Genomics FAQs
How do I get in touch?
Contact Maike Paramor (mp600@cam.ac.uk)
What if I have a request that is not on your list?
We will always try and accommodate new protocols that we have not previously done. It makes our work exciting and may benefit other groups eventually. Contact us!
How do I submit my samples?
Please contact us to arrange a handover, and please fill in the online submission form here.
How much does it cost?
For smaller projects, I can provide a price list. We will prepare quotations for larger projects and grant applications. Please contact Maike Paramor for details.
What are your turnaround times?
It will depend on the type of project, but in general we are aiming to have all incoming projects fulfilled within 2 weeks.
Who can access the facility?
The NGS facility is prioritising projects from the Stem Cell Institute, however, we are also accepting a wide range of projects from across the University, and from companies.
How will I receive the sequencing data?
Once your sequencing run has finished, we will send you information on how to download the data over FTP. The output will be the FASTQ files, and some quality reports and demultiplexing statistics.
Do you provide bioinformatics support?
The Cambridge Stem Cell Institute has a very experienced bioinformatics facility, please contact Irina Mohorianu (iim22@cam.ac.uk) for further details.
How do I fill out the online submission form?
Details about this here.
How much data do I need
It depends on your individual requirements!
Here are some guidelines: https://emea.illumina.com/science/education/sequencing-coverage.html
What is the difference between the HiSeq4000 and the Novaseq?
The Hiseq4000 is the older sequencer, it has 8 lanes per flowcell and a 4 colour scheme. It also has longer run times, and therefore 2 run types are offered as standard: SE50 and PE150.
The Novaseq is newer, faster, and more flexible. It uses a 2 colour scheme, and has different sized flowcells which adjust to different output needs. For larger runs, it might be necessary to do a QC run on a Miseq first.
Here is a table to guide you through the output of each option:
|
Machine, flow cell, run type |
million reads per lane/flowcell |
|
HiSeq4000_PE150 |
350 |
|
HiSeq4000_SE50 |
350 |
|
NovaSeq6000_S1_UpTo100_Standard |
1600 |
|
NovaSeq6000_S1_UpTo100_Xp |
800 |
|
NovaSeq6000_S1_UpTo200_Standard |
1600 |
|
NovaSeq6000_S1_UpTo200_Xp |
800 |
|
NovaSeq6000_S1_UpTo300_Standard |
1600 |
|
NovaSeq6000_S1_UpTo300_Xp |
800 |
|
NovaSeq6000_S2_UpTo100_Standard |
4100 |
|
NovaSeq6000_S2_UpTo100_Xp |
2050 |
|
NovaSeq6000_S2_UpTo200_Standard |
4100 |
|
NovaSeq6000_S2_UpTo200_Xp |
2050 |
|
NovaSeq6000_S2_UpTo300_Standard |
4100 |
|
NovaSeq6000_S2_UpTo300_Xp |
2050 |
|
NovaSeq6000_S4_UpTo200_Standard |
10000 |
|
NovaSeq6000_S4_UpTo200_Xp |
2500 |
|
NovaSeq6000_S4_UpTo300_Standard |
10000 |
|
NovaSeq6000_S4_UpTo300_Xp |
2500 |
|
NovaSeq6000_SP_UpTo100_Standard |
700 |
|
NovaSeq6000_SP_UpTo100_Xp |
350 |
|
NovaSeq6000_SP_UpTo300_Standard |
700 |
|
NovaSeq6000_SP_UpTo300_Xp |
350 |
What are the main library kits you are using?
- Illumina small RNA library kit
- Qiagen QIAseq FastSelect kit
- NEB PolyA kit
- NEB Ultra II directional RNA kit
- Nextflex rapid DNA kit
- NEB Adapters for multiplexing up to 96 samples
- Thruplex DNA-seq kit
- Nextera XT kit with 384 barcodes
- NuGen Ovation RNA-Seq Systems 1–16 for Model Organisms
- NuGen Ovation RRBS Methyl-Seq System 1-16 with TrueMethyl oxBS
- SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian
- Smartseq2 method for single cells / very low RNA amounts
- Covaris E220 evolution instrument for DNA/RNA shearing and chromatin shearing
What do I do if my samples fail your QC?
We would normally ask you to either replace those samples that failed the QC, or continue the project without them. In some cases it might be necessary to work with degraded RNA samples, and in those cases we have the appropriate kits available that deal with degraded RNA.