title: ChIP-Seq analysis of H3K27ac in human HUES64 cells; DNA_Lib 834

status: Public on Jun 24 2013

description:
sample_term_id: NTR_0000853
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 834
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.14602
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.8178
****************
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: GSM1112775_BI.HUES64.H3K27ac.DNA_Lib_834.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 834.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of HUES64 Cell Line H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27ac ChIP-Seq on the HUES64 Cell Line, Library DNA_Lib 834, 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.17208
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 27,755,104
FINDPEAKS_SCORE: 0.069
FINDPEAKS_PERCENTILE: 7
HOTSPOT_SCORE: 0.1401
HOTSPOT_PERCENTILE: 13
IROC_SCORE: 0.9552
IROC_PERCENTILE: 8
POISSON_SCORE: 0.2365
POISSON_PERCENTILE: 8
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

ANALYSIS FILE NAME: GSM1112775_BI.HUES64.H3K27ac.DNA_Lib_834.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 834.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of HUES64 Cell Line H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27ac ChIP-Seq read mappings from the HUES64 Cell Line, Library DNA_Lib 834, 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.17391
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: HUES64 H3K27ac 34
BROWSER_TRACK_DESCRIPTION: BI HUES64 Cell Line Histone H3K27ac Library DNA_Lib 834 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 27,755,104
FINDPEAKS_SCORE: 0.069
FINDPEAKS_PERCENTILE: 7
HOTSPOT_SCORE: 0.1401
HOTSPOT_PERCENTILE: 13
IROC_SCORE: 0.9552
IROC_PERCENTILE: 8
POISSON_SCORE: 0.2365
POISSON_PERCENTILE: 8
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

source_name: Harvard University Embryonic Stem Cells; DNA_Lib 834

value: HUES64 Cell Line

tag: sra sample accession

tag: lineage

value: embrionic stem cell

tag: medium

value: KSR

tag: passage

tag: line

tag: batch

value: ES cell HUES_64-2

value: Cell Line

value: undifferentiated

tag: Sex

value: Unknown

value: Harvard University

value: cell/nuclei lysis

value: Histone H3K27ac


title: ChIP-Seq analysis of H3K36me3 in human CD56+ ectoderm cells; DNA_Lib 1808

type: SRA

city: Cambridge

first: BROAD

last: INSTITUTE

state: MA

country: USA

institute: Broad Institute

description:
sample_term_id: CL_0000221
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 1808
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.13166
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.13314
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

library_source: genomic

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

ANALYSIS FILE NAME: GSM997253_BI.hESC_Derived_CD56+_Ectoderm_Cultured_Cells.H3K36me3.DNA_Lib_1808.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 1808.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of hESC Derived CD56+ Ectoderm Cultured Cells H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K36me3 ChIP-Seq on the hESC Derived CD56+ Ectoderm Cultured Cells, Library DNA_Lib 1808, 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.17272
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: 14,395,248
FINDPEAKS_SCORE: 0.2591
FINDPEAKS_PERCENTILE: 45
HOTSPOT_SCORE: 0.2929
HOTSPOT_PERCENTILE: 49
IROC_SCORE: 0.9649
IROC_PERCENTILE: 38
POISSON_SCORE: 0.4579
POISSON_PERCENTILE: 40
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM997253_BI.hESC_Derived_CD56+_Ectoderm_Cultured_Cells.H3K36me3.DNA_Lib_1808.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 1808.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of hESC Derived CD56+ Ectoderm Cultured Cells H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K36me3 ChIP-Seq read mappings from the hESC Derived CD56+ Ectoderm Cultured Cells, Library DNA_Lib 1808, 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.17455
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: hDCEcto H3K36me3 08
BROWSER_TRACK_DESCRIPTION: BI hESC Derived CD56+ Ectoderm Cultured Cells Histone H3K36me3 Library DNA_Lib 1808 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 14,395,248
FINDPEAKS_SCORE: 0.2591
FINDPEAKS_PERCENTILE: 45
HOTSPOT_SCORE: 0.2929
HOTSPOT_PERCENTILE: 49
IROC_SCORE: 0.9649
IROC_PERCENTILE: 38
POISSON_SCORE: 0.4579
POISSON_PERCENTILE: 40
MAXIMUM_REPLICATE_CORRELATION: NA

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

molecule: genomic DNA

organism: Homo sapiens

source_name: CD56+ ectodermal germ layer cells derived in vitro from embrionic stem cells by culture in the presence of inhibitors of the BMP, TGFbeta, and WNT signaling pathways.; DNA_Lib 1808

extract_protocol: Library construction protocol: Single read - Illumina

tag: sample alias

value: BioSam 707

tag: sample common name

value: ectoderm

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

tag: molecule

value: genomic DNA

tag: disease

value: presumed normal

value: CD56+ ectoderm

value: adherence

value: BioSAli 877

value: Male

value: Harvard

value: Protein A-Sepharose 4B

value: 0.5 to 3 million cells

value: ~1 ug

value: 10 ul bed volume

value: Abcam

value: Histone H3K36me3

value: Branson


title: ChIP-Seq analysis of WCE in human CD56+ mesoderm cells; DNA_Lib 1318

description:
sample_term_id: CL_0000222
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 1318
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.13183
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.11768
****************
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: GSM997270_BI.hESC_Derived_CD56+_Mesoderm_Cultured_Cells.Input.DNA_Lib_1318.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 1318.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of hESC Derived CD56+ Mesoderm Cultured Cells Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Input ChIP-Seq on the hESC Derived CD56+ Mesoderm Cultured Cells, Library DNA_Lib 1318, 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.17280
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: 15,680,034
FINDPEAKS_SCORE: 0.0061
FINDPEAKS_PERCENTILE: 60
HOTSPOT_SCORE: 0.076
HOTSPOT_PERCENTILE: 81
IROC_SCORE: 0.9593
IROC_PERCENTILE: 56
POISSON_SCORE: 0.098
POISSON_PERCENTILE: 73
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM997270_BI.hESC_Derived_CD56+_Mesoderm_Cultured_Cells.Input.DNA_Lib_1318.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 1318.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of hESC Derived CD56+ Mesoderm Cultured Cells Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Input ChIP-Seq read mappings from the hESC Derived CD56+ Mesoderm Cultured Cells, Library DNA_Lib 1318, 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.17463
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: hDCM Input 18
BROWSER_TRACK_DESCRIPTION: BI hESC Derived CD56+ Mesoderm Cultured Cells ChIP-Seq Input Library DNA_Lib 1318 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 15,680,034
FINDPEAKS_SCORE: 0.0061
FINDPEAKS_PERCENTILE: 60
HOTSPOT_SCORE: 0.076
HOTSPOT_PERCENTILE: 81
IROC_SCORE: 0.9593
IROC_PERCENTILE: 56
POISSON_SCORE: 0.098
POISSON_PERCENTILE: 73
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

source_name: HUES64 differentiated with Activin A, BMP4, VEGF and bFGF for 24 hours, then with BMP4, VEGF and bFGF for an additional 4 days. ; DNA_Lib 1318

value: BioSam 577

value: mesoderm

value: 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: BioSAli 713

value: Cell Line

value: intermediate

value: standard

value: cell/nuclei lysis

value: ChIP-Seq Input

value: Input


title: ChIP-Seq analysis of H3K36me3 in human CD25- Th cells; DNA_Lib 2271

status: Public on Jul 18 2013

description:
sample_term_id: CL_0000492
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 2271
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.13154
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.13313
****************
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: GSM997241_BI.CD4+_CD25-_Th_Primary_Cells.H3K36me3.Donor_332.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 2271.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of CD4+ CD25- Th Primary Cells H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K36me3 ChIP-Seq on CD4+ CD25- Th Primary Cells, Donor Donor 332, 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.17282
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: 13,162,098
FINDPEAKS_SCORE: 0.2962
FINDPEAKS_PERCENTILE: 58
HOTSPOT_SCORE: 0.3224
HOTSPOT_PERCENTILE: 58
IROC_SCORE: 0.9764
IROC_PERCENTILE: 47
POISSON_SCORE: 0.475
POISSON_PERCENTILE: 49
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM997241_BI.CD4+_CD25-_Th_Primary_Cells.H3K36me3.Donor_332.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 2271.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of CD4+ CD25- Th Primary Cells H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K36me3 ChIP-Seq read mappings from CD4+ CD25- Th Primary Cells, Donor Donor 332, 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.17465
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: CCT H3K36me3 32 71
BROWSER_TRACK_DESCRIPTION: BI CD4+ CD25- Th Primary Cells Histone H3K36me3 Donor 332 Library DNA_Lib 2271 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 13,162,098
FINDPEAKS_SCORE: 0.2962
FINDPEAKS_PERCENTILE: 58
HOTSPOT_SCORE: 0.3224
HOTSPOT_PERCENTILE: 58
IROC_SCORE: 0.9764
IROC_PERCENTILE: 47
POISSON_SCORE: 0.475
POISSON_PERCENTILE: 49
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

source_name: CD25- Th  is one of  CD4+  T cell subsets  that purified by microbeads, LS column and FACS ; DNA_Lib 2271

value: BioSam 715

value: CD4+ CD25- Th Primary Cells

value: normal

value: genomic DNA

tag: markers

value: CD4+ T cell

value: CD25- Th

value: Unknown

value: Primary Cell

value: Donor 332

value: Dana Farber

value: Protein A-Sepharose 4B

value: 0.5 to 3 million cells


title: ChIP-Seq analysis of WCE in human CD56+ mesoderm cells; DNA_Lib 1317

description:
sample_term_id: CL_0000222
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 1317
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.13185
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.11767
****************
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: GSM997272_BI.hESC_Derived_CD56+_Mesoderm_Cultured_Cells.Input.DNA_Lib_1317.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 1317.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of hESC Derived CD56+ Mesoderm Cultured Cells Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Input ChIP-Seq on the hESC Derived CD56+ Mesoderm Cultured Cells, Library DNA_Lib 1317, 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.17279
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: 16,175,248
FINDPEAKS_SCORE: 0.006
FINDPEAKS_PERCENTILE: 59
HOTSPOT_SCORE: 0.0726
HOTSPOT_PERCENTILE: 78
IROC_SCORE: 0.9543
IROC_PERCENTILE: 52
POISSON_SCORE: 0.0925
POISSON_PERCENTILE: 68
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM997272_BI.hESC_Derived_CD56+_Mesoderm_Cultured_Cells.Input.DNA_Lib_1317.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 1317.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of hESC Derived CD56+ Mesoderm Cultured Cells Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Input ChIP-Seq read mappings from the hESC Derived CD56+ Mesoderm Cultured Cells, Library DNA_Lib 1317, 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.17462
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: hDCM Input 17
BROWSER_TRACK_DESCRIPTION: BI hESC Derived CD56+ Mesoderm Cultured Cells ChIP-Seq Input Library DNA_Lib 1317 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 16,175,248
FINDPEAKS_SCORE: 0.006
FINDPEAKS_PERCENTILE: 59
HOTSPOT_SCORE: 0.0726
HOTSPOT_PERCENTILE: 78
IROC_SCORE: 0.9543
IROC_PERCENTILE: 52
POISSON_SCORE: 0.0925
POISSON_PERCENTILE: 68
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

source_name: HUES64 differentiated with Activin A, BMP4, VEGF and bFGF for 24 hours, then with BMP4, VEGF and bFGF for an additional 4 days. ; DNA_Lib 1317

value: BioSam 575

value: mesoderm

value: 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 712

value: Cell Line

value: intermediate

value: Male

value: Harvard

value: Branson


title: ChIP-Seq analysis of H3K27ac in human HUES64 cells; DNA_Lib 2069

description:
sample_term_id: NTR_0000853
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 2069
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.13162
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.13319
****************
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: GSM997249_BI.HUES64.H3K27ac.DNA_Lib_2069.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 2069.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of HUES64 Cell Line H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27ac ChIP-Seq on the HUES64 Cell Line, Library DNA_Lib 2069, 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.17222
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: 19,992,368
FINDPEAKS_SCORE: 0.3782
FINDPEAKS_PERCENTILE: 55
HOTSPOT_SCORE: 0.4139
HOTSPOT_PERCENTILE: 54
IROC_SCORE: 0.9945
IROC_PERCENTILE: 49
POISSON_SCORE: 0.4434
POISSON_PERCENTILE: 44
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

ANALYSIS FILE NAME: GSM997249_BI.HUES64.H3K27ac.DNA_Lib_2069.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 2069.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of HUES64 Cell Line H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27ac ChIP-Seq read mappings from the HUES64 Cell Line, Library DNA_Lib 2069, 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.17405
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: HUES64 H3K27ac 69
BROWSER_TRACK_DESCRIPTION: BI HUES64 Cell Line Histone H3K27ac Library DNA_Lib 2069 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 19,992,368
FINDPEAKS_SCORE: 0.3782
FINDPEAKS_PERCENTILE: 55
HOTSPOT_SCORE: 0.4139
HOTSPOT_PERCENTILE: 54
IROC_SCORE: 0.9945
IROC_PERCENTILE: 49
POISSON_SCORE: 0.4434
POISSON_PERCENTILE: 44
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

source_name: Harvard University ES Cell 64 AKA HUES 64; DNA_Lib 2069

value: BioSam 825

value: HUES64 Cell Line

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

value: genomic DNA

value: BioSAli 1030

value: cell/nuclei lysis

value: ~1 ug

value: 10 ul bed volume

value: Active Motif

value: Histone H3K27ac


title: ChIP-Seq analysis of H3K9me3 in human CD56+ ectoderm cells; DNA_Lib 1811

description:
sample_term_id: CL_0000221
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 1811
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.13186
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.13314
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM997273_BI.hESC_Derived_CD56+_Ectoderm_Cultured_Cells.H3K9me3.DNA_Lib_1811.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 1811.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of hESC Derived CD56+ Ectoderm Cultured Cells H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K9me3 ChIP-Seq on the hESC Derived CD56+ Ectoderm Cultured Cells, Library DNA_Lib 1811, 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.17205
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: 5,924,332
FINDPEAKS_SCORE: 0.1503
FINDPEAKS_PERCENTILE: 83
HOTSPOT_SCORE: 0.2056
HOTSPOT_PERCENTILE: 75
IROC_SCORE: 0.8647
IROC_PERCENTILE: 71
POISSON_SCORE: 0.4412
POISSON_PERCENTILE: 92
MAXIMUM_REPLICATE_CORRELATION: 0.59

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

ANALYSIS FILE NAME: GSM997273_BI.hESC_Derived_CD56+_Ectoderm_Cultured_Cells.H3K9me3.DNA_Lib_1811.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 1811.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of hESC Derived CD56+ Ectoderm Cultured Cells H3K9me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K9me3 ChIP-Seq read mappings from the hESC Derived CD56+ Ectoderm Cultured Cells, Library DNA_Lib 1811, 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.17388
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: hDCEcto H3K9me3 11
BROWSER_TRACK_DESCRIPTION: BI hESC Derived CD56+ Ectoderm Cultured Cells Histone H3K9me3 Library DNA_Lib 1811 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 5,924,332
FINDPEAKS_SCORE: 0.1503
FINDPEAKS_PERCENTILE: 83
HOTSPOT_SCORE: 0.2056
HOTSPOT_PERCENTILE: 75
IROC_SCORE: 0.8647
IROC_PERCENTILE: 71
POISSON_SCORE: 0.4412
POISSON_PERCENTILE: 92
MAXIMUM_REPLICATE_CORRELATION: 0.59

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

source_name: CD56+ ectodermal germ layer cells derived in vitro from embrionic stem cells by culture in the presence of inhibitors of the BMP, TGFbeta, and WNT signaling pathways.; DNA_Lib 1811

value: BioSam 707

value: ectoderm

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

value: presumed normal

value: CD56+ ectoderm

value: adherence

value: BioSAli 877

value: Protein A-Sepharose 4B

value: 0.5 to 3 million cells

value: Abcam

value: Histone H3K9me3


title: ChIP-Seq analysis of WCE in human chondrogenic dif cells; Lib EpiLabSPL Row 1385

description:
sample_term_id: CL_0000138
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib EpiLabSPL Row 1385
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8052
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5951
****************
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: GSM772791_BI.Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.Input.58.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100726:14--ChIP:MC:20100713:14:chondrogenic dif cells:WCE-Lib EpiLabSPL Row 1385.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Input ChIP-Seq on Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells, Donor 58, 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.17257
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: 36,875,494
FINDPEAKS_SCORE: NA
FINDPEAKS_PERCENTILE: NA
HOTSPOT_SCORE: NA
HOTSPOT_PERCENTILE: NA
IROC_SCORE: NA
IROC_PERCENTILE: NA
POISSON_SCORE: NA
POISSON_PERCENTILE: NA
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM772791_BI.Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.Input.58.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100726:14--ChIP:MC:20100713:14:chondrogenic dif cells:WCE-Lib EpiLabSPL Row 1385.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Input ChIP-Seq read mappings from Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells, Donor 58, 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.17440
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: CfBMDMSC Input 58
BROWSER_TRACK_DESCRIPTION: BI Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells ChIP-Seq Input Donor 58 Library Lib:MC:20100726:14--ChIP:MC:20100713:14:chondrogenic dif cells:WCE EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 36,875,494
FINDPEAKS_SCORE: NA
FINDPEAKS_PERCENTILE: NA
HOTSPOT_SCORE: NA
HOTSPOT_PERCENTILE: NA
IROC_SCORE: NA
IROC_PERCENTILE: NA
POISSON_SCORE: NA
POISSON_PERCENTILE: NA
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: chondrocytes derived via in vitro culture from mesenchymal stem cells; Lib EpiLabSPL Row 1385

value: healthy

value: genomic DNA

value: Medium:NA; Differentiation Method:alginate hydrogel scaffold (SR Herlofsen et al, Tissue Eng Part A. 2011)

value: chondrogenic dif cells

value: Unknown

value: Primary Cell Culture

value: Rikshospitalet University Hospital

value: standard

value: SDS lysis

value: ChIP-Seq Input

value: Input

value: Bioruptor


title: ChIP-Seq analysis of WCE in human CD56+ ectoderm cells; DNA_Lib 1812

description:
sample_term_id: CL_0000221
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 1812
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.13161
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.13314
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM997248_BI.hESC_Derived_CD56+_Ectoderm_Cultured_Cells.Input.DNA_Lib_1812.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 1812.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of hESC Derived CD56+ Ectoderm Cultured Cells Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Input ChIP-Seq on the hESC Derived CD56+ Ectoderm Cultured Cells, Library DNA_Lib 1812, 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.17266
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: 16,480,226
FINDPEAKS_SCORE: 0.0075
FINDPEAKS_PERCENTILE: 81
HOTSPOT_SCORE: 0.0467
HOTSPOT_PERCENTILE: 70
IROC_SCORE: 0.9721
IROC_PERCENTILE: 67
POISSON_SCORE: 0.067
POISSON_PERCENTILE: 54
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM997248_BI.hESC_Derived_CD56+_Ectoderm_Cultured_Cells.Input.DNA_Lib_1812.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 1812.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of hESC Derived CD56+ Ectoderm Cultured Cells Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Input ChIP-Seq read mappings from the hESC Derived CD56+ Ectoderm Cultured Cells, Library DNA_Lib 1812, 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.17449
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: hDCEcto Input 12
BROWSER_TRACK_DESCRIPTION: BI hESC Derived CD56+ Ectoderm Cultured Cells ChIP-Seq Input Library DNA_Lib 1812 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 16,480,226
FINDPEAKS_SCORE: 0.0075
FINDPEAKS_PERCENTILE: 81
HOTSPOT_SCORE: 0.0467
HOTSPOT_PERCENTILE: 70
IROC_SCORE: 0.9721
IROC_PERCENTILE: 67
POISSON_SCORE: 0.067
POISSON_PERCENTILE: 54
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

source_name: CD56+ ectodermal germ layer cells derived in vitro from embrionic stem cells by culture in the presence of inhibitors of the BMP, TGFbeta, and WNT signaling pathways.; DNA_Lib 1812

value: BioSam 707

value: ectoderm

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

value: presumed normal

value: CD56+ ectoderm

value: adherence

value: BioSAli 877

value: Cell Line

value: Male

value: Harvard

value: cell/nuclei lysis

value: Branson


title: ChIP-Seq analysis of WCE in human CD19 cells; Lib EpiLabSPL Row 1819

description:
sample_term_id: CL_0000236
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib EpiLabSPL Row 1819
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8014
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.2303
****************
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: GSM772753_BI.CD19_Primary_Cells.Input.CD19_0_0_00.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib EpiLabSPL Row 1819.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of CD19 Primary Cells Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Input ChIP-Seq on CD19 Primary Cells, Donor CD19_0/0/00, 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.17239
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: 38,284,082
FINDPEAKS_SCORE: 0.005
FINDPEAKS_PERCENTILE: 27
HOTSPOT_SCORE: 0.0032
HOTSPOT_PERCENTILE: 16
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.0181
POISSON_PERCENTILE: 6
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

ANALYSIS FILE NAME: GSM772753_BI.CD19_Primary_Cells.Input.CD19_0_0_00.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib EpiLabSPL Row 1819.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of CD19 Primary Cells Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Input ChIP-Seq read mappings from CD19 Primary Cells, Donor CD19_0/0/00, 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.17422
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: CD19 Input 0 19
BROWSER_TRACK_DESCRIPTION: BI CD19 Primary Cells ChIP-Seq Input Donor CD19_0/0/00 Library Lib EpiLabSPL Row 1819 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 38,284,082
FINDPEAKS_SCORE: 0.005
FINDPEAKS_PERCENTILE: 27
HOTSPOT_SCORE: 0.0032
HOTSPOT_PERCENTILE: 16
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.0181
POISSON_PERCENTILE: 6
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

source_name: flow sorted CD19+ cells from cord blood; Lib EpiLabSPL Row 1819

value: CD19 Primary Cells

value: genomic DNA

value: FHCRC

value: Primary Cell

value: Female

value: not passaged

value: standard


title: ChIP-Seq analysis of WCE in human chondrogenic dif cells; Lib EpiLabSPL Row 1727

description:
sample_term_id: CL_0000138
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib EpiLabSPL Row 1727
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8042
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5932
****************
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: GSM772781_BI.Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.Input.60.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib EpiLabSPL Row 1727-Lib:MC:20100729:11--ChIP:MC:20100726:11:chondrogenic dif cells:H3K27Me3.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Input ChIP-Seq on Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells, Donor 60, 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.17258
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: 62,557,620
FINDPEAKS_SCORE: NA
FINDPEAKS_PERCENTILE: NA
HOTSPOT_SCORE: NA
HOTSPOT_PERCENTILE: NA
IROC_SCORE: NA
IROC_PERCENTILE: NA
POISSON_SCORE: NA
POISSON_PERCENTILE: NA
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM772781_BI.Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.Input.60.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib EpiLabSPL Row 1727-Lib:MC:20100729:11--ChIP:MC:20100726:11:chondrogenic dif cells:H3K27Me3.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Input ChIP-Seq read mappings from Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells, Donor 60, 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.17441
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: CfBMDMSC Input 60 27
BROWSER_TRACK_DESCRIPTION: BI Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells ChIP-Seq Input Donor 60 Library Lib EpiLabSPL Row 1727 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 62,557,620
FINDPEAKS_SCORE: NA
FINDPEAKS_PERCENTILE: NA
HOTSPOT_SCORE: NA
HOTSPOT_PERCENTILE: NA
IROC_SCORE: NA
IROC_PERCENTILE: NA
POISSON_SCORE: NA
POISSON_PERCENTILE: NA
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: chondrocytes derived via in vitro culture from mesenchymal stem cells; Lib EpiLabSPL Row 1727

value: healthy

value: Medium:NA; Differentiation Method:alginate hydrogel scaffold (SR Herlofsen et al, Tissue Eng Part A. 2011)

value: chondrogenic dif cells

value: Unknown

value: Primary Cell Culture

value: Rikshospitalet University Hospital

value: SDS lysis

value: ChIP-Seq Input

value: Input

value: Bioruptor


title: ChIP-Seq analysis of H3K27me3 in human CD56+ ectoderm cells; DNA_Lib 1807

description:
sample_term_id: CL_0000221
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 1807
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.13160
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.13314
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

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

ANALYSIS FILE NAME: GSM997247_BI.hESC_Derived_CD56+_Ectoderm_Cultured_Cells.H3K27me3.DNA_Lib_1807.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 1807.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of hESC Derived CD56+ Ectoderm Cultured Cells H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27me3 ChIP-Seq on the hESC Derived CD56+ Ectoderm Cultured Cells, Library DNA_Lib 1807, 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.17202
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 7,448,571
FINDPEAKS_SCORE: 0.4156
FINDPEAKS_PERCENTILE: 95
HOTSPOT_SCORE: 0.4614
HOTSPOT_PERCENTILE: 95
IROC_SCORE: 0.989
IROC_PERCENTILE: 96
POISSON_SCORE: 0.5293
POISSON_PERCENTILE: 93
MAXIMUM_REPLICATE_CORRELATION: 0.53

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

ANALYSIS FILE NAME: GSM997247_BI.hESC_Derived_CD56+_Ectoderm_Cultured_Cells.H3K27me3.DNA_Lib_1807.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 1807.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of hESC Derived CD56+ Ectoderm Cultured Cells H3K27me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27me3 ChIP-Seq read mappings from the hESC Derived CD56+ Ectoderm Cultured Cells, Library DNA_Lib 1807, 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.17385
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: hDCEcto H3K27me3 07
BROWSER_TRACK_DESCRIPTION: BI hESC Derived CD56+ Ectoderm Cultured Cells Histone H3K27me3 Library DNA_Lib 1807 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 7,448,571
FINDPEAKS_SCORE: 0.4156
FINDPEAKS_PERCENTILE: 95
HOTSPOT_SCORE: 0.4614
HOTSPOT_PERCENTILE: 95
IROC_SCORE: 0.989
IROC_PERCENTILE: 96
POISSON_SCORE: 0.5293
POISSON_PERCENTILE: 93
MAXIMUM_REPLICATE_CORRELATION: 0.53

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

source_name: CD56+ ectodermal germ layer cells derived in vitro from embrionic stem cells by culture in the presence of inhibitors of the BMP, TGFbeta, and WNT signaling pathways.; DNA_Lib 1807

value: BioSam 707

value: ectoderm

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

value: presumed normal

value: CD56+ ectoderm

value: adherence

value: BioSAli 877

value: Cell Line

value: Male

value: Harvard

value: Protein A-Sepharose 4B

value: 0.5 to 3 million cells

value: cell/nuclei lysis

value: ~1 ug

value: 10 ul bed volume

value: Millipore

value: Histone H3K27me3

value: Branson


title: Calbicans_WT_vs_DeletionStrain_YPD_6h_Biolrep3_Techrep1

status: Public on Mar 25 2013

type: RNA

city: Stuttgart

first: Steffen

last: Rupp

address: Nobelstr. 12

department: MBT

country: Germany

institute: Fraunhofer IGB

description: Dye Swap to Calbicans_WT_vs_DeletionStrain_YPD_6h_Biolrep3_Techrep2, Biolrep 3 of 3

hyb_protocol: 40 µL cDNA eluate, 6.5 µL SDS solution (1 %), 13 µL 20 x SSC and 15.5 µL RNase-free ddH2O were mixed and denatured at 100°C for 3 min. Hybridization was done over night (20 h) at 65 °C using LifterSlips (25 x 44 mm, VWR, Darmstadt, Germany). After hybridization, the LifterSlips were removed while rinsing for 1 min using 2 x SSC, 0.2 % SDS. Subsequently, DNA microarrays were washed for 10 min 2 x SSC, 0.2 % SDS, for 10 min in 2 x SSC and for 10 min in 0.2 x SSC. Afterwards, DNA microarrays were dried with compressed N2 gas, and stored protected from light in the dark until scanned.

scan_protocol: The completely dried DNA microarrays were scanned using the Genepix microarray scanner 4300A (Molecular Devices, Sunnyvale, CA) (resolution,  10 µm; PMT setting: 550 - 800 PMT). Pictures of both channels were saved as 16-bit TIFF files.

data_processing: Raw data were created using Molecular Devices imaging software GenePix Pro 7.0 (Molecular Devices, Sunnyvale, CA).  The data were statistically analyzed using the software R (V. 2.10.1), the limma package (V. 3.2.1) and the statmod package (V. 1.4.2) (1, 2). An empirical Bayes method was chosen to take into account that in the classical t test, small variance values of the gene of interest tend to lead to high t-test statistics and therefore, erroneously, to a higher probability of significant differential expression (3). Background correction was performed using “normexp” with an offset of 50 (4). The data was normalized “print-tip-loess” (5). Spots which were classified as not found by the image analysis software were ignored for fitting of the linear model.  As thousands of hypotheses can be tested with DNA microarrays, the chance to make an α error increases with the number of hypotheses. Therefore, multiple-hypothesis testing was performed (6). Multiple-hypothesis testing correction was performed by the method of Benjamini and Hochberg, which controls the false discovery rate (FDR) (7). The quotient between expected false-positive genes and all differentially expressed genes allows an adjusted P value to be calculated, which can be used to make predictions about differential gene expression. Genes were regarded as differentially expressed and followed up, when the adjusted P values were 0.001, therefore nominally controlling the expected FDR to less than 0.001.  [1. R. (2009) R: A language and environment for statistical computing. R Foundation for Statistical Computing., RDevelopment Core Team.] [2. Smyth, G. K. (2005) Limma: Linear models for microarray data., In Bioinformatics and Computational Biology Solutions using R and Bioconductor (Gentleman, R., Carrey, V., Dudoit, S., Irizzary, I., Huber, W., Ed.), pp 397-420, Springer, New York.] [3. Lönnstedt, I., and Speed, T. P. (2002) Replicated microarray data., Stat.Sin. 12, 31-46.] [4. Ritchie, M. E., Silver, J., Oshlack, A., Holmes, M., Diyagama, D., Holloway, A., and Smyth, G. K. (2007) A comparison of background correction methods for two-colour microarrays, Bioinformatics 23, 2700-2707.] [5. Smyth, G. K., and Speed, T. (2003) Normalization of cDNA microarray data, Methods 31, 265-273.] [6. Dudoit, S., Popper Schaffer, J., and Boldrick, J. C. (2003) Multiple hypothesis testing in microarray experiments, Stat. Sci. 28, 71-103.] [7. Benjamini, Y., and Hochberg, Y. (1995) Controlling the false discovery rate: A practical and powerful approach to multiple testing., J. R. Stat. Soc. B 57, 289-300.]

molecule: total RNA

organism: Candida albicans

label_protocol: Fluorescently labeled cDNA was synthesized by reverse transcription of total RNA using SuperScript III (Invitrogen, Karlsruhe, Germany) and Cy3- or Cy5-dUTPs (GE Healthcare Europe, Germany) according to the following protocol: 23 µg (alphaMEM) or 25 µg (YPD) of total RNA was mixed with 3 µl of 50 µM Anchored Oligo(dT)18 oligonucleotide (Roche, Mannheim, Germany), 4 µl of dNTP-mix (5 mM of dATP, dGTP and dCTP as well as 0,8 mM of dTTP) and DEPC- H2O in a volume of 19 µl and incubated for 5 min at 65°C. After cooling on ice, 4 µl of 10 x RT buffer (200 mM Tris-HCl (pH 8.4), 500 mM KCl), 8 µl of 25 mM MgCl2, 4 µl of 0,1 M DTT, 80 U RNaseOUT, 400 U of SuperScript III RT enzyme as well as 1 µl of Cy3- or Cy5-dUTP was added to the reaction The reverse transcription and labeling reaction was carried out for 50 min at 50°C (light protected) and stopped by denaturation of the enzyme at 85°C for 5 min. RNA was eliminated by addition of 4 U RNase H (Invitrogen, Karlsruhe, Germany) for 20 min at 37°C. The corresponding Cy3- or Cy5 labeled cDNA fractions (of SC5314 and the deletion strains) were pooled and column purified (LabelStar Kit, Qiagen).

growth_protocol: 100 mL YPD (10 g yeast extract, 20 g bacto peptone and 20 g glucose per litre) were inoculated from an ON culture (10 mL YPD medium 30°C) to an OD of 0.1 and grown for 6 h at 30°C.

extract_protocol: Disruption was carried out using a Mixer Mill MM 200 (Retsch, Haan, Germany) with a shaking frequency of 30/s. The resulting powder was resuspended in lysis buffer RLT (Qiagen, Hilden, Germany) supplemented with 0.01 % (v/v) of ß-mercaptoethanol. The extraction of total RNA was performed according to Qiagen`s Mechanical Disruption Protocol for the isolation of total RNA from Yeast using the RNeasy Midi Kit. The RNA was precipitated using lithium chloride: 500 µL 4 M LiCl-solution was added to 500 µL RNA-solution and incubated at -20°C over night. RNA was centrifuged at 4°C and 13,000 g for 30 min, washed three times with 70 % ethanol and the precipitate dried for 5 min at 37 °C. RNA was redissolved in 50 - 150 µL RNase free ddH2O. Only RNA with a 260 nm/280 nm ratio of 1.8 to 2 as well as a 260 nm/230 nm ratio of 1.8 was used for DNA microarrays.  23 - 25 μg of total-RNA in a volume of maximal 19 μL was used for reverse transcription and labeling.

treatment_protocol: Cells were centrifuged (1200 g, 3 min) and the supernatant discarded. Subsequently, cells were resuspended in the remaining medium and dropped into liquid N2 to generate cell beads for RNA isolation. The experiment was performed three times.

tag: strain

tag: genotype/variation

value: wild type


title: Calbicans_WT_vs_DeletionStrain_YPD_6h_Biolrep2_Techrep1

description: Dye Swap to Calbicans_WT_vs_DeletionStrain_YPD_6h_Biolrep2_Techrep2, Biolrep 2 of 3


title: PBMC_nonagenarian 81136

status: Public on Jan 10 2013

city: Tampere

first: Saara

last: Marttila

address: Biokatu 6

department: School of Medicine

country: Finland

institute: University of Tampere

hyb_protocol: 1,500 ng of labeled cRNA was hybridized overnight according to the Illumina protocol

scan_protocol: Beadscan

data_processing: The preprocessing, filtering and analysis of the data were performed with the Chipster v2.0 program (Kallio, M.A., et al. MBC Genomics 12, 507 (2011)).The lumi pipeline was used for data preprocessing and normalization. Array_Address_ID was used as a probe identifier, background correction was performed with the bgAdjust.affy package, and the data were vst transformed and normalized with the rsn method.

label: biotin

source_name: Human PBMC

label_protocol: Labeled cRNA was prepared from 330 ng of total RNA using an Illumina TotalPrep RNA Amplification Kit (Ambion Inc., TX, USA) with overnight incubation according to the manufacturer’s protocol.

growth_protocol: Study subjects did not have any infections or received any vaccinations in the 30 (nonagenarians) or 14 (young controls) days prior to blood sample collection

extract_protocol: RNA was purified using an miRNeasy mini kit (Qiagen, CA, USA) according to the manufacturer`s protocol using on-column DNase digestion (AppliChem GmbH, Darmstadt, Germany)

treatment_protocol: Blood was collected to EDTA-containing tubes between 8 and 12 am. Leucocytes were separated with a density gradient and stored in RNAlater.

tag: tissue

value: PBMC

tag: age

value: Female

tag: cmv serostatus

value: pos.

tag: cf-dna (ug/ml)

tag: cmv titer


title: PBMC_nonagenarian 81074


title: Calbicans_WT_vs_DeletionStrain_YPD_6h_Biolrep2_Techrep2

description: Dye Swap to Calbicans_WT_vs_DeletionStrain_YPD_6h_Biolrep2_Techrep1, Biolrep 2 of 3


title: Calbicans_WT_vs_DeletionStrain_alphaMEM_6h_Biolrep2_Techrep1

description: Dye Swap to Calbicans_WT_vs_DeletionStrain_alphaMEM_6h_Biolrep2_Techrep2, Biolrep 2 of 3

growth_protocol: 100 mL Minimum Essential Medium Alpha (alpha-MEM; Gibco, Invitrogen, Darmstadt, Germany), supplemented with 2% (w/v) glucose were inoculated from an ON culture (10 mL YPD medium 30°C) to an OD of 0.1 and grown for 6 h at 37°C.


title: Calbicans_WT_vs_DeletionStrain_alphaMEM_6h_Biolrep2_Techrep2

description: Dye Swap to Calbicans_WT_vs_DeletionStrain_alphaMEM_6h_Biolrep2_Techrep1, Biolrep 2 of 3


title: Calbicans_WT_vs_DeletionStrain_YPD_6h_Biolrep1_Techrep2

description: Dye Swap to Calbicans_WT_vs_DeletionStrain_YPD_6h_Biolrep1_Techrep1, Biolrep 1 of 3


title: Calbicans_WT_vs_DeletionStrain_alphaMEM_6h_Biolrep3_Techrep2

description: Dye Swap to Calbicans_WT_vs_DeletionStrain_alphaMEM_6h_Biolrep3_Techrep1, Biolrep 3 of 3


title: Calbicans_WT_vs_DeletionStrain_YPD_6h_Biolrep3_Techrep2

description: Dye Swap to Calbicans_WT_vs_DeletionStrain_YPD_6h_Biolrep3_Techrep1, Biolrep 3 of 3


title: Calbicans_WT_vs_DeletionStrain_alphaMEM_6h_Biolrep3_Techrep1

description: Dye Swap to Calbicans_WT_vs_DeletionStrain_alphaMEM_6h_Biolrep3_Techrep2, Biolrep 3 of 3


title: Calbicans_WT_vs_DeletionStrain_alphaMEM_6h_Biolrep1_Techrep1

description: Dye Swap to Calbicans_WT_vs_DeletionStrain_alphaMEM_6h_Biolrep1_Techrep2, Biolrep 1 of 3


title: PBMC_nonagenarian 81012


title: PBMC_nonagenarian 81019


title: PBMC_young control 42036


title: Calbicans_WT_vs_DeletionStrain_alphaMEM_6h_Biolrep1_Techrep2

description: Dye Swap to Calbicans_WT_vs_DeletionStrain_alphaMEM_6h_Biolrep1_Techrep1, Biolrep 1 of 3


title: PBMC_nonagenarian 81059


title: PBMC_nonagenarian 81064


title: PBMC_young control 42033

value: neg.


title: PBMC_nonagenarian 81084


title: PBMC_young control 42035


title: PBMC_young control 42031


title: PBMC_young control 42030


title: PBMC_young control 42038


title: PBMC_nonagenarian 81018


title: PBMC_young control 42037


title: PBMC_young control 42034


title: PBMC_young control 42032


title: Calbicans_WT_vs_DeletionStrain_YPD_6h_Biolrep1_Techrep1

description: Dye Swap to Calbicans_WT_vs_DeletionStrain_YPD_6h_Biolrep1_Techrep2, Biolrep 1 of 3


title: PBMC_young control 42029


title: PBMC_young control 42023


title: PBMC_young control 42019


title: PBMC_young control 42021


title: PBMC_young control 42014


title: PBMC_young control 42028


title: PBMC_young control 42027


title: PBMC_young control 42022


title: PBMC_young control 42006


title: PBMC_young control 42018


title: PBMC_young control 42017


title: PBMC_young control 42020


title: PBMC_nonagenarian 28895


title: PBMC_young control 42005


title: PBMC_young control 42008


title: PBMC_young control 42009


title: PBMC_nonagenarian 28861


title: PBMC_young control 42010


title: PBMC_young control 42013


title: PBMC_nonagenarian 28868


title: PBMC_young control 42007


title: PBMC_young control 42025


title: PBMC_nonagenarian 28812


title: PBMC_young control 42016


title: PBMC_nonagenarian 28897


title: PBMC_nonagenarian 28807


title: PBMC_nonagenarian 28816


title: PBMC_nonagenarian 28803


title: PBMC_nonagenarian 28736


title: PBMC_nonagenarian 28760


title: PBMC_nonagenarian 28735


title: PBMC_nonagenarian 28706


title: PBMC_nonagenarian 28752


title: PBMC_nonagenarian 28798


title: PBMC_nonagenarian 28675


title: PBMC_nonagenarian 81025


title: PBMC_nonagenarian 28698


title: PBMC_nonagenarian 28636


title: PBMC_nonagenarian 28664


title: PBMC_nonagenarian 28649


title: PBMC_nonagenarian 28695


title: PBMC_nonagenarian 28663


title: PBMC_nonagenarian 28778


title: PBMC_nonagenarian 28782


title: PBMC_nonagenarian 28806


title: PBMC_nonagenarian 28704


title: PBMC_nonagenarian 28623


title: PBMC_nonagenarian 28657


title: PBMC_nonagenarian 28647


title: PBMC_nonagenarian 28622


title: PBMC_nonagenarian 28720


title: PBMC_nonagenarian 28716


title: PBMC_nonagenarian 28726


title: PBMC_nonagenarian 28615


title: PBMC_young control 42024


title: PBMC_nonagenarian 28611


title: PBMC_nonagenarian 28603


title: PBMC_nonagenarian 28594


title: PBMC_nonagenarian 28614


title: PBMC_nonagenarian 28581


title: PBMC_nonagenarian 28582


title: PBMC_nonagenarian 28592


title: PBMC_nonagenarian 28588


title: PBMC_nonagenarian 28591


title: PBMC_nonagenarian 28542


title: PBMC_nonagenarian 28575


title: PBMC_nonagenarian 28509


title: PBMC_nonagenarian 28544


title: PBMC_nonagenarian 28489


title: PBMC_nonagenarian 28502


title: PBMC_nonagenarian 28453


title: PBMC_nonagenarian 28448


title: PBMC_nonagenarian 28498


title: PBMC_nonagenarian 28456


title: PBMC_nonagenarian 28612


title: PBMC_nonagenarian 28583


title: PBMC_nonagenarian 28600


title: PBMC_nonagenarian 28487


title: PBMC_nonagenarian 28515


title: PBMC_nonagenarian 28501


title: PBMC_nonagenarian 28559


title: PBMC_nonagenarian 28472


title: PBMC_nonagenarian 28396


title: PBMC_nonagenarian 28401


title: PBMC_nonagenarian 28438


title: PBMC_nonagenarian 28406


title: PBMC_nonagenarian 28381


title: PBMC_nonagenarian 28667


title: PBMC_nonagenarian 28393


title: PBMC_nonagenarian 28417


title: PBMC_nonagenarian 28395


title: PBMC_nonagenarian 28306


title: PBMC_nonagenarian 28376


title: PBMC_nonagenarian 28290


title: PBMC_nonagenarian 28319


title: PBMC_nonagenarian 28301


title: PBMC_nonagenarian 28289


title: PBMC_nonagenarian 28291


title: PBMC_nonagenarian 28368


title: PBMC_nonagenarian 28288


title: PBMC_nonagenarian 28378


title: PBMC_nonagenarian 28298


title: PBMC_nonagenarian 28286


title: PBMC_nonagenarian 28370


title: PBMC_nonagenarian 28303


title: PBMC_nonagenarian 28358


title: PBMC_nonagenarian 28341


title: PBMC_nonagenarian 28330


title: PBMC_nonagenarian 28346


title: PBMC_nonagenarian 28399


title: PBMC_nonagenarian 28284


title: PBMC_nonagenarian 28269


title: PBMC_nonagenarian 28258


title: PBMC_nonagenarian 28233


title: PBMC_nonagenarian 28243


title: PBMC_nonagenarian 28277


title: PBMC_nonagenarian 28182


title: PBMC_nonagenarian 28223


title: PBMC_nonagenarian 28212


title: PBMC_nonagenarian 28242


title: PBMC_nonagenarian 28237


title: PBMC_nonagenarian 28183


title: PBMC_nonagenarian 28189


title: PBMC_nonagenarian 28179


title: PBMC_nonagenarian 28191


title: PBMC_nonagenarian 28193


title: PBMC_nonagenarian 28247


title: PBMC_nonagenarian 28202


title: PBMC_nonagenarian 28175


title: PBMC_nonagenarian 28200


title: PBMC_nonagenarian 28172


title: PBMC_nonagenarian 28232


title: PBMC_nonagenarian 28198


title: PBMC_nonagenarian 28272


title: PBMC_nonagenarian 28204


title: PBMC_nonagenarian 28429


title: PBMC_nonagenarian 28147


title: PBMC_nonagenarian 28119


title: PBMC_nonagenarian 28112


title: PBMC_nonagenarian 28140


title: PBMC_nonagenarian 28131


title: PBMC_nonagenarian 28127


title: PBMC_nonagenarian 28148


title: PBMC_nonagenarian 28123


title: PBMC_nonagenarian 28106


title: PBMC_nonagenarian 28629


title: PBMC_nonagenarian 28032


title: PBMC_nonagenarian 28087


title: PBMC_nonagenarian 28028


title: PBMC_nonagenarian 28035


title: PBMC_nonagenarian 28073


title: PBMC_nonagenarian 28020


title: PBMC_nonagenarian 28015


title: PBMC_nonagenarian 28058


title: PBMC_nonagenarian 28078


title: PBMC_nonagenarian 28059


title: PBMC_nonagenarian 28048


title: fibroblast_K2_untreated_1h_rep2

status: Public on Jan 01 2013

city: Gdańsk

first: Magdalena

last: Gabig-Cimińska

address: Wita Stwosza 59

department: of Medical Biology and Genetics

country: Poland

institute: University of Gdańsk

description: replicate 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using quantile normalization with Illumina GenomeStudio software package  (gene expression module version 1.9.0).

label_protocol: Biotinylated cRNA was prepared with the Ambion TotalPrepAmp Kit for Illumina arrays

growth_protocol: Fibroblasts were cultured from cryo-preserved cells in Dulbecco’s modified Eagle’s medium containing 10% fetal bovine serum and 1% antibiotic/antimycotic solution at 37 oC in a humidified atmosphere of 5% CO2. 10E5 cells were seeded in 6-well plates and grown to a confluence of approximately 80 %.

extract_protocol: Total RNA was extracted from cells using the High Pure RNA Isolation Kit in accordance with the prescribed protocol, quantified with Quant iT RiboGreen Assay Kit

treatment_protocol: The medium was replaced by fresh medium non-supplemented, containing dimethyl sulfooxide (DMSO) added to a final concentration of 0.05%, or genistein at 30, 60 and 100 µM concentrations, with 0.05% DMSO. The experimental treatment was carried out for 1h, 24 h and 48 h period.

tag: cell line

value: HDFa

tag: cell type

value: fibroblasts


title: PBMC_nonagenarian 28042


title: fibroblast_K2_untreated_24h_rep2

description: replicate 2


title: fibroblast_K2_untreated_48h_rep2

description: replicate 2


title: fibroblast_K2_untreated_24h_rep1

description: replicate 1


title: fibroblast_K2_untreated_1h_rep1

description: replicate 1


title: 14_48_years_old_f

status: Public on Dec 03 2012

city: Leiden

first: Marius

last: Gheorghe

address: Einthovenweg 20

department: Human Genetics

country: Netherlands

institute: LUMC

description: SAMPLE 14

hyb_protocol: According to Illumina protocols

scan_protocol: According to Illumina protocols

data_processing: Microarray measurements were normalized using the quantile method. The quality of the data was assessed by principal component analysis (PCA). Human subjects were grouped into controls, pre-symptomatic, and symptomatic subjects. P-value cut-off of 0.05 were used due to high inter-individual variation. Probe annotation was done using the illuminaHumanv3BeadID package in R.

source_name: vastus laterlalis

extract_protocol:
Human quadriceps muscle samples were collected with the needle or by an open surgical procedure from anonymous healthy individuals that gave informed consent. Only age and gender are noted for those.
Total RNA was extracted from skeletal muscles using RNA Bee (Amsbio) according to the manufacturer's instructions. RNA integration number (RIN) was determined with RNA 6000 Nano (Agilent Technologies). RNA with RIN >7 were used for subsequent steps. RNA labeling was performed with the Illumina® TotalPrep RNA Amplification kit (Ambion) according to the manufacturer's protocol, and subsequently was hybridized to Illumina Human v3 Bead arrays.

tag: gender

value: female

value: muscles

value: 48 years old


title: 13_47_years_old_f

description: SAMPLE 13

label_protocol: RNA labeling was performed with the Illumina® TotalPrep RNA Amplification kit (Ambion) according to the manufacturer's protocol, and subsequently was hybridized to Illumina Human v3 Bead arrays.

value: 47 years old


title: 12_45_years_old_f

description: SAMPLE 12

value: 45 years old


title: fibroblast_K2_untreated_48h_rep1

description: replicate 1


title: 11_44_years_old_m

description: SAMPLE 11

value: male

value: 44 years old


title: 5_40_years_old_m

description: SAMPLE 5

value: 40 years old


title: 4_39_years_old_m

description: SAMPLE 4

value: 39 years old


title: 7_42_years_old_f

description: SAMPLE 7

value: 42 years old


title: 6_41_years_old_m

description: SAMPLE 6

value: 41 years old


title: 10_43_years_old_m

description: SAMPLE 10

value: 43 years old


title: 3_37_years_old_f

description: SAMPLE 3

value: 37 years old


title: 2_36_years_old_m

description: SAMPLE 2

value: 36 years old


title: EL798

status: Public on Oct 10 2012

type: genomic

city: Vancouver

first: Michael

middle: S.

last: Kobor

state: BC

address: 950 West 28th Avenue

department: Medical Genetics

country: Canada

institute: Centre for Molecular Medicine and Therapeutics / University of British Columbia

description: PBMC sample

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol

scan_protocol: BeadChips were imaged using iScan with standard recommended Illumina scanner setting

data_processing: Raw intensities extracted using GenomeStudio v2010.1. Color correction, background normalization and quantile normalization were done using the standard protocol suggested in the Bioconductor lumi package.

label: Cy3 and Cy5

source_name: PBMC

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was isolated using Qiagen AllPrep DNA/RNA mini kit according to manufacturer's instructions

tag: age (y)

value: Female

tag: smoker

value: no

tag: early (low vs. high ses in early life)

value: High

tag: current (low vs. high ses at present)

value: Low

tag: alcohol (drinks per week)

tag: bmi

tag: exercise (minutes per week)

tag: stress (perceived stress scale questionnaire)

tag: depression (center for epidemiologic studies depression scale)

tag: sleep (perceived quality; pittsburgh sleep quality index)

tag: birth control (current use of oral contraceptives)

tag: ethnicity (caucasian or other ethnicity)

value: Others

tag: pbimw (measures of recalled maternal warmth based on a questionnaire called the parental bonding inventory)

tag: pbifw (measures of recalled paternal warmth based on a questionnaire called the parental bonding inventory)

tag: total cortisol  (total cortisol release over 3 days in arbitrary units)

tag: dslope (diurnal rhythm of cortisol in arbitrary units)

tag: pam3csk4 (il-6 response to pam3csk4 in pg/ml)

tag: pgn (il6 response to peptidoglycan in pg/ml)

tag: pic (il6 response to ppoly i

tag: lps (il6 response to lipopolysaccharide in pg/ml)

tag: flagellin (il6 response to flagelin in pg/ml)

tag: zymosan (il6 response to zymosan in pg/ml)

tag: ssr (il6 response to single-stranded rna in pg/ml)

tag: imiquimod (il6 response to imiquimod in pg/ml)

tag: odn (il6 response to oligodeoxyribonucleotide in pg/ml)

tag: il1b (il6 response to interleukin-1b in pg/ml)

tag: pma (il6 response to phorbol-12-myristate-13-acetatein pg/ml)

tag: wbc count (total white blood cells per 10(9) liter/blood)

tag: neutrophils (neutrophils per 10(9) liter/blood)

tag: lymphocytes (lymphocytes per 10(9) liter/blood)

tag: monocytes (monocytes per 10(9) liter/blood)

tag: basophils (basophils per 10(9) liter/blood)

tag: eosinophils (eosinophils per 10(9) liter/blood)

tag: neutrophil% (percent of wbc that are neutrophils)

tag: lymphocyte% (percent of wbc that are lymphocytes)

tag: monocyte% (percent of wbc that are monocytes)

tag: basophil% (percent of wbc that are basophils)

tag: eosinophil% (percent of wbc that are eosinoophils)


title: EL796

description: PBMC sample

tag: age (y)

tag: gender

value: Male

tag: smoker

tag: early (low vs. high ses in early life)

tag: current (low vs. high ses at present)

tag: alcohol (drinks per week)

tag: bmi

tag: exercise (minutes per week)

tag: stress (perceived stress scale questionnaire)

tag: depression (center for epidemiologic studies depression scale)

tag: sleep (perceived quality; pittsburgh sleep quality index)

tag: birth control (current use of oral contraceptives)

tag: ethnicity (caucasian or other ethnicity)

value: European

tag: pbimw (measures of recalled maternal warmth based on a questionnaire called the parental bonding inventory)

tag: pbifw (measures of recalled paternal warmth based on a questionnaire called the parental bonding inventory)

tag: total cortisol  (total cortisol release over 3 days in arbitrary units)

tag: dslope (diurnal rhythm of cortisol in arbitrary units)

tag: pam3csk4 (il-6 response to pam3csk4 in pg/ml)

tag: pgn (il6 response to peptidoglycan in pg/ml)

tag: pic (il6 response to ppoly i

tag: lps (il6 response to lipopolysaccharide in pg/ml)

tag: flagellin (il6 response to flagelin in pg/ml)

tag: zymosan (il6 response to zymosan in pg/ml)


title: EL802

description: PBMC sample

tag: age (y)

tag: gender

tag: smoker

tag: early (low vs. high ses in early life)

tag: current (low vs. high ses at present)

tag: alcohol (drinks per week)

tag: bmi

value: c in pg/ml):639

tag: ssr (il6 response to single-stranded rna in pg/ml)

tag: imiquimod (il6 response to imiquimod in pg/ml)

tag: odn (il6 response to oligodeoxyribonucleotide in pg/ml)

tag: il1b (il6 response to interleukin-1b in pg/ml)

tag: pma (il6 response to phorbol-12-myristate-13-acetatein pg/ml)

tag: wbc count (total white blood cells per 10(9) liter/blood)

tag: neutrophils (neutrophils per 10(9) liter/blood)

tag: lymphocytes (lymphocytes per 10(9) liter/blood)

tag: monocytes (monocytes per 10(9) liter/blood)

tag: basophils (basophils per 10(9) liter/blood)

tag: eosinophils (eosinophils per 10(9) liter/blood)

tag: neutrophil% (percent of wbc that are neutrophils)

tag: lymphocyte% (percent of wbc that are lymphocytes)

tag: monocyte% (percent of wbc that are monocytes)

tag: basophil% (percent of wbc that are basophils)

tag: eosinophil% (percent of wbc that are eosinoophils)


title: EL792

description: PBMC sample

tag: age (y)

tag: gender

tag: smoker

tag: early (low vs. high ses in early life)

tag: current (low vs. high ses at present)

tag: alcohol (drinks per week)

tag: bmi

tag: exercise (minutes per week)

tag: stress (perceived stress scale questionnaire)

tag: depression (center for epidemiologic studies depression scale)

tag: sleep (perceived quality; pittsburgh sleep quality index)

tag: birth control (current use of oral contraceptives)

value: yes

tag: ethnicity (caucasian or other ethnicity)

tag: pbimw (measures of recalled maternal warmth based on a questionnaire called the parental bonding inventory)

tag: pbifw (measures of recalled paternal warmth based on a questionnaire called the parental bonding inventory)

tag: total cortisol  (total cortisol release over 3 days in arbitrary units)

tag: dslope (diurnal rhythm of cortisol in arbitrary units)

tag: pam3csk4 (il-6 response to pam3csk4 in pg/ml)

tag: pgn (il6 response to peptidoglycan in pg/ml)

tag: pic (il6 response to ppoly i

tag: lps (il6 response to lipopolysaccharide in pg/ml)

tag: flagellin (il6 response to flagelin in pg/ml)

tag: zymosan (il6 response to zymosan in pg/ml)


title: EL805

description: PBMC sample

tag: age (y)

tag: gender

tag: smoker

tag: early (low vs. high ses in early life)

tag: current (low vs. high ses at present)

tag: alcohol (drinks per week)

tag: bmi

tag: ssr (il6 response to single-stranded rna in pg/ml)

tag: imiquimod (il6 response to imiquimod in pg/ml)

tag: odn (il6 response to oligodeoxyribonucleotide in pg/ml)

tag: il1b (il6 response to interleukin-1b in pg/ml)

tag: pma (il6 response to phorbol-12-myristate-13-acetatein pg/ml)

tag: wbc count (total white blood cells per 10(9) liter/blood)

tag: neutrophils (neutrophils per 10(9) liter/blood)

tag: lymphocytes (lymphocytes per 10(9) liter/blood)

tag: monocytes (monocytes per 10(9) liter/blood)

tag: basophils (basophils per 10(9) liter/blood)

tag: eosinophils (eosinophils per 10(9) liter/blood)

tag: neutrophil% (percent of wbc that are neutrophils)

tag: lymphocyte% (percent of wbc that are lymphocytes)

tag: monocyte% (percent of wbc that are monocytes)

tag: basophil% (percent of wbc that are basophils)

tag: eosinophil% (percent of wbc that are eosinoophils)


title: EL795

description: PBMC sample

tag: age (y)

tag: gender

tag: smoker

tag: early (low vs. high ses in early life)

tag: current (low vs. high ses at present)

tag: alcohol (drinks per week)

tag: bmi

tag: exercise (minutes per week)

tag: stress (perceived stress scale questionnaire)

tag: depression (center for epidemiologic studies depression scale)

tag: sleep (perceived quality; pittsburgh sleep quality index)

tag: birth control (current use of oral contraceptives)

tag: ethnicity (caucasian or other ethnicity)

tag: pbimw (measures of recalled maternal warmth based on a questionnaire called the parental bonding inventory)

tag: pbifw (measures of recalled paternal warmth based on a questionnaire called the parental bonding inventory)

tag: total cortisol  (total cortisol release over 3 days in arbitrary units)

tag: dslope (diurnal rhythm of cortisol in arbitrary units)

tag: pam3csk4 (il-6 response to pam3csk4 in pg/ml)

tag: pgn (il6 response to peptidoglycan in pg/ml)

tag: pic (il6 response to ppoly i

tag: lps (il6 response to lipopolysaccharide in pg/ml)

tag: flagellin (il6 response to flagelin in pg/ml)

tag: zymosan (il6 response to zymosan in pg/ml)


title: EL797

description: PBMC sample

tag: age (y)

tag: gender

tag: smoker

tag: early (low vs. high ses in early life)

tag: current (low vs. high ses at present)

tag: alcohol (drinks per week)

tag: bmi

tag: ssr (il6 response to single-stranded rna in pg/ml)

tag: imiquimod (il6 response to imiquimod in pg/ml)

tag: odn (il6 response to oligodeoxyribonucleotide in pg/ml)

tag: il1b (il6 response to interleukin-1b in pg/ml)

tag: pma (il6 response to phorbol-12-myristate-13-acetatein pg/ml)

tag: wbc count (total white blood cells per 10(9) liter/blood)

tag: neutrophils (neutrophils per 10(9) liter/blood)

tag: lymphocytes (lymphocytes per 10(9) liter/blood)

tag: monocytes (monocytes per 10(9) liter/blood)

tag: basophils (basophils per 10(9) liter/blood)

tag: eosinophils (eosinophils per 10(9) liter/blood)

tag: neutrophil% (percent of wbc that are neutrophils)

tag: lymphocyte% (percent of wbc that are lymphocytes)

tag: monocyte% (percent of wbc that are monocytes)

tag: basophil% (percent of wbc that are basophils)

tag: eosinophil% (percent of wbc that are eosinoophils)


title: EL799

description: PBMC sample

tag: age (y)

tag: gender

tag: smoker

tag: early (low vs. high ses in early life)

tag: current (low vs. high ses at present)

tag: alcohol (drinks per week)

tag: bmi

tag: exercise (minutes per week)

tag: stress (perceived stress scale questionnaire)

tag: depression (center for epidemiologic studies depression scale)

tag: sleep (perceived quality; pittsburgh sleep quality index)

tag: birth control (current use of oral contraceptives)

tag: ethnicity (caucasian or other ethnicity)

tag: pbimw (measures of recalled maternal warmth based on a questionnaire called the parental bonding inventory)

tag: pbifw (measures of recalled paternal warmth based on a questionnaire called the parental bonding inventory)

tag: total cortisol  (total cortisol release over 3 days in arbitrary units)

tag: dslope (diurnal rhythm of cortisol in arbitrary units)

tag: pam3csk4 (il-6 response to pam3csk4 in pg/ml)

tag: pgn (il6 response to peptidoglycan in pg/ml)

tag: pic (il6 response to ppoly i

tag: lps (il6 response to lipopolysaccharide in pg/ml)

tag: flagellin (il6 response to flagelin in pg/ml)

tag: zymosan (il6 response to zymosan in pg/ml)


title: EL803

description: PBMC sample

tag: age (y)

tag: gender

tag: smoker

tag: early (low vs. high ses in early life)

tag: current (low vs. high ses at present)

tag: alcohol (drinks per week)

tag: bmi

tag: ssr (il6 response to single-stranded rna in pg/ml)

tag: imiquimod (il6 response to imiquimod in pg/ml)

tag: odn (il6 response to oligodeoxyribonucleotide in pg/ml)

tag: il1b (il6 response to interleukin-1b in pg/ml)

tag: pma (il6 response to phorbol-12-myristate-13-acetatein pg/ml)

tag: wbc count (total white blood cells per 10(9) liter/blood)

tag: neutrophils (neutrophils per 10(9) liter/blood)

tag: lymphocytes (lymphocytes per 10(9) liter/blood)

tag: monocytes (monocytes per 10(9) liter/blood)

tag: basophils (basophils per 10(9) liter/blood)

tag: eosinophils (eosinophils per 10(9) liter/blood)

tag: neutrophil% (percent of wbc that are neutrophils)

tag: lymphocyte% (percent of wbc that are lymphocytes)

tag: monocyte% (percent of wbc that are monocytes)

tag: basophil% (percent of wbc that are basophils)

tag: eosinophil% (percent of wbc that are eosinoophils)


title: EL804

description: PBMC sample

tag: age (y)

tag: gender

tag: smoker

tag: early (low vs. high ses in early life)

tag: current (low vs. high ses at present)

tag: alcohol (drinks per week)

tag: bmi

tag: exercise (minutes per week)

tag: stress (perceived stress scale questionnaire)

tag: depression (center for epidemiologic studies depression scale)

tag: sleep (perceived quality; pittsburgh sleep quality index)

tag: birth control (current use of oral contraceptives)

tag: ethnicity (caucasian or other ethnicity)

tag: pbimw (measures of recalled maternal warmth based on a questionnaire called the parental bonding inventory)

tag: pbifw (measures of recalled paternal warmth based on a questionnaire called the parental bonding inventory)

tag: total cortisol  (total cortisol release over 3 days in arbitrary units)

tag: dslope (diurnal rhythm of cortisol in arbitrary units)

tag: pam3csk4 (il-6 response to pam3csk4 in pg/ml)

tag: pgn (il6 response to peptidoglycan in pg/ml)

tag: pic (il6 response to ppoly i

tag: lps (il6 response to lipopolysaccharide in pg/ml)

tag: flagellin (il6 response to flagelin in pg/ml)

tag: zymosan (il6 response to zymosan in pg/ml)


title: 1_35_years_old_f

description: SAMPLE 1

tag: gender

value: female

tag: tissue

value: muscles

tag: age

value: 35 years old


title: EL793

description: PBMC sample

tag: age (y)

tag: smoker

tag: early (low vs. high ses in early life)

tag: current (low vs. high ses at present)

tag: alcohol (drinks per week)

tag: bmi

tag: exercise (minutes per week)

tag: stress (perceived stress scale questionnaire)

tag: depression (center for epidemiologic studies depression scale)

tag: ssr (il6 response to single-stranded rna in pg/ml)

tag: imiquimod (il6 response to imiquimod in pg/ml)

tag: odn (il6 response to oligodeoxyribonucleotide in pg/ml)

tag: il1b (il6 response to interleukin-1b in pg/ml)

tag: pma (il6 response to phorbol-12-myristate-13-acetatein pg/ml)

tag: wbc count (total white blood cells per 10(9) liter/blood)

tag: neutrophils (neutrophils per 10(9) liter/blood)

tag: lymphocytes (lymphocytes per 10(9) liter/blood)

tag: monocytes (monocytes per 10(9) liter/blood)

tag: basophils (basophils per 10(9) liter/blood)

tag: eosinophils (eosinophils per 10(9) liter/blood)

tag: neutrophil% (percent of wbc that are neutrophils)

tag: lymphocyte% (percent of wbc that are lymphocytes)

tag: monocyte% (percent of wbc that are monocytes)

tag: basophil% (percent of wbc that are basophils)

tag: eosinophil% (percent of wbc that are eosinoophils)


title: EL790

description: PBMC sample

tag: age (y)

tag: gender

tag: smoker

tag: early (low vs. high ses in early life)

tag: current (low vs. high ses at present)

tag: alcohol (drinks per week)

tag: bmi

tag: exercise (minutes per week)

tag: stress (perceived stress scale questionnaire)

tag: depression (center for epidemiologic studies depression scale)

tag: sleep (perceived quality; pittsburgh sleep quality index)

tag: birth control (current use of oral contraceptives)

tag: ethnicity (caucasian or other ethnicity)

tag: pbimw (measures of recalled maternal warmth based on a questionnaire called the parental bonding inventory)

tag: pbifw (measures of recalled paternal warmth based on a questionnaire called the parental bonding inventory)

tag: total cortisol  (total cortisol release over 3 days in arbitrary units)

tag: dslope (diurnal rhythm of cortisol in arbitrary units)

tag: pam3csk4 (il-6 response to pam3csk4 in pg/ml)

tag: pgn (il6 response to peptidoglycan in pg/ml)

tag: pic (il6 response to ppoly i

tag: lps (il6 response to lipopolysaccharide in pg/ml)

tag: flagellin (il6 response to flagelin in pg/ml)

tag: zymosan (il6 response to zymosan in pg/ml)


title: EL800

description: PBMC sample

tag: age (y)

tag: gender

tag: smoker

tag: early (low vs. high ses in early life)

tag: current (low vs. high ses at present)

tag: alcohol (drinks per week)

tag: bmi

tag: ssr (il6 response to single-stranded rna in pg/ml)

tag: imiquimod (il6 response to imiquimod in pg/ml)

tag: odn (il6 response to oligodeoxyribonucleotide in pg/ml)

tag: il1b (il6 response to interleukin-1b in pg/ml)

tag: pma (il6 response to phorbol-12-myristate-13-acetatein pg/ml)

tag: wbc count (total white blood cells per 10(9) liter/blood)

tag: neutrophils (neutrophils per 10(9) liter/blood)

tag: lymphocytes (lymphocytes per 10(9) liter/blood)

tag: monocytes (monocytes per 10(9) liter/blood)

tag: basophils (basophils per 10(9) liter/blood)

tag: eosinophils (eosinophils per 10(9) liter/blood)

tag: neutrophil% (percent of wbc that are neutrophils)

tag: lymphocyte% (percent of wbc that are lymphocytes)

tag: monocyte% (percent of wbc that are monocytes)

tag: basophil% (percent of wbc that are basophils)

tag: eosinophil% (percent of wbc that are eosinoophils)


title: EL791

description: PBMC sample

tag: age (y)

tag: gender

tag: smoker

tag: early (low vs. high ses in early life)

tag: current (low vs. high ses at present)

tag: alcohol (drinks per week)

tag: bmi

tag: exercise (minutes per week)

tag: stress (perceived stress scale questionnaire)

tag: depression (center for epidemiologic studies depression scale)

tag: sleep (perceived quality; pittsburgh sleep quality index)

tag: birth control (current use of oral contraceptives)

tag: ethnicity (caucasian or other ethnicity)

tag: pbimw (measures of recalled maternal warmth based on a questionnaire called the parental bonding inventory)

tag: pbifw (measures of recalled paternal warmth based on a questionnaire called the parental bonding inventory)

tag: total cortisol  (total cortisol release over 3 days in arbitrary units)

tag: dslope (diurnal rhythm of cortisol in arbitrary units)

tag: pam3csk4 (il-6 response to pam3csk4 in pg/ml)

tag: pgn (il6 response to peptidoglycan in pg/ml)

tag: pic (il6 response to ppoly i

tag: lps (il6 response to lipopolysaccharide in pg/ml)

tag: flagellin (il6 response to flagelin in pg/ml)

tag: zymosan (il6 response to zymosan in pg/ml)


title: EL787

description: PBMC sample

tag: age (y)

tag: gender

tag: smoker

tag: early (low vs. high ses in early life)

tag: current (low vs. high ses at present)

tag: alcohol (drinks per week)

tag: bmi

value: c in pg/ml):36.1

tag: ssr (il6 response to single-stranded rna in pg/ml)

tag: imiquimod (il6 response to imiquimod in pg/ml)

tag: odn (il6 response to oligodeoxyribonucleotide in pg/ml)

tag: il1b (il6 response to interleukin-1b in pg/ml)

tag: pma (il6 response to phorbol-12-myristate-13-acetatein pg/ml)

tag: wbc count (total white blood cells per 10(9) liter/blood)

tag: neutrophils (neutrophils per 10(9) liter/blood)

tag: lymphocytes (lymphocytes per 10(9) liter/blood)

tag: monocytes (monocytes per 10(9) liter/blood)

tag: basophils (basophils per 10(9) liter/blood)

tag: eosinophils (eosinophils per 10(9) liter/blood)

tag: neutrophil% (percent of wbc that are neutrophils)

tag: lymphocyte% (percent of wbc that are lymphocytes)

tag: monocyte% (percent of wbc that are monocytes)

tag: basophil% (percent of wbc that are basophils)

tag: eosinophil% (percent of wbc that are eosinoophils)


title: 9_43_years_old_m

description: SAMPLE 9

tag: gender

value: male

tag: tissue

tag: age


title: EL789

description: PBMC sample

tag: age (y)

tag: smoker

tag: early (low vs. high ses in early life)

tag: current (low vs. high ses at present)

tag: alcohol (drinks per week)

tag: bmi

tag: exercise (minutes per week)

tag: stress (perceived stress scale questionnaire)

tag: depression (center for epidemiologic studies depression scale)

tag: sleep (perceived quality; pittsburgh sleep quality index)

tag: birth control (current use of oral contraceptives)

tag: ethnicity (caucasian or other ethnicity)

tag: pbimw (measures of recalled maternal warmth based on a questionnaire called the parental bonding inventory)

tag: pbifw (measures of recalled paternal warmth based on a questionnaire called the parental bonding inventory)

tag: total cortisol  (total cortisol release over 3 days in arbitrary units)

tag: dslope (diurnal rhythm of cortisol in arbitrary units)

tag: pam3csk4 (il-6 response to pam3csk4 in pg/ml)

tag: pgn (il6 response to peptidoglycan in pg/ml)

tag: pic (il6 response to ppoly i

value: c in pg/ml):559

tag: lps (il6 response to lipopolysaccharide in pg/ml)

tag: flagellin (il6 response to flagelin in pg/ml)

tag: zymosan (il6 response to zymosan in pg/ml)

tag: ssr (il6 response to single-stranded rna in pg/ml)

tag: imiquimod (il6 response to imiquimod in pg/ml)

tag: odn (il6 response to oligodeoxyribonucleotide in pg/ml)


title: 8_42_years_old_m

description: SAMPLE 8

tag: gender

tag: tissue

tag: age

value: 42 years old


title: EL788

description: PBMC sample

tag: age (y)

tag: smoker

tag: early (low vs. high ses in early life)

tag: current (low vs. high ses at present)

tag: alcohol (drinks per week)

tag: bmi

tag: exercise (minutes per week)

tag: stress (perceived stress scale questionnaire)

tag: depression (center for epidemiologic studies depression scale)

tag: sleep (perceived quality; pittsburgh sleep quality index)

tag: birth control (current use of oral contraceptives)

tag: ethnicity (caucasian or other ethnicity)

value: c in pg/ml):259

tag: il1b (il6 response to interleukin-1b in pg/ml)

tag: pma (il6 response to phorbol-12-myristate-13-acetatein pg/ml)

tag: wbc count (total white blood cells per 10(9) liter/blood)

tag: neutrophils (neutrophils per 10(9) liter/blood)

tag: lymphocytes (lymphocytes per 10(9) liter/blood)

tag: monocytes (monocytes per 10(9) liter/blood)

tag: basophils (basophils per 10(9) liter/blood)

tag: eosinophils (eosinophils per 10(9) liter/blood)

tag: neutrophil% (percent of wbc that are neutrophils)

tag: lymphocyte% (percent of wbc that are lymphocytes)

tag: monocyte% (percent of wbc that are monocytes)

tag: basophil% (percent of wbc that are basophils)

tag: eosinophil% (percent of wbc that are eosinoophils)


title: EL786

description: PBMC sample

tag: age (y)

tag: gender

value: Female

tag: smoker

tag: early (low vs. high ses in early life)

tag: current (low vs. high ses at present)

tag: alcohol (drinks per week)

tag: bmi

tag: exercise (minutes per week)

tag: stress (perceived stress scale questionnaire)

tag: depression (center for epidemiologic studies depression scale)

tag: pbimw (measures of recalled maternal warmth based on a questionnaire called the parental bonding inventory)

tag: pbifw (measures of recalled paternal warmth based on a questionnaire called the parental bonding inventory)

tag: total cortisol  (total cortisol release over 3 days in arbitrary units)

tag: dslope (diurnal rhythm of cortisol in arbitrary units)

tag: pam3csk4 (il-6 response to pam3csk4 in pg/ml)

tag: pgn (il6 response to peptidoglycan in pg/ml)

tag: pic (il6 response to ppoly i

value: c in pg/ml):273

tag: lps (il6 response to lipopolysaccharide in pg/ml)

tag: flagellin (il6 response to flagelin in pg/ml)

tag: zymosan (il6 response to zymosan in pg/ml)

tag: ssr (il6 response to single-stranded rna in pg/ml)

tag: imiquimod (il6 response to imiquimod in pg/ml)

tag: odn (il6 response to oligodeoxyribonucleotide in pg/ml)


title: EL785

description: PBMC sample

tag: age (y)

tag: gender

tag: smoker

value: no

tag: early (low vs. high ses in early life)

value: High

tag: current (low vs. high ses at present)

tag: alcohol (drinks per week)

tag: bmi

tag: sleep (perceived quality; pittsburgh sleep quality index)

tag: birth control (current use of oral contraceptives)

tag: ethnicity (caucasian or other ethnicity)

tag: il1b (il6 response to interleukin-1b in pg/ml)

tag: pma (il6 response to phorbol-12-myristate-13-acetatein pg/ml)

tag: wbc count (total white blood cells per 10(9) liter/blood)

tag: neutrophils (neutrophils per 10(9) liter/blood)

tag: lymphocytes (lymphocytes per 10(9) liter/blood)

tag: monocytes (monocytes per 10(9) liter/blood)

tag: basophils (basophils per 10(9) liter/blood)

tag: eosinophils (eosinophils per 10(9) liter/blood)

tag: neutrophil% (percent of wbc that are neutrophils)

tag: lymphocyte% (percent of wbc that are lymphocytes)

tag: monocyte% (percent of wbc that are monocytes)

tag: basophil% (percent of wbc that are basophils)

tag: eosinophil% (percent of wbc that are eosinoophils)