title: ChIP-Seq analysis of H3K9me3 in human CD56+ ectoderm cells; DNA_Lib 3192

description:
sample_term_id: CL_0000221
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 3192
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.15383
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.15412
****************
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: GSM1112826_BI.hESC_Derived_CD56+_Ectoderm_Cultured_Cells.H3K9me3.DNA_Lib_3192.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 3192.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of hESC Derived CD56+ Ectoderm Cultured Cells H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K9me3 ChIP-Seq on the hESC Derived CD56+ Ectoderm Cultured Cells, Library DNA_Lib 3192, 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.17248
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 12,629,414
FINDPEAKS_SCORE: 0.0384
FINDPEAKS_PERCENTILE: 46
HOTSPOT_SCORE: 0.181
HOTSPOT_PERCENTILE: 65
IROC_SCORE: 0.6423
IROC_PERCENTILE: 17
POISSON_SCORE: 0.3278
POISSON_PERCENTILE: 60
MAXIMUM_REPLICATE_CORRELATION: 0.59

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

ANALYSIS FILE NAME: GSM1112826_BI.hESC_Derived_CD56+_Ectoderm_Cultured_Cells.H3K9me3.DNA_Lib_3192.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 3192.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of hESC Derived CD56+ Ectoderm Cultured Cells H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K9me3 ChIP-Seq read mappings from the hESC Derived CD56+ Ectoderm Cultured Cells, Library DNA_Lib 3192, 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.17431
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: hDCEcto H3K9me3 92
BROWSER_TRACK_DESCRIPTION: BI hESC Derived CD56+ Ectoderm Cultured Cells Histone H3K9me3 Library DNA_Lib 3192 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 12,629,414
FINDPEAKS_SCORE: 0.0384
FINDPEAKS_PERCENTILE: 46
HOTSPOT_SCORE: 0.181
HOTSPOT_PERCENTILE: 65
IROC_SCORE: 0.6423
IROC_PERCENTILE: 17
POISSON_SCORE: 0.3278
POISSON_PERCENTILE: 60
MAXIMUM_REPLICATE_CORRELATION: 0.59

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

source_name: CD56+ ectodermal germ layer cells derived in vitro from embrionic stem cells by culture in the presence of inhibitors of the BMP, TGFbeta, and WNT signaling pathways.; DNA_Lib 3192

value: BioSam 1247

value: ectoderm

value: CD56 ectoderm - Days 0-5:DMEM F12, 15% KSR, Dorsomorphin (2um), A83-01 (2um), PNU 74654 (2um)

value: CD56+ ectoderm

value: adherence

value: BioSAli 1890

value: Cell Line

value: intermediate

value: Male

value: Harvard

value: Protein A-Sepharose 4B

value: Abcam

value: Histone H3K9me3


title: ChIP-Seq analysis of H3K4me1 in human HUES64 derived CD184+ cells; DNA_Lib 3190

status: Public on Jun 24 2013

type: SRA

city: Cambridge

first: BROAD

last: INSTITUTE

state: MA

country: USA

institute: Broad Institute

description:
sample_term_id: CL_0000223
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 3190
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.15385
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.15413
****************
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: GSM1112828_BI.hESC_Derived_CD184+_Endoderm_Cultured_Cells.H3K4me1.DNA_Lib_3190.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 3190.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of hESC Derived CD184+ Endoderm Cultured Cells H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K4me1 ChIP-Seq on the hESC Derived CD184+ Endoderm Cultured Cells, Library DNA_Lib 3190, 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.17322
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 20,389,560
FINDPEAKS_SCORE: 0.1741
FINDPEAKS_PERCENTILE: 33
HOTSPOT_SCORE: 0.0
HOTSPOT_PERCENTILE: 2
IROC_SCORE: 0.9449
IROC_PERCENTILE: 41
POISSON_SCORE: 0.4341
POISSON_PERCENTILE: 35
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

ANALYSIS FILE NAME: GSM1112828_BI.hESC_Derived_CD184+_Endoderm_Cultured_Cells.H3K4me1.DNA_Lib_3190.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 3190.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of hESC Derived CD184+ Endoderm Cultured Cells H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K4me1 ChIP-Seq read mappings from the hESC Derived CD184+ Endoderm Cultured Cells, Library DNA_Lib 3190, 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.17505
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: hDCE H3K4me1 90
BROWSER_TRACK_DESCRIPTION: BI hESC Derived CD184+ Endoderm Cultured Cells Histone H3K4me1 Library DNA_Lib 3190 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 20,389,560
FINDPEAKS_SCORE: 0.1741
FINDPEAKS_PERCENTILE: 33
HOTSPOT_SCORE: 0.0
HOTSPOT_PERCENTILE: 2
IROC_SCORE: 0.9449
IROC_PERCENTILE: 41
POISSON_SCORE: 0.4341
POISSON_PERCENTILE: 35
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

molecule: genomic DNA

organism: Homo sapiens

source_name: CD184+ endoderm differentiated in vitro from stem cells; DNA_Lib 3190

extract_protocol: Library construction protocol: Single read - Illumina

value: CD184+ endoderm cultured cells

tag: sample alias

value: BioSam 1246

tag: sample common name

tag: lineage

value: endoderm

tag: medium

value: RPMI 100ng/mL Activin A 50ng/mL Wnt3a

tag: disease

value: presumed normal

tag: passage

tag: line

value: HUES64 derived CD184+

value: in vitro culture

tag: batch

value: BioSAli 1888

value: differentiated

tag: Sex

value: 0.5 to 3 million cells

value: cell/nuclei lysis

value: ~1 ug

value: 10 ul bed volume

value: Histone H3K4me1

value: Branson


title: ChIP-Seq analysis of H3K27ac in human CD56+ mesoderm cells; DNA_Lib 3195

description:
sample_term_id: CL_0000222
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 3195
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.15382
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.15410
****************
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: GSM1112825_BI.hESC_Derived_CD56+_Mesoderm_Cultured_Cells.H3K27ac.DNA_Lib_3195.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 3195.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of hESC Derived CD56+ Mesoderm Cultured Cells H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27ac ChIP-Seq on the hESC Derived CD56+ Mesoderm Cultured Cells, Library DNA_Lib 3195, 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.17236
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 15,403,364
FINDPEAKS_SCORE: 0.3454
FINDPEAKS_PERCENTILE: 47
HOTSPOT_SCORE: 0.0
HOTSPOT_PERCENTILE: 6
IROC_SCORE: 0.9923
IROC_PERCENTILE: 42
POISSON_SCORE: 0.4623
POISSON_PERCENTILE: 52
MAXIMUM_REPLICATE_CORRELATION: 0.54

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

ANALYSIS FILE NAME: GSM1112825_BI.hESC_Derived_CD56+_Mesoderm_Cultured_Cells.H3K27ac.DNA_Lib_3195.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 3195.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of hESC Derived CD56+ Mesoderm Cultured Cells H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27ac ChIP-Seq read mappings from the hESC Derived CD56+ Mesoderm Cultured Cells, Library DNA_Lib 3195, 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.17419
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: hDCM H3K27ac 95
BROWSER_TRACK_DESCRIPTION: BI hESC Derived CD56+ Mesoderm Cultured Cells Histone H3K27ac Library DNA_Lib 3195 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 15,403,364
FINDPEAKS_SCORE: 0.3454
FINDPEAKS_PERCENTILE: 47
HOTSPOT_SCORE: 0.0
HOTSPOT_PERCENTILE: 6
IROC_SCORE: 0.9923
IROC_PERCENTILE: 42
POISSON_SCORE: 0.4623
POISSON_PERCENTILE: 52
MAXIMUM_REPLICATE_CORRELATION: 0.54

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

source_name: HUES64 differentiated with Activin A, BMP4, VEGF and bFGF for 24 hours, then with BMP4, VEGF and bFGF for an additional 4 days. ; DNA_Lib 3195

value: BioSam 1249

value: mesoderm

value: CD56 mesoderm - Day 0-1:DMEM F12, 0.5% FBS, Activin A (100ng/mL) BMP4 (100ng/mL), VEGF (100ng/mL), and bFGF (20ng/mL). Days 1-5:DMEM F12, 0.5% FBS, BMP4 (100ng/mL), VEGF (100ng/mL), and bFGF (20ng/mL)

value: CD56+ mesoderm

value: adherence

value: BioSAli 1892

value: Cell Line

value: intermediate

value: Male

value: Harvard

value: Protein A-Sepharose 4B

value: Active Motif

value: Histone H3K27ac


title: Bisulfite-Seq analysis of WGBS_Lib 21 derived from human CD56+ ectoderm cells; WGBS_Lib 21

description:
sample_term_id: CL_0000221
assay_term_id: OBI_0001863
nucleic_acid_term_id: SO_0000352
Design description: WGBS REMC Sequencing on Illumina
Library name: WGBS_Lib 21
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.15057
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.13314
****************
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: GSM1112821_BI.hESC_Derived_CD56+_Ectoderm_Cultured_Cells.Bisulfite-Seq.WGBS_Lib_21.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: WGBS_Lib 21.hg19.level.2.release.9
ANALYSIS TITLE: Methylation Proportion Graphs of hESC Derived CD56+ Ectoderm Cultured Cells Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from hESC Derived CD56+ Ectoderm Cultured Cells, Donor WGBS_Lib 21 were processed into graphs of methylation proportions. Methylation proportions were calculated as (methylated calls / (methylated calls + unmethylated calls)) for all CpGs covered by at least 4 reads. Reads from the + and - strands were combined for methylation proportion calculations.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.18738
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
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: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: hDCEcto BS 21
BROWSER_TRACK_DESCRIPTION: BI hESC Derived CD56+ Ectoderm Cultured Cells Bisulfite-Seq Library WGBS_Lib 21 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 638,014,763
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 99.28
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE: 74
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

source_name: CD56+ ectodermal germ layer cells derived in vitro from embrionic stem cells by culture in the presence of inhibitors of the BMP, TGFbeta, and WNT signaling pathways.; WGBS_Lib 21

extract_protocol: Library construction protocol: Genomic DNA (1.5~5µg) was fragmented to 100-500 bp using a Covaris S2. Purified DNA fragments were end-repaired. After A-tailing, the DNA fragments were ligated with methylated paired-end adapters. Adapter-attached DNA fragments of 300-400 bp, which contain 150-250 bp genomic DNA inserts, were gel-purified. The purified DNA fragments were subjected to two cycles of sodium bisulfite conversion using the EpiTect Bisulfite kit (Qiagen). Adapter-attached, bisulfite-converted DNA molecules were enriched by PCR using PfuTurboCx Hotstart DNA polymerase (Stratagene). The PCR amplified DNA fragments were subjected to a second gel size selection to remove PCR primers and adapter dimers. The enriched library was quantified using a Qubit fluorometer and Quant-iT dsDNA HS Assay Kit. Library sequencing was performed using 101 BP PE Illumina technology.

tag: sra sample accession

value: ectoderm

value: Days 0-5:DMEM F12, 15% KSR, Dorsomorphin (2um), A83-01 (2um), PNU 74654 (2um)

value: presumed normal

value: CD56+ ectoderm

value: BioSAli 877

value: 2x5hrs Epitect Kit

value: 5 ug

value: Covaris shearing, duty cycle 5%, intensity 5, cycles / burst 200, duration 9 minutes

value: T4 Ligase (2,000U/ul) 16C o/n

value: Illumina paired end adapter

value: Standard Protocol (Smith et al., Methods 48, 226-232)

value: DNA Methylation

value: Smith et al., Methods 48, 226-232

value: SPRI Beads

value: Pfu Turbo Cx hot start

value: Covaris S2 (TM)


title: Bisulfite-Seq analysis of WGBS_Lib 20 derived from human CD56+ ectoderm cells; WGBS_Lib 20

description:
sample_term_id: CL_0000221
assay_term_id: OBI_0001863
nucleic_acid_term_id: SO_0000352
Design description: WGBS REMC Sequencing on Illumina
Library name: WGBS_Lib 20
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.15056
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.13321
****************
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: GSM1112820_BI.hESC_Derived_CD56+_Ectoderm_Cultured_Cells.Bisulfite-Seq.WGBS_Lib_20.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: WGBS_Lib 20.hg19.level.2.release.9
ANALYSIS TITLE: Methylation Proportion Graphs of hESC Derived CD56+ Ectoderm Cultured Cells Bisulfite-Seq Data
ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from hESC Derived CD56+ Ectoderm Cultured Cells, Donor WGBS_Lib 20 were processed into graphs of methylation proportions. Methylation proportions were calculated as (methylated calls / (methylated calls + unmethylated calls)) for all CpGs covered by at least 4 reads. Reads from the + and - strands were combined for methylation proportion calculations.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.18737
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Bisulfite-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
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: 2bp containing CpGs
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: hDCEcto BS 20
BROWSER_TRACK_DESCRIPTION: BI hESC Derived CD56+ Ectoderm Cultured Cells Bisulfite-Seq Library WGBS_Lib 20 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 701,626,695
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 99.34
BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE: 77
MAXIMUM_REPLICATE_CORRELATION: 0.99

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

source_name: CD56+ ectodermal germ layer cells derived in vitro from embrionic stem cells by culture in the presence of inhibitors of the BMP, TGFbeta, and WNT signaling pathways.; WGBS_Lib 20

value: adherence

value: BioSAli 876

value: Cell Line

value: Male

value: Harvard


title: ChIP-Seq analysis of H3K27ac in human CD56+ ectoderm cells; DNA_Lib 3191

description:
sample_term_id: CL_0000221
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 3191
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.15386
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.15412
****************
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: GSM1112829_BI.hESC_Derived_CD56+_Ectoderm_Cultured_Cells.H3K27ac.DNA_Lib_3191.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 3191.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of hESC Derived CD56+ Ectoderm Cultured Cells H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27ac ChIP-Seq on the hESC Derived CD56+ Ectoderm Cultured Cells, Library DNA_Lib 3191, 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.17300
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 10,593,619
FINDPEAKS_SCORE: 0.1578
FINDPEAKS_PERCENTILE: 16
HOTSPOT_SCORE: 0.0
HOTSPOT_PERCENTILE: 6
IROC_SCORE: 0.8933
IROC_PERCENTILE: 2
POISSON_SCORE: 0.4308
POISSON_PERCENTILE: 39
MAXIMUM_REPLICATE_CORRELATION: 0.4

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

ANALYSIS FILE NAME: GSM1112829_BI.hESC_Derived_CD56+_Ectoderm_Cultured_Cells.H3K27ac.DNA_Lib_3191.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 3191.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of hESC Derived CD56+ Ectoderm Cultured Cells H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27ac ChIP-Seq read mappings from the hESC Derived CD56+ Ectoderm Cultured Cells, Library DNA_Lib 3191, 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.17483
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: hDCEcto H3K27ac 91
BROWSER_TRACK_DESCRIPTION: BI hESC Derived CD56+ Ectoderm Cultured Cells Histone H3K27ac Library DNA_Lib 3191 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 10,593,619
FINDPEAKS_SCORE: 0.1578
FINDPEAKS_PERCENTILE: 16
HOTSPOT_SCORE: 0.0
HOTSPOT_PERCENTILE: 6
IROC_SCORE: 0.8933
IROC_PERCENTILE: 2
POISSON_SCORE: 0.4308
POISSON_PERCENTILE: 39
MAXIMUM_REPLICATE_CORRELATION: 0.4

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

source_name: CD56+ ectodermal germ layer cells derived in vitro from embrionic stem cells by culture in the presence of inhibitors of the BMP, TGFbeta, and WNT signaling pathways.; DNA_Lib 3191

value: BioSam 1247

value: ectoderm

value: CD56 ectoderm - Days 0-5:DMEM F12, 15% KSR, Dorsomorphin (2um), A83-01 (2um), PNU 74654 (2um)

value: presumed normal

value: CD56+ ectoderm

value: BioSAli 1890

value: intermediate

value: Protein A-Sepharose 4B

value: 0.5 to 3 million cells

value: cell/nuclei lysis

value: ~1 ug

value: 10 ul bed volume

value: Active Motif

value: Histone H3K27ac

value: Branson


title: Full length RNASeq of fly heads_zt15

first: Sabah

last: Kadri

state: Massachusetts

address: 7 Cambridge Center

department: Computational Biology

institute: Broad institute

description:
Drosophila melanogaster: full-length and 3' RNA-Seq data only.
Sample 3
Processed data file: dm3.full.scores.rpk.txt (linked as supplementary file on Series record)

library_source: transcriptomic

data_processing:
Reads mapping to rRNA were filtered out and tophat v1.4.1 was used for alignment to dm3 with segment length 20 and maximum multi-hits 15.
Gene expression matrices for end RNASeq were generated using the software package, ESAT (http://garberlab.umassmed.edu/software/esat/) and Scripture (Guttman et al. 2010) for full length RNA-Seq
Genome_build: Release 5
Supplementary_files_format_and_content: dm3.wt226.heat7.dge.table: gene expression matrix
Supplementary_files_format_and_content: dm3.full.scores.rpk.txt (linked as supplementary file on Series record): gene expression matrix

molecule: total RNA

organism: Drosophila melanogaster

source_name: fly head

growth_protocol: Fly samples: Canton S (CS) wild type flies were reared at 25 °C on a standard diet (yeast: 38gr/L, Yellow corn mill: 91gr/L, agar: 10gr/L, molassas: 8.7% v/v, propanoic acid (BioLab): 0.9% v/v, Tegasept solution (Sigma-Aldrich; 300g/L in EtOH (BioLab)): 0.8% v/v)). Flies were kept in 12-h light:12-h dark cycles at 25 °C.

extract_protocol:
50ng-1ug of total RNA is polyA selected using Oligo-dT beads (Invitrogen) and then fragmented using Ambion Fragmentation buffer using incubation time of 1 min 50sec at 70C. Extractions for ExoCAGE and 3' RNASeq are carried out as described in the paper.
Fragmented RNA is cleaned-up using 2.5X volume on SPRI beads (Agencourt) and then subjected to second polyA enrichment step using additional polyA selection on beads. For 3' end targeting, enriched RNA is processed as described in the paper, which is the same way as in Full-Length protocol starting with hybrid degradation and so on.

tag: cell/tissue type

value: head of fly

tag: strain

value: Canton S

tag: timepoint/developmental stage

value: 3hr after lights are off


title: ChIP-Seq analysis of H3K27ac in human CD56+ ectoderm cells; DNA_Lib 3194

description:
sample_term_id: CL_0000221
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 3194
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.15381
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.15411
****************
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: GSM1112824_BI.hESC_Derived_CD56+_Ectoderm_Cultured_Cells.H3K27ac.DNA_Lib_3194.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 3194.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of hESC Derived CD56+ Ectoderm Cultured Cells H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27ac ChIP-Seq on the hESC Derived CD56+ Ectoderm Cultured Cells, Library DNA_Lib 3194, 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.17302
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 7,084,169
FINDPEAKS_SCORE: 0.1549
FINDPEAKS_PERCENTILE: 15
HOTSPOT_SCORE: 0.0
HOTSPOT_PERCENTILE: 6
IROC_SCORE: 0.9343
IROC_PERCENTILE: 5
POISSON_SCORE: 0.3927
POISSON_PERCENTILE: 28
MAXIMUM_REPLICATE_CORRELATION: 0.4

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

ANALYSIS FILE NAME: GSM1112824_BI.hESC_Derived_CD56+_Ectoderm_Cultured_Cells.H3K27ac.DNA_Lib_3194.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 3194.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of hESC Derived CD56+ Ectoderm Cultured Cells H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27ac ChIP-Seq read mappings from the hESC Derived CD56+ Ectoderm Cultured Cells, Library DNA_Lib 3194, 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.17485
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: hDCEcto H3K27ac 94
BROWSER_TRACK_DESCRIPTION: BI hESC Derived CD56+ Ectoderm Cultured Cells Histone H3K27ac Library DNA_Lib 3194 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 7,084,169
FINDPEAKS_SCORE: 0.1549
FINDPEAKS_PERCENTILE: 15
HOTSPOT_SCORE: 0.0
HOTSPOT_PERCENTILE: 6
IROC_SCORE: 0.9343
IROC_PERCENTILE: 5
POISSON_SCORE: 0.3927
POISSON_PERCENTILE: 28
MAXIMUM_REPLICATE_CORRELATION: 0.4

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

source_name: CD56+ ectodermal germ layer cells derived in vitro from embrionic stem cells by culture in the presence of inhibitors of the BMP, TGFbeta, and WNT signaling pathways.; DNA_Lib 3194

value: BioSam 1248

value: ectoderm

value: adherence

value: BioSAli 1891

value: Cell Line

value: Male

value: Harvard


title: 3' RNASeq of fly heads_zt3

description:
Drosophila melanogaster: full-length and 3' RNA-Seq data only.
Sample 1
Processed data file: dm3.wt226.heat7.dge.table.txt (linked below)

value: 3hr after lights are on


title: poly-A-SNU-719

status: Public on Jun 23 2013

city: New Orleans

first: Erik

middle: K

last: Flemington

state: LA

address: 1430 Tulane Ave., SL79

department: Pathology

institute: Tulane Health Sciences Center

description: Poly-A selected RNA

data_processing:
alignments to hg19 (UCSC) using novoalign (v.2.08.02) using default settings
read counts were calculated using HT-seq count using the interesection-strict option and the GRCh37.70 annotation file.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include read counts for each sample

source_name: Gastric carcinoma cell line

growth_protocol: Cells were grown in RPMI supplemented with 10% FBS in a humidified chamber with 5% CO2.

extract_protocol:
RNA was extracted using the Trizol protocol.
Two separate cDNA libraries were prepared from polyA selected and from Ribo-Zero selected RNAs using the Illumina Truseq Stranded Total RNA Sample Prep Kit (RS-122-2101).

tag: cell line

value: gastric carcinoma cell line SNU-719

tag: infection

value: EBV


title: ribo-zero-SNU-719

description: Ribo-Zero selected RNA


title: ES_Dex-_Wild-type_ChIPSeq

city: Kyoto

first: Masaki

last: Shigeta

state: Kyoto

address: 465 Kajii-cho, Kawaramachi-street, Hitokojiagaru, Kamigyo-ku

department: Department of Anatomy and Developmental Biology

country: Japan

institute: Kyoto prefectural university of medicine

data_processing:
Basecalls and QV (Quality Value) were performed by using CASAVA version 1.8.1
Adapter-trimming was examined by cutadapt tool (http://code.google.com/p/cutadapt) to remove adapter sequences and N (Read1 AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAG, Read2 AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT) from DNA sequencing reads.
Adapter-trimmed ChIP-seq reads were uploaded to DNAnexus server and mapped to the mm9 genome assembly using  DNAnexus software tools (https://dnanexus.com).
Data were filtered using the following specifications
DKO-specific GATA-4 peaks were called using DNAnexus software tools with the following setting: Experiment type (ChIP-Seq / Peaks), Experiment (Sample 2: Flk1+Dex+DKO_ChIPSeq), Background (Sample 1: Flk1+Dex+wild-type_ChIPSeq), ChIP candidate threshold (5.0), Experiment to background (or control) enrichment (3.0), Enable FDR calculation (Yes), Gene annotations (RefSeq Genes), Maximum gene distance (5000)

The 'Flk1_DKO_GATA-4.peaks.txt' is based on comparison analysis between 'Flk1+Dex+DKO' and 'ES_Dex-_DKO' samples.
The 'Flk1_wild-type_GATA-4.peaks.txt' is based on comparison analysis between 'Flk1+Dex+Wild-type' and 'ES_Dex-_Wild-type' samples.

Genome_build: NCBI v37, mm9

Supplementary_files_format_and_content: Result data files (text format, available on Series records) were exported using DNAnexus software tools; peak_index, chromosome_name, position, expt_height, back_height, enrichment, neg_log1-_qvalue, rank, gene_name, gene_dist, gene_5p_dist, dna_around_peaks (option; 1-500 bps), were represented.

organism: Mus musculus

growth_protocol:
For Flk1+ progenitor: 5.4 x 10^5 ES for WT, 6.5 x 10^5 ES cells for DKO, were plated onto OP9 culture in 15-cm dish containing alpha-MEM medium (GIBCO) containing 10% fetal bovine serum (FBS; ThermoTrace) and 0.05 mM 2-mercaptroethanol. ES cell-derived Flk1+ progenitors were routinely generated at day.4.5.
For ES cells: Both WT and DKO ES cells were routinely maintained in GMEM (Gibco) containing 10% fetal calf serum (FCS; Thermo Scientific), 1 x sodium pyruvate (1 mM; Gibco), 1 x non-essential amino acids (NEAA; Gibco), 0.1 mM  2-mercaptroethanol (Nakarai Tesque) and 1000 U/ml leukemia inhibitory factor (LIF) on a 0.1% (v/v) gelatin-coated dish.

extract_protocol:
Lysates were clarified from sonicated nuclei and GATA-4-DNA complexes were isolated with the 3 type of antibody mixture (GATA4 (Santacruz, sc-1237, lot K1611), GATA4 (Santacruz, sc-25310, lot J0611), GATA4 (BD pharmingen, L97-56, lot 17576)
Libraries were prepared according to Illumina's instructions accompanying the ChIP-Seq DNA Sample Prep Kit (Catalog # IP-102-1001). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (3' to 5' exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 18 cycles and library fragments of 300~400 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on theIllumina Hiseq following the manufacturer's protocols.

treatment_protocol: Dex (100nM) was treated for 3 hours before trypsinization of cell cultures and then Flk1+ progenitors were collected by a immunomagnetic system (MACS, Miltenyi Biotech), immediatedly crosslinked with 1% formaldehyde.

tag: parental cell line

value: J1 derived from 129  background

tag: genotype/variation

value: wild type

tag: cell type

value: embryonic stem (ES) cells

tag: differentiation day

value: undifferentiated

tag: chip antibody (mixed)

tag: chip antibody info

value: Santa Cruz, sc-1237, lot K1611

value: Santa Cruz, sc-25310, lot J0611

value: BD pharmingen, L97-56, lot 17576


title: Flk1+Dex+DKO_ChIPSeq

value: sorted Flk1+ mesoderm progenitor cells (ES-derived)

tag: clone name


title: ES_Dex-_DKO_ChIPSeq


title: Flk1+Dex+Wild-type_ChIPSeq


title: ChIP-Seq Input of Fetal Adrenal Gland; Histone.DS23062

status: Public on Jun 22 2013

city: Seattle

first: Northwest

last: REMC

state: WA

institute: University of Washington

description:
sample_term_id: UBERON_0002369
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Input
Library name: Histone.DS23062
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.16299
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.15682
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM1160207_UW.Fetal_Adrenal_Gland.Input.H-24800.Histone.DS23062.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS23062-Histone.DS23062.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Fetal Adrenal Gland Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Input ChIP-Seq on Fetal Adrenal Gland, Donor H-24800, were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.16859
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 25,519,490
FINDPEAKS_SCORE: 0.0055
FINDPEAKS_PERCENTILE: 42
HOTSPOT_SCORE: 0.0061
HOTSPOT_PERCENTILE: 35
IROC_SCORE: 0.0
IROC_PERCENTILE: 25
POISSON_SCORE: 0.0313
POISSON_PERCENTILE: 31
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1160207_UW.Fetal_Adrenal_Gland.Input.H-24800.Histone.DS23062.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS23062-Histone.DS23062.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Adrenal Gland Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Input ChIP-Seq read mappings from Fetal Adrenal Gland, Donor H-24800, were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.16955
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: FAG Input 00 62
BROWSER_TRACK_DESCRIPTION: UW Fetal Adrenal Gland ChIP-Seq Input Donor H-24800 Library Histone.DS23062 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 25,519,490
FINDPEAKS_SCORE: 0.0055
FINDPEAKS_PERCENTILE: 42
HOTSPOT_SCORE: 0.0061
HOTSPOT_PERCENTILE: 35
IROC_SCORE: 0.0
IROC_PERCENTILE: 25
POISSON_SCORE: 0.0313
POISSON_PERCENTILE: 31
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: Fetal Adrenal Gland primary tissue, day 97; Histone.DS23062

tag: sample alias

tag: disease

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

value: Primary Tissue

value: Fetal Adrenal Gland

value: UW

value: fetal

value: day 97

value: ChIP-Seq Input

value: Diagenode Bioruptor

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

value: Input


title: ChIP-Seq Input of Fetal Placenta; Histone.DS23024

description:
sample_term_id: UBERON_0001987
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Input
Library name: Histone.DS23024
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.16257
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.15690
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM1160206_UW.Fetal_Placenta.Input.H-24996.Histone.DS23024.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS23024-Histone.DS23024.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Fetal Placenta Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Input ChIP-Seq on Fetal Placenta, Donor H-24996, were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.16829
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 18,296,461
FINDPEAKS_SCORE: 0.006
FINDPEAKS_PERCENTILE: 60
HOTSPOT_SCORE: 0.0317
HOTSPOT_PERCENTILE: 63
IROC_SCORE: 0.9579
IROC_PERCENTILE: 52
POISSON_SCORE: 0.0612
POISSON_PERCENTILE: 51
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1160206_UW.Fetal_Placenta.Input.H-24996.Histone.DS23024.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS23024-Histone.DS23024.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Placenta Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Input ChIP-Seq read mappings from Fetal Placenta, Donor H-24996, were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.16925
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: FP Input 96 24
BROWSER_TRACK_DESCRIPTION: UW Fetal Placenta ChIP-Seq Input Donor H-24996 Library Histone.DS23024 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 18,296,461
FINDPEAKS_SCORE: 0.006
FINDPEAKS_PERCENTILE: 60
HOTSPOT_SCORE: 0.0317
HOTSPOT_PERCENTILE: 63
IROC_SCORE: 0.9579
IROC_PERCENTILE: 52
POISSON_SCORE: 0.0612
POISSON_PERCENTILE: 51
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: Fetal Placenta primary tissue, day 113; Histone.DS23024

value: Fetal Placenta

value: day 113

value: Female


title: Histone H3K9me3 ChIP-Seq of Fetal Placenta; Histone.DS23311

description:
sample_term_id: UBERON_0001987
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Histone H3K9me3 ChIP-Seq
Library name: Histone.DS23311
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.16289
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.15690
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM1160204_UW.Fetal_Placenta.H3K9me3.H-24996.Histone.DS23311.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS23311-Histone.DS23311.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Fetal Placenta H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K9me3 ChIP-Seq on Fetal Placenta, Donor H-24996, were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.16888
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 24,015,629
FINDPEAKS_SCORE: 0.1462
FINDPEAKS_PERCENTILE: 80
HOTSPOT_SCORE: 0.2452
HOTSPOT_PERCENTILE: 84
IROC_SCORE: 0.911
IROC_PERCENTILE: 84
POISSON_SCORE: 0.3539
POISSON_PERCENTILE: 74
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1160204_UW.Fetal_Placenta.H3K9me3.H-24996.Histone.DS23311.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS23311-Histone.DS23311.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Placenta H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K9me3 ChIP-Seq read mappings from Fetal Placenta, Donor H-24996, were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.16984
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: FP H3K9me3 96 11
BROWSER_TRACK_DESCRIPTION: UW Fetal Placenta Histone H3K9me3 Donor H-24996 Library Histone.DS23311 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 24,015,629
FINDPEAKS_SCORE: 0.1462
FINDPEAKS_PERCENTILE: 80
HOTSPOT_SCORE: 0.2452
HOTSPOT_PERCENTILE: 84
IROC_SCORE: 0.911
IROC_PERCENTILE: 84
POISSON_SCORE: 0.3539
POISSON_PERCENTILE: 74
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: Fetal Placenta primary tissue, day 113; Histone.DS23311

value: Histone H3K9me3

value: Millipore A/G agarose beads

value: 30ul A/G bead slurry

value: Active Motif


title: Histone H3K9me3 ChIP-Seq of Fetal Muscle, Trunk; Histone.DS23309

description:
sample_term_id: UBERON_0001774
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Histone H3K9me3 ChIP-Seq
Library name: Histone.DS23309
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.16305
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.16267
****************
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: GSM1160203_UW.Fetal_Muscle_Trunk.H3K9me3.H-24851.Histone.DS23309.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS23309-Histone.DS23309.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Fetal Muscle Trunk H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K9me3 ChIP-Seq on Fetal Muscle Trunk, Donor H-24851, 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.16849
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 19,403,700
FINDPEAKS_SCORE: 0.0764
FINDPEAKS_PERCENTILE: 62
HOTSPOT_SCORE: 0.1387
HOTSPOT_PERCENTILE: 48
IROC_SCORE: 0.8309
IROC_PERCENTILE: 52
POISSON_SCORE: 0.3206
POISSON_PERCENTILE: 56
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1160203_UW.Fetal_Muscle_Trunk.H3K9me3.H-24851.Histone.DS23309.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS23309-Histone.DS23309.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Muscle Trunk H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K9me3 ChIP-Seq read mappings from Fetal Muscle Trunk, Donor H-24851, 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.16945
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: FMT H3K9me3 51 09
BROWSER_TRACK_DESCRIPTION: UW Fetal Muscle Trunk Histone H3K9me3 Donor H-24851 Library Histone.DS23309 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 19,403,700
FINDPEAKS_SCORE: 0.0764
FINDPEAKS_PERCENTILE: 62
HOTSPOT_SCORE: 0.1387
HOTSPOT_PERCENTILE: 48
IROC_SCORE: 0.8309
IROC_PERCENTILE: 52
POISSON_SCORE: 0.3206
POISSON_PERCENTILE: 56
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: Fetal Muscle, Trunk primary tissue, day 115; Histone.DS23309

tag: sample common name

value: Fetal Muscle, Trunk

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

value: day 115


title: Histone H3K9me3 ChIP-Seq of Fetal Adrenal Gland; Histone.DS23066

description:
sample_term_id: UBERON_0002369
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Histone H3K9me3 ChIP-Seq
Library name: Histone.DS23066
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.16295
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.15682
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM1160201_UW.Fetal_Adrenal_Gland.H3K9me3.H-24800.Histone.DS23066.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS23066-Histone.DS23066-Histone.DS23066.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Fetal Adrenal Gland H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K9me3 ChIP-Seq on Fetal Adrenal Gland, Donor H-24800, were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.16828
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 17,602,118
FINDPEAKS_SCORE: 0.2216
FINDPEAKS_PERCENTILE: 90
HOTSPOT_SCORE: 0.2623
HOTSPOT_PERCENTILE: 90
IROC_SCORE: 0.9046
IROC_PERCENTILE: 80
POISSON_SCORE: 0.4298
POISSON_PERCENTILE: 88
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1160201_UW.Fetal_Adrenal_Gland.H3K9me3.H-24800.Histone.DS23066.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS23066-Histone.DS23066-Histone.DS23066.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Adrenal Gland H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K9me3 ChIP-Seq read mappings from Fetal Adrenal Gland, Donor H-24800, were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.16924
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: FAG H3K9me3 00 66
BROWSER_TRACK_DESCRIPTION: UW Fetal Adrenal Gland Histone H3K9me3 Donor H-24800 Library Histone.DS23066 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 17,602,118
FINDPEAKS_SCORE: 0.2216
FINDPEAKS_PERCENTILE: 90
HOTSPOT_SCORE: 0.2623
HOTSPOT_PERCENTILE: 90
IROC_SCORE: 0.9046
IROC_PERCENTILE: 80
POISSON_SCORE: 0.4298
POISSON_PERCENTILE: 88
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: Fetal Adrenal Gland primary tissue, day 97; Histone.DS23066

value: Primary Tissue

value: Fetal Adrenal Gland

value: UW

value: Male


title: Histone H3K9me3 ChIP-Seq of CD19 Primary Cells; Histone.DS23314

description:
sample_term_id: CL_0000236
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Histone H3K9me3 ChIP-Seq
Library name: Histone.DS23314
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.16292
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.6973
****************
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: GSM1160205_UW.CD19_Primary_Cells.H3K9me3.RO_01701.Histone.DS23314.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS23314-Histone.DS23314.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of CD19 Primary Cells H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K9me3 ChIP-Seq on CD19 Primary Cells, Donor RO 01701, were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.16839
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 19,645,845
FINDPEAKS_SCORE: 0.2915
FINDPEAKS_PERCENTILE: 94
HOTSPOT_SCORE: 0.3784
HOTSPOT_PERCENTILE: 96
IROC_SCORE: 0.9446
IROC_PERCENTILE: 96
POISSON_SCORE: 0.4645
POISSON_PERCENTILE: 92
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM1160205_UW.CD19_Primary_Cells.H3K9me3.RO_01701.Histone.DS23314.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS23314-Histone.DS23314.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of CD19 Primary Cells H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K9me3 ChIP-Seq read mappings from CD19 Primary Cells, Donor RO 01701, were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.16935
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: CD19 H3K9me3 01 14
BROWSER_TRACK_DESCRIPTION: UW CD19 Primary Cells Histone H3K9me3 Donor RO 01701 Library Histone.DS23314 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 19,645,845
FINDPEAKS_SCORE: 0.2915
FINDPEAKS_PERCENTILE: 94
HOTSPOT_SCORE: 0.3784
HOTSPOT_PERCENTILE: 96
IROC_SCORE: 0.9446
IROC_PERCENTILE: 96
POISSON_SCORE: 0.4645
POISSON_PERCENTILE: 92
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

source_name: flow sorted CD19+ Cells, year 37; Histone.DS23314

value: FHCRC HEIMFELD

value: Primary Cell

value: CD19 Primary Cells

tag: markers

value: year 37

value: Hispanic

value: Diagenode Bioruptor


title: Histone H3K4me3 ChIP-Seq of Fetal Placenta; Histone.DS23300

description:
sample_term_id: UBERON_0001987
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Histone H3K4me3 ChIP-Seq
Library name: Histone.DS23300
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.16254
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.15690
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM1160199_UW.Fetal_Placenta.H3K4me3.H-24996.Histone.DS23300.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS23300-Histone.DS23300.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Fetal Placenta H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K4me3 ChIP-Seq on Fetal Placenta, Donor H-24996, were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.16848
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 19,861,909
FINDPEAKS_SCORE: 0.2694
FINDPEAKS_PERCENTILE: 27
HOTSPOT_SCORE: 0.281
HOTSPOT_PERCENTILE: 23
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.2824
POISSON_PERCENTILE: 20
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1160199_UW.Fetal_Placenta.H3K4me3.H-24996.Histone.DS23300.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS23300-Histone.DS23300.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Placenta H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K4me3 ChIP-Seq read mappings from Fetal Placenta, Donor H-24996, were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.16944
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: FP H3K4me3 96 00
BROWSER_TRACK_DESCRIPTION: UW Fetal Placenta Histone H3K4me3 Donor H-24996 Library Histone.DS23300 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 19,861,909
FINDPEAKS_SCORE: 0.2694
FINDPEAKS_PERCENTILE: 27
HOTSPOT_SCORE: 0.281
HOTSPOT_PERCENTILE: 23
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.2824
POISSON_PERCENTILE: 20
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: Fetal Placenta primary tissue, day 113; Histone.DS23300

value: Fetal Placenta

value: fetal

value: day 113

value: Female

value: Histone H3K4me3

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

value: Invitrogen Dynabeads

value: Cell Signaling

value: lot 2


title: Histone H3K4me3 ChIP-Seq of Fetal Muscle, Trunk; Histone.DS23302

description:
sample_term_id: UBERON_0001774
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Histone H3K4me3 ChIP-Seq
Library name: Histone.DS23302
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.16277
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.16267
****************
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: GSM1160200_UW.Fetal_Muscle_Trunk.H3K4me3.H-24851.Histone.DS23302.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS23302-Histone.DS23302.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Fetal Muscle Trunk H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K4me3 ChIP-Seq on Fetal Muscle Trunk, Donor H-24851, 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.16856
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 32,749,026
FINDPEAKS_SCORE: 0.4001
FINDPEAKS_PERCENTILE: 54
HOTSPOT_SCORE: 0.4076
HOTSPOT_PERCENTILE: 46
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.4055
POISSON_PERCENTILE: 46
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1160200_UW.Fetal_Muscle_Trunk.H3K4me3.H-24851.Histone.DS23302.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS23302-Histone.DS23302.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Muscle Trunk H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K4me3 ChIP-Seq read mappings from Fetal Muscle Trunk, Donor H-24851, 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.16952
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: FMT H3K4me3 51 02
BROWSER_TRACK_DESCRIPTION: UW Fetal Muscle Trunk Histone H3K4me3 Donor H-24851 Library Histone.DS23302 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 32,749,026
FINDPEAKS_SCORE: 0.4001
FINDPEAKS_PERCENTILE: 54
HOTSPOT_SCORE: 0.4076
HOTSPOT_PERCENTILE: 46
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.4055
POISSON_PERCENTILE: 46
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: Fetal Muscle, Trunk primary tissue, day 115; Histone.DS23302

value: Fetal Muscle, Trunk

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

value: Primary Tissue

value: UW

value: day 115


title: Histone H3K36me3 ChIP-Seq of Fetal Muscle, Trunk; Histone.DS23037

description:
sample_term_id: UBERON_0001774
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Histone H3K36me3 ChIP-Seq
Library name: Histone.DS23037
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.16283
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.16267
****************
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: GSM1160195_UW.Fetal_Muscle_Trunk.H3K36me3.H-24851.Histone.DS23037.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS23037-Histone.DS23037.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Fetal Muscle Trunk H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K36me3 ChIP-Seq on Fetal Muscle Trunk, Donor H-24851, 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.16833
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 31,272,004
FINDPEAKS_SCORE: 0.3567
FINDPEAKS_PERCENTILE: 71
HOTSPOT_SCORE: 0.3371
HOTSPOT_PERCENTILE: 67
IROC_SCORE: 0.9908
IROC_PERCENTILE: 76
POISSON_SCORE: 0.5529
POISSON_PERCENTILE: 71
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1160195_UW.Fetal_Muscle_Trunk.H3K36me3.H-24851.Histone.DS23037.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS23037-Histone.DS23037.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Muscle Trunk H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K36me3 ChIP-Seq read mappings from Fetal Muscle Trunk, Donor H-24851, 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.16929
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: FMT H3K36me3 51 37
BROWSER_TRACK_DESCRIPTION: UW Fetal Muscle Trunk Histone H3K36me3 Donor H-24851 Library Histone.DS23037 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 31,272,004
FINDPEAKS_SCORE: 0.3567
FINDPEAKS_PERCENTILE: 71
HOTSPOT_SCORE: 0.3371
HOTSPOT_PERCENTILE: 67
IROC_SCORE: 0.9908
IROC_PERCENTILE: 76
POISSON_SCORE: 0.5529
POISSON_PERCENTILE: 71
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: Fetal Muscle, Trunk primary tissue, day 115; Histone.DS23037

value: Histone H3K36me3

value: Millipore A/G agarose beads

value: 30ul A/G bead slurry

value: Active Motif


title: Histone H3K27me3 ChIP-Seq of Fetal Placenta; Histone.DS23312

description:
sample_term_id: UBERON_0001987
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Histone H3K27me3 ChIP-Seq
Library name: Histone.DS23312
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.16251
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.15690
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM1160193_UW.Fetal_Placenta.H3K27me3.H-24996.Histone.DS23312.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS23312-Histone.DS23312.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Fetal Placenta H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27me3 ChIP-Seq on Fetal Placenta, Donor H-24996, were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.16869
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 19,321,162
FINDPEAKS_SCORE: 0.0784
FINDPEAKS_PERCENTILE: 55
HOTSPOT_SCORE: 0.1949
HOTSPOT_PERCENTILE: 59
IROC_SCORE: 0.8766
IROC_PERCENTILE: 48
POISSON_SCORE: 0.375
POISSON_PERCENTILE: 59
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1160193_UW.Fetal_Placenta.H3K27me3.H-24996.Histone.DS23312.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS23312-Histone.DS23312.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Placenta H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27me3 ChIP-Seq read mappings from Fetal Placenta, Donor H-24996, were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.16965
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: FP H3K27me3 96 12
BROWSER_TRACK_DESCRIPTION: UW Fetal Placenta Histone H3K27me3 Donor H-24996 Library Histone.DS23312 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 19,321,162
FINDPEAKS_SCORE: 0.0784
FINDPEAKS_PERCENTILE: 55
HOTSPOT_SCORE: 0.1949
HOTSPOT_PERCENTILE: 59
IROC_SCORE: 0.8766
IROC_PERCENTILE: 48
POISSON_SCORE: 0.375
POISSON_PERCENTILE: 59
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: Fetal Placenta primary tissue, day 113; Histone.DS23312

value: Fetal Placenta

value: fetal

value: Histone H3K27me3

value: Diagenode Bioruptor

value: Millipore


title: Histone H3K27me3 ChIP-Seq of Fetal Adrenal Gland; Histone.DS23067

description:
sample_term_id: UBERON_0002369
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Histone H3K27me3 ChIP-Seq
Library name: Histone.DS23067
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.16260
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.15682
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM1160192_UW.Fetal_Adrenal_Gland.H3K27me3.H-24800.Histone.DS23067.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS23067-Histone.DS23067-Histone.DS23067.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Fetal Adrenal Gland H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27me3 ChIP-Seq on Fetal Adrenal Gland, Donor H-24800, were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.16817
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 33,695,621
FINDPEAKS_SCORE: 0.5081
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.5049
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9947
IROC_PERCENTILE: 98
POISSON_SCORE: 0.6198
POISSON_PERCENTILE: 98
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1160192_UW.Fetal_Adrenal_Gland.H3K27me3.H-24800.Histone.DS23067.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS23067-Histone.DS23067-Histone.DS23067.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Adrenal Gland H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27me3 ChIP-Seq read mappings from Fetal Adrenal Gland, Donor H-24800, were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.16913
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: FAG H3K27me3 00 67
BROWSER_TRACK_DESCRIPTION: UW Fetal Adrenal Gland Histone H3K27me3 Donor H-24800 Library Histone.DS23067 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 33,695,621
FINDPEAKS_SCORE: 0.5081
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.5049
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9947
IROC_PERCENTILE: 98
POISSON_SCORE: 0.6198
POISSON_PERCENTILE: 98
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: Fetal Adrenal Gland primary tissue, day 97; Histone.DS23067

value: Fetal Adrenal Gland

value: day 97

value: Male

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


title: Histone H3K27ac ChIP-Seq of Fetal Adrenal Gland; Histone.DS23304

description:
sample_term_id: UBERON_0002369
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Histone H3K27ac ChIP-Seq
Library name: Histone.DS23304
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.16271
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.15682
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM1160190_UW.Fetal_Adrenal_Gland.H3K27ac.H-24800.Histone.DS23304.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS23304-Histone.DS23304.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Fetal Adrenal Gland H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27ac ChIP-Seq on Fetal Adrenal Gland, Donor H-24800, were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.16854
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 19,537,147
FINDPEAKS_SCORE: 0.5027
FINDPEAKS_PERCENTILE: 75
HOTSPOT_SCORE: 0.5179
HOTSPOT_PERCENTILE: 74
IROC_SCORE: 0.9985
IROC_PERCENTILE: 80
POISSON_SCORE: 0.5797
POISSON_PERCENTILE: 75
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1160190_UW.Fetal_Adrenal_Gland.H3K27ac.H-24800.Histone.DS23304.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS23304-Histone.DS23304.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Adrenal Gland H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27ac ChIP-Seq read mappings from Fetal Adrenal Gland, Donor H-24800, were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.16950
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: FAG H3K27ac 00 04
BROWSER_TRACK_DESCRIPTION: UW Fetal Adrenal Gland Histone H3K27ac Donor H-24800 Library Histone.DS23304 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 19,537,147
FINDPEAKS_SCORE: 0.5027
FINDPEAKS_PERCENTILE: 75
HOTSPOT_SCORE: 0.5179
HOTSPOT_PERCENTILE: 74
IROC_SCORE: 0.9985
IROC_PERCENTILE: 80
POISSON_SCORE: 0.5797
POISSON_PERCENTILE: 75
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: Fetal Adrenal Gland primary tissue, day 97; Histone.DS23304

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

value: Histone H3K27ac

value: Invitrogen Dynabeads


title: Full length RNASeq of fly heads_zt3

description:
Drosophila melanogaster: full-length and 3' RNA-Seq data only.
Sample 2
Processed data file: dm3.full.scores.rpk.txt (linked as supplementary file on Series record)

value: head of fly

value: Canton S

value: 3hr after lights are on


title: Histone H3K27me3 ChIP-Seq of Fetal Muscle, Trunk; Histone.DS23036

description:
sample_term_id: UBERON_0001774
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Histone H3K27me3 ChIP-Seq
Library name: Histone.DS23036
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.16280
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.16267
****************
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: GSM1160191_UW.Fetal_Muscle_Trunk.H3K27me3.H-24851.Histone.DS23036.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS23036-Histone.DS23036.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Fetal Muscle Trunk H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27me3 ChIP-Seq on Fetal Muscle Trunk, Donor H-24851, 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.16825
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 19,229,877
FINDPEAKS_SCORE: 0.4621
FINDPEAKS_PERCENTILE: 98
HOTSPOT_SCORE: 0.494
HOTSPOT_PERCENTILE: 98
IROC_SCORE: 0.981
IROC_PERCENTILE: 91
POISSON_SCORE: 0.597
POISSON_PERCENTILE: 96
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1160191_UW.Fetal_Muscle_Trunk.H3K27me3.H-24851.Histone.DS23036.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS23036-Histone.DS23036.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Muscle Trunk H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27me3 ChIP-Seq read mappings from Fetal Muscle Trunk, Donor H-24851, 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.16921
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: FMT H3K27me3 51 36
BROWSER_TRACK_DESCRIPTION: UW Fetal Muscle Trunk Histone H3K27me3 Donor H-24851 Library Histone.DS23036 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 19,229,877
FINDPEAKS_SCORE: 0.4621
FINDPEAKS_PERCENTILE: 98
HOTSPOT_SCORE: 0.494
HOTSPOT_PERCENTILE: 98
IROC_SCORE: 0.981
IROC_PERCENTILE: 91
POISSON_SCORE: 0.597
POISSON_PERCENTILE: 96
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: Fetal Muscle, Trunk primary tissue, day 115; Histone.DS23036

value: Fetal Muscle, Trunk

value: Primary Tissue

value: UW

value: day 115

value: Female

value: Millipore A/G agarose beads

value: 30ul A/G bead slurry


title: Reference Epigenome: ChIP-Seq Input from Human Spleen Tissue; renlab.Input.STL001SX.01.01

city: La Jolla

first: UCSD AND

last: SALK

state: CA

address: Health Sciences Drive

institute: University of California, San Diego

description:
sample_term_id: UBERON_0002106
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Input from Human Spleen Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AY355
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.16027
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.15438
****************
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: GSM1127188_UCSD.Spleen.Input.STL001.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.Input.STL001SX.01.01.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Spleen Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Input ChIP-Seq on Spleen, Donor STL001, 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.16404
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 8,703,771
FINDPEAKS_SCORE: 0.02
FINDPEAKS_PERCENTILE: 96
HOTSPOT_SCORE: 0.19
HOTSPOT_PERCENTILE: 98
IROC_SCORE: 0.7
IROC_PERCENTILE: 28
POISSON_SCORE: 0.3
POISSON_PERCENTILE: 93
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM1127188_UCSD.Spleen.Input.STL001.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.Input.STL001SX.01.01.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Spleen Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Input ChIP-Seq read mappings from Spleen, Donor STL001, 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.16558
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: Spleen Input 01 55
BROWSER_TRACK_DESCRIPTION: UCSD Spleen ChIP-Seq Input Donor STL001 Library AY355 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 8,703,771
FINDPEAKS_SCORE: 0.02
FINDPEAKS_PERCENTILE: 96
HOTSPOT_SCORE: 0.19
HOTSPOT_PERCENTILE: 98
IROC_SCORE: 0.7
IROC_PERCENTILE: 28
POISSON_SCORE: 0.3
POISSON_PERCENTILE: 93
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

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

value: Spleen

value: Shin Lin, Stanford University

value: Autopsy

value: healthy, no prior medical history (NO diabetes, hypertension, coronary artery disease, cancer)

value: Caucasian and African American

value: ChIP-Seq Input

value: Biorupter

value: Input

value: 500 micrograms