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Wellcome - MRC

Cambridge Stem Cell Institute

Studying at Cambridge

 

Genomics

Preparation of DNA/RNA libraries for Next Generation Sequencing projects

Next Generation Sequencing has become indispensable for most research projects. The Stem Cell Institute Genomics Facility offers support to all research groups to produce high quality libraries, drawing on many years of expertise. This facility provides a reliable and fast turnaround for standard library preparation. We have experience in a wide variety of different library preparation techniques, and we are always happy to try out new things as well.

Services

  • Project planning and advice
  • Covaris shearing of DNA/RNA samples; chromatin samples
  • Transcriptome/mRNA libraries
  • Small RNA libraries
  • Single cell transcriptome libraries
  • ChIP-seq libraries
  • Genomic resequencing libraries
  • WGBS projects
  • RRBS projects
  • Exome sequencing
  • ATAC libraries
  • Low input RNA and DNA libraries
  • Specialist techniques (tRNA, riboseq, Chirp, MNase, RNA bisulfite seq, CRISPR, transposon mutagenesis screens, …)
  • Individual projects and non-established methods will be considered!

Currently available preparations/kits

  • Illumina small RNA library kit
  • Illumina RiboZero kit
  • NEB PolyA kit
  • NEB Ultra II directional RNA kit
  • Nextflex directional RNA seq kit
  • Nextflex rapid DNA kit
  • Nextflex adapters for multiplexing up to 48 samples
  • Thruplex DNA-seq kit
  • NEBNext and Kapa Hyperprep reagents for standard Illumina DNA libraries and ChIP libraries
  • Nextera and Nextera XT kit
  • NuGen Ovation RNA-Seq Systems 1–16 for Model Organisms
  • SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian
  • Smartseq2 method for single cells / very low RNA amounts
  • NimbleGen SeqCap EZ exome library kits
  • Covaris E220 evolution instrument for DNA/RNA shearing and chromatin shearing

Sequencing

The sequencing itself is not done in-house, but we have a collaboration with the CIGC here in Cambridge which allows us access to the latest Illumina sequencing technology.

If you are using the NGS library facility, the sequencing will be submitted directly to the genome core at CIGC. If you are making your own libraries and would like access to the sequencing core, your group will need to set up an account with CIGC, and submit the SLX submission files for approval to Maike Paramor (mp600@cam.ac.uk).

Data Analysis

The SCI has a bioinformatics facility, which will provide support with any aspect of your data analysis.

Contact

The Gene Service Facility is managed by Dr Maike Paramor.

The Academic chair for this facility is Dr Paul Bertone.

How to book

Please find here the sample submission form, which you can download and fill in.

When submitting samples, please follow these simple guidelines:

Always make sure you have got the best possible quality of your RNA or DNA - to get good libraries, you need good starting material! Quantify your nucleic acid with a fluorescent dye (Qubit, picogreen), and avoid the nanodrop!

Total RNA for standard RNA-seq projects (2-5ug) will have to be DNAse digested and submitted in RNAse free water, the volume should not exceed 30 ul. Aim for bionalayzer RIN values for >8. We routinely do this quality check for you, so you do not have to have access to a bioanalyzer.

If quantity of total RNA is limited, please discuss options with me. The volume needs to be considerably smaller for low input samples.

Genomic DNA should be free of RNA, and you should check the integrity and size on a 1% gel before submitting.

Clean ChIP DNA should be submitted after you have done the chromatin immunoprecipitation in a volume not larger than 15ul. Do not attempt to measure ChIP DNA in a nanodrop, it will not be accurate enough. Please let me know if your fragments are longer than 500bp.

To make an equipment booking, please go to the online Booking System.