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Microarray Service Details

Project and Assay Design Workflow

Microarray Project Workflow

LMT staff is available to discuss the design of your microarray experiments, such as number of samples, type of arrays to use, and suitable labeling kits for your projects.  Experienced users may skip the consultation step and make a CSAS request through the online request system.  Subsequent to placing a CSAS request, the LMT service manager will send you a cost estimate through the online system based on the information you provided.  You can then decide to accept or reject the cost estimate.  Upon accepting the cost estimate, the request will need to go through additional approval from OD/OSTP and your AO.  Once the request is fully approved, samples can be sent to the LMT and we can start sample processing.  

Sample Processing Workflow (Affymetrix)

Affymetrix Sample Workflow

Once samples are received, LMT staff will first check RNA quality and concentration using Agilent Bioanalyzer and NanoDrop.  You will be informed about the RNA QC results within 48 hours along with the decision/recommendation about the necessity of replacement samples.  If samples pass RNA QC, they will be put in the queue for processing in batches.  About 100 ng of total RNA samples are reverse transcribed and labeled by biotin.  If the labeling reaction is successful and passes labeling QC, samples are hybridized overnight to Affymetrix GeneChip microarrays. Wash/stain/scan of the microarray is carried out under strictly controlled conditions with the Affymetrix Fluidics Station and Scanner.  Data is collected and final QC is performed.  Raw data is sent to you (.cel file, which is suitable for most microarray analysis software) unless analysis is requested.   The entire process generally takes 2-3 weeks.

Sample Processing Workflow (NanoString)

 NanoString Sample Workflow

Once samples are received, LMT staff will check RNA quality and concentration using Agilent Bioanalyzer and/or NanoDrop.  You will be informed about the RNA QC results within 48 hours along with the decision/recommendation about the necessity of replacement samples.  If samples pass RNA QC, they will be put in the queue for processing in batches.  For NanoString, samples are processed in batches of 12.  With exception to the miRNA assay, samples (100 ng of total RNA) are hybridized to color barcoded codeset probes without any amplification or other processing.  For the miRNA assay, samples are first ligated to form hybrid molecules which hybridize to the color-barcoded codeset probes better. Wash/stain/scan is carried out under strictly controlled conditions with the NanoString nCounter instrument. You will be sent a collected Excel spreadsheet of counts for each sample and each probe along with the raw data. 

Page last updated July 29, 2011 @ 9:43 am