title: T11_Obese_Normalized

description: Gene expression of obese participant


title: 60376_532

status: Public on Nov 01 2015

type: RNA

city: Rennes

first: carlos

last: blanco

address: 263 avenue Général Leclerc

department: SVE

country: France

institute: université rennes 1

description: replicate 1

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

molecule: total RNA

organism: Dickeya dadantii 3937

source_name: D.dadantii 3937_M63

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: Dickeya dadantii 3937 was grown to mild exponential growth phase (OD 600nm 0.4) in M63 medium (Miller, 1972, Experiments in molecular genetics. Press, C. S. H. L., Cold spring Harbor, New York)

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA) and the RNAprotect reagent (Qiagen) and DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen). RNA quality and concentration was determined by analysis with an Agilent 2100 bioanalyzer at the Harvard-Partners Center for Genetics and Genomics (Harvard Medical School, Cambridge, MA USA).

tag: growth media

value: M63 medium


title: 60379_532

description: replicate 2


title: T15_Obese_Normalized

city: Tempe

first: Samantha

middle: Elaine

last: Day

state: AZ

address: University Dr. and Mill Ave.

country: USA

institute: Arizona State University

description: Gene expression of obese participant

hyb_protocol: Cy3-labeled cRNA was fragmented using Agilent Gene Expression Hybridization kit and hybridized to the SurePrint G3 Human Gene Expression 8x60K v2 Microarray  at 65C for 17 hours.

scan_protocol: After washing using Agilent's protocol (see manufacturer's instruction), slides were scanned with an Agilent C scanner.

data_processing: Feature extraction software version 12.0.1.1  (Agilent) was used for analysis.

organism: Homo sapiens

source_name: Vastus lateralis muscle

label_protocol: Total RNA was amplified and labeled using the Low Input Quick Amp Labeling Kit (Agilent) and quantified for Cy3 dye labeled cRNA concentration.

extract_protocol: Muscle biopsy specimens were homogenized in TRIzol solution using a Polytron. Total RNA was purified with RNeasy MinElute Cleanup Kit (Qiagen).

treatment_protocol: Participants underwent euglycemic hyperinsulinemic clamps with muscle biopsies. The biopsies were immediately frozen in liquid nitrogen.

tag: tissue

value: Vastus lateralis muscle

tag: Sex

value: Male

tag: age

tag: obese status

value: obese


title: T14_Obese_Normalized

description: Gene expression of obese participant

value: Female


title: Tregs stimulated in the presence of media. Replicate #3

city: Cleveland

first: Yibayiri

middle: Osee

last: Sanogo

state: OH

address: 9500 S Euclid Ave

department: Genomics Core

institute: Cleveland Clinic Foundation

description: 48hrs -IL-27_3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

label: biotin

organism: Mus musculus

source_name: regulatory T cells

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

growth_protocol: CD4+Foxp3GFP+ 5x10^5 cells/ml stimulated with CD3/28 coated dynabeads added IL-2 (100u/ml) for 48hrs

extract_protocol: RNA was extracted with QIAGEN RNeasy mini kit followed by clean-up and DNase I treatment in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: cell type

value: regulatory T cells


title: Tregs stimulated in the presence of media. Replicate #4

description: 48hrs -IL-27_4


title: 60392_532

description: replicate 2

source_name: D.dadantii 3937_0.3M NaCl M63

growth_protocol: Dickeya dadantii 3937 was grown to mild exponential growth phase (OD 600nm 0.4) in M63 medium containing 03 M NaCl .

value: 0.3 M NaCl M63 medium


title: Tregs stimulated in the presence of IL-27. Replicate #4


title: Tregs stimulated in the presence of IL-27. Replicate #2

description: 48hrs +-IL-27_2


title: T07_Obese_Normalized

description: Gene expression of obese participant


title: T10_Obese_Normalized

description: Gene expression of obese participant


title: Tregs stimulated in the presence of IL-27. Replicate #1

description: 48hrs +IL-27_1


title: Tregs stimulated in the presence of media. Replicate #1

description: 48hrs -IL-27_1


title: Tregs stimulated in the presence of media. Replicate #2

description: 48hrs  -IL-27_2


title: T24_Lean_Normalized

description: Gene expression of lean participant

value: lean


title: A549_mock_12h_2

city: Berlin

first: Daniel

last: Bourquain

state: Berlin

address: Seestraße 10

department: Centre for Biological Threats and Special Pathogens 1

country: Germany

institute: Robert Koch Institute

hyb_protocol: The hybridization procedure was performed according to the Agilent 60-mer oligo microarray processing protocol using the Agilent Gene Expression Hybridization Kit (Agilent Technologies). Briefly, 600 ng Cy3-labeled fragmented cRNA in hybridization buffer was hybridized overnight (17 hours, 65 °C) to Agilent Whole Human Genome Oligo Microarrays 8x60K using Agilent’s recommended hybridization chamber and oven. Finally, the microarrays were washed once with the Agilent Gene Expression Wash Buffer 1 for 1 min at room temperature followed by a second wash with preheated Agilent Gene Expression Wash Buffer 2 (37 °C) for 1 min. The last washing step was performed with acetonitrile.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s  Microarray Scanner System (Agilent Technologies).

data_processing: The Agilent Feature Extraction Software (FES) was used to read out and process the microarray image files. For determination of differential gene expression FES derived output data files were further analyzed using the Rosetta Resolver gene expression data analysis system (Rosetta Biosoftware).

label_protocol: For the linear T7-based amplification step, 100 ng of each total RNA sample was used. To produce Cy3-labeled cRNA, the RNA samples were amplified and labeled using the Agilent Low Input Quick Amp Labeling Kit (Agilent Technologies) following the manufacturer’s protocol. Yields of cRNA and the dye-incorporation rate were measured with the ND-1000  Spectrophotometer (NanoDrop Technologies).

growth_protocol: A549 human lung carcinoma epithelial cells (DSMZ ACC 107) were cultured under standard conditions in 12-well cell culture plates

extract_protocol: TRIzol® extraction, according to manufacturer's protocol

treatment_protocol: Cells were infected with the described viruses at MOI of 5.0 and the virus was adsorbed for 1h. Mock infections were performed using culture medium free of any virus.

tag: cell line

tag: inoculum

value: non-infected


title: T20_Lean_Normalized

description: Gene expression of lean participant


title: T18_Lean_Normalized

description: Gene expression of lean participant


title: Unaffected liver mouse 4033 dye swap

type: genomic

city: Boston

first: Lee

middle: Alan

last: Albacker

state: MA

address: 200 Longwood Ave

department: Department of Systems Biology

institute: Harvard Medical School

hyb_protocol: Arrays were hybridized in hybridization buffer (Agilent) in a hybridization oven and sequentially washed.

scan_protocol: Images were scanned with a Agilent Technologies Scanner G2505C US22502664

data_processing: Agilent feature extraction (v 9.1.3.1) was used for background subtraction and linear normalization

molecule: genomic DNA

source_name: unaffected liver tissue

label_protocol: 3 ug of genomic DNA was labeled using Agilent labeling kits

extract_protocol: Genomic DNA using Machery-Nagel DNA extraction kit occording to manufacturers instructions, subsequent steps performed at BioMicroCenter MIT

value: unaffected liver tissue

tag: strain

tag: genotype

value: 13.9 months

value: male

source_name: normal liver tissue

value: liver

value: female


title: A549_mock_12h_1


title: T27_Lean_Normalized

description: Gene expression of lean participant


title: Tregs stimulated in the presence of IL-27. Replicate #3

description: 48hrs +IL-27_3


title: Unaffected liver mouse 4033


title: A549_TULV_12h_2

value: TULV Moravia Ve6P3951129


title: Hepatocellular carcinoma 1 mouse 4033

source_name: tumor tissue

value: liver tumor tissue


title: A549_TULV_12h_1


title: Hepatocellular carcinoma 1 mouse 4033 dye swap


title: Hepatocellular carcinoma 2 mouse 4033 dye swap


title: Unaffected liver mouse 3760 dye swap

value: 13.8 months


title: A549_DOBV_Dobrava_12h_2

value: DOBV Dobrava (genotype Dobrava Slo 97110)


title: A549_DOBV_Sochi_12h_2

value: DOBV Sochi (genotype Sochi Ap/Sochi/hu )


title: T16_Lean_Normalized

description: Gene expression of lean participant

value: Vastus lateralis muscle


title: T03_Lean_Normalized

description: Gene expression of lean participant


title: Unaffected liver mouse 3151

value: 16.4 months


title: Hepatocellular carcinoma 2 mouse 4033


title: A549_DOBV_Sochi_12h_1


title: T06_Lean_Normalized

description: Gene expression of lean participant

value: Male


title: T09_Lean_Normalized

description: Gene expression of lean participant

value: Female


title: Hepatocellular carcinoma 2 mouse 3760


title: Unaffected liver mouse 3151 dye swap


title: Hepatocellular carcinoma 2 mouse 3151 dye swap


title: T04_Lean_Normalized

description: Gene expression of lean participant


title: T08_Lean_Normalized

description: Gene expression of lean participant


title: Hepatocellular carcinoma 1 mouse 3151 dye swap


title: A549_DOBV_Kurkino_12h_2

value: DOBV Kurkino (genotype Kurkino GER/08/131/Af)


title: Hepatocellular carcinoma 2 mouse 3151


title: A549_DOBV_Dobrava_12h_1


title: Hepatocellular adenoma 3690

scan_protocol: Images were scanned with a GenePix 4000B

data_processing: Feature extraction using Genepix Pro 6.0.1.25, Log2 ratios calculated using R package snapCGH by Darin Takemoto

extract_protocol: Genomic DNA using Machery-Nagel DNA extraction kit occording to manufacturers instructions, hybridization performed at Partners array core

value: liver tumor

value: 18.1 months


title: DCs_hypoxia_HIF1A-silenced_A.fumigatus-stimulated_rep3

city: Wuerzburg

first: Mirjam

last: Fliesser

state: Bavaria

address: Josef-Schneider-Str. 2

department: Medical Clinic II

institute: University Hospital Wuerzburg

description:
DC_hyp_si_AF_rep3
E13R019c08.CEL

hyb_protocol: Standard Affymetrix GeneTitan hybridization protocol

scan_protocol: Standard Affymetrix GeneTitan scan protocol

data_processing: Affymetrix Expression Console 1.3.1

source_name: A. fumigatus stimulated, HIF-1α silenced dendritic cells, hypoxia

label_protocol: Standard Affymetrix 3´- expression profiling kit

growth_protocol: DCs were differentiated with IL4 and GMCSF from monocytes over 5 days. Three independent experiments with cells from different blood donors were performed.

extract_protocol: Qiagen RNeasy Mini Kit

treatment_protocol: siRNA directed agains HIF1A or non-silencing control siRNA was transfected via electroporation.  1x10^6 DCs were stimulated with 1x10^6 inactivated A. fumigatus germ tubes at normoxia or hypoxia (1 % O2) for 6 h.

value: human monocyte-derived dendritic cells

tag: genotype/variation

value: HIF-1α silenced

tag: stimulated with

value: inactivated germ tubes of A. fumigatus

tag: culture condition

value: hypoxia (1 % O2)


title: Unaffected liver mouse 3760

value: unaffected liver tissue

value: male

value: liver

value: female


title: A549_DOBV_Kurkino_12h_1


title: Hepatocellular carcinoma 3643

value: 10.3 months


title: Hepatocellular carcinoma 3643 swap


title: Hepatocellular adenoma 3690 swap


title: Hepatocellular carcinoma 1 mouse 3151

value: liver tumor tissue


title: Hepatocellular carcinoma 3605 swap

value: 19.3 months


title: Hepatocellular carcinoma 3605


title: DCs_hypoxia_HIF1A-silenced_A.fumigatus-stimulated_rep1

description:
DC_hyp_si_AF_rep1
E13R019a08.CEL


title: DCs_hypoxia_HIF1A-silenced_A.fumigatus-stimulated_rep2

description:
DC_hyp_si_AF_rep2
E13R019b08.CEL


title: DCs_hypoxia_HIF1A-silenced_unstimulated_rep3

description:
DC_hyp_si_unst_rep3
E13R019c07.CEL

source_name: unstimulated, HIF-1α silenced dendritic cells, hypoxia


title: Hepatocellular adenoma 4007 swap

value: 20.7 months


title: Hepatocellular carcinoma 3308

value: 24.7 months


title: Hepatocellular adenoma 4007


title: DCs_hypoxia_nonsilenced_A.fumigatus-stimulated_rep2

description:
DC_hyp_ns_AF_rep2
E13R019b06.CEL

source_name: A. fumigatus stimulated, non-silenced dendritic cells, hypoxia

value: HIF-1α non-silenced


title: Hepatocellular adenoma 4757

value: 20.1 months


title: Hepatocellular carcinoma 3308 swap

value: liver tumor


title: Hepatocellular carcinoma 2985

value: 15.9 months


title: DCs_hypoxia_nonsilenced_A.fumigatus-stimulated_rep1

description:
DC_hyp_ns_AF_rep1
E13R019a06.CEL

value: human monocyte-derived dendritic cells


title: DCs_hypoxia_HIF1A-silenced_unstimulated_rep1

description:
DC_hyp_si_unst_rep1
E13R019a07.CEL

value: HIF-1α silenced


title: Hepatocellular carcinoma 3055 swap

value: 8.5 months


title: DCs_hypoxia_HIF1A-silenced_unstimulated_rep2

description:
DC_hyp_si_unst_rep2
E13R019b07.CEL

value: hypoxia (1 % O2)


title: Hepatocellular adenoma 3296 swap

value: 11.1 months


title: Hepatocellular carcinoma 2985 swap

value: male


title: Hepatocellular adenoma 4757 swap

value: liver


title: P43T14

city: Jena

first: S.

last: Lambeck

address: Erlanger Allee 101

institute: JUH

description:
in vivo
SAMPLE 81

hyb_protocol: Hybridization is performed according to the Illumina “WGGEX Direct Hybridization Assay Guide. Biotinylated probes were prepared from 750 ng of total RNA, using the TargetAmp™-Nano Labeling Kit for Illumina® Expression BeadChip®. Amplification of RNA was in agreement to the protocol of the Illumina® for the BeadArray Reader 500 X.

scan_protocol: Arrays were readout with the detection system iScan from Illumina.

data_processing: Raw data was pre-processed using GenomeStudio (v 1.9.0). Robust spline normalization (rsn) and detection filtering were performed via the lumi package within Bioconductor and R statistics software (version 3.13). Detection (p<0.01) was required in at least ten samples (out of 90). Candidates were validated by RT-PCR. Annotation was mapped using HumanHT-12_V4_0_R2_15002873_B from Illumina. Analyses were perfomed with respect to individual resolved fold changes (T0-adjusted) as well as global.

source_name: P43_Systemic Inflammation

label_protocol: Amplification and biotinylation of RNA were carried out using the TargetAmp™-Nano Labeling Kit for Illumina® Expression BeadChip®. Alexa Fluor 555 Streptavidin (Invitrogen, Karlsruhe). 0,75 µg cRNA of each sample was hybridized on  Human-HT-12-V4 bead chips.

growth_protocol: All samples were taken after official registration and written consent.

extract_protocol:
Blood was drawn after ICU admission and prepared with  PAXgene reagent (PreAnalytix®, Qiagen, Hilden, Germany). 0,75 µg cRNA of each sample was hybridized on a Human-HT-12-V4  Expression BeadChips from Illumina®. Amplification of RNA was in agreement to the protocol of the Illumina® for the BeadArray Reader 500 X.
Blood was drawn on (D0) and after admission (D1-D21) and prepared with PAXgene reagent (PreAnalytix®, Qiagen, Hilden, Germany). 200ng of total RNA of each sample were reversely transcribed and amplified using the TargetAmp-Nano Labeling Kit for Illumina Expression BeadChips (Epicentre, Biozym, Hessisch Oldendorf) a Biorad MJ Thermal Cycler (Biorad, München). All cRNA samples were quantified with a NanoDrop spectrophotometer (Nanodrop-Technologies) before proceeding to sample hybridization. Samples were prepared for hybridization according to the Illumina WGGEX Direct Hybridization Assay Guide (Illumina).

treatment_protocol: High standard protocol.

tag: subject id

tag: subject status

value: patients with multi-system trauma (ISS ≥ 17 points)

tag: gender

tag: subject subgroup

value: patients with systemic inflammation without infection

tag: time point

value: day 14 after trauma

value: circulating leukocytes


title: Hepatocellular adenoma 3433 swap

tag: tissue

value: 11 months

value: female


title: DCs_hypoxia_nonsilenced_unstimulated_rep2

description:
DC_hyp_ns_unst_rep2
E13R019b05.CEL

source_name: unstimulated, non-silenced dendritic cells, hypoxia

value: HIF-1α non-silenced


title: DCs_hypoxia_nonsilenced_unstimulated_rep1

description:
DC_hyp_ns_unst_rep1
E13R019a05.CEL


title: DCs_hypoxia_nonsilenced_A.fumigatus-stimulated_rep3

description:
DC_hyp_ns_AF_rep3
E13R019c06.CEL

value: inactivated germ tubes of A. fumigatus


title: P43T21

description:
in vivo
SAMPLE 82

value: day 21 after trauma


title: P43T10

description:
in vivo
SAMPLE 80

value: day 10 after trauma


title: Hepatocellular carcinoma 2827

value: liver tumor

value: 21.2 months

tag: Sex


title: Hepatocellular adenoma 3296

tag: age


title: Hepatocellular carcinoma 3055

value: 8.5 months


title: DCs_hypoxia_nonsilenced_unstimulated_rep3

description:
DC_hyp_ns_unst_rep3
E13R019c05.CEL

value: human monocyte-derived dendritic cells

value: hypoxia (1 % O2)


title: Hepatocellular carcinoma 3548 swap

value: 13.5 months

value: male


title: Hepatocellular carcinoma 2827 swap

value: liver


title: P43T05

description:
in vivo
SAMPLE 78

value: patients with multi-system trauma (ISS ≥ 17 points)

value: patients with systemic inflammation without infection

value: day 5 after trauma


title: P43T07

description:
in vivo
SAMPLE 79

value: day 7 after trauma

value: circulating leukocytes


title: Hepatocellular adenoma 1895

value: 12 months

value: female


title: DCs_normoxia_HIF1A-silenced_A.fumigatus-stimulated_rep3

description:
DC_norm_si_AF_rep3
E13R019c04.CEL

source_name: A. fumigatus stimulated, HIF-1α silenced dendritic cells, normoxia

value: HIF-1α silenced

value: inactivated germ tubes of A. fumigatus

value: normoxia


title: P43T02

description:
in vivo
SAMPLE 76

value: day 2 after trauma


title: MtuR mutant_late exp_2 vs. S. uberis 0140J_late exp_3

city: Sutton Bonington

first: Sharon

last: Egan

state: Leicestershire

address: Sutton Bonington Campus

department: School of Veterinary Medicine and Sciences

country: United Kingdom

institute: University of Nottingham

description: Array 1_4

hyb_protocol: Cy3- and Cy5-labelled probes were mixed together in the appropriate combinations, with the fragmented RNA and hybridization buffer applied to the microarray hybridization chamber (Agilent Technologies) and incubated at 65°C for 17 hours with 10 RPM rotation. Following hybridization, microarrays were washed using Gene Expression Wash Buffer (Agilent Technologies).

scan_protocol: Arrays were scanned on an Agilent C scanner at 5 um using the XDR function at 10%. The images were then feature extracted using Agilent Feature Extraction version 10.5.1.1 using the GE2_105_Jan09 extraction protocol.

data_processing: Data were loess and scale normalized and analyzed for differential expression using limma. Linear models were fitted to the data to compare the MtuR mutant with the wild-type 0140J strain at both early and late logarithmic growth phases. The resultant p-values were adjusted for the false discovery rate. Genes were considered to be differentially expressed if the difference between the two strains was greater than 4 fold by analysis of the duplicate probes for each gene, and the comparison of the data sets preferentially showed an adjusted P-value of <0.001.

organism: Streptococcus uberis

source_name: bacterial RNA, MtuR, late exponential growth phase

label_protocol: Fluorescently labeled probes for microarray hybridization were generated from 500ng total RNA using the MessageAmp II-Bacteria RNA amplification kit (Ambion) according to the manufacturer’s instructions. A total of 5µg of the resulting amplified antisense RNA (aRNA) was purified using the RNeasy minElute clean up kit (Qiagen), and hybridisation was performed using the Gene expression hybridization kit (Agilent). Samples were labeled with either Cy3 or Cy5 NHS ester reactive dyes (GE healthcare) according to the manufacturer’s instructions.

growth_protocol: Aliquots (30-60ml) of either S. uberis 0140J or MtuR mutant cultures were grown in Todd Hewit Broth (THB) with the addition of 1mM manganese at 37°C. Cultures were harvested at OD550nm of 0.43 for early logarithmic or OD550nm of 0.78 for late logarithmic growth phases.

extract_protocol: Total RNA was extracted by resuspension of cells in 1ml of RLT buffer (Qiagen) containing 1% (v/v) β-mercaptoethanol (Sigma-Aldrich). Cells were mechanically disrupted in a Mini-beadbeater-8 (Biospec) using acid-washed glass beads (Sigma). Following disruption, glass beads and cell debris were removed by centrifugation (17,000 × g, 10 sec). Supernatants were removed and mixed with an equal volume of 70% ethanol. Total RNA was extracted using an RNeasy column (Qiagen) according to the manufacturer’s instructions, with RNA finally eluted in 50µl of nuclease-free water. Contaminating DNA was removed from samples by DNase treatment using the DNA-free™ DNase Treatment kit (Ambion), and the resulting samples were further purified by ethanol precipitation.

treatment_protocol: Two volumes of RNAprotect Bacterial Reagent (Qiagen) were immediately added to each sample, and the samples were incubated for 5 min at room temp. Samples were centrifuged (5,000 × g, 10 min), the supernatant was discarded and the cell pellets were stored at -80°C until RNA extraction was performed.

tag: background/strain

value: MtuR mutant

tag: growth phase

value: late exponential

tag: replicate

source_name: bacterial RNA, 0140J, late exponential growth phase

value: wild-type


title: DCs_normoxia_HIF1A-silenced_A.fumigatus-stimulated_rep2

description:
DC_norm_si_AF_rep2
E13R019b04.CEL

tag: cell type

value: human monocyte-derived dendritic cells


title: DCs_normoxia_HIF1A-silenced_unstimulated_rep3

description:
DC_norm_si_unst_rep3
E13R019c03.CEL

source_name: unstimulated, HIF-1α silenced dendritic cells, normoxia


title: S. uberis 0140J_late exp_1 vs. MtuR mutant_late exp_3

description: Array 1_5


title: Hepatocellular adenoma 3433

value: liver tumor

tag: strain

value: 11 months

value: male


title: Hepatocellular adenoma 1895 swap

tag: genotype

value: liver


title: MtuR mutant_early exp_3 vs. S. uberis 0140J_early exp_2

description: Array 1_2

source_name: bacterial RNA, MtuR, early exponential growth phase

tag: genotype/variation

value: early exponential

source_name: bacterial RNA, 0140J, early exponential growth phase


title: P43T03

description:
in vivo
SAMPLE 77

value: patients with multi-system trauma (ISS ≥ 17 points)

value: patients with systemic inflammation without infection

value: day 3 after trauma


title: DCs_normoxia_HIF1A-silenced_unstimulated_rep2

description:
DC_norm_si_unst_rep2
E13R019b03.CEL

tag: stimulated with


title: MtuR mutant_late exp_1 vs. S. uberis 0140J_late exp_2

description: Array 1_6


title: DCs_normoxia_HIF1A-silenced_unstimulated_rep1

description:
DC_norm_si_unst_rep1
E13R019a03.CEL

tag: culture condition


title: AR1189_02

city: sakura

first: Hideaki

last: Bujo

address: 564-1 shimoshizu

country: Japan

institute: Toho University Sakura hospital

description: Gene expression after HFD 4w

hyb_protocol: 0.6ug of Cy3-labelled cRNA was then fragmented at 60°C for 30 min in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Mouse GE 8x60K Microarray for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 min at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute at 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565CA) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green PMT to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: WT BAT

label_protocol: Cyanine-3 (Cy3)-labeled cRNA was prepared from 0.1ug total RNA using the Low Input Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

growth_protocol: C57Bl6/J mice were purchased from Charles River. Lr11 -/- mice were generated as previously described on a C57Bl6/J background and compared to wild-type littermates.

extract_protocol: All animal tissues for RNA extraction were snap frozen in liquid nitrogen at the time of collection abd later ground to a fine powder using a sterile pestle and mortar on liquid nitrogen.

treatment_protocol: High Fat Diet (HFD) was administered ad-libitum from weaning. HFD consisted of 60% calories from fat (D12492, Research Diets, NJ, USA)

value: wild type

value: brown adipose


title: P43T00

description:
in vivo
SAMPLE 74

extract_protocol:
Blood was drawn before ICU admission and prepared with  PAXgene reagent (PreAnalytix®, Qiagen, Hilden, Germany). 0,75 µg cRNA of each sample was hybridized on a Human-HT-12-V4  Expression BeadChips from Illumina®. Amplification of RNA was in agreement to the protocol of the Illumina® for the BeadArray Reader 500 X.
Blood was drawn on (D0) and after admission (D1-D21) and prepared with PAXgene reagent (PreAnalytix®, Qiagen, Hilden, Germany). 200ng of total RNA of each sample were reversely transcribed and amplified using the TargetAmp-Nano Labeling Kit for Illumina Expression BeadChips (Epicentre, Biozym, Hessisch Oldendorf) a Biorad MJ Thermal Cycler (Biorad, München). All cRNA samples were quantified with a NanoDrop spectrophotometer (Nanodrop-Technologies) before proceeding to sample hybridization. Samples were prepared for hybridization according to the Illumina WGGEX Direct Hybridization Assay Guide (Illumina).

tag: subject id

value: within the first 6 h after trauma (day 0)

value: circulating leukocytes


title: DCs_normoxia_HIF1A-silenced_A.fumigatus-stimulated_rep1

description:
DC_norm_si_AF_rep1
E13R019a04.CEL

value: HIF-1α silenced

value: inactivated germ tubes of A. fumigatus

value: normoxia


title: Hepatocellular carcinoma 3548

value: 13.5 months

value: female


title: AR1189_09

description: Gene expression after HFD 4w


title: DCs_normoxia_nonsilenced_A.fumigatus-stimulated_rep3

description:
DC_norm_ns_AF_rep3
E13R019c02.CEL

source_name: A. fumigatus stimulated, non-silenced dendritic cells, normoxia

value: human monocyte-derived dendritic cells

value: HIF-1α non-silenced


title: P42T21

description:
in vivo
SAMPLE 73

tag: subject status

value: male

value: patients with secondary sepsis after trauma

value: day 21 after trauma


title: AR1189_04

description: Gene expression after HFD 4w

source_name: Lr11 -/- BAT

tag: gender


title: P43T01

description:
in vivo
SAMPLE 75

value: patients with multi-system trauma (ISS ≥ 17 points)

tag: subject subgroup

value: day 1 after trauma


title: P42T14

description:
in vivo
SAMPLE 72

tag: time point

value: day 14 after trauma


title: AR1189_03

description: Gene expression after HFD 4w

tag: tissue


title: S. uberis 0140J_early exp_1 vs. MtuR mutant_early exp_2

description: Array 1_1

value: wild-type

value: early exponential

value: MtuR mutant


title: AR0964_17

description: Gene expression after HFD 4w

value: brown adipose


title: AR0964_16

description: Gene expression after HFD 4w

value: wild type


title: P42T10

description:
in vivo
SAMPLE 71

value: day 10 after trauma

value: circulating leukocytes


title: AR1189_06

description: Gene expression after HFD 4w

source_name: WT scWAT

value: white adipose


title: DCs_normoxia_nonsilenced_A.fumigatus-stimulated_rep2

description:
DC_norm_ns_AF_rep2
E13R019b02.CEL

value: inactivated germ tubes of A. fumigatus

value: normoxia


title: P42T07

description:
in vivo
SAMPLE 70

value: day 7 after trauma


title: AR1189_07

description: Gene expression after HFD 4w

source_name: Lr11 -/- scWAT

value: male


title: AR1189_08

description: Gene expression after HFD 4w


title: Wild type, bio rep 3

city: Baltimore

first: Arnob

last: Banerjee

state: MD

address: 20 Penn St

institute: University of Maryland Baltimore

description:
Gene expression data from MEP cells from C57BL/6 mice
WT C57BL/6 3

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Gene 2.0 ST Arrays. GeneChips were washed and stained in the Affymetrix GeneChip Fluidiics Station 450.

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

data_processing: The data were analyzed with Affymetrix Expression Console software version 1.4.1.46, using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: C57BL/6 MEP cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA.

extract_protocol: RNA was extracted using RNAqueous (Ambion) per manufacturers instructions.

treatment_protocol: MEP cells were labeled with fluorochrome conjugated antibodies and sorted from fresh whole bone marrow by flow cytometric cell sorting.

value: Wild type

value: bone marrow megakaryoerythroid progenitor cells


title: AR0964_14

description: Gene expression after HFD 4w


title: Wild-type, bio rep 2

description:
Gene expression data from MEP cells from C57BL/6 mice
WT C57BL/6 2

value: Wild-type


title: P42T03

description:
in vivo
SAMPLE 68

value: patients with multi-system trauma (ISS ≥ 17 points)

value: patients with secondary sepsis after trauma

value: day 3 after trauma


title: AR0964_15

description: Gene expression after HFD 4w


title: DCs_normoxia_nonsilenced_A.fumigatus-stimulated_rep1

description:
DC_norm_ns_AF_rep1
E13R019a02.CEL

value: human monocyte-derived dendritic cells

value: HIF-1α non-silenced


title: AR1189_05

description: Gene expression after HFD 4w


title: T-bet knockout, bio rep 2

description:
Gene expression data from MEP cells from T-bet knockout mice
T-bet KO 2

source_name: T-bet deficient MEP cells

value: T-bet knockout


title: 15-08-042-0

city: Aurora

first: David

last: Schwartz

state: CO

address: Anschutz Medical Campus

department: Medicine

institute: University of Colorado, Anschutz Medical Campus

description: bisulfite

hyb_protocol: standard Illumina protocol

scan_protocol: standard Illumina protocol

data_processing: SWAN normalization method

source_name: nasal-epithelium

label_protocol: DNA was bisulfite converted using the EZ DNA Methylation-Gold Kit (Zymo) followed by labeling following Illumina protocol

extract_protocol: Allprep kit (Qiagen) for DNA and RNA

value: nasal-epithelium

tag: asthma

value: FALSE

tag: lnige

value: Female

value: No

value: Yes

tag: site

value: Washington D.C.


title: P42T01

description:
in vivo
SAMPLE 66

value: day 1 after trauma

value: circulating leukocytes


title: DCs_normoxia_nonsilenced_unstimulated_rep1

description:
DC_norm_ns_unst_rep1
E13R019a01.CEL

source_name: unstimulated, non-silenced dendritic cells, normoxia

value: normoxia


title: P42T05

description:
in vivo
SAMPLE 69

value: male

value: day 5 after trauma


title: P42T00

description:
in vivo
SAMPLE 65

value: patients with multi-system trauma (ISS ≥ 17 points)

value: within the first 6 h after trauma (day 0)


title: Wild-type, bio rep 1

description:
Gene expression data from MEP cells from C57BL/6 mice
WT C57BL/6 1

value: Wild-type

value: bone marrow megakaryoerythroid progenitor cells


title: T-bet knockout, bio rep 1

description:
Gene expression data from MEP cells from T-bet knockout mice
T-bet KO 1


title: IRF4-5

city: New York

first: Ulf

last: Klein

state: NY

address: 1130 St. Nicholas Avenue

department: Herbert Irving Comprehensive Cancer Center

institute: Columbia University

description: Gene expression data

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Mouse Genome 430 2.0 Gene Expression Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: B lymphocytes

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA.

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

treatment_protocol: B cells from 12-week old irf4-/- and irf4+/+ littermate mice were isolated by magnetic depletion of non-B cells from splenic mononuclear cells and cultured for 3 days in RPMI+10%FBS with 1mg/ml anti-mouse CD40 antibody and 20ng/ml IL-4

value: MACS-purified mature B cells

tag: treatment

value: stimulated in vitro with CD40+IL-4


title: P36T21

description:
in vivo
SAMPLE 64

value: patients with secondary sepsis after trauma

value: day 21 after trauma


title: IRF4-3

description: Gene expression data


title: P36T14

description:
in vivo
SAMPLE 63

value: day 14 after trauma


title: 15-08-035-5

description: bisulfite

value: nasal-epithelium

value: TRUE

value: Male

tag: age

value: No


title: T-bet knockout, bio rep 3

description:
Gene expression data from MEP cells from T-bet knockout mice
T-bet KO 3

value: T-bet knockout

tag: cell type


title: IRF4-2

description: Gene expression data

tag: strain


title: DCs_normoxia_nonsilenced_unstimulated_rep3

description:
DC_norm_ns_unst_rep3
E13R019c01.CEL

value: human monocyte-derived dendritic cells

value: HIF-1α non-silenced

value: normoxia


title: 15-08-036-4

description: bisulfite

value: FALSE

value: Female

value: Yes

value: Washington D.C.


title: DCs_normoxia_nonsilenced_unstimulated_rep2

description:
DC_norm_ns_unst_rep2
E13R019b01.CEL


title: P42T02

description:
in vivo
SAMPLE 67

value: patients with multi-system trauma (ISS ≥ 17 points)

value: male

value: day 2 after trauma

value: circulating leukocytes


title: 15-08-034-0

description: bisulfite


title: IRF4-4

description: Gene expression data

value: MACS-purified mature B cells

value: stimulated in vitro with CD40+IL-4


title: P36T10

description:
in vivo
SAMPLE 62

value: patients with secondary sepsis after trauma

value: day 10 after trauma


title: WT-3

description: Gene expression data


title: IRF4-1

description: Gene expression data


title: WT-5

description: Gene expression data


title: WT-4

description: Gene expression data


title: WT-1

description: Gene expression data


title: P36T05

description:
in vivo
SAMPLE 60

value: day 5 after trauma


title: WT-2

description: Gene expression data


title: P36T03

description:
in vivo
SAMPLE 59

value: day 3 after trauma


title: P36T07

description:
in vivo
SAMPLE 61

value: day 7 after trauma


title: CD8-Control-BiologicalReplicate3

city: Seattle

first: Matthias

last: Stephan

state: WA

address: 1100 Fairview Ave. N.

department: Program in Immunology

institute: Fred Hutchinson Cancer Research Center

hyb_protocol: The fragmented cRNA is added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control), and hybridized to a microarray chip overnight at 45°C. The hybridization solution is then removed.  The chips are transferred to a fluidics instrument that performs washes to remove cRNA that has not hybridized to its complementary oligonucleotide probe. The bound cRNA is then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors are then added using biotinylated anti-streptavidin antibody and additional SAPE.

scan_protocol: Each cRNA bound at its complementary oligonucleotide is excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions are captured.

data_processing: Array normalization and expression value calculation were performed using DNA-Chip Analyzer (www.dchip.org; Li & Wong 2001a)

source_name: CD8 T cells transduced with empty Plko.3g lentiviral vector

label_protocol: 1 ug RNA is converted into cDNA using a T7 promoter-tailed oligo-dT primer in the synthesis of the first cDNA strand; second strand cDNA synthesis is then carried out.  The double-stranded cDNA is used as the template in an in vitro transcription (IVT) reaction catalyzed by T7 polymerase and containing biotinylated CTP and UTP in addition to the four unmodified ribonucleoside triphosphates.  The biotinylated complementary RNA (cRNA) is purified from the IVT reaction mixture using magnetic particles. The purified cRNA is fragmented in order to facilitate the subsequent hybridization step.

growth_protocol: Negatively selected CD8 T cells were expanded in vitro with Il-7 and Il-15 in RPMI media containing 10% FCS for 2 days

extract_protocol: Trizol RNA preperation, followed by Qiagen Rneasy column cleanup according to manufacturer's instructions.

treatment_protocol: Cells were transduved  with control or pre-miR31 expressing lentiviral vectors,  cultured in IL-2 for 3 days, then infected cells were sorted by expression of GFP marker.

value: OT-I TCR transgenic

value: CD8 T-cells

tag: transduced

value: empty Plko.3g lentiviral vector


title: P36T02

description:
in vivo
SAMPLE 58


title: 15-08-025-8

description: bisulfite

value: nasal-epithelium

value: FALSE

value: Female

value: No


title: 15-08-028-9

description: bisulfite

value: TRUE

value: Male

value: Yes

value: Washington D.C.


title: P36T01

description:
in vivo
SAMPLE 57

value: patients with multi-system trauma (ISS ≥ 17 points)

value: male

value: day 1 after trauma

value: circulating leukocytes


title: 15-08-026-2

description: bisulfite


title: CD8-miR31-BiologicalReplicate2

source_name: CD8 T cells transduced with pre-miR-31 expressing Plko.3g lentiviral vector

tag: genotype/variation


title: CD8-Control-BiologicalReplicate2


title: 15-08-023-6

description: bisulfite


title: 15-08-027-0

description: bisulfite


title: P36T00

description:
in vivo
SAMPLE 56

value: patients with secondary sepsis after trauma

value: within the first 6 h after trauma (day 0)


title: CD8-miR31-BiologicalReplicate3

value: OT-I TCR transgenic

value: pre-miR-31 expressing Plko.3g lentiviral vector


title: 15-08-011-3

description: bisulfite


title: 15-08-017-8

description: bisulfite


title: 15-08-012-1

description: bisulfite


title: CD8-miR31-BiologicalReplicate1

value: CD8 T-cells


title: P35T14

description:
in vivo
SAMPLE 55

source_name: P35_Systemic Inflammation

value: patients with systemic inflammation without infection

value: day 14 after trauma


title: HBL1 ND-2158 vs ND-1659 - 24 hours - mAdbID:125747

city: Bethesda

first: Louis

middle: M.

last: Staudt

address: 9000 Rockville Pike, Bldg 10, Rm 4N114

department: Lymphoid Malignancies Branch

institute: National Cancer Institute

description: mAdb experiment ID: 125747

hyb_protocol: Agilent Hybridization Other: According to the manufacture's recommended protocol (Two-Color Microarray-Based Gene Expression Analysis, Agilent).

scan_protocol: Scan_MicronsPerPixelX: 5 Scan_MicronsPerPixelY: 5 Scan_ScannerName: Agilent Technologies Scanner G2505C US45102888

data_processing:
Agilent Data Processing Protocol
Calculation Method: Images were auto gridded, analyzed and data extracted using Agilent Feature Extraction Software. Spot values were normalized using the default linear-lowess normalization.
FeatureExtractor_Version: 10.1.1.1
Protocol_Name: GE2-v5_10_Apr08 (Read Only)

source_name: HBL1 ND-2158 Treated - 24 hours

label_protocol:
Agilent Labeling-Cy5
Other: Total RNA was reverse transcribed to cDNA using T7 Promoter Primer and MMLV-RT. Then the cDNA was converted to aRNA polymerase, which simultaneously amplifies target material and incorporates cyanine 3- or cyanine 5-labeled CTP (Two-Color Microarray-Based Gene Expression Analysis Protocol, Agilent).

extract_protocol:
TRIzol and RNeasy Kit
Other: Total RNA was prepared by TRIzol (Invitrogen) extraction followed by clean-up using the RNeasy kit (Qiagen).

treatment_protocol:
Treatment type: small molecule
Agent: ND-2158
Treatment dose: 10 uM
Treatment time: 24 hours

tag: cell line

value: ABC DLBCL cells

tag: disease state

value: activated B cell-like (ABC) subtype of diffuse large B cell lymphoma (DLBCL)

source_name: HBL1 ND-1659 Control Treated - 24 hours

label_protocol:
Agilent Labeling-Cy3
Other: Total RNA was reverse transcribed to cDNA using T7 Promoter Primer and MMLV-RT. Then the cDNA was converted to aRNA polymerase, which simultaneously amplifies target material and incorporates cyanine 3- or cyanine 5-labeled CTP (Two-Color Microarray-Based Gene Expression Analysis Protocol, Agilent).

treatment_protocol:
Treatment type: small molecule
Agent: ND-1659
Treatment dose: 10 uM
Treatment time: 24 hours


title: 15-08-013-2

description: bisulfite

value: nasal-epithelium

value: FALSE

value: No


title: 15-08-018-4

description: bisulfite

value: TRUE

value: Female

value: Yes

value: Washington D.C.


title: P35T07

description:
in vivo
SAMPLE 53

tag: subject id

value: patients with multi-system trauma (ISS ≥ 17 points)

value: male

value: day 7 after trauma

value: circulating leukocytes


title: 15-08-020-4

description: bisulfite


title: P35T05

description:
in vivo
SAMPLE 52

tag: subject status

value: day 5 after trauma


title: OCI-Ly3 ND-2158 vs ND-1659 - 6 hours - mAdbID:125774

description: mAdb experiment ID: 125774

source_name: OCI-Ly3 ND-2158 Treated - 6 hours

treatment_protocol:
Treatment type: small molecule
Agent: ND-2158
Treatment dose: 10 uM
Treatment time: 6 hours

source_name: OCI-Ly3 ND-1659 Control Treated - 6 hours

treatment_protocol:
Treatment type: small molecule
Agent: ND-1659
Treatment dose: 10 uM
Treatment time: 6 hours


title: CD8-Control-BiologicalReplicate4

value: OT-I TCR transgenic

value: CD8 T-cells

value: empty Plko.3g lentiviral vector


title: HBL1 ND-2158 vs ND-1659 - 36 hours - mAdbID:125748

description: mAdb experiment ID: 125748

source_name: HBL1 ND-2158 Treated - 36 hours

treatment_protocol:
Treatment type: small molecule
Agent: ND-2158
Treatment dose: 10 uM
Treatment time: 36 hours

value: ABC DLBCL cells

source_name: HBL1 ND-1659 Control Treated - 36 hours

treatment_protocol:
Treatment type: small molecule
Agent: ND-1659
Treatment dose: 10 uM
Treatment time: 36 hours


title: OCI-Ly10 ND-2158 vs ND-1659 - 12 hours - mAdbID:125742

description: mAdb experiment ID: 125742

source_name: OCI-Ly10 ND-2158 Treated - 12 hours

treatment_protocol:
Treatment type: small molecule
Agent: ND-2158
Treatment dose: 10 uM
Treatment time: 12 hours

value: activated B cell-like (ABC) subtype of diffuse large B cell lymphoma (DLBCL)

source_name: OCI-Ly10 ND-1659 Control Treated - 12 hours

treatment_protocol:
Treatment type: small molecule
Agent: ND-1659
Treatment dose: 10 uM
Treatment time: 12 hours


title: OCI-Ly3 ND-2158 vs ND-1659 - 24 hours - mAdbID:125776

description: mAdb experiment ID: 125776

source_name: OCI-Ly3 ND-2158 Treated - 24 hours

source_name: OCI-Ly3 ND-1659 Control Treated - 24 hours


title: P35T03

description:
in vivo
SAMPLE 51

tag: gender

value: patients with systemic inflammation without infection

value: day 3 after trauma


title: CD8-miR31-BiologicalReplicate4

value: pre-miR-31 expressing Plko.3g lentiviral vector


title: OCI-Ly3 ND-2158 vs ND-1659 - 12 hours - mAdbID:125775

description: mAdb experiment ID: 125775

source_name: OCI-Ly3 ND-2158 Treated - 12 hours

source_name: OCI-Ly3 ND-1659 Control Treated - 12 hours


title: OCI-Ly3 ND-2158 vs ND-1659 - 36 hours - mAdbID:125777

description: mAdb experiment ID: 125777

source_name: OCI-Ly3 ND-2158 Treated - 36 hours

source_name: OCI-Ly3 ND-1659 Control Treated - 36 hours


title: CD8-Control-BiologicalReplicate1

source_name: CD8 T cells transduced with empty Plko.3g lentiviral vector


title: OCI-Ly10 ND-2158 vs ND-1659 - 24 hours - mAdbID:125743

description: mAdb experiment ID: 125743

source_name: OCI-Ly10 ND-2158 Treated - 24 hours

source_name: OCI-Ly10 ND-1659 Control Treated - 24 hours


title: HBL1 ND-2158 vs ND-1659 - 6 hours - mAdbID:125745

description: mAdb experiment ID: 125745

source_name: HBL1 ND-2158 Treated - 6 hours

source_name: HBL1 ND-1659 Control Treated - 6 hours


title: HBL1 ND-2158 vs ND-1659 - 12 hours - mAdbID:125746

description: mAdb experiment ID: 125746

source_name: HBL1 ND-2158 Treated - 12 hours

source_name: HBL1 ND-1659 Control Treated - 12 hours


title: OCI-Ly10 ND-2158 vs ND-1659 - 6 hours - mAdbID:125741

description: mAdb experiment ID: 125741

source_name: OCI-Ly10 ND-2158 Treated - 6 hours

source_name: OCI-Ly10 ND-1659 Control Treated - 6 hours


title: 15-08-003-4

description: bisulfite

source_name: nasal-epithelium

value: nasal-epithelium

value: FALSE

value: Male

value: No


title: TMD8 ND-2158 vs ND-1659 - 36 hours - mAdbID:125693

description: mAdb experiment ID: 125693

source_name: TMD8 ND-2158 Treated - 36 hours

source_name: TMD8 ND-1659 Control Treated - 36 hours


title: TMD8 ND-2158 vs ND-1659 - 12 hours - mAdbID:125691

description: mAdb experiment ID: 125691

source_name: TMD8 ND-2158 Treated - 12 hours

source_name: TMD8 ND-1659 Control Treated - 12 hours


title: S. uberis 0140J_early exp_3 vs. MtuR mutant_early exp_1

description: Array 1_3

source_name: bacterial RNA, 0140J, early exponential growth phase

tag: background/strain

value: wild-type

tag: growth phase

value: early exponential

tag: replicate

source_name: bacterial RNA, MtuR, early exponential growth phase

value: MtuR mutant


title: OCI-Ly10 ND-2158 vs ND-1659 - 36 hours - mAdbID:125744

description: mAdb experiment ID: 125744

source_name: OCI-Ly10 ND-2158 Treated - 36 hours

source_name: OCI-Ly10 ND-1659 Control Treated - 36 hours


title: TMD8 ND-2158 vs ND-1659 - 24 hours - mAdbID:125692

description: mAdb experiment ID: 125692

source_name: TMD8 ND-2158 Treated - 24 hours

source_name: TMD8 ND-1659 Control Treated - 24 hours


title: P35T01

description:
in vivo
SAMPLE 49

source_name: P35_Systemic Inflammation

value: patients with multi-system trauma (ISS ≥ 17 points)

value: male

tag: subject subgroup

tag: time point

value: day 1 after trauma

value: circulating leukocytes


title: P35T02

description:
in vivo
SAMPLE 50

value: day 2 after trauma


title: XX329, biological rep 3

city: changchun

first: bao

last: qi

state: jilin province

address: 5268, renmindajie

country: China

institute: northeast normal university

description:
XX329-3
Gene expression data from leaf of resynthesized allohexaploid wheat using Extracted tetra as maternal parent

hyb_protocol: Followed Expression Analysis Technical Manual, 2001, Affymetrix.

data_processing: The raw CEL data were normalized with the Robust Multichip Average (RMA) method using the R software 'limma' package. Genes that were differentially expressed among genotypes were identified by performing a t-moderated test ebayes (P value<0.05).

organism: Triticum aestivum

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: All plants were grown in chambers under controlled conditions at 24/20°C day/night of 16 h day-length.

tag: tissue

value: leaf


title: XX329 mix, biological rep 3

description:
XX329 mix-3
Gene expression data from leaf RNA mix by Extracted tetra (2/3) and TQ18(1/3)

scan_protocol: Followed Expression Analysis Technical Manual, 2001, Affymetrix.


title: P34T10

description:
in vivo
SAMPLE 45

source_name: P34_Systemic Inflammation

value: female

value: day 10 after trauma


title: P34T21

description:
in vivo
SAMPLE 47

value: patients with systemic inflammation without infection

value: day 21 after trauma


title: 15-07-034-1

description: bisulfite

value: nasal-epithelium

tag: asthma

tag: lnige

value: Female

value: Yes

tag: site

value: New York


title: 15-08-008-1

description: bisulfite

value: FALSE

tag: age

value: No

value: Washington D.C.


title: XX329 mix, biological rep 1

description:
XX329 mix-1
Gene expression data from leaf RNA mix by Extracted tetra (2/3) and TQ18(1/3)


title: P34T14

description:
in vivo
SAMPLE 46

value: patients with multi-system trauma (ISS ≥ 17 points)

value: day 14 after trauma

tag: cell type


title: 15-07-029-2

description: bisulfite


title: TTR13, biological rep 2

description:
TTR13-2
Gene expression data from leaf of T. turgidum ssp. durum

organism: Triticum turgidum subsp. durum

source_name: leaf of T. turgidum ssp. durum


title: XX329, biological rep 2

description:
XX329-2
Gene expression data from leaf of resynthesized allohexaploid wheat using Extracted tetra as maternal parent


title: XX329 mix, biological rep 2

description:
XX329 mix-2
Gene expression data from leaf RNA mix by Extracted tetra (2/3) and TQ18(1/3)


title: P35T10

description:
in vivo
SAMPLE 54

value: male


title: XX329, biological rep 1

description:
XX329-1
Gene expression data from leaf of resynthesized allohexaploid wheat using Extracted tetra as maternal parent


title: 15-08-002-3

description: bisulfite

value: TRUE


title: 15-08-007-5

description: bisulfite


title: 15-07-030-2

description: bisulfite


title: TTR13, biological rep 3

description:
TTR13-3
Gene expression data from leaf of T. turgidum ssp. durum


title: TMD8 ND-2158 vs ND-1659 - 6 hours - mAdbID:125690

description: mAdb experiment ID: 125690

source_name: TMD8 ND-2158 Treated - 6 hours

value: ABC DLBCL cells

value: activated B cell-like (ABC) subtype of diffuse large B cell lymphoma (DLBCL)

source_name: TMD8 ND-1659 Control Treated - 6 hours


title: TTR13, biological rep 1

description:
TTR13-1
Gene expression data from leaf of T. turgidum ssp. durum

value: leaf


title: P35T00

description:
in vivo
SAMPLE 48

value: within the first 6 h after trauma (day 0)

value: circulating leukocytes


title: 15-07-023-7

description: bisulfite

value: Male


title: TQ18, biological rep 2

description:
TQ18-2
Gene expression data from leaf of Aegilops tauschii

organism: Aegilops tauschii

source_name: leaf of Aegilops tauschii


title: TQ18, biological rep 3

description:
TQ18-3
Gene expression data from leaf of Aegilops tauschii


title: P34T01

description:
in vivo
SAMPLE 40

value: female

value: patients with systemic inflammation without infection

value: day 1 after trauma


title: 15-07-021-6

description: bisulfite

source_name: nasal-epithelium

value: nasal-epithelium

value: Yes

value: New York


title: TAA10, biological rep 3

description:
TAA10-3
Gene expression data from leaf of T. aestivum

source_name: leaf of T. aestivum


title: TD265, biological rep 2

description:
TD265-2
Gene expression data from leaf of T. turgidum ssp. dicoccoides

organism: Triticum dicoccoides

source_name: leaf of T. turgidum ssp. dicoccoides


title: P34T07

description:
in vivo
SAMPLE 44

value: day 7 after trauma


title: P34T00

description:
in vivo
SAMPLE 39

value: patients with multi-system trauma (ISS ≥ 17 points)


title: P19T21

description:
in vivo
SAMPLE 38

source_name: P19_Systemic Inflammation

value: day 21 after trauma


title: 15-07-018-0

description: bisulfite

value: No


title: Chick-whole-lung-E18-rep3

first: Maria

last: Loscertales

state: Ma

address: 185 Cambridge St

department: Pediatric Surgery

institute: Massachusetts General Hospital

hyb_protocol: Samples were hybridized by Roche Applied Science as previously described by Nuwaysir et al. Genome Res. 2002 Nov;12(11):1749-55

scan_protocol: Samples were scanned by Roche Applied Science as previously described by Nuwaysir et al. Genome Res. 2002 Nov;12(11):1749-55

data_processing:
Microarray raw data was normalized by RMA (Robust Multi-array Analysis)
Data processing was performed by Roche Applied Science as previously described by Nuwaysir et al. Genome Res. 2002 Nov;12(11):1749-55

organism: Gallus gallus

source_name: Whole chick lung extract, embryonic day 18

label_protocol: Samples were labeled by Roche Applied Science as previously described by Nuwaysir et al. Genome Res. 2002 Nov;12(11):1749-55

growth_protocol: Timed fertilized white leghorn eggs (SPAFAS, CT, USA) were incubated in a humidified incubator (Khul, NJ) at 380 C and staged by embryonic day (E)

extract_protocol: Total RNA was isolated from embryonic chick lungs harvested at embryonic days E14, E15, E16, and E18; RNeasy Mini Kit (Quiagen; Valencia, CA, USA) was used to isolate total RNA

treatment_protocol: No treatment prior to lung harvesting

tag: breed

value: white leghorn

value: embryonic day 18

value: whole lung


title: TQ18, biological rep 1

description:
TQ18-1
Gene expression data from leaf of Aegilops tauschii

value: leaf


title: 15-07-020-0

description: bisulfite

value: TRUE


title: TD265, biological rep 1

description:
TD265-1
Gene expression data from leaf of T. turgidum ssp. dicoccoides


title: 15-08-024-3

description: bisulfite

value: FALSE

value: Washington D.C.


title: 15-06-008-0

description: bisulfite

value: Male

value: Detroit


title: TAA10, biological rep 1

description:
TAA10-1
Gene expression data from leaf of T. aestivum


title: P34T05

description:
in vivo
SAMPLE 43

value: female

value: patients with systemic inflammation without infection

value: day 5 after trauma

value: circulating leukocytes


title: TD265, biological rep 3

description:
TD265-3
Gene expression data from leaf of T. turgidum ssp. dicoccoides


title: P19T14

description:
in vivo
SAMPLE 37

value: male

value: day 14 after trauma


title: 15-07-013-3

description: bisulfite

value: nasal-epithelium

value: Female

value: Yes

value: New York


title: P34T02

description:
in vivo
SAMPLE 41

value: patients with multi-system trauma (ISS ≥ 17 points)

value: day 2 after trauma


title: Extracted-tetra, biological rep 3

description:
Extracted-tetra-3
Gene expression data from leaf of Extracted-tetra

organism: Triticum turgidum

source_name: leaf of Extracted-tetra

value: leaf


title: P34T03

description:
in vivo
SAMPLE 42

value: day 3 after trauma


title: Extracted-tetra, biological rep 1

description:
Extracted-tetra-1
Gene expression data from leaf of Extracted-tetra


title: 15-07-005-3

description: bisulfite

value: TRUE

value: No


title: TAA10, biological rep 2

description:
TAA10-2
Gene expression data from leaf of T. aestivum


title: Extracted-tetra, biological rep 2

description:
Extracted-tetra-2
Gene expression data from leaf of Extracted-tetra


title: P19T10

description:
in vivo
SAMPLE 36

value: day 10 after trauma


title: 15-06-006-7

description: bisulfite

value: Detroit


title: Chick-whole-lung-E18-rep2

value: white leghorn

value: embryonic day 18

value: whole lung


title: Blackbird, biological rep 1

description:
Blackbird-1
Gene expression data from leaf of T. turgidum ssp. carthlicum

organism: Triticum carthlicum

source_name: leaf of T. turgidum ssp. carthlicum


title: P19T01

description:
in vivo
SAMPLE 31

value: male

value: patients with systemic inflammation without infection

value: day 1 after trauma

value: circulating leukocytes


title: Chick-whole-lung-E16-rep3

source_name: Whole chick lung extract, embryonic day 16

value: embryonic day 16


title: P19T02

description:
in vivo
SAMPLE 32


title: Allo-960 mix, biological rep 2

description:
Allo-960 mix-2
Gene expression data from leaf RNA mix by Blackbird(2/3) and 30A(1/3)


title: 15-06-002-2

description: bisulfite

value: nasal-epithelium

value: Female

value: Yes


title: Allo-960 mix, biological rep 1

description:
Allo-960 mix-1
Gene expression data from leaf RNA mix by Blackbird(2/3) and 30A(1/3)

value: leaf


title: Blackbird, biological rep 2

description:
Blackbird-2
Gene expression data from leaf of T. turgidum ssp. carthlicum


title: Chick-whole-lung-E15-rep2

source_name: Whole chick lung extract, embryonic day 15

value: embryonic day 15


title: 15-05-032-3

description: bisulfite

value: TRUE

value: Denver


title: Chick-whole-lung-E16-rep1


title: 15-06-004-6

description: bisulfite

value: Male

value: No


title: P19T03

description:
in vivo
SAMPLE 33

value: patients with multi-system trauma (ISS ≥ 17 points)

value: day 3 after trauma


title: 15-05-037-5

description: bisulfite


title: 15-06-007-9

description: bisulfite

value: Detroit


title: P19T07

description:
in vivo
SAMPLE 35

value: male

value: day 7 after trauma


title: Chick-whole-lung-E18-rep1

value: white leghorn

value: embryonic day 18

value: whole lung


title: Chick-whole-lung-E15-rep3


title: P19T00

description:
in vivo
SAMPLE 30

value: patients with systemic inflammation without infection

value: within the first 6 h after trauma (day 0)

value: circulating leukocytes


title: Allo-960S7, biological rep 2

description:
Allo-960S7-2
Gene expression data from leaf of newly synthesized wheat Allo-960 at selfed generations 7

value: leaf


title: Blackbird, biological rep 3

description:
Blackbird-3
Gene expression data from leaf of T. turgidum ssp. carthlicum


title: Chick-whole-lung-E16-rep2

value: embryonic day 16


title: Allo-960 mix, biological rep 3

description:
Allo-960 mix-3
Gene expression data from leaf RNA mix by Blackbird(2/3) and 30A(1/3)


title: P19T05

description:
in vivo
SAMPLE 34

value: day 5 after trauma


title: 15-05-031-0

description: bisulfite

value: nasal-epithelium

value: FALSE

value: Yes

value: Denver


title: 15-05-024-9

description: bisulfite

value: TRUE

value: Male

value: No


title: Allo-960S7, biological rep 3

description:
Allo-960S7-3
Gene expression data from leaf of newly synthesized wheat Allo-960 at selfed generations 7


title: P17T21

description:
in vivo
SAMPLE 29

source_name: P17_Systemic Inflammation

value: patients with multi-system trauma (ISS ≥ 17 points)

value: male

value: day 21 after trauma


title: P17T14

description:
in vivo
SAMPLE 28

value: day 14 after trauma


title: Chick-whole-lung-E15-rep1

value: white leghorn

value: embryonic day 15

value: whole lung


title: Chick-whole-lung-E14-rep3

source_name: Whole chick lung extract, embryonic day 14

value: embryonic day 14


title: P17T07

description:
in vivo
SAMPLE 26

value: patients with systemic inflammation without infection

value: day 7 after trauma

value: circulating leukocytes


title: 15-05-022-0

description: bisulfite

value: nasal-epithelium

value: Female


title: Chick-whole-lung-E14-rep2


title: 15-05-012-6

description: bisulfite

value: Yes

value: Denver


title: P17T05

description:
in vivo
SAMPLE 25

value: day 5 after trauma


title: 30A, biological rep 3

description:
30A-3
Gene expression data from leaf of Aegilops tauschii

value: leaf


title: P17T10

description:
in vivo
SAMPLE 27

value: patients with multi-system trauma (ISS ≥ 17 points)

value: day 10 after trauma


title: Allo-960S7, biological rep 1

description:
Allo-960S7-1
Gene expression data from leaf of newly synthesized wheat Allo-960 at selfed generations 7


title: 15-05-006-4

description: bisulfite

value: FALSE

value: No


title: 15-05-005-5

description: bisulfite

value: TRUE

value: Male


title: 4T1-A2

city: Sapporo

first: Hirotake

last: ABE

state: Japan/Hokkaido

address: Kita15-Nishi7, Kitaku

department: Institute for Genetic Medicine

institute: Hokkaido University

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ml containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ml of 2x Agilent hybridization Buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent Mouse Gene Expression 4x44K Microarray Kit (G4122F) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to XDR Hi 100%, Lo 10%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v5_91_0806 and Grid: 014868_D_20060807) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Mouse breast cancer cell line

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng RNA using the Low Input Quick Amp. labeling kit, one-colot (Agilent) according to the manufacturer's instructions.

extract_protocol: RNA was prepared using the RNeasy Plus Mini kit (QIAGEN) following the manufacturer's recommendations. RNA was quantified using spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies).

tag: parental cell line


title: P17T03

description:
in vivo
SAMPLE 24

value: male

value: day 3 after trauma


title: Chick-whole-lung-E14-rep1

value: white leghorn

value: embryonic day 14

value: whole lung


title: 30A, biological rep 1

description:
30A-1
Gene expression data from leaf of Aegilops tauschii


title: 30A, biological rep 2

description:
30A-2
Gene expression data from leaf of Aegilops tauschii


title: 4T1-S2


title: 15-04-009-4

description: bisulfite

value: nasal-epithelium

value: Dallas


title: 15-05-004-0

description: bisulfite

value: Yes


title: 15-05-017-4

description: bisulfite

value: Denver


title: 4T1-S1


title: 4T1-A1


title: wt CD8 SP thymocytes II

city: Heidelberg

first: Fabian

last: Brunk

address: Im Neuenheimer Feld 280

institute: German Cancer Research Center

description: replicate 2 CD8 SP wt

scan_protocol: Scanning of the microarray was done by using a Beadstation array scanner; settings were adjusted to a scaling factor of 1 and PMT settings at 430. The data extraction was done for all beads individually and outliers were removed when > 2.5 MAD (median absolute deviation). All remaining data points were used for the calculation of the mean average signal for a given probe and the standard deviation for each probe was calculated.

data_processing: data were normalized using quantile normalization in R.

source_name: CD8 SP thymocytes

label_protocol: Biotin-labeled cRNA for hybridization was prepared according to Illumina`s recommended sample labeling procedure based on the modified Eberwine protocol (Eberwine et al. 1992). In brief, 200 ng total RNA was used for cDNA synthesis, followed by an in vitro transcription step for amplification and labeling to synthesize biotin-labelled cRNA using the MessageAmp II RNA amplification kit (Ambion) and biotin-16-UTP (Roche)

growth_protocol: primary mouse thymocytes isolated from thymi of young adult mice

extract_protocol: RNA was isolated using the QIAGEN RNeasy Plus Micro Kit according to the manufactor's instructions. Quality control was performed using the Agilent Bioanalyser.

treatment_protocol: conditional gene knock-out (FoxN1-Cre driven deletion of (Exon3 of) Gpr177/Wls)

value: 4-6 weeks

tag: strain

tag: genotype/variation

value: wt


title: P17T00

description:
in vivo
SAMPLE 21

tag: subject id

tag: subject status

value: patients with multi-system trauma (ISS ≥ 17 points)

value: patients with systemic inflammation without infection

value: within the first 6 h after trauma (day 0)

value: circulating leukocytes


title: P16T28

description:
in vivo
SAMPLE 20

tag: gender

value: female

value: patients with secondary sepsis after trauma

value: day 28 after trauma


title: 15-04-006-0

description: bisulfite

value: FALSE

value: Male

value: No


title: wt CD8 SP thymocytes III

description: replicate 3 CD8 SP wt


title: FoxN1-Gpr177 CD4 SP thymocytes III

description: replicate 3 CD4 SP cKO

source_name: CD4 SP thymocytes


title: FoxN1-Gpr177 CD8 SP thymocytes II

description: replicate 2 CD8 SP cKO


title: P17T02

description:
in vivo
SAMPLE 23

value: male

value: day 2 after trauma


title: ATLL cells_3 [exon level]

city: lyon

first: franck

last: mortreux

address: 46 allee d'Italie

institute: oncovirology and Biotherapies, UMR5239, LBMC

hyb_protocol: As per manufacturer (Affymetrix).

scan_protocol: The arrays were scanned using the GeneChip Scanner 3000. Then CEL files were generated using the Affymetrix GeneChip Command Console software (AGCC) 3.0.

data_processing:
Raw data were normalized using Partek Genomic Suite v.6.5 (Partek Incorporated, St. Louis, Missouri 63005): The normalization was performed using quantile method including RMA background correction and probe sequence adjustment.
Probe group file: HuEx-1_0-st-v2.r2.pgf
Meta-probeset file: HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

source_name: ATLL cells, no PHA

label_protocol: As per manufacturer (Affymetrix).

extract_protocol: RNA was extracted using Trizol/Glycogen reagent. RNA was quantified using a NanoDrop spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer.

treatment_protocol: T-cell clones, but not ATLL cells, were exposed or not to PHA.

value: monoclonal T-cell clone

tag: htlv1 infection

value: yes

tag: activated by pha

value: no


title: wt CD8 SP thymocytes I

description: replicate 1 CD8 SP wt

value: 4-6 weeks


title: P17T01

description:
in vivo
SAMPLE 22

treatment_protocol: High standard protocol.

tag: subject subgroup

value: day 1 after trauma


title: ATLL cells_2 [exon level]


title: ATLL cells_1 [exon level]


title: P16T21

description:
in vivo
SAMPLE 19

value: patients with multi-system trauma (ISS ≥ 17 points)

tag: time point

value: day 21 after trauma


title: FoxN1-Gpr177 CD4 SP thymocytes II

description: replicate 2 CD4 SP cKO


title: P16T14

description:
in vivo
SAMPLE 18

value: day 14 after trauma


title: ExVivo_TCD4+_HTLV1negative_5 [exon level]

source_name: ExVivo_TCD4+_HTLV1negative clone obtained by limiting dilution culture of PBMC of HTLV-1 carriers, PHA

tag: tissue


title: 15-04-003-9

description: bisulfite

value: nasal-epithelium

tag: asthma

value: TRUE

value: Yes

value: Dallas


title: P16T10

description:
in vivo
SAMPLE 17

value: female

value: patients with secondary sepsis after trauma

value: day 10 after trauma

value: circulating leukocytes


title: ExVivo_TCD4+_HTLV1negative_6 [exon level]

source_name: ExVivo_TCD4+_HTLV1negative clone obtained by limiting dilution culture of PBMC of HTLV-1 carriers, no PHA


title: FoxN1-Gpr177 CD4 SP thymocytes I

description: replicate 1 CD4 SP cKO


title: 15-02-053-1

description: bisulfite

source_name: nasal-epithelium

value: FALSE

tag: lnige

value: Male

value: No

value: Boston


title: 15-04-001-8

description: bisulfite

value: Female

tag: site


title: wt CD4 SP thymocytes III

description: replicate 3 CD4 SP wt

tag: age

value: 4-6 weeks

value: wt


title: 15-02-049-9

description: bisulfite


title: 15-02-047-5

description: bisulfite


title: ExVivo_TCD4+_HTLV1positive_2 [exon level]

source_name: ExVivo_TCD4+_HTLV1positive clone obtained by limiting dilution culture of PBMC of HTLV-1 carriers, no PHA

value: monoclonal T-cell clone

tag: cell type

value: yes

value: no


title: 15-04-005-6

description: bisulfite

value: nasal-epithelium

value: TRUE


title: ExVivo_TCD4+_HTLV1positive_1 [exon level]

source_name: ExVivo_TCD4+_HTLV1positive clone obtained by limiting dilution culture of PBMC of HTLV-1 carriers, PHA


title: P16T05

description:
in vivo
SAMPLE 15

value: patients with multi-system trauma (ISS ≥ 17 points)

value: day 5 after trauma


title: wt CD4 SP thymocytes II

description: replicate 2 CD4 SP wt


title: wt CD4 SP thymocytes I

description: replicate 1 CD4 SP wt


title: P16T07

description:
in vivo
SAMPLE 16

value: female

value: patients with secondary sepsis after trauma

value: day 7 after trauma


title: 15-02-041-0

description: bisulfite

value: FALSE

value: Yes


title: ExVivo_TCD4+_HTLV1positive_4 [exon level]


title: ExVivo_TCD4+_HTLV1positive_6 [exon level]


title: P16T02

description:
in vivo
SAMPLE 13

value: day 2 after trauma

value: circulating leukocytes


title: ExVivo_TCD4+_HTLV1positive_3 [exon level]


title: FoxN1-Gpr177 DP thymocytes II

description: replicate 2 DP cKO

source_name: DP thymocytes


title: P16T01

description:
in vivo
SAMPLE 12

value: day 1 after trauma


title: FoxN1-Gpr177 DP thymocytes III

description: replicate 3 DP cKO

value: 4-6 weeks


title: wt DP thymocytes III

description: replicate 3 DP wt

value: wt


title: P16T03

description:
in vivo
SAMPLE 14

value: day 3 after trauma


title: 15-02-035-8

description: bisulfite

value: Female

value: No

value: Boston


title: P09T26

description:
in vivo
SAMPLE 10

value: male

value: day 26 after trauma


title: ExVivo_TCD4+_HTLV1positive_5 [exon level]

value: monoclonal T-cell clone

value: yes

value: no


title: wt DP thymocytes I

description: replicate 1 DP wt


title: 15-02-030-4

description: bisulfite

value: nasal-epithelium


title: ExVivo_TCD4+_HTLV1negative_4 [exon level]


title: ExVivo_TCD4+_HTLV1negative_3 [exon level]


title: 15-02-038-9

description: bisulfite

value: TRUE


title: P09T14

description:
in vivo
SAMPLE 8

value: patients with multi-system trauma (ISS ≥ 17 points)

value: patients with secondary sepsis after trauma

value: day 14 after trauma


title: P16T00

description:
in vivo
SAMPLE 11

value: female

value: within the first 6 h after trauma (day 0)

value: circulating leukocytes


title: 15-02-028-7

description: bisulfite

value: FALSE

value: Yes


title: P09T21

description:
in vivo
SAMPLE 9

value: day 21 after trauma


title: wt DP thymocytes II

description: replicate 2 DP wt

value: 4-6 weeks

value: wt


title: P09T06

description:
in vivo
SAMPLE 6

value: male

value: day 6 after trauma


title: 15-02-040-6

description: bisulfite

value: Male

value: No

value: Boston


title: FoxN1-Gpr177 CD8 SP thymocytes I

description: replicate 1 CD8 SP cKO


title: 15-02-025-6

description: bisulfite

value: nasal-epithelium


title: ExVivo_TCD4+_HTLV1negative_1 [exon level]

value: monoclonal T-cell clone

value: no

value: yes


title: P09T05

description:
in vivo
SAMPLE 5

value: patients with multi-system trauma (ISS ≥ 17 points)

value: patients with secondary sepsis after trauma

value: day 5 after trauma


title: ExVivo_TCD4+_HTLV1negative_2 [exon level]


title: P09T10

description:
in vivo
SAMPLE 7

value: day 10 after trauma

value: circulating leukocytes


title: 15-02-015-3

description: bisulfite

value: TRUE

value: Female

value: Yes


title: 15-02-014-8

description: bisulfite

value: FALSE


title: 15-02-026-0

description: bisulfite


title: P09T01

description:
in vivo
SAMPLE 2

value: male

value: day 1 after trauma


title: HP035_4

city: Cambridge

first: Liam

last: Masterson

state: Cambridgeshire

address: Hills road

department: Pathology

institute: University of Cambridge

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R. The data were filtered before normalisation removing any probe with a detection p-value above 0.01 for all samples. If a probe is detected (detection p-value<0.01) in at least one sample it will be kept. This is done to remove non expressed probe and avoid adding to much noise during the normalisation process.

source_name: Invasive SCC

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

value: patients with primary oropharyngeal squamous cell carcinoma

tag: age (yrs)

tag: smoker status

value: Never

tag: performance status (ecog)

tag: subsite

value: Tongue base

tag: Stage

value: IV

tag: hpv status

value: Pos

value: invasive squamous cell carcinoma


title: 15-02-016-9

description: bisulfite

value: nasal-epithelium

tag: gender

value: Male

value: No

value: Boston


title: 15-02-019-5

description: bisulfite


title: P09T03

description:
in vivo
SAMPLE 4

tag: subject id

tag: subject status

value: patients with multi-system trauma (ISS ≥ 17 points)

value: patients with secondary sepsis after trauma

value: day 3 after trauma

value: circulating leukocytes


title: 15-02-017-6

description: bisulfite

value: TRUE

value: Yes


title: P09T00

description:
in vivo
SAMPLE 1

value: male

tag: subject subgroup

value: within the first 6 h after trauma (day 0)


title: 15-02-011-1

description: bisulfite

value: Female


title: P09T02

description:
in vivo
SAMPLE 3

tag: time point

value: day 2 after trauma


title: FoxN1-Gpr177 DP thymocytes I

description: replicate 1 DP cKO

value: 4-6 weeks

tag: strain

tag: genotype/variation


title: HP035_1

source_name: Normal epithelium

value: patients with primary oropharyngeal squamous cell carcinoma

value: Never

value: Tongue base

value: IV

value: Pos

tag: tissue

value: site-matched normal epithelial


title: keratinocytes, postnatal day 35, from genotype negative littermate, biological rep4

city: Huddinge

last: Eriksson

address: Hälsovägen 7

department: Biosciences and Nutrition

country: Sweden

institute: Karolinska Institutet

description: mouse ID: E925_07

hyb_protocol: A total of 5.5 μg of labeled and fragmented single-stranded cDNA was hybridized to the arrays and incubated in a 45º C oven for 16-18 hours, 60 rpm rotation (Affymetrix Gene Chip Hybridization Oven 640). Arrays were washed and stained using the FS450_0001 fluidic script (Affymetrix Gene Chip Fluidics Station 450)

scan_protocol: Scanning was performed by Affymetrix Gene Chip scanner 3000 7G.

data_processing:
The core meta probe set and control probes were analyzed in Partek Genomic Suite v.6.6 (Partek Inc., St. Louis, MO, USA). RMA background correction algorithm was selected and adjusted for GC content (GC-RMA). For the normalization of probe signals a quantile normalization and median polish probe set summarization was used and converted to log2 scale.
probe group file: MoEx-1_0-st-v1.r2.pgf
meta-probeset file: MoEx-1_0-st-v1.r2.dt1.mm9.core.mps

source_name: skin keratinocytes, postnatal day 24, from genotype negative littermate

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

growth_protocol: Mice were housed in the experimental animal facility with a 12-hour light/dark cycle, a temperature of 20-22°C and 50-75% air humidity (Karolinska Hospital, Huddinge, Sweden). They were supplied with R36 pellets (Lactamin, Sweden) and drinking water ad libitum and aged up to desired age.

extract_protocol: Mice were euthanized by cervical dislocation and the fur was trimmed before the skin was taken and placed into Ca2+ free PBS (d-PBS; Invitrogen). Subcutaneous tissue was removed, and the skin was floated on trypsin (T4424; Sigma-Aldrich) for 2 h at 32°C. After incubation, the epidermis was scraped into S-minimal essential medium (S-MEM; Invitrogen) supplemented with 0.01% soybean trypsin inhibitor (T9128; Sigma-Aldrich) and 0.5% BSA (bovine albumin fraction V solution (7.5%); Invitrogen) and gently mixed with a magnetic stirrer at room temperature for 20 min. The cell suspension was filtered through a 70-mm cell strainer (BD Falcon, Becton Dickinson, Franklin Lakes, NJ, USA), and viable cells were counted after staining with tryphan blue. Keratinocyte total RNA was thereafter  immediatel extracted with Trizol and RNA  integrity was assessed by the Agilent 2100 Bioanalyzer. The RNA quality criteria for proceeding with exon arrays were a 18S/28S ratio above 1.5 and an RNA integrity number (RIN-value) ≥ 8.0. For array hybridization and Whole Transcript Sense Target Labeling Synthesis, 200 ng of RNA was processed using the Gene Chip WT cDNA Synthesis Kit, (Affymetrix) (Rosengardten et al., 2011)

value: FVB/NCrl

value: skin

tag: age (days)

value: Male

tag: genotype

value: K5tTA-; tetop-LA G608G- (F1-line VF1-07)

tag: treatment

value: Drinking water was supplied with 100 μg ml−1 doxycycline (D9891; Sigma-Aldrich, St. Louis, MO, USA) and 2.5% sucrose during embryogenesis, which was replaced with normal water on postnatal day 0 (Rosengardten et al., 2011). Doxycyline treatment during embryogenesis keeps the transgene turned off.


title: HP034_1

hyb_protocol: Standard Illumina hybridization protocol

tag: age (yrs)

value: Tonsil


title: HP034_4

value: male

tag: smoker status

value: invasive squamous cell carcinoma


title: 15-02-013-0

description: bisulfite

value: nasal-epithelium

tag: asthma

value: FALSE

tag: lnige

tag: age

value: No

value: Yes

tag: site

value: Boston


title: 15-02-010-7

description: bisulfite

value: TRUE

tag: gender


title: keratinocytes, postnatal day 35, from genotype negative littermate, biological rep2

description: mouse ID: E924_05


title: keratinocytes, postnatal day 35, from genotype negative littermate, biological rep3

description: mouse ID: E925_04


title: HP032_4

value: patients with primary oropharyngeal squamous cell carcinoma

tag: subject id

value: Former

tag: performance status (ecog)

tag: subsite

value: Tongue base

tag: Stage

value: IV

tag: hpv status

value: Neg


title: keratinocytes, postnatal day 35, from genotype negative littermate, biological rep1

description: mouse ID: E924_02

tag: strain

value: FVB/NCrl

value: skin

value: Female


title: keratinocytes, postnatal day 35, from transgenic mouse expressing progerin and lamin A, biological rep4

description: mouse ID: E925_08

source_name: skin keratinocytes, postnatal day 24, from transgenic mouse expressing progerin and lamin A

tag: tissue

value: Male

value: K5tTA+; tetop-LA G608G+ (F1-line VF1-07)

value: Drinking water was supplied with 100 μg ml−1 doxycycline (D9891; Sigma-Aldrich, St. Louis, MO, USA) and 2.5% sucrose during embryogenesis, which was replaced with normal water on postnatal day 0 (Rosengardten et al., 2011). Doxycyline treatment during embryogenesis keeps the transgene turned off.


title: HP032_1

tag: subject status

value: male

value: site-matched normal epithelial


title: IMR32 cells_Control 2c_rep3

city: Verona

first: Alberto

last: Ferrarini

state: Veneto

address: Strada le Grazie, 15

department: Scientific and Technological Department

country: Italy

institute: University of Verona

hyb_protocol: Hybridization and washing procedures were performed according to the NimbleGen Arrays User’s Guide (V 5.1).

scan_protocol: Each microarray was scanned using an Axon GenePix 4400 A at 532 nm and GenePix Pro7 software (Molecular Devices, Sunnyvale, CA, USA).

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction.

source_name: IMR32 cells_Control 2c

label_protocol: cDNA synthesis and labeling reactions were performed according to the NimbleGen Arrays User’s Guide (V 5.1).

growth_protocol: Neuroblastoma cells adherent onto Petri dishes at standard density were collected  after mild treatment with Trypsin-PBS solution (5 mg/L).

extract_protocol: Total RNA was extracted from 3.5 x 106  cells with Qiagen RNAeasy Mini Kit (Qiagen S.p.A., Milan, Italy) following the manufacturer’s instructions (Animal cells Spin protocol), including genomic DNA elimination step in column.  The qualitative parameters A260/A280>1.8, A260/A230>1.7; RNA integrity number>7 were evaluated.

tag: cell line

value: IMR-32 (ATCC N. CCL-127)

tag: cell type

value: neuroblastoma


title: 15-02-020-2

description: bisulfite

value: nasal-epithelium

value: No

value: Yes

value: Boston


title: HP021_5

value: patients with primary oropharyngeal squamous cell carcinoma

tag: age (yrs)

value: Never

value: Tonsil

value: Pos

value: invasive squamous cell carcinoma


title: keratinocytes, postnatal day 35, from transgenic mouse expressing progerin and lamin A, biological rep2

description: mouse ID: E924_08

value: skin

tag: age (days)

tag: genotype

tag: treatment


title: 15-02-005-0

description: bisulfite

tag: asthma

value: TRUE

tag: lnige

value: Female

tag: age


title: HP030_1

tag: subject id

tag: gender

tag: smoker status

value: Tongue base

value: IV


title: keratinocytes, postnatal day 35, from transgenic mouse expressing progerin and lamin A, biological rep3

description: mouse ID: E925_06

value: Male

value: K5tTA+; tetop-LA G608G+ (F1-line VF1-07)

value: Drinking water was supplied with 100 μg ml−1 doxycycline (D9891; Sigma-Aldrich, St. Louis, MO, USA) and 2.5% sucrose during embryogenesis, which was replaced with normal water on postnatal day 0 (Rosengardten et al., 2011). Doxycyline treatment during embryogenesis keeps the transgene turned off.


title: IMR32 cells_Gelsemium 2c_rep3

source_name: IMR32 cells_Gelsemium 2c

value: IMR-32 (ATCC N. CCL-127)

value: neuroblastoma


title: 15-02-008-4

description: bisulfite

value: nasal-epithelium

value: FALSE

value: No

value: Yes

tag: site


title: IMR32 cells_Gelsemium 2c_rep2


title: keratinocytes, postnatal day 24, from genotype negative littermate, biological rep4

description: mouse ID: E952_05

value: FVB/NCrl

value: K5tTA-; tetop-LA G608G- (F1-line VF1-07)


title: HP021_1

value: patients with primary oropharyngeal squamous cell carcinoma

value: male

value: Never

tag: performance status (ecog)

tag: subsite

value: Tonsil

tag: Stage

tag: hpv status

value: Pos

value: site-matched normal epithelial


title: IMR32 cells_Gelsemium 2c_rep1

tag: cell line


title: IMR32 cells_Control 2c_rep2

tag: cell type


title: HP019_3

tag: subject status

tag: age (yrs)

value: female

value: III

tag: tissue

value: invasive squamous cell carcinoma


title: HP030_4

value: Tongue base

value: IV


title: keratinocytes, postnatal day 35, from transgenic mouse expressing progerin and lamin A, biological rep1

description: mouse ID: E924_07

tag: strain

value: skin

tag: age (days)

value: Male

tag: genotype

value: K5tTA+; tetop-LA G608G+ (F1-line VF1-07)

tag: treatment

value: Drinking water was supplied with 100 μg ml−1 doxycycline (D9891; Sigma-Aldrich, St. Louis, MO, USA) and 2.5% sucrose during embryogenesis, which was replaced with normal water on postnatal day 0 (Rosengardten et al., 2011). Doxycyline treatment during embryogenesis keeps the transgene turned off.


title: SHSY5Y cells_Control 30c_rep4

source_name: SHSY5Y cells_Control 30c

value: SHSY5Y (ATCC N. CRL-2266)

value: neuroblastoma


title: HP020_4

value: patients with primary oropharyngeal squamous cell carcinoma

tag: subject id

value: Current

value: Neg


title: IMR32 cells_Control 2c_rep1

value: IMR-32 (ATCC N. CCL-127)


title: keratinocytes, postnatal day 24, from genotype negative littermate, biological rep1

description: mouse ID: E952_07

value: FVB/NCrl

tag: gender

value: Female

value: K5tTA-; tetop-LA G608G- (F1-line VF1-07)


title: keratinocytes, postnatal day 24, from genotype negative littermate, biological rep3

description: mouse ID: E949_05


title: keratinocytes, postnatal day 24, from genotype negative littermate, biological rep2

description: mouse ID: E952_08


title: HP020_1

value: male

tag: smoker status

value: Tonsil

value: III

value: site-matched normal epithelial


title: HP019_2

value: female

value: Never

value: Pos


title: HP014_1

value: IV


title: SHSY5Y cells_Control 30c_rep2

value: SHSY5Y (ATCC N. CRL-2266)


title: HP017_2

value: Tongue base


title: HP017_3

value: patients with primary oropharyngeal squamous cell carcinoma

value: invasive squamous cell carcinoma


title: SHSY5Y cells_Control 5c_rep4

source_name: SHSY5Y cells_Control 5c

value: neuroblastoma


title: keratinocytes, postnatal day 24, from transgenic mouse expressing progerin and lamin A, biological rep2

description: mouse ID: E952_06

value: skin

value: K5tTA+; tetop-LA G608G+ (F1-line VF1-07)

value: Drinking water was supplied with 100 μg ml−1 doxycycline (D9891; Sigma-Aldrich, St. Louis, MO, USA) and 2.5% sucrose during embryogenesis, which was replaced with normal water on postnatal day 0 (Rosengardten et al., 2011). Doxycyline treatment during embryogenesis keeps the transgene turned off.


title: HP013_6


title: SHSY5Y cells_Control 30c_rep1


title: SHSY5Y cells_Control 30c_rep3


title: 15-02-039-1

description: bisulfite

value: nasal-epithelium

tag: asthma

value: FALSE

tag: lnige

value: Male

tag: age

value: No

value: Yes

tag: site

value: Boston


title: SHSY5Y cells_Control 9c_rep4

source_name: SHSY5Y cells_Control 9c


title: SHSY5Y cells_Control 9c_rep3


title: keratinocytes, postnatal day 24, from transgenic mouse expressing progerin and lamin A, biological rep3

description: mouse ID: E949_04


title: HP010_1

value: male

value: Never

tag: performance status (ecog)

tag: subsite

tag: Stage

tag: hpv status

value: site-matched normal epithelial


title: A13_white.adipose.tissue_18months, biological rep3

description: mouse ID: A13

source_name: wild-type, abdominal white adipose tissue, 18 months

extract_protocol: Mice were euthanized by cervical dislocation.Tissues were dissected and immediately transferred to liquid N2 to be stored at -80° C prior to homogenization and RNA extraction. Total RNA was extracted with Trizol  and  purified using an RNeasy cleanup kit. The RNA integrity was assessed by the Agilent 2100 Bioanalyzer. The RNA quality criteria for proceeding with exon arrays were a 18S/28S ratio above 1.5 and an RNA integrity number (RIN-value) ≥ 8.0. For array hybridization and Whole Transcript Sense Target Labeling Synthesis, 200 ng of RNA was processed using the Gene Chip WT cDNA Synthesis Kit, (Affymetrix)

treatment_protocol: No treatments

value: abdominal white adipose

tag: age (months)

value: wild-type


title: A15_white.adipose.tissue _18months, biological rep5

description: mouse ID: A15

tag: tissue


title: keratinocytes, postnatal day 24, from transgenic mouse expressing progerin and lamin A, biological rep1

description: mouse ID: E949_09

tag: strain

value: Female


title: HP010_3

tag: subject status

value: patients with primary oropharyngeal squamous cell carcinoma

tag: age (yrs)

value: Tongue base

value: IV

value: Pos

value: invasive squamous cell carcinoma


title: SHSY5Y cells_Control 5c_rep3

tag: cell line

value: SHSY5Y (ATCC N. CRL-2266)

tag: cell type

value: neuroblastoma


title: A11_white.adipose.tissue_18months, biological rep2

description: mouse ID: A11

tag: gender

tag: genotype


title: HP014_4

tag: subject id

tag: smoker status

value: Current

value: Tonsil


title: SHSY5Y cells_Control 9c_rep1


title: HP013_2


title: SHSY5Y cells_Control 9c_rep2


title: A10_white.adipose.tissue_18months, biological rep1

description: mouse ID: A10


title: FoxN1-Gpr177 CD8 SP thymocytes III

description: replicate 3 CD8 SP cKO

source_name: CD8 SP thymocytes

tag: age

value: 4-6 weeks

tag: genotype/variation


title: A9_white.adipose.tissue_4months, biological rep5

description: mouse ID: A9

source_name: wild-type, abdominal white adipose tissue, 4 months


title: keratinocytes, postnatal day 24, from transgenic mouse expressing progerin and lamin A, biological rep4

description: mouse ID: E949_06

value: skin

tag: age (days)

value: Male

value: K5tTA+; tetop-LA G608G+ (F1-line VF1-07)

tag: treatment

value: Drinking water was supplied with 100 μg ml−1 doxycycline (D9891; Sigma-Aldrich, St. Louis, MO, USA) and 2.5% sucrose during embryogenesis, which was replaced with normal water on postnatal day 0 (Rosengardten et al., 2011). Doxycyline treatment during embryogenesis keeps the transgene turned off.


title: A14_white.adipose.tissue_18months, biological rep4

description: mouse ID: A14

value: abdominal white adipose

value: male


title: liver_H0021_2

city: Düsseldorf

first: Wasco

last: Wruck

address: Moorenstr. 5

institute: Universitätsklinikum Düsseldorf

description: replicate 2

data_processing: The data were normalised using rank invariant normalisation with BeadStudio version 3 (Illumina)

source_name: primary hepatocytes_low steatosis

label_protocol: Illumina Gene Expression protocols contain a first- and second-strand reverse transcription step, followed by a single in vitro transcription (IVT) amplification that incorporates biotin-labeled nucleotides. Subsequent steps include array hybridization, washing, blocking, and streptavadin-Cy3 staining. Fluorescence emission by Cy3 is quantitatively detected for downstream analysis.

extract_protocol: The RNA was isolated using RNeasy Mini Kit (Quiagen), and DNase digestion (RNase-free DNase Set, Quiagen) has been applied on the columns during isolation.

value: primary hepatocytes

tag: grade of steatosis

value: m

tag: bmi


title: SHSY5Y cells_Control 4c_rep2

source_name: SHSY5Y cells_Control 4c


title: liver_H0018_2

description: replicate 2

source_name: primary hepatocytes_high steatosis

value: high

value: f


title: SHSY5Y cells_Control 3c_rep4

source_name: SHSY5Y cells_Control 3c


title: HP003_3

value: patients with primary oropharyngeal squamous cell carcinoma

value: Never

tag: performance status (ecog)

tag: subsite

value: Tongue base

tag: Stage

value: III

tag: hpv status

value: Pos

value: site-matched normal epithelial


title: liver_H0012_2

description: replicate 2

tag: tissue

value: low


title: SHSY5Y cells_Control 4c_rep4

tag: cell line

value: SHSY5Y (ATCC N. CRL-2266)

value: neuroblastoma


title: SHSY5Y cells_Control 4c_rep1

tag: cell type


title: SHSY5Y cells_Control 3c_rep1


title: SHSY5Y cells_Control 5c_rep1


title: SHSY5Y cells_Control 3c_rep2


title: liver_H0022_1

description: replicate 1

tag: gender


title: liver_H0021_1

description: replicate 1


title: SHSY5Y cells_Control 5c_rep2


title: SHSY5Y cells_Control 3c_rep3


title: A6_white.adipose.tissue_4months, biological rep2

description: mouse ID: A6

tag: strain

tag: age (months)

tag: genotype

value: wild-type


title: HP003_5

tag: subject status

tag: subject id

tag: age (yrs)

tag: smoker status

value: invasive squamous cell carcinoma


title: A7_white.adipose.tissue_4months, biological rep3

description: mouse ID: A7

value: abdominal white adipose


title: A8_white.adipose.tissue_4months, biological rep4

description: mouse ID: A8

value: male


title: A29_ventral.skin_28months, biological rep3

description: mouse ID: A29

source_name: wild-type, ventral skin, 28 months

value: ventral skin


title: liver_H0018_1

description: replicate 1

value: primary hepatocytes

tag: grade of steatosis

tag: age


title: liver_H0012_1

description: replicate 1

tag: bmi


title: A28_ventral.skin_28months, biological rep2

description: mouse ID: A28


title: A5_white.adipose.tissue_4months, biological rep1

description: mouse ID: A5


title: A30_ventral.skin_28months, biological rep4

description: mouse ID: A30


title: A27_ventral.skin_28months, biological rep1

description: mouse ID: A27


title: A31_ventral.skin_28months, biological rep5

description: mouse ID: A31


title: A15_ventral.skin_18months, biological rep5

description: mouse ID: A15

source_name: wild-type, ventral skin, 18 months


title: SHSY5Y cells_Control 2c_rep4

source_name: SHSY5Y cells_Control 2c


title: liver_H0022_2

description: replicate 2

value: high

value: m


title: A14_ventral.skin_18months, biological rep4

description: mouse ID: A14


title: SHSY5Y cells_Control 2c_rep3


title: SHSY5Y cells_Control 4c_rep3


title: liver_H0011_2

description: replicate 2

value: f


title: SHSY5Y cells_Gelsemium 30c_rep1

source_name: SHSY5Y cells_Gelsemium 30c


title: SHSY5Y cells_Control 2c_rep1


title: liver_H0008_1

description: replicate 1


title: SHSY5Y cells_Gelsemium 30c_rep4


title: liver_H0008_2

description: replicate 2


title: liver_H0011_1

description: replicate 1


title: A12_ventral.skin_18months, biological rep3

description: mouse ID: A12


title: SHSY5Y cells_Gelsemium 30c_rep2


title: liver_H0007_1

description: replicate 1


title: A11_ventral.skin_18months, biological rep2

description: mouse ID: A11


title: SHSY5Y cells_Gelsemium 30c_rep3


title: liver_H0007_2

description: replicate 2


title: liver_H0004_2

description: replicate 2


title: SHSY5Y cells_Control 2c_rep2


title: A7_ventral.skin_4months, biological rep3

description: mouse ID: A7

source_name: wild-type, ventral skin, 4 months


title: 6JA3_ventral.skin_4months, biological rep2

description: mouse ID: 6JA3


title: SHSY5Y cells_Gelsemium 9c_rep4

source_name: SHSY5Y cells_Gelsemium 9c


title: SHSY5Y cells_Gelsemium 9c_rep3


title: A8_ventral.skin_4months, biological rep4

description: mouse ID: A8


title: liver_H0009_1

description: replicate 1


title: liver_H0004_1

description: replicate 1


title: A10_ventral.skin_18months, biological rep1

description: mouse ID: A10


title: A14_thymus_18months, biological rep5

description: mouse ID: A14

source_name: wild-type, thymus, 18 months

value: thymus


title: 6JA2_ventral.skin_4months, biological rep1

description: mouse ID: 6JA2


title: SHSY5Y cells_Gelsemium 9c_rep2


title: SHSY5Y cells_Gelsemium 9c_rep1


title: SHSY5Y cells_Gelsemium 5c_rep2

source_name: SHSY5Y cells_Gelsemium 5c


title: SHSY5Y cells_Gelsemium 5c_rep1


title: A13_thymus_18months, biological rep4

description: mouse ID: A13


title: 5125_NT

city: Austin

first: Grace

last: Chappell

state: TX

address: 9390 Research Blvd, Bldg 2, Ste. #100

department: Health Sciences

institute: ToxStrategies, Inc.

description: biological replicate 25 of 26

hyb_protocol: Equal amounts (minimum 3500 ng) of Cy3-labeled reference DNA  and Cy5-labeled sample DNA were hybridized on the same array (Agilent 4x44K CGH microarray),  hybridized and washed according to the manufacturer's (Agilent) protocol.

scan_protocol: The signals from both Cy3 and Cy5 on the hybridized array were detected by laser scanner (Agilent G2565 Series scanner Model C).

data_processing: The images were converted to digital data by Agilent Feature Extraction Software (v 8.5.1.1).  Samples underwent background subtraction and LOWESS normalization.

source_name: Liver tumor from a male mouse treated with DEN+CCl12

label_protocol: Genomic DNA (minimum 500ng) from samples (reference and samples) were digested by restrict enzymes (Alu I and Rsa I). The fragmented DNA was labeled with either Cy3-dUTP or Cy5-dUTP, amplified with Exo(-) Klenow,  and purified.

extract_protocol: Total DNA was extracted using a Qiagen DNEasy kit according to the manufacturer's instructions

treatment_protocol: At 2 weeks of age, mice were injected i.p. with DEN (1mg/kg) in sterile saline (15 µl/g). At 8 weeks of age (6 weeks after a single injection of DEN or vehicle as detailed above), and were injected i.p. twice weekly with CCl4 (0.2ml/kg) diluted in olive oil vehicle for 14 additional weeks.  Mice were maintained on animal chow with free access to food/water for the duration of the study. Vehicle-control mice were injected with sterile saline and olive oil vehicles in place of DEN and CCl4, respectively. Liver tumors were separated at the time of sacrifice, and both tumor and non-tumor tissues were flash frozen in liquid nitrogen

value: liver non-tumor

tag: Sex

source_name: pooled DNA from normal liver from vehicle-control mice

value: liver


title: SHSY5Y cells_Gelsemium 5c_rep3


title: SHSY5Y cells_Gelsemium 5c_rep4


title: A8_thymus_4months, biological rep4

description: mouse ID: A8

source_name: wild-type, thymus, 4 months


title: 5126_NT

description: biological replicate 26 of 26

source_name: Non-tumor fibrotic liver tissue from a male mouse treated with DEN+CCl6


title: A10_thymus_18months, biological rep1

description: mouse ID: A10


title: SHSY5Y cells_Gelsemium 4c_rep2

source_name: SHSY5Y cells_Gelsemium 4c


title: SHSY5Y cells_Gelsemium 4c_rep1


title: A12_thymus_18months, biological rep3

description: mouse ID: A12


title: 5123_Tumor

description: biological replicate 23 of 26

source_name: Non-tumor fibrotic liver tissue from a male mouse treated with DEN+CCl11

value: liver tumor


title: A7_thymus_4months, biological rep3

description: mouse ID: A7


title: SHSY5Y cells_Gelsemium 4c_rep3


title: 5126_Tumor

description: biological replicate 26 of 26

source_name: Liver tumor from a male mouse treated with DEN+CCl6


title: 5123_NT

description: biological replicate 23 of 26

source_name: Liver tumor from a male mouse treated with DEN+CCl10


title: A9_thymus_4months, biological rep5

description: mouse ID: A9


title: 5125_Tumor

description: biological replicate 25 of 26

source_name: Non-tumor fibrotic liver tissue from a male mouse treated with DEN+CCl13


title: 5124_NT

description: biological replicate 24 of 26

source_name: Liver tumor from a male mouse treated with DEN+CCl11


title: 5120_Tumor

description: biological replicate 20 of 26

source_name: Non-tumor fibrotic liver tissue from a male mouse treated with DEN+CCl10


title: A6_thymus_4months, biological rep2

description: mouse ID: A6


title: liver_H0009_2

description: replicate 2

source_name: primary hepatocytes_low steatosis


title: A9_ventral.skin_4months, biological rep5

description: mouse ID: A9