New Recharge Rates
The recharge rates at our Core Labs have stayed unchanged for the last three years while reagent prices have increased annually. Thus, we have to adjust the rates to be able to continue offering atâcost sequencing services. Details of the the new rates â which went into effect on October 1st â are available on the
DNA Technologies Core website.
We will, of course, honor the date limited quotes for the previous rates provided in recent weeks. Please also note that Agilent has significantly increased the prices for their Bioanalyzer reagents, especially for the High Sensitivity DNA reagents. Thus we have introduced separate rates for the RNA and DNA 12000 supplies ($36) and HS DNA supplies ($56).
Illumina RNA-Seq Pilot Grant Program Winners
Coinciding with the Illumina sequencing symposium on August 28th (see below), Illumina announced a UC Davis RNA-Seq Pilot Grant Program offering 4 grants. Each grant includes the preparation of 12 RNA-seq libraries and the sequencing of one HiSeq lane. We have received 27 grant applications of which 20 were judged to be very well suited for the pilot grant program. The proposals included studies of a wide selection of organisms among them bacteria, anemones, wheat, spinach, sturgeons, flies, dinoflagellates, and frogs and a wide selection of tissues and samples (e.g. gills, breast milk, stem cells, bee antennae). Further, the studies aim to answer developmental, disease related, as well as evolutionary questions. In short we received a large number of excellent proposals for which we thank the participants. The following four proposals were selected as the winners of the RNA-Seq Grant Program:
- Kai Battenberg, Plant Sciences: Elucidating the evolutionary origin of root nodule symbiosis: When did key genes gain function?
- Anupam Mitra, UCDHS - Dermatology: Transcriptome wide analysis in an in vitro milieu of scleroderma.
- Anne Frances Armstrong, Population Biology: Gene regulation by thyroid hormone in an echinoid echinoderm.
- Elva Diaz, Pharmacology: Cortical neuron specific gene expression mediated by Ephrin-B3-dependent synapse development.
HiSeq - new Real Time Base Caller - PhiX
The latest software update for Illumina HiSeq 2500 systems increases the tolerance for low complexity sequencing libraries and often improves base calling quality in general thanks to a new Base Caller (RTA 1.18.61). This Base Caller requires, similar to the MiSeqs, by default a small amount of PhiX spike-in into every lane. Please note that only if you are not de-multiplexing your HiSeq data (or let us do it) your reads could thus include some PhiX data. Almost all adapters now include barcodes which allow for filtering. Illumina flags reads identified as coming from the PhiX controls in the header line of the reads in the fastq format to enable filtering of the PhiX reads. The flag is located in field 9 of the header. If the read aligns to PhiX, this will field will be non-zero. If the read does not correspond to the PhiX genome field 9 will be zero. Please see the examples below:
Aligned to PhiX
@HWI-M02034:55:000000000-A85G4:1:1101:21460:1468 1:N:
18:
Clean - Not aligned to PhiX
@HWI-M02034:55:000000000-A85G4:1:1101:21468:1472 1:N:
0:
Please contact us with any questions about the data.
Summary of the Illumina Sequencing Symposium on August 28th
The Genome Center symposium was well attended and presented applications of the latest NGS technologies in synthetic long read sequencing, RNA-seq, 16S rRNA metagenomic profiling. I want to explicitly thank
Jenna Morgan Lang who filled in (on very short notice) with a thought provoking presentation on the variability of 16S sequencing data (among other things). Ours thanks also go to the other presenters Rajiv McCoy, Stanford University, Chia-Lin Wei, DOE Joint Genome Institute, Christopher Hopkins, Illumina, as well as to everybody who joined us.
