A "much-tweeted" manuscript was recently published on Biorxiv, investigating the barcode mis-assignment issues affecting HiSeq 3000, 4000, and HiSeq X, reported in our last newsletter. Please see the manuscript here: Sinha et al.
New High-Throughput Gene-Expression Analysis Services (3'Tag-Seq)
The DNA Technologies and the Bioinformatics Cores have been working for more than half a year with a simplified RNA-Seq protocol that promises to drastically reduce the costs of many gene-expression studies, while fully maintaining the precision of the analysis.
The new approach is called 3'Tag-Seq (or TagSeq, 3'Tag-RNA-Seq, Digital RNA-seq but these names have also been used for a variety of different protocols).
PacBio Sequel Version 2 Chemistry
We have recently beta-tested the new PacBio Sequel chemistry (V2). The tests have demonstrated significant yield and read-length improvements. All current and future Sequel runs will be carried out with the new chemistry. In addition to the V2 chemistry change, the Sequel software has been updated and allows now for 10 hour movie recordings (previously the limit was 6 hours, as it still is for the RSII).
We will be open before, after, and between the holidays and closed only on official UC holidays. The UC holidays are Friday the 23rd, Monday the 26th, Friday the 30th, and Monday the 2nd.Happy Holidays! The DNA Tech Core Staff.
Please joins us for the seminar: Simultaneous “multi-omic” measurement of gene fusions, mRNA, & proteins at 800-plex using single-molecule optical barcodes.Thursday, December 1st: 2pm to 3 pm Genome Center Auditorium (GBSF, #1005)
Refreshments provided. Please RSVP using this link.
ABSTRACT
The ability to measure changes to DNA, RNA, and protein is crucial to developing a comprehensive understanding of biology in the genomics era
Pacific Biosciences (PacBio) has recently published a high quality de novo genome assembly for Arabidopsis based on the data of only two Sequel SMRT-cells. The Sequel is the second generation PacBio sequencer and generates up to 7x more reads per SMRT-cell compared to the first generation PacBio RSII sequencer.
The UC Davis DNA Technologies and Expression Analysis Cores have been designated a Campus Research Core Facility
From the official announcement:
" .... This designation provides a strategic platform to ensure state-of-the-art research capabilities provided in a cost-efficient manner. The designated laboratories are expected to develop and represent best practices for core facility operation and emerge as centers of excellence for the university.
We would like to thank everybody who participated in our user survey!
Your input is highly appreciated and will help us improve our services.
The results are available here: https://www.surveymonkey.com/results/SM-Q67N6H9J/
73 DNA Technologies and Expression Analysis Core users did participate.
Our latest generation Illumina HiSeq3000 sequencer has been upgraded to a HiSeq4000. This means the option to run two flowcells in parallel was enabled. Thus, the sequencer offers now twice the throughput. The chemistry and reagents do not change as should the yields per lane and the high quality of the data.
Please note, we will not be open for business between 21 December and 4 January. The last day to sign up for shared instrument use, to drop off samples, or to receive data, is Friday December 18th.
Happy Christmas – we look forward to seeing you in the New Year!
The DNA Technologies Core now offers the following new services: METHYL-Seq
Whole Genome Bisulfite Sequencing (WGBS) and
Reduced Representation Bisulfite Seq (RRBS)
Mate Pair library preps and sequencing
Nextera based mate pair with insert sizes ranging from 2 kb to 12 kb
Reduced Representation Sequencing
e.g.for the purpose of genotyping
Please see our homepage for a complete list of services and
The Genome Center has acquired a HiSeq 3000 sequencer to be able to provide faster sequencing at significantly reduced per-base-costs. The new sequencer is already delivered and will be installed this week and then tested. Please note that for some samples the library preps should be adjusted for the HiSeq 3000.
The new sequencer is more than three times faster than the HiSeq 2500 and yields about 65% more reads per lane.
UCD Genome Center - DNA Technologies and Expression Analysis Cores News Bulletin, April 2015
New Latest Generation Illumina Sequencer
Dear DNA Technologies Core users,
The Genome Center has acquired a HiSeq 3000 sequencer to be able to providefaster sequencing at significantly reduced per-base-costs. The new sequencer is already delivered and will be installed this week and then tested.
