title: Chromatin accessibility assay of Fetal Kidney; DNase.DS21096

description:
sample_term_id: UBERON_0002113
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DNase.DS21096
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.14459
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.14458
****************
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: GSM1027342_UW.Fetal_Kidney.ChromatinAccessibility.H-24608.DNase.DS21096.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNase.DS21096.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Fetal Kidney Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Kidney, Donor H-24608, Library DNase.DS21096 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.17594
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 49,763,171
FINDPEAKS_SCORE: 0.5945
FINDPEAKS_PERCENTILE: 96
HOTSPOT_SCORE: 0.5762
HOTSPOT_PERCENTILE: 96
IROC_SCORE: 0.9958
IROC_PERCENTILE: 89
POISSON_SCORE: 0.6154
POISSON_PERCENTILE: 96
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

ANALYSIS FILE NAME: GSM1027342_UW.Fetal_Kidney.ChromatinAccessibility.H-24608.DNase.DS21096.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNase.DS21096.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Kidney Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Kidney, Donor H-24608, Library DNase.DS21096 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.17548
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 150bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: FK DNase 08 96
BROWSER_TRACK_DESCRIPTION: UW Fetal Kidney DNase Hypersensitivity Donor H-24608 Library DNase.DS21096 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 49,763,171
FINDPEAKS_SCORE: 0.5945
FINDPEAKS_PERCENTILE: 96
HOTSPOT_SCORE: 0.5762
HOTSPOT_PERCENTILE: 96
IROC_SCORE: 0.9958
IROC_PERCENTILE: 89
POISSON_SCORE: 0.6154
POISSON_PERCENTILE: 96
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

source_name: Fetal Kidney primary tissue, day 85; DNase.DS21096

value: Fetal Kidney

value: Chromatin Accessibility


title: Chromatin accessibility assay of Fetal Kidney, Right; DNase.DS21044

status: Public on Nov 01 2012

type: SRA

city: Seattle

first: Northwest

last: REMC

state: WA

country: USA

institute: University of Washington

description:
sample_term_id: UBERON_0004539
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DNase.DS21044
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.14336
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.14335
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

library_source: genomic

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

ANALYSIS FILE NAME: GSM1027340_UW.Fetal_Kidney_Right.ChromatinAccessibility.H-24595.DNase.DS21044.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNase.DS21044.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Fetal Kidney Right Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Kidney Right, Donor H-24595, Library DNase.DS21044 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.17612
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 27,606,399
FINDPEAKS_SCORE: 0.399
FINDPEAKS_PERCENTILE: 52
HOTSPOT_SCORE: 0.3886
HOTSPOT_PERCENTILE: 52
IROC_SCORE: 0.9928
IROC_PERCENTILE: 50
POISSON_SCORE: 0.459
POISSON_PERCENTILE: 54
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM1027340_UW.Fetal_Kidney_Right.ChromatinAccessibility.H-24595.DNase.DS21044.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNase.DS21044.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Kidney Right Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Kidney Right, Donor H-24595, Library DNase.DS21044 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.17566
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 150bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: FKR DNase 95 44
BROWSER_TRACK_DESCRIPTION: UW Fetal Kidney Right DNase Hypersensitivity Donor H-24595 Library DNase.DS21044 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 27,606,399
FINDPEAKS_SCORE: 0.399
FINDPEAKS_PERCENTILE: 52
HOTSPOT_SCORE: 0.3886
HOTSPOT_PERCENTILE: 52
IROC_SCORE: 0.9928
IROC_PERCENTILE: 50
POISSON_SCORE: 0.459
POISSON_PERCENTILE: 54
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

molecule: genomic DNA

organism: Homo sapiens

source_name: Fetal Kidney, Right primary tissue, day 108; DNase.DS21044

extract_protocol: Library construction protocol: Single read - Illumina

tag: sample alias

tag: sample common name

value: Fetal Kidney, Right

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 108

value: Male

value: Qiagen minElut


title: 10_1_c FAIRE-seq

status: Public on Nov 02 2012

city: Daejeon, Seoul

first: kwoneel

last: kim

address: Gwahangno, Yuseong gu

country: South Korea

institute: KAIST

data_processing:
Raw data processing was carried out by means of Illumina data pipeline (ELAND and CASAVA). To identify the peaks of the reads, we ran F-seq with the default parameters. Small-sized peaks (< 15 bp) were extended in both directions such that all the peaks are 15 bp long at least. To identify all possible open chromatin regions (OCRs), we merged the extended peak positions of the 96 yeast strains by using BEDTools. Overlapping peaks were merged into a single peak.
Genome build: sacCer2

organism: Saccharomyces cerevisiae

source_name: yeast extract

growth_protocol: We obtained the BY-RM cross strains from the original authors (Science 296, 752-755 & PNAS 102, 1572-1577). Each yeast strain was grown with 200ml YPD medium in conical flask and incubated under shaking condition at 200 rpm overnight to 1.5 of the value of A600.

extract_protocol:
High-throughput sequencing of the 96 FAIRE libraries was performed on eight lanes of a single flow cell of HiSeq 2000 with 100 bp run length. Illumina’s Multiplexing Sample Preparation Oligonucleotide Kit was used to sequence twelve samples in each lane.
library_strategy: FAIRE-seq

treatment_protocol: The yeast cell was fixed by 37% formaldehyde (final 1%) for 20 minutes at room temperature. To stop fixation, 2.5M glycine (final 125 mM) was added and mixed swirling for 5 minutes at room temperature. The fixed cell was harvested by centrifugation at 3000 rpm for 5 minutes, and the pellet cells was rinsed twice with 10ml cold PBS and stored at -70ºC after removing all supernatant. Fixed cell was re-suspended in 300ul ChIP lysis buffer (50mM HEPES-KOH, pH7.5, 140mM NaCl, 1% Triton-X 100, 0.1% Sodium deoxycholate, 1mM EDTA) and protease inhibitor (Roche Inc. #1697498) per 0.12g of cells. Glass bead (425-600 micron diameter, Sigma #G8772) was added an equal volume to each sample and mixed 5 times 30 seconds by vortex mixer with 30 second incubation on ice. Then glass beads were filtered by puncture bottom of tube with a 20-26G needle and centrifugation. The samples were sonicated for 20 cycles (30 seconds ON and 30 seconds OFF) using a Bioruptor sonicator. DNA isolation was done by adding an equal volume of phenol-chloroform (Amresco. AMR-0883-2, phenol : chloroform : isoamyl alcohol 25:24:1), vortexing vigorously for 30 seconds and centrifuged at 13000 rpm for 10 minutes at 4ºC. The aqueous phase was isolated and the stored in a separate tube. The DNA was precipitated by addition of sodium acetate (final 0.3M) and two times the volume of 95% ethanol and incubated at -20ºC overnight. The precipitate was centrifuged at 13000 rpm for 20 minutes at 4ºC. Then the pellet was washed with 70% ethanol and dried at room temperature. The pellet was resuspended in dH2O with the addition of RNase A (final 100ug/mL), and then incubated at 37ºC for 2 hours. DNA fragments of 100-350 bp were eluted from 2% agarose gel.

tag: strain

value: BY4716xRM11_1a segregant


title: Chromatin accessibility assay of Fetal Kidney, Left; DNase.DS20953

description:
sample_term_id: UBERON_0004538
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DNase.DS20953
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.14451
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.14450
****************
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: GSM1027338_UW.Fetal_Kidney_Left.ChromatinAccessibility.H-24582.DNase.DS20953.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNase.DS20953.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Fetal Kidney Left Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Kidney Left, Donor H-24582, Library DNase.DS20953 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.17598
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 52,245,433
FINDPEAKS_SCORE: 0.4677
FINDPEAKS_PERCENTILE: 72
HOTSPOT_SCORE: 0.4543
HOTSPOT_PERCENTILE: 72
IROC_SCORE: 0.9931
IROC_PERCENTILE: 59
POISSON_SCORE: 0.5112
POISSON_PERCENTILE: 72
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM1027338_UW.Fetal_Kidney_Left.ChromatinAccessibility.H-24582.DNase.DS20953.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNase.DS20953.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Kidney Left Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Kidney Left, Donor H-24582, Library DNase.DS20953 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.17552
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 150bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: FKL DNase 82 53
BROWSER_TRACK_DESCRIPTION: UW Fetal Kidney Left DNase Hypersensitivity Donor H-24582 Library DNase.DS20953 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 52,245,433
FINDPEAKS_SCORE: 0.4677
FINDPEAKS_PERCENTILE: 72
HOTSPOT_SCORE: 0.4543
HOTSPOT_PERCENTILE: 72
IROC_SCORE: 0.9931
IROC_PERCENTILE: 59
POISSON_SCORE: 0.5112
POISSON_PERCENTILE: 72
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

source_name: Fetal Kidney, Left primary tissue, day 87; DNase.DS20953

value: Fetal Kidney, Left

value: day 87

value: Female


title: Ho16-b

status: Public on Nov 07 2012

city: Derio

first: Rosa

last: Barrio

address: Bizkaia Technology Park

country: Spain

institute: CIC bioGUNE

library_source: transcriptomic

data_processing:
Illumina RTA 1.5.35.0 & Illumina RTA 1.9.35
SCS_2.5 & SCS_2.9
Aligment with BOWTIE
Differential Expression by Deseq
GO with FatiGO tool
Genome_build: d_melanogaster_fb5_22
Supplementary_files_format_and_content: DE comparisons of the groups considered in the present study. The included fields are:
Id: gene ID
baseMean: mean expression level (at the base scale) as a joint estimate from both conditions
baseMeanA: mean expression level (at the base scale) as an estimate for condition A
baseMeanB: mean expression level (at the base scale) as an estimate for condition B
foldChange: fold change from the first to the second condition
log2FoldChange: the logarithm (to basis 2) of the fold change
pval: significance of this fold change
padj: p values, adjusted for multiple testing with the Benjamini-Hochberg procedure, which controls false discovery rate (FDR)
resVarA: the ratio of the single gene estimates for the base variance to the fitted value in condition A
resVarB: the ratio of the single gene estimates for the base variance to the fitted value in condition B

molecule: total RNA

organism: Drosophila melanogaster

source_name: Pool of 50 embryos

growth_protocol: Standard Drosophila Husbandry protocols

extract_protocol: mRNA Sequencing Sample Preparation (Illumina Inc.)

treatment_protocol: No treatment

tag: Stage

value: early stage 16 (13-14 hours of egg development at 25°C)

tag: genotype


title: Chromatin accessibility assay of Fetal Spinal Cord; DNase.DS20956

description:
sample_term_id: UBERON_0002240
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DNase.DS20956
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.14293
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.14292
****************
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: GSM1027339_UW.Fetal_Spinal_Cord.ChromatinAccessibility.H-24582.DNase.DS20956.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNase.DS20956.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Fetal Spinal Cord Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Spinal Cord, Donor H-24582, Library DNase.DS20956 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.17630
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 27,247,950
FINDPEAKS_SCORE: 0.3667
FINDPEAKS_PERCENTILE: 46
HOTSPOT_SCORE: 0.3645
HOTSPOT_PERCENTILE: 46
IROC_SCORE: 0.9895
IROC_PERCENTILE: 22
POISSON_SCORE: 0.43
POISSON_PERCENTILE: 46
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM1027339_UW.Fetal_Spinal_Cord.ChromatinAccessibility.H-24582.DNase.DS20956.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNase.DS20956.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Spinal Cord Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Spinal Cord, Donor H-24582, Library DNase.DS20956 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.17584
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 150bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: FSC DNase 82 56
BROWSER_TRACK_DESCRIPTION: UW Fetal Spinal Cord DNase Hypersensitivity Donor H-24582 Library DNase.DS20956 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 27,247,950
FINDPEAKS_SCORE: 0.3667
FINDPEAKS_PERCENTILE: 46
HOTSPOT_SCORE: 0.3645
HOTSPOT_PERCENTILE: 46
IROC_SCORE: 0.9895
IROC_PERCENTILE: 22
POISSON_SCORE: 0.43
POISSON_PERCENTILE: 46
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

source_name: Fetal Spinal, Cord primary tissue, day 87; DNase.DS20956

value: Fetal Spinal Cord


title: Chromatin accessibility assay of Fetal Placenta; DNase.DS20793

description:
sample_term_id: UBERON_0001987
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DNase.DS20793
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.14304
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.14303
****************
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: GSM1027332_UW.Fetal_Placenta.ChromatinAccessibility.H-24510.DNase.DS20793.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNase.DS20793.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Fetal Placenta Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Placenta, Donor H-24510, Library DNase.DS20793 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.17631
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 49,087,167
FINDPEAKS_SCORE: 0.5474
FINDPEAKS_PERCENTILE: 93
HOTSPOT_SCORE: 0.5384
HOTSPOT_PERCENTILE: 93
IROC_SCORE: 0.9963
IROC_PERCENTILE: 91
POISSON_SCORE: 0.5695
POISSON_PERCENTILE: 91
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

ANALYSIS FILE NAME: GSM1027332_UW.Fetal_Placenta.ChromatinAccessibility.H-24510.DNase.DS20793.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNase.DS20793.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Placenta Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Placenta, Donor H-24510, Library DNase.DS20793 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.17585
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 150bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: FP DNase 10 93
BROWSER_TRACK_DESCRIPTION: UW Fetal Placenta DNase Hypersensitivity Donor H-24510 Library DNase.DS20793 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 49,087,167
FINDPEAKS_SCORE: 0.5474
FINDPEAKS_PERCENTILE: 93
HOTSPOT_SCORE: 0.5384
HOTSPOT_PERCENTILE: 93
IROC_SCORE: 0.9963
IROC_PERCENTILE: 91
POISSON_SCORE: 0.5695
POISSON_PERCENTILE: 91
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

source_name: Fetal Placenta primary tissue, day 105; DNase.DS20793

value: Fetal Placenta

value: day 105


title: Chromatin accessibility assay of Fetal Muscle, Back; DNase.DS20789

description:
sample_term_id: UBERON_0002324
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DNase.DS20789
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.14320
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.14319
****************
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: GSM1027330_UW.Fetal_Muscle_Back.ChromatinAccessibility.H-24510.DNase.DS20789.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNase.DS20789.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Fetal Muscle Back Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Muscle Back, Donor H-24510, Library DNase.DS20789 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.17615
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 36,054,353
FINDPEAKS_SCORE: 0.4386
FINDPEAKS_PERCENTILE: 63
HOTSPOT_SCORE: 0.4315
HOTSPOT_PERCENTILE: 65
IROC_SCORE: 0.9929
IROC_PERCENTILE: 52
POISSON_SCORE: 0.4928
POISSON_PERCENTILE: 63
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM1027330_UW.Fetal_Muscle_Back.ChromatinAccessibility.H-24510.DNase.DS20789.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNase.DS20789.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Muscle Back Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Muscle Back, Donor H-24510, Library DNase.DS20789 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.17569
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 150bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: FMB DNase 10 89
BROWSER_TRACK_DESCRIPTION: UW Fetal Muscle Back DNase Hypersensitivity Donor H-24510 Library DNase.DS20789 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 36,054,353
FINDPEAKS_SCORE: 0.4386
FINDPEAKS_PERCENTILE: 63
HOTSPOT_SCORE: 0.4315
HOTSPOT_PERCENTILE: 65
IROC_SCORE: 0.9929
IROC_PERCENTILE: 52
POISSON_SCORE: 0.4928
POISSON_PERCENTILE: 63
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

source_name: Fetal Muscle, Back primary tissue, day 105; DNase.DS20789

value: Fetal Muscle, Back

value: Chromatin Accessibility


title: Chromatin accessibility assay of Fetal Renal Cortex; DNase.DS20445

description:
sample_term_id: UBERON_0001225
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DNase.DS20445
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.14355
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.14354
****************
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: GSM1027323_UW.Fetal_Renal_Cortex.ChromatinAccessibility.H-24477.DNase.DS20445.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNase.DS20445.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Fetal Renal Cortex Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Renal Cortex, Donor H-24477, Library DNase.DS20445 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.17624
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 63,386,725
FINDPEAKS_SCORE: 0.3482
FINDPEAKS_PERCENTILE: 43
HOTSPOT_SCORE: 0.3328
HOTSPOT_PERCENTILE: 41
IROC_SCORE: 0.9859
IROC_PERCENTILE: 9
POISSON_SCORE: 0.4024
POISSON_PERCENTILE: 43
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM1027323_UW.Fetal_Renal_Cortex.ChromatinAccessibility.H-24477.DNase.DS20445.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNase.DS20445.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Renal Cortex Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Renal Cortex, Donor H-24477, Library DNase.DS20445 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.17578
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 150bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: FRC DNase 77 45
BROWSER_TRACK_DESCRIPTION: UW Fetal Renal Cortex DNase Hypersensitivity Donor H-24477 Library DNase.DS20445 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 63,386,725
FINDPEAKS_SCORE: 0.3482
FINDPEAKS_PERCENTILE: 43
HOTSPOT_SCORE: 0.3328
HOTSPOT_PERCENTILE: 41
IROC_SCORE: 0.9859
IROC_PERCENTILE: 9
POISSON_SCORE: 0.4024
POISSON_PERCENTILE: 43
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

source_name: Fetal Kidney, renal, cortex primary tissue, day 103; DNase.DS20445

value: Fetal Renal Cortex

value: genomic DNA

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

value: day 103


title: Chromatin accessibility assay of Fetal Muscle, Leg; DNase.DS20797

description:
sample_term_id: UBERON_0001383
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DNase.DS20797
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.14308
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.14307
****************
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: GSM1027333_UW.Fetal_Muscle_Leg.ChromatinAccessibility.H-24510.DNase.DS20797.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNase.DS20797.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Fetal Muscle Leg Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Muscle Leg, Donor H-24510, Library DNase.DS20797 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.17629
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 36,788,139
FINDPEAKS_SCORE: 0.4692
FINDPEAKS_PERCENTILE: 74
HOTSPOT_SCORE: 0.4596
HOTSPOT_PERCENTILE: 74
IROC_SCORE: 0.9935
IROC_PERCENTILE: 61
POISSON_SCORE: 0.5236
POISSON_PERCENTILE: 74
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM1027333_UW.Fetal_Muscle_Leg.ChromatinAccessibility.H-24510.DNase.DS20797.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNase.DS20797.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Muscle Leg Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Muscle Leg, Donor H-24510, Library DNase.DS20797 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.17583
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 150bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: FML DNase 10 97
BROWSER_TRACK_DESCRIPTION: UW Fetal Muscle Leg DNase Hypersensitivity Donor H-24510 Library DNase.DS20797 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 36,788,139
FINDPEAKS_SCORE: 0.4692
FINDPEAKS_PERCENTILE: 74
HOTSPOT_SCORE: 0.4596
HOTSPOT_PERCENTILE: 74
IROC_SCORE: 0.9935
IROC_PERCENTILE: 61
POISSON_SCORE: 0.5236
POISSON_PERCENTILE: 74
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

source_name: Fetal Muscle, Leg primary tissue, day 105; DNase.DS20797

value: Fetal Muscle, Leg

value: Primary Tissue

value: UW

value: fetal


title: Digital Genomic Footprinting assay of Penis Foreskin Keratinocytes Primary Cells; DGF.DS18692

description:
sample_term_id: CL_1001606
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Digital Genomic Footprinting determination via DNase-seq
Library name: DGF.DS18692
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.14367
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSF-UBC%2FSAMPLE%2FEDACC.5490
****************
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: GSM1027350_UW.Penis_Foreskin_Keratinocyte_Primary_Cells.Digital_Genomic_Footprinting.skin01.DGF.DS18692.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DGF.DS18692.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Penis Foreskin Keratinocyte Primary Cells Digital Genomic Footprinting Data
ANALYSIS DESCRIPTION: Illumina reads produced by Digital Genomic Footprinting on Penis Foreskin Keratinocyte Primary Cells, Donor skin01, Library DGF.DS18692 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.15149
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Digital Genomic Footprinting
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: 289,580,124
NUMBER_OF_DIGITAL_GENOMIC_FOOTPRINTING_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 11
FINDPEAKS_SCORE: 0.5142
FINDPEAKS_PERCENTILE: 73
HOTSPOT_SCORE: 0.5314
HOTSPOT_PERCENTILE: 73
IROC_SCORE: 0.9936
IROC_PERCENTILE: 55
POISSON_SCORE: 0.5945
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1027350_UW.Penis_Foreskin_Keratinocyte_Primary_Cells.Digital_Genomic_Footprinting.skin01.DGF.DS18692.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DGF.DS18692.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Penis Foreskin Keratinocyte Primary Cells Digital Genomic Footprinting Data
ANALYSIS DESCRIPTION: Illumina Digital Genomic Footprinting read mappings from  Penis Foreskin Keratinocyte Primary Cells, Donor skin01, Library DGF.DS18692 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.15160
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Digital Genomic Footprinting
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 150bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: PFK DGF 01 92
BROWSER_TRACK_DESCRIPTION: UW Penis Foreskin Keratinocyte Primary Cells Digital Genomic Footprinting Donor skin01 Library DGF.DS18692 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 289,580,124
NUMBER_OF_DIGITAL_GENOMIC_FOOTPRINTING_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 11
FINDPEAKS_SCORE: 0.5142
FINDPEAKS_PERCENTILE: 73
HOTSPOT_SCORE: 0.5314
HOTSPOT_PERCENTILE: 73
IROC_SCORE: 0.9936
IROC_PERCENTILE: 55
POISSON_SCORE: 0.5945
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: Penis, Foreskin, Keratinocyte Primary Cells skin01; DGF.DS18692

value: Penis, Foreskin, Keratinocyte skin01

value: SFVAMC Dermatology

value: Primary Cell Culture

value: Keratinocyte

tag: markers

value: Invitrogen 154CF + HKGS + .07mM Ca

value: Neonate

value: Disease Free

value: Male

tag: karyotype

tag: parity

value: Digital Genomic Footprinting

value: Qiagen minElut


title: Chromatin accessibility assay of Fetal Kidney, Left; DNase.DS20920

description:
sample_term_id: UBERON_0004538
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DNase.DS20920
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.14455
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.14454
****************
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: GSM1027336_UW.Fetal_Kidney_Left.ChromatinAccessibility.H-24568.DNase.DS20920.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNase.DS20920.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Fetal Kidney Left Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Kidney Left, Donor H-24568, Library DNase.DS20920 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.17589
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 60,393,843
FINDPEAKS_SCORE: 0.44
FINDPEAKS_PERCENTILE: 65
HOTSPOT_SCORE: 0.423
HOTSPOT_PERCENTILE: 61
IROC_SCORE: 0.9906
IROC_PERCENTILE: 28
POISSON_SCORE: 0.4954
POISSON_PERCENTILE: 65
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

ANALYSIS FILE NAME: GSM1027336_UW.Fetal_Kidney_Left.ChromatinAccessibility.H-24568.DNase.DS20920.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNase.DS20920.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Kidney Left Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Kidney Left, Donor H-24568, Library DNase.DS20920 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.17543
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 150bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: FKL DNase 68 20
BROWSER_TRACK_DESCRIPTION: UW Fetal Kidney Left DNase Hypersensitivity Donor H-24568 Library DNase.DS20920 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 60,393,843
FINDPEAKS_SCORE: 0.44
FINDPEAKS_PERCENTILE: 65
HOTSPOT_SCORE: 0.423
HOTSPOT_PERCENTILE: 61
IROC_SCORE: 0.9906
IROC_PERCENTILE: 28
POISSON_SCORE: 0.4954
POISSON_PERCENTILE: 65
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

source_name: Fetal Kidney, Left primary tissue, day 98; DNase.DS20920

value: Fetal Kidney, Left

value: genomic DNA

value: day 98

value: Female

value: Chromatin Accessibility


title: Chromatin accessibility assay of Fetal Kidney; DNase.DS20786

description:
sample_term_id: UBERON_0002113
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DNase.DS20786
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.14463
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:
**********************************************************************

ANALYSIS FILE NAME: GSM1027329_UW.Fetal_Kidney.ChromatinAccessibility.H-24510.DNase.DS20786.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNase.DS20786.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Fetal Kidney Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Kidney, Donor H-24510, Library DNase.DS20786 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.17610
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 30,234,213
FINDPEAKS_SCORE: 0.4889
FINDPEAKS_PERCENTILE: 83
HOTSPOT_SCORE: 0.4868
HOTSPOT_PERCENTILE: 85
IROC_SCORE: 0.9946
IROC_PERCENTILE: 80
POISSON_SCORE: 0.5449
POISSON_PERCENTILE: 85
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM1027329_UW.Fetal_Kidney.ChromatinAccessibility.H-24510.DNase.DS20786.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNase.DS20786.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Kidney Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Kidney, Donor H-24510, Library DNase.DS20786 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.17564
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 150bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: FK DNase 10 86
BROWSER_TRACK_DESCRIPTION: UW Fetal Kidney DNase Hypersensitivity Donor H-24510 Library DNase.DS20786 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 30,234,213
FINDPEAKS_SCORE: 0.4889
FINDPEAKS_PERCENTILE: 83
HOTSPOT_SCORE: 0.4868
HOTSPOT_PERCENTILE: 85
IROC_SCORE: 0.9946
IROC_PERCENTILE: 80
POISSON_SCORE: 0.5449
POISSON_PERCENTILE: 85
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

source_name: Fetal Kidney primary tissue, day 105; DNase.DS20786

value: Fetal Kidney

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

value: Primary Tissue

value: UW

value: day 105


title: Chromatin accessibility assay of Fetal Stomach; DNase.DS20791

description:
sample_term_id: UBERON_0000945
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DNase.DS20791
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.14257
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.14256
****************
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: GSM1027331_UW.Fetal_Stomach.ChromatinAccessibility.H-24510.DNase.DS20791.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNase.DS20791.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Fetal Stomach Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Stomach, Donor H-24510, Library DNase.DS20791 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.17617
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 37,208,954
FINDPEAKS_SCORE: 0.2631
FINDPEAKS_PERCENTILE: 11
HOTSPOT_SCORE: 0.275
HOTSPOT_PERCENTILE: 13
IROC_SCORE: 0.9848
IROC_PERCENTILE: 7
POISSON_SCORE: 0.3301
POISSON_PERCENTILE: 15
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM1027331_UW.Fetal_Stomach.ChromatinAccessibility.H-24510.DNase.DS20791.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNase.DS20791.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Stomach Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Stomach, Donor H-24510, Library DNase.DS20791 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.17571
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 150bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: FS DNase 10 91
BROWSER_TRACK_DESCRIPTION: UW Fetal Stomach DNase Hypersensitivity Donor H-24510 Library DNase.DS20791 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 37,208,954
FINDPEAKS_SCORE: 0.2631
FINDPEAKS_PERCENTILE: 11
HOTSPOT_SCORE: 0.275
HOTSPOT_PERCENTILE: 13
IROC_SCORE: 0.9848
IROC_PERCENTILE: 7
POISSON_SCORE: 0.3301
POISSON_PERCENTILE: 15
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

source_name: Fetal Stomach primary tissue, day 105; DNase.DS20791

value: Fetal Stomach

value: fetal


title: Chromatin accessibility assay of Fetal Renal Pelvis; DNase.DS20570

description:
sample_term_id: UBERON_0001224
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DNase.DS20570
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.14344
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.14343
****************
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: GSM1027324_UW.Fetal_Renal_Pelvis.ChromatinAccessibility.H-24493.DNase.DS20570.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNase.DS20570.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Fetal Renal Pelvis Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Renal Pelvis, Donor H-24493, Library DNase.DS20570 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.17628
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 47,531,755
FINDPEAKS_SCORE: 0.4752
FINDPEAKS_PERCENTILE: 78
HOTSPOT_SCORE: 0.4663
HOTSPOT_PERCENTILE: 76
IROC_SCORE: 0.993
IROC_PERCENTILE: 57
POISSON_SCORE: 0.5331
POISSON_PERCENTILE: 80
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM1027324_UW.Fetal_Renal_Pelvis.ChromatinAccessibility.H-24493.DNase.DS20570.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNase.DS20570.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Renal Pelvis Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Renal Pelvis, Donor H-24493, Library DNase.DS20570 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.17582
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 150bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: FRP DNase 93 70
BROWSER_TRACK_DESCRIPTION: UW Fetal Renal Pelvis DNase Hypersensitivity Donor H-24493 Library DNase.DS20570 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 47,531,755
FINDPEAKS_SCORE: 0.4752
FINDPEAKS_PERCENTILE: 78
HOTSPOT_SCORE: 0.4663
HOTSPOT_PERCENTILE: 76
IROC_SCORE: 0.993
IROC_PERCENTILE: 57
POISSON_SCORE: 0.5331
POISSON_PERCENTILE: 80
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

source_name: Fetal Kidney, renal, pelvis primary tissue, day 89; DNase.DS20570

value: Fetal Renal Pelvis

value: day 89


title: Chromatin accessibility assay of Heart; DNase.DS20383

description:
sample_term_id: UBERON_0000948
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DNase.DS20383
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.14534
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.14533
****************
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: GSM1027322_UW.Heart.ChromatinAccessibility.STL001.DNase.DS20383.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNase.DS20383.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Heart Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Heart, Donor STL001, Library DNase.DS20383 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.17601
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 42,520,289
FINDPEAKS_SCORE: 0.2991
FINDPEAKS_PERCENTILE: 24
HOTSPOT_SCORE: 0.2876
HOTSPOT_PERCENTILE: 22
IROC_SCORE: 0.9883
IROC_PERCENTILE: 13
POISSON_SCORE: 0.3792
POISSON_PERCENTILE: 37
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1027322_UW.Heart.ChromatinAccessibility.STL001.DNase.DS20383.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNase.DS20383.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Heart Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Heart, Donor STL001, Library DNase.DS20383 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.17555
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 150bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: Heart DNase 01 83
BROWSER_TRACK_DESCRIPTION: UW Heart DNase Hypersensitivity Donor STL001 Library DNase.DS20383 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 42,520,289
FINDPEAKS_SCORE: 0.2991
FINDPEAKS_PERCENTILE: 24
HOTSPOT_SCORE: 0.2876
HOTSPOT_PERCENTILE: 22
IROC_SCORE: 0.9883
IROC_PERCENTILE: 13
POISSON_SCORE: 0.3792
POISSON_PERCENTILE: 37
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: Adult Heart primary tissue, year 3; DNase.DS20383

value: Heart

value: Lin Laboratory

value: Washington University, St. Louis

value: After the donor aorta and inferior mesenteric vein (IMV) were cannulated, the aorta was flushed with 5L of 4degC cooled histidine-tryptophan-ketoglutarate solution (HTK) and the IMV was flushed with 3L of HTK which results in the perfusion of all intra-abdominal organs with preservative solution. The abdominal cavity was cooled topically with ice during perfusion. The relevant tissues were then removed and transported to a local laboratory within 1 hour. There, the tissues were minced with a blade and 1gm of tissue was placed into a cryovial with 1mL of freezing solution (freezing solution 50mL:25mL DMEM, 10mL Normosol-R, 10mL 25% BSA, 5mL DMSO, 1 tablet protease inhibitor) for 15min on ice. The cyrovial was then placed in a 1inch-thick styrofoam container, and then placed into -80C freezer, resulting in a slow freezing to -80C over an 1hour period.

value: year 3

value: Male


title: Chromatin accessibility assay of Fetal Stomach; DNase.DS20079

description:
sample_term_id: UBERON_0000945
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DNase.DS20079
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.14253
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.14252
****************
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: GSM1027318_UW.Fetal_Stomach.ChromatinAccessibility.H-24365.DNase.DS20079.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNase.DS20079.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Fetal Stomach Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Stomach, Donor H-24365, Library DNase.DS20079 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.17632
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 67,936,041
FINDPEAKS_SCORE: 0.2929
FINDPEAKS_PERCENTILE: 20
HOTSPOT_SCORE: 0.2857
HOTSPOT_PERCENTILE: 20
IROC_SCORE: 0.9895
IROC_PERCENTILE: 22
POISSON_SCORE: 0.3634
POISSON_PERCENTILE: 20
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM1027318_UW.Fetal_Stomach.ChromatinAccessibility.H-24365.DNase.DS20079.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNase.DS20079.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Stomach Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Stomach, Donor H-24365, Library DNase.DS20079 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.17586
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 150bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: FS DNase 65 79
BROWSER_TRACK_DESCRIPTION: UW Fetal Stomach DNase Hypersensitivity Donor H-24365 Library DNase.DS20079 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 67,936,041
FINDPEAKS_SCORE: 0.2929
FINDPEAKS_PERCENTILE: 20
HOTSPOT_SCORE: 0.2857
HOTSPOT_PERCENTILE: 20
IROC_SCORE: 0.9895
IROC_PERCENTILE: 22
POISSON_SCORE: 0.3634
POISSON_PERCENTILE: 20
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

source_name: Fetal Stomach primary tissue, day 96; DNase.DS20079

value: genomic DNA

value: day 96

value: Female

value: Qiagen minElut


title: Chromatin accessibility assay of Fetal Brain; DNase.DS20780

description:
sample_term_id: UBERON_0000955
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DNase.DS20780
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.14467
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.14466
****************
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: GSM1027328_UW.Fetal_Brain.ChromatinAccessibility.H-24510.DNase.DS20780.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNase.DS20780.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Fetal Brain Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Brain, Donor H-24510, Library DNase.DS20780 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.17623
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 42,789,897
FINDPEAKS_SCORE: 0.4921
FINDPEAKS_PERCENTILE: 85
HOTSPOT_SCORE: 0.4807
HOTSPOT_PERCENTILE: 83
IROC_SCORE: 0.9945
IROC_PERCENTILE: 76
POISSON_SCORE: 0.5285
POISSON_PERCENTILE: 76
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM1027328_UW.Fetal_Brain.ChromatinAccessibility.H-24510.DNase.DS20780.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNase.DS20780.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Brain Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Brain, Donor H-24510, Library DNase.DS20780 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.17577
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 150bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: FB DNase 10 80
BROWSER_TRACK_DESCRIPTION: UW Fetal Brain DNase Hypersensitivity Donor H-24510 Library DNase.DS20780 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 42,789,897
FINDPEAKS_SCORE: 0.4921
FINDPEAKS_PERCENTILE: 85
HOTSPOT_SCORE: 0.4807
HOTSPOT_PERCENTILE: 83
IROC_SCORE: 0.9945
IROC_PERCENTILE: 76
POISSON_SCORE: 0.5285
POISSON_PERCENTILE: 76
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

source_name: Fetal Brain primary tissue, day 105; DNase.DS20780

value: Fetal Brain

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

value: Primary Tissue

value: Chromatin Accessibility


title: Chromatin accessibility assay of Fetal Renal Pelvis; DNase.DS20027

description:
sample_term_id: UBERON_0001224
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DNase.DS20027
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.14348
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.14347
****************
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: GSM1027317_UW.Fetal_Renal_Pelvis.ChromatinAccessibility.H-24365.DNase.DS20027.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNase.DS20027.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Fetal Renal Pelvis Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Renal Pelvis, Donor H-24365, Library DNase.DS20027 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.17591
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 26,890,998
FINDPEAKS_SCORE: 0.4752
FINDPEAKS_PERCENTILE: 78
HOTSPOT_SCORE: 0.4747
HOTSPOT_PERCENTILE: 78
IROC_SCORE: 0.9947
IROC_PERCENTILE: 83
POISSON_SCORE: 0.5297
POISSON_PERCENTILE: 78
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM1027317_UW.Fetal_Renal_Pelvis.ChromatinAccessibility.H-24365.DNase.DS20027.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNase.DS20027.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Renal Pelvis Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Renal Pelvis, Donor H-24365, Library DNase.DS20027 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.17545
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 150bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: FRP DNase 65 27
BROWSER_TRACK_DESCRIPTION: UW Fetal Renal Pelvis DNase Hypersensitivity Donor H-24365 Library DNase.DS20027 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 26,890,998
FINDPEAKS_SCORE: 0.4752
FINDPEAKS_PERCENTILE: 78
HOTSPOT_SCORE: 0.4747
HOTSPOT_PERCENTILE: 78
IROC_SCORE: 0.9947
IROC_PERCENTILE: 83
POISSON_SCORE: 0.5297
POISSON_PERCENTILE: 78
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

source_name: Fetal Kidney, renal, pelvis primary tissue, day 96; DNase.DS20027

value: UW

value: fetal


title: Chromatin accessibility assay of Fetal Testes; DNase.DS20170

description:
sample_term_id: UBERON_0000473
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DNase.DS20170
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.14261
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.14260
****************
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: GSM1027319_UW.Fetal_Testes.ChromatinAccessibility.H23914_H24089_H24218_H24244.DNase.DS20170.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNase.DS20170.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Fetal Testes Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Testes, Donor H23914_H24089_H24218_H24244, Library DNase.DS20170 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.17609
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 48,133,230
FINDPEAKS_SCORE: 0.4014
FINDPEAKS_PERCENTILE: 54
HOTSPOT_SCORE: 0.3884
HOTSPOT_PERCENTILE: 50
IROC_SCORE: 0.993
IROC_PERCENTILE: 57
POISSON_SCORE: 0.442
POISSON_PERCENTILE: 50
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM1027319_UW.Fetal_Testes.ChromatinAccessibility.H23914_H24089_H24218_H24244.DNase.DS20170.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNase.DS20170.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Testes Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Testes, Donor H23914_H24089_H24218_H24244, Library DNase.DS20170 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.17563
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 150bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: FT DNase 44 70
BROWSER_TRACK_DESCRIPTION: UW Fetal Testes DNase Hypersensitivity Donor H23914_H24089_H24218_H24244 Library DNase.DS20170 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 48,133,230
FINDPEAKS_SCORE: 0.4014
FINDPEAKS_PERCENTILE: 54
HOTSPOT_SCORE: 0.3884
HOTSPOT_PERCENTILE: 50
IROC_SCORE: 0.993
IROC_PERCENTILE: 57
POISSON_SCORE: 0.442
POISSON_PERCENTILE: 50
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

source_name: Fetal Testes primary tissue, pool; DNase.DS20170

value: Fetal Testes

value: pool


title: Chromatin accessibility assay of Fetal Adrenal Gland; DNase.DS19583

description:
sample_term_id: UBERON_0002369
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DNase.DS19583
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.14471
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.14470
****************
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: GSM1027311_UW.Fetal_Adrenal_Gland.ChromatinAccessibility.H-24279.DNase.DS19583.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNase.DS19583.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Fetal Adrenal Gland Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Adrenal Gland, Donor H-24279, Library DNase.DS19583 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.17605
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 51,684,653
FINDPEAKS_SCORE: 0.282
FINDPEAKS_PERCENTILE: 15
HOTSPOT_SCORE: 0.2782
HOTSPOT_PERCENTILE: 15
IROC_SCORE: 0.9913
IROC_PERCENTILE: 30
POISSON_SCORE: 0.3284
POISSON_PERCENTILE: 13
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM1027311_UW.Fetal_Adrenal_Gland.ChromatinAccessibility.H-24279.DNase.DS19583.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNase.DS19583.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Adrenal Gland Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Adrenal Gland, Donor H-24279, Library DNase.DS19583 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.17559
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 150bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: FAG DNase 79 83
BROWSER_TRACK_DESCRIPTION: UW Fetal Adrenal Gland DNase Hypersensitivity Donor H-24279 Library DNase.DS19583 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 51,684,653
FINDPEAKS_SCORE: 0.282
FINDPEAKS_PERCENTILE: 15
HOTSPOT_SCORE: 0.2782
HOTSPOT_PERCENTILE: 15
IROC_SCORE: 0.9913
IROC_PERCENTILE: 30
POISSON_SCORE: 0.3284
POISSON_PERCENTILE: 13
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

source_name: Fetal Adrenal Gland primary tissue, day 101; DNase.DS19583

value: Fetal Adrenal Gland

value: day 101


title: Chromatin accessibility assay of Fetal Muscle, Back; DNase.DS21048

description:
sample_term_id: UBERON_0002324
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DNase.DS21048
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.14316
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.14315
****************
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: GSM1027341_UW.Fetal_Muscle_Back.ChromatinAccessibility.H-24595.DNase.DS21048.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNase.DS21048.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Fetal Muscle Back Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Muscle Back, Donor H-24595, Library DNase.DS21048 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.17600
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 33,397,194
FINDPEAKS_SCORE: 0.4354
FINDPEAKS_PERCENTILE: 61
HOTSPOT_SCORE: 0.419
HOTSPOT_PERCENTILE: 59
IROC_SCORE: 0.9943
IROC_PERCENTILE: 70
POISSON_SCORE: 0.4807
POISSON_PERCENTILE: 61
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM1027341_UW.Fetal_Muscle_Back.ChromatinAccessibility.H-24595.DNase.DS21048.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNase.DS21048.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Muscle Back Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Muscle Back, Donor H-24595, Library DNase.DS21048 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.17554
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 150bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: FMB DNase 95 48
BROWSER_TRACK_DESCRIPTION: UW Fetal Muscle Back DNase Hypersensitivity Donor H-24595 Library DNase.DS21048 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 33,397,194
FINDPEAKS_SCORE: 0.4354
FINDPEAKS_PERCENTILE: 61
HOTSPOT_SCORE: 0.419
HOTSPOT_PERCENTILE: 59
IROC_SCORE: 0.9943
IROC_PERCENTILE: 70
POISSON_SCORE: 0.4807
POISSON_PERCENTILE: 61
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

source_name: Fetal Muscle, Back primary tissue, day 108; DNase.DS21048

value: Fetal Muscle, Back

value: day 108


title: Chromatin accessibility assay of Fetal Thymus; DNase.DS19675

description:
sample_term_id: UBERON_0002370
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DNase.DS19675
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.14265
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.14264
****************
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: GSM1027313_UW.Fetal_Thymus.ChromatinAccessibility.H-24297.DNase.DS19675.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNase.DS19675.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Fetal Thymus Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Thymus, Donor H-24297, Library DNase.DS19675 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.17618
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 51,155,098
FINDPEAKS_SCORE: 0.3381
FINDPEAKS_PERCENTILE: 41
HOTSPOT_SCORE: 0.3244
HOTSPOT_PERCENTILE: 37
IROC_SCORE: 0.9979
IROC_PERCENTILE: 100
POISSON_SCORE: 0.364
POISSON_PERCENTILE: 22
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM1027313_UW.Fetal_Thymus.ChromatinAccessibility.H-24297.DNase.DS19675.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNase.DS19675.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Thymus Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Thymus, Donor H-24297, Library DNase.DS19675 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.17572
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 150bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: FT DNase 97 75
BROWSER_TRACK_DESCRIPTION: UW Fetal Thymus DNase Hypersensitivity Donor H-24297 Library DNase.DS19675 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 51,155,098
FINDPEAKS_SCORE: 0.3381
FINDPEAKS_PERCENTILE: 41
HOTSPOT_SCORE: 0.3244
HOTSPOT_PERCENTILE: 37
IROC_SCORE: 0.9979
IROC_PERCENTILE: 100
POISSON_SCORE: 0.364
POISSON_PERCENTILE: 22
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

source_name: Fetal Thymus primary tissue, day 104; DNase.DS19675

value: Fetal Thymus

value: day 104

value: Male


title: Chromatin accessibility assay of Fetal Renal Cortex; DNase.DS20018

description:
sample_term_id: UBERON_0001225
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DNase.DS20018
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.14364
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.14363
****************
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: GSM1027314_UW.Fetal_Renal_Cortex.ChromatinAccessibility.H-24342.DNase.DS20018.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNase.DS20018.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Fetal Renal Cortex Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Renal Cortex, Donor H-24342, Library DNase.DS20018 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.17604
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 38,527,776
FINDPEAKS_SCORE: 0.4966
FINDPEAKS_PERCENTILE: 87
HOTSPOT_SCORE: 0.4873
HOTSPOT_PERCENTILE: 87
IROC_SCORE: 0.9946
IROC_PERCENTILE: 80
POISSON_SCORE: 0.5569
POISSON_PERCENTILE: 87
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM1027314_UW.Fetal_Renal_Cortex.ChromatinAccessibility.H-24342.DNase.DS20018.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNase.DS20018.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Renal Cortex Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Renal Cortex, Donor H-24342, Library DNase.DS20018 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.17558
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 150bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: FRC DNase 42 18
BROWSER_TRACK_DESCRIPTION: UW Fetal Renal Cortex DNase Hypersensitivity Donor H-24342 Library DNase.DS20018 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 38,527,776
FINDPEAKS_SCORE: 0.4966
FINDPEAKS_PERCENTILE: 87
HOTSPOT_SCORE: 0.4873
HOTSPOT_PERCENTILE: 87
IROC_SCORE: 0.9946
IROC_PERCENTILE: 80
POISSON_SCORE: 0.5569
POISSON_PERCENTILE: 87
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

source_name: Fetal Kidney, renal, cortex primary tissue, day 96; DNase.DS20018

value: Fetal Renal Cortex

value: genomic DNA

value: day 96

value: Female


title: Chromatin accessibility assay of Fetal Renal Pelvis; DNase.DS20022

description:
sample_term_id: UBERON_0001224
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DNase.DS20022
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.14351
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.14350
****************
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: GSM1027315_UW.Fetal_Renal_Pelvis.ChromatinAccessibility.H-24342.DNase.DS20022.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNase.DS20022.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Fetal Renal Pelvis Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Renal Pelvis, Donor H-24342, Library DNase.DS20022 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.17626
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 45,629,831
FINDPEAKS_SCORE: 0.4586
FINDPEAKS_PERCENTILE: 67
HOTSPOT_SCORE: 0.4471
HOTSPOT_PERCENTILE: 70
IROC_SCORE: 0.9923
IROC_PERCENTILE: 46
POISSON_SCORE: 0.5092
POISSON_PERCENTILE: 70
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM1027315_UW.Fetal_Renal_Pelvis.ChromatinAccessibility.H-24342.DNase.DS20022.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNase.DS20022.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Renal Pelvis Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Renal Pelvis, Donor H-24342, Library DNase.DS20022 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.17580
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 150bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: FRP DNase 42 22
BROWSER_TRACK_DESCRIPTION: UW Fetal Renal Pelvis DNase Hypersensitivity Donor H-24342 Library DNase.DS20022 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 45,629,831
FINDPEAKS_SCORE: 0.4586
FINDPEAKS_PERCENTILE: 67
HOTSPOT_SCORE: 0.4471
HOTSPOT_PERCENTILE: 70
IROC_SCORE: 0.9923
IROC_PERCENTILE: 46
POISSON_SCORE: 0.5092
POISSON_PERCENTILE: 70
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

source_name: Fetal Kidney, renal, pelvis primary tissue, day 96; DNase.DS20022

value: Fetal Renal Pelvis

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

value: Primary Tissue

value: Qiagen minElut


title: Chromatin accessibility assay of Fetal Spinal Cord; DNase.DS19260

description:
sample_term_id: UBERON_0002240
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DNase.DS19260
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.14296
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.14295
****************
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: GSM1027308_UW.Fetal_Spinal_Cord.ChromatinAccessibility.H-24244.DNase.DS19260.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNase.DS19260.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Fetal Spinal Cord Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Spinal Cord, Donor H-24244, Library DNase.DS19260 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.17602
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 37,879,953
FINDPEAKS_SCORE: 0.2967
FINDPEAKS_PERCENTILE: 22
HOTSPOT_SCORE: 0.2924
HOTSPOT_PERCENTILE: 24
IROC_SCORE: 0.9896
IROC_PERCENTILE: 24
POISSON_SCORE: 0.3756
POISSON_PERCENTILE: 33
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM1027308_UW.Fetal_Spinal_Cord.ChromatinAccessibility.H-24244.DNase.DS19260.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNase.DS19260.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Spinal Cord Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Spinal Cord, Donor H-24244, Library DNase.DS19260 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.17556
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 150bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: FSC DNase 44 60
BROWSER_TRACK_DESCRIPTION: UW Fetal Spinal Cord DNase Hypersensitivity Donor H-24244 Library DNase.DS19260 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 37,879,953
FINDPEAKS_SCORE: 0.2967
FINDPEAKS_PERCENTILE: 22
HOTSPOT_SCORE: 0.2924
HOTSPOT_PERCENTILE: 24
IROC_SCORE: 0.9896
IROC_PERCENTILE: 24
POISSON_SCORE: 0.3756
POISSON_PERCENTILE: 33
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

source_name: Fetal Spinal, Cord primary tissue, day 96; DNase.DS19260

value: Fetal Spinal Cord

value: UW

value: fetal

value: Chromatin Accessibility