RS19035.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RNA.RS19035.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Muscle Leg mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina mRNA-Seq read mappings from Fetal Muscle Leg, Donor H-24111 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.17135
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: FML mRNA 11 35
BROWSER_TRACK_DESCRIPTION: UW Fetal Muscle Leg mRNA-Seq Donor H-24111 Library lib-RNA.RS19035 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 58,100,616
PERCENT_READS_MAPPING_TO_UCSC_GENES: 89.35
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 24
MAXIMUM_REPLICATE_CORRELATION: 0.57

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

source_name: Fetal Muscle, Leg primary tissue, day 105; RNA.RS19035

value: Fetal Muscle, Leg


title: RNA-Seq (Total RNA) Fetal Muscle, Leg; RNA.RS19034

description:
sample_term_id: UBERON_0001383
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: RNA-Seq (Total RNA) Fetal Muscle, Leg
Library name: lib-RNA.RS19034
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15610
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.9846
****************
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: GSM1101705_UW.Fetal_Muscle_Leg.mRNA-Seq.H-24089.lib-RNA.RS19034.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RNA.RS19034.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Fetal Muscle Leg mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by mRNA-Seq on Fetal Muscle Leg, Donor H-24089 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.16686
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 34,818,958
PERCENT_READS_MAPPING_TO_UCSC_GENES: 94.0
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 55
MAXIMUM_REPLICATE_CORRELATION: 0.57

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

ANALYSIS FILE NAME: GSM1101705_UW.Fetal_Muscle_Leg.mRNA-Seq.H-24089.lib-RNA.RS19034.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RNA.RS19034.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Muscle Leg mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina mRNA-Seq read mappings from Fetal Muscle Leg, Donor H-24089 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.17149
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: FML mRNA 89 34
BROWSER_TRACK_DESCRIPTION: UW Fetal Muscle Leg mRNA-Seq Donor H-24089 Library lib-RNA.RS19034 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 34,818,958
PERCENT_READS_MAPPING_TO_UCSC_GENES: 94.0
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 55
MAXIMUM_REPLICATE_CORRELATION: 0.57

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

source_name: Fetal Muscle, Leg primary tissue, day 96; RNA.RS19034

value: day 96


title: RNA-Seq (Total RNA) Fetal Muscle, Back; RNA.RS19032

description:
sample_term_id: UBERON_0002324
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: RNA-Seq (Total RNA) Fetal Muscle, Back
Library name: lib-RNA.RS19032
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15676
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.9879
****************
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: GSM1101703_UW.Fetal_Muscle_Back.mRNA-Seq.H-24078.lib-RNA.RS19032.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RNA.RS19032.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Fetal Muscle Back mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by mRNA-Seq on Fetal Muscle Back, Donor H-24078 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.16710
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 31,972,356
PERCENT_READS_MAPPING_TO_UCSC_GENES: 94.13
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 58
MAXIMUM_REPLICATE_CORRELATION: 0.65

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

ANALYSIS FILE NAME: GSM1101703_UW.Fetal_Muscle_Back.mRNA-Seq.H-24078.lib-RNA.RS19032.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: RNA.RS19032.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Muscle Back mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina mRNA-Seq read mappings from Fetal Muscle Back, Donor H-24078 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.17173
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: FMB mRNA 78 32
BROWSER_TRACK_DESCRIPTION: UW Fetal Muscle Back mRNA-Seq Donor H-24078 Library lib-RNA.RS19032 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 31,972,356
PERCENT_READS_MAPPING_TO_UCSC_GENES: 94.13
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 58
MAXIMUM_REPLICATE_CORRELATION: 0.65

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

source_name: Fetal Muscle, Back primary tissue, day 127; RNA.RS19032

value: Fetal Muscle, Back

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

value: day 127