Glossary

This glossary provides defintions for some terms commonly encountered when using the GSAF LIMS system.

1. Job - an individual project for a particular client, marked by an identifier called a "job number". Job numbers are of the form "JAxxyyy", where "xx" are the last two digits of the current year. For example, all jobs started in 2011 are of the form "JA11xxx".
   
   
2. Sample - an individual preparation of DNA or RNA. Most samples are processed into a library, amplified on beads via emPCR, and sequenced on the appropriate platform. Sometimes samples are pooled together after being appropriately barcoded; this new pool is NOT a new "sample"; in other words, it does not get entered into the ZOHO as a new "sample". (Pools are usually referred to as "sample sets".)
   
   
3. QC ("Quality Control") - procedures run to verify certain characteristics of a sample, to ensure it meets the criteria for emPCR and sequencing. Different QC types have different identifiers:
   1. BA (Bioanalyzer) - a gel electrophoresis procedure run on a small chip, usually used to determine the size distribution of a sample. It is also used to determine if a sample is present or not, but usually not used as a quantitative measure. The identifier is of the form "QBxxyyy".
   2. Fluorimetry - Used to determine the concentration of 454 Rapid Libraries for 454 emPCR. The identifier is of the form "QFxxyyy".
   3. qPCR - quantitve PCR, used to determine the concentration of SOLiD and 454 Fragment/Mate-Paired Libraries for emPCR. The identifier is of the form "QAxxyyy".
      
      
4.  Sample Set - a set of samples that has been used in one individual emPCR. If a pool of samples is used in an emPCR, then the pool constitutes one sample set. If only a single sample is amplified on beads via emPCR (which is often the case), that single sample MUST BE TREATED as a sample set, even though it seems redundant. A simple rule for sample sets is: "one blue dot tube, one sample set". There is no strictly defined naming convention for a sample set, so any name that clearly conveys the contents of the sample set is acceptable.
   
   
5. emPCR (emulsion PCR) - the process by which finished libraries are amplified on beads for sequencing. The 454 allows for 3 sizes of emPCR: small volume (SV), medium volume (MV), and large volume (LV). The SOLiD allows for two scales of emPCR: mini-scale and full-scale. Whenever emulsion PCRs are set up, they are assigned an "EA number", of the form "EAxxyyy". Multiple emPCRs can be assigned to the same EA number if they are set up simultaneously. However, only one sample set can go into an emPCR. Amplifying multiple samples on the same set of beads is equivalent to pooling them, and so the sample set would be a pool including all of those samples. Each emPCR generates exactly one bead lot.
   
   
6. Bead Lots: The enriched beads resulting from a single emPCR. One EA can result in multiple bead lots, one for each emPCR that was set up. The general form of the bead lot identifier is "Samplesetname_EAnumber". For example, if the sample set "Test1" went into an emPCR under EA11222, then the associated bead lot would be "Test1_EA11222".
   
   
7. Sequencing Run: An actual sequencing run in which appropriate quality beads containing amplified template are sequenced on the appropriate platform. The general form of the sequencing run identifier is "SAxxyyy".