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NGS Monthly Update: HiSeq Upgrade, a Website, and much more...

last modified May 01, 2014 06:44 PM

Dear users of the CIGC NGS Service,
 
We have a lot of news for you this month, including more data from the HiSeq, a new website, and changes to the “Progress” field in LabLink.
 

HiSeq Upgrade imminent

Illumina have released their “v4” sequencing kits that will allow us to run the 8-lane flowcell in half the time (PE100 in 6 days!), and generate one third more reads per lane (max 300M read per lane!). We are not yet using these reagents because we are waiting for our instrument to be upgraded. This upgrade is only affecting the High Output mode, and NOT rapid run, so the service we offer you will change when we move to v4 reagents. We will keep you informed of the date of this change by email. Changes at that time will include:

  • We will no longer operate the HiSeq in Rapid Run mode unless you specifically ask us to at submission and we will recommend that you provide multiples of 2 lanes, or risk waiting indefinitely for another submission.
  • Our submission form will offer “HiSeq”, “HiSeq Rapid Run” and “HiSeq 2000” workflow options
  • You will receive more data per lane (up to 300M reads)
  • Our per-lane charges will increase to reflect the increase in reagent price
  • Therefore you may need to pool more samples per lane to benefit from the potential cost saving

For more information, check out James’ blog entry. We will contact you again to let you know when the upgrade is taking place.
 

New Website

The CRUK-CI genomics core website has been launched! http://genomics.cruk.cam.ac.uk
Please feedback and let us know what you would like to see here. This is an information resource only and does not replace the LabLink submission page.
 

Upcoming Changes to Lablink “Progress” Field

The “Progress” field in lablink is used to let you know how processing is going for your submission. We have had feedback that it doesn’t work when a library is submitted for more than one lane of sequencing, and also that sometimes it doesn’t update. We will shortly be changing how this field works to help with both of these problems. The new format will tell you i) if your library has been accepted into our lims system, ii) how many lanes have been clustered, iii) how many lanes have completed sequencing and data have been published. We can only add status updates for a process that has completed so unfortunately we can’t tell you when your sample is actually on the sequencer.
 
For example:
When a library is accepted but has not be processed: Accepted
When a library is accepted and has been clustered, but data is not yet available: Accepted. Clustered: 1
When a library is accepted and has been clustered, and data is available: Accepted. Clustered:1. Published:1.
When a library is accepted, 3 lanes have been clustered but only 2 are published so far: Accepted. Clustered:3. Published:2.
 
If you have any questions about the progress field, please email genomics-helpdesk@cruk.cam.ac.uk.
 

Library Pooling Instructions

We have produced a new submission instruction how-to guide with recommendations for quantification, quality checking, and pooling before submission (attached). The step we were most regularly asked about is pooling:

A simple method to pool libraries:
1) Quantify and QC all of your libraries
2) Select a concentration for pooling, often the lowest concentration of your library set. This should be above our submission minimum of 10nM.
3) Dilute all of your libraries to that concentration. Use Illumina Resuspension Buffer, EB, or Library Dilution Buffer (10mM Tris pH 8.5 with 0.1% Tween, available from CIGC).
4) Combine an equal volume of all of your libraries in your pool tube.
5) We recommend that you re-quantify your pool and dilute again to reach our submission requirements (10nM-20nM).
 

SLX Submission Forms

We continue to receive many submissions which request SE40 sequencing. We no longer offer this length and all submissions are being treated as SE50, but the “SE40” entries are causing us problems when planning flowcells for clustering, so if you use this your sequencing could be delayed accidentally. It appears that many users have saved old versions of the SLX submission form and are re-using them. Please always download the latest version of the SLX submission form and do not use an old copy saved on your local computer.
 

Genomics Helpdesk

If you have any queries about our NGS service, any concerns or questions about a submission, or wish to enquire about any aspect of the CRUK-CI genomics core services, email genomics-helpdesk@cruk.cam.ac.uk.
 

Product Updates

  • New England Biolabs recently presented information to the genomics core on their library prep kits, including DNA (details) and RNA (details)
  • New England Biolabs Methylated adapters: NEB announce they have produced adapters for making illumina-compatible libraries which are methylated, and therefore suitable for bisulphite sequencing. View product details
  • Active Motif Launched a ChIPSeq kit specifically for T cells, B cells, monocytes and other PBMCs. Click for details
  • Active Motif provide a selection of ChIP-validated antibodies which may be of interest: Click for more details
  • Illumina Truseq RNA Access Library Prep Kit for FFPE: Illumina announce an RNASeq library prep kit aimed at FFPE samples or samples with low quality/quantity of RNA. If this works well it could unlock a massive array of samples for transcriptome studies in cancer biology. Click for more details
  • Upcoming Illumina Webinars: including “Library QC with the Bioanalyzer”, “Nextera: Sample Preparation and Troubleshooting” Click for more details
  • Illumina Targeted RNASeq: Illumina launch on online course for designing targeted RNASeq experiments in DesignStudio. DesignStudio™: TruSeq® Targeted RNA Expression
  • Illumina Kit Health & Safety: Illumina created a web-based search tool to retrieve all safety information relating to your kit. Are your MSDS up to date? Click for more details
  • Illumina Nextera XT kit expanded: Now available with 384 indexes

 
 
Best regards,
CIGC NGS team