Sample Submission Guidelines and Requirements Version 1.0 Status Final Date 4 June 2012 Sample Submission Guidelines and requirements Version Date 4 June 2012 1.0 Table of Contents 1. Introduction .............................................................................................................. 3 2. General Requirements............................................................................................... 3 3. DNA .......................................................................................................................... 4 4. RNA .......................................................................................................................... 4 5. Blood, blood products and tissue samples.................................................................. 5 6. Proteins: ................................................................................................................... 6 Centre for Proteomic and Genomic Research Institute of infectious Diseases and Molecular Medicine, Faculty of Health Sciences, UCT Wernher and Beit Building South, Lab S2.09, Anzio Road, Observatory. Page 2 of 7 Sample Submission Guidelines and requirements Version Date 4 June 2012 1.0 1. Introduction These guidelines have been drafted by the CPGR to ensure the following: 1.1. Chain of custody for samples and the authority to carry out testing is maintained 1.2. Testing is not delayed by the receipt of samples that do not meet the stringent quality criteria required for high end omics projects. 1.3. No uncertainty of measurement is introduced by contaminants or additives that may adversely affect the testing of samples. The purpose of these guidelines is to ensure that testing and analysis is completed in the shortest possible time, to the highest possible standards. Samples that do not conform to the requirements of this guideline will not be accepted for testing. Queries can be directed to the platform manager or project manager dealing with your project, or submitted to [email protected]. 2. General Requirements 2.1. Samples must be submitted in clearly labeled tubes, preferably with a printed label containing a barcode. 2.2. Samples must be accompanied by a shipping manifest. To maintain chain of custody, two paper copies of the manifest must accompany the samples. The copies will be signed and one copy returned as proof of delivery/acceptance. An electronic copy of the manifest must be sent prior to delivery of the samples to [email protected] 2.3. The sample volume and sample concentration must be included. 2.4. Samples must be submitted in a cryobox and the position of the samples must be indicated on the manifest. If you do not have a cryobox, the CPGR will provide one or more at a fee. 2.5. Plastics such as cryovials, microtubes or plates can be purchased from the CPGR. 2.6. Samples must be submitted at the correct temperature. 2.7. The hazardous or infectious nature of samples must be indicated. Centre for Proteomic and Genomic Research Institute of infectious Diseases and Molecular Medicine, Faculty of Health Sciences, UCT Wernher and Beit Building South, Lab S2.09, Anzio Road, Observatory. Page 3 of 7 Sample Submission Guidelines and requirements Date 4 June 2012 Version 1.0 2.8. Samples that need to be handled in a BSL III or BSL IV Laboratory environment cannot be accepted. 2.9. Samples containing radioactive substances cannot be accepted. 2.10. The following details must be provided: 2.10.1. Processing, isolation, extraction, or purification methods. 2.10.2. Any freeze thaw cycles. 2.10.3. Fate of the left over samples (destroyed, stored, returned). 2.10.4. Date and time of sample collection. 3. DNA 3.1. Samples may be submitted in 96 well plates (for 24+samples) or microtubes 3.2. The sample list and plate layout must be sent to the CPGR as an electronic manifest in the CPGR’s template. 3.3. Initial QC data including gel electrophoresis carried out in your lab must be sent to CPGR electronically. Submitted DNA must be of suitable integrity. 3.4. The DNA must meet the following criteria:: 260/280 ratios between 1.8 – 2.1 260/230 ratios greater than 1.5 3.5. Visibly contaminated samples may not be included 3.6. Degraded or RNA contaminated samples may not be included 3.7. Samples must be transported on dry ice (Solid CO2) 3.8. The elution buffer must be clearly indicated and an aliquot included for CPGR QC purposes 4. RNA 4.1. Samples may be submitted in 96 well plates (for 24+samples) or microtubes: 4.2. The sample list and plate layout must be sent to the CPGR as an electronic manifest in the CPGR’s template. A copy of the template can be found here Centre for Proteomic and Genomic Research Institute of infectious Diseases and Molecular Medicine, Faculty of Health Sciences, UCT Wernher and Beit Building South, Lab S2.09, Anzio Road, Observatory. Page 4 of 7 Sample Submission Guidelines and requirements Date 4 June 2012 Version 1.0 4.3. Initial QCs including bioanalyser results carried out in your lab must be sent to CPGR electronically. Submitted RNA must be of suitable integrity. 4.4. The RNA criteria to be met are: 260/280 ratios between 1.8 and 2.1: 260/230 ratios greater or equal to 1.5: RIN Value greater than 7 4.5. Visibly contaminated samples may not be included 4.6. Samples must be transported on dry ice (Solid CO2) 4.7. Degraded or DNA contaminated samples may not be included 4.8. The elution buffer must be clearly indicated and an aliquot included for CPGR QC purposes. N.B. RNA should not be eluted in DEPC treated water 5. Blood, blood products and tissue samples 5.1. Fresh whole blood samples must be submitted within 4 hours of collection for processing. 5.2. Where blood has been stored in a stabilization reagent, please indicate details of the stabilization reagent (e.g. RNAlater, Paxgene) 5.3. Cryopreserved samples must be submitted in polypropylene tubes or cryovials. Glass vials will not be accepted. The correct cryoagent must be used for transport and handling (vapour phase nitrogen (-160oC) ordry ice (-80oC, solid CO2) 5.4. Viable samples submitted in nitrogen must be stored in a cryovial containing an internal threaded lid and a silicone gasket. 5.5. The following must be clearly indicated before samples are submitted: 5.5.1. Time and date of collection 5.5.2. Anticoagulant used in plasma samples such as EDTA, ACD, Na Citrate, Na Fl etc 5.5.3. Fixatives such as formalin, 5.5.4. cryopreservatives such as glycerol or DMSO, Centre for Proteomic and Genomic Research Institute of infectious Diseases and Molecular Medicine, Faculty of Health Sciences, UCT Wernher and Beit Building South, Lab S2.09, Anzio Road, Observatory. Page 5 of 7 Sample Submission Guidelines and requirements Date 4 June 2012 Version 1.0 5.5.5. Detergents such as SDS 5.5.6. Denaturants, for example urea 5.6. To prevent unnecessary thawing of samples, serum samples should be aliquoted into individual cryotubes. “PCR-strip” like tubes should never be used. 5.7. Tissue samples must include the wet mass of the tissue and the origin of the tissue. 6. Proteins: 6.1. Isolated or purified proteins submitted for PMF analysis must be submitted in the following formats: 6.1.1. Desiccated gel pieces in a low binding eppendorph or glass vial. Gel pieces may be stained with Coomassie or Maldi Compatible Silver Stain. The approximate molecular mass of the protein must be indicated. A photograph of the gel must accompany the gel pieces. 6.1.2. Lyopholised powder in a low binding eppendoprh or glass vial. The molecular mass and purity of the sample must be indicated. 6.1.3. In a tryptic digest compatible buffer 6.2. Protein samples submitted for iTRAQ analysis must be submitted in the following format: 6.2.1. iTRAQ compatible buffer 6.2.2. in a glass vial. 6.2.3. Exogenous protein spikes must be included during extraction. Both the extraction buffer and exogenous proteins are available from the CPGR. 6.3. Blood, blood products or tissue samples submitted for protein extraction must include the criteria in section 5 Centre for Proteomic and Genomic Research Institute of infectious Diseases and Molecular Medicine, Faculty of Health Sciences, UCT Wernher and Beit Building South, Lab S2.09, Anzio Road, Observatory. Page 6 of 7 Page 7 of 7