Services
The Microarray Core Facility offers a user fee microarray service for the academic researchers in the Czech Republic using Affymetrix GeneChip arrays. The core facility is equipped to process RNA and DNA samples on most of the types of GeneChips (expression, genotyping, resequencing, exon and tiling chips). The facility staff has been trained and approved for sample processing on GeneChip arrays by Affymetrix application specialists.
The facility staff will carry out the complete Affymetrix protocol required for the particular chip type starting from the input RNA/DNA sample including all necessary quality controls of the input material and intermediate products. The input samples have to meet requirements on quality and quantity to obtain successful result of the experiment. The facility staff can provide you with advice on sample preparation.
The samples are processed with respect to the capacity of the core facility on the "first come first served" principle. Small experiments may be also scheduled for processing in groups to allow reagent consumption in batches. The GeneChips and reagents are ordered by the facility staff as necessary for each experiment.
Full chip service description
The facility privides "full chip service" only, which starts from the RNA/DNA samples and ends by exporting the results from GCOS software. Only by this approach, it is possible to have the whole procedure of sample preparation under the control and to guarantee the best quality of the results if the input samples satisfied requirements. The researchers are required to collect cells or tissues, isolate total RNA/mRNA (or genomic DNA) and check the quality and quantity of the samples before their submitting to the core facility.
The "full chip service" includes:
- An initial check of the sample quality and quantity on Agilent 2100 Bioanalyzer and NanoDrop spectrophotometer.
- The complete Affymetrix protocol specific for each chip type including:
- first and second strand cDNA synthesis, in vitro transcription and biotin-labelling of cRNA, cRNA fragmentation (for expression, exon and tiling chips)
- rRNA subtraction (for exon and tiling chips)
- reverse transcription of cRNA into cDNA (for exon chips)
- genomic DNA digestion, adaptor ligation, PCR (for genotyping chips)
- hybridization, washing, straining and scanning (for all chip types)
- Quality and yield controls of the intermediate products on Agilent 2100 Bioanalyzer and NanoDrop spectrophotometer.
- Quality inspection of the scanned images and data review using the control probes present on the chip.
- Export of the output files from GCOS software and delivery to the user on CD/DVD media or by download.
Procedure for ordering microarray analysis
- If you intend to carry out microarray experiments, please contact the core facility staff at least several weeks in advance and discuss details on availability of chips, price, sample preparation, scheduling your work and other technical information.
- Send an obligatory order for microarray sample processing to the core facility. The order has to be signed by an authorized person of your institution.
- Fill out the sample submission form and indicate all required information. Send the sample submission form together with your samples to the core facility for processing.
- After completion of the experiment the results will be exported from GCOS software and delivered to you on CD/DVD or by download.
- An invoice for sample processing will be sent to you for payment.