title: RNA-Seq analysis of cDNA_Lib 17 derived from human HUES64 cells; cDNA_Lib 17

description:
sample_term_id: NTR_0000853
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: mRNA-Seq for REMC on Illumina
Library name: cDNA_Lib 17
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.15431
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.15436
****************
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: GSM1112834_BI.HUES64.mRNA-Seq.cDNA_Lib_17.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: cDNA_Lib 17.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of HUES64 Cell Line mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by mRNA-Seq on the HUES64 Cell Line, Library cDNA_Lib 17 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.16654
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 156,910,092
PERCENT_READS_MAPPING_TO_UCSC_GENES: 88.48
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 20
MAXIMUM_REPLICATE_CORRELATION: 0.67

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

ANALYSIS FILE NAME: GSM1112834_BI.HUES64.mRNA-Seq.cDNA_Lib_17.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: cDNA_Lib 17.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of HUES64 Cell Line mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina mRNA-Seq read mappings from the HUES64 Cell Line, Library cDNA_Lib 17 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.16663
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: HUES64 mRNA 17
BROWSER_TRACK_DESCRIPTION: BI HUES64 Cell Line mRNA-Seq Library cDNA_Lib 17 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 156,910,092
PERCENT_READS_MAPPING_TO_UCSC_GENES: 88.48
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 20
MAXIMUM_REPLICATE_CORRELATION: 0.67

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

source_name: Harvard University ES Cell 64 AKA HUES 64; cDNA_Lib 17

value: BioSam 1282

value: HUES64 Cell Line

value: HUES general media - KO DMEM, 20% KSR, bFGF (10ng/mL)

value: presumed normal

value: BioSAli 1950

value: Cell Line

value: undifferentiated

value: 3' cDNA ligation

value: Our protocol using T4 RNA ligase from NEB

value: ILLUMINA A1+B1, C1+D1, E1+F1, G1+H1

value: around 10ng

value: 3x RLT + 15/20 ul of Silane + 0.4x EtOn, eluted in 100ul, recleaned using 0.95X SPRI

value: yes

value: OligodT - Dynabeads mRNA purification kit (Invitrogen)

value: 98C 30 sec, 8 cycles of: 98C for 10 sec, 67C for 20 sec, 72C for 20 min, then 72C for 30 seconds, hold 4C

value: Qiagen AllPrep DNA/RNA/Protein Mini Kit

value: Adapter ligated cDNA made by reverse transcription of RNA

value: Phusion High Fidelity

value: 12 pmoles of each/50 ul of reaction

value: 70C for 4 min in Ambion Fragmentation Buffer

value: NO

value: mRNA-Seq

value: We synthesized first-strand cDNA using affinity-script reverse transcriptase


title: RNA-Seq analysis of cDNA_Lib 18 derived from human HUES64 cells; cDNA_Lib 18

status: Public on Jun 22 2013

type: SRA

city: Cambridge

first: BROAD

last: INSTITUTE

state: MA

country: USA

institute: Broad Institute

description:
sample_term_id: NTR_0000853
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: mRNA-Seq for REMC on Illumina
Library name: cDNA_Lib 18
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.15434
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.15435
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

library_source: transcriptomic

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

ANALYSIS FILE NAME: GSM1112837_BI.HUES64.mRNA-Seq.cDNA_Lib_18.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: cDNA_Lib 18.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of HUES64 Cell Line mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by mRNA-Seq on the HUES64 Cell Line, Library cDNA_Lib 18 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.16655
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 114,256,450
PERCENT_READS_MAPPING_TO_UCSC_GENES: 88.2
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 19
MAXIMUM_REPLICATE_CORRELATION: 0.67

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

ANALYSIS FILE NAME: GSM1112837_BI.HUES64.mRNA-Seq.cDNA_Lib_18.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: cDNA_Lib 18.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of HUES64 Cell Line mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina mRNA-Seq read mappings from the HUES64 Cell Line, Library cDNA_Lib 18 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.16664
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: HUES64 mRNA 18
BROWSER_TRACK_DESCRIPTION: BI HUES64 Cell Line mRNA-Seq Library cDNA_Lib 18 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 114,256,450
PERCENT_READS_MAPPING_TO_UCSC_GENES: 88.2
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 19
MAXIMUM_REPLICATE_CORRELATION: 0.67

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

molecule: total RNA

organism: Homo sapiens

source_name: Harvard University ES Cell 64 AKA HUES 64; cDNA_Lib 18

extract_protocol: Library construction protocol: Direct RNA-seq method based on RNA 3' linker ligation, unpublished

tag: sample alias

value: BioSam 1283

tag: sample common name

value: HUES64 Cell Line

tag: lineage

tag: medium

value: HUES general media - KO DMEM, 20% KSR, bFGF (10ng/mL)

tag: disease

value: presumed normal

tag: passage

tag: line

tag: batch

value: BioSAli 1951

value: Cell Line

value: undifferentiated

tag: Sex

value: Male

value: Harvard


title: RNA-Seq analysis of cDNA_Lib 16 derived from human CD56+ mesoderm cells; cDNA_Lib 16

description:
sample_term_id: CL_0000222
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: mRNA-Seq for REMC on Illumina
Library name: cDNA_Lib 16
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.15430
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.15415
****************
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: GSM1112833_BI.hESC_Derived_CD56+_Mesoderm_Cultured_Cells.mRNA-Seq.cDNA_Lib_16.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: cDNA_Lib 16.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of hESC Derived CD56+ Mesoderm Cultured Cells mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by mRNA-Seq on the hESC Derived CD56+ Mesoderm Cultured Cells, Library cDNA_Lib 16 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.16662
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 108,453,952
PERCENT_READS_MAPPING_TO_UCSC_GENES: 89.48
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 25
MAXIMUM_REPLICATE_CORRELATION: 0.69

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

ANALYSIS FILE NAME: GSM1112833_BI.hESC_Derived_CD56+_Mesoderm_Cultured_Cells.mRNA-Seq.cDNA_Lib_16.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: cDNA_Lib 16.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of hESC Derived CD56+ Mesoderm Cultured Cells mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina mRNA-Seq read mappings from the hESC Derived CD56+ Mesoderm Cultured Cells, Library cDNA_Lib 16 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.16671
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: hDCM mRNA 16
BROWSER_TRACK_DESCRIPTION: BI hESC Derived CD56+ Mesoderm Cultured Cells mRNA-Seq Library cDNA_Lib 16 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 108,453,952
PERCENT_READS_MAPPING_TO_UCSC_GENES: 89.48
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 25
MAXIMUM_REPLICATE_CORRELATION: 0.69

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

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. ; cDNA_Lib 16

value: BioSam 1250

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 1893

value: intermediate

value: 3' cDNA ligation

value: Our protocol using T4 RNA ligase from NEB

value: ILLUMINA A1+B1, C1+D1, E1+F1, G1+H1

value: around 10ng

value: 3x RLT + 15/20 ul of Silane + 0.4x EtOn, eluted in 100ul, recleaned using 0.95X SPRI

value: yes

value: OligodT - Dynabeads mRNA purification kit (Invitrogen)

value: 98C 30 sec, 8 cycles of: 98C for 10 sec, 67C for 20 sec, 72C for 20 min, then 72C for 30 seconds, hold 4C

value: Qiagen AllPrep DNA/RNA/Protein Mini Kit


title: Reference Epigenome: ChIP-Seq Input from Human Liver Tissue; renlab.Input.STL011LI.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_0002107
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Input from Human Liver Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AY359
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.15141
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.15104
****************
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: GSM1059458_UCSD.Adult_Liver.Input.STL011.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.Input.STL011LI.01.01.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Adult Liver Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Input ChIP-Seq on Adult Liver, Donor STL011, 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.16468
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: 32,560,516
FINDPEAKS_SCORE: 0.01
FINDPEAKS_PERCENTILE: 93
HOTSPOT_SCORE: 0.04
HOTSPOT_PERCENTILE: 67
IROC_SCORE: 0.9652
IROC_PERCENTILE: 58
POISSON_SCORE: 0.14
POISSON_PERCENTILE: 80
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM1059458_UCSD.Adult_Liver.Input.STL011.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.Input.STL011LI.01.01.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Adult Liver Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Input ChIP-Seq read mappings from Adult Liver, Donor STL011, 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.16622
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: AL Input 11 59
BROWSER_TRACK_DESCRIPTION: UCSD Adult Liver ChIP-Seq Input Donor STL011 Library AY359 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 32,560,516
FINDPEAKS_SCORE: 0.01
FINDPEAKS_PERCENTILE: 93
HOTSPOT_SCORE: 0.04
HOTSPOT_PERCENTILE: 67
IROC_SCORE: 0.9652
IROC_PERCENTILE: 58
POISSON_SCORE: 0.14
POISSON_PERCENTILE: 80
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

molecule: genomic DNA

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

value: Adult Liver

tag: molecule

value: genomic DNA

value: coronary artery disease

value: Shin Lin, Stanford University

value: Primary Tissue

value: Liver

value: Autopsy

value: coronary artery disease. No history of hypertension or diabetes.

value: Male

value: Caucasian

value: ChIP-Seq Input

value: Biorupter

value: Input

value: 500 micrograms


title: Reference Epigenome: ChIP-Seq Input from Human Bladder Tissue; renlab.Input.STL001BL.02.01

description:
sample_term_id: UBERON_0001255
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Input from Human Bladder Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: CY49
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.15137
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.11880
****************
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: GSM1059457_UCSD.Bladder.Input.STL003.CY49.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.Input.STL001BL.02.01-renlab.Input.STL001BL.01.01.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Bladder Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Input ChIP-Seq on Bladder, 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.16356
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: 25,221,478
FINDPEAKS_SCORE: 0.01
FINDPEAKS_PERCENTILE: 93
HOTSPOT_SCORE: 0.02
HOTSPOT_PERCENTILE: 59
IROC_SCORE: 0.9677
IROC_PERCENTILE: 60
POISSON_SCORE: 0.07
POISSON_PERCENTILE: 52
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM1059457_UCSD.Bladder.Input.STL003.CY49.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.Input.STL001BL.02.01-renlab.Input.STL001BL.01.01.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Bladder Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Input ChIP-Seq read mappings from Bladder, 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.16510
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: Bladder Input 03 49
BROWSER_TRACK_DESCRIPTION: UCSD Bladder ChIP-Seq Input Donor STL001 Library CY49 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 25,221,478
FINDPEAKS_SCORE: 0.01
FINDPEAKS_PERCENTILE: 93
HOTSPOT_SCORE: 0.02
HOTSPOT_PERCENTILE: 59
IROC_SCORE: 0.9677
IROC_PERCENTILE: 60
POISSON_SCORE: 0.07
POISSON_PERCENTILE: 52
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

value: Bladder

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

value: Caucasian and African American


title: Reference Epigenome: ChIP-Seq Analysis of H3K4me1 in Human Thymus Tissue; renlab.H3K4me1.STL001TH.01.01

description:
sample_term_id: UBERON_0002370
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K4me1 in Human Thymus Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AY476
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.15100
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.13369
****************
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: GSM1059446_UCSD.Thymus.H3K4me1.STL001.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4me1.STL001TH.01.01.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Thymus H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K4me1 ChIP-Seq on Thymus, 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.16455
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: 15,676,809
FINDPEAKS_SCORE: 0.23
FINDPEAKS_PERCENTILE: 46
HOTSPOT_SCORE: 0.3
HOTSPOT_PERCENTILE: 42
IROC_SCORE: 0.9821
IROC_PERCENTILE: 60
POISSON_SCORE: 0.38
POISSON_PERCENTILE: 21
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1059446_UCSD.Thymus.H3K4me1.STL001.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4me1.STL001TH.01.01.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Thymus H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K4me1 ChIP-Seq read mappings from Thymus, 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.16609
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: Thymus H3K4me1 01 76
BROWSER_TRACK_DESCRIPTION: UCSD Thymus Histone H3K4me1 Donor STL001 Library AY476 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 15,676,809
FINDPEAKS_SCORE: 0.23
FINDPEAKS_PERCENTILE: 46
HOTSPOT_SCORE: 0.3
HOTSPOT_PERCENTILE: 42
IROC_SCORE: 0.9821
IROC_PERCENTILE: 60
POISSON_SCORE: 0.38
POISSON_PERCENTILE: 21
MAXIMUM_REPLICATE_CORRELATION: NA

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

value: Thymus

value: Histone H3K4me1

value: magnetic anti-rabbit

value: 5 micrograms

value: Abcam


title: Reference Epigenome: ChIP-Seq Analysis of H3K4me1 in Human Liver Tissue; renlab.H3K4me1.STL011LI.01.01

description:
sample_term_id: UBERON_0002107
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K4me1 in Human Liver Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: CY127
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.15139
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.15104
****************
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: GSM1059451_UCSD.Adult_Liver.H3K4me1.STL011.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4me1.STL011LI.01.01.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Adult Liver H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K4me1 ChIP-Seq on Adult Liver, Donor STL011, 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.16438
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: 20,160,273
FINDPEAKS_SCORE: 0.15
FINDPEAKS_PERCENTILE: 27
HOTSPOT_SCORE: 0.25
HOTSPOT_PERCENTILE: 25
IROC_SCORE: 0.9356
IROC_PERCENTILE: 27
POISSON_SCORE: 0.38
POISSON_PERCENTILE: 21
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

ANALYSIS FILE NAME: GSM1059451_UCSD.Adult_Liver.H3K4me1.STL011.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4me1.STL011LI.01.01.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Adult Liver H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K4me1 ChIP-Seq read mappings from Adult Liver, Donor STL011, 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.16592
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: AL H3K4me1 11 27
BROWSER_TRACK_DESCRIPTION: UCSD Adult Liver Histone H3K4me1 Donor STL011 Library CY127 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 20,160,273
FINDPEAKS_SCORE: 0.15
FINDPEAKS_PERCENTILE: 27
HOTSPOT_SCORE: 0.25
HOTSPOT_PERCENTILE: 25
IROC_SCORE: 0.9356
IROC_PERCENTILE: 27
POISSON_SCORE: 0.38
POISSON_PERCENTILE: 21
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

value: Adult Liver

value: genomic DNA

value: coronary artery disease

value: Shin Lin, Stanford University

value: Primary Tissue

value: Liver


title: Reference Epigenome: ChIP-Seq Analysis of H3K4me1 in Human Aorta Tissue; renlab.H3K4me1.STL002AO.01.01

description:
sample_term_id: UBERON_0000947
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K4me1 in Human Aorta Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: CY163
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.15121
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.14007
****************
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: GSM1059448_UCSD.Aorta.H3K4me1.STL002.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4me1.STL002AO.01.01.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Aorta H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K4me1 ChIP-Seq on Aorta, Donor STL002, 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.16402
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 22,882,515
FINDPEAKS_SCORE: 0.01
FINDPEAKS_PERCENTILE: 4
HOTSPOT_SCORE: 0.14
HOTSPOT_PERCENTILE: 6
IROC_SCORE: 0.7354
IROC_PERCENTILE: 4
POISSON_SCORE: 0.28
POISSON_PERCENTILE: 2
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

ANALYSIS FILE NAME: GSM1059448_UCSD.Aorta.H3K4me1.STL002.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4me1.STL002AO.01.01.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Aorta H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K4me1 ChIP-Seq read mappings from Aorta, Donor STL002, 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.16556
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: Aorta H3K4me1 02 63
BROWSER_TRACK_DESCRIPTION: UCSD Aorta Histone H3K4me1 Donor STL002 Library CY163 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 22,882,515
FINDPEAKS_SCORE: 0.01
FINDPEAKS_PERCENTILE: 4
HOTSPOT_SCORE: 0.14
HOTSPOT_PERCENTILE: 6
IROC_SCORE: 0.7354
IROC_PERCENTILE: 4
POISSON_SCORE: 0.28
POISSON_PERCENTILE: 2
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

value: Aorta

value: iron deficiency, bipolar

value: Autopsy

value: iron deficiency, bipolar disease (NO diabetes, hypertension, coronary artery disease, cancer)

value: Female

value: Caucasian

value: Biorupter


title: Reference Epigenome: ChIP-Seq Input from Human Sigmoid Colon Tissue; renlab.Input.STL001SG.01.01

description:
sample_term_id: UBERON_0001159
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Input from Human Sigmoid Colon Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: CY114
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.15111
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.12265
****************
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: GSM1059456_UCSD.Sigmoid_Colon.Input.STL001.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.Input.STL001SG.02.01-renlab.Input.STL001SG.01.01.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Sigmoid Colon Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Input ChIP-Seq on Sigmoid Colon, 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.16456
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: 46,242,102
FINDPEAKS_SCORE: 0.0
FINDPEAKS_PERCENTILE: 2
HOTSPOT_SCORE: 0.01
HOTSPOT_PERCENTILE: 44
IROC_SCORE: 0.9627
IROC_PERCENTILE: 51
POISSON_SCORE: 0.11
POISSON_PERCENTILE: 74
MAXIMUM_REPLICATE_CORRELATION: NA

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

SPECIAL NOTE: generated from combined data in GSM1120362, GSM1059456 (thus .bed files on these records are identical)

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

ANALYSIS FILE NAME: GSM1059456_UCSD.Sigmoid_Colon.Input.STL001.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.Input.STL001SG.02.01-renlab.Input.STL001SG.01.01.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Sigmoid Colon Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Input ChIP-Seq read mappings from Sigmoid Colon, 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.16610
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: SC Input 01 91
BROWSER_TRACK_DESCRIPTION: UCSD Sigmoid Colon ChIP-Seq Input Donor STL001 Library CY191 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 46,242,102
FINDPEAKS_SCORE: 0.0
FINDPEAKS_PERCENTILE: 2
HOTSPOT_SCORE: 0.01
HOTSPOT_PERCENTILE: 44
IROC_SCORE: 0.9627
IROC_PERCENTILE: 51
POISSON_SCORE: 0.11
POISSON_PERCENTILE: 74
MAXIMUM_REPLICATE_CORRELATION: NA

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

SPECIAL NOTE: generated from combined data in GSM1120362, GSM1059456 (thus .wig files on these records are identical)

source_name: Sigmoid Colon tissue; renlab.Input.STL001SG.01.01

value: Sigmoid Colon

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

value: Male

value: Caucasian and African American

value: ChIP-Seq Input

value: Input

value: 500 micrograms


title: Reference Epigenome: ChIP-Seq Analysis of H3K4me1 in Human Adrenal Gland Tissue; renlab.H3K4me1.STL003AD.01.01

description:
sample_term_id: UBERON_0002369
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K4me1 in Human Adrenal Gland Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AY474
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.15127
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.11638
****************
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: GSM1059449_UCSD.Adrenal_Gland.H3K4me1.STL003.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4me1.STL003AD.01.01.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Adrenal Gland H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K4me1 ChIP-Seq on Adrenal Gland, Donor STL003, 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.16423
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: 12,972,750
FINDPEAKS_SCORE: 0.02
FINDPEAKS_PERCENTILE: 8
HOTSPOT_SCORE: 0.18
HOTSPOT_PERCENTILE: 13
IROC_SCORE: 0.7208
IROC_PERCENTILE: 2
POISSON_SCORE: 0.31
POISSON_PERCENTILE: 6
MAXIMUM_REPLICATE_CORRELATION: 0.95

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

ANALYSIS FILE NAME: GSM1059449_UCSD.Adrenal_Gland.H3K4me1.STL003.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4me1.STL003AD.01.01.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Adrenal Gland H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K4me1 ChIP-Seq read mappings from Adrenal Gland, Donor STL003, 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.16577
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: AG H3K4me1 03 74
BROWSER_TRACK_DESCRIPTION: UCSD Adrenal Gland Histone H3K4me1 Donor STL003 Library AY474 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 12,972,750
FINDPEAKS_SCORE: 0.02
FINDPEAKS_PERCENTILE: 8
HOTSPOT_SCORE: 0.18
HOTSPOT_PERCENTILE: 13
IROC_SCORE: 0.7208
IROC_PERCENTILE: 2
POISSON_SCORE: 0.31
POISSON_PERCENTILE: 6
MAXIMUM_REPLICATE_CORRELATION: 0.95

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

source_name: Adrenal Gland tissue; renlab.H3K4me1.STL003AD.01.01

value: Adrenal Gland

value: genomic DNA

value: Shin Lin, Stanford University

value: polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)

value: Histone H3K4me1

value: magnetic anti-rabbit

value: 5 micrograms

value: Abcam


title: Reference Epigenome: ChIP-Seq Analysis of H3K4me1 in Human Adrenal Gland Tissue; renlab.H3K4me1.STL002AD.01.01

description:
sample_term_id: UBERON_0002369
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K4me1 in Human Adrenal Gland Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: CY99
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.15113
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.13995
****************
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: GSM1059447_UCSD.Adrenal_Gland.H3K4me1.STL002.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4me1.STL002AD.01.01.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Adrenal Gland H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K4me1 ChIP-Seq on Adrenal Gland, Donor STL002, 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.16421
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: 12,248,977
FINDPEAKS_SCORE: 0.15
FINDPEAKS_PERCENTILE: 27
HOTSPOT_SCORE: 0.27
HOTSPOT_PERCENTILE: 31
IROC_SCORE: 0.9065
IROC_PERCENTILE: 23
POISSON_SCORE: 0.38
POISSON_PERCENTILE: 21
MAXIMUM_REPLICATE_CORRELATION: 0.95

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

ANALYSIS FILE NAME: GSM1059447_UCSD.Adrenal_Gland.H3K4me1.STL002.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4me1.STL002AD.01.01.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Adrenal Gland H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K4me1 ChIP-Seq read mappings from Adrenal Gland, Donor STL002, 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.16575
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: AG H3K4me1 02 99
BROWSER_TRACK_DESCRIPTION: UCSD Adrenal Gland Histone H3K4me1 Donor STL002 Library CY99 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 12,248,977
FINDPEAKS_SCORE: 0.15
FINDPEAKS_PERCENTILE: 27
HOTSPOT_SCORE: 0.27
HOTSPOT_PERCENTILE: 31
IROC_SCORE: 0.9065
IROC_PERCENTILE: 23
POISSON_SCORE: 0.38
POISSON_PERCENTILE: 21
MAXIMUM_REPLICATE_CORRELATION: 0.95

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

source_name: Adrenal Gland tissue; renlab.H3K4me1.STL002AD.01.01

value: iron deficiency, bipolar

value: Primary Tissue

value: Autopsy

value: iron deficiency, bipolar disease (NO diabetes, hypertension, coronary artery disease, cancer)

value: Female

value: Caucasian


title: Reference Epigenome: ChIP-Seq Analysis of H3K4me1 in Human Right Ventricle Tissue; renlab.H3K4me1.STL001RV.01.01

description:
sample_term_id: UBERON_0002080
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K4me1 in Human Right Ventricle Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: CY102
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.15098
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.14086
****************
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: GSM1059445_UCSD.Right_Ventricle.H3K4me1.STL001.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4me1.STL001RV.01.01.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Right Ventricle H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K4me1 ChIP-Seq on Right Ventricle, 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.16352
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: 14,693,625
FINDPEAKS_SCORE: 0.09
FINDPEAKS_PERCENTILE: 15
HOTSPOT_SCORE: 0.23
HOTSPOT_PERCENTILE: 19
IROC_SCORE: 0.8736
IROC_PERCENTILE: 17
POISSON_SCORE: 0.37
POISSON_PERCENTILE: 15
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM1059445_UCSD.Right_Ventricle.H3K4me1.STL001.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4me1.STL001RV.01.01.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Right Ventricle H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K4me1 ChIP-Seq read mappings from Right Ventricle, 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.16506
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: RV H3K4me1 01 02
BROWSER_TRACK_DESCRIPTION: UCSD Right Ventricle Histone H3K4me1 Donor STL001 Library CY102 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 14,693,625
FINDPEAKS_SCORE: 0.09
FINDPEAKS_PERCENTILE: 15
HOTSPOT_SCORE: 0.23
HOTSPOT_PERCENTILE: 19
IROC_SCORE: 0.8736
IROC_PERCENTILE: 17
POISSON_SCORE: 0.37
POISSON_PERCENTILE: 15
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

source_name: Right Ventricle tissue; renlab.H3K4me1.STL001RV.01.01

value: Right Ventricle

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

value: Male

value: Caucasian and African American

value: Biorupter


title: Reference Epigenome: ChIP-Seq Analysis of H3K36me3 in Human Liver Tissue; renlab.H3K36me3.STL011LI.01.01

description:
sample_term_id: UBERON_0002107
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K36me3 in Human Liver Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: CY125
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.15105
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.15104
****************
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: GSM1059442_UCSD.Adult_Liver.H3K36me3.STL011.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K36me3.STL011LI.01.01.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Adult Liver H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K36me3 ChIP-Seq on Adult Liver, Donor STL011, 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.16492
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: 15,546,705
FINDPEAKS_SCORE: 0.16
FINDPEAKS_PERCENTILE: 27
HOTSPOT_SCORE: 0.25
HOTSPOT_PERCENTILE: 27
IROC_SCORE: 0.9229
IROC_PERCENTILE: 24
POISSON_SCORE: 0.39
POISSON_PERCENTILE: 22
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

ANALYSIS FILE NAME: GSM1059442_UCSD.Adult_Liver.H3K36me3.STL011.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K36me3.STL011LI.01.01.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Adult Liver H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K36me3 ChIP-Seq read mappings from Adult Liver, Donor STL011, 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.16646
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: AL H3K36me3 11 25
BROWSER_TRACK_DESCRIPTION: UCSD Adult Liver Histone H3K36me3 Donor STL011 Library CY125 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 15,546,705
FINDPEAKS_SCORE: 0.16
FINDPEAKS_PERCENTILE: 27
HOTSPOT_SCORE: 0.25
HOTSPOT_PERCENTILE: 27
IROC_SCORE: 0.9229
IROC_PERCENTILE: 24
POISSON_SCORE: 0.39
POISSON_PERCENTILE: 22
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

value: Adult Liver

value: genomic DNA

value: coronary artery disease

value: Shin Lin, Stanford University

value: Liver

value: coronary artery disease. No history of hypertension or diabetes.

value: Histone H3K36me3

value: 500 micrograms


title: RNA-Seq analysis of cDNA_Lib 11 derived from human HUES64 derived CD184+ cells; cDNA_Lib 11

description:
sample_term_id: CL_0000223
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: mRNA-Seq for REMC on Illumina
Library name: cDNA_Lib 11
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.15789
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.15414
****************
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: GSM1112847_BI.hESC_Derived_CD184+_Endoderm_Cultured_Cells.mRNA-Seq.cDNA_Lib_11.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: cDNA_Lib 11.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of hESC Derived CD184+ Endoderm Cultured Cells mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by mRNA-Seq on the hESC Derived CD184+ Endoderm Cultured Cells, Library cDNA_Lib 11 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.16659
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 117,869,974
PERCENT_READS_MAPPING_TO_UCSC_GENES: 89.93
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 28
MAXIMUM_REPLICATE_CORRELATION: 0.62

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

ANALYSIS FILE NAME: GSM1112847_BI.hESC_Derived_CD184+_Endoderm_Cultured_Cells.mRNA-Seq.cDNA_Lib_11.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: cDNA_Lib 11.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of hESC Derived CD184+ Endoderm Cultured Cells mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina mRNA-Seq read mappings from the hESC Derived CD184+ Endoderm Cultured Cells, Library cDNA_Lib 11 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.16668
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: hDCE mRNA 11
BROWSER_TRACK_DESCRIPTION: BI hESC Derived CD184+ Endoderm Cultured Cells mRNA-Seq Library cDNA_Lib 11 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 117,869,974
PERCENT_READS_MAPPING_TO_UCSC_GENES: 89.93
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 28
MAXIMUM_REPLICATE_CORRELATION: 0.62

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

source_name: CD184+ endoderm differentiated in vitro from stem cells; cDNA_Lib 11

value: CD184+ endoderm cultured cells

value: BioSam 1245

value: endoderm

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

value: presumed normal

value: HUES64 derived CD184+

value: in vitro culture

value: BioSAli 1887

value: Cell Line

value: differentiated

value: Harvard

value: 3' cDNA ligation

value: Our protocol using T4 RNA ligase from NEB

value: ILLUMINA A1+B1, C1+D1, E1+F1, G1+H1

value: around 10ng

value: 3x RLT + 15/20 ul of Silane + 0.4x EtOn, eluted in 100ul, recleaned using 0.95X SPRI

value: yes

value: OligodT - Dynabeads mRNA purification kit (Invitrogen)

value: 98C 30 sec, 8 cycles of: 98C for 10 sec, 67C for 20 sec, 72C for 20 min, then 72C for 30 seconds, hold 4C

value: Qiagen AllPrep DNA/RNA/Protein Mini Kit

value: Adapter ligated cDNA made by reverse transcription of RNA

value: Phusion High Fidelity

value: 12 pmoles of each/50 ul of reaction

value: 70C for 4 min in Ambion Fragmentation Buffer

value: NO

value: mRNA-Seq

value: We synthesized first-strand cDNA using affinity-script reverse transcriptase


title: Reference Epigenome: ChIP-Seq Analysis of H3K36me3 in Human Bladder Tissue; renlab.H3K36me3.STL001BL.01.01

description:
sample_term_id: UBERON_0001255
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K36me3 in Human Bladder Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: CY122
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.15129
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.11880
****************
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: GSM1059441_UCSD.Bladder.H3K36me3.STL003.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K36me3.STL001BL.01.01.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Bladder H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K36me3 ChIP-Seq on Bladder, 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.16399
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: 17,042,394
FINDPEAKS_SCORE: 0.05
FINDPEAKS_PERCENTILE: 6
HOTSPOT_SCORE: 0.18
HOTSPOT_PERCENTILE: 10
IROC_SCORE: 0.8266
IROC_PERCENTILE: 8
POISSON_SCORE: 0.31
POISSON_PERCENTILE: 10
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM1059441_UCSD.Bladder.H3K36me3.STL003.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K36me3.STL001BL.01.01.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Bladder H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K36me3 ChIP-Seq read mappings from Bladder, 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.16553
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: Bladder H3K36me3 03 22
BROWSER_TRACK_DESCRIPTION: UCSD Bladder Histone H3K36me3 Donor STL001 Library CY122 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 17,042,394
FINDPEAKS_SCORE: 0.05
FINDPEAKS_PERCENTILE: 6
HOTSPOT_SCORE: 0.18
HOTSPOT_PERCENTILE: 10
IROC_SCORE: 0.8266
IROC_PERCENTILE: 8
POISSON_SCORE: 0.31
POISSON_PERCENTILE: 10
MAXIMUM_REPLICATE_CORRELATION: NA

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

value: Bladder

value: genomic DNA

value: Shin Lin, Stanford University

value: Primary Tissue

value: Autopsy

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

value: Male

value: Caucasian and African American

value: Histone H3K36me3

value: Biorupter

value: 500 micrograms

value: magnetic anti-rabbit

value: 5 micrograms

value: Abcam


title: Reference Epigenome: ChIP-Seq Analysis of H3K36me3 in Human Esophagus Tissue; renlab.H3K36me3.STL002EG.01.01

description:
sample_term_id: UBERON_0001043
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K36me3 in Human Esophagus Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: CY177
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.15834
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.14001
****************
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: GSM1120346_UCSD.Esophagus.H3K36me3.STL002.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K36me3.STL002EG.01.01.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Esophagus H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K36me3 ChIP-Seq on Esophagus, Donor STL002, 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.16422
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: 25,082,103
FINDPEAKS_SCORE: 0.01
FINDPEAKS_PERCENTILE: 4
HOTSPOT_SCORE: 0.11
HOTSPOT_PERCENTILE: 2
IROC_SCORE: 0.75
IROC_PERCENTILE: 2
POISSON_SCORE: 0.26
POISSON_PERCENTILE: 2
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

ANALYSIS FILE NAME: GSM1120346_UCSD.Esophagus.H3K36me3.STL002.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K36me3.STL002EG.01.01.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Esophagus H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K36me3 ChIP-Seq read mappings from Esophagus, Donor STL002, 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.16576
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: Esophagus H3K36me3 02 77
BROWSER_TRACK_DESCRIPTION: UCSD Esophagus Histone H3K36me3 Donor STL002 Library CY177 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 25,082,103
FINDPEAKS_SCORE: 0.01
FINDPEAKS_PERCENTILE: 4
HOTSPOT_SCORE: 0.11
HOTSPOT_PERCENTILE: 2
IROC_SCORE: 0.75
IROC_PERCENTILE: 2
POISSON_SCORE: 0.26
POISSON_PERCENTILE: 2
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

value: Esophagus

tag: sra sample accession

value: iron deficiency, bipolar

value: iron deficiency, bipolar disease (NO diabetes, hypertension, coronary artery disease, cancer)

value: Female

value: Caucasian


title: Reference Epigenome: ChIP-Seq Analysis of H3K36me3 in Human Aorta Tissue; renlab.H3K36me3.STL002AO.01.01

description:
sample_term_id: UBERON_0000947
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K36me3 in Human Aorta Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: CY161
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.15117
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.14007
****************
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: GSM1059440_UCSD.Aorta.H3K36me3.STL002.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K36me3.STL002AO.01.01.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Aorta H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K36me3 ChIP-Seq on Aorta, Donor STL002, 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.16405
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: 19,698,554
FINDPEAKS_SCORE: 0.01
FINDPEAKS_PERCENTILE: 4
HOTSPOT_SCORE: 0.14
HOTSPOT_PERCENTILE: 4
IROC_SCORE: 0.7527
IROC_PERCENTILE: 4
POISSON_SCORE: 0.27
POISSON_PERCENTILE: 4
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

ANALYSIS FILE NAME: GSM1059440_UCSD.Aorta.H3K36me3.STL002.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K36me3.STL002AO.01.01.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Aorta H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K36me3 ChIP-Seq read mappings from Aorta, Donor STL002, 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.16559
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: Aorta H3K36me3 02 61
BROWSER_TRACK_DESCRIPTION: UCSD Aorta Histone H3K36me3 Donor STL002 Library CY161 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 19,698,554
FINDPEAKS_SCORE: 0.01
FINDPEAKS_PERCENTILE: 4
HOTSPOT_SCORE: 0.14
HOTSPOT_PERCENTILE: 4
IROC_SCORE: 0.7527
IROC_PERCENTILE: 4
POISSON_SCORE: 0.27
POISSON_PERCENTILE: 4
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

value: Aorta

value: genomic DNA

value: Shin Lin, Stanford University


title: Reference Epigenome: ChIP-Seq Analysis of H3K36me3 in Human Adrenal Gland Tissue; renlab.H3K36me3.STL002AD.01.01

description:
sample_term_id: UBERON_0002369
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K36me3 in Human Adrenal Gland Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: CY97
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.15102
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.13995
****************
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: GSM1059439_UCSD.Adrenal_Gland.H3K36me3.STL002.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K36me3.STL002AD.01.01.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Adrenal Gland H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K36me3 ChIP-Seq on Adrenal Gland, Donor STL002, 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.16375
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: 11,581,916
FINDPEAKS_SCORE: 0.16
FINDPEAKS_PERCENTILE: 27
HOTSPOT_SCORE: 0.26
HOTSPOT_PERCENTILE: 31
IROC_SCORE: 0.9184
IROC_PERCENTILE: 20
POISSON_SCORE: 0.36
POISSON_PERCENTILE: 16
MAXIMUM_REPLICATE_CORRELATION: 0.95

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

ANALYSIS FILE NAME: GSM1059439_UCSD.Adrenal_Gland.H3K36me3.STL002.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K36me3.STL002AD.01.01.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Adrenal Gland H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K36me3 ChIP-Seq read mappings from Adrenal Gland, Donor STL002, 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.16529
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: AG H3K36me3 02 97
BROWSER_TRACK_DESCRIPTION: UCSD Adrenal Gland Histone H3K36me3 Donor STL002 Library CY97 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 11,581,916
FINDPEAKS_SCORE: 0.16
FINDPEAKS_PERCENTILE: 27
HOTSPOT_SCORE: 0.26
HOTSPOT_PERCENTILE: 31
IROC_SCORE: 0.9184
IROC_PERCENTILE: 20
POISSON_SCORE: 0.36
POISSON_PERCENTILE: 16
MAXIMUM_REPLICATE_CORRELATION: 0.95

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

source_name: Adrenal Gland tissue; renlab.H3K36me3.STL002AD.01.01

value: Adrenal Gland

value: Primary Tissue

value: Autopsy


title: Reference Epigenome: ChIP-Seq Analysis of H3K4me1 in Human Lung Tissue; renlab.H3K4me1.STL001LG.01.01

description:
sample_term_id: UBERON_0002048
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K4me1 in Human Lung Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: CY166
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.15107
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.13947
****************
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: GSM1059443_UCSD.Lung.H3K4me1.STL001.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4me1.STL001LG.01.01.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Lung H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K4me1 ChIP-Seq on Lung, 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.16350
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: 24,794,026
FINDPEAKS_SCORE: 0.2
FINDPEAKS_PERCENTILE: 38
HOTSPOT_SCORE: 0.29
HOTSPOT_PERCENTILE: 38
IROC_SCORE: 0.9427
IROC_PERCENTILE: 35
POISSON_SCORE: 0.47
POISSON_PERCENTILE: 52
MAXIMUM_REPLICATE_CORRELATION: 0.95

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

ANALYSIS FILE NAME: GSM1059443_UCSD.Lung.H3K4me1.STL001.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4me1.STL001LG.01.01.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Lung H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K4me1 ChIP-Seq read mappings from Lung, 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.16504
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: Lung H3K4me1 01 66
BROWSER_TRACK_DESCRIPTION: UCSD Lung Histone H3K4me1 Donor STL001 Library CY166 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 24,794,026
FINDPEAKS_SCORE: 0.2
FINDPEAKS_PERCENTILE: 38
HOTSPOT_SCORE: 0.29
HOTSPOT_PERCENTILE: 38
IROC_SCORE: 0.9427
IROC_PERCENTILE: 35
POISSON_SCORE: 0.47
POISSON_PERCENTILE: 52
MAXIMUM_REPLICATE_CORRELATION: 0.95

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

value: Lung

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

value: Male

value: Caucasian and African American

value: Histone H3K4me1


title: Reference Epigenome: ChIP-Seq Analysis of H3K36me3 in Human Lung Tissue; renlab.H3K36me3.STL001LG.01.01

description:
sample_term_id: UBERON_0002048
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K36me3 in Human Lung Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: CY164
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.15092
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.13947
****************
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: GSM1059437_UCSD.Lung.H3K36me3.STL001.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K36me3.STL001LG.01.01.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Lung H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K36me3 ChIP-Seq on Lung, 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.16457
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 21,217,698
FINDPEAKS_SCORE: 0.22
FINDPEAKS_PERCENTILE: 39
HOTSPOT_SCORE: 0.28
HOTSPOT_PERCENTILE: 41
IROC_SCORE: 0.9594
IROC_PERCENTILE: 37
POISSON_SCORE: 0.44
POISSON_PERCENTILE: 35
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

ANALYSIS FILE NAME: GSM1059437_UCSD.Lung.H3K36me3.STL001.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K36me3.STL001LG.01.01.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Lung H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K36me3 ChIP-Seq read mappings from Lung, 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.16611
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: Lung H3K36me3 01 64
BROWSER_TRACK_DESCRIPTION: UCSD Lung Histone H3K36me3 Donor STL001 Library CY164 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 21,217,698
FINDPEAKS_SCORE: 0.22
FINDPEAKS_PERCENTILE: 39
HOTSPOT_SCORE: 0.28
HOTSPOT_PERCENTILE: 41
IROC_SCORE: 0.9594
IROC_PERCENTILE: 37
POISSON_SCORE: 0.44
POISSON_PERCENTILE: 35
MAXIMUM_REPLICATE_CORRELATION: 0.96

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

value: Histone H3K36me3

value: Biorupter

value: 500 micrograms

value: magnetic anti-rabbit

value: 5 micrograms

value: Abcam


title: Reference Epigenome: ChIP-Seq Analysis of H3K9me3 in Human Liver Tissue; renlab.H3K9me3.STL011LI.01.01

description:
sample_term_id: UBERON_0002107
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K9me3 in Human Liver Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AY531
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.15897
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.15104
****************
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: GSM1120361_UCSD.Adult_Liver.H3K9me3.STL011.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K9me3.STL011LI.01.01.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Adult Liver H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K9me3 ChIP-Seq on Adult Liver, Donor STL011, 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.16447
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: 45,960,586
FINDPEAKS_SCORE: 0.01
FINDPEAKS_PERCENTILE: 8
HOTSPOT_SCORE: 0.05
HOTSPOT_PERCENTILE: 8
IROC_SCORE: 0.85
IROC_PERCENTILE: 69
POISSON_SCORE: 0.16
POISSON_PERCENTILE: 5
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM1120361_UCSD.Adult_Liver.H3K9me3.STL011.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K9me3.STL011LI.01.01.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Adult Liver H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K9me3 ChIP-Seq read mappings from Adult Liver, Donor STL011, 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.16601
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: AL H3K9me3 11 31
BROWSER_TRACK_DESCRIPTION: UCSD Adult Liver Histone H3K9me3 Donor STL011 Library AY531 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 45,960,586
FINDPEAKS_SCORE: 0.01
FINDPEAKS_PERCENTILE: 8
HOTSPOT_SCORE: 0.05
HOTSPOT_PERCENTILE: 8
IROC_SCORE: 0.85
IROC_PERCENTILE: 69
POISSON_SCORE: 0.16
POISSON_PERCENTILE: 5
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

value: Adult Liver

value: coronary artery disease

value: Liver

value: coronary artery disease. No history of hypertension or diabetes.

value: Caucasian

value: Histone H3K9me3


title: RNA-Seq analysis of cDNA_Lib 15 derived from human CD56+ mesoderm cells; cDNA_Lib 15

description:
sample_term_id: CL_0000222
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: mRNA-Seq for REMC on Illumina
Library name: cDNA_Lib 15
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.15432
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: GSM1112835_BI.hESC_Derived_CD56+_Mesoderm_Cultured_Cells.mRNA-Seq.cDNA_Lib_15.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: cDNA_Lib 15.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of hESC Derived CD56+ Mesoderm Cultured Cells mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by mRNA-Seq on the hESC Derived CD56+ Mesoderm Cultured Cells, Library cDNA_Lib 15 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.16661
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 111,865,476
PERCENT_READS_MAPPING_TO_UCSC_GENES: 89.35
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 24
MAXIMUM_REPLICATE_CORRELATION: 0.69

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

ANALYSIS FILE NAME: GSM1112835_BI.hESC_Derived_CD56+_Mesoderm_Cultured_Cells.mRNA-Seq.cDNA_Lib_15.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: cDNA_Lib 15.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of hESC Derived CD56+ Mesoderm Cultured Cells mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina mRNA-Seq read mappings from the hESC Derived CD56+ Mesoderm Cultured Cells, Library cDNA_Lib 15 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.16670
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: hDCM mRNA 15
BROWSER_TRACK_DESCRIPTION: BI hESC Derived CD56+ Mesoderm Cultured Cells mRNA-Seq Library cDNA_Lib 15 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 111,865,476
PERCENT_READS_MAPPING_TO_UCSC_GENES: 89.35
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 24
MAXIMUM_REPLICATE_CORRELATION: 0.69

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

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. ; cDNA_Lib 15

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: presumed normal

value: CD56+ mesoderm

value: adherence

value: BioSAli 1892

value: Cell Line

value: intermediate

value: Harvard

value: 3' cDNA ligation

value: Our protocol using T4 RNA ligase from NEB

value: ILLUMINA A1+B1, C1+D1, E1+F1, G1+H1

value: around 10ng

value: 3x RLT + 15/20 ul of Silane + 0.4x EtOn, eluted in 100ul, recleaned using 0.95X SPRI

value: yes

value: OligodT - Dynabeads mRNA purification kit (Invitrogen)

value: 98C 30 sec, 8 cycles of: 98C for 10 sec, 67C for 20 sec, 72C for 20 min, then 72C for 30 seconds, hold 4C

value: Qiagen AllPrep DNA/RNA/Protein Mini Kit

value: Adapter ligated cDNA made by reverse transcription of RNA

value: Phusion High Fidelity

value: 12 pmoles of each/50 ul of reaction

value: 70C for 4 min in Ambion Fragmentation Buffer

value: NO

value: mRNA-Seq

value: We synthesized first-strand cDNA using affinity-script reverse transcriptase


title: Reference Epigenome: ChIP-Seq Analysis of H3K36me3 in Human Right Ventricle Tissue; renlab.H3K36me3.STL001RV.01.01

description:
sample_term_id: UBERON_0002080
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H3K36me3 in Human Right Ventricle Tissue. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: CY100
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.15096
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.14086
****************
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: GSM1059438_UCSD.Right_Ventricle.H3K36me3.STL001.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K36me3.STL001RV.01.01.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Right Ventricle H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K36me3 ChIP-Seq on Right Ventricle, 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.16391
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: 12,535,740
FINDPEAKS_SCORE: 0.15
FINDPEAKS_PERCENTILE: 22
HOTSPOT_SCORE: 0.25
HOTSPOT_PERCENTILE: 27
IROC_SCORE: 0.9003
IROC_PERCENTILE: 16
POISSON_SCORE: 0.37
POISSON_PERCENTILE: 18
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

ANALYSIS FILE NAME: GSM1059438_UCSD.Right_Ventricle.H3K36me3.STL001.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K36me3.STL001RV.01.01.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Right Ventricle H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K36me3 ChIP-Seq read mappings from Right Ventricle, 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.16545
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: RV H3K36me3 01 00
BROWSER_TRACK_DESCRIPTION: UCSD Right Ventricle Histone H3K36me3 Donor STL001 Library CY100 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 12,535,740
FINDPEAKS_SCORE: 0.15
FINDPEAKS_PERCENTILE: 22
HOTSPOT_SCORE: 0.25
HOTSPOT_PERCENTILE: 27
IROC_SCORE: 0.9003
IROC_PERCENTILE: 16
POISSON_SCORE: 0.37
POISSON_PERCENTILE: 18
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

source_name: Right Ventricle tissue; renlab.H3K36me3.STL001RV.01.01

value: Right Ventricle

value: genomic DNA

value: Shin Lin, Stanford University

value: Primary Tissue

value: Autopsy

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

value: Male

value: Caucasian and African American

value: Histone H3K36me3

value: Biorupter

value: 500 micrograms

value: magnetic anti-rabbit

value: 5 micrograms

value: Abcam