Single-Cell Pilot Grants Call — Lexogen RNA-Seq Lunch & Learn this Thursday, March 15th — Dovetail Genomics: Building the Best Genomes on Earth , April 18th

Dear DNA Tech Core users, the March news is:

1) a Pilot and Feasibility Project Grants Call by the Office of Research    (apply for single-cell gene expression projects)
2) the Lexogen RNA-Seq Lunch & Learn Seminar — this Thursday, March 15th — 12:30pm
3) Dovetail Genomics and the Genome Center – Building the Best Genomes on Earth — April 18th  — 1pm

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1) Pilot and Feasibility Project Grants Call 

The Office of Research has issued a program supporting pilot and feasibility projects for UC Davis investigators.   For the DNA Technologies Core these funding opportunities will be focusing onsingle-cell gene expressions studies.   Hereby we are collaborating with both the Bioinformatics Core and the Flowcytometry Core.

Single-cell gene expressions studies reveal expression changes that are undetectable via conventional RNA-seq from tissue samples.  The latter can only provide transcriptome data averages for the entire sample, confounding transcripts of multiple cell types and cell-cycle stages.  In contrast single-cell RNA-seq (scRNA-seq) allows to resolve the cellular heterogeneity.

The DNA Technologies Core offers two protocols for scRNA-seq:

  1.      Plate-based scRNA-seqlibrary prep and sequencing  (e.g. after flow-sorting).
  2. Droplet-based high-throughput scRNA-seq library prep and sequencing (using the 10X Genomics system)
  • Please inquire with the Flowcytometry Core if your project will involve cell sorting.
    The Bioinformatics Core has lot of experience in single-cell data analysis.  Both cores will aim to support Pilot and Feasibility Project Grant applications for their efforts.
  • The DNA Technologies Core must provide an estimate for services that you apply for, so please contact dnatech@ucdavis.edu before you apply to the Campus Program for Pilot and Feasibility Project Grant funds.
  • For more details please see the call at this page:
    http://research.ucdavis.edu/research/core-facilities-services/core-resources/
    Award preference will be given to projects that will generate long-term use, preliminary data for a new extramural grant or manuscript submissions.  Funding from this program will be granted to Academic Senate and Academic Federation members with PI status with the following constraints:
  • (1) Who have not used the requested facility in the past 2 years, or
  • (2) Investigators who will explore the utilization of equipment and services offered by the facility that they have not used before
  • These funds must be utilized within 12 months.
    ·         Please direct administrative questions to dmporter@ucdavis.edu

Application deadlines are:  March 23;  June 15; September 14; & December 14, 2018

2) Lexogen RNA-Seq Lunch & Learn Seminar on March 15th

Please join the Genome Center DNA Technologies and Bioinformatics Cores for a Lunch & Learn Seminar sponsored by Lexogen!

 

When:  Thursday March 15, 12:30 – 1:30pm

Where:  UC Davis GBSF Auditorium

Speaker:  Alex Mojcher, Application Scientist, Lexogen, Inc.
Lexogen Inc. has developed a complete line of reagent kits for working with the transcriptome to make your life easier. The talk will cover topics from RNA extraction, rRNA depletion and mRNA enrichment, to library prep kits for small RNA, whole transcriptome and expression profiling. Lexogen also introduced a Metabolic RNA-Seq kit for measuring nascent RNA levels in cells, globin blockers for working with blood samples and spike-in RNA variant controls for experimental quality control.

This seminar will include a technical overview of these products and will describe how to make sequencing libraries without fragmenting your RNA to get unparalleled strand specificity. They will also show you how to make expression profiling easy and affordable.

Please register at https://registration.genomecenter.ucdavis.edu/events/Lexogen_March_15_2018/  so we can get an accurate headcount for lunch.
Questions?  Contact Kristy Ramsey (kristy.ramsey@lexogen.com) or see the attachment.

3) Reserve the date: Dovetail Genomics and the Genome Center – Together, Building the Best Genomes on Earth — on April 18th

Dovetail Genomics and UC Davis – Together, Building the Best Genomes on Earth

Sponsored by the DNA Technologies and Bioinformatics Core Facilities

Wednesday April 18, 1pm

Auditorium Room 1005

This will also be a Lunch & Learn Seminar: please register:

https://registration.genomecenter.ucdavis.edu/events/Dovetail_April_18_2018/

Learn how the DNA Technologies and Bioinformatics Core Facilities are now providing the Dovetail Genomics Hi-C technology with HiRise software.

A contiguous and accurate genome assembly is a crucial first step in fully understanding the biology of any organism.  A high-quality genome assembly will make any downstream analyses, like gene annotation, synteny, comparative genomics and population genetics far easier and more reliable.

Dovetail Genomics has assembled and scaffolded more than 1000 genomes over the past five years.  We are routinely delivering chromosome-scale assemblies to our customers, built using our Dovetail Hi-C protocol and HiRise scaffolding software.  We have now released this protocol as an easy-to-use kit with cloud-based software.

This seminar will provide an overview of the Dovetail genome scaffolding technologies, and details on the new Hi-C Kit with HiRise software.  We will discuss why Dovetail is superior to other scaffolding methods, and how you too can take advantage of this unique technology.

 

———————————————————————————————–

Lutz Froenicke, PhD

DNA Technologies and Expression Analysis Cores
UC Davis Genome Center
Lab: (530) 754-9143
dnatech.genomecenter.ucdavis.edu

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