title: Double heterozygous (EN-/GsbN-) embryos versus Wild-type - Biological replicate 3 - technical replicate 2

status: Public on Jan 01 2014

city: Montpellier

first: Florence

last: Maschat

address: 141 rue de la cardonille

country: France

institute: IGF

hyb_protocol: Cy3 and Cy5 labelled aRNA samples were mixed in equal proportions (700 pmol) and fragmented with the RNA Fragmentation Reagents (Ambion) to enhance aRNA hybridization, dried up to 60ul of final volume, and hybridized on INDAC oligonucleotide microarrays. Labeled probes (60 µl) were mixed with 60 µl of 4X hybridization buffer and 120 µl of deionised formamide, denatured at 95°C for 5min and hybridized at 37°C for 12 hours with the Automated Slide Processor (ASP) of Amersham. Slides were successively washed at 37°C in 1X SCC/0.2% SDS for 20 min, in 0.1X SCC/0.2% SDS for 2x10 min, in 0.1X SCC for 10 min, rinsed in isopropanol and air dried.

scan_protocol: Images were obtained with a GenePix 4200AL (Axon Instruments) at 10 um resolution and 5% of laser power.

data_processing: The rawdata were normalized by Loess (Limma Package).

organism: Drosophila melanogaster

source_name: En/GsbN double heterozygous Embryos

label_protocol: Amino allyl aRNA was labelled according the Dye Coupling and Labeled aRNA Cleanup protocol of the Amino Allyl MessageAmpTM II aRNA Amplification Kit (Ambion) 700 pmol of incorporated dye was used for hybridization.

growth_protocol: Embryos were raised at 25°C

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

value: embryo

tag: genotype/variation

value: En/GsbN double heterozygous

source_name: Wild-type Oregon embryo

value: wild type


title: Double heterozygous (EN-/GsbN-) embryos  versus Wild-type - Biological replicate 3 - technical replicate 1

type: RNA

molecule: total RNA

tag: tissue


title: Double heterozygous (EN-/GsbN-) embryos   versus Wild-type  - Biological replicate 1 - technical replicate 1


title: siCAF1_3

status: Public on Dec 31 2013

city: Paris

first: Pierre

last: de la Grange

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

institute: GenoSplice technology

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 42° for 5 minutes centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). • Transfer 200μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0001

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data were processed using EASANA from GenoSplice technology. GC background correction were applied to probe intensities (core), gene and exon level expression were summarized from the corrected intensities and then quantile normalized.
probe group file; HuEx-1_0-st-v2.r2.pgf
meta-probeset file; HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

label: biotin

organism: Homo sapiens

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

growth_protocol: MCF7 stable cell lines were routinely maintained in DMEM supplemented with 10% foetal bovine serum, penicillin/streptomycin ,blasticidin 3µg/mL in a humidified atmosphere of 5% CO2 at 37°C

extract_protocol: total RNA purified using TRI-Reagent (Sigma),

tag: cell line

tag: sirna

value: siRNA siRNA duplexes targeting hCAF1


title: siCAF1_2


title: Double heterozygous (EN-/GsbN-) embryos versus Wild-type - Biological replicate 2 - technical replicate 2

description: Double heterozygous (EN-/GsbN-) embryos - versus Wild-type  - Biological replicate 2 - technical replicate 2


title: Double heterozygous (EN-/GsbN-) embryos versus Wild-type - Biological replicate 2 - technical replicate 1


title: Double heterozygous (EN-/GsbN-) embryos versus Wild-type - Biological replicate 1 - technical replicate 2


title: Yellow fever vaccinated NDs; Group 4: CD4 T lymphocytes; ND 57 before YFV

status: Public on Jan 06 2014

city: Berlin

first: Pawel

last: Durek

address: Charitéplatz 1

country: Germany

institute: Deutsches Rheuma-Forschungszentrum

description: Purified CD4 T lymphocytes isolated from healthy individual ND57 before yellow fever vaccination

hyb_protocol: Labeling and hybridization of total RNA was performed using the GeneChip 3’ IVT Expression Kit from Affymetrix according to the manufacturers instruction. Briefly, after total RNA extraction, 100 ng of total RNA from each cell sample was reverse transcribed, cDNA was extracted and used as template for in vitro-transcription to generate biotinylated cRNA. cRNA was fragmented and 15 µg cRNA hybridized to each of the GeneChip arrays. The HG-U133 Plus 2.0 GeneChip arrays were loaded with the hybridization cocktail, hybridized at 45 °C rotating for 16 h in a hybridization oven 640 (Affymetrix), washed and stained with streptavidin-phycoerythrin using the Affymetrix GeneChip Fluidics Workstation 450.

scan_protocol: Arrays were scanned with an Affymetrix GeneChip Scanner 3000, using the GCOS software version 1.4 from Affymetrix.

data_processing: Data were analyzed according to High Performance Chip Data Analysis (HPCDA, unpublished - Joachim R. Grün) with the Bioretis database (http://www.bioretis-analysis.de/) using the default filter parameters for decreased and increased gene lists (description of database c.f. open access paper Menssen et al., 2009; PubMedID: 19265543). Chip data included in the Bioretis database were analyzed using the GeneChip Operating Software (GCOS, Affymetrix), version 1.4. Microarrays were globally normalized and scaled to a trimmed mean expression value of 150. Quality checks were performed according to the manufacturer's recommendations. All chips of one SLE group were compared to each of any other ND group, and the following parameters of absolute and comparative analysis were included in the Bioretis database: expression heights (Signals) and mean, median and standard deviation of Signals of both groups, call for presence of transcripts (Absent, A; Marginal, M; Present, P), p-value for presence or absence of transcripts, log2 value of fold change (Signal Log Ratio, SLR) and the fold change as mean values, call for the significance of differentially expression (Change Call: Increase, I; Marginal I, MI; Decrease, D; Marginal D, MD; No Change, NC), and the p value for that call. Additionally – not calculated with GCOS – t-tests of log Signals and SLRs were included in the database. For each present transcript the significance of differential expression between the groups of arrays was either calculated using strict Bonferroni corrected Welch t-tests between SLR values of Experiment group vs. Baseline group and SLR values within both groups (the latter always giving a mean SLR value of zero) or more than 50% of non-parametrically calculated Change calls (Mann-Whitney U test, GCOS) have to be in the same direction. Compared were Grp1 vs. Grp4 (24 comparisons, that means at least 13 Change Calls have to be in increased or decreased direction and/or p-value < 1.3856E-08), Grp1 vs. Grp5 (24 comparisons, p-value < 1.386E-08), Grp2 vs. Grp6 (16 comparisons, p-value < 2.286E-08), Grp2 vs. Grp7 (16 comparisons, p-value < 2.286E-08), Grp3 vs. Grp8 (12 comparisons, p-value < 3.048E-08) and Grp3 vs. Grp9 (12 comparisons, p-value < 3.048E-08). Significantly differentially expressed genes, were filtered using both default parameter sets of filter criteria; these are a combination of four different queries. Filter criteria were developed with various data sets of GeneChips and validated with the Affymetrix Latin Square dataset as shown in Menssen et al., 2009. You can find these validation experiments in BioRetis without registering, using the public content and public login. Click on view single results, select any existing Analysis beginning with first 3 letters "SGU" and click on "Next". Click on "Chose an existing parameterset" and select "JRG_Increase" for increased or "JRG_Decrease" for decreased probesets and click on "Fill". At the bottom of the site check the box named "* use Bonferroni correction" and click on "Search only" to get the list of significantly changed increased or decreased probesets, respectively. The Affymetrix Latin Square dataset, consisting of 42 chips in 14 experiments with three replicates each were analyzed in BioRetis with all possible 3 vs. 3 chip comparisons (one direction).

label: Biotin

source_name: CD4 T lymphocytes from whole blood

extract_protocol: Total RNA was extracted using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s instruction, including the recommended DNase digestion. The purity and integrity of RNA were assessed for each sample using an Agilent 2100 Bioanalyzer with the RNA 6000 Nano LabChip and amount was checked with a NanoDrop ND-1000 spectrophotometer. Contaminating genomic DNA was removed by an on-column DNA digestion step (Qiagen).

treatment_protocol: A total of 50 ml peripheral blood was collected in Vacutainer heparin tubes (Becton-Dickinson, Heidelberg, Germany), and erythrocytes were lysed in EL buffer (Qiagen, Hilden, Germany). Subsequently, granulocytes were depleted using CD15-conjugated microbeads (MACS, Miltenyi Biotec, Bergisch Gladbach, Germany). The CD15-depleted fraction was stained with a CD14-fluorescein isothiocyanate (FITC) antibody (Becton-Dickinson), a CD16-APC-Cy7 antibody (Becton-Dickinson), a CD3-Vioblue antibody (Becton-Dickinson) and a CD4-FITC antibody (Becton-Dickinson). Using a FACSAria cell sorter (Becton-Dickinson), CD4pos T cells, CD16neg monocytes and CD16pos monocytes were isolated with purities and viabilities of >97%. After sorting, the cells were immediately lysed with RLT buffer (Qiagen) and frozen at -70 °C.

tag: blood donor

value: Healthy individual (ND)

tag: vaccination

tag: cell type

tag: flow cytometric cell sorting


title: siCAF1_1


title: siCTRL_1

value: non-targeting control siRNA (mock)


title: SLE-patients; Group 1: CD4 T lymphocytes; active SLE 7

description: Purified CD4 T lymphocytes isolated from active SLE-patient 7

label_protocol: Labeling and hybridization of total RNA was performed using the GeneChip 3’ IVT Expression Kit from Affymetrix according to the manufacturers instruction. Briefly, after total RNA extraction, 100 ng of total RNA from each cell sample was reverse transcribed, cDNA was extracted and used as template for in vitro-transcription to generate biotinylated cRNA. cRNA was fragmented and 15 µg cRNA hybridized to each of the GeneChip arrays. The HG-U133 Plus 2.0 GeneChip arrays were loaded with the hybridization cocktail, hybridized at 45 °C rotating for 16 h in a hybridization oven 640 (Affymetrix), washed and stained with streptavidin-phycoerythrin using the Affymetrix GeneChip Fluidics Workstation 450.

value: SLE patient


title: ChorionicVilli_CPM16_3rd_10

status: Public on Jan 15 2014

type: genomic

city: Vancouver

first: Wendy

last: Robinson

state: BC

address: 950 W 28th Ave

department: Medical Genetics

country: Canada

institute: University of British Columbia

hyb_protocol: Illumina HumanMethylation450 BeadChip Protocol

scan_protocol: Arrays were imaged using Illumina iScan on a two-color channel

data_processing: GenomeStudio 2011.1 software and R version 2.14.0

label: Cy5 and Cy3

molecule: genomic DNA

source_name: placental chorionic villus

extract_protocol: Genomic DNA was purified using the Dneasy Blood and Tissue kit (Qiagen) followed by bisufite conversion using the EZ DNA methylation kit (Zymo) following manufacturer's protocols.

tag: gestational age (weeks)

tag: Sex

value: F

tag: genotype

value: confined placental mosaicism

value: placental chorionic villus


title: siCTRL_2


title: S. solea 24 dph_B

status: Public on Sep 20 2013

city: Legnaro (PD)

first: Serena

last: Ferraresso

state: Padova

address: Viale dell'Università

department: Dept of Comparative Biomedicine and Food Science

country: Italy

institute: University of Padova

description: Solea solea

hyb_protocol: Hybridized according to Agilent One-Color Microarray-Based Gene Expression Analysis protocol

scan_protocol: Array was scanned according to standard Agilent protocol at a resolution of 5 microns modifying default setting to scan the slide twice at two different sensitivity settings (XDRHi 100% and XDRLo 10%) yielding two .tif images.  Agilent FE software then generated one FE file per sample.

data_processing: Data processed with FeatureExtraction v9.5 and quantile normalized using R2.6.1 statistical software

label: Cyanine 3

organism: Solea solea

source_name: whole larvae collected at 24 dph

label_protocol: Amplified and labeled according to Agilent One-Color Microarray-Based Gene Expression Analysis protocol

extract_protocol: Extracted according to QiAgen RNeasy MiniKit protocol for tissue samples

tag: condition

value: pool of 5 larvae collected at 24 dph


title: S. solea 6 dph_C

description: Solea solea

source_name: whole larvae collected at 6 dph

value: pool of 10 larvae collected at 6 dph


title: S. solea 24 dph_C

description: Solea solea


title: S. solea 18 dph_C

description: Solea solea

source_name: whole larvae collected at 18 dph

value: pool of 5 larvae collected at 18 dph


title: S. solea 33 dph_A

description: Solea solea

source_name: whole larvae collected at 33 dph

value: pool of 5 larvae collected at 33 dph


title: S. solea 24 dph_D

description: Solea solea


title: S. solea 11 dph_C

description: Solea solea

source_name: whole larvae collected at 11 dph

value: pool of 10 larvae collected at 11 dph


title: S. solea 33 dph_D

description: Solea solea


title: S. solea 33 dph_B

description: Solea solea


title: S. solea 33 dph_C

description: Solea solea


title: S. solea 18 dph_A

description: Solea solea


title: S. solea 6 dph_A

description: Solea solea


title: S. solea 13 dph_C

description: Solea solea

source_name: whole larvae collected at 13 dph

value: pool of 10 larvae collected at 13 dph


title: S. solea 4 dph_C

description: Solea solea

source_name: whole larvae collected at 4 dph

value: pool of 10 larvae collected at 4 dph


title: S. solea 13 dph_D

description: Solea solea


title: S. solea 11 dph_B

description: Solea solea


title: S. solea 18 dph_B

description: Solea solea


title: S. solea 18 dph_D

description: Solea solea


title: Yellow fever vaccinated NDs; Group 7: CD16neg, inflammatory monocytes; ND 54 seven days after YFV

description: Purified CD16-negative monocytes isolated from healthy individual ND54, 7 days after yellow fever vaccination

source_name: CD16neg, inflammatory monocytes from whole blood

value: 7 days after Yellow Fever vaccination

value: CD16 negative


title: S. solea 11 dph_D

description: Solea solea


title: S. solea 6 dph_B

description: Solea solea


title: S. solea 4 dph_B

description: Solea solea


title: S. solea 11 dph_A

description: Solea solea


title: S. solea 4 dph_D

description: Solea solea


title: S. solea 13 dph_B

description: Solea solea


title: S. solea 4 dph_A

description: Solea solea


title: ChIP-Seq analysis of H3K4me1 in human HUES64 derived CD184+ cells; DNA_Lib 2067

status: Public on Jul 18 2013

type: SRA

city: Cambridge

first: BROAD

last: INSTITUTE

state: MA

country: USA

institute: Broad Institute

description:
sample_term_id: CL_0000223
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 2067
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.13164
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9460
****************
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: GSM997251_BI.hESC_Derived_CD184+_Endoderm_Cultured_Cells.H3K4me1.DNA_Lib_2067.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 2067.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of hESC Derived CD184+ Endoderm Cultured Cells H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K4me1 ChIP-Seq on the hESC Derived CD184+ Endoderm Cultured Cells, Library DNA_Lib 2067, 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.17287
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: 15,483,017
FINDPEAKS_SCORE: 0.2576
FINDPEAKS_PERCENTILE: 50
HOTSPOT_SCORE: 0.3689
HOTSPOT_PERCENTILE: 57
IROC_SCORE: 0.9522
IROC_PERCENTILE: 43
POISSON_SCORE: 0.5141
POISSON_PERCENTILE: 61
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

ANALYSIS FILE NAME: GSM997251_BI.hESC_Derived_CD184+_Endoderm_Cultured_Cells.H3K4me1.DNA_Lib_2067.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 2067.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of hESC Derived CD184+ Endoderm Cultured Cells H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K4me1 ChIP-Seq read mappings from the hESC Derived CD184+ Endoderm Cultured Cells, Library DNA_Lib 2067, 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.17470
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: hDCE H3K4me1 67
BROWSER_TRACK_DESCRIPTION: BI hESC Derived CD184+ Endoderm Cultured Cells Histone H3K4me1 Library DNA_Lib 2067 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 15,483,017
FINDPEAKS_SCORE: 0.2576
FINDPEAKS_PERCENTILE: 50
HOTSPOT_SCORE: 0.3689
HOTSPOT_PERCENTILE: 57
IROC_SCORE: 0.9522
IROC_PERCENTILE: 43
POISSON_SCORE: 0.5141
POISSON_PERCENTILE: 61
MAXIMUM_REPLICATE_CORRELATION: 0.97

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

source_name: CD184+ endoderm differentiated in vitro from stem cells; DNA_Lib 2067

extract_protocol: Library construction protocol: Single read - Illumina

value: CD184+ endoderm cultured cells

tag: sample alias

tag: sample common name

tag: lineage

tag: medium

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

tag: molecule

value: genomic DNA

tag: disease

value: presumed normal

tag: passage

tag: line

value: HUES64 derived CD184+

value: in vitro culture

tag: batch

value: BioSAli 137

value: Cell Line

value: differentiated

value: Male

value: Harvard University

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: Abcam

value: Histone H3K4me1

value: Branson


title: S. solea 24 dph_A

description: Solea solea

value: pool of 5 larvae collected at 24 dph


title: ChIP-Seq analysis of H3K27ac in human BM-MSC cells; DNA_Lib 996

description:
sample_term_id: EFO_0000586
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 996
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.14619
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3895
****************
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: GSM1112792_BI.Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K27ac.57.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 996.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27ac ChIP-Seq on Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells, Donor 57, 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.17289
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 17,898,335
FINDPEAKS_SCORE: 0.6961
FINDPEAKS_PERCENTILE: 94
HOTSPOT_SCORE: 0.6937
HOTSPOT_PERCENTILE: 94
IROC_SCORE: 0.9996
IROC_PERCENTILE: 94
POISSON_SCORE: 0.719
POISSON_PERCENTILE: 94
MAXIMUM_REPLICATE_CORRELATION: 0.95

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

ANALYSIS FILE NAME: GSM1112792_BI.Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K27ac.57.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 996.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27ac ChIP-Seq read mappings from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells, Donor 57, 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.17472
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: BMDMSC H3K27ac 57 96
BROWSER_TRACK_DESCRIPTION: BI Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K27ac Donor 57 Library DNA_Lib 996 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 17,898,335
FINDPEAKS_SCORE: 0.6961
FINDPEAKS_PERCENTILE: 94
HOTSPOT_SCORE: 0.6937
HOTSPOT_PERCENTILE: 94
IROC_SCORE: 0.9996
IROC_PERCENTILE: 94
POISSON_SCORE: 0.719
POISSON_PERCENTILE: 94
MAXIMUM_REPLICATE_CORRELATION: 0.95

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

source_name: "bone marrow was aspirated from the iliac crest, isolated by density gradient and adhesion to plastic, and expanded in monolayer culture, containing 10% FBS"; DNA_Lib 996

tag: sra sample accession

value: healthy

tag: markers

value: BM-MSC

value: Unknown

value: Primary Cell Culture

value: Rikshospitalet University Hospital

value: Active Motif

value: Histone H3K27ac


title: ChIP-Seq analysis of H3K27ac in human HUES 48 cells; DNA_Lib 2068

description:
sample_term_id: NTR_0000848
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 2068
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.13163
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.13320
****************
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: GSM997250_BI.HUES48.H3K27ac.DNA_Lib_2068.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 2068.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of HUES48 Cell Line H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K27ac ChIP-Seq on the HUES48 Cell Line, Library DNA_Lib 2068, 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.17273
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 18,754,313
FINDPEAKS_SCORE: 0.4641
FINDPEAKS_PERCENTILE: 69
HOTSPOT_SCORE: 0.5043
HOTSPOT_PERCENTILE: 72
IROC_SCORE: 0.9928
IROC_PERCENTILE: 44
POISSON_SCORE: 0.5395
POISSON_PERCENTILE: 69
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM997250_BI.HUES48.H3K27ac.DNA_Lib_2068.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 2068.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of HUES48 Cell Line H3K27ac ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K27ac ChIP-Seq read mappings from the HUES48 Cell Line, Library DNA_Lib 2068, 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.17456
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: HUES48 H3K27ac 68
BROWSER_TRACK_DESCRIPTION: BI HUES48 Cell Line Histone H3K27ac Library DNA_Lib 2068 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 18,754,313
FINDPEAKS_SCORE: 0.4641
FINDPEAKS_PERCENTILE: 69
HOTSPOT_SCORE: 0.5043
HOTSPOT_PERCENTILE: 72
IROC_SCORE: 0.9928
IROC_PERCENTILE: 44
POISSON_SCORE: 0.5395
POISSON_PERCENTILE: 69
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: Harvard University ES cell number 48 AKA HUES 48; DNA_Lib 2068

value: BioSam 824

value: HUES48 Cell Line

value: embrionic stem cell

value: DMEM

value: genomic DNA

value: presumed normal

value: HUES48 stem cells

value: in vitro culture

value: BioSAli 1028

value: Cell Line

value: undifferentiated

value: Female

value: Harvard


title: S. solea 1 dph_D

description: Solea solea

source_name: whole larvae collected at 1 dph

value: pool of 10 larvae collected at 1 dph


title: S. solea 1 dph_C

description: Solea solea


title: S. solea 1 dph_B

description: Solea solea


title: S. solea 1 dph_A

description: Solea solea


title: B-cell lymphoma, Dog 51

status: Public on Jul 02 2013

city: Chapel Hill

first: Kristy

middle: L

last: Richards

state: NC

address: 1062 Genetic Medicine Bldg.

department: Medicine

institute: University of North Carolina

description: Gene expression data from canine B-cell lymphoma patient

hyb_protocol: Following fragmentation at 94°C for 35 min, the aRNA was prepared for hybridization according to the Affymetrix Expession Analysis Technical Manual. The hybridization cocktail was hybridized to the arrays at 45°C for 16 hours. The arrays were washed with the Affymetrix Fluidics Station 450 wash stations.

scan_protocol: The arrays were scanned with the Affymetrix GeneChip Scanner 3000 7G Plus with Autoloader.

data_processing:
Basic data analysis and quality of the arrays was carried out using Affymetrix Expression Console software
Microarray data were normalized using RMA implemented by the Bioconductor package in R10, version 2.12.1.

organism: Canis lupus familiaris

source_name: Fine needle aspirate

label_protocol: One microgram of total RNA was processed for microarray hybridization to Affymetrix GeneChips using the MessageAmp II-Biotin Enhanced Kit from Ambion according to manufacturer's instructions

growth_protocol: Client owned pet dogs presented for veterinary care

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Biopsies were obtained prior to treatment and B-cell lymphomas were identified by flow cytometry and/or immunohistochemistry for B-cell markers

tag: vet path diagnosis

value: unknown

tag: ighv status

value: ongoing

tag: pfs time

tag: pfs indicator

tag: OS time

tag: os indicator


title: B-cell lymphoma, Dog 45

source_name: Lymph node

value: MZL


title: B-cell lymphoma, Dog 48

value: DLBCL

value: static


title: B-cell lymphoma, Dog 52

value: ND


title: B-cell lymphoma, Dog 49


title: B-cell lymphoma, Dog 55


title: B-cell lymphoma, Dog 50


title: B-cell lymphoma, Dog 46


title: B-cell lymphoma, Dog 57


title: B-cell lymphoma, Dog 44


title: B-cell lymphoma, Dog 56


title: B-cell lymphoma, Dog 53


title: B-cell lymphoma, Dog 58


title: B-cell lymphoma, Dog 43


title: B-cell lymphoma, Dog 40


title: B-cell lymphoma, Dog 42


title: B-cell lymphoma, Dog 54


title: B-cell lymphoma, Dog 39


title: B-cell lymphoma, Dog 41


title: B-cell lymphoma, Dog 37


title: B-cell lymphoma, Dog 47


title: B-cell lymphoma, Dog 36


title: B-cell lymphoma, Dog 35


title: B-cell lymphoma, Dog 34


title: B-cell lymphoma, Dog 38


title: B-cell lymphoma, Dog 33


title: B-cell lymphoma, Dog 31


title: B-cell lymphoma, Dog 32


title: B-cell lymphoma, Dog 29


title: B-cell lymphoma, Dog 24


title: B-cell lymphoma, Dog 26


title: B-cell lymphoma, Dog 25


title: S. solea 6 dph_D

description: Solea solea

tag: condition

value: pool of 10 larvae collected at 6 dph


title: B-cell lymphoma, Dog 30


title: siCTRL_3

tag: cell line

tag: sirna

value: non-targeting control siRNA (mock)


title: B-cell lymphoma, Dog 19


title: B-cell lymphoma, Dog 15


title: B-cell lymphoma, Dog 13


title: B-cell lymphoma, Dog 16


title: B-cell lymphoma, Dog 10


title: B-cell lymphoma, Dog 28


title: B-cell lymphoma, Dog 22


title: B-cell lymphoma, Dog 12


title: B-cell lymphoma, Dog 14


title: B-cell lymphoma, Dog 27


title: B-cell lymphoma, Dog 11


title: B-cell lymphoma, Dog 17


title: B-cell lymphoma, Dog 20


title: B-cell lymphoma, Dog 18


title: B-cell lymphoma, Dog 21


title: B-cell lymphoma, Dog 5


title: B-cell lymphoma, Dog 8


title: B-cell lymphoma, Dog 6


title: B-cell lymphoma, Dog 7


title: B-cell lymphoma, Dog 23


title: B-cell lymphoma, Dog 9


title: ChIP-Seq analysis of H3K36me3 in human HUES64 derived CD184+ cells; DNA_Lib 842

status: Public on Jun 24 2013

description:
sample_term_id: CL_0000223
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 842
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.14632
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9460
****************
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: GSM1112805_BI.hESC_Derived_CD184+_Endoderm_Cultured_Cells.H3K36me3.DNA_Lib_842.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 842.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of hESC Derived CD184+ Endoderm Cultured Cells H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K36me3 ChIP-Seq on the hESC Derived CD184+ Endoderm Cultured Cells, Library DNA_Lib 842, 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.17238
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: 15,944,617
FINDPEAKS_SCORE: 0.1753
FINDPEAKS_PERCENTILE: 25
HOTSPOT_SCORE: 0.2431
HOTSPOT_PERCENTILE: 20
IROC_SCORE: 0.9229
IROC_PERCENTILE: 22
POISSON_SCORE: 0.4197
POISSON_PERCENTILE: 27
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM1112805_BI.hESC_Derived_CD184+_Endoderm_Cultured_Cells.H3K36me3.DNA_Lib_842.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 842.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of hESC Derived CD184+ Endoderm Cultured Cells H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K36me3 ChIP-Seq read mappings from the hESC Derived CD184+ Endoderm Cultured Cells, Library DNA_Lib 842, 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.17421
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: hDCE H3K36me3 42
BROWSER_TRACK_DESCRIPTION: BI hESC Derived CD184+ Endoderm Cultured Cells Histone H3K36me3 Library DNA_Lib 842 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 15,944,617
FINDPEAKS_SCORE: 0.1753
FINDPEAKS_PERCENTILE: 25
HOTSPOT_SCORE: 0.2431
HOTSPOT_PERCENTILE: 20
IROC_SCORE: 0.9229
IROC_PERCENTILE: 22
POISSON_SCORE: 0.4197
POISSON_PERCENTILE: 27
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

source_name: CD184+ endoderm differentiated in vitro from stem cells; DNA_Lib 842

value: CD184+ endoderm cultured cells

tag: sample common name

tag: lineage

tag: medium

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

value: presumed normal

value: HUES64 derived CD184+

value: BioSAli 137

value: differentiated

tag: Sex

value: Male

value: Harvard University

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: Abcam

value: Histone H3K36me3

value: Branson


title: B-cell lymphoma, Dog 4

value: unknown

value: ongoing


title: B-cell lymphoma, Dog 1


title: B-cell lymphoma, Dog 3

value: DLBCL

value: static


title: B-cell lymphoma, Dog 2


title: ChorionicVilli_Control_17 (methylation)

status: Public on Jun 21 2013

description: Sample name: PL58

data_processing:
GenomeStudio 2011.1 software and R version 2.14.0
Unmethylated and methylated signal intensities matrix linked as supplementary file on the Series record.

label_protocol: Illumina HumanMethylation450 BeadChip Protocol

tag: tissue

value: placental chorionic villus

value: Control

tag: gestational age (weeks)

tag: fetus gender

value: Female


title: ChorionicVilli_Control_6 (methylation)

description: Sample name: PL56v1v2


title: ChorionicVilli_Control_16 (methylation)

description: Sample name: PL43

value: Male


title: ChorionicVilli_Control_14 (methylation)

description: Sample name: PL59


title: ChorionicVilli_Control_1 (methylation)

description: Sample name: PL112


title: ChorionicVilli_Control_12 (methylation)

description: Sample name: PL104


title: ChorionicVilli_Control_8 (methylation)

description: Sample name: PL65v1v2


title: ChorionicVilli_Control_3 (methylation)

description: Sample name: PL25v1v2


title: ChorionicVilli_Control_19 (methylation)

description: Sample name: PL102


title: ChorionicVilli_EOPET_20 (methylation)

description: Sample name: PM138

value: EOPET


title: ChorionicVilli_Control_15 (methylation)

description: Sample name: PL32


title: ChorionicVilli_Control_11 (methylation)

description: Sample name: PL113v1v2


title: ChorionicVilli_EOPET_18 (methylation)

description: Sample name: PL130


title: ChorionicVilli_Control_7 (methylation)

description: Sample name: PL64v1v2


title: ChorionicVilli_Control_2 (methylation)

description: Sample name: PL11v2v3


title: ChorionicVilli_Control_10 (methylation)

description: Sample name: PL96v1v2


title: ChorionicVilli_Control_20 (methylation)

description: Sample name: PL21


title: ChorionicVilli_Control_18 (methylation)

description: Sample name: PM87


title: ChorionicVilli_Control_5 (methylation)

description: Sample name: PL33v1v2


title: ChorionicVilli_Control_4 (methylation)

description: Sample name: PL26v1v2


title: ChorionicVilli_EOPET_19 (methylation)

description: Sample name: PM64


title: ChorionicVilli_Control_13 (methylation)

description: Sample name: PL38


title: ChorionicVilli_EOPET_17 (methylation)

description: Sample name: PM49


title: ChorionicVilli_EOPET_12 (methylation)

description: Sample name: PL131


title: ChorionicVilli_Control_9 (methylation)

description: Sample name: PL76v1v2


title: ChorionicVilli_EOPET_13 (methylation)

description: Sample name: PM80


title: ChorionicVilli_EOPET_14 (methylation)

description: Sample name: PM36


title: ChorionicVilli_EOPET_11 (methylation)

description: Sample name: PM67


title: ChorionicVilli_CONTROL_5 (expression)

description: Sample name: PL33

hyb_protocol: Standard Illumina beadarray hybridization protocol for gene expression profiling

scan_protocol: Illumina hiScan machine using standard Illumina Settings

data_processing:
GenomeStudio-  Background Subtraction and Quantile Normalization
Non-normalized data matrix linked as supplementary file on the Series record.

source_name: ChorionicVilli

label_protocol: Standard Illumina Protocol

extract_protocol: RNA was extracted from tissues stored at -80 in RNAlater using an RNeasy kit (Qiagen)

value: Chorionic Villi


title: ChorionicVilli_CONTROL_7 (expression)

description: Sample name: PL76


title: ChorionicVilli_EOPET_16 (methylation)

description: Sample name: PM99

source_name: placental chorionic villus


title: ChorionicVilli_CONTROL_6 (expression)

description: Sample name: PL11


title: ChorionicVilli_CONTROL_3 (expression)

description: Sample name: PL65


title: ChorionicVilli_CONTROL_2 (expression)

description: Sample name: PL64


title: ChorionicVilli_EOPET_6 (expression)

description: Sample name: PM86


title: ChorionicVilli_CONTROL_1 (expression)

description: Sample name: PL113


title: ChorionicVilli_EOPET_10 (methylation)

description: Sample name: PM129v1v2


title: ChorionicVilli_EOPET_7 (expression)

description: Sample name: PM116


title: ChorionicVilli_EOPET_5 (expression)

description: Sample name: PM51


title: ChorionicVilli_EOPET_8 (expression)

description: Sample name: PM129


title: ChorionicVilli_EOPET_7 (methylation)

description: Sample name: PM86v1v2


title: ChorionicVilli_EOPET_8 (methylation)

description: Sample name: PM97v1v2


title: ChorionicVilli_EOPET_4 (expression)

description: Sample name: PM43


title: ChorionicVilli_EOPET_3 (expression)

description: Sample name: PM39


title: ChorionicVilli_EOPET_2 (expression)

description: Sample name: PM21


title: ChorionicVilli_CONTROL_4 (expression)

description: Sample name: PL56


title: ChorionicVilli_EOPET_2 (methylation)

description: Sample name: PM15v1v3


title: ChorionicVilli_EOPET_15 (methylation)

description: Sample name: PM6


title: 129_Sv_3_Tal1_Ko_d6_4302

status: Public on Jun 18 2013

description: Gene-expression profiling of three biological replicates was performed at day 6 during the differentiation process of Tal-1-/- J1 ESCs (3 samples). Samples were analyzed using mouse Genome 430-2 arrays (Affymetrix).

hyb_protocol: Labeling and hybridization of total RNA was performed using the GeneChip 3’ IVT Express Kit from Affymetrix according to the manufacturers instruction. Briefly, after total RNA extraction, 100 ng of total RNA from each cell sample was reverse transcribed, cDNA was extracted, biotinylated cRNA was transcribed, fragmented, and 15 µg cRNA hybridized to each of the GeneChip arrays. The MG430Av2 GeneChip arrays were loaded with the hybridization cocktail, hybridized at 45 °C rotating for 16 h in a hybridization oven 640 (Affymetrix), washed and stained with streptavidin-phycoerythrin using the Affymetrix GeneChip Fluidics Workstation 400.

scan_protocol: Arrays were scanned with an Affymetrix GeneChip Scanner 3000, using the GCOS software from Affymetrix.

data_processing: Data were analyzed according to High Performance Chip Data Analysis (HPCDA, unpublished - Joachim R. Gruen) with the Bioretis database (http://www.bioretis-analysis.de/) using the default filter parameters for decreased and increased gene lists (description of database c.f. open access paper Menssen et al., 2009; PubMedID: 19265543). Chip data included in the Bioretis database were analyzed using the GeneChip Operating Software (GCOS, Affymetrix), version 1.4. Microarrays were globally normalized and scaled to a trimmed mean expression value of 150. Quality checks were performed according to the manufacturer's recommendations. All 3 chips of one group were compared to each 3 chips of any other group, and the following parameters of absolute and comparative analysis were included in the Bioretis database: expression heights (Signals) and mean, median and standard deviation of Signals of both groups, call for presence of transcripts (Absent, A; Marginal, M; Present, P), p-value for presence or absence of transcripts, log2 value of fold change (Signal Log Ratio, SLR) and the fold change as mean values, call for the significance of differentially expression (Change Call: Increase, I; Marginal I, MI; Decrease, D; Marginal D, MD; No Change, NC), and the p value for that call. Additionally – not calculated with GCOS – t-tests of log Signals and SLRs were included in the database. For each present transcript the significance of differential expression between the groups of arrays was either calculated using strict Bonferroni corrected Welch t-tests between 9 SLR values of Experiment group vs. Baseline group and 12 SLR values within both groups (the latter 12 giving a mean SLR value of zero; p-value had to be <= 5.279E-08) or more than 50% of non-parametrically calculated Change calls (Mann-Whitney U test, GCOS) i.e. 5 or more of all 9 Change calls have to be in the same direction. Significantly differentially expressed genes, were filtered using both default parameter sets of filter criteria; these are a combination of four different queries. Filter criteria were developed with various data sets of GeneChips and validated with the Affymetrix Latin Square dataset as shown in Menssen et al., 2009. You can find these validation experiments in BioRetis without registering, using the public content and public login. Click on view single results, select any existing Analysis beginning with first 3 letters "SGU" and click on "Next". Click on "Chose an existing parameterset" and select "JRG_Increase" for increased or "JRG_Decrease" for decreased probesets and click on "Fill". At the bottom of the site check the box named "* use Bonferroni correction" and click on "Search only" to get the list of significantly changed increased or decreased probesets, respectively. The Affymetrix Latin Square dataset, consisting of 42 chips in 14 experiments with three replicates each were analyzed in BioRetis with all possible 3 vs. 3 chip comparisons (one direction).

organism: Mus musculus

source_name: Group5: 6 days differentiated Flk1+ Tal-1-/- ES cells

growth_protocol: Undifferentiated ESCs were plated at on pre-seeded confluent, non-irradiated OP9 stromal cells (day 0) and cultured in αMEM supplemented with 20% FCS (Gibco-Invitrogen). On day 4, 5, and 6 of differentiation “in vitro”, cells were harvested by trypsinization and FACS purified for Flk-1+ cells (98% purity).

extract_protocol: Total RNA was extracted using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s instruction, including the recommended DNase digest. The amount, purity, and integrity of RNA were assessed for each sample using an Agilent 2100 Bioanalyzer with the RNA 6000 Nano LabChip and a NanoDrop ND-1000 spectrophotometer. Contaminating genomic DNA was removed by an on-column DNA digestion step (Qiagen).

tag: strain

tag: cell type

value: embryonic stem

tag: time

value: 6 days

tag: differentiation

value: differentiated Flk1+ Tal-1-/-  ES cells


title: ChorionicVilli_EOPET_6 (methylation)

description: Sample name: PM51v1v2


title: 129_Sv_2_Tal1_Ko_d6_4302

label_protocol: Labeling and hybridization of total RNA was performed using the GeneChip 3’ IVT Express Kit from Affymetrix according to the manufacturers instruction. Briefly, after total RNA extraction, 100 ng of total RNA from each cell sample was reverse transcribed, cDNA was extracted, biotinylated cRNA was transcribed, fragmented, and 15 µg cRNA hybridized to each of the GeneChip arrays. The MG430Av2 GeneChip arrays were loaded with the hybridization cocktail, hybridized at 45 °C rotating for 16 h in a hybridization oven 640 (Affymetrix), washed and stained with streptavidin-phycoerythrin using the Affymetrix GeneChip Fluidics Workstation 400.


title: ChorionicVilli_EOPET_1 (expression)

description: Sample name: PM12


title: 129_Sv_1_Tal1_Ko_d6_4302


title: 129_Sv_3_Runx1_Ko_d6_4302

description: Gene-expression profiling of three biological replicates was performed at day 6 during the differentiation process of Runx1-/- J1 ESCs (3 samples). Samples were analyzed using mouse Genome 430-2 arrays (Affymetrix).

source_name: Group4: 6 days differentiated Flk1+ Runx1-/- ES cells

value: differentiated Flk1+ Runx1-/- ES cells


title: ChorionicVilli_EOPET_3 (methylation)

description: Sample name: PM21v1v2


title: 129_Sv_2_Runx1_Ko_d6_4302


title: ChorionicVilli_CONTROL_8 (expression)

description: Sample name: PL96


title: ChorionicVilli_EOPET_9 (methylation)

description: Sample name: PM116v1v2


title: ChorionicVilli_EOPET_4 (methylation)

description: Sample name: PM39v2v3


title: 129_Sv_3_WT_d6_4302

description: Gene-expression profiling of three biological replicates was performed at day 6 during the differentiation process of WT J1 ESCs (3 samples). Samples were analyzed using mouse Genome 430-2 arrays (Affymetrix).

source_name: Group3: 6 days differentiated Flk1+ WT ES cells

value: differentiated Flk1+ WT ES cells


title: ChorionicVilli_EOPET_1 (methylation)

description: Sample name: PM12v5


title: 129_Sv_1_WT_d6_4302


title: 129_Sv_1_Runx1_Ko_d6_4302


title: 129_Sv_2_WT_d5_4302

description: Gene-expression profiling of three biological replicates was performed at day 5 during the differentiation process of WT J1 ESCs (3 samples). Samples were analyzed using mouse Genome 430-2 arrays (Affymetrix).

source_name: Group2: 5 days differentiated Flk1+ WT ES cells

value: 5 days


title: 129_Sv_2_WT_d6_4302


title: 129_Sv_3_WT_d4_4302

description: Gene-expression profiling of three biological replicates was performed at day 4 during the differentiation process of WT J1 ESCs (3 samples). Samples were analyzed using mouse Genome 430-2 arrays (Affymetrix).

source_name: Group1: 4 days differentiated Flk1+ WT ES cells

value: 4 days


title: 129_Sv_3_WT_d5_4302


title: Group4: preB cells after 24h induction with doxycycline_6

status: Public on Jun 05 2013

description:
Grp4_C57B6_6_SCfl_mir221_24h_430_2
Gene expression profiles of un-induced preB cells prepared from tissue culture were compared using Affymetrix MG430Av2 GeneChip arrays. After total RNA extraction, reverse transcription, cDNA extraction, the biotinylated cRNA was transcribed, fragmented, and 15 µg cRNA hybridized in triplicates for each of the four groups to the GeneChip arrays. Twelve chips in these four groups were hybridized and analyzed: Group4 are preB cells induced for miR-221 expression after 24h

data_processing: Data were analyzed according to High Performance Chip Data Analysis (HPCDA, unpublished - Joachim R. Grün) with the Bioretis database (http://www.bioretis-analysis.de/) using the default filter parameters for decreased and increased gene lists (description of database c.f. open access paper Menssen et al., 2009; PubMedID: 19265543). Chip data included in the Bioretis database were analyzed using the GeneChip Operating Software (GCOS, Affymetrix), version 1.4. Microarrays were globally normalized and scaled to a trimmed mean expression value of 150. Quality checks were performed according to the manufacturer's recommendations. All 3 chips of one group were compared to each 3 chips of any other group (results, compared to 16h chips were ignored in this study), and the following parameters of absolute and comparative analysis were included in the Bioretis database: expression heights (Signals) and mean, median and standard deviation of Signals of both groups, call for presence of transcripts (Absent, A; Marginal, M; Present, P), p-value for presence or absence of transcripts, log2 value of fold change (Signal Log Ratio, SLR) and the fold change as mean values, call for the significance of differentially expression (Change Call: Increase, I; Marginal I, MI; Decrease, D; Marginal D, MD; No Change, NC), and the p value for that call. Additionally -- not calculated with GCOS -- t-tests of log Signals and SLRs were included in the database. For each present transcript the significance of differential expression between the groups of arrays was either calculated using strict Bonferroni corrected Welch t-tests between 9 SLR values of Experiment group vs. Baseline group and 12 SLR values within both groups (the latter 12 giving a mean SLR value of zero; p-value had to be <= 5.279E-08) or more than 50% of non-parametrically calculated Change calls (Mann-Whitney U test, GCOS) i.e. 5 or more of all 9 Change calls have to be in the same direction. Significantly differentially expressed genes, were filtered using both default parameter sets of filter criteria; these are a combination of four different queries. Filter criteria were developed with various data sets of GeneChips and validated with the Affymetrix Latin Square dataset as shown in Menssen et al., 2009. You can find these validation experiments in BioRetis without registering, using the public content and public login. Click on view single results, select any existing Analysis beginning with first 3 letters "SGU" and click on "Next". Click on "Chose an existing parameterset" and select "JRG_Increase" for increased or "JRG_Decrease" for decreased probesets and click on "Fill". At the bottom of the site check the box named "* use Bonferroni correction" and click on "Search only" to get the list of significantly changed increased or decreased probesets, respectively. The Affymetrix Latin Square dataset, consisting of 42 chips in 14 experiments with three replicates each were analyzed in BioRetis with all possible 3 vs. 3 chip comparisons (one direction).

source_name: Grp4-6 preB cells after 24h induction for miR-221 expression with doxycycline

growth_protocol: PreB cells derived from wild type fetal liver (C57BL/6, CD45.1pos) at day 18 of gestation were grown on a confluent layer of gamma-irradiated (30Gy) M-CSF-deficient OP9 stromal cells in IMDM medium (Gibco) supplemented with 2% FCS (Sigma-Aldrich), 0.03% Primatone-RL (Quest) and 1% mouse IL7 conditioned media as described by Rolink et al, 1991.

extract_protocol: Total RNA was extracted using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s instruction, including the recommended DNase digest. The purity and integrity of RNA were assessed for each sample using an Agilent 2100 Bioanalyzer with the RNA 6000 Nano LabChip and amount was checked with a NanoDrop ND-1000 spectrophotometer. Contaminating genomic DNA was removed by an on-column DNA digestion step (Qiagen).

treatment_protocol: MiR-221 expression was induced by adding 1 mg/ml doxycycline to the cell culture media and samples were taken at 8, 16, or 24h after induction.

value: fetal liver

value: preB-cells

tag: induction of mir-221


title: Group4: preB cells after 24h induction with doxycycline_4

description:
Grp4_C57B6_4_SCfl_mir221_24h_430_2
Gene expression profiles of un-induced preB cells prepared from tissue culture were compared using Affymetrix MG430Av2 GeneChip arrays. After total RNA extraction, reverse transcription, cDNA extraction, the biotinylated cRNA was transcribed, fragmented, and 15 µg cRNA hybridized in triplicates for each of the four groups to the GeneChip arrays. Twelve chips in these four groups were hybridized and analyzed: Group4 are preB cells induced for miR-221 expression after 24h

source_name: Grp4-4 preB cells after 24h induction for miR-221 expression with doxycycline


title: Group2: preB cells after 8h induction with doxycycline_6

description:
Grp2_C57B6_6_SCfl_mir221_8h_430_2
Gene expression profiles of un-induced preB cells prepared from tissue culture were compared using Affymetrix MG430Av2 GeneChip arrays. After total RNA extraction, reverse transcription, cDNA extraction, the biotinylated cRNA was transcribed, fragmented, and 15 µg cRNA hybridized in triplicates for each of the four groups to the GeneChip arrays. Twelve chips in these four groups were hybridized and analyzed: Group2 are preB cells induced for miR-221 expression after 8h

source_name: Grp2-6: preB cells after 8h induction for miR-221 expression with doxycycline

value: 8 h


title: Group2: preB cells after 8h induction with doxycycline_5

description:
Grp2_C57B6_5_SCfl_mir221_8h_430_2
Gene expression profiles of un-induced preB cells prepared from tissue culture were compared using Affymetrix MG430Av2 GeneChip arrays. After total RNA extraction, reverse transcription, cDNA extraction, the biotinylated cRNA was transcribed, fragmented, and 15 µg cRNA hybridized in triplicates for each of the four groups to the GeneChip arrays. Twelve chips in these four groups were hybridized and analyzed: Group2 are preB cells induced for miR-221 expression after 8h

source_name: Grp2-5: preB cells after 8h induction for miR-221 expression with doxycycline


title: Group4: preB cells after 24h induction with doxycycline_5

description:
Grp4_C57B6_5_SCfl_mir221_24h_430_2
Gene expression profiles of un-induced preB cells prepared from tissue culture were compared using Affymetrix MG430Av2 GeneChip arrays. After total RNA extraction, reverse transcription, cDNA extraction, the biotinylated cRNA was transcribed, fragmented, and 15 µg cRNA hybridized in triplicates for each of the four groups to the GeneChip arrays. Twelve chips in these four groups were hybridized and analyzed: Group4 are preB cells induced for miR-221 expression after 24h

source_name: Grp4-5 preB cells after 24h induction for miR-221 expression with doxycycline


title: Group3: preB cells after 16h induction with doxycycline; not used in this publication_6

description:
Grp3_C57B6_6_SCfl_mir221_16h_430_2
Gene expression profiles of un-induced preB cells prepared from tissue culture were compared using Affymetrix MG430Av2 GeneChip arrays. After total RNA extraction, reverse transcription, cDNA extraction, the biotinylated cRNA was transcribed, fragmented, and 15 µg cRNA hybridized in triplicates for each of the four groups to the GeneChip arrays. Twelve chips in these four groups were hybridized and analyzed: Group3 are preB cells induced for miR-221 expression after 16h. The 16h chips were not used in this publication, because miR-221 expression did not reach the maximum at this time point and so did not give us additional information.

source_name: Grp3-6 preB cells after 16h induction for miR-221 expression with doxycycline


title: Group3: preB cells after 16h induction with doxycycline; not used in this publication_5

description:
Grp3_C57B6_5_SCfl_mir221_16h_430_2
Gene expression profiles of un-induced preB cells prepared from tissue culture were compared using Affymetrix MG430Av2 GeneChip arrays. After total RNA extraction, reverse transcription, cDNA extraction, the biotinylated cRNA was transcribed, fragmented, and 15 µg cRNA hybridized in triplicates for each of the four groups to the GeneChip arrays. Twelve chips in these four groups were hybridized and analyzed: Group3 are preB cells induced for miR-221 expression after 16h. The 16h chips were not used in this publication, because miR-221 expression did not reach the maximum at this time point and so did not give us additional information.

source_name: Grp3-5 preB cells after 16h induction for miR-221 expression with doxycycline


title: 129_Sv_1_WT_d5_4302


title: 129_Sv_1_WT_d4_4302


title: ChorionicVilli_EOPET_5 (methylation)

description: Sample name: PM43v1v2


title: Group2: preB cells after 8h induction with doxycycline_4

description:
Grp2_C57B6_4_SCfl_mir221_8h_430_2
Gene expression profiles of un-induced preB cells prepared from tissue culture were compared using Affymetrix MG430Av2 GeneChip arrays. After total RNA extraction, reverse transcription, cDNA extraction, the biotinylated cRNA was transcribed, fragmented, and 15 µg cRNA hybridized in triplicates for each of the four groups to the GeneChip arrays. Twelve chips in these four groups were hybridized and analyzed: Group2 are preB cells induced for miR-221 expression after 8h

source_name: Grp2-4: preB cells after 8h induction for miR-221 expression with doxycycline


title: Group1: preB cells without induction_5

description:
Grp1_C57B6_5_SCfl_mir221_0h_430_2
Gene expression profiles of un-induced preB cells prepared from tissue culture were compared using Affymetrix MG430Av2 GeneChip arrays. After total RNA extraction, reverse transcription, cDNA extraction, the biotinylated cRNA was transcribed, fragmented, and 15 µg cRNA hybridized in triplicates for each of the four groups to the GeneChip arrays. Twelve chips in these four groups were hybridized and analyzed: Group1 are un-induced preB cells

source_name: Grp1-5: preB cells without induction

value: 0 h


title: 129_Sv_2_WT_d4_4302


title: Group3: preB cells after 16h induction with doxycycline; not used in this publication_4

description:
Grp3_C57B6_4_SCfl_mir221_16h_430_2
Gene expression profiles of un-induced preB cells prepared from tissue culture were compared using Affymetrix MG430Av2 GeneChip arrays. After total RNA extraction, reverse transcription, cDNA extraction, the biotinylated cRNA was transcribed, fragmented, and 15 µg cRNA hybridized in triplicates for each of the four groups to the GeneChip arrays. Twelve chips in these four groups were hybridized and analyzed: Group3 are preB cells induced for miR-221 expression after 16h. The 16h chips were not used in this publication, because miR-221 expression did not reach the maximum at this time point and so did not give us additional information.

source_name: Grp3-4 preB cells after 16h induction for miR-221 expression with doxycycline


title: Group1: preB cells without induction_6

description:
Grp1_C57B6_6_SCfl_mir221_0h_430_2
Gene expression profiles of un-induced preB cells prepared from tissue culture were compared using Affymetrix MG430Av2 GeneChip arrays. After total RNA extraction, reverse transcription, cDNA extraction, the biotinylated cRNA was transcribed, fragmented, and 15 µg cRNA hybridized in triplicates for each of the four groups to the GeneChip arrays. Twelve chips in these four groups were hybridized and analyzed: Group1 are un-induced preB cells

source_name: Grp1-6: preB cells without induction


title: non-AD_FC, biological rep17

status: Public on Apr 17 2013

city: Fukuoka

first: Yusaku

last: Nakabeppu

state: Fukuoka

address: 3-1-1 Maidashi Higashi-ku

department: Department of Immunobiology and Neuroscience

country: Japan

institute: Medical Institute of Bioregulation, Kyushu University

hyb_protocol: Following fragmentation, 5.5 µg of cDNA were hybridized for 17 hr at 45℃ on Affymetrix Human Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip® Scanner 3000 7G.

data_processing: CEL files were imported into Affymetrix Expression Console Software, and CHP files were generated.

source_name: Frontal cortex of non-AD brain

label_protocol: The Ambion WT Expression Kit and the GeneChip WT Terminal Labeling and Controls Kit (Affymetrix) were used to generate amplified and biotinylated sense-strand DNA targets from expressed transcripts (100 ng of total RNA).

growth_protocol: We examined postmortem human brains donated for the Hisayama study.

extract_protocol: Total RNA was isolated using a combination of Isogen (Nippon Gene) and the RNeasy Mini Kit (Qiagen), according to the manufacturers’ instructions.

treatment_protocol: During autopsy dissection, parts of the frontal cortex, temporal cortex and hippocampus were cut out from each brain, and preserved at –80°C until RNA preparation.

value: Frontal cortex

tag: age

value: M


title: Group1: preB cells without induction_4

description:
Grp1_C57B6_4_SCfl_mir221_0h_430_2
Gene expression profiles of un-induced preB cells prepared from tissue culture were compared using Affymetrix MG430Av2 GeneChip arrays. After total RNA extraction, reverse transcription, cDNA extraction, the biotinylated cRNA was transcribed, fragmented, and 15 µg cRNA hybridized in triplicates for each of the four groups to the GeneChip arrays. Twelve chips in these four groups were hybridized and analyzed: Group1 are un-induced preB cells

source_name: Grp1-4: preB cells without induction


title: Cyto 20% oxygen 0Vitd (expression) 92

status: Public on Jan 18 2013

data_processing: GenomeStudio-  Background Subtraction and Quantile Normalization

source_name: cultured cytotrophoblast, 20% oxygen conditions, 0 nmvitamin D

growth_protocol: Cultures were plated at a density of 300,000 cells/cm2 and maintained in Dulbecco's modified Eagle's medium containing 10% fetal bovine serum, 20 mmol/liter HEPES pH 7.4 , penicillin (100 units/ml), streptomycin (100 μg/ml), and fungizone (0.25 μg/ml) at 37°C in a 5% carbon dioxide/air atmosphere.

extract_protocol: RNA was purified from cultured trophoblasts using TriReagent

treatment_protocol: The cells from each placenta were in standard conditions of 5% carbon dioxide/air until exposure to <1% oxygen conditions (<1% O2/5%CO2/10%H2/balance N2), 8% oxygen conditions (8% O2/5%CO2/10%H2/balance N2) or standard conditions with or without active vitamin D (1α, 25-dihydroxyvitamin D3) (10 nM or 100 nM), while the other half of the cells were exposed to <1% oxygen, 8%, or standard conditions for 24 h with or without active vitamin D.

value: Isolated Cytotrophoblast

tag: treatment

value: 20% oxygen conditions, 0 nm vitamin D


title: Cyto 20% oxygen 0Vitd (expression) 95


title: chorionic villus_control_26

status: Public on Mar 04 2013

description:
Sample name: PL26v1v2
sample consists of combined chorionic DNA sampled from two independent villi

data_processing:
GenomeStudio 2011.1 software and R version 2.14.0
Processed data: Normalized Average Beta consisting of background subtraction in GenomeStudio, color correction (lumi Bioconductor package) and probe type correction (SWAN, bioconductor package).
Raw data: Unmethylated and methylated signal intensities. Signal_intensities.txt linked as supplementary file on Series record.

source_name: placental chorionic villus, control

extract_protocol: Genomic DNA was purified using the Dneasy Blood and Tissue kit followed by bisufite conversion using the ES DNA methylation kit following manufacturer's protocols.

value: male

tag: gestational age

value: 32 wks 0 days


title: Cyto 8% oxygen 100Vitd (expression) 95

source_name: cultured cytotrophoblast, 8% oxygen conditions, 100 nmvitamin D

value: 8% oxygen conditions, 100 nm vitamin D


title: Cyto 8% oxygen 10Vitd (expression) 95

source_name: cultured cytotrophoblast, 8% oxygen conditions, 10 nmvitamin D

value: 8% oxygen conditions, 10 nm vitamin D


title: Cyto 20% oxygen 10Vitd (expression) 95

source_name: cultured cytotrophoblast, 20% oxygen conditions, 10 nmvitamin D

value: 20% oxygen conditions, 10 nm vitamin D


title: Cyto 20% oxygen 100Vitd (expression) 95

source_name: cultured cytotrophoblast, 20% oxygen conditions, 100 nmvitamin D

value: 20% oxygen conditions, 100 nm vitamin D


title: Cyto 8% oxygen 0Vitd (expression) 95

source_name: cultured cytotrophoblast, 8% oxygen conditions, 0 nmvitamin D

value: 8% oxygen conditions, 0 nm vitamin D


title: chorionic villus_control_33

description:
Sample name: PL33v1v2
sample consists of combined chorionic DNA sampled from two independent villi

value: 32 wks 6 days


title: buccal_control_004

description: Sample name: C004

source_name: buccal swab, control

value: female

value: 4.4 yrs


title: blood_control_067

description: Sample name: A067 B

source_name: peripheral blood leukocytes, control

value: 46 yrs


title: chorionic villus_control_56

description:
Sample name: PL56v1v2
sample consists of combined chorionic DNA sampled from two independent villi

value: 32 wks 4 days


title: blood_control_674

description: Sample name: A674 B

value: 29 yrs


title: chorionic villus_control_64

description:
Sample name: PL64v1v2
sample consists of combined chorionic DNA sampled from two independent villi

value: 26 wks 0 days


title: Cyto 8% oxygen 10Vitd (expression) 92


title: blood_control_642

description: Sample name: A642 B

value: 61 yrs


title: buccal_control_047

description: Sample name: C047

value: 4 yrs


title: blood_control_442

description: Sample name: A422 B

value: 22 yrs


title: Cyto 8% oxygen 100Vitd (expression) 92

value: Isolated Cytotrophoblast


title: Cyto 1% oxygen 10Vitd (expression) 95

source_name: cultured cytotrophoblast, 1% oxygen conditions, 10 nmvitamin D

value: 1% oxygen conditions, 10 nm vitamin D


title: buccal_control_077

description: Sample name: C077

value: male

value: 4.6 yrs


title: Cyto 1% oxygen 100Vitd (expression) 95

source_name: cultured cytotrophoblast, 1% oxygen conditions, 100 nmvitamin D

value: 1% oxygen conditions, 100 nm vitamin D


title: buccal_control_024

description: Sample name: C024

value: 4.5 yrs


title: Syncytio 20% oxygen 100Vitd (methylation) 91

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

data_processing: GenomeStudio-  Background Subtraction. R- Colour Correction and Quantile Normalization using Methyllumi package

source_name: cultured syncytiotrophoblast, 20% oxygen conditions, 100 nmvitamin D

extract_protocol: Genomic DNA was purified from cultured trophoblasts using Wizard® Genomic DNA Purification Kit

treatment_protocol: Half of the cells from each placenta were continued in standard conditions of 5% carbon dioxide/air for 48 h until exposure to <1% oxygen conditions (<1% O2/5%CO2/10%H2/balance N2), 8% oxygen conditions (8% O2/5%CO2/10%H2/balance N2) or standard conditions with or without active vitamin D (1α, 25-dihydroxyvitamin D3) (10 nM or 100 nM), while the other half of the cells were exposed to <1% oxygen, 8%, or standard conditions for 24 h with or without active vitamin D.

value: Fused Cytotrophoblast cells (syncitiotrophoblast)

value: 20% oxygen conditions, 100 nm vitamin D


title: Syncytio 8% oxygen 100Vitd (methylation) 91

source_name: cultured syncytiotrophoblast, 8% oxygen conditions, 100 nmvitamin D

value: 8% oxygen conditions, 100 nm vitamin D


title: Cyto 8% oxygen 0Vitd (expression) 92

value: 8% oxygen conditions, 0 nm vitamin D


title: Cyto 1% oxygen 100Vitd (expression) 92


title: Syncytio 20% oxygen 100Vitd (methylation) 93


title: Syncytio 20% oxygen 0Vitd (methylation) 91

source_name: cultured syncytiotrophoblast, 20% oxygen conditions, 0 nmvitamin D

value: 20% oxygen conditions, 0 nm vitamin D


title: Cyto 1% oxygen 0Vitd (expression) 95

source_name: cultured cytotrophoblast, 1% oxygen conditions, 0 nmvitamin D

value: 1% oxygen conditions, 0 nm vitamin D


title: Syncytio 1% oxygen 100Vitd (methylation) 91

source_name: cultured syncytiotrophoblast, 1% oxygen conditions, 100 nmvitamin D


title: Syncytio 8% oxygen 0Vitd (methylation) 91

source_name: cultured syncytiotrophoblast, 8% oxygen conditions, 0 nmvitamin D


title: Syncytio 1% oxygen 0Vitd (methylation) 91

source_name: cultured syncytiotrophoblast, 1% oxygen conditions, 0 nmvitamin D


title: Cyto 1% oxygen 10Vitd (expression) 92


title: Syncytio 20% oxygen 10Vitd (methylation) 91

source_name: cultured syncytiotrophoblast, 20% oxygen conditions, 10 nmvitamin D

value: 20% oxygen conditions, 10 nm vitamin D


title: Syncytio 1% oxygen 10Vitd (methylation) 91

source_name: cultured syncytiotrophoblast, 1% oxygen conditions, 10 nmvitamin D


title: Syncytio 20% oxygen 10Vitd (methylation) 93


title: Syncytio 8% oxygen 10Vitd (methylation) 91

source_name: cultured syncytiotrophoblast, 8% oxygen conditions, 10 nmvitamin D

value: 8% oxygen conditions, 10 nm vitamin D


title: Syncytio 20% oxygen 10Vitd (methylation) 65


title: Syncytio 20% oxygen 100Vitd (methylation) 65


title: Syncytio 20% oxygen 0Vitd (methylation) 65


title: Syncytio 20% oxygen 0Vitd (methylation) 93


title: Syncytio 1% oxygen 10Vitd (methylation) 65


title: Syncytio 8% oxygen 100Vitd (methylation) 65


title: Syncytio 8% oxygen 0Vitd (methylation) 65


title: Syncytio 1% oxygen 10Vitd (methylation) 93


title: Syncytio 8% oxygen 10Vitd (methylation) 93


title: Syncytio 8% oxygen 100Vitd (methylation) 93


title: Syncytio 20% oxygen 100Vitd (methylation) 95


title: Syncytio 1% oxygen 0Vitd (methylation) 93


title: Syncytio 1% oxygen 0Vitd (methylation) 95


title: Syncytio 1% oxygen 100Vitd (methylation) 95


title: Syncytio 1% oxygen 100Vitd (methylation) 93


title: Syncytio 1% oxygen 0Vitd (methylation) 65


title: Syncytio 20% oxygen 10Vitd (methylation) 95


title: Syncytio 8% oxygen 0Vitd (methylation) 93


title: Syncytio 20% oxygen 10Vitd (methylation) 92


title: Syncytio 1% oxygen 100Vitd (methylation) 65


title: Syncytio 20% oxygen 100Vitd (methylation) 92


title: Syncytio 8% oxygen 10Vitd (methylation) 65


title: Syncytio 20% oxygen 0Vitd (methylation) 92


title: Syncytio 8% oxygen 100Vitd (methylation) 92


title: Syncytio 8% oxygen 0Vitd (methylation) 95


title: Syncytio 8% oxygen 0Vitd (methylation) 92


title: Syncytio 8% oxygen 100Vitd (methylation) 95


title: Syncytio 1% oxygen 10Vitd (methylation) 95


title: Syncytio 8% oxygen 10Vitd (methylation) 92


title: Syncytio 20% oxygen 0Vitd (methylation) 95


title: Syncytio 1% oxygen 100Vitd (methylation) 92


title: Syncytio 1% oxygen 0Vitd (methylation) 92


title: Syncytio 8% oxygen 10Vitd (methylation) 95


title: Cyto 20% oxygen 10Vitd (methylation) 91

source_name: cultured cytotrophoblast, 20% oxygen conditions, 10 nmvitamin D


title: Cyto 20% oxygen 100Vitd (methylation) 65

source_name: cultured cytotrophoblast, 20% oxygen conditions, 100 nmvitamin D


title: Cyto 8% oxygen 10Vitd (methylation) 91

source_name: cultured cytotrophoblast, 8% oxygen conditions, 10 nmvitamin D


title: Cyto 20% oxygen 100Vitd (methylation) 91


title: Cyto 20% oxygen 0Vitd (methylation) 91

source_name: cultured cytotrophoblast, 20% oxygen conditions, 0 nmvitamin D


title: Cyto 20% oxygen 100Vitd (methylation) 93


title: Cyto 1% oxygen 10Vitd (methylation) 91


title: Cyto 8% oxygen 10Vitd (methylation) 65


title: Cyto 8% oxygen 10Vitd (methylation) 95


title: Cyto 20% oxygen 100Vitd (methylation) 95


title: Cyto 20% oxygen 0Vitd (methylation) 93


title: Cyto 8% oxygen 100Vitd (methylation) 91

source_name: cultured cytotrophoblast, 8% oxygen conditions, 100 nmvitamin D


title: Cyto 1% oxygen 0Vitd (methylation) 91


title: Cyto 8% oxygen 0Vitd (methylation) 65

source_name: cultured cytotrophoblast, 8% oxygen conditions, 0 nmvitamin D


title: Cyto 8% oxygen 100Vitd (methylation) 65


title: Cyto 1% oxygen 100Vitd (methylation) 65

source_name: cultured cytotrophoblast, 1% oxygen conditions, 100 nmvitamin D


title: Syncytio 1% oxygen 10Vitd (methylation) 92


title: Cyto 1% oxygen 100Vitd (methylation) 95


title: Cyto 8% oxygen 0Vitd (methylation) 91


title: Cyto 20% oxygen 10Vitd (methylation) 65


title: Cyto 20% oxygen 0Vitd (methylation) 65


title: Cyto 1% oxygen 10Vitd (methylation) 95

source_name: cultured cytotrophoblast, 1% oxygen conditions, 10 nmvitamin D


title: Cyto 1% oxygen 10Vitd (methylation) 65


title: Cyto 20% oxygen 10Vitd (methylation) 95


title: Cyto 8% oxygen 10Vitd (methylation) 93


title: Cyto 20% oxygen 10Vitd (methylation) 93


title: Cyto 20% oxygen 0Vitd (methylation) 95


title: Cyto 8% oxygen 100Vitd (methylation) 95


title: Cyto 1% oxygen 0Vitd (methylation) 65


title: blood from HIV negative women_MCH116451

status: Public on Nov 11 2012

city: winnipge

first: binhua

last: liang

address: 1015 Arlington Street

institute: National Microbiology Laboratory

description:
Gene expression data from whole blood of HIV negative women
MCH116451.CHP
CH116451.CEL

hyb_protocol: done in the Centre For Applied Genomics, Hospitals for Sick Children, Toronto.

data_processing: Background substraction and probe signal summarization was analyzed uing R Bioconductor software. And the data were analyzed by Affymetrix MAS5 package, followed by Array Assist software. The ratio of the genometic means of expression analysis of the relevant genes to estimate P values and a P value of 0.05 or less were considered significant.  Only genes with differences between the resistance and mormal controls > 1.3 fold and p value of 0.005  and called as present in at least 50% of the samples tested were considered as differentially expressed.

source_name: human blood in HIV negative women

extract_protocol: Total RNA was extracted in Nairobi according to the manufacturer's protocol (Qiagen)

value: whole blood

tag: hiv status

value: HIV negative


title: blood from HIV negative women_MCH116459

description:
Gene expression data from whole blood of HIV negative women
MCH116459.CHP
CH116459.CEL

scan_protocol: done in the Centre For Applied Genomics, Hospitals for Sick Children, Toronto.


title: Cyto 1% oxygen 100Vitd (methylation) 91


title: blood from HIV negative women_MCH116715

description:
Gene expression data from whole blood of HIV negative women
MCH116715.CHP
CH116715.CEL

label_protocol: done in the Centre For Applied Genomics, Hospitals for Sick Children, Toronto.


title: Cyto 8% oxygen 100Vitd (methylation) 93


title: blood from HIV negative women_MCH116588

description:
Gene expression data from whole blood of HIV negative women
MCH116588.CHP
CH116588.CEL


title: Cyto 1% oxygen 0Vitd (methylation) 95


title: Cyto 8% oxygen 0Vitd (methylation) 93


title: Cyto 1% oxygen 100Vitd (methylation) 93


title: blood from HIV negative women_MCH116044

description:
Gene expression data from whole blood of HIV negative women
MCH116044.CHP
CH116044.CEL


title: blood from HIV negative women_MCH115693

description:
Gene expression data from whole blood of HIV negative women
MCH115693.CHP
CH115693.CEL


title: blood from HIV negative women_MCH115735

description:
Gene expression data from whole blood of HIV negative women
MCH115735.CHP
CH115735.CEL


title: blood from HIV negative women_MCH115647

description:
Gene expression data from whole blood of HIV negative women
MCH115647.CHP
CH115647.CEL


title: blood from HIV negative women_MCH117270

description:
Gene expression data from whole blood of HIV negative women
MCH117270.CHP
CH117270.CEL


title: Cyto 1% oxygen 0Vitd (methylation) 93


title: Cyto 8% oxygen 0Vitd (methylation) 95


title: blood from HIV negative women_MCH115621

description:
Gene expression data from whole blood of HIV negative women
MCH115621.CHP
CH115621.CEL


title: Cyto 1% oxygen 10Vitd (methylation) 92


title: Cyto 20% oxygen 100Vitd (methylation) 92


title: blood from HIV negative women_MCH115150

description:
Gene expression data from whole blood of HIV negative women
MCH115150.CHP
CH115150.CEL


title: Cyto 20% oxygen 0Vitd (methylation) 92


title: Cyto 20% oxygen 10Vitd (methylation) 92


title: blood from HIV negative women_MCH115641

description:
Gene expression data from whole blood of HIV negative women
MCH115641.CHP
CH115641.CEL


title: blood from HIV negative women_MCH114383

description:
Gene expression data from whole blood of HIV negative women
MCH114383.CHP
CH114383.CEL


title: blood from HIV negative women_MCH115344A

description:
Gene expression data from whole blood of HIV negative women
MCH115344A.CHP
CH115344A.CEL


title: Cyto 1% oxygen 100Vitd (methylation) 92


title: blood from HIV negative women_MCH115490

description:
Gene expression data from whole blood of HIV negative women
MCH115490.CHP
CH115490.CEL


title: blood from HIV negative women_MCH114277

description:
Gene expression data from whole blood of HIV negative women
MCH114277.CHP
CH114277.CEL


title: blood from HIV negative women_MCH114451

description:
Gene expression data from whole blood of HIV negative women
MCH114451.CHP
CH114451.CEL


title: blood from HIV negative women_MCH113929

description:
Gene expression data from whole blood of HIV negative women
MCH113929.CHP
CH113929.CEL


title: blood from HIV negative women_MCH113261

description:
Gene expression data from whole blood of HIV negative women
MCH113261.CHP
CH113261.CEL


title: blood from HIV negative women_MCH113754

description:
Gene expression data from whole blood of HIV negative women
MCH113754.CHP
CH113754.CEL


title: Cyto 8% oxygen 100Vitd (methylation) 92


title: blood from HIV negative women_MCH11318

description:
Gene expression data from whole blood of HIV negative women
MCH111318.CHP
CH111318.CEL


title: Cyto 1% oxygen 0Vitd (methylation) 92


title: Cyto 8% oxygen 10Vitd (methylation) 92


title: blood from HIV negative women_MCH11280

description:
Gene expression data from whole blood of HIV negative women
MCH11280.CHP
CH11280.CEL


title: blood from HIV negative women_MCH113039

description:
Gene expression data from whole blood of HIV negative women
MCH113039.CHP
CH113039.CEL


title: blood from HIV negative women_MCH1112406

description:
Gene expression data from whole blood of HIV negative women
MCH1112406.CHP
CH1112406.CEL


title: Cyto 8% oxygen 0Vitd (methylation) 92


title: blood from HIV negative women_MCH113186

description:
Gene expression data from whole blood of HIV negative women
MCH113186.CHP
CH113186.CEL


title: blood from HIV negative women_MCH103621A

description:
Gene expression data from whole blood of HIV negative women
MCH103621A.CHP
CH103621A.CEL


title: blood from HIV negative women_MCH112406

description:
Gene expression data from whole blood of HIV negative women
MCH112406.CHP
CH112406.CEL


title: blood from HIV negative women_MCH105849

description:
Gene expression data from whole blood of HIV negative women
MCH105849.CHP
CH105849.CEL


title: blood from HIV negative women_MCH114185

description:
Gene expression data from whole blood of HIV negative women
MCH114185.CHP
CH114185.CEL


title: blood from HIV negative women_MCH102749

description:
Gene expression data from whole blood of HIV negative women
MCH102749.CHP
CH102749.CEL


title: blood from HIV negative women_MCH108172

description:
Gene expression data from whole blood of HIV negative women
MCH108172.CHP
CH108172.CEL


title: blood from HIV negative women_MCH106844

description:
Gene expression data from whole blood of HIV negative women
MCH106844.CHP
CH106844.CEL


title: Cyto 1% oxygen 10Vitd (methylation) 93


title: blood from HIV negative women_MCH106527

description:
Gene expression data from whole blood of HIV negative women
MCH106527.CHP
CH106527.CEL


title: blood from HIV negative women_MCH103621

description:
Gene expression data from whole blood of HIV negative women
MCH103621.CHP
CH103621.CEL


title: blood from HIV negative women_MCH104341

description:
Gene expression data from whole blood of HIV negative women
MCH104341.CHP
CH104341.CEL


title: blood from HIV negative women_MCH106447

description:
Gene expression data from whole blood of HIV negative women
MCH106447.CHP
CH106447.CEL


title: blood from HIV negative women_MCH102577

description:
Gene expression data from whole blood of HIV negative women
MCH102577.CHP
CH102577.CEL


title: blood from HIV negative women_MCH100367

description:
Gene expression data from whole blood of HIV negative women
MCH100367.CHP
CH100367.CEL


title: blood from HIV negative women_MCH104651

description:
Gene expression data from whole blood of HIV negative women
MCH104651.CHP
CH104651.CEL


title: blood from HIV negative women_MCH100129-84

description:
Gene expression data from whole blood of HIV negative women
MCH100129-84.CHP
CH100129-84.CEL


title: blood from HIV resistant women_ML2057

description:
Gene expression data from whole blood of HIV resistant women
ML2057.CHP
ML2057.CEL

source_name: human blood in HIV resistant women

value: HIV resistant


title: blood from HIV negative women_MCH115344

description:
Gene expression data from whole blood of HIV negative women
MCH115344.CHP
CH115344.CEL


title: blood from HIV resistant women_ML1949

description:
Gene expression data from whole blood of HIV resistant women
ML1949.CHP
ML1949.CEL


title: blood from HIV resistant women_ML2018

description:
Gene expression data from whole blood of HIV resistant women
ML2018.CHP
ML2018.CEL


title: blood from HIV resistant women_ML2038

description:
Gene expression data from whole blood of HIV resistant women
ML2038.CHP
ML2038.CEL


title: blood from HIV resistant women_ML2016

description:
Gene expression data from whole blood of HIV resistant women
ML2016.CHP
ML2016.CEL


title: blood from HIV resistant women_ML1833

description:
Gene expression data from whole blood of HIV resistant women
ML1833.CHP
ML1833.CEL


title: blood from HIV resistant women_ML1953

description:
Gene expression data from whole blood of HIV resistant women
ML1953.CHP
ML1953.CEL


title: blood from HIV resistant women_ML1871

description:
Gene expression data from whole blood of HIV resistant women
ML1871.CHP
ML1871.CEL


title: blood from HIV resistant women_ML1814

description:
Gene expression data from whole blood of HIV resistant women
ML1814.CHP
ML1814.CEL


title: blood from HIV negative women_MCH102749A

description:
Gene expression data from whole blood of HIV negative women
MCH102749A.CHP
CH102749A.CEL


title: blood from HIV resistant women_ML1860

description:
Gene expression data from whole blood of HIV resistant women
ML1860.CHP
ML1860.CEL


title: blood from HIV resistant women_ML1808

description:
Gene expression data from whole blood of HIV resistant women
ML1808.CHP
ML1808.CEL


title: RNA-Seq analysis of cDNA_Lib 9 and 10 derived from human HUES64 derived CD184+ cells; cDNA_Lib 9/10

status: Public on Sep 05 2012

description:
sample_term_id: CL_0000223
assay_term_id: OBI_0001271
nucleic_acid_term_id: SO_0000871
Design description: mRNA-Seq for REMC on Illumina
Library name: cDNA_Lib 9/10
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.12714
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.12719
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

library_source: transcriptomic

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

ANALYSIS FILE NAME: GSM997220_BI.hESC_Derived_CD184+_Endoderm_Cultured_Cells.mRNA-Seq.cDNA_Lib_9-10.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: cDNA_Lib 9/10.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of hESC Derived CD184+ Endoderm Cultured Cells mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by mRNA-Seq on hESC Derived CD184+ Endoderm Cultured Cells, Library cDNA_Lib 9-10 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.13715
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 221,370,018
NUMBER_OF_MRNA-SEQ_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 22
PERCENT_READS_MAPPING_TO_UCSC_GENES: 92.54
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 86
MAXIMUM_REPLICATE_CORRELATION: NA

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

ANALYSIS FILE NAME: GSM997220_BI.hESC_Derived_CD184+_Endoderm_Cultured_Cells.mRNA-Seq.cDNA_Lib_9-10.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: cDNA_Lib 9/10.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of hESC Derived CD184+ Endoderm Cultured Cells mRNA-Seq Data
ANALYSIS DESCRIPTION: Illumina mRNA-Seq read mappings from hESC Derived CD184+ Endoderm Cultured Cells, Library cDNA_Lib 9-10 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.13718
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: mRNA-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 8
BROWSER_TRACK_NAME: hDCE mRNA 10
BROWSER_TRACK_DESCRIPTION: BI hESC Derived CD184+ Endoderm Cultured Cells mRNA-Seq Library cDNA_Lib 9/10 EA Release 8

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 221,370,018
NUMBER_OF_MRNA-SEQ_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 22
PERCENT_READS_MAPPING_TO_UCSC_GENES: 92.54
PERCENT_READS_MAPPING_TO_UCSC_GENES_PERCENTILE: 86
MAXIMUM_REPLICATE_CORRELATION: NA

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

source_name: CD184+ endoderm differentiated in vitro from stem cells; cDNA_Lib 9/10

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

value: CD184+ endoderm cultured cells

tag: sample alias

value: BioSam 828

value: endoderm

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

tag: disease

value: presumed normal

tag: passage

tag: line

value: HUES64 derived CD184+

value: in vitro culture

tag: batch

value: BioSAli 1032

value: Cell Line

value: differentiated

value: Male

value: Harvard

value: 3' cDNA ligation

value: Our protocol using T4 RNA ligase from NEB

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

value: around 10ng

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

value: yes

value: OligodT - Dynabeads mRNA purification kit (Invitrogen)

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

value: Qiagen AllPrep DNA/RNA/Protein Mini Kit

value: Adapter ligated cDNA made by reverse transcription of RNA

value: Phusion High Fidelity

value: 12 pmoles of each/50 ul of reaction

value: 70C for 4 min in Ambion Fragmentation Buffer

value: NO

value: mRNA-Seq

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


title: blood from HIV negative women_MCH105510

description:
Gene expression data from whole blood of HIV negative women
MCH105510.CHP
CH105510.CEL

tag: tissue

value: whole blood

value: HIV negative


title: blood from HIV resistant women_ML1817

description:
Gene expression data from whole blood of HIV resistant women
ML1817.CHP
ML1817.CEL

value: HIV resistant


title: Monocytes from healthy donor number 13, technical replicate

status: Public on Jun 14 2012

description:
peripheral blood monocyte: in the first step, monocyte from whole blood were depleted from granulocytes by CD15 MACS beads, and in the second step they were sorted from remaining peripheral blood leukocyte by CD14 labelling
Gene expression data of peripheral blood monocytes isolated from healthy donor number 13, it is technical replicates and it is labelled as ND_113

hyb_protocol: label protocol for 14 SLE chips (including SLE test samples), 8 RA chips (RA1 to RA 11, without RA test samples) and 12 ND chips: 50µg/ml of labeled cRNA was hybridized at 45°C for 16h using the Affymetrix GeneChip hybridization oven. Washing and staining was performed on the Affymetrix Fluidics 450 using the EukGE-WS2v4 protocol. label protocol for 3 TNF_1.5h chips, 7 IFNa2a_1.5h chips, 7 IFNg_1.5h chips, 11 Un_1.5h chips and 8 Un_0h chips: 50µg/ml of labeled cRNA was hybridized at 45°C for 16h using the Affymetrix GeneChip hybridization oven. Washing and staining was performed on the Affymetrix Fluidics 450 using the EukGE-WS2v5 protocol. label protocol for 4 RA test chips: RA_1_test, RA_18 test, RA_88_test and RA_98 test: 50µg/ml of labeled cRNA was hybridized at 45°C for 16h using the Affymetrix GeneChip hybridization oven. Washing and staining was performed on the Affymetrix Fluidics 450 using the FS450_0001 protocol.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000

data_processing: Data were processed with GCOS 1.4 (TGT = 150) and subsequently imported and further analyzed in the online database (www.bioretis.de)

source_name: peripheral blood monocytes

label_protocol:
label protocol for 14 SLE chips (including SLE test samples), 8 RA chips (RA1 to RA 11, without RA test samples) and 12 ND chips: 3-5 µg of total RNA was amplified and labelled using the GeneChip® one-cycle target labelling and control reagents (Affymetrix)
label protocol for 3 TNF_1.5h chips, 7 IFNa2a_1.5h chips, 7 IFNg_1.5h chips, 11 Un_1.5h chips and 8 Un_0h chips: 300 ng of total RNA was amplified and labelled using the MessageAmp™ II-Biotin Enhanced Single Round aRNA Amplification Kit according to Affymetrix instruction
label protocol for 4 RA test chips: RA_1_test, RA_18 test, RA_88_test and RA_98 test: 100 ng of total RNA was amplified and labelled using the GeneChip® one-cycle target labelling and control reagents (Affymetrix)

extract_protocol: RNA was collected by using the RNeasy mini kit (Qiagen)

treatment_protocol: only for Affymetrix chips where monocytes were stimulated in vitro by TNFα, IFNα2a and IFNγ

value: Monocytes

tag: individual

value: healthy donor number 13

tag: disease state

value: healthy


title: Monocytes from healthy donor number 20

description:
peripheral blood monocyte: in the first step, monocyte from whole blood were depleted from granulocytes by CD15 MACS beads, and in the second step they were sorted from remaining peripheral blood leukocyte by CD14 labelling
Gene expression data of peripheral blood monocytes isolated from healthy donor number 20, labelled as ND_20

value: healthy donor number 20


title: Monocytes from healthy donor number 14, technical replicate

description:
peripheral blood monocyte: in the first step, monocyte from whole blood were depleted from granulocytes by CD15 MACS beads, and in the second step they were sorted from remaining peripheral blood leukocyte by CD14 labelling
Gene expression data of peripheral blood monocytes isolated from healthy donor number 14, it is technical replicates and it is labelled as ND_114

value: healthy donor number 14


title: Monocytes from healthy donor number 13

description:
peripheral blood monocyte: in the first step, monocyte from whole blood were depleted from granulocytes by CD15 MACS beads, and in the second step they were sorted from remaining peripheral blood leukocyte by CD14 labelling
Gene expression data of peripheral blood monocytes isolated from healthy donor number 13, labelled as ND_13


title: vestibular macula (bv/+) at E16.5, biological rep4

status: Public on Oct 21 2012

city: Coralville

first: Botond

last: Banfi

state: Iowa

address: 2501 Crosspark Road

department: Anatomy and Cell Biology

institute: University of Iowa

description:
pooled vestibular maculas from the utricule and saccule
vm_Het_4

hyb_protocol: Standard Affymetrix protocol.

scan_protocol: Affymetrix Model 7G upgraded scanner

data_processing:
Raw microarray CEL files were imported into Partek Genomics Suite. Signal intensities for the probe-sets were quantile normalized and median polished using Robust Multichip Average background correction. Prior to analysis, two data sets were generated: the first data set contained probe-set intensity data that were not corrected for a batch effect [available as a Series Supplementary file], and the second data set contained probe-set intensity data that were batch-corrected [included in the sample data table] in Partek Genomics Suite (batch 1: Het(bv+)_1, Het(bv+)_2, and Homoz(bvbv)_1; batch 2: Het(bv+)_3, Het(bv+)_4, Homoz(bvbv)_2, Homoz(bvbv)_3). The downstream analysis of the batch-corrected and non-corrected data sets was identical. The signal intensities of exon probe-sets were used to calculate the overall expression level of each gene represented in MJAY. Normalized probe-set intensities (Inorm) were calculated by dividing the background-subtracted signal intensities of exon and exon-junction probe-sets by the background-subtracted gene-expression signal of the corresponding gene. We used 2 (in log2 scale) as background level for exon and exon-exon junction probe-sets and 3 (in log2 scale) as background level for gene expression data. Probe-sets that do not match any NCBI reference transcript were filtered out.
MJAY_r2.pgf
MJAY_r2.full.mps

source_name: vestibular macula (bv/+) at E16.5

label_protocol: Sense-strand cDNA targets were generated using the NuGEN WT-Ovation Exon Module and biotinylated using the NuGEN FL-Ovation cDNA Biotin Module.

growth_protocol: Mouse vestibular maculas isolated by laser capture microdissection from mouse embryos at E16.5

extract_protocol: Inner ears of mouse embryos (E16.5) were embedded in Tissue-Tek O.C.T. Compound and frozen in liquid nitrogen. The embryos were genotyped, and the selected inner ear samples were cryosectioned. Sections were further processed for laser-capture microdissection using the Arcturus Histogene Frozen Section Staining kit. The manufacturer’s staining protocol was modified in that RNAse inhibitor (ProtectRNA, Sigma) was added to every solution in the kit that contains more than 5% water. The vestibular macula was captured from the inner ear sections using the Laser Capture Microdissection system (Pixcell II). RNA was isolated from the captured tissue using the PicoPure RNA isolation kit (Arcturus). RNA samples for microarray analysis were processed using the NuGEN WT-Ovation Pico RNA Amplification System, NuGEN WT-Ovation Exon Module, and NuGEN FL-Ovation cDNA Biotin Module.

treatment_protocol: not applicable

tag: background strain

value: Bronx waltzer (bv)

tag: genotype

value: heterozygous (bv/+)

tag: developmental stage

value: vestibular maculas


title: Monocytes from healthy donor number 11

description:
peripheral blood monocyte: in the first step, monocyte from whole blood were depleted from granulocytes by CD15 MACS beads, and in the second step they were sorted from remaining peripheral blood leukocyte by CD14 labelling
Gene expression data of peripheral blood monocytes isolated from healthy donor number 11, labelled as ND_11

tag: cell type

value: healthy donor number 11


title: Monocytes from healthy donor number 3

description:
peripheral blood monocyte: in the first step, monocyte from whole blood were depleted from granulocytes by CD15 MACS beads, and in the second step they were sorted from remaining peripheral blood leukocyte by CD14 labelling
Gene expression data of peripheral blood monocytes isolated from healthy donor number 3, labelled as ND_3

value: healthy donor number 3