Single-Cell Sequencing Powered by 10X Genomics
One of the newest cutting edge tools available in our lab is our 10x Genomics Chromium Controller, which allows us to prepare samples for a variety of downstream analysis. This micro-fluidic system allows for the barcoding and labelling of single-cells as well as DNA fragments, preparing them for sequencing on our illumina sequencers. Researchers interested in the full suite of solutions on the10X platform are encouraged to contact us prior to submitting samples, as timing and viability of cells is essential for successful processing. During the consultation period we will address any researcher questions and discuss sample preparation. When the experimental details are agreed upon, the core can provide the researcher with a custom cost estimate for the project if desired.
The first use case for the 10X instrument is single-cell transcriptome profiling. Using this protocol, all transcripts within a single cell are tagged with a unique molecular identifier, allowing bioinformaticsts the ability to properly identify the unique transcriptome of each cell. Paired with clustering and dimension reduction techniques, populations of cells sharing similar profiles emerge and can be analyzed using differential expression techniques, as well as temporal analysis of cellular trajectory.
Working with researcher Dr. Rose-Anne Romano from the University of Buffalo’s Department of Oral Biology, single-cell sequencing analysis of a mouse salivary-gland looked at the roll of transcription factor p63 and smooth muscle actin and their roll on cell-fate determination. For this publication, ~1,000 cells were captured by the 10X controller, followed by sequencing on the illumina 2500 instrument. The resulting sequencing experiment was followed by in-depth analysis at our core facility, working one-on-one with Dr. Romano, resulting in rapid turn around from sequence to publication.
The 10X platform also has the ability to preform V(D)J immune profiling experiments for mouse and human models. This can aid researchers who are interested in immune response, by profiling the clonality, diversity, and antigen specificity at a single-cellular level. This preparation assembles and annotates the full length V(D)J gene sequences, and can be paired with the above transcriptomic pipeline to measure both cell surface protein expression and full gene expression on a cellular level.
A recent addition to the 10X portfolio is the ability to assay chromatin accessibility at single-cell resolution. The combination of ATAC-Seq (assay for transposase accessible chromatin) with the 10X single-cell barcoding system allows for researchers to gain insight into the roll chromatin conformation has a roll in DNA-protein binding. This preparation starts by loading between 500 and 10,000 nuclei into the 10X controller. Researchers interested in this protocol are encouraged to contact us for more details.
For projects interested in genome, exome, and denovo assembly projects, the 10X Controller also allows for the molecular tagging of high-molecular weight DNA. This linked-read technology provides long-range information using cost-effective short-read sequencing platforms like our illumina platforms. This platform is particularly powerful for SNP,SNV and Indel analysis, as well as for whole-genome denovo assembly.