email : Webview : CDS Summer 2023 Newsletter

Summer 2023 Newsletter

Creative Data Solutions (CDS) is a Vanderbilt University Shared Resource that provides bioinformatics and research informatics services to Vanderbilt investigators.

Open Position

In response to increased demand for our services, we are recruiting a new CDS team member, who will perform bioinformatics analyses of genomic data sets, develop and implement (genetic and other) statistical models, and contribute to research studies. The ideal candidate will have experience in analyzing large-scale next-generation sequencing data like whole genome sequencing (WGS) and low-pass WGS, DNA genotyping arrays, and a strong understanding of statistical analysis methods including statistical genetics. More details are available via Vanderbilt’s job site.

New Services
Over the past six months we have implemented several new approaches:

Courtesy of Fluent BioSciences

PIPseq data processing. We are pleased to announce data processing analysis support for PIPseq (Fluent Biosciences), a microfluidics-free scRNA-seq method that produces high-quality data using a simplified emulsification technique. The output we can generate includes 10X Genomics-compatible barcode and matrix data, which can readily be used with analysis tools such as Seurat, Single Cell Experiment and Scanpy.

NGS pre-sequencing consultation. We are launching a new consultation approach intended as a pre-sequencing “flight check”, either before and/or after library preparation. Our goals are to 1) ensure that sequencing results can be analyzed with sufficient statistical power, 2) minimize batch effects and 3) simplify downstream analysis, thereby reducing cost and turn-around time. For now, we will focus on transcriptomics and epigenomics, and offer a metadata and experiment design review. We will assess best practices for number of replicates, assess confounding variables, library QC results (if available), what type of transcripts or regulatory elements you are targeting, discuss species- and cell type-specific challenges, etc.

Try it out! Explore a 45K cell data (Shrestha et al, JCI 2021) with VITESSCE.

Publication of single cell RNA-Seq interactive apps. We now offer the ability to publish your single cell RNA-Seq data and metadata as web-hosted interactive applications, such as CELLxGENE (expression data only) or VITESSCE (expression, epigenomics, spatial, multimodal). In addition to depositing your data to funder-approved data repositories, this is a great way to make your data accessible to non-technical users to browse and interact with.

Data Management and Sharing Plans

Please contact us if you need help submitting a DMS plan with your next NIH grant. We’ve helped multiple investigators develop their plans and are knowledgeable about the data submission requirements for various repositories.

To discuss a new project, please contact us at data@vanderbilt.edu. For other information, please visit our website at https://cds.vanderbilt.edu and https://www.twitter.com/vandydata.

Jean-Philippe (JP) Cartailler, Ph.D.
Shristi Shresta, Ph.D.
Matt Cottam, Ph.D.