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Affymetrix Citation

Instrumentation

The Center for Genome Research and Biocomputing Core Laboratories offer a Affymetrix GeneChip® service that enables transcriptome analyses using model organisms. The chips are prefabricated by Affymetrix. The Affymetrix GeneChip® system consists of:

  • a GeneChip® Scanner 3000
  • Affymetrix GeneChip® Fluidics Station 450,
  • and Affymetrix GeneChip® Hybridization Oven 640.
    Affymetrix imageAffymetrix image

Citation

Labeling, Hybridization and Scanning Protocols followed are from the Affmetrix image GeneChip® Expression Analysis Technical Manual ( 701021 Rev. 5)

Long Citation Example

RNA Labeling and Affymetrix Expression Array processing - RNA integrity screening, Probe synthesis, hybridization and scanning were conducted by the Center for Genome Research and Biocomputing Core Laboratories at Oregon State University, Corvallis OR. 5 µg of total RNA was used to generate biotinylated complementary RNA (cRNA) for each treatment group using the One-Cycle Target Labeling protocol (Affymetrix, Santa Clara, CA) from the GeneChip® Expression Analysis Technical Manual ( 701021 Rev. 5 ).   In short, isolated total RNA was checked for integrity and concentration using the RNA 6000 Nano LabChip kit on the Agilent Bioanalyzer 2100 (Agilent Technologies, Inc., Palo Alto, CA).   Poly-A RNA control kit RNA and zebrafish RNA were reverse transcribed using a T7-(dT) 24 primer and Superscript II reverse transcriptase (Invitrogen, Carlsbad, CA) and double stranded cDNA was synthesized and purified with GeneChip® Sample Cleanup Modules (Affymetrix, Santa Clara, CA). Biotinylated cRNA was synthesized from the double stranded cDNA using T7 RNA polymerase and a biotin-conjugated pseudouridine containing nucleotide mixture provided in the IVT Labeling Kit (Affymetrix, Santa Clara, CA) . Prior to hybridization, the cRNA was purified with GeneChip® Sample Cleanup Modules (Affymetrix, Santa Clara, CA), and fragmented. 10 µg from each experimental sample along with Affymetrix eukaryotic hybridization controls were hybridized for 16 hours to zebrafish genome arrays (Zebrafish430_2) in an Affymetrix GeneChip® Hybridization Oven 640. Affymetrix GeneChip® Fluidics Station 450 was used to wash and stain the arrays with streptavidin-phycoerythrin (Moleculer Probes, Eugene, OR), biotinylated anti-streptavidin (Vector Laboratories, Burlingame, CA) according to the standard antibody amplification protocol for eukaryotic targets. Arrays were scanned with an Affymetrix GeneChip® Scanner 3000 at 570nm. The Affymetrix eukaryotic hybridization control kit and Poly-A RNA control kit were used to ensure efficiency of hybridization and cRNA amplification. All cRNA was synthesized at the same time. Hybridizations were conducted with one replicate of all times and treatments concurrently. Each array image was visually screened to discount for signal artifacts, scratches or debris.