title: Chromatin accessibility assay of Fetal Renal Pelvis, Right; DS18961

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: DS18961
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.9955
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.9954
****************
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: GSM817204_UW.Fetal_Renal_Pelvis_Right.ChromatinAccessibility.H-24169.DS18961.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS18961.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of Fetal Renal Pelvis Right Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Renal Pelvis Right, Donor H-24169, Library DS18961 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.12624
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 26,852,213
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.3824
FINDPEAKS_PERCENTILE: 52
HOTSPOT_SCORE: 0.3761
HOTSPOT_PERCENTILE: 52
IROC_SCORE: 0.9923
IROC_PERCENTILE: 38
POISSON_SCORE: 0.4452
POISSON_PERCENTILE: 51
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

ANALYSIS FILE NAME: GSM817204_UW.Fetal_Renal_Pelvis_Right.ChromatinAccessibility.H-24169.DS18961.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS18961.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Renal Pelvis Right Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Renal Pelvis Right, Donor H-24169, Library DS18961 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.12687
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 150bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 6
BROWSER_TRACK_NAME: FRPR DNase 69 61
BROWSER_TRACK_DESCRIPTION: UW Fetal Renal Pelvis Right DNase Hypersensitivity Donor H-24169 Library DS18961 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 26,852,213
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.3824
FINDPEAKS_PERCENTILE: 52
HOTSPOT_SCORE: 0.3761
HOTSPOT_PERCENTILE: 52
IROC_SCORE: 0.9923
IROC_PERCENTILE: 38
POISSON_SCORE: 0.4452
POISSON_PERCENTILE: 51
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

source_name: Fetal Kidney, renal, pelvis, Right primary tissue, day 120; DS18961

value: Fetal Renal Pelvis, Right

value: genomic DNA

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

value: Primary Tissue

value: UW

value: fetal

value: day 120

value: Male

value: Chromatin Accessibility

value: Qiagen minElut

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


title: Reference Epigenome: ChIP-Seq Analysis of H4K8ac in Mesenchymal Stem Cells; renlab.H4K8ac.MSC.02.01

status: Public on Oct 15 2011

type: SRA

city: La Jolla

first: UCSD AND

last: SALK

state: CA

address: Health Sciences Drive

country: USA

institute: University of California, San Diego

description:
sample_term_id: EFO_0000586
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H4K8ac in Mesenchymal Stem Cells. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AK287
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.10234
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.10206
****************
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: GSM818059_UCSD.H1_Derived_Mesenchymal_Stem_Cells.H4K8ac.AK287.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H4K8ac.MSC.02.01.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of H1 Derived Mesenchymal Stem Cells Histone H4K8ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H4K8ac ChIP-Seq on H1 Derived Mesenchymal Stem Cells, Library AK287, 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.12387
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 45,004,747
NUMBER_OF_H4K8ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 3
FINDPEAKS_SCORE: 0.2523
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.4164
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.981
IROC_PERCENTILE: 100
POISSON_SCORE: 0.4766
POISSON_PERCENTILE: 67
MAXIMUM_REPLICATE_CORRELATION: 0.94

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

ANALYSIS FILE NAME: GSM818059_UCSD.H1_Derived_Mesenchymal_Stem_Cells.H4K8ac.AK287.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H4K8ac.MSC.02.01.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Derived Mesenchymal Stem Cells Histone H4K8ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H4K8ac ChIP-Seq read mappings from the H1 Derived Mesenchymal Stem Cells, Library AK287, 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.12460
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 6
BROWSER_TRACK_NAME: HDMSC H4K8ac 87
BROWSER_TRACK_DESCRIPTION: UCSD H1 Derived Mesenchymal Stem Cells Histone H4K8ac Library AK287 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 45,004,747
NUMBER_OF_H4K8ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 3
FINDPEAKS_SCORE: 0.2523
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.4164
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.981
IROC_PERCENTILE: 100
POISSON_SCORE: 0.4766
POISSON_PERCENTILE: 67
MAXIMUM_REPLICATE_CORRELATION: 0.94

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

molecule: genomic DNA

organism: Homo sapiens

source_name: Human embryonic stem cells received from the James Thomson laboratory.  Cells are from the H1 line and are differentiated into mesenchymal stem cells.; renlab.H4K8ac.MSC.02.01

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

tag: sample alias

tag: sample common name

value: H1 Derived Mesenchymal Stem Cells

tag: molecule

tag: disease

value: James Thomson Laboratory

value: Cell Line

tag: line

tag: lineage

value: Embryonic Stem Cell

value: Embryonic stem cell differentiated into mesenchymal stem cells

value: Publication in progress

tag: passage

tag: medium

tag: Sex

tag: batch

value: Histone H4K8ac

value: Biorupter

value: 500 micrograms

value: magnetic anti-rabbit

value: 5 micrograms

value: Millipore


title: Ltap_antiJ_JBP2KO_BrdU

city: SEATTLE

first: Gowthaman

last: Ramasamy

state: WASHINGTON

address: 307 WESTLAKE AVE N

department: GHBC

institute: SEATTLE BIOMEDICAL RESEARCH INSTITUTE

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

organism: Leishmania tarentolae

source_name: Procyclic Promastigotes

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

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

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

tag: strain

value: Parrot

tag: developmental stage

value: Procyclic Promastigotes

tag: genotype/variation

tag: treatment

value: BrdU

tag: chip antibody

value: antiJ


title: fertile_donor1

status: Public on Oct 16 2011

city: Detroit

first: Stephen

middle: A

last: Krawetz

state: MI

address: 275 E. Hancock, CS Mott Center

department: Obstetrics and Gynecology

institute: Wayne State University

library_source: transcriptomic

data_processing: Alignment: Sequence reads obtained from Bustard (Illumina Genome Analyzer II) were mapped to the human (February, 2009) genome using Novoalign (2.05.33MT). Aligned sequence reads for each of the three samples were separated into two classes.  Those reads mapping to a unique region on the genome were classified as Uniquely Mapped (UM).  Sequence reads mapping to 2–10 locations were classified as Multiple Mapped (MM).

molecule: total RNA

source_name: spermatozoa

extract_protocol: samples were thawed and the sperm cells were separated from contaminants through a 50% Percoll cushion.  The sperm cells were then processed for separate extraction of small (<200 b) and large (> 200b) RNA using Qiagen Rneasy kit

treatment_protocol: semen samples were frozen upon reception.

tag: tissue

value: Spermatozoa


title: Reference Epigenome: ChIP-Seq Analysis of H3K27ac in Neural Progenitor Cells; renlab.H3K27ac.NPC.03.01

description:
sample_term_id: CL_0000047
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K27ac in Neural Progenitor Cells. Sequencing was done on the Illumina Genome Analyzer IIx platform.
Library name: AK220
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.10101
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.10100
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM818031_UCSD.H1_Derived_Neuronal_Progenitor_Cultured_Cells.H3K27ac.AK220.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27ac.NPC.03.01.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of H1 Derived Neuronal Progenitor Cultured Cells Histone H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27ac ChIP-Seq on H1 Derived Neuronal Progenitor Cultured Cells, Library AK220, 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.12383
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 34,903,612
NUMBER_OF_H3K27ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 5
FINDPEAKS_SCORE: 0.1162
FINDPEAKS_PERCENTILE: 20
HOTSPOT_SCORE: 0.1409
HOTSPOT_PERCENTILE: 20
IROC_SCORE: 0.9936
IROC_PERCENTILE: 60
POISSON_SCORE: 0.2129
POISSON_PERCENTILE: 20
MAXIMUM_REPLICATE_CORRELATION: 0.54

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

ANALYSIS FILE NAME: GSM818031_UCSD.H1_Derived_Neuronal_Progenitor_Cultured_Cells.H3K27ac.AK220.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K27ac.NPC.03.01.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Derived Neuronal Progenitor Cultured Cells Histone H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K27ac ChIP-Seq read mappings from the H1 Derived Neuronal Progenitor Cultured Cells, Library AK220, 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.12456
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 6
BROWSER_TRACK_NAME: HDNP H3K27ac 20
BROWSER_TRACK_DESCRIPTION: UCSD H1 Derived Neuronal Progenitor Cultured Cells Histone H3K27ac Library AK220 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 34,903,612
NUMBER_OF_H3K27ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 5
FINDPEAKS_SCORE: 0.1162
FINDPEAKS_PERCENTILE: 20
HOTSPOT_SCORE: 0.1409
HOTSPOT_PERCENTILE: 20
IROC_SCORE: 0.9936
IROC_PERCENTILE: 60
POISSON_SCORE: 0.2129
POISSON_PERCENTILE: 20
MAXIMUM_REPLICATE_CORRELATION: 0.54

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

source_name: Human embryonic stem cells received from the James Thomson laboratory.  Cells are from the H1 line and are differentiated into neural progenitor cells.; renlab.H3K27ac.NPC.03.01

value: genomic DNA

value: Embryonic stem cell differentiated into neural progenitor cells

value: Male

value: Histone H3K27ac

value: Active Motif


title: Chromatin accessibility assay of Fetal Renal Cortex, Left; DS18931

city: Seattle

first: Northwest

last: REMC

state: WA

institute: University of Washington

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: DS18931
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.10018
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.10017
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM817203_UW.Fetal_Renal_Cortex_Left.ChromatinAccessibility.H-24169.DS18931.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS18931.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of Fetal Renal Cortex Left Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Renal Cortex Left, Donor H-24169, Library DS18931 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.12623
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 23,113,025
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.3662
FINDPEAKS_PERCENTILE: 48
HOTSPOT_SCORE: 0.3653
HOTSPOT_PERCENTILE: 49
IROC_SCORE: 0.993
IROC_PERCENTILE: 46
POISSON_SCORE: 0.44
POISSON_PERCENTILE: 46
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

ANALYSIS FILE NAME: GSM817203_UW.Fetal_Renal_Cortex_Left.ChromatinAccessibility.H-24169.DS18931.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS18931.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Renal Cortex Left Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Renal Cortex Left, Donor H-24169, Library DS18931 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.12686
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 150bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 6
BROWSER_TRACK_NAME: FRCL DNase 69 31
BROWSER_TRACK_DESCRIPTION: UW Fetal Renal Cortex Left DNase Hypersensitivity Donor H-24169 Library DS18931 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 23,113,025
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.3662
FINDPEAKS_PERCENTILE: 48
HOTSPOT_SCORE: 0.3653
HOTSPOT_PERCENTILE: 49
IROC_SCORE: 0.993
IROC_PERCENTILE: 46
POISSON_SCORE: 0.44
POISSON_PERCENTILE: 46
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

source_name: Fetal Kidney, renal, cortex, Left primary tissue, day 120; DS18931

extract_protocol: Library construction protocol: Single read - Illumina

value: Fetal Renal Cortex, Left

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

value: Primary Tissue

value: UW

value: fetal

value: day 120

value: Chromatin Accessibility

value: Qiagen minElut

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


title: Chromatin accessibility assay of Fetal Renal Cortex, Right; DS18928

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: DS18928
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.10004
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.10003
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM817202_UW.Fetal_Renal_Cortex_Right.ChromatinAccessibility.H-24169.DS18928.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS18928.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of Fetal Renal Cortex Right Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Renal Cortex Right, Donor H-24169, Library DS18928 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.12622
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 28,371,473
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.3548
FINDPEAKS_PERCENTILE: 43
HOTSPOT_SCORE: 0.3477
HOTSPOT_PERCENTILE: 44
IROC_SCORE: 0.9917
IROC_PERCENTILE: 32
POISSON_SCORE: 0.4292
POISSON_PERCENTILE: 43
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

ANALYSIS FILE NAME: GSM817202_UW.Fetal_Renal_Cortex_Right.ChromatinAccessibility.H-24169.DS18928.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS18928.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Renal Cortex Right Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Renal Cortex Right, Donor H-24169, Library DS18928 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.12685
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 150bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 6
BROWSER_TRACK_NAME: FRCR DNase 69 28
BROWSER_TRACK_DESCRIPTION: UW Fetal Renal Cortex Right DNase Hypersensitivity Donor H-24169 Library DS18928 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 28,371,473
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.3548
FINDPEAKS_PERCENTILE: 43
HOTSPOT_SCORE: 0.3477
HOTSPOT_PERCENTILE: 44
IROC_SCORE: 0.9917
IROC_PERCENTILE: 32
POISSON_SCORE: 0.4292
POISSON_PERCENTILE: 43
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

source_name: Fetal Kidney, renal, cortex, Right primary tissue, day 120; DS18928

value: Fetal Renal Cortex, Right


title: Reference Epigenome: ChIP-Seq Analysis of H3K9ac in Neural Progenitor Cells; renlab.H3K9ac.NPC.01.01

description:
sample_term_id: CL_0000047
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K9ac in Neural Progenitor Cells. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AK263
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.10184
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.10100
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM818052_UCSD.H1_Derived_Neuronal_Progenitor_Cultured_Cells.H3K9ac.AK263.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K9ac.NPC.01.01.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of H1 Derived Neuronal Progenitor Cultured Cells Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K9ac ChIP-Seq on H1 Derived Neuronal Progenitor Cultured Cells, Library AK263, 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.12389
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 30,954,772
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 9
FINDPEAKS_SCORE: 0.1958
FINDPEAKS_PERCENTILE: 67
HOTSPOT_SCORE: 0.4971
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9871
IROC_PERCENTILE: 56
POISSON_SCORE: 0.4961
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM818052_UCSD.H1_Derived_Neuronal_Progenitor_Cultured_Cells.H3K9ac.AK263.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K9ac.NPC.01.01.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of H1 Derived Neuronal Progenitor Cultured Cells Histone H3K9ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K9ac ChIP-Seq read mappings from the H1 Derived Neuronal Progenitor Cultured Cells, Library AK263, 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.12462
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 6
BROWSER_TRACK_NAME: HDNP H3K9ac 63
BROWSER_TRACK_DESCRIPTION: UCSD H1 Derived Neuronal Progenitor Cultured Cells Histone H3K9ac Library AK263 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 30,954,772
NUMBER_OF_H3K9ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 9
FINDPEAKS_SCORE: 0.1958
FINDPEAKS_PERCENTILE: 67
HOTSPOT_SCORE: 0.4971
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9871
IROC_PERCENTILE: 56
POISSON_SCORE: 0.4961
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: Human embryonic stem cells received from the James Thomson laboratory.  Cells are from the H1 line and are differentiated into neural progenitor cells.; renlab.H3K9ac.NPC.01.01

value: James Thomson Laboratory

value: Cell Line

value: Embryonic Stem Cell

value: Publication in progress

value: Histone H3K9ac

value: Biorupter

value: 500 micrograms

value: magnetic anti-rabbit

value: 5 micrograms


title: LtaP_antiJ_WT

value: Parrot

value: Procyclic Promastigotes

value: WT

value: antiJ


title: Reference Epigenome: ChIP-Seq Analysis of H2BK5ac in IMR90 Cells; renlab.H2BK5ac.IMR90.03.01

description:
sample_term_id: EFO_0001196
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H2BK5ac in IMR90 Cells. Sequencing was done on the Illumina Genome Analyzer platform.
Library name: YL281
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.10138
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.10137
****************
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: GSM818017_UCSD.IMR90.H2BK5ac.YL281.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H2BK5ac.IMR90.03.01.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of IMR90 Cell Line Histone H2BK5ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H2BK5ac ChIP-Seq on IMR90 Cell Line, Library YL281, 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.12395
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 48,290,850
NUMBER_OF_H2BK5ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 7
FINDPEAKS_SCORE: 0.3038
FINDPEAKS_PERCENTILE: 71
HOTSPOT_SCORE: 0.3651
HOTSPOT_PERCENTILE: 71
IROC_SCORE: 0.9505
IROC_PERCENTILE: 71
POISSON_SCORE: 0.3953
POISSON_PERCENTILE: 71
MAXIMUM_REPLICATE_CORRELATION: 0.1

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

ANALYSIS FILE NAME: GSM818017_UCSD.IMR90.H2BK5ac.YL281.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H2BK5ac.IMR90.03.01.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of IMR90 Cell Line Histone H2BK5ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H2BK5ac ChIP-Seq read mappings from the IMR90 Cell Line, Library YL281, 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.12468
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 6
BROWSER_TRACK_NAME: IMR90 H2BK5ac 81
BROWSER_TRACK_DESCRIPTION: UCSD IMR90 Cell Line Histone H2BK5ac Library YL281 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 48,290,850
NUMBER_OF_H2BK5ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 7
FINDPEAKS_SCORE: 0.3038
FINDPEAKS_PERCENTILE: 71
HOTSPOT_SCORE: 0.3651
HOTSPOT_PERCENTILE: 71
IROC_SCORE: 0.9505
IROC_PERCENTILE: 71
POISSON_SCORE: 0.3953
POISSON_PERCENTILE: 71
MAXIMUM_REPLICATE_CORRELATION: 0.1

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

source_name: IMR90 Cell Line, additional biological replicate; renlab.H2BK5ac.IMR90.03.01

value: IMR90 Cell Line

value: genomic DNA

value: ATCC

value: Fetal lung fibroblast

value: Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)

value: Female

value: Histone H2BK5ac

value: Active Motif


title: Chromatin accessibility assay of Fetal Muscle, Leg; DS18844

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: DS18844
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.9839
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.9838
****************
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: GSM817201_UW.Fetal_Muscle_Leg.ChromatinAccessibility.H-24143.DS18844.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS18844.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of Fetal Muscle Leg Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Muscle Leg, Donor H-24143, Library DS18844 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.12621
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 21,258,233
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.2763
FINDPEAKS_PERCENTILE: 13
HOTSPOT_SCORE: 0.2828
HOTSPOT_PERCENTILE: 13
IROC_SCORE: 0.9893
IROC_PERCENTILE: 17
POISSON_SCORE: 0.3617
POISSON_PERCENTILE: 16
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM817201_UW.Fetal_Muscle_Leg.ChromatinAccessibility.H-24143.DS18844.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS18844.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Muscle Leg Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Muscle Leg, Donor H-24143, Library DS18844 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.12684
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 150bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 6
BROWSER_TRACK_NAME: FML DNase 43 44
BROWSER_TRACK_DESCRIPTION: UW Fetal Muscle Leg DNase Hypersensitivity Donor H-24143 Library DS18844 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 21,258,233
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.2763
FINDPEAKS_PERCENTILE: 13
HOTSPOT_SCORE: 0.2828
HOTSPOT_PERCENTILE: 13
IROC_SCORE: 0.9893
IROC_PERCENTILE: 17
POISSON_SCORE: 0.3617
POISSON_PERCENTILE: 16
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

source_name: Fetal Muscle, Leg primary tissue, day 115; DS18844

value: Fetal Muscle, Leg

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

value: Primary Tissue

value: UW

value: fetal

value: day 115

value: Chromatin Accessibility

value: Qiagen minElut

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


title: Reference Epigenome: ChIP-Seq Analysis of H3K23ac in BMP4 Mesendoderm Cells; renlab.H3K23ac.BMP4M.01.01

description:
sample_term_id: NTR_0000856
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K23ac in BMP4 Mesendoderm Cells. Sequencing was done on the Illumina Genome Analayzer IIx platform.
Library name: AK173
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.10094
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.7808
****************
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: GSM818025_UCSD.H1_BMP4_Derived_Mesendoderm_Cultured_Cells.H3K23ac.AK173.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K23ac.BMP4M.01.01.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of H1 BMP4 Derived Mesendoderm Cultured Cells Histone H3K23ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K23ac ChIP-Seq on H1 BMP4 Derived Mesendoderm Cultured Cells, Library AK173, 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.12404
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 28,515,068
NUMBER_OF_H3K23ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 6
FINDPEAKS_SCORE: 0.0077
FINDPEAKS_PERCENTILE: 17
HOTSPOT_SCORE: 0.0609
HOTSPOT_PERCENTILE: 50
IROC_SCORE: 0.4652
IROC_PERCENTILE: 17
POISSON_SCORE: 0.2237
POISSON_PERCENTILE: 50
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM818025_UCSD.H1_BMP4_Derived_Mesendoderm_Cultured_Cells.H3K23ac.AK173.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K23ac.BMP4M.01.01.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of H1 BMP4 Derived Mesendoderm Cultured Cells Histone H3K23ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K23ac ChIP-Seq read mappings from the H1 BMP4 Derived Mesendoderm Cultured Cells, Library AK173, 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.12477
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 6
BROWSER_TRACK_NAME: HBDM H3K23ac 73
BROWSER_TRACK_DESCRIPTION: UCSD H1 BMP4 Derived Mesendoderm Cultured Cells Histone H3K23ac Library AK173 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 28,515,068
NUMBER_OF_H3K23ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 6
FINDPEAKS_SCORE: 0.0077
FINDPEAKS_PERCENTILE: 17
HOTSPOT_SCORE: 0.0609
HOTSPOT_PERCENTILE: 50
IROC_SCORE: 0.4652
IROC_PERCENTILE: 17
POISSON_SCORE: 0.2237
POISSON_PERCENTILE: 50
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: Human embryonic stem cells received from the James Thomson laboratory.  Cells are from the H1 line and are differentiated into mesendoderm by treatment with BMP4.; renlab.H3K23ac.BMP4M.01.01

value: James Thomson Laboratory

value: Cell Line

value: Embryonic Stem Cell

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

value: H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days

value: Between 20 and 30

value: Male

value: Histone H3K23ac

value: Biorupter

value: 500 micrograms

value: magnetic anti-rabbit

value: 5 micrograms

value: Upstate


title: Ltap_antiJ_JBP2KO

value: Parrot

value: Procyclic Promastigotes

value: antiJ


title: USC_ChipSeq_HeLa-S3_Input_UCDavis

status: Public on Oct 18 2011

city: Stanford

first: ENCODE

last: DCC

address: 300 Pasteur Dr

institute: ENCODE DCC

tag: lab

value: USC

tag: lab description

value: Farnham - University of Southern California

tag: datatype

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

tag: cell

tag: cell organism

value: human

tag: cell description

value: cervical carcinoma

tag: cell karyotype

value: cancer

tag: cell lineage

value: ectoderm

tag: cell sex

value: F

tag: treatment description

value: No special treatment or protocol applies

tag: antibody

value: Input

tag: antibody description

value: Control signal which may be subtracted from experimental raw signal before peaks are called.

tag: control

value: UCDavis

tag: control description

value: Input library was prepared at UC Davis.

tag: controlid


title: LtaP_JBP2KO_BrdU_SL_repeat1

extract_protocol: First strand cDNA synthesis was performed using 1 μg of DNAse-treated total RNA using Superscript III (Invitrogen) and primer (5’- TCCGATCTCTNNNNNNN-3’). The RNA from DNA/RNA heteroduplexes was degraded using 2 U of RNAse H (Invitrogen) and purified using QIAquick PCR purification kit (Qiagen). Second strand synthesis reactions were performed using 3’-5’ exo- Klenow Fragment (New England Biolabs). The resulting double strand DNA was purified using a QIAquick PCR purification kit. Enrichment of DNA fragments with adapters was performed by PCR using primers 5’-CAAGCAGAAGACGGCATACGAGCTCTTCCGATCTCT-3’ and 5’-AATGATACGGCGACCACCGACACTCTTTCCCTACATCAGTTTCTGTACTTTA-3’. The resulting enriched fragments were QIAquick PCR purified and eluted.

tag: strain

value: Parrot

tag: developmental stage

tag: rna subtype

value: total RNA

tag: genotype/variation

tag: treatment

value: BrdU


title: Chromatin accessibility assay of Penis Foreskin Keratinocytes Primary Cells; DS18695

description:
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS18695
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.9790
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: GSM817195_UW.Penis_Foreskin_Keratinocyte_Primary_Cells.ChromatinAccessibility.skin01.DS18695.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS18695.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of Penis Foreskin Keratinocyte Primary Cells Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Penis Foreskin Keratinocyte Primary Cells, Donor skin01, Library DS18695 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.12615
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 34,521,027
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.455
FINDPEAKS_PERCENTILE: 71
HOTSPOT_SCORE: 0.4944
HOTSPOT_PERCENTILE: 87
IROC_SCORE: 0.9963
IROC_PERCENTILE: 89
POISSON_SCORE: 0.5389
POISSON_PERCENTILE: 83
MAXIMUM_REPLICATE_CORRELATION: 1.0

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

ANALYSIS FILE NAME: GSM817195_UW.Penis_Foreskin_Keratinocyte_Primary_Cells.ChromatinAccessibility.skin01.DS18695.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS18695.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of Penis Foreskin Keratinocyte Primary Cells Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Penis Foreskin Keratinocyte Primary Cells, Donor skin01, Library DS18695 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.12678
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 150bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 6
BROWSER_TRACK_NAME: PFK DNase 01 95
BROWSER_TRACK_DESCRIPTION: UW Penis Foreskin Keratinocyte Primary Cells DNase Hypersensitivity Donor skin01 Library DS18695 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 34,521,027
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.455
FINDPEAKS_PERCENTILE: 71
HOTSPOT_SCORE: 0.4944
HOTSPOT_PERCENTILE: 87
IROC_SCORE: 0.9963
IROC_PERCENTILE: 89
POISSON_SCORE: 0.5389
POISSON_PERCENTILE: 83
MAXIMUM_REPLICATE_CORRELATION: 1.0

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

source_name: Penis, Foreskin, Keratinocyte Primary Cells skin01; DS18695

tag: sample alias

value: Penis, Foreskin, Keratinocyte skin01

tag: sample common name

tag: molecule

value: genomic DNA

tag: disease

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: Chromatin Accessibility

value: Qiagen minElut

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


title: Chromatin accessibility assay of H1 BMP4 Derived Mesendoderm Cultured Cells; DS18732

description:
sample_term_id: NTR_0000856
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS18732
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.10113
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.7805
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM817198_UW.H1_BMP4_Derived_Mesendoderm_Cultured_Cells.ChromatinAccessibility.DS18732.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS18732.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of H1 BMP4 Derived Mesendoderm Cultured Cells Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on the H1 BMP4 Derived Mesendoderm Cultured Cells, Library DS18732 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.12618
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 25,261,865
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.2847
FINDPEAKS_PERCENTILE: 19
HOTSPOT_SCORE: 0.3046
HOTSPOT_PERCENTILE: 24
IROC_SCORE: 0.9885
IROC_PERCENTILE: 14
POISSON_SCORE: 0.3994
POISSON_PERCENTILE: 27
MAXIMUM_REPLICATE_CORRELATION: 1.0

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

ANALYSIS FILE NAME: GSM817198_UW.H1_BMP4_Derived_Mesendoderm_Cultured_Cells.ChromatinAccessibility.DS18732.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS18732.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of H1 BMP4 Derived Mesendoderm Cultured Cells Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  the H1 BMP4 Derived Mesendoderm Cultured Cells, Library DS18732 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.12681
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 150bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 6
BROWSER_TRACK_NAME: HBDM DNase 32
BROWSER_TRACK_DESCRIPTION: UW H1 BMP4 Derived Mesendoderm Cultured Cells DNase Hypersensitivity Donor  Library DS18732 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 25,261,865
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.2847
FINDPEAKS_PERCENTILE: 19
HOTSPOT_SCORE: 0.3046
HOTSPOT_PERCENTILE: 24
IROC_SCORE: 0.9885
IROC_PERCENTILE: 14
POISSON_SCORE: 0.3994
POISSON_PERCENTILE: 27
MAXIMUM_REPLICATE_CORRELATION: 1.0

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

source_name: Human embryonic stem cells received from the James Thomson laboratory.  Cells are from the H1 line and are differentiated into mesendoderm by treatment with BMP4.; DS18732

value: James Thomson Laboratory

value: Cell Line

tag: line

tag: lineage

value: Embryonic Stem Cell

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

value: H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days

tag: passage

value: Between 20 and 30

tag: medium

tag: Sex

tag: batch


title: Chromatin accessibility assay of Fetal Stomach; DS18821

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: DS18821
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.9807
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.9806
****************
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: GSM817199_UW.Fetal_Stomach.ChromatinAccessibility.H-24125.DS18821.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS18821.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of Fetal Stomach Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Stomach, Donor H-24125, Library DS18821 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.12619
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 35,596,116
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.2472
FINDPEAKS_PERCENTILE: 8
HOTSPOT_SCORE: 0.2551
HOTSPOT_PERCENTILE: 8
IROC_SCORE: 0.9902
IROC_PERCENTILE: 22
POISSON_SCORE: 0.3394
POISSON_PERCENTILE: 8
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

ANALYSIS FILE NAME: GSM817199_UW.Fetal_Stomach.ChromatinAccessibility.H-24125.DS18821.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS18821.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Stomach Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Stomach, Donor H-24125, Library DS18821 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.12682
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 150bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 6
BROWSER_TRACK_NAME: FS DNase 25 21
BROWSER_TRACK_DESCRIPTION: UW Fetal Stomach DNase Hypersensitivity Donor H-24125 Library DS18821 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 35,596,116
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.2472
FINDPEAKS_PERCENTILE: 8
HOTSPOT_SCORE: 0.2551
HOTSPOT_PERCENTILE: 8
IROC_SCORE: 0.9902
IROC_PERCENTILE: 22
POISSON_SCORE: 0.3394
POISSON_PERCENTILE: 8
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

source_name: Fetal Stomach primary tissue, day 101; DS18821

value: Fetal Stomach

value: genomic DNA

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

value: Primary Tissue

value: UW

value: fetal

value: day 101

value: Unknown


title: Chromatin accessibility assay of Penis Foreskin Keratinocytes Primary Cells; DS18692

description:
sample_term_id: CL_1001606
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS18692
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.9793
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: GSM817194_UW.Penis_Foreskin_Keratinocyte_Primary_Cells.ChromatinAccessibility.skin01.DS18692.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS18692.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of Penis Foreskin Keratinocyte Primary Cells Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Penis Foreskin Keratinocyte Primary Cells, Donor skin01, Library 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.12614
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 31,933,090
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.525
FINDPEAKS_PERCENTILE: 94
HOTSPOT_SCORE: 0.5566
HOTSPOT_PERCENTILE: 95
IROC_SCORE: 0.9978
IROC_PERCENTILE: 95
POISSON_SCORE: 0.5961
POISSON_PERCENTILE: 94
MAXIMUM_REPLICATE_CORRELATION: 0.0

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

ANALYSIS FILE NAME: GSM817194_UW.Penis_Foreskin_Keratinocyte_Primary_Cells.ChromatinAccessibility.skin01.DS18692.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS18692.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of Penis Foreskin Keratinocyte Primary Cells Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Penis Foreskin Keratinocyte Primary Cells, Donor skin01, Library 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.12677
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 150bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 6
BROWSER_TRACK_NAME: PFK DNase 01 92
BROWSER_TRACK_DESCRIPTION: UW Penis Foreskin Keratinocyte Primary Cells DNase Hypersensitivity Donor skin01 Library DS18692 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 31,933,090
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.525
FINDPEAKS_PERCENTILE: 94
HOTSPOT_SCORE: 0.5566
HOTSPOT_PERCENTILE: 95
IROC_SCORE: 0.9978
IROC_PERCENTILE: 95
POISSON_SCORE: 0.5961
POISSON_PERCENTILE: 94
MAXIMUM_REPLICATE_CORRELATION: 0.0

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

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

value: Penis, Foreskin, Keratinocyte skin01

value: SFVAMC Dermatology

value: Primary Cell Culture

value: Keratinocyte

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

value: Neonate

value: Disease Free

value: Male

value: Chromatin Accessibility


title: Chromatin accessibility assay of Penis Foreskin Keratinocytes Primary Cells; DS18718

description:
sample_term_id: CL_1001606
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS18718
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.9858
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSF-UBC%2FSAMPLE%2FEDACC.9573
****************
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: GSM817197_UW.Penis_Foreskin_Keratinocyte_Primary_Cells.ChromatinAccessibility.skin02.DS18718.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS18718.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of Penis Foreskin Keratinocyte Primary Cells Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Penis Foreskin Keratinocyte Primary Cells, Donor skin02, Library DS18718 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.12617
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 38,613,097
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.4743
FINDPEAKS_PERCENTILE: 86
HOTSPOT_SCORE: 0.5138
HOTSPOT_PERCENTILE: 92
IROC_SCORE: 0.9966
IROC_PERCENTILE: 92
POISSON_SCORE: 0.5546
POISSON_PERCENTILE: 92
MAXIMUM_REPLICATE_CORRELATION: 1.0

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

ANALYSIS FILE NAME: GSM817197_UW.Penis_Foreskin_Keratinocyte_Primary_Cells.ChromatinAccessibility.skin02.DS18718.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS18718.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of Penis Foreskin Keratinocyte Primary Cells Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Penis Foreskin Keratinocyte Primary Cells, Donor skin02, Library DS18718 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.12680
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 150bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 6
BROWSER_TRACK_NAME: PFK DNase 02 18
BROWSER_TRACK_DESCRIPTION: UW Penis Foreskin Keratinocyte Primary Cells DNase Hypersensitivity Donor skin02 Library DS18718 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 38,613,097
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.4743
FINDPEAKS_PERCENTILE: 86
HOTSPOT_SCORE: 0.5138
HOTSPOT_PERCENTILE: 92
IROC_SCORE: 0.9966
IROC_PERCENTILE: 92
POISSON_SCORE: 0.5546
POISSON_PERCENTILE: 92
MAXIMUM_REPLICATE_CORRELATION: 1.0

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

source_name: Penis, Foreskin, Keratinocyte Primary Cells skin02; DS18718

value: Penis, Foreskin, Keratinocyte skin02

value: Qiagen minElut

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


title: LtaP_JBP2KO_SL_repeat1

tag: strain

value: Parrot

tag: developmental stage

value: Procyclic Promastigotes

value: total RNA


title: LtaP_WT_SL_repeat1

tag: rna subtype

tag: genotype/variation

value: WT


title: LtaP_JBP2KO_BrdU_smallRNA

source_name: mixed

extract_protocol: Total RNA from was isolated from the stationary phase wild type L. tarentolae, L. tarentolae JBP2-/- (KO) and KO grown in BrdU (KO+BrdU) using TRIzol reagent (Invitrogen). 2 μg of total RNA was treated with RNase A or RNase T1 or both in a 25-μl reaction at 25oC. The RNA was purified with phenol-chloroform, ethanol precipitated and dissolved in 10 μl RNase-free water.The RNA from each sample was size separated in TBE gel and the 18-35 bp slices were cut and pulverized. The RNA was eluted, precipitated and ligated to the 5’ small RNA adapter 5’ GUUCAGAGUUCUACAGUCCGACGAUC  using T4 RNA ligase and a second size selection was performed to isolate the 40-65 bp fragments. The 3’ adapter 5’-P-UCGUAUGCCGUCUUCUGCUUGUidT was ligated using T4 RNA ligase followed by the third urea TBE gel to collect the 70-120 bp sized molecules that were reverse transcribed with SSII (Invitrogen) and the SRA RT primer 5’ CAAGCAGAAGACGGCATACGA followed by PCR amplification with Phusion polymerase enzyme (Finnzymes Oy) using Illumina primers (GX1: 5’ CAAGCAGAAGACGGCATACGA and GX2: 5’ AATGATACGGCGACCACCGACAGGTTCAGAGTTCTACAGTCCGA).

value: mixed

value: small RNA

tag: treatment

value: BrdU


title: LtaP_JBP2KO_smallRNA


title: Chromatin accessibility assay of Fetal Spinal Cord; DS18501

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: DS18501
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.10165
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.10164
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM817189_UW.Fetal_Spinal_Cord.ChromatinAccessibility.H-24111.DS18501.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS18501.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of Fetal Spinal Cord Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Spinal Cord, Donor H-24111, Library DS18501 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.12609
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 41,428,248
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.2842
FINDPEAKS_PERCENTILE: 16
HOTSPOT_SCORE: 0.2938
HOTSPOT_PERCENTILE: 19
IROC_SCORE: 0.9799
IROC_PERCENTILE: 2
POISSON_SCORE: 0.4248
POISSON_PERCENTILE: 40
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM817189_UW.Fetal_Spinal_Cord.ChromatinAccessibility.H-24111.DS18501.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS18501.hg19.level.2.release.6
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-24111, Library DS18501 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.12672
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 150bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 6
BROWSER_TRACK_NAME: FSC DNase 11 01
BROWSER_TRACK_DESCRIPTION: UW Fetal Spinal Cord DNase Hypersensitivity Donor H-24111 Library DS18501 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 41,428,248
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.2842
FINDPEAKS_PERCENTILE: 16
HOTSPOT_SCORE: 0.2938
HOTSPOT_PERCENTILE: 19
IROC_SCORE: 0.9799
IROC_PERCENTILE: 2
POISSON_SCORE: 0.4248
POISSON_PERCENTILE: 40
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: Fetal Spinal, Cord primary tissue, day 105; DS18501

tag: sample alias

tag: sample common name

value: Fetal Spinal Cord

value: genomic DNA

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

value: Primary Tissue

value: UW

value: fetal

value: day 105


title: Chromatin accessibility assay of Fetal Muscle, Arm; DS18559

description:
sample_term_id: UBERON_0001499
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS18559
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.9896
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.9895
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM817191_UW.Fetal_Muscle_Arm.ChromatinAccessibility.H-24125.DS18559.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS18559.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of Fetal Muscle Arm Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Muscle Arm, Donor H-24125, Library DS18559 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.12611
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 25,532,758
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.4409
FINDPEAKS_PERCENTILE: 65
HOTSPOT_SCORE: 0.4349
HOTSPOT_PERCENTILE: 65
IROC_SCORE: 0.9949
IROC_PERCENTILE: 78
POISSON_SCORE: 0.4981
POISSON_PERCENTILE: 67
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM817191_UW.Fetal_Muscle_Arm.ChromatinAccessibility.H-24125.DS18559.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS18559.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Muscle Arm Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Muscle Arm, Donor H-24125, Library DS18559 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.12674
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 150bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 6
BROWSER_TRACK_NAME: FMA DNase 25 59
BROWSER_TRACK_DESCRIPTION: UW Fetal Muscle Arm DNase Hypersensitivity Donor H-24125 Library DS18559 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 25,532,758
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.4409
FINDPEAKS_PERCENTILE: 65
HOTSPOT_SCORE: 0.4349
HOTSPOT_PERCENTILE: 65
IROC_SCORE: 0.9949
IROC_PERCENTILE: 78
POISSON_SCORE: 0.4981
POISSON_PERCENTILE: 67
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

source_name: Fetal Muscle, Arm primary tissue, day 101; DS18559

value: Fetal Muscle, Arm

tag: molecule

tag: disease

value: day 101

value: Unknown

value: Chromatin Accessibility


title: Chromatin accessibility assay of Fetal Renal Pelvis, Left; DS18666

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: DS18666
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.9980
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.9979
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM817193_UW.Fetal_Renal_Pelvis_Left.ChromatinAccessibility.H-24111.DS18666.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS18666.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of Fetal Renal Pelvis Left Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Renal Pelvis Left, Donor H-24111, Library DS18666 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.12613
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 24,641,687
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.3916
FINDPEAKS_PERCENTILE: 56
HOTSPOT_SCORE: 0.3899
HOTSPOT_PERCENTILE: 56
IROC_SCORE: 0.9936
IROC_PERCENTILE: 51
POISSON_SCORE: 0.4597
POISSON_PERCENTILE: 56
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

ANALYSIS FILE NAME: GSM817193_UW.Fetal_Renal_Pelvis_Left.ChromatinAccessibility.H-24111.DS18666.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS18666.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Renal Pelvis Left Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Renal Pelvis Left, Donor H-24111, Library DS18666 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.12676
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 150bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 6
BROWSER_TRACK_NAME: FRPL DNase 11 66
BROWSER_TRACK_DESCRIPTION: UW Fetal Renal Pelvis Left DNase Hypersensitivity Donor H-24111 Library DS18666 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 24,641,687
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.3916
FINDPEAKS_PERCENTILE: 56
HOTSPOT_SCORE: 0.3899
HOTSPOT_PERCENTILE: 56
IROC_SCORE: 0.9936
IROC_PERCENTILE: 51
POISSON_SCORE: 0.4597
POISSON_PERCENTILE: 56
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

source_name: Fetal Kidney, renal, pelvis, Left primary tissue, day 105; DS18666

value: Fetal Renal Pelvis, Left

value: Male

value: Qiagen minElut

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


title: Chromatin accessibility assay of Fetal Renal Pelvis, Right; DS18663

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: DS18663
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.9960
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.9959
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM817192_UW.Fetal_Renal_Pelvis_Right.ChromatinAccessibility.H-24111.DS18663.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS18663.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of Fetal Renal Pelvis Right Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Renal Pelvis Right, Donor H-24111, Library DS18663 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.12612
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 32,467,482
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.4073
FINDPEAKS_PERCENTILE: 60
HOTSPOT_SCORE: 0.398
HOTSPOT_PERCENTILE: 59
IROC_SCORE: 0.9922
IROC_PERCENTILE: 37
POISSON_SCORE: 0.4744
POISSON_PERCENTILE: 59
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

ANALYSIS FILE NAME: GSM817192_UW.Fetal_Renal_Pelvis_Right.ChromatinAccessibility.H-24111.DS18663.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS18663.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Renal Pelvis Right Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Renal Pelvis Right, Donor H-24111, Library DS18663 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.12675
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 150bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 6
BROWSER_TRACK_NAME: FRPR DNase 11 63
BROWSER_TRACK_DESCRIPTION: UW Fetal Renal Pelvis Right DNase Hypersensitivity Donor H-24111 Library DS18663 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 32,467,482
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.4073
FINDPEAKS_PERCENTILE: 60
HOTSPOT_SCORE: 0.398
HOTSPOT_PERCENTILE: 59
IROC_SCORE: 0.9922
IROC_PERCENTILE: 37
POISSON_SCORE: 0.4744
POISSON_PERCENTILE: 59
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

source_name: Fetal Kidney, renal, pelvis, Right primary tissue, day 105; DS18663

value: Fetal Renal Pelvis, Right


title: LtaP_JBP2KO_SL

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

source_name: Procyclic Promastigotes

value: Parrot

value: Procyclic Promastigotes

value: total RNA


title: LtaP_JBP2KO_BrdU_SL

value: BrdU


title: LtaP_WT_SL

value: WT


title: Chromatin accessibility assay of Fetal Renal Cortex, Left; DS18542

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: DS18542
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.10022
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.10021
****************
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: GSM817190_UW.Fetal_Renal_Cortex_Left.ChromatinAccessibility.H-24111.DS18542.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS18542.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of Fetal Renal Cortex Left Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Renal Cortex Left, Donor H-24111, Library DS18542 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.12610
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 38,748,041
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.2846
FINDPEAKS_PERCENTILE: 17
HOTSPOT_SCORE: 0.2936
HOTSPOT_PERCENTILE: 17
IROC_SCORE: 0.9874
IROC_PERCENTILE: 10
POISSON_SCORE: 0.4099
POISSON_PERCENTILE: 32
MAXIMUM_REPLICATE_CORRELATION: 0.95

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

ANALYSIS FILE NAME: GSM817190_UW.Fetal_Renal_Cortex_Left.ChromatinAccessibility.H-24111.DS18542.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS18542.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Renal Cortex Left Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Renal Cortex Left, Donor H-24111, Library DS18542 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.12673
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 150bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 6
BROWSER_TRACK_NAME: FRCL DNase 11 42
BROWSER_TRACK_DESCRIPTION: UW Fetal Renal Cortex Left DNase Hypersensitivity Donor H-24111 Library DS18542 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 38,748,041
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.2846
FINDPEAKS_PERCENTILE: 17
HOTSPOT_SCORE: 0.2936
HOTSPOT_PERCENTILE: 17
IROC_SCORE: 0.9874
IROC_PERCENTILE: 10
POISSON_SCORE: 0.4099
POISSON_PERCENTILE: 32
MAXIMUM_REPLICATE_CORRELATION: 0.95

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

source_name: Fetal Kidney, renal, cortex, Left primary tissue, day 105; DS18542

value: Fetal Renal Cortex, Left

value: genomic DNA

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

value: Primary Tissue

value: UW


title: Chromatin accessibility assay of Fetal Stomach; DS18389

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: DS18389
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.9811
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.9810
****************
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: GSM817173_UW.Fetal_Stomach.ChromatinAccessibility.H-24078.DS18389.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS18389.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of Fetal Stomach Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Stomach, Donor H-24078, Library DS18389 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.12593
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 31,429,350
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.32
FINDPEAKS_PERCENTILE: 30
HOTSPOT_SCORE: 0.3204
HOTSPOT_PERCENTILE: 32
IROC_SCORE: 0.9898
IROC_PERCENTILE: 19
POISSON_SCORE: 0.3935
POISSON_PERCENTILE: 22
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

ANALYSIS FILE NAME: GSM817173_UW.Fetal_Stomach.ChromatinAccessibility.H-24078.DS18389.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS18389.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Stomach Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Stomach, Donor H-24078, Library DS18389 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.12656
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 150bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 6
BROWSER_TRACK_NAME: FS DNase 78 89
BROWSER_TRACK_DESCRIPTION: UW Fetal Stomach DNase Hypersensitivity Donor H-24078 Library DS18389 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 31,429,350
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.32
FINDPEAKS_PERCENTILE: 30
HOTSPOT_SCORE: 0.3204
HOTSPOT_PERCENTILE: 32
IROC_SCORE: 0.9898
IROC_PERCENTILE: 19
POISSON_SCORE: 0.3935
POISSON_PERCENTILE: 22
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

source_name: Fetal Stomach primary tissue, day 127; DS18389

value: Fetal Stomach

value: fetal

value: day 127


title: Chromatin accessibility assay of Fetal Thymus; DS18382

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: DS18382
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.9802
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.9801
****************
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: GSM817172_UW.Fetal_Thymus.ChromatinAccessibility.H-24078.DS18382.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS18382.hg19.level.1.release.6
ANALYSIS TITLE: Mapping of Fetal Thymus Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fetal Thymus, Donor H-24078, Library DS18382 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.12592
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 85,102,252
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.3253
FINDPEAKS_PERCENTILE: 32
HOTSPOT_SCORE: 0.3092
HOTSPOT_PERCENTILE: 25
IROC_SCORE: 0.9878
IROC_PERCENTILE: 11
POISSON_SCORE: 0.3536
POISSON_PERCENTILE: 13
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM817172_UW.Fetal_Thymus.ChromatinAccessibility.H-24078.DS18382.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS18382.hg19.level.2.release.6
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Thymus Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Fetal Thymus, Donor H-24078, Library DS18382 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.12655
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 150bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 6
BROWSER_TRACK_NAME: FT DNase 78 82
BROWSER_TRACK_DESCRIPTION: UW Fetal Thymus DNase Hypersensitivity Donor H-24078 Library DS18382 EA Release 6

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 85,102,252
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 63
FINDPEAKS_SCORE: 0.3253
FINDPEAKS_PERCENTILE: 32
HOTSPOT_SCORE: 0.3092
HOTSPOT_PERCENTILE: 25
IROC_SCORE: 0.9878
IROC_PERCENTILE: 11
POISSON_SCORE: 0.3536
POISSON_PERCENTILE: 13
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

source_name: Fetal Thymus primary tissue, day 127; DS18382

value: Fetal Thymus

value: Male

value: Chromatin Accessibility