Affymetrix GeneChip Murine Genome U74Av2 [MG_U74Av2]

Microarray analysis of gene expression with age in individual nematodes

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Effect of the overexpression of the oncogenic form of the Vav2 protein in the NIH3T3 cell line under serum deprivation conditions. oncovav2-transformed NIH3T3 cells grown in serum-deprived medium (Vav2SD) are compared to the parental NIH3T3 controls under the same growth conditions (ContSD). Vav2SD cells are also compared to the oncovav2-transformed NIH3T3 cells growing exponentially and the NIH3T3 growing exponentially.

Transcription profiling of mouse NIH3T3 cells transformed with oncovav2 deprived of Serum

Effect of the overexpression of the oncogenic form of the Vav2 protein in the NIH3T3 cell line under serum deprivation conditions. oncovav2-transformed NIH3T3 cells grown in serum-deprived medium (Vav2SD) are compared to the parental NIH3T3 controls under the same growth conditions (ContSD). Vav2SD cells are also compared to the oncovav2-transformed NIH3T3 cells growing exponentially and the NIH3T3 growing exponentially.


Affymetrix:Protocol:ExpressionStat

Title: Affymetrix CHP Analysis (ExpressionStat). Description:

Affymetrix:Protocol:Hybridization-EukGE-WS2v4

Title: Fluidics Station Protocol. Description:

P-AFFY-6

Title: Affymetrix CEL analysis. Description:

P-MEXP-4249

Cell line. Temperature: 37ºC, CO2: 5%. Exponential growth conditions: DMEM was supplemeted with Pen/Strep and 10%FCS. 

P-MEXP-4250

Cell line exponential conditions. Cells allowed to grow to 75% confluency in DMEM 10%FCS. Total RNA extracted using Qiagen RNeasy MiniKit according to manufacturer's instructions and resulting RNA stores at -80ºC until further use.

P-MEXP-4251

Total RNA was extracted using the RNeasy Mini Kit (Qiagen, Hilden, Germany)according to the manufacturer's instructions. Extracted total RNA was used to synthesize double stranded cDNA using the SuperScript Choice System (Gibco BRL) which incorporates a T7 RNA polymerase promoter. 

P-MEXP-4253

Cell line. Temperature: 37ºC, CO2: 5%. Serum deprivation growth conditions: DMEM was supplemeted with Pen/Strep, no serum added.

P-MEXP-4254

Cell line serum deprivation conditions. Cells allowed to grow for 48 hours in DMEM without serum. Total RNA extracted using Qiagen RNeasy MiniKit according to manufacturer's instructions and resulting RNA stores at -80ºC until further use.

P-MEXP-4255

Biotin-labeled antisense cRNA was obtained using the BioArray High-Yield RNA Transcript Labeling Kit transcription kit (ENZO Diagnostics Inc.) using 5 mg of total RNAs and the oligo dT primer 5’ GGCCAGTGA-ATTGTAATACGACTCACTATAGGGAGGCGG-(dT)24. cRNas were purified using the RNeasy columns and then 20 mg of cRNAs was fragmented at 94ºC for 30 min in 40 ml of 40 mM Tris-acetate, pH 8.1, 100 mM KOAc, 30 mM MgOAc. The fragmented samples were checked in an agarose gel to verify their quality and then added to a hybridisation cocktail containing Control oligonucleotide B2 (50 pM) and Eukaryotic Hybridisation controls (BioB, BioC, BioD, cre) at 1.5, 5, 25 and 100 pM final concentration respectively from the GeneChip Eukaryotic Hybridization Control Kit, herring sperm DNA (0.1 mg/ml) and acetylated BSA (0.5 mg/ml). 

P-MEXP-4256

Probe aray was equilibrated to RT and prehybridised with 1x hybridisation buffer (100mM MES, 1M [Na+], 20mM EDTA, 0.01% Tween 20)at 45ºC for 10 min with rotation. The hybridisation cocktail was heated to 99ºC for 5 min in a heat block, transferred to 45ºC heat block for 5 min and spun at maximum speed in a microfuge for 5 min. 200 ul of the hybridsation mixture were used to fill the affymetrix cartridge after removal of the hybridisation buffer and the arrays were hybridised at 60ºC for 16 hours with rotation in the Affymetrix GeneChip Hyb Oven 640. GeneChips were washed and marked with streptavivin phycoerythrin in the Fluidics Station (Affymetrix, Inc.) using the protocol EukGE-WS2 provided by the program MAS 5.0 (Affymetrix, Inc.).

Transcription profiling of mouse NIH3T3 cells transformed with oncovav2 deprived of Serum

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