December News Letter

Dear DNA Technologies Core Users,

  • We are happy to announce that we are now offering 10X Genomics Linked-Read sequencing services using the GemCode technology. This exiting technology is currently applied for haplotype phasing and the delineation of structural rearrangements. However other applications will emerge soon. Please see the details below.
  • We are co-hosting a Single-Cell Genomics workshop on December 11th:
    Preparing for Single Cell Genomics – Tips, Tricks and Secret Hacks to Improve your Success”. Please also see the bottom of the email for details. There will be two sessions: a morning workshop in Sacramento and a afternoon workshop in Davis.

Date: Friday December 11, 2015
UCDMC 10 a.m.-11:30a.m.
Davis 1:30 p.m.-3:30 p.m.

  • We can now accept tissue and blood samples for sequencing and genotyping analyses, thanks to a collaboration with the Real-time PCR and Research Diagnostics Core (also known as Taqman Core). The core manager Samantha Mapes and her team have many years of experience in extraction sequencing worthy DNA and total RNA samples from both animal and plant tissues.
  • Reluctantly we have to say Good Bye to our staff member Charlotte Acharya who has been managing the HiSeq runs and the Sciclone robot and has helped us in a lot of other ways for the last one and a half years. We wish Charlotte all the best in her new position as lab manager of the UC Davis Strawberry Breeding program and a lot of fun returning to working with plants.
  • The recharge rates for the HiSeq 3000 SR50 lanes have dropped (to $1127 per lane) thanks to Illumina now delivering single-read flow-cells for the new generation of sequencers. Unfortunately the quality for the first batches of these flowcells was inconsistent which caused some delays in our sequencing schedule for which we apologize. The latest flowcells generate great data.
  • Our website features a new page summarizing the sample requirements for the wide array of sequencing, genotyping, and sample QC services we are offering. We hope this will be helpful planning your experiments. Please let us know which additional information you would like to see.

New Services: 10x Genomics Linked Reads


The DNA Technologies Core, ​together with the ​Langley lab, has acquired a 10X Genomics Gem Code instrument that will allow the generation of “linked reads” that could reach up to 150 kb (depending on the integrity of the DNA sample). The applications currently supported by the 10X Genomics software are human haplotype phasing and structural variant detection. However, the technology will be valuable also for genome scaffolding, structural variant detection in other species.
The 10X technology generates generates barcoded sequencing libraries in hundreds of thousands of nanoliter volume oil droplets using up to 700,000 different barcodes. Thus it allows to analyze individual HMW DNA molecules to be analyzed by Illumina sequencing using the limiting dilution principle. Please see the 10X Genomics webpage for currently supported applications. Only 1 ng DNA sample is required for the library preparation.

Details: Single Cell Genomics Workshop

Save the date for these technical workshops:
“Preparing for Single Cell Genomics – Tips, Tricks and Secret Hacks to Improve your Success”

Friday December 11, 2015:

UCDMC 10 a.m.-11:30a.m.
UC Davis Medical Center
Center for Health and Technology
Room 1347 LH
4610 X Street, Sacramento, CA, 95817

Davis 1:30 p.m.-3:30 p.m.
Tupper Hall, Room 2133 (ground floor)
1:30-3:30 p.m.

Single cell genomics uncovers biological heterogeneity that is not readily apparent by other means. Recently, the National Institutes of Health announced four new funding opportunities (detailed below) to support the development of innovative genomic technologies across a broad range of research areas including single-cell genomics, sample preparation, transcriptomics and epigenomics, and genome-wide functional analysis. These seminars, led by Maxine McClain, Senior Applications Scientist with the Fluidigm Corporation, will discuss considerations for sample prep and experimental design when isolating high-quality cDNA from single cells. Applications will include single cell qPCR with the Fluidigm BioMark system (located in the Flow Cytometry core, Tupper Hall) and single cell RNAseq using the Fluidigm C1 platform (located in the DNA Technologies core, GBSF), as well as the new HT800 chip for the C1 system.

Two sessions are offered and light refreshments will be provided.

Morning – Sacramento
UC Davis Medical Center
Center for Health and Technology
Room 1347 LH
4610 X Street, Sacramento, CA, 95817
10:00 – 11:30 a.m.
There are several two-hour parking spaces available next to the building for visitors.

Afternoon – Davis
UC Davis Health Sciences District
Tupper Hall, Room 2133 (ground floor)
1:30-3:30 p.m.

Please mark your calendars to join us and see below for information on the funding announcement from the NIH.

Bridget McLaughlin & Lutz Froenicke

Hosted by:
UC Davis Flow Cytometry Shared Resource
DNA Technologies Core at the UC Davis Genome Center
Fluidigm Corporation


 

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