DNA Services

This cutting-edge long-read sequencing instrument offers exciting new capabilities. Its applications span a wide range, including de novo genome assembly for both eukaryotic and prokaryotic species, the most cost-effective genome resequencing using long reads, sequencing of long amplicons including full-length 16S, and full-length mRNA sequencing from bulk or single-cell RNAseq samples. The standout advantage of the REVIO lies in its significantly reduced sequencing cost. Compared to the Sequel, it produces three times the data for the same cost, making it an best choice for researchers for their long-reads needs. We eagerly anticipate discussing how long-read sequencing can enhance your research endeavors. Feel free to reach out for further details! 😊

The Single-Cell and Spatial Transcriptomics workshop was a huge success. This workshop included presentations of all the latest applications, technologies, and instrumentation. A recording of all the lectures can be accessed in the link below. If you are considering utilizing single-cell or spatial transcriptomics, please watch the recording to become familiarized with the most up to date information. https://mediaspace.illinois.edu/media/t/1_n3a5pevn

Chris Wright and Alvaro Hernandez loading the NovaSeq X Plus The NovaSeq X Plus is the latest and most advanced DNA sequencing instrument currently available, able to sequence up to 20 billion DNA fragments in just one day. To translate this to samples, the output is 6 Tb of genomic information, equivalent to 2,000 human genomes, 6,000 soybean genomes, or 1 million bacterial genomes! In addition, The X Plus system reduces current sequencing costs by up to **50%**, further enabling PIs to extend their funding into new or more complex research, utilizing genomics, transcriptomics, epigenomics, single-cell multiomics, spatial transcriptomics and proteomics, and metagenomics at a significantly lower cost compared to any other sequencing technology.

•Single cell RNA-sequencing reveals the complete temporal sequence of transcription factors that pattern Drosophila medulla neuroblasts. Hailun Zhu, Sihai Dave Zhao*, Alokananda Ray, Yu Zhang and Xin Li*.  In preparation.   •Single-cell analyses of the corneal epithelium: Unique cell types and gene expression profiles. Surabhi Sonam, Sushant Bangru, Kimberly J. Perry, Auinash Kalsotra, Jonathan J. Henry. bioRxiv 2020.08.06.240036. –https://doi.org/10.1101/2020.08.06.240036 •Meta-analysis of honey bee neurogenomic response links Deformed wing virus type A to precocious behavioral maturation. Traniello, I.M., Bukhari, S.A., Kevill, J. et al. Sci Rep 10, 3101 (2020). –https://doi.org/10.1038/s41598-020-59808-4 •Cellular plasticity balances the metabolic and proliferation dynamics of a regenerating liver. Ullas V. Chembazhi, Sushant Bangru, Mikel Hernaez, Auinash Kalsotra –https://doi.org/10.1101/2020.05.29.124263 •A common pattern of influenza A virus single cell gene expression heterogeneity governs the innate antiviral response to infection. J. Cristobal Vera, Jiayi Sun, Yen Ting Lin, Jenny Drnevic, Ruian Ke, Christopher B. Brooke. bioRxiv 858373.  –https://doi.org/10.1101/858373 •Progesterone Receptor Serves the Ovary as a Trigger of Ovulation and a Terminator of Inflammation. Park CJ, Lin PC, Zhou S, et al.  Cell Rep. 2020;31(2):107496. –https://doi.org/10.1016/j.celrep.2020.03.060

Our new shiny Sequel II is here. We believe that this instrument is a game changer for denovo assembly and annotation of eukaryotic genomes, for sequencing of full-length 16S from metagenomic samples, sequencing of PCR amplicons or DNA fragments with high accuracy and full characterization of transcriptomes, including splice variants . Let us know if you have any project that can benefit from long highly accurate/error-corrected reads.

We just received our second NovaSeq 6000. The addition of this instrument, the latest technology from Illumina, will ensure the fastest possible turnaround time. A section of our museum of obsolete technology with a HiSeq 4000, a HiSeq 2500, a cBot, and a Neoprep (yayy). In total, it has over $2M in equipment, some only 3 years old. Hello progress!

We showcased the University of Illinois NGS capabilities.

Description: The DNA Services lab is hosting a lunch seminar on the exciting applications of single cell genomics!  We hope you can join us for an informative seminar on single cell RNA sequencing, including new single-cell applications of Immune Profiling and ATAC-Seq.  Please register (see link below) so that we can ensure seating and pizza for all. See information below regarding a program to support two 2 single-cell projects for UIUC faculty grant proposals. Featured Speakers: Andrew Steelman, PhD, Assistant Professor, University of Illinois – ‘Differences in glial activation during upper-respiratory viral infection are revealed using 10x single cell RNA-seq’ Dr. Steelman will present an overview of a 10x single-cell experiment performed in collaboration with Dr. Romana Nowak on influenza infected versus non-infected mice glial cells, discussing his techniques for cell preparation and results including identification of cell populations, percentages of cells expressing selective genes and downstream analysis of the dataset. Melissa Leone, Sales Executive, 10x Genomics * Reveal cellular heterogeneity and profile unique cell types individually with the Chromium Single Cell Gene Expression Solution * Simultaneously examine the cellular context of the adaptive immune response and immune repertoires of T and B cells in human or mouse on a cell-by-cell basis with the Chromium Single Cell Immune Profiling Solution * Perform single cell epigenomics with the Chromium Single Cell Assay for Transposase Accessible Chromatin (ATAC) Solution Please Register, seating is limited: https://10x_seminar_univofillinois.eventbrite.com Date/time: October 17th, at 11:45am to 1pm (seminar starts at noon) Location:               612 IGB (lower floor of gatehouse) Questions?  Contact Alvaro Hernandez aghernan@illinois.edu or Chris Wright clwright@illinois.edu

Our NovaSeq 6000 has been installed and it is producing GREAT data. Each lane produces ~ 5 billion reads 150nt in length (2.5 billion clusters sequenced from both ends) with amazing quality scores. This is a cost effective system for projects that require high depth or that have a large number of samples. It has an output equivalent to over 6 lanes in the HiSeq 4000, but for a portion of the cost. The first sequenced projects included several single-cell transcriptomics, 10x Genomics libraries for de novo genome assemblies and shotgun genomics libraries. This picture shows flowcells from the NovaSeq 6000, HiSeq 4000, and HiSeq 2500, in that order:

We received the GridION (Oxford Nanopore)! Let us know if you have any project for direct RNA sequencing, de novo assembly of microbial and larger genomes, sequencing of full length 16S or ITS or other projects that can benefit from very long sequence reads (up to 120kb) and single-molecule sequencing.