title: WT1

description: Replicate 1 of 3.

tag: genotype/variation


title: NTKO3

status: Public on Sep 01 2014

type: RNA

city: Chicago

first: Relja

last: Popovic

address: 303 East Superior Street

country: USA

institute: Northwestern University

description: Replicate 3 of 3.

hyb_protocol: cRNA was hybridized to the Illumina HumanWG-6 v3.0 Expression BeadChip using standard protocols (provided by Illumina).

scan_protocol: The arrays were scanned on an Illumina BeadArray Reader.

data_processing: The data was processed using GenomeStudio.

molecule: total RNA

organism: Homo sapiens

source_name: NTKO cells

label_protocol: Biotin-UTP labeled using the Illumina TotalPrep RNA Amplification Kit (Ambion).

growth_protocol: Cells were grown in RPMI 1640 supplemented with 10% FBS and 1% Pen/Strep.

extract_protocol: Total RNA was extracted using the RNeasy Mini Kit from Qiagen (Cat. No. 74104) in accordance with the prescribed protocol provided with the kit.

tag: parental cell line

tag: cell type

value: multiple myeloma cell line

value: wild type MMSET allele inactivated


title: norm-HUL-PRE-DMO-24H-R-2-CD_(HG-U133_Plus_2).CEL

city: Brussels

first: Tatyana

last: Doktorova

state: Belgium

address: Laarbeeklaan 103, building G

department: FAFY

country: Belgium

institute: VUB

description: Control D

hyb_protocol: We used standard Affymetrix hybridisation rotocols

scan_protocol: We used standard Affymetrix scanning parameters

data_processing: The Affymetrix IDs were alternatively remapped to the alternative IDs from Brainarray  (http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/CDF_download.asp), thus the ensemb version 61 was used (http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/14.1.0/ensg.download/HGU133Plus2_Hs_ENSG_14.1.0.zip).  All samples were  further normalized by GC-RMA algorithm. As the number of controls were less than the number of treatments, the same controls were used several to normalize data from several treatments.

label: biotin

source_name: HepaRG cell line

label_protocol: We used standard Affymetrix labeling protocols

growth_protocol: The human hepatoma-derived HepaRG cells (Biopredic International, France) were cultivated as previously described  by A. Guillouzo et al. 168 (2007) 66-73.  and P. Gripon et al 99 (2002) 15655-15660. At day 13 of cultivation, dimethylsulfoxide (DMSO)-containing medium (2%) was added for 7 days . At day 19 exposure with the selected compounds was initiated.

extract_protocol: Samples for RNA isolation were collected after 24 and 72 hours of exposure. Minimum three independent biological experiments were conducted for each compound. The total RNA extraction (RNA extraction kit, Qiagen), including a DNase digestion step, was done according to the manufacturer’s instructions.

treatment_protocol: The cells were individually exposed to 15 prototypical compounds for 24h and 72 hours at IC10 concentrations, i.e. 5 GTX (N-nitrosomorpholine, NMP, IC10=0.216mM; Hydroquinone, HQO, IC10=0.15mM; Hydrazine dihydrochloride, HHC, IC10=0.86mM; 2-acetylaminofluorene, TAF, IC10=0.0408mM; 2-amino-3-methylimidazo(4,5-f)quinoline, AMQ, IC10=0.003mM), 5 NGTX (Fumonisin B1, FMB, IC10=2.4mM; Cyclosporine A, CsA, IC10=0.0026mM; Acetamide, ACE, IC10=5.9; Diethylhexyl Phthalate, DHP, IC10=10mM; Ethanol, ETH, IC10=10mM), 5 NC (4-acetylaminofluorene, FAF, IC10=0.22; D,L-Menthol, DLM, IC10=1.2mM; Benzoin, BEN, IC10=0.345mM; Benzyl Alcohol, BEA, IC10=6.5mM; Triclosan, TRI, IC10=0.022mM).

tag: cell line

value: HepaRG cell line

tag: treatment

value: Control D

tag: replicate


title: femur_wt_rep1

city: Neuherberg

first: Martin

last: Irmler

state: Bayern

address: Ingolstaedter Landstrasse 1

department: Institute of Experimental Genetics

country: Germany

institute: Helmholtz Zentrum München GmbH

description: replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol using HiScan

data_processing: The data were normalised using cubic spline normalisation with Illumina GenomeStudio 2011.1

organism: Mus musculus

source_name: femur

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 with QIAGEN RNeasy midi kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with gel electrophoreses.

tag: strain

tag: genotype

value: wild type

tag: tissue

value: femur

tag: age

value: 17 weeks

tag: mouse id


title: norm-HUL-PRE-CPD-24H-R-3-CD_(HG-U133_Plus_2).CEL

description: Treatment with D

value: Treatment with D


title: white adipose tissue_AEA001_rep2

description: replicate 2

source_name: white adipose tissue

value: AEA001 - Ednra mutant

value: white adipose tissue


title: WT2

description: Replicate 2 of 3.

source_name: KMS11 cells

value: WT


title: norm-HUL-PRE-CPD-24H-R-1-CD_(HG-U133_Plus_2).CEL

description: Treatment with D


title: white adipose tissue_AEA001_rep3

description: replicate 3


title: white adipose tissue_AEA001_rep1

description: replicate 1


title: norm-HUL-PRE-CPD-24H-R-2-CD_(HG-U133_Plus_2).CEL

description: Treatment with D


title: white adipose tissue_wt_rep4

description: replicate 4


title: norm-BPI-2101-FDMSO-72H-R1_(HG-U133_Plus_2).CEL

description: Control F

value: Control F


title: white adipose tissue_wt_rep3

description: replicate 3


title: norm-BPI-2005-FDMSO-72H-R1_(HG-U133_Plus_2).CEL

description: Control F


title: white adipose tissue_wt_rep1

description: replicate 1


title: norm-BPI-1802-FDMSO-72H-R1_(HG-U133_Plus_2).CEL

description: Control F


title: norm-BPI-0202-F-72H-R1_(HG-U133_Plus_2).CEL

description: Treatment with F

value: Treatment with F


title: norm-BPI-1305-FDMSO-72H-R1_(HG-U133_Plus_2).CEL

description: Control F


title: Ali35 brain mut rep 3

description: replicate 3

data_processing: The data were normalised using cubic spline normalisation with Illumina Genomestudio 2011.1

source_name: Ali35 brain

value: 3 days

value: brain

value: Ali35 mutant


title: white adipose tissue_wt_rep2

description: replicate 2


title: norm-BPI-1105-FDMSO-24H-R1_(HG-U133_Plus_2).CEL

description: Control F


title: WT brain rep 3

description: replicate 3

source_name: wt brain


title: Ali35 brain mut rep 1

description: replicate 1


title: norm-HUL-PRE-DMO-24H-R-1-CD2_(HG-U133_Plus_2).CEL

description: Control D


title: norm-BPI-1802-F-72H-R1_(HG-U133_Plus_2).CEL

description: Treatment with F


title: WT brain rep 4

description: replicate 4


title: WT brain rep 1

description: replicate 1


title: norm-BPI-2101-F-72H-R1_(HG-U133_Plus_2).CEL

description: Treatment with F


title: norm-BPI-1006-FDMSO-72H-R1_(HG-U133_Plus_2).CEL

description: Control F


title: Ali35 brain mut rep 2

description: replicate 2


title: Ali35 brain mut rep 4

description: replicate 4


title: norm-BPI-0402-FDMSO-24H-R1_(HG-U133_Plus_2).CEL

description: Control F


title: norm-BPI-1602-FDMSO-24H-R1_(HG-U133_Plus_2).CEL

description: Control F


title: Ali35 bone mut rep 4

description: replicate 4

source_name: Ali35 bone

value: 120 days

value: bone


title: norm-BPI-1805-FDMSO-24H-R1_(HG-U133_Plus_2).CEL

description: Control F


title: norm-BPI-0202-FDMSO-72H-R1_(HG-U133_Plus_2).CEL

description: Control F


title: Ali35 bone mut rep 2

description: replicate 2


title: WT brain rep 2

description: replicate 2


title: norm-BPI-0806-FDMSO-24H-R1_(HG-U133_Plus_2).CEL

description: Control F


title: norm-BPI-1901-FDMSO-24H-R1_(HG-U133_Plus_2).CEL

description: Control F


title: Ali35 bone mut rep 1

description: replicate 1


title: norm-BPI-1901-F-24H-R1_(HG-U133_Plus_2).CEL

description: Treatment with F


title: WT bone rep 4

description: replicate 4

source_name: wt bone


title: norm-BPI-1602-F-24H-R1_(HG-U133_Plus_2).CEL

description: Treatment with F


title: ICEclc_10mM3CBA_exponential_2961

city: Lausanne

first: Jan

middle: Roelof

last: van der Meer

address: Bâtiment Biophore, Quartier UNIL-Sorge

department: Department of Fundamental Microbiology

country: Switzerland

institute: University of Lausanne

description:
ICEclcB13 in Pseudomonas putida UWC1.
Gene expression in exponential phase during growth on 10mM trichlorobenzaote (3CBA) as substrate.
REPLICATES:
ICEclc_10mM3CBA_exponential_2961_replicate1
ICEclc_10mM3CBA_exponential_2961_replicate2
ICEclc_10mM3CBA_exponential_2961_replicate3
ICEclc_10mM3CBA_exponential_2961_replicate4

hyb_protocol: 60 ng of labeled cDNA was then loaded onto each microarray, hybridized for 17 hours at 65ºC, and washed and scanned as described for labeled cRNA in the One-Color Microarray-Based Gene Expression Analysis Manual (Agilent). The fragmentation step (heating to 60ºC for 30 minutes) was omitted.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 8x15k 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% and XDR Lo:10%.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5.1.1 (Agilent) using default parameters (protocols GE1-v5_95_Feb07 or GE1_105_Dec08 and Grid: 020923_D_F_20080708) to obtain background subtracted and spatially detrended Processed Signal intensities. Data were then transported to GeneSpring GX v11.0, Generic Single Color experiment, thresholding 1.0, Quantile normalization, no baseline transformation performed. Data were grouped according to genotypes, filtered on expression value (20-100th percentile), analysed for significance (Oneway ANOVA unequal variance, corrected p-value cut-off 0.05, assymptotic p-value  computation, Benjamini-Hochberg multiple testing correction).

organism: Pseudomonas putida UWC1

label_protocol: cDNA was synthesized from total RNA and directly labeled with cyanine-3-dCTP using a modification of a protocol described elsewhere (Charbonnier et al. 2005). Briefly, each 50-µL reaction contained 10 µg of total RNA, 1.25 µg of random hexanucleotide primers (Promega), 100 µM each of unlabeled dATP, dGTP, and dTTP (Invitrogen), 25 µM of unlabeled dCTP (Invitrogen), 25 µM of cyanine-3-labeled dCTP (Perkin-Elmer), 25 U SUPERase•In (Ambion), and 400 U Superscript II reverse transcriptase (Invitrogen). Reactions were performed by heating at 42ºC for 2 hours followed by 70ºC for 10 min. RNA was then removed by adding 100 mM NaOH, heating to 65ºC for 20 min, and neutralizing with 100 mM HCl and 300 mM sodium acetate (pH 5.2). Labeled cDNA products were purified using the MinElute PCR purification kit (Qiagen) and the quantity and incorporation frequency of cyanine-3-labeled dCTP were calculated using the MICROARRAY function on a NanoDrop Spectrophotometer.

growth_protocol: ICEclc-bearing P. putida UWC1 strains were cultivated in minimal medium (MM) based on the type 21C medium (Gerhardt et al. 1981). This MM was complemented with 10mM 3CBA and the bacteria were grown at 30°C. Bacterial growth was assessed from culture turbidity at 600 nm (OD600). Cells were recovered at (i) OD600= 0.5 (exponential phase) and (ii) 48h after the beginning of the stationary phase. For RNA isolation, 100 ml of culture was immediately harvested by centrifugation (at 15,000 × g for 1 min at 4°C) and the supernatant was decanted. Cell pellets were resuspended in 4 ml RNAprotect Bacteria Reagent (QIAGEN GmbH). After 5 min incubation, the suspensions were centrifuged again (at 5,000 × g for 5 min at room temperature); the supernatant was discarded and pellets were stored at -80°C.

extract_protocol: Prior to RNA extraction, frozen pellets were slowly thawed, then resuspended in 0.5 ml TES buffer [10 mM Tris-HCl (pH 8.0), 1 mM EDTA, 100 mM NaCl], followed by addition of and mixing with 0.25 ml lysis solution [20 mM sodium acetate (pH 5.5), 1 mM EDTA, 0.5% SDS]. After that, the total RNA was further purified by the hot acid-phenol method as described previously [Baumann et al. 1996]. RNA samples were purified from contaminating DNA by treatment with 50 U of DNase I (RNase free; Roche) during 1 h at 37°C. Finally, the RNA was dissolved in 50 µl diethylpyrocarbonate (DEPC)-treated water and quantified by absorbance at 260 and 280 nm on a NanoDrop spectrophotometer (Witec AG). The integrity of RNA was determined by agarose gel electrophoresis and the absence of DNA was verified by PCR.

tag: grown on substrate

tag: growth phase

value: exponential phase


title: ICEclc_10mM3CBA_exponential_3543

description:
ICEclcB13 in Pseudomonas putida UWC1.
Gene expression in exponential phase during growth on 10mM trichlorobenzaote (3CBA) as substrate.
REPLICATES:
ICEclc_10mM3CBA_exponential_3543_replicate1
ICEclc_10mM3CBA_exponential_3543_replicate2
ICEclc_10mM3CBA_exponential_3543_replicate3
ICEclc_10mM3CBA_exponential_3543_replicate4


title: ICEclc_10mM3CBA_stationary_4321

description:
ICEclcB13 in Pseudomonas putida UWC1.
Gene expression 48hours after entrance in stationary phase after growth on 10mM trichlorobenzaote (3CBA) as substrate.
REPLICATES:
ICEclc_10mM3CBA_stationary_4321_replicate1
ICEclc_10mM3CBA_stationary_4321_replicate2
ICEclc_10mM3CBA_stationary_4321_replicate3
ICEclc_10mM3CBA_stationary_4321_replicate4

source_name: 4321 stat

value: ∆'tciR

value: stationary phase


title: Ali35 bone mut rep 3

description: replicate 3


title: norm-BPI-1802-EDMSO-72H-R1_(HG-U133_Plus_2).CEL

description: Control E

value: HepaRG cell line

value: Control E


title: ICEclc_10mM3CBA_stationary_2961

description:
ICEclcB13 in Pseudomonas putida UWC1.
Gene expression 48hours after entrance in stationary phase after growth on 10mM trichlorobenzaote (3CBA) as substrate.
REPLICATES:
ICEclc_10mM3CBA_stationary_2961_replicate1
ICEclc_10mM3CBA_stationary_2961_replicate2
ICEclc_10mM3CBA_stationary_2961_replicate3
ICEclc_10mM3CBA_stationary_2961_replicate4

source_name: 2961 stat


title: norm-BPI-2101-EDMSO-72H-R1_(HG-U133_Plus_2).CEL

description: Control E


title: norm-BPI-1305-EDMSO-72H-R1_(HG-U133_Plus_2).CEL

description: Control E


title: ICEclc_10mM3CBA_stationary_3543

description:
ICEclcB13 in Pseudomonas putida UWC1.
Gene expression 48hours after entrance in stationary phase after growth on 10mM trichlorobenzaote (3CBA) as substrate.
REPLICATES:
ICEclc_10mM3CBA_stationary_3543_replicate1
ICEclc_10mM3CBA_stationary_3543_replicate2
ICEclc_10mM3CBA_stationary_3543_replicate3
ICEclc_10mM3CBA_stationary_3543_replicate4

source_name: 3543 stat


title: ICEclc_10mM3CBA_stationary_4372

description:
ICEclcB13 in Pseudomonas putida UWC1.
Gene expression 48hours after entrance in stationary phase after growth on 10mM trichlorobenzaote (3CBA) as substrate.
REPLICATES:
ICEclc_10mM3CBA_stationary_4372_replicate1
ICEclc_10mM3CBA_stationary_4372_replicate2
ICEclc_10mM3CBA_stationary_4372_replicate3

source_name: 4372 stat


title: ICEclc_10mM3CBA_exponential_4321

description:
ICEclcB13 in Pseudomonas putida UWC1.
Gene expression in exponential phase during growth on 10mM trichlorobenzaote (3CBA) as substrate.
REPLICATES:
ICEclc_10mM3CBA_exponential_4321_replicate1
ICEclc_10mM3CBA_exponential_4321_replicate2
ICEclc_10mM3CBA_exponential_4321_replicate3


title: WT bone rep 2

description: replicate 2

value: wild type


title: norm-BPI-0202-EDMSO-72H-R1_(HG-U133_Plus_2).CEL

description: Control E


title: norm-BPI-2005-EDMSO-72H-R1_(HG-U133_Plus_2).CEL

description: Control E


title: norm-BPI-2005-E-72H-R1_(HG-U133_Plus_2).CEL

description: Treatment with E

value: Treatment with E


title: WT bone rep 3

description: replicate 3


title: norm-BPI-1006-E-72H-R1_(HG-U133_Plus_2).CEL

description: Treatment with E


title: norm-BPI-1006-EDMSO-72H-R1_(HG-U133_Plus_2).CEL

description: Control E


title: WT bone rep 1

description: replicate 1


title: norm-BPI-1305-E-72H-R1_(HG-U133_Plus_2).CEL

description: Treatment with E


title: norm-BPI-1105-EDMSO-24H-R1_(HG-U133_Plus_2).CEL

description: Control E


title: ICEclc_10mM3CBA_stationary_2737

description:
ICEclcB13 in Pseudomonas putida UWC1.
Gene expression 48hours after entrance in stationary phase after growth on 10mM trichlorobenzaote (3CBA) as substrate.
REPLICATES:
ICEclc_10mM3CBA_stationary_2737_replicate1
ICEclc_10mM3CBA_stationary_2737_replicate2
ICEclc_10mM3CBA_stationary_2737_replicate3
ICEclc_10mM3CBA_stationary_2737_replicate4

source_name: 2737 stat


title: ICEclc_10mM3CBA_stationary_4322

description:
ICEclcB13 in Pseudomonas putida UWC1.
Gene expression 48hours after entrance in stationary phase after growth on 10mM trichlorobenzaote (3CBA) as substrate.
REPLICATES:
ICEclc_10mM3CBA_stationary_4322_replicate1
ICEclc_10mM3CBA_stationary_4322_replicate2
ICEclc_10mM3CBA_stationary_4322_replicate3
ICEclc_10mM3CBA_stationary_4322_replicate4

source_name: 4322 stat

value: ∆'mfsR


title: ICEclc_10mM3CBA_exponential_2737

description:
ICEclcB13 in Pseudomonas putida UWC1.
Gene expression in exponential phase during growth on 10mM trichlorobenzaote (3CBA) as substrate.
REPLICATES:
ICEclc_10mM3CBA_exponential_2737_replicate1
ICEclc_10mM3CBA_exponential_2737_replicate2
ICEclc_10mM3CBA_exponential_2737_replicate3
ICEclc_10mM3CBA_exponential_2737_replicate4


title: ICEclc_10mM3CBA_exponential_4372

description:
ICEclcB13 in Pseudomonas putida UWC1.
Gene expression in exponential phase during growth on 10mM trichlorobenzaote (3CBA) as substrate.
REPLICATES:
ICEclc_10mM3CBA_exponential_4372_replicate1
ICEclc_10mM3CBA_exponential_4372_replicate2
ICEclc_10mM3CBA_exponential_4372_replicate3
ICEclc_10mM3CBA_exponential_4372_replicate4


title: norm-BPI-1901-EDMSO-24H-R1_(HG-U133_Plus_2).CEL

description: Control E


title: ICEclc_10mM3CBA_exponential_4322

description:
ICEclcB13 in Pseudomonas putida UWC1.
Gene expression in exponential phase during growth on 10mM trichlorobenzaote (3CBA) as substrate.
REPLICATES:
ICEclc_10mM3CBA_exponential_4322_replicate1
ICEclc_10mM3CBA_exponential_4322_replicate2
ICEclc_10mM3CBA_exponential_4322_replicate3
ICEclc_10mM3CBA_exponential_4322_replicate4


title: norm-BPI-1805-EDMSO-24H-R1_(HG-U133_Plus_2).CEL

description: Control E


title: norm-BPI-0806-EDMSO-24H-R1_(HG-U133_Plus_2).CEL

description: Control E


title: norm-BPI-0806-E-24H-R1_(HG-U133_Plus_2).CEL

description: Treatment with E


title: norm-BPI-1105-E-24H-R1_(HG-U133_Plus_2).CEL

description: Treatment with E


title: Mm_mouse_3_t_0

city: Amsterdam

first: Oskar

last: Bruning

address: Science Park 904

department: SILS

country: Netherlands

institute: University of Amsterdam

hyb_protocol: Each hybridization mixture was made up from 750 ng Test (Cy3) and 750 µg Reference (Cy5) sample.  Samples were dried and 1.98 µl of water was added. The hybridization cocktail was made according to the manufacturer’s instructions (Nimblegen Arrays User’s Guide – Gene Expression Arrays Version 5.0, Roche Nimblegen). 5.22 µl from this mix was added to each sample. The samples were incubated for 5 min at 65°C and 5 min at 42°C prior to loading. Hybridization samples were loaded onto 12x135k custom designed microarrays against E. coli (OID 38205, Design 120315). Microarrays were hybridized for 18 hours at 42°C with the NimbleGen Hybridization System 4 (Roche Nimblegen).

scan_protocol: the slides were washed according to the Nimblegen Arrays User’s Guide – Gene Expression Arrays Version 5.0 and scanned in an ozone-free room with a Agilent DNA microarray scanner G2565CA (Agilent Technologies). Feature extraction was performed with NimbleScan v2.6 (Roche Nimblegen).

data_processing: The raw data from all arrays was subjected to multiple quality control checks, i.e. visual inspection of the scans, testing against criteria for foreground and background signals, testing for consistent performance of the labeling dyes, checking for spatial effects through pseudo-color plots, and inspection of pre- and post-normalized data with box plots, ratio-intensity (RI) plots and PCA plots. Within array normalization was performed using LOESS. Between array normalization was run on the Cy3-channel by summarizing (Genebank id's) the intensity values of the probes in a probe set using the robust multi-array average (RMA) algorithm.

label_protocol: Per test sample, 5 µg total RNA combined with 1 µg random octamers (Biolegio) in 4.5 µl was heated to 65°C for 10 min to denature the RNA and was allowed to cool in an ice-waterbath for 10 min. This 4.5 µl was made to 10 µl with a first strand mastermix containing final concentrations of 50 mM Tris-Cl (pH 8.3), 3 mM MgCl2, 75 mM KCl, 200 mM Raffinose (Sigma-Aldrich), 0.015% Triton X-100, 30 ng Actinomycin-D (Sigma-Aldrich), 0.01M DTT, 0.5 mM dGAC, 0.35 mM dUTP, 0.15 mM dUTP-Cy3 (test) or dUTP-Cy5 (common reference) (GE Healthcare) and 200U SuperScript-II (Life Technologies).  This mixture was incubated for 2 min at 25°C, 120 min at 42°C and 15 min at 70°C. Finally, 1.5 µl of 2.5M NaOH was added to hydrolyze the remaining RNA by heating for 10 min at 70°C. 8.5 µl 2M MOPS was added for neutralization and the labeled cDNA was purified with the E.Z.N.A. MicroElute RNA Clean-up Kit (Omega Biotek). Dye incorporation and cDNA yield was measured on the NanoDrop ND-1000 (Thermo Scientific) yielding 2-2.5 µg per sample and a FOI > 10 pmol/µg. The common reference was made by an equimolar pool of all test samples (5 µg per sample) and subsequently labeled as the test samples with Cy5 incorporation.

growth_protocol: Wild-type (WT; p53+/+) mice were used for UV exposure studies. All mice used were males of 7-10 weeks of age and at least 10 times backcrossed in SKH hairless strain. Mice received normal feed and water ad libitum.

extract_protocol: At different time points after UV-B exposure, both treated and untreated mice were anaesthetized by isoflurane. 1.5mm biopsies were sampled from the back.  by punching a half moon shape on folded skin. Biopsies were immediately snap frozen in liquid nitrogen and stored at -80°C until further processing. Total RNA was isolated using the RNeasy mini kit (Qiagen, Valencia, CA). RNA was assessed for quality with the Bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA).

treatment_protocol: All mouse treatments have been approved by the institute's Experimental Animal Ethical Committee and carried out in accordance with national legislation. Mice were UVB irradiated at different doses (90, 180, 360, 450, 720 J/m2) in a chamber containing Phillips TL12 lamps. Control mice were mock treated.

tag: time (hours)

value: skin

value: Wild-type (WT; p53+/+)


title: norm-BPI-2005-DMSO-72H-R1_(HG-U133_Plus_2).CEL

description: Control D

value: Control D


title: norm-BPI-1602-EDMSO-24H-R1_(HG-U133_Plus_2).CEL

description: Control E


title: Mm_mouse_3_t_12


title: Mm_mouse_4_t_3


title: norm-BPI-1006-DMSO-72H-R1_(HG-U133_Plus_2).CEL

description: Control D


title: Mm_mouse_4_t_6


title: Mm_mouse_3_t_48


title: Mm_mouse_3_t_24


title: norm-BPI-2101-DMSO-72H-R1_(HG-U133_Plus_2).CEL

description: Control D


title: Mm_mouse_3_t_1


title: norm-BPI-1305-DMSO-72H-R1_(HG-U133_Plus_2).CEL

description: Control D


title: norm-BPI-1802-DMSO-72H-R1_(HG-U133_Plus_2).CEL

description: Control D


title: Mm_mouse_3_t_3


title: norm-BPI-2101-D-72H-R1_(HG-U133_Plus_2).CEL

description: Treatment with D

value: Treatment with D


title: Mm_mouse_4_t_1


title: norm-BPI-0202-DMSO-72H-R1_(HG-U133_Plus_2).CEL

description: Control D


title: Mm_mouse_4_t_24


title: norm-BPI-1802-D-72H-R1_(HG-U133_Plus_2).CEL

description: Treatment with D


title: norm-BPI-0202-D-72H-R1_(HG-U133_Plus_2).CEL

description: Treatment with D


title: Mm_mouse_2_t_12


title: Mm_mouse_1_t_48


title: norm-BPI-1805-DMSO-24H-R1_(HG-U133_Plus_2).CEL

description: Control D


title: Mm_mouse_1_t_0


title: norm-BPI-0806-DMSO-24H-R1_(HG-U133_Plus_2).CEL

description: Control D


title: norm-BPI-0402-DMSO-24H-R1_(HG-U133_Plus_2).CEL

description: Control D


title: Mm_mouse_2_t_1


title: Mm_mouse_1_t_24


title: norm-BPI-1105-DMSO-24H-R1_(HG-U133_Plus_2).CEL

description: Control D


title: Mm_mouse_2_t_6


title: norm-BPI-1602-DMSO-24H-R1_(HG-U133_Plus_2).CEL

description: Control D


title: Mm_mouse_1_t_6


title: norm-BPI-0402-D-24H-R1_(HG-U133_Plus_2).CEL

description: Treatment with D


title: norm-BPI-1901-D-24H-R1_(HG-U133_Plus_2).CEL

description: Treatment with D


title: norm-BPI-1602-D-24H-R1_(HG-U133_Plus_2).CEL

description: Treatment with D


title: Mm_mouse_1_t_12


title: Mm_mouse_2_t_0


title: Mm_mouse_2_t_24


title: femur_wt_rep4

description: replicate 4

value: femur

value: 17 weeks


title: Mm_mouse_2_t_48


title: norm-BPI-1901-DMSO-24H-R1_(HG-U133_Plus_2).CEL

description: Control D


title: Inhibition of mannosidase

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

country: Japan

institute: Toray Industries,Inc.

description: Man

hyb_protocol: Hybridized for 16 h at 37 C with rotary shaking (250 rpm). Hybridization buffer and washing protocol were according to the protocol supplied by TORAY Industries, Inc.

scan_protocol: 3D-Gene Scanner (Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction (Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with the mean intensity of the background signal determined by all blank spots' signal intensities of 95% confidence intervals. Measurements of both duplicate spots with the signal intensities greater than 2 standard deviations (SD) of the background signal intensity were considered to be valid. A relative expression level of a given mRNA was calculated by comparing the signal intensities of the averaged valid spots with their mean value throughout the microarray experiments.

source_name: cervical carcinoma cells, inhibition of mannosidase

label_protocol: cDNA and Amino Allyl aRNA was synthesized by the Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion#1753). CyeDye coupling and fragmentation were performed as per the protocol supplied by TORAY Industries, Inc.

extract_protocol: Sample extraction for array hybridization was carried out as described in the RNeasy Mini instructions.

treatment_protocol: HeLa cells (RCB0007) were treated with a small molecule inhibitor and then were cultured at 37°C.

value: HeLa

value: cervical carcinoma cells

tag: inhibition

value: mannosidase


title: Inhibition of glucosidase

description: Glc

source_name: cervical carcinoma cells, inhibition of glucosidase

value: glucosidase


title: Inhibition of fucosidase

description: Fuc

source_name: cervical carcinoma cells, inhibition of fucosidase

value: fucosidase


title: norm-BPI-0402-F-24H-R1_(HG-U133_Plus_2).CEL

description: Treatment with F

source_name: HepaRG cell line

value: Treatment with F


title: Control

description: Con

source_name: cervical carcinoma cells, untreated


title: norm-VUB-1008-TRIDMSO-72-R-2-1G_(HG-U133_Plus_2).CEL

description: Control TRI

value: HepaRG cell line

value: Control TRI


title: ΔF2 H5N1-infected vs. Mock-infected replicates 3

city: Jouy-en-Josas

first: Ronan

last: Le Goffic

state: Please select one below:

address: Domaine de Vilvert

department: SA

country: France

institute: INRA

description: Biological replicate 3 of 5. ΔF2 H5N1-infected vs mock-infected

hyb_protocol: An equal amount of 800 ng of cyanine 3 and cyanine 5 labeled cRNA were hybridized for each sample. The hybridization and the washing steps were performed following the manufacturer’s recommendations.

scan_protocol: The arrays were scanned using an Agilent G2505C scanner, and the scan protocol used a resolution of 5 µm and a 20 bit dynamic range.

data_processing: The tiff images resulting from arrays scanning were analyzed using the Feature Extraction software version 10.7.3.1 (Agilent) using the GE2_107_Sep09 protocol. For each channel, the median of the signal intensity was used without background subtraction.

organism: Gallus gallus

source_name: ΔF2 H5N1 infected chicken 8

label_protocol: Fluorescently labeled cRNAs were obtained using the two colors Low Input Quick Amp Labeling Kit (Agilent Technologies) and starting from 100 ng of total RNA for each sample. supplemented with known synthetic RNA (two-color RNA spike-in kit, Agilent Technologies).

growth_protocol: Specific pathogen free white Leghorn chickens at 40 days old were obtained from Fallowfield, Ottawa CFIA laboratory. They were floor housed in heated BSL3 animal cubicles and allowed 1 week of acclimatization before the start of experiments.

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

treatment_protocol: Five chickens per group were inoculated intranasally with 10E3 PFU per chicken of either wt or ΔF2 Nig06 H5N1 in 0.5 ml sterile PBS distributed into both nares. Blood was collected from the wing vein of anaesthetized chickens on days 0 and 2 post infection.

tag: breed

value: white Leghorn

value: blood

source_name: mock infected chicken 8


title: wt H5N1-infected vs. Mock-infected replicates 5

description: Biological replicate 5 of 5. wt H5N1-infected vs mock-infected

source_name: wt H5N1 infected chicken 5

source_name: mock infected chicken 5


title: Mm_mouse_1_t_3


title: ΔF2 H5N1-infected vs. Mock-infected replicates 2

description: Biological replicate 2 of 5. ΔF2 H5N1-infected vs mock-infected

source_name: ΔF2 H5N1 infected chicken 7

source_name: mock infected chicken 7


title: wt H5N1-infected vs. Mock-infected replicates 3

description: Biological replicate 3 of 5. wt H5N1-infected vs mock-infected

source_name: wt H5N1 infected chicken 3

source_name: mock infected chicken 3


title: ΔF2 H5N1-infected vs. Mock-infected replicates 4

description: Biological replicate 4 of 5. ΔF2 H5N1-infected vs mock-infected

source_name: ΔF2 H5N1 infected chicken 9

source_name: mock infected chicken 9


title: ΔF2 H5N1-infected vs. Mock-infected replicates 1

description: Biological replicate 1 of 5. ΔF2 H5N1-infected vs mock-infected

source_name: ΔF2 H5N1 infected chicken 6

source_name: mock infected chicken 6


title: norm-VUB-1009-TRI-72-R-3-1_(HG-U133_Plus_2).CEL

description: Treatment with TRI

value: Treatment with TRI


title: norm-VUB-1007-TRIDMSO-72-R-1-1L_(HG-U133_Plus_2).CEL

description: Control TRI


title: norm-VUB-1009-TRIDMSO-72-R-3-1G_(HG-U133_Plus_2).CEL

description: Control TRI


title: ΔF2 H5N1-infected vs. Mock-infected replicates 5

description: Biological replicate 5 of 5. ΔF2 H5N1-infected vs mock-infected

source_name: ΔF2 H5N1 infected chicken 10

source_name: mock infected chicken 10


title: norm-VUB-1008-TRI-72-R-2-1_(HG-U133_Plus_2).CEL

description: Treatment with TRI


title: norm-BPI-0402-EDMSO-24H-R1_(HG-U133_Plus_2).CEL

description: Control E

value: Control E


title: E.coli O157 Sakai pH5.5 2.5h biological rep2

city: Birmingham

last: Turan

address: University of Birmingham, Edgbaston

country: United Kingdom

institute: University of Birmingham

description: Gene expression data from E.coli  O157 Sakai at pH5.5 for 2.5h

hyb_protocol: Following labeling, 80pmoles of labeled probe was hybridized for 16 hr at 42C on E.coli whole genome arrays. GeneChips were washed using Adwawash.

scan_protocol: GeneChips were scanned using the Perkin-Elmer Scanarray Scanner 4200.

data_processing: The data were analyzed with Scanarray express microarray analysis system and quantile normalization was used in R package to normalise the data.

organism: Escherichia coli O157:H7 str. Sakai

label_protocol: GE healthcare Cyscibe indirect labeling kit

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

tag: wildtype


title: E.coli O157 Sakai pH5.5 2h biological rep3

description: Gene expression data from E.coli  O157 Sakai at pH5.5 for 2h


title: E.coli O157 Sakai pH5.5 2.5h biological rep3


title: Mm_mouse_4_t_0

value: skin

value: Wild-type (WT; p53+/+)


title: wt H5N1-infected vs. Mock-infected replicates 1

description: Biological replicate 1 of 5. wt H5N1-infected vs mock-infected

source_name: wt H5N1 infected chicken 1

source_name: mock infected chicken 1


title: E.coli O157 Sakai pH5.5 2h biological rep2


title: E.coli O157 Sakai pH5.5 2.5h biological rep1


title: wt H5N1-infected vs. Mock-infected replicates 2

description: Biological replicate 2 of 5. wt H5N1-infected vs mock-infected

source_name: wt H5N1 infected chicken 2

source_name: mock infected chicken 2


title: Mm_mouse_4_t_48


title: norm-VUB-1007-TRI-72-R-1-1_(HG-U133_Plus_2).CEL

description: Treatment with TRI

source_name: HepaRG cell line


title: norm-VUB-1009-TRIDMSO-24-R-3-1B_(HG-U133_Plus_2).CEL

description: Control TRI


title: norm-BPI-1805-E-24H-R1_(HG-U133_Plus_2).CEL

description: Treatment with E

value: Treatment with E


title: wt H5N1-infected vs. Mock-infected replicates 4

description: Biological replicate 4 of 5. wt H5N1-infected vs mock-infected

source_name: wt H5N1 infected chicken 4

source_name: mock infected chicken 4


title: E.coli O157 Sakai pH5.5 2h biological rep1


title: E.coli O157 Sakai pH5.5 1.5h biological rep1

description: Gene expression data from E.coli  O157 Sakai at pH5.5 for 1.5h


title: E.coli O157 Sakai pH5.5 1h biological rep3

description: Gene expression data from E.coli  O157 Sakai at pH5.5 for 1h


title: E.coli O157 Sakai pH5.5 1.5h biological rep2


title: CVL125 Selected sample 4

city: Zürich

first: Christian

last: Heichinger

state: Zürich

address: Zollikerstrasse 107

department: Institute of Plant Biology

institute: Zürich University

description: gene expression data of 25-day-old plants which experienced 5 generations of selection and 2 generations without selection

hyb_protocol: Labeled cDNA was hybridized to AGRONOMICS1 Chips using standardized assays and reagents for Affymetrix Fluidics Station 450

scan_protocol: GeneChips were scanned using the Affymetrix Scanner 3000 7G with autoloader

data_processing: Expression signals were normalized using the Robust Multichip Average (RMA) approach, defined in custom functions for analyzing AGRONOMICS1 Chip data (http://www.agron-omics.eu/index.php/resource_center/tiling-array/tools-and-protocols), implemented in R and bioconductor which also requires the aroma.affymetrix package. Log2 RMA expression values (summarized by gene) were generated using Agronomics R script and are available on associated GSE entry.

organism: Arabidopsis thaliana

source_name: CVL125 Selected sample

label_protocol: Biotinylated cRNA were prepared according to the standarf Affymetrix protocol from 1 microgram cDNA

growth_protocol: Sterilized seeds were initially sown on MA agar plates and stratified at 4°C for three days. After 12 days seedlings of CVL39 and CVL125 were transferred to pots in a general soil mix and grown under long-day conditions (23°C, 16 h light, 8 h dark). On day 25 the above ground parts of one individual were harvested in an Eppendorf tube containing glass beads and flash frozen in liquid nitrogen for RNA extraction.

extract_protocol: Approximately half of the frozen whole plant tissue from 25-day old plants was used for RNA extractions. Total RNA was isolated with the TRIzol® Reagent (Invitrogen) and treated with DNAse (Applied Biosystems, AM1906) to remove any contaminating DNA. 2 µg of RNA were reverse transcribed using standard Invitrogen reagents and protocols. cDNA samples were subjected to RNAse H digestion to remove any remaining RNA/DNA hybrid complexes (Invitrogen). The quality of RNA (integrity and purity) and cDNA was assessed with the 2100 Bioanalyzer pico Chip (Agilent Technologies). cDNA was quantified with the NanoDrop 1000TM Spectrophotometer (Thermo SCIENTIFIC) and diluted to 100 ng/µl with sterile dH2O.

value: Recombinant inbred lines CVL125

value: Whole above ground plant

value: 25 days


title: norm-VUB-1008-TRIDMSO-24-R-2-1B_(HG-U133_Plus_2).CEL

description: Control TRI


title: norm-VUB-1007-TRI-24-R-1-1_(HG-U133_Plus_2).CEL

description: Treatment with TRI


title: E.coli O157 Sakai pH5.5 1.5h biological rep3


title: norm-VUB-1009-TAFDMSO-72-R-3-1G_(HG-U133_Plus_2).CEL

description: Control TAF

value: Control TAF


title: E.coli O157 Sakai pH5.5 1h biological rep2


title: E.coli O157 Sakai pH5.5 1h biological rep1


title: CVL125 Selected sample 3


title: E.coli O157 Sakai pH5.5 30min biological rep3

description: Gene expression data from E.coli  O157 Sakai at pH5.5 for 30min


title: norm-VUB-1007-TAF-72-R-1-1_(HG-U133_Plus_2).CEL

description: Treatment with TAF

value: Treatment with TAF


title: E.coli O157 Sakai pH5.5 10min biological rep2

description: Gene expression data from E.coli  O157 Sakai at pH5.5 for 10min


title: norm-VUB-1009-TRI-24-R-3-1_(HG-U133_Plus_2).CEL

description: Treatment with TRI


title: E.coli O157 Sakai pH5.5 30min biological rep1


title: E.coli O157 Sakai pH5.5 30min biological rep2


title: norm-VUB-1008-TRI-24-R-2-1_(HG-U133_Plus_2).CEL

description: Treatment with TRI


title: norm-VUB-1009-TAF-72-R-3-1_(HG-U133_Plus_2).CEL

description: Treatment with TAF


title: CVL125 Selected sample 1


title: CVL125 Selected sample 2


title: norm-VUB-1007-TRIDMSO-24-R-1-1F_(HG-U133_Plus_2).CEL

description: Control TRI


title: norm-VUB-1007-TAFDMSO-72-R-1-1O_(HG-U133_Plus_2).CEL

description: Control TAF


title: E.coli O157 Sakai pH5.5 10min biological rep1


title: norm-VUB-1008-TAF-72-R-2-1_(HG-U133_Plus_2).CEL

description: Treatment with TAF


title: CVL125 Ancestral sample 4

description: gene expression data of 25-day-old plants which did not undergo selection

source_name: CVL125 Ancestral sample


title: E.coli O157 Sakai pH5.5 10min biological rep3


title: CVL125 Ancestral sample 3


title: CVL125 Ancestral sample 2


title: E.coli O157 Sakai pH5.5 30sec biological rep3

description: Gene expression data from E.coli  O157 Sakai at pH5.5 for 30sec


title: norm-VUB-1008-TAFDMSO-72-R-2-1G_(HG-U133_Plus_2).CEL

description: Control TAF


title: norm-VUB-1008-TAFDMSO-24-R-2-1B_(HG-U133_Plus_2).CEL

description: Control TAF


title: CVL125 Ancestral sample 1


title: CVL39 Selected sample 4

source_name: CVL39 Selected sample

value: Recombinant inbred lines CVL39


title: norm-VUB-1009-TAFDMSO-24-R-3-1B_(HG-U133_Plus_2).CEL

description: Control TAF


title: E.coli O157 Sakai pH5.5 30sec biological rep1


title: CVL39 Selected sample 3


title: CVL39 Selected sample 2


title: norm-VUB-1007-TAFDMSO-24-R-1-1I_(HG-U133_Plus_2).CEL

description: Control TAF


title: CVL39 Selected sample 1


title: E.coli O157 Sakai pH5.5 30sec biological rep2


title: E.coli O157 Sakai pH7 1h biological rep2

description: Gene expression data from E.coli  O157 Sakai at pH7 for 1h


title: E.coli O157 Sakai pH7 1h biological rep3

description: Gene expression data from E.coli  O157 Sakai at pH7 for1h


title: norm-VUB-1007-TAF-24-R-1-1_(HG-U133_Plus_2).CEL

description: Treatment with TAF


title: MEFs with lipid only replicate 4

city: Bethesda

first: Ji

last: Luo

state: MD

address: 10 Center Drive, 10/3B43c

institute: National Cancer Institute

description: negative control

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized to the Mouse Gene ST 2.0 microarrays according to the standard Ammymetrix protocol provided by the manufacturer.

scan_protocol: GeneChips were scanned using a GeneArray Scanner.

data_processing: The data was analyzed with Partek Genomics Suite 6.6 using default analysis settings.

source_name: Kras/Hras/Nras-triple knockout MEFs expressing recombinant Nras

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol provided by the manufacturer.

growth_protocol: Cells were cultured in DMDM with 10% FBS in 37C incubator with 5% CO2.

extract_protocol: Total RNA were extract using trizol followed by RNA clean up kit (Qiagen).

treatment_protocol: Cells were transfected with siKRAS234 (sense UUGACGAUACAGCUAAUUCAUA) and siKRAS355 (sense strand CAGGUCAAGAGGAGUACAGUUA) at 0.2, 2, 20 and 50nM in triplicates for 72 hours.  Six replicates of lipid-only transfection were included as control.

value: Mouse embryonic fibroblasts


title: MEFs with lipid only replicate 5

description: negative control


title: E.coli K12 pH5.5 2.5h biological rep3

description: Gene expression data from E.coli K12 at pH5.5 for 2.5h

organism: Escherichia coli str. K-12 substr. MG1655

source_name: E.coli K12 pH5.5 2.5h biological rep3


title: norm-VUB-1008-DM-72-R-2-1I_(HG-U133_Plus_2).CEL

description: Control NMP

value: Control NMP


title: CVL39 Ancestral sample 4

source_name: CVL39 Ancestral sample


title: MEFs with lipid only replicate 6

description: negative control


title: E.coli K12 pH5.5 2.5h biological rep2

source_name: E.coli K12 pH5.5 2.5h biological rep2


title: CVL39 Ancestral sample 3


title: norm-VUB-1008-TAF-24-R-2-1_(HG-U133_Plus_2).CEL

description: Treatment with TAF

value: HepaRG cell line


title: norm-VUB-1007-DM-72-R-1-1N_(HG-U133_Plus_2).CEL

description: Control NMP


title: MEFs with lipid only replicate 3

description: negative control


title: norm-VUB-1009-DM-72-R-3-1I_(HG-U133_Plus_2).CEL

description: Control NMP


title: MEFs with lipid only replicate 1

description: negative control


title: E.coli O157 Sakai pH7 1h biological rep1


title: E.coli K12 pH5.5 2.5h biological rep1

source_name: E.coli K12 pH5.5 2.5h biological rep1


title: CVL39 Ancestral sample 2


title: norm-VUB-1009-TAF-24-R-3-1_(HG-U133_Plus_2).CEL

description: Treatment with TAF


title: CVL39 Ancestral sample 1


title: E.coli K12 pH5.5 2 h biological rep3

description: Gene expression data from E.coli K12 at pH5.5 for 2h

source_name: E.coli K12 pH5.5 2 h biological rep3


title: MEFs with siKRAS_355, 50nM, replicate 3

description: siKRAS_355 dependent gene expression change


title: MEFs with lipid only replicate 2

description: negative control


title: MEFs with siKRAS_355, 50nM, replicate 2


title: norm-VUB-1009-NMP-72-R-3-1_(HG-U133_Plus_2).CEL

description: Treatment with NMP

value: Treatment with NMP


title: E.coli K12 pH5.5 2 h biological rep1

source_name: E.coli K12 pH5.5 2 h biological rep1


title: norm-VUB-1009-DM-24-R-3-1D_(HG-U133_Plus_2).CEL

description: Control NMP


title: norm-VUB-1007-NMP-72-R-1-1_(HG-U133_Plus_2).CEL

description: Treatment with NMP


title: E.coli K12 pH5.5 1.5h biological rep2

description: Gene expression data from E.coli K12 at pH5.5 for 1.5h

source_name: E.coli K12 pH5.5 1.5h biological rep2


title: E.coli K12 pH5.5 2 h biological rep2

source_name: E.coli K12 pH5.5 2 h biological rep2


title: MEFs with siKRAS_355, 20nM, replicate 1


title: MEFs with siKRAS_355, 20nM, replicate 2


title: norm-VUB-1008-DM-24-R-2-1D_(HG-U133_Plus_2).CEL

description: Control NMP


title: E.coli K12 pH5.5 1.5h biological rep3

source_name: E.coli K12 pH5.5 1.5h biological rep3


title: norm-VUB-1007-DM-24-R-1-1H_(HG-U133_Plus_2).CEL

description: Control NMP


title: norm-VUB-1008-NMP-72-R-2-1_(HG-U133_Plus_2).CEL

description: Treatment with NMP


title: MEFs with siKRAS_355, 20nM, replicate 3


title: E.coli K12 pH5.5 1h biological rep3

description: Gene expression data from E.coli K12 at pH5.5 for 1h

source_name: E.coli K12 pH5.5 1h biological rep3


title: E.coli K12 pH5.5 1.5h biological rep1

source_name: E.coli K12 pH5.5 1.5h biological rep1


title: E.coli K12 pH5.5 1h biological rep1

source_name: E.coli K12 pH5.5 1h biological rep1


title: MEFs with siKRAS_355, 50nM, replicate 1


title: Late Time1 vs Time2

city: Edmonton

first: Chelsea

last: Ju

state: Alberta

address: CW 405, Biological Sciences Centre

department: Biological Sciences

country: Canada

institute: University of Alberta

description: 10 biological replicates were used

hyb_protocol: Performed according to El Kayal et al. 2011 (Plant Cell Environ, 34 (2011), pp. 480–500).

data_processing: The raw data was first corrected for background noise by subtracting the local median background value. Data normalization was divided into two stages: within-array and between-array normalization. Print-tip loess detrending procedure was applied to remove the spatial artifacts within each array, and quantile correction was employed to map every value on any chip to the corresponding quantile of the standard distribution. The normalized data was fitted into linear models for each gene. Prior to the statistical analysis, low expressed genes (low intensity) were filtered out to reduce the false discovery rate. The statistical analysis was applied for each gene using empirical Bayes statstic to obtain the p-values, and these p-values were further adjusted by Benjamini-Hockberg procedure. A list of statistically significant differentially expressed (DE) genes was defined as having the adjusted p-value lower than 0.01.

organism: Picea glauca

source_name: Time 1 Late Tree

growth_protocol: Plants were grown under full illumination, 16 h days/8 h nights, 20°C days/20° nights, 50-60% humidity. Fertilization: 0.5g/L 20-20-20

treatment_protocol: The population was visually scored from 2006-2008 for a number of traits, including bud set, under both natural environmental conditions

tag: time point

value: Time 1 = early stage of bud formation

tag: daylight

value: 16 h days/8 h nights

value: shoot tips

tag: developmental stage

value: Late Tree= late bud set phenotype

source_name: Time 2 Late Tree

value: Time 2 =  mid stage of bud formation


title: E.coli K12 pH5.5 1h biological rep2

source_name: E.coli K12 pH5.5 1h biological rep2


title: MEFs with siKRAS_355, 2nM, replicate 1

tag: cell type


title: MEFs with siKRAS_355, 2nM, replicate 2


title: E.coli K12 pH5.5 30min biological rep3_b

description: Gene expression data from E.coli K12 at pH5.5 for 30min

source_name: E.coli K12 pH5.5 30min biological rep3


title: Time1 Early vs Late

description: 6 biological replicates were used

scan_protocol: Performed according to El Kayal et al. 2011 (Plant Cell Environ, 34 (2011), pp. 480–500).

source_name: Time 1 Early Tree

value: Early Tree= early bud set phenotype


title: Time2 Early vs Late

description: 5 biological replicates were used

source_name: Time 2 Early Tree

label_protocol: Performed according to El Kayal et al. 2011 (Plant Cell Environ, 34 (2011), pp. 480–500).


title: norm-VUB-1009-NMP-24-R-3-1_(HG-U133_Plus_2).CEL

description: Treatment with NMP

source_name: HepaRG cell line

tag: cell line

tag: treatment


title: MEFs with siKRAS_355, 2nM, replicate 3

source_name: Kras/Hras/Nras-triple knockout MEFs expressing recombinant Nras


title: norm-VUB-1008-NMP-24-R-2-1_(HG-U133_Plus_2).CEL

description: Treatment with NMP

tag: replicate


title: norm-VUB-1008-HQODMSO-72-R-2-1G_(HG-U133_Plus_2).CEL

description: Control HQO

value: Control HQO


title: norm-VUB-1007-NMP-24-R-1-1_(HG-U133_Plus_2).CEL

description: Treatment with NMP


title: norm-VUB-1009-HQODMSO-72-R-3-1G_(HG-U133_Plus_2).CEL

description: Control HQO


title: E.coli K12 pH5.5 30min biological rep2_b

source_name: E.coli K12 pH5.5 30min biological rep2


title: MEFs with siKRAS_355, 0.2nM, replicate 3


title: E.coli K12 pH5.5 30min biological rep1_b

source_name: E.coli K12 pH5.5 30min biological rep1


title: E.coli K12 pH5.5 10min biological rep3_b

description: Gene expression data from E.coli K12 at pH5.5 for 10min

source_name: E.coli K12 pH5.5 10min biological rep3


title: MEFs with siKRAS_234 ,50nM, replicate 3

description: siKRAS_234 dependent gene expression change


title: MEFs with siKRAS_355, 0.2nM, replicate 2


title: MEFs with siKRAS_355, 0.2nM, replicate 1


title: norm-VUB-1007-HQODMSO-72-R-1-1L_(HG-U133_Plus_2).CEL

description: Control HQO


title: MEFs with siKRAS_234, 50nM, replicate 2


title: Early Time1 vs Time2

description: 8 biological replicates were used

extract_protocol: Performed according to El Kayal et al. 2011 (Plant Cell Environ, 34 (2011), pp. 480–500).


title: norm-VUB-1009-HQO-72-R-3-1_(HG-U133_Plus_2).CEL

description: Treatment with HQO

value: Treatment with HQO


title: E.coli K12 pH5.5 30sec biological rep3_b

description: Gene expression data from E.coli K12 at pH5.5 for 30sec

source_name: E.coli K12 pH5.5 30sec biological rep3


title: norm-VUB-1007-HQO-72-R-1-1_(HG-U133_Plus_2).CEL

description: Treatment with HQO


title: MEFs with siKRAS_234, 50nM, replicate 1


title: norm-VUB-1008-HQO-72-R-2-2_(HG-U133_Plus_2).CEL

description: Treatment with HQO


title: E.coli K12 pH5.5 10min biological rep2_b

source_name: E.coli K12 pH5.5 10min biological rep2


title: norm-VUB-1009-HQODMSO-24-R-3-1B_(HG-U133_Plus_2).CEL

description: Control HQO


title: norm-VUB-1007-HQODMSO-24-R-1-1F_(HG-U133_Plus_2).CEL

description: Control HQO


title: E.coli K12 pH5.5 10min biological rep1_b

source_name: E.coli K12 pH5.5 10min biological rep1


title: norm-VUB-1008-HQODMSO-24-R-2-1B_(HG-U133_Plus_2).CEL

description: Control HQO


title: MEFs with siKRAS_234, 20nM, replicate 2


title: MEFs with siKRAS_234, 20nM, replicate 1


title: MEFs with siKRAS_234, 2nM, replicate 1


title: E.coli K12 pH5.5 30sec biological rep1_b

source_name: E.coli K12 pH5.5 30sec biological rep1


title: MEFs with siKRAS_234, 2nM, replicate 3


title: norm-VUB-1008-HQO-24-R-2-1_(HG-U133_Plus_2).CEL

description: Treatment with HQO


title: MDA_MB_231-CNTRL-DMSO-3

city: Kansas City

first: Chris

middle: W

last: Seidel

state: MO

department: Genomics

institute: Stowers Institute

description:
dmso_3
Gene expression from MDA-MB-231 cells after exposure to DMSO for 30 hrs, replicate 3.

hyb_protocol: Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 and processed with AGCC v3.0 software.

data_processing: Array intensities were processed using the RMA algorithm in the affy library (version affy_1.28.1) from Bioconductor in R version 2.12.

source_name: MDA-MB-231 breast cancer cells, DMSO

label_protocol: Biotinylated cRNA was prepared according to the Ambion Biotin Enhanced MessageAmp II aRNA amplification kit (according to manual rev. C rev 5/16/2008) from 1 ug total RNA.

growth_protocol: MDA-MB-231 cells were obtained from the American Type Culture Collection. All cell lines were maintained in DMEM (GIBCO) supplemented with 10% FBS, Pen/Strep, and Glutamax (GIBCO) in a humidified atmosphere at 370C with 5% CO2.

extract_protocol: Cells were lysed in Trizol (Invitrogen) three days after transfection, RNA was extracted and then processed through an RNeasy column (QIAGEN) using the RNA clean-up protocol.

treatment_protocol: SAHA or DMSO was added directly to the culture media for a final concentration of 2 uM, and cells were collected after 30 hrs of incubation.

value: human breast cancer cell line

tag: drug

value: DMSO


title: norm-VUB-1009-HQO-24-R-3-1_(HG-U133_Plus_2).CEL

description: Treatment with HQO


title: MEFs with siKRAS_234, 0.2nM, replicate 3


title: norm-VUB-1007-HQO-24-R-1-1_(HG-U133_Plus_2).CEL

description: Treatment with HQO


title: E.coli K12 pH7 1h biological rep2_b

description: Gene expression data from E.coli K12 at pH7 for 1h

source_name: E.coli K12 pH7 1h biological rep2


title: MEFs with siKRAS_234, 20nM, replicate 3


title: norm-VUB-1009-DP-72-R-3-1I_(HG-U133_Plus_2).CEL

description: Control HHC

value: Control HHC


title: E.coli K12 pH7 1h biological rep1_b

source_name: E.coli K12 pH7 1h biological rep1


title: MDA_MB_231-DRUG-SAHA-1

description:
saha_1
Gene expression from MDA-MB-231 cells after exposure to HDAC inhibitor SAHA for 30 hrs, replicate 1.

source_name: MDA-MB-231 breast cancer cells, SAHA

value: suberoylanilide hydroxamic acid (SAHA)


title: E.coli K12 pH7 1h biological rep3_b

source_name: E.coli K12 pH7 1h biological rep3


title: MEFs with siKRAS_234, 0.2nM, replicate 2


title: MEFs with siKRAS_234, 2nM, replicate 2


title: MDA_MB_231-CNTRL-DMSO-1

description:
dmso_1
Gene expression from MDA-MB-231 cells after exposure to DMSO for 30 hrs, replicate 1.


title: norm-VUB-1007-DP-72-R-1-1N_(HG-U133_Plus_2).CEL

description: Control HHC


title: MDA_MB_231-ING2-RNAi-3

description:
ing2.3
Gene expression from MDA-MB-231 cells after transfection with ING2 targeting siRNA, replicate 3.

source_name: MDA-MB-231 breast cancer cells, ING2 siRNA

treatment_protocol: ING2 expression is knocked down in human breast cancer cells (MDA-MB-231 cell line) using siRNA #116981 (Ambion) and Dharmafect 1 (Dharmacon). RNA was collected 4 days post-transfection.

tag: sirna

value: ING2 targeting


title: norm-VUB-1009-HHC-72-R-3-1_(HG-U133_Plus_2).CEL

description: Treatment with HHC

value: Treatment with HHC


title: MDA_MB_231-DRUG-SAHA-2

description:
saha_2
Gene expression from MDA-MB-231 cells after exposure to HDAC inhibitor SAHA for 30 hrs, replicate 2.


title: E.coli K12 pH5.5 5 1h biological rep3

description: Gene expression data from E.coli K12 at pH5.5 for 60min

source_name: E.coli K12 pH5.5 5 1h  biological rep3


title: E.coli K12 pH5.5 5 1h biological rep2

source_name: E.coli K12 pH5.5 5 1h  biological rep2


title: norm-VUB-1008-HHC-72-R-2-2_(HG-U133_Plus_2).CEL

description: Treatment with HHC

source_name: HepaRG cell line


title: E.coli K12 pH5.5 5 1h biological rep1

source_name: E.coli K12 pH5.5 5 1h  biological rep1


title: norm-VUB-1008-DP-72-R-2-1I_(HG-U133_Plus_2).CEL

description: Control HHC


title: MDA_MB_231-CNTRL-DMSO-2

description:
dmso_2
Gene expression from MDA-MB-231 cells after exposure to DMSO for 30 hrs, replicate 2.


title: MDA_MB_231-ING2-RNAi-1

description:
ing2.1
Gene expression from MDA-MB-231 cells after transfection with ING2 targeting siRNA, replicate 1.


title: MixFemale_rep4

city: Gainesville

first: Erica

middle: Karin

last: Brockmeier

state: FL

address: 2187 Mowry Road

institute: University of Florida

description: Gene expression after 48 hour exposure to levonorgestrel (100 ng/L) and mifepristone (100 ng/L)

hyb_protocol: Hybridization of 600 ng purified cRNA was completed with the Gene Expression hybridization kit (Agilent, Santa Clara, USA). Cy3-labeled cRNA was incubated with blocking agent and fragmentation buffer at 60 C for 30 minutes. Hybridization buffer was then added to the sample and 40 μL of the sample was added to the gasket. The microarray slide was  incubated with the gasket for 17 hours at 65 C while spinning at 10 rpm. The slide was then washed and dried, and scanning was conducted at the University of Florida gene expression core by the Microarray Scanner (Agilent, Santa Clara, USA).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scannerusing one color scan setting for 8x15k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) to obtain background subtracted Processed Signal intensities.

organism: Gambusia holbrooki

source_name: 100 ng/L levonorgestrel and 100 ng/L mifepristone, replicate 4

label_protocol: The Low RNA Input Amplification Kit for one color (Cy3) (Agilent, Santa Clara, USA) was used to synthesize cRNA. 200 ng RNA and RNA spike-in controls were incubated with T7 primer mix and cDNA synthesis immediately proceeded primer annealing. In vitro transcription and Cy3 incorporation was then conducted and purification of Cy3-labeled cRNA was completed using the RNeasy kit (QIAGEN, Hilden, Germany). cRNA concentrations and specific activities were determined by the Nanodrop (ThermoScientific, Waltham, USA).

growth_protocol: G. holbrooki were captured using pole nets from a pristine river in a New South Wales (NSW) national park

extract_protocol: Liver samples in RNALater were thawed on ice, blotted dry of excess RNAlater, and homogenized in 1mL of TRIzol (Invitrogen, Grand Island, USA). After precipitation in isopropanol and washing with ethanol, RNA was rehydrated with RNAsecure Reagent (Ambion, Grand Island, USA). RNA was DNase treated using Turbo DNase (Ambion, Grand Island, USA). RNA quality and quantity was assessed using the Nanodrop (ThermoScientific, Waltham, USA) and the 2100 BioAnalyzer (Agilent, Santa Clara, USA).

treatment_protocol: G. holbrooki adult males and females were exposed to one of the following conditions: vehicle control (ethanol), 100 ng/L of levonorgestrel, 100 ng/L of mifepristone, or a mixture of both levonorgestrel and mifepristone. All exposures were conducted for 48 hours with water changed and chemicals renewed daily.

tag: tissue

value: liver

tag: gender

value: female


title: MifeFemale_rep3

description: Gene expression after 48 hour exposure to mifepristone (100 ng/L)

source_name: 100 ng/L mifepristone, replicate 3


title: MixFemale_rep3

source_name: 100 ng/L levonorgestrel and 100 ng/L mifepristone, replicate 3

value: 48 hour exposure to levonorgestrel (100 ng/L) and mifepristone (100 ng/L)


title: E.coli K12 pH5.5 55min biological rep1

description: Gene expression data from E.coli K12 at pH5.5 for 55min

source_name: E.coli K12 pH5.5 55min biological rep1


title: MEFs with siKRAS_234, 0.2nM, replicate 1

source_name: Kras/Hras/Nras-triple knockout MEFs expressing recombinant Nras

value: Mouse embryonic fibroblasts


title: MDA_MB_231-CNTRL-RNAi-3

description:
cntrl.3
Gene expression from MDA-MB-231 cells after transfection with non-targeting siRNA, replicate 3.

source_name: MDA-MB-231 breast cancer cells, control siRNA

value: non-targeting


title: MifeFemale_rep4

source_name: 100 ng/L mifepristone, replicate 4

value: 48 hour exposure to mifepristone (100 ng/L)


title: E.coli K12 pH5.5 55min biological rep3

source_name: E.coli K12 pH5.5 55min biological rep3


title: MDA_MB_231-ING2-RNAi-2

description:
ing2.2
Gene expression from MDA-MB-231 cells after transfection with ING2 targeting siRNA, replicate 2.


title: ControlFemale_rep4

description: Gene expression after 48 hour exposure to vehicle control (0.001% ethanol).

source_name: Vehicle control, replicate 4


title: MixFemale_rep2

source_name: 100 ng/L levonorgestrel and 100 ng/L mifepristone, replicate 2


title: E.coli K12 pH5.5 50min biological rep2

description: Gene expression data from E.coli K12 at pH5.5 for 50min

source_name: E.coli K12 pH5.5 50min biological rep2


title: E.coli K12 pH5.5 50min biological rep3

source_name: E.coli K12 pH5.5 50min biological rep3


title: E.coli K12 pH5.5 55min biological rep2

source_name: E.coli K12 pH5.5 55min biological rep2


title: MDA_MB_231-CNTRL-RNAi-2

description:
cntrl.2
Gene expression from MDA-MB-231 cells after transfection with non-targeting siRNA, replicate 2.


title: E.coli K12 pH5.5 45min biological rep3

description: Gene expression data from E.coli K12 at pH5.5 for 45min

source_name: E.coli K12 pH5.5 45min biological rep3


title: norm-VUB-1008-DP-24-R-2-1D_(HG-U133_Plus_2).CEL

description: Control HHC

value: HepaRG cell line


title: MDA_MB_231-CNTRL-RNAi-1

description:
cntrl.1
Gene expression from MDA-MB-231 cells after transfection with non-targeting siRNA, replicate 1.


title: E.coli K12 pH5.5 50min biological rep1

source_name: E.coli K12 pH5.5 50min biological rep1


title: norm-VUB-1007-HHC-72-R-1-1_(HG-U133_Plus_2).CEL

description: Treatment with HHC

source_name: HepaRG cell line


title: pooled untreated xenograft, technical rep 2

city: Budapest

first: Andras

last: Furedi

state: HU

address: Magyar tudosok krt 2

department: Molecular Life Sciences

country: Hungary

institute: HUN-REN RCNS

description: Gene expression data from untreated HT-29 xenograft

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome HGU133 Plus2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 using FS450_001 fluidics script.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip3000 Scanner with 7G upgrade.

data_processing: The data were analyzed with  R using gcrma Bioconductor package. Preprocessing and normalization were performed by GCRMA method.

source_name: opposite side of 4h post-treatment

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

growth_protocol: HT-29 human colorectal adenocarcinoma cells were grown in DMEM+ GlutaMax, high-glucose (4.5 g/l) medium. After the detachin and purification protocol 0.1 ml suspension of 10^7/ml HT29 tumor cells were injected into both femoral regions of 6 to 8-week old Balb/c (nu/nu) mice.

extract_protocol: Macrodissected tissue sections were collected into prechilled 2 ml eppendorf tubes and stored at -80 C. Total RNA were extracted by Roche MagNA Pure LC RNA Isolation Tissue Kit according to the manufacturer's protocol.

treatment_protocol: After 18 days 30 min electromagnetic heat treatment, sampling time 4h post-treatment

tag: xenograft cell line

tag: xenograft cell type

value: colon adenocarcinoma

tag: host

value: Balb/c (nu/nu) mice


title: norm-VUB-1009-HHC-24-R-3-1_(HG-U133_Plus_2).CEL

description: Treatment with HHC


title: LevoFemale_rep3

description: Gene expression after 48 hour exposure to levonorgestrel (100 ng/L)

source_name: 100 ng/L levonorgestrel, replicate 3


title: LevoFemale_rep2

source_name: 100 ng/L levonorgestrel, replicate 2

value: 48 hour exposure to levonorgestrel (100 ng/L)


title: norm-VUB-1009-DP-24-R-3-1D_(HG-U133_Plus_2).CEL

description: Control HHC


title: norm-VUB-1007-DP-24-R-1-1H_(HG-U133_Plus_2).CEL

description: Control HHC


title: LevoFemale_rep4

source_name: 100 ng/L levonorgestrel, replicate 4


title: E.coli K12 pH5.5 45min biological rep1

source_name: E.coli K12 pH5.5 45min biological rep1


title: E.coli K12 pH5.5 45min biological rep2

source_name: E.coli K12 pH5.5 45min biological rep2


title: pooled untreated xenograft, technical rep 1


title: norm-VUB-1007-HHC-24-R-1-1_(HG-U133_Plus_2).CEL

description: Treatment with HHC


title: norm-VUB-1009-DP-72-R-3-1J_(HG-U133_Plus_2).CEL

description: Control FMB

value: Control FMB


title: pooled 4h thermo-treated xenograft, technical rep 1

description: Gene expression data from 4h thermo-treated HT-29 xenograft

source_name: 4h post-treatment


title: pooled 4h thermo-treated xenograft, technical rep 2


title: norm-VUB-1008-DP-72-R-2-1J_(HG-U133_Plus_2).CEL

description: Control FMB


title: pooled control xenograft, technical rep 2

description: Gene expression data from control HT-29 xenograft

source_name: control HT-29 xenograft


title: MifeFemale_rep2

source_name: 100 ng/L mifepristone, replicate 2


title: ControlFemale_rep3

source_name: Vehicle control, replicate 3

value: 48 hour exposure to vehicle control (0.001% ethanol).


title: MifeFemale_rep1

source_name: 100 ng/L mifepristone, replicate 1


title: norm-VUB-1008-HHC-24-R-2-1_(HG-U133_Plus_2).CEL

description: Treatment with HHC


title: E.coli K12 pH5.5 40min biological rep1

description: Gene expression data from E.coli K12 at pH5.5 for 40min

source_name: E.coli K12 pH5.5 40min biological rep1


title: E.coli K12 pH5.5 40min biological rep2

source_name: E.coli K12 pH5.5 40min biological rep2


title: E.coli K12 pH5.5 40min biological rep3

source_name: E.coli K12 pH5.5 40min biological rep3


title: E.coli K12 pH5.5 35min biological rep3

description: Gene expression data from E.coli K12 at pH5.5 for 35min

source_name: E.coli K12 pH5.5 35min biological rep3


title: norm-VUB-1007-DP-72-R-1-1P_(HG-U133_Plus_2).CEL

description: Control FMB


title: ControlFemale_rep1

source_name: Vehicle control, replicate 1


title: ControlFemale_rep2

source_name: Vehicle control, replicate 2


title: MixFemale_rep1

source_name: 100 ng/L levonorgestrel and 100 ng/L mifepristone, replicate 1


title: pooled control xenograftt, technical rep 1


title: norm-VUB-1009-FMB-72-R-3-1_(HG-U133_Plus_2).CEL

description: Treatment with FMB

source_name: HepaRG cell line

value: Treatment with FMB


title: norm-VUB-1007-FMB-72-R-1-1_(HG-U133_Plus_2).CEL

description: Treatment with FMB


title: LevoMale_rep4

value: male


title: norm-VUB-1008-FMB-72-R-2-2_(HG-U133_Plus_2).CEL

description: Treatment with FMB


title: LevoFemale_rep1

source_name: 100 ng/L levonorgestrel, replicate 1


title: VA(-) virus infection sample2

city: Kobe

first: Kenji

last: Yoshida

address: 2-2-2, Minatojima Minamimachim Chuo-ku

department: Regenerative & Cellular Medicine

institute: Sumitomo Dainippon Pharma Co.,Ltd.

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45C on GeneChip® Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station FS450-0001.

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000 7G

data_processing: Data analysis was carried out by Expression Console 1.1 (Affymetrix). Detection and signal were obtained by MAS5 algorithm with default settings. Global normalization was performed to make average signal intensity of all probesets equal to 100.

source_name: A549 VA(-) virus infection at 24hr

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol

growth_protocol: A549 with/without virus was cultured in normal DMEM+FCS media.

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

treatment_protocol: Virus infection period was 24 hours.

value: alveolar basal epithelial cells

tag: infected with

value: virus-associated RNA-deleted (VA-)adeviral vectors (AdVs)


title: VA(-) virus infection sample3


title: E.coli K12 pH5.5 35min biological rep2

source_name: E.coli K12 pH5.5 35min biological rep2


title: VA(+) virus infection sample3

source_name: A549 VA(+) virus infection at 24hr

value: virus-associated RNA (VA+) adeviral vectors (AdVs)


title: MifeMale_rep4

source_name: 100 ng/L mifepristone, replicate 4

value: liver


title: E.coli K12 pH5.5 35min biological rep1

source_name: E.coli K12 pH5.5 35min biological rep1


title: VA(+) virus infection sample2


title: E.coli K12 pH5.5 30min biological rep3

description: Gene expression data from E.coli K12 at pH5.5 for 30min

source_name: E.coli K12 pH5.5 30min biological rep3


title: VA(-) virus infection sample1


title: norm-VUB-1007-DP-24-R-1-1J_(HG-U133_Plus_2).CEL

description: Control FMB


title: LevoMale_rep3

source_name: 100 ng/L levonorgestrel, replicate 3


title: norm-VUB-1009-DP-24-R-3-1E_(HG-U133_Plus_2).CEL

description: Control FMB


title: E.coli K12 pH5.5 30min biological rep2

source_name: E.coli K12 pH5.5 30min biological rep2


title: E.coli K12 pH5.5 30min biological rep1

source_name: E.coli K12 pH5.5 30min biological rep1


title: ControlMale_rep3

source_name: Vehicle control, replicate 3


title: norm-VUB-1008-DP-24-R-2-1E_(HG-U133_Plus_2).CEL

description: Control FMB


title: VA(+) virus infection sample1


title: Mock infection sample3

source_name: A549 mock infection at 24hr

value: mock control


title: LevoMale_rep2

source_name: 100 ng/L levonorgestrel, replicate 2


title: Mock infection sample2


title: E.coli K12 pH5.5 30sec biological rep2_b

description: Gene expression data from E.coli K12 at pH5.5 for 30sec

source_name: E.coli K12 pH5.5 30sec biological rep2


title: Mock infection sample1


title: ControlMale_rep2

source_name: Vehicle control, replicate 2


title: norm-VUB-1008-FMB-24-R-2-1_(HG-U133_Plus_2).CEL

description: Treatment with FMB


title: norm-VUB-1009-FMB-24-R-3-1_(HG-U133_Plus_2).CEL

description: Treatment with FMB


title: norm-VUB-1007-FMB-24-R-1-1_(HG-U133_Plus_2).CEL

description: Treatment with FMB


title: norm-VUB-1009-DMSO-72-R-3-1G_(HG-U133_Plus_2).CEL

description: Control FAF

value: Control FAF


title: E.coli K12 pH5.5 25min biological rep2

description: Gene expression data from E.coli K12 at pH5.5 for 25min

source_name: E.coli K12 pH5.5 25min biological rep2


title: E.coli K12 pH5.5 25min biological rep1

source_name: E.coli K12 pH5.5 25min biological rep1


title: E.coli K12 pH5.5 20min biological rep3

description: Gene expression data from E.coli K12 at pH5.5 for 20min

source_name: E.coli K12 pH5.5 20min biological rep3


title: E.coli K12 pH5.5 25min biological rep3

source_name: E.coli K12 pH5.5 25min biological rep3


title: norm-VUB-1008-DMSO-72-R-2-1G_(HG-U133_Plus_2).CEL

description: Control FAF

source_name: HepaRG cell line


title: MixMale_rep2

description: Gene expression after 48 hour exposure to levonorgestrel (100 ng/L) and mifepristone (100 ng/L)

source_name: 100 ng/L levonorgestrel and 100 ng/L mifepristone, replicate 2


title: E.coli K12 pH5.5 20min biological rep2

source_name: E.coli K12 pH5.5 20min biological rep2


title: MifeMale_rep2

description: Gene expression after 48 hour exposure to mifepristone (100 ng/L)

source_name: 100 ng/L mifepristone, replicate 2


title: MifeMale_rep3

source_name: 100 ng/L mifepristone, replicate 3


title: H460R-3

city: Columbus

first: Alessandra

last: Drusco

state: Ohio

address: 460 W 12th Ave

institute: The Ohio State University

description: Gene expression from acquired TRAIL-resistant cells

hyb_protocol: Samples were hybridized using Herring sperm DNA, Acetylated BSA (50mg/ml), BioArray Eukaryotic Hybridization Controls (Enzo Life Science) Heat 65c for 5 mins, 99c for 5 mins

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G using Command Console

data_processing: Data were normalized by the RMA algorithm (Quantiles Normalization)

source_name: TRAIL-resistant H460 cells

label_protocol: Samples were enzimatically labeled using BioArray High Yield RNA Transcript Labeling kit (Enzo)

growth_protocol: The cells were grown with RPMI supplemented 10% FBS at 37C

extract_protocol: Trizol extraction was performed following the manufacturer's protocol

treatment_protocol: NSCLC H460 cells  were  treated  with TRAIL daily for a period of 6 months.

tag: genotype/variation

value: acquired TRAIL-resistance


title: MixMale_rep3

source_name: 100 ng/L levonorgestrel and 100 ng/L mifepristone, replicate 3

value: 48 hour exposure to levonorgestrel (100 ng/L) and mifepristone (100 ng/L)


title: E.coli K12 pH5.5 20min biological rep1

source_name: E.coli K12 pH5.5 20min biological rep1

tag: wildtype


title: ControlMale_rep1

description: Gene expression after 48 hour exposure to vehicle control (0.001% ethanol).

source_name: Vehicle control, replicate 1


title: H460R-4


title: H460R-2


title: E.coli K12 pH5.5 15min biological rep2

description: Gene expression data from E.coli K12 at pH5.5 for 15min

source_name: E.coli K12 pH5.5 15min biological rep2


title: MixMale_rep1

source_name: 100 ng/L levonorgestrel and 100 ng/L mifepristone, replicate 1


title: H460S-4

description: Gene expression from control cell

source_name: TRAIL-sensitive H460 cells

value: control


title: H460R-1


title: norm-VUB-1007-DMSO-72-R-1-1L_(HG-U133_Plus_2).CEL

description: Control FAF

value: HepaRG cell line


title: E.coli K12 pH5.5 15min biological rep3

source_name: E.coli K12 pH5.5 15min biological rep3


title: H460S-3

description: Gene expression from control cell


title: MifeMale_rep1

source_name: 100 ng/L mifepristone, replicate 1

value: 48 hour exposure to mifepristone (100 ng/L)


title: H460S-2

description: Gene expression from control cell


title: E.coli K12 pH5.5 10min biological rep3

description: Gene expression data from E.coli K12 at pH5.5 for 10min

source_name: E.coli K12 pH5.5 10min biological rep3


title: E.coli K12 pH5.5 5min biological rep3

description: Gene expression data from E.coli K12 at pH5.5 for 5min

source_name: E.coli K12 pH5.5 5min biological rep3


title: norm-VUB-1007-DMSO-24-R-1-1F_(HG-U133_Plus_2).CEL

description: Control FAF


title: E.coli K12 pH5.5 10min biological rep2

source_name: E.coli K12 pH5.5 10min biological rep2


title: norm-VUB-1008-DMSO-24-R-2-1B_(HG-U133_Plus_2).CEL

description: Control FAF

source_name: HepaRG cell line


title: norm-VUB-1009-FAF-72-R-3-1_(HG-U133_Plus_2).CEL

description: Treatment with FAF

value: Treatment with FAF


title: E.coli K12 pH5.5 10min biological rep1

source_name: E.coli K12 pH5.5 10min biological rep1


title: norm-VUB-1009-FAF-24-R-3-1_(HG-U133_Plus_2).CEL

description: Treatment with FAF


title: H460S-1

description: Gene expression from control cell


title: CSES22 ES from T2

city: Jerusalem

first: Uri

last: Ben-David

address: Givat-Ram

department: Genetics

country: Israel

institute: Hebrew University

hyb_protocol: Affymetrix protocol, 11ug cRNA

scan_protocol: GeneChip scanner 3000 7G, GeneChip Operating Software v1.4

data_processing: Affymetrix Expression Console MAS5

source_name: CSES22 pluripotent cells recovered from teratoma

label_protocol: 200ng total RNA, Affymetrix protocol

growth_protocol: Cells were grown on gelatin-coated plates using Knockout DMEM supplemented with 15 % FBS (Hyclone), 5% KnockOutTM Serum Replacement (Invitrogen), 1 mM glutamine (Invitrogen), 1% nonessential amino acids (Invitrogen), 0.1 mM beta-mercaptoethanol (Sigma) and 8 ng/ml FGF2 (R&D systems)].  Cultures were passaged every 5 to 7 days either manually or enzymatically with collagenase type IV (Invitrogen; 1.5 mg/ml).

extract_protocol: total RNA was isolated from pluripotent-like cells recovred from 3w old teratoma using 5 Prime RNA isolation kit

value: Undifferentiated human embryonic stem cells recovered from teratoma

tag: genotype


title: norm-VUB-1008-FAF-72-R-2-1_(HG-U133_Plus_2).CEL

description: Treatment with FAF

data_processing: The Affymetrix IDs were alternatively remapped to the alternative IDs from Brainarray  (http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/CDF_download.asp), thus the ensemb version 61 was used (http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/14.1.0/ensg.download/HGU133Plus2_Hs_ENSG_14.1.0.zip).  All samples were  further normalized by GC-RMA algorithm. As the number of controls were less than the number of treatments, the same controls were used several to normalize data from several treatments.


title: E.coli K12 pH5.5 15min biological rep1

source_name: E.coli K12 pH5.5 15min biological rep1


title: norm-VUB-1009-DMSO-24-R-3-1B_(HG-U133_Plus_2).CEL

description: Control FAF


title: E.coli K12 pH5.5 5min biological rep2

source_name: E.coli K12 pH5.5 5min biological rep2


title: norm-VUB-1008-FAF-24-R-2-1_(HG-U133_Plus_2).CEL

description: Treatment with FAF


title: norm-VUB-1009-ETHDMSO-72-R-3-1H_(HG-U133_Plus_2).CEL

description: Control ETH

value: Control ETH


title: LevoMale_rep1

source_name: 100 ng/L levonorgestrel, replicate 1

value: 48 hour exposure to levonorgestrel (100 ng/L)


title: HiPS18_late T2

source_name: HiPS18 teratoma from late passage T12-iPS cells

growth_protocol: Cells differentiated in-vivo following injection of undifferentiated pluripotent cells into the kidney of immunodeficient mice

extract_protocol: total RNA was isolated from 3w old teratoma using 5 Prime RNA isolation kit

value: In-vivo differentiated human induced pluripotent stem cells


title: HiPS18 ES from T2

source_name: HiPS18 pluripotent-like cells recovered from teratoma

value: Undifferentiated human induced pluripotent stem cells recovered from teratoma


title: E.coli K12 pH5.5 5min biological rep1

source_name: E.coli K12 pH5.5 5min biological rep1


title: norm-VUB-1008-ETHDMSO-72-R-2-1H_(HG-U133_Plus_2).CEL

description: Control ETH

extract_protocol: Samples for RNA isolation were collected after 24 and 72 hours of exposure. Minimum three independent biological experiments were conducted for each compound. The total RNA extraction (RNA extraction kit, Qiagen), including a DNase digestion step, was done according to the manufacturer’s instructions.


title: CSES45p20 T3

source_name: CSES45 teratoma from T12-ES cells

value: In-vivo differentiated human embryonic stem cells


title: norm-VUB-1007-FAF-24-R-1-1_(HG-U133_Plus_2).CEL

description: Treatment with FAF


title: HiPS18 ES from T1


title: E.coli K12 pH5.5 30sec biological rep2

source_name: E.coli K12 pH5.5 30sec biological rep2


title: HiPS18_early T2

source_name: HiPS18 teratoma from early passage diploid iPS cells

tag: passage

value: passage 35


title: CSES22p35 T2

source_name: CSES22 teratoma from T12-ES cells


title: E.coli K12 pH5.5 30sec biological rep3

source_name: E.coli K12 pH5.5 30sec biological rep3


title: norm-VUB-1007-FAF-72-R-1-2_(HG-U133_Plus_2).CEL

description: Treatment with FAF


title: norm-VUB-1007-ETHDMSO-72-R-1-1O_(HG-U133_Plus_2).CEL

description: Control ETH


title: norm-VUB-1009-ETH-72-R-3-1_(HG-U133_Plus_2).CEL

description: Treatment with ETH

value: Treatment with ETH


title: CSES26p17 T1(2)

source_name: CSES26 teratoma from ES cells


title: E.coli K12 pH7 1h biological rep2

description: Gene expression data from E.coli K12 at pH7 for 1h

source_name: E.coli K12 pH7 1h biological rep2


title: E.coli K12 pH5.5 30sec biological rep1

source_name: E.coli K12 pH5.5 30sec biological rep1


title: CSES15p24 T1

source_name: CSES15 teratoma from ES cells

value: passage 52


title: E.coli K12 pH7 1h biological rep3

description: Gene expression data from E.coli K12 at pH7 for1h

source_name: E.coli K12 pH7 1h biological rep3


title: CSES25p23 T2

source_name: CSES25 teratoma from ES cells


title: norm-VUB-1008-ETH-72-R-2-1_(HG-U133_Plus_2).CEL

description: Treatment with ETH

source_name: HepaRG cell line


title: CSES7p10 T1

source_name: CSES7 teratoma from ES cells


title: CSES45p20 ES

source_name: CSES45 undifferentiated ES cells

extract_protocol: total RNA was isolated from undifferentiated pluripotent stem cells grown on MEFs with standard human ES culture medium using 5 Prime RNA isolation kit

value: Undifferentiated human embryonic stem cells

value: passage 22


title: E.coli K12 pH7 30min biological rep2

description: Gene expression data from E.coli K12 at pH7 for 30 min

source_name: E.coli K12 pH7 30min biological rep2


title: CSES22p34 ES

source_name: CSES22 undifferentiated ES cells

value: passage 34


title: E.coli K12 pH7 1h biological rep1

source_name: E.coli K12 pH7 1h biological rep1


title: norm-VUB-1009-ETH-24-R-3-1_(HG-U133_Plus_2).CEL

description: Treatment with ETH


title: norm-VUB-1007-ETHDMSO-24-R-1-1I_(HG-U133_Plus_2).CEL

description: Control ETH


title: norm-VUB-1009-ETHDMSO-24-R-3-1C_(HG-U133_Plus_2).CEL

description: Control ETH


title: E.coli K12 pH7 30min biological rep1

source_name: E.coli K12 pH7 30min biological rep1


title: norm-VUB-1008-ETHDMSO-24-R-2-1C_(HG-U133_Plus_2).CEL

description: Control ETH


title: norm-VUB-1008-ETH-24-R-2-1_(HG-U133_Plus_2).CEL

description: Treatment with ETH


title: norm-VUB-1007-ETH-72-R-1-1_(HG-U133_Plus_2).CEL

description: Treatment with ETH


title: LN229-miR-127-3p

city: hangzhou

first: jie

last: liu

address: yuhangtang road 866

country: China

institute: zcni

description: miR-127-3p overexpression LN229

hyb_protocol: Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hours at 45 ℃ on GeneChip U133_plus 2.0 Array. GeneChips were washed and stained in the Affymetrix fluidics Station 450.

scan_protocol: The chips were scanned with the affymetrix genechip 7G plus, and AGCC is used for the image processing

data_processing: Genespring 10.0 is used for automatically normalizing the chip data and analyzing the fold change

source_name: LN229 human glioblastoma cell line with miR-127-3p overexpression

label_protocol: Start with 250ng total RNA, and Biotinylated cRNA were prepared according to the standard Affymetrix protocol, in which, GeneChip 3 IVT Express Kit (Lot no.901228) is used in the experiment.

growth_protocol: cells were cultured in DMEM with 10% FBS

extract_protocol: total RNA was extracted with Trizol according to the manufacturer's protocol

treatment_protocol: MiR-127-3p was overexpressed with pSUPER.neo-miR-127-3p or pSUPER.neo in LN229

value: LN229 glioblastoma cell line

value: miR-127-3p overexpression


title: norm-VUB-1007-ETH-24-R-1-1_(HG-U133_Plus_2).CEL

city: Brussels

last: Doktorova

institute: VUB

description: Treatment with ETH

hyb_protocol: We used standard Affymetrix hybridisation rotocols

scan_protocol: We used standard Affymetrix scanning parameters

label_protocol: We used standard Affymetrix labeling protocols

value: HepaRG cell line


city: Beijing

first: Wentao

last: Liu

address: 22 Zhongguancun South Avenue

institute: Peking University School and Hospital of Stomatology

description: Gene expression data from hBMSCs cultured on aligned nanofibers at day 14

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45°C on GeneChip Wheat Genome Array in the Affymetrix Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the affymetrix scanner 3000 7G.The scanned images were first assessed by visual inspection then analyzed to generate raw data files saved as CEL files using the default setting of AGCC.

data_processing: The data were normalized using Robust Multi-array Average(RMA) .

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 200ng total RNA (3' IVT Express Kit User Manual, 2008, Affymetrix).

growth_protocol: The cell culture medium contained 10% Fetal Bovine Serum, 10 µg/ml glutamine, and 100 IU/ml penicillin-streptomycin. The medium was changed every 2–3 days.

treatment_protocol: hBMSCs were seeded on random and aligned nanofibers and flat polymer films with/without OS were harvested at 4, 7, 14 and 21 days, the total RNA was extracted for microarray analysis.

value: bone marrow mesenchymal stem cells


description: Gene expression data from hBMSCs cultured on aligned nanofibers at day 21


description: Gene expression data from hBMSCs cultured on aligned nanofibers at day 7


description: Gene expression data from hBMSCs cultured on aligned nanofibers at day 4


title: norm-VUB-1008-DLMDMSO-72-R-2-1F_(HG-U133_Plus_2).CEL

first: Tatyana

address: Laarbeeklaan 103, building G

description: Control DLM

value: Control DLM


title: norm-VUB-1009-DLMDMSO-72-R-3-1F_(HG-U133_Plus_2).CEL

description: Control DLM


title: E.coli K12 pH7 30min biological rep3

source_name: E.coli K12 pH7 30min biological rep3


title: LN229-control

description: LN229 control

source_name: LN229 human glioblastoma cell line with control overexpression

value: control overexpression


title: norm-VUB-1009-DLM-72-R-3-1_(HG-U133_Plus_2).CEL

description: Treatment with DLM

value: Treatment with DLM


description: Gene expression data from hBMSCs cultured on random nanofibers at day 21


title: norm-VUB-1007-DMSO-24-R-1-1I_(HG-U133_Plus_2).CEL

description: Control DLM


title: norm-VUB-1007-DLM-72-R-1-1_(HG-U133_Plus_2).CEL

description: Treatment with DLM


title: hBMSCs induced with OS at day 21

description: Gene expression data from hBMSCs induced with OS at day 21

source_name: hBMSCs induced with OS at day 21


description: Gene expression data from hBMSCs cultured on random nanofibers at day 14


title: hBMSCs induced with OS at day 7

description: Gene expression data from hBMSCs induced with OS at day 7

source_name: hBMSCs induced with OS at day 7


title: hBMSCs induced with OS at day 14

description: Gene expression data from hBMSCs induced with OS at day 14

source_name: hBMSCs induced with OS at day 14


title: norm-VUB-1008-DLMDMSO-24-R-2-1A_(HG-U133_Plus_2).CEL

description: Control DLM


title: hBMSCs induced with OS at day 4

description: Gene expression data from hBMSCs induced with OS at day 4

source_name: hBMSCs induced with OS at day 4


title: hBMSCs cultured on flat films at day 14

description: Gene expression data from hBMSCs cultured on flat films at day 14

source_name: hBMSCs cultured on flat films at day 14


title: norm-VUB-1008-DLM-72-R-2-1_(HG-U133_Plus_2).CEL

description: Treatment with DLM


title: hBMSCs cultured on flat films at day 21

description: Gene expression data from hBMSCs cultured on flat films at day 21

source_name: hBMSCs cultured on flat films at day 21


title: norm-VUB-1009-DLMDMSO-24-R-3-1A_(HG-U133_Plus_2).CEL

description: Control DLM


title: norm-VUB-1009-DLM-24-R-3-1_(HG-U133_Plus_2).CEL

description: Treatment with DLM


description: Gene expression data from hBMSCs cultured on random nanofibers at day 7


description: Gene expression data from hBMSCs cultured on random nanofibers at day 4


title: norm-VUB-1008-DLM-24-R-2-1_(HG-U133_Plus_2).CEL

description: Treatment with DLM


title: norm-VUB-1007-DLM-24-R-1-1_(HG-U133_Plus_2).CEL

description: Treatment with DLM


title: hBMSCs cultured on flat films at day 7

description: Gene expression data from hBMSCs cultured on flat films at day 7

source_name: hBMSCs cultured on flat films at day 7


title: norm-VUB-1009-DHPDMSO-72-R-3-1H_(HG-U133_Plus_2).CEL

description: Control DHP

source_name: HepaRG cell line

value: Control DHP


title: colonocytes from aldosterone treated rat, biological rep1

city: Rehovot

first: Haim

last: Garty

address: Hertzel 234

department: Biological Chemistry

institute: The Weizmann Institute of Science

description: Gene expression data from surface colonocytes of aldosterone treated rat

hyb_protocol: The labeling assay yielded labeled single-stranded DNA that was fragmented and hybridized to Affymetrix Rat Exon 1.0 ST Arrays according to manufacturer’s protocols. Shortly, Samples were heated at 90° for 5 minutes, then 45° for 5 minutes, centrifuged at max speed for 1 minute and then 200µl were transferred to each array. Hybridization lasted 16 hours at 45° at 60rpm.

scan_protocol: Hybridized Affymetrix Rat Exon 1.0 ST Arrays were washed by Affymetrix GeneChip Fluidics Station 450 (protocol FS450_0001) and scanned by Affymetrix GeneChip Scanner 3000 7G.

data_processing: Quality control assessment was carried out through the Expression Console software (Affymetrix, Inc., US). Statistical analysis of microarray data was performed using the Partek® Genomics Suite (Partek Inc., St. Louis, Missouri 63141) software. CEL files were imported to Partek GS and the data was preprocessed and normalized using the RMA (Robust Multichip Average) algorithm. To identify differentially expressed genes among the different treatments, a mixed model ANOVA analysis of variance was applied.

organism: Rattus norvegicus

label_protocol: Biotinylated sense-strand DNA for hybridization to Affymetrix exon arrays was prepared with the Affymetrix GeneChip whole transcript sense target labeling assay, using the standard 1 μg total RNA method according to the manufacturer’s protocols (Affymetrix, 900854). Ribosomal RNA reduction was performed using the RiboMinus Human/Mouse Transcriptome Isolation Kit (Invitrogen, K1550-01).

growth_protocol: Bilaterally adrenalectomized rats were maintained for 4 days under a 12 hr light/dark cycle with free access to standard rat chow and drinking water containing 0.9% NaCl.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions (MRC Cincinnati OH 45212).

treatment_protocol: One group of 2 rats was injected subcutaneousely (sc) with a single dose of 50 µg/100g body weight aldosterone. In addition, these rats were implanted sc with osmotic minipumps which were filled with aldosterone dissolved in polyethylene glycol 300 at a concentration designed to achieve delivery rates of 10µg/kg*hr. Another group of 2 rats was injected with the vehicle and implanted with osmotic minipumps delivering PEG300. After 2 hours of aldosterone/vehicle treatment rats were euthanized using CO2 gas. Distal colons were excised and surface colonocytes were dissociated during 40 min ex-vivo shaking of inverted colons in a solution containing either 100 nM aldosterone or vehicle.

value: distal colon

tag: background strain

value: wistar rat

tag: age

value: 12 weeks


title: colonocytes from aldosterone treated rat, biological rep2


title: colonocytes from vehicle treated rat, biological rep2

description: Gene expression data from surface colonocytes of control rat

source_name: colonocytes from vehicle treated rat


title: colonocytes from vehicle treated rat, biological rep1


title: norm-VUB-1007-DHP-72-R-1-1_(HG-U133_Plus_2).CEL

description: Treatment with DHP

growth_protocol: The human hepatoma-derived HepaRG cells (Biopredic International, France) were cultivated as previously described  by A. Guillouzo et al. 168 (2007) 66-73.  and P. Gripon et al 99 (2002) 15655-15660. At day 13 of cultivation, dimethylsulfoxide (DMSO)-containing medium (2%) was added for 7 days . At day 19 exposure with the selected compounds was initiated.

tag: cell line

value: Treatment with DHP


title: norm-VUB-1008-DHP-72-R-2-1_(HG-U133_Plus_2).CEL

description: Treatment with DHP

tag: treatment


title: norm-VUB-1009-DHP-72-R-3-1_(HG-U133_Plus_2).CEL

description: Treatment with DHP

tag: replicate


title: hBMSCs cultured on flat films at day 4

description: Gene expression data from hBMSCs cultured on flat films at day 4

source_name: hBMSCs cultured on flat films at day 4

tag: cell type


title: solitary colorectal cancer sample_3267

type: genomic

city: Barcelona

first: Juanjo

last: Lozano

address: C/ Rosselló 153

department: Plataforma de Bioinformatica

country: Spain

institute: CIBEREHD

description: solitary colorectal cancer :3267

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

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: BeadStudio software v3.2 and beta-value correction using metillumi R package

label: Cy5 and Cy3

molecule: genomic DNA

source_name: tumor colorectal tissue

label_protocol: Standard Illumina Protocol

growth_protocol: Frozen samples were thawed and genomic DNA was isolated using QIAamp DNA Mini Kit (Qiagen, Valencia, CA) according to the manufacturer’s instructions.

extract_protocol: Frozen tumor colorectal tissues were obtained at surgery from all patients, and immediately stored at -80º until use. In patients with multiple lesions, tissue sample was obtained from one of the tumors (the most advanced or the largest one when multiple tumors had the same tumor stage)

treatment_protocol: Bisulfite treatment was carried out on genomic DNA using the EZ DNA Methylation-Gold Kit (Zymo Research, Orange, CA) according to the manufacturer’s protocol.

tag: type colorectal cancer

value: solitary colorectal cancer

value: Female

tag: age (years)

tag: tumor location

value: distal

tag: cimp-h/l status

value: CIMP-L

tag: kras mutation status

value: mutated


title: solitary colorectal cancer sample_7422

description: solitary colorectal cancer :7422

tag: gender

value: Proximal

value: wild type


title: solitary colorectal cancer sample_3383

description: solitary colorectal cancer :3383

value: Male


title: norm-VUB-1007-DHPDMSO-72-R-1-1M_(HG-U133_Plus_2).CEL

description: Control DHP

value: HepaRG cell line


title: solitary colorectal cancer sample_5616

description: solitary colorectal cancer :5616


title: solitary colorectal cancer sample_885

description: solitary colorectal cancer :885


title: solitary colorectal cancer sample_883A

description: solitary colorectal cancer :883A

value: Not Available


title: norm-VUB-1008-DHPDMSO-24-R-2-1C_(HG-U133_Plus_2).CEL

description: Control DHP


title: norm-VUB-1008-CsADMSO-72-R-2-1H_(HG-U133_Plus_2).CEL

description: Control CsA

value: Control CsA


title: solitary colorectal cancer sample_942

description: solitary colorectal cancer :942


title: norm-VUB-1009-CsADMSO-72-R-3-1H_(HG-U133_Plus_2).CEL

description: Control CsA


title: norm-VUB-1009-DHP-24-R-3-1_(HG-U133_Plus_2).CEL

description: Treatment with DHP


title: norm-VUB-1007-DHPDMSO-24-R-1-1G_(HG-U133_Plus_2).CEL

description: Control DHP


title: norm-VUB-1008-DHP-24-R-2-1_(HG-U133_Plus_2).CEL

description: Treatment with DHP


title: norm-VUB-1009-DHPDMSO-24-R-3-1C_(HG-U133_Plus_2).CEL

description: Control DHP


title: norm-VUB-1007-DHP-24-R-1-1_(HG-U133_Plus_2).CEL

description: Treatment with DHP


title: solitary colorectal cancer sample_5085

description: solitary colorectal cancer :5085


title: norm-VUB-1007-CsADMSO-72-R-1-1M_(HG-U133_Plus_2).CEL

description: Control CsA


title: solitary colorectal cancer sample_4146

description: solitary colorectal cancer :4146


title: norm-VUB-1009-CsA-24-R-3-1_(HG-U133_Plus_2).CEL

description: Treatment with CsA

value: Treatment with CsA


title: norm-VUB-1007-DMSO-72-R-1-1O_(HG-U133_Plus_2).CEL

description: Control DLM

value: Control DLM


title: solitary colorectal cancer sample_3268

description: solitary colorectal cancer :3268


title: norm-VUB-1007-BENDMSO-72-R-1-1K_(HG-U133_Plus_2).CEL

description: Control BEN

value: Control BEN


title: norm-VUB-1007-CsA-72-R-1-1_(HG-U133_Plus_2).CEL

description: Treatment with CsA


title: norm-VUB-1009-BEN-72-R-3-1_(HG-U133_Plus_2).CEL

description: Treatment with BEN

value: Treatment with BEN


title: norm-VUB-1007-CsA-24-R-1-1_(HG-U133_Plus_2).CEL

description: Treatment with CsA


title: norm-VUB-1007-CsADMSO-24-R-1-1G_(HG-U133_Plus_2).CEL

description: Control CsA


title: solitary colorectal cancer sample_5467

description: solitary colorectal cancer :5467


title: norm-VUB-1009-CsADMSO-24-R-3-1C_(HG-U133_Plus_2).CEL

description: Control CsA


title: solitary colorectal cancer sample_3226

description: solitary colorectal cancer :3226


title: solitary colorectal cancer sample_7124

description: solitary colorectal cancer :7124


title: solitary colorectal cancer sample_5442

description: solitary colorectal cancer :5442


title: norm-VUB-1008-CsADMSO-24-R-2-1C_(HG-U133_Plus_2).CEL

description: Control CsA


title: solitary colorectal cancer sample_6068

description: solitary colorectal cancer :6068


title: solitary colorectal cancer sample_7564

description: solitary colorectal cancer :7564

value: CIMP-H


title: solitary colorectal cancer sample_1562

description: solitary colorectal cancer :1562


title: solitary colorectal cancer sample_13064

description: solitary colorectal cancer :13064


title: solitary colorectal cancer sample_3183

description: solitary colorectal cancer :3183


title: norm-VUB-1009-BENDMSO-72-R-3-1F_(HG-U133_Plus_2).CEL

description: Control BEN


title: norm-VUB-1008-BENDMSO-72-R-2-1F_(HG-U133_Plus_2).CEL

description: Control BEN


title: solitary colorectal cancer sample_887

description: solitary colorectal cancer :887


title: solitary colorectal cancer sample_13109

description: solitary colorectal cancer :13109


title: norm-VUB-1007-BEN-24-R-1-1_(HG-U133_Plus_2).CEL

description: Treatment with BEN


title: norm-VUB-1008-CsA-72-R-2-1_(HG-U133_Plus_2).CEL

description: Treatment with CsA


title: norm-VUB-1007-BEN-72-R-1-1_(HG-U133_Plus_2).CEL

description: Treatment with BEN


title: norm-VUB-1008-CsA-24-R-2-1_(HG-U133_Plus_2).CEL

description: Treatment with CsA


title: norm-VUB-1008-BEN-72-R-2-1_(HG-U133_Plus_2).CEL

description: Treatment with BEN


title: norm-VUB-1008-BENDMSO-24-R-2-1A_(HG-U133_Plus_2).CEL

description: Control BEN


title: norm-VUB-1009-CsA-72-R-3-1_(HG-U133_Plus_2).CEL

description: Treatment with CsA


title: norm-VUB-1008-BEN-24-R-2-1_(HG-U133_Plus_2).CEL

description: Treatment with BEN


title: solitary colorectal cancer sample_888

description: solitary colorectal cancer :888


title: synchronous colorectal cancer sample_4662

description: synchronous colorectal cancer :4662

value: synchronous colorectal cancer


title: synchronous colorectal cancer sample_5642

description: synchronous colorectal cancer :5642


title: solitary colorectal cancer sample_703

description: solitary colorectal cancer :703

value: solitary colorectal cancer


title: solitary colorectal cancer sample_743

description: solitary colorectal cancer :743

value: Female


title: norm-VUB-1008-DHPDMSO-72-R-2-1H_(HG-U133_Plus_2).CEL

description: Control DHP

value: Control DHP


title: solitary colorectal cancer sample_24058

description: solitary colorectal cancer :24058

value: distal

value: CIMP-L


title: norm-VUB-1007-BENDMSO-24-R-1-1E_(HG-U133_Plus_2).CEL

description: Control BEN


title: synchronous colorectal cancer sample_5725

description: synchronous colorectal cancer :5725


title: norm-VUB-1009-BEA-72-R-3-1_(HG-U133_Plus_2).CEL

description: Treatment with BEA

value: Treatment with BEA


title: solitary colorectal cancer sample_5082

description: solitary colorectal cancer :5082

value: mutated


title: synchronous colorectal cancer sample_5284

description: synchronous colorectal cancer :5284


title: solitary colorectal cancer sample_1022

description: solitary colorectal cancer :1022


title: norm-VUB-1007-DMSO-72-R-1-1M_(HG-U133_Plus_2).CEL

description: Control BEA

value: Control BEA


title: norm-VUB-1009-BENDMSO-24-R-3-1A_(HG-U133_Plus_2).CEL

description: Control BEN

value: HepaRG cell line


title: norm-VUB-1008-DMSO-72-R-2-1H_(HG-U133_Plus_2).CEL

description: Control BEA


title: norm-VUB-1009-DMSO-72-R-3-1H_(HG-U133_Plus_2).CEL

description: Control BEA


title: norm-VUB-1008-BEA-72-R-2-1_(HG-U133_Plus_2).CEL

description: Treatment with BEA


title: solitary colorectal cancer sample_5449

description: solitary colorectal cancer :5449

value: Male

value: wild type


title: solitary colorectal cancer sample_2103

description: solitary colorectal cancer :2103


title: synchronous colorectal cancer sample_502

description: synchronous colorectal cancer :502


title: norm-VUB-1009-BEN-24-R-3-1_(HG-U133_Plus_2).CEL

description: Treatment with BEN


title: norm-VUB-1007-BEA-72-R-1-1_(HG-U133_Plus_2).CEL

description: Treatment with BEA


title: synchronous colorectal cancer sample_2282

description: synchronous colorectal cancer :2282

value: Not Available


title: synchronous colorectal cancer sample_3126

description: synchronous colorectal cancer :3126


title: synchronous colorectal cancer sample_7742

description: synchronous colorectal cancer :7742

value: Proximal


title: norm-VUB-1008-DMSO-24-R-2-1C_(HG-U133_Plus_2).CEL

description: Control BEA


title: norm-VUB-1008-BEA-24-R-2-1_(HG-U133_Plus_2).CEL

description: Treatment with BEA


title: norm-VUB-1009-DMSO-24-R-3-1C_(HG-U133_Plus_2).CEL

description: Control BEA


title: synchronous colorectal cancer sample_742B(D1)

description: synchronous colorectal cancer :742B(D1)


title: synchronous colorectal cancer sample_4147

description: synchronous colorectal cancer :4147


title: norm-VUB-1008-AMQDMSO-72-R-2-1F_(HG-U133_Plus_2).CEL

description: Control AMQ

value: Control AMQ