The genomics core offers several different library prep methods to Cambridge Institute scientists, we don’t generally offer these services to external users. We offer the following default methods (but can run pretty much anything you’d like, so do ask):
- RNA-seq: Illumina stranded mRNA
- ChIP-seq: Thruplex library prep for ChIP
- Genomes: Illumina PCR-free or Nextera
- Exomes: Illumina rapid (Nextera) exome 37Mb
- Amplicons: Fluidigm Access Arrays
Things to remember for library prep submissions:
- Is your request for something outside the defaults? If so please talk to us first.
- Have you been to an experimental design meeting? You’ll need to if you want the Bioinformatics core to analyse your data. Email to book a slot.
- Review submission requirements before preparing your samples
- Do you have at least 24 samples? If not you may need to wait for other samples to come into the core before we start processing.
- Submit samples in a labeled 96-well plate arranging your samples by columns (A1 – H1, A2 – H2, etc.)
- Leave well G:12 and H:12 on your plate empty, we use these wells for DNA or RNA controls during processing.
- Submit your plate of DNA/RNA to CRUK-CI Genomics Core room 026 in freezer 026/10
- Make sure your samples are submitted at the correct concentration and volumes. We cannot adjust your plate for you and will reject your submission.
- If appropriate you will have a randomised plate layout, created using metadata provided by you, please make sure your samples are in this format. We cannot reformat your plate for you and will reject your submission.
- Quantify your nucleic acid using a fluorescent dye, e.g. Invitrogen Qubit or PicoGreen. Do not use the Nanodrop.
- Dilute your nucleic acid in nuclease-free water (RNA) or elution buffer (DNA)
For large dilutions: Dilute to a medium concentration value, re-quantify and do a second dilution to the final goal concentration.
- If submitting DNA, check the quality of each sample (if possible) or a representative subsample on a 1% Agarose gel to check for high molecular weight DNA.
- If submitting RNA, check the quality of each sample on the Bioanalyzer and check for a RIN >8.
- For a ChIPseq experiment, perform the chromatin immunoprecipitation and submit the ChIP’ed DNA. We do not specify a minimum quantity for a ChIPseq experiment, please submit what you have. Include at least one input control (5.5ng in 15ul)