The GRCF is excited to now offer a wide and growing range of genomics applications for single cells, including RNA-seq, gene expression profiling by qPCR and DNA amplification for whole-genome or targeted (exome or PCR-based analysis) through two workflows: 10x  Genomics Chromium platform (similar to Drop Seq) and Fluidigm’s C1 Single Cell Auto-Prep.


Drop Seq technology as presented through the 10x Genomics Chromium Platform 10x genomics chromium pictureoffers a high throughput molecular barcoding and analysis suite that delivers cell-by-cell 3’end counting of mRNA transcripts for many tens of thousands of cells per run- similar to the popular DropSeq technology. This technology supports a broad range of applications, including cancer-cell transcriptomics and cell-type identification and discovery.  Because the platform works with short read sequencers, it integrates easily into the existing GRCF RNAseq workflow allowing for an end to end service.

 

10x workflow

Click Here for a 10x Genomic Single Cell Overview

 


Fluidigm’s C1 Single-Cell Auto Prep system offers within specific cell size ranges,  isolation  and processing of up to 96 cells  to produce pre-amplified cDNA or amplified genomic DNA for downstream analysis, including sequencing on Illumina platforms.  The most commonly used application for the C1 single-cell system is currently RNA-seq.  The whole process from cell capture to sequence-ready libraries can be done quickly and efficiently to deliver gene expression data from many diverse cell populations.

 

C1_workflow2


 

Aside from numbers of cells that can be assayed and the uniform cell size requirements of the C1, the chief distinction between the platforms is that 10X currently only provides sequence at the 3’ end of mRNAs while the C1 produces random-primed cDNAs anywhere in the RNA.  Further, the well-characterized pipeline and unique software, allows the GRCF to offer analysis for 10X Genomics data. In both systems, the GRCF cost for sequencing will vary based on read length.

Single cell genomics through the GRCF is a  joint effort between the GRCF Biorepository & Cell Center and GRCF DNA services center to allow for a one-stop single cell isolation, sequencing and analysis service.

Contact us today for more information or to schedule for your experiment!

410-614-5201

bioprocessing@jhmi.edu