All equipment of the CFNGS is provided by the Bopp Lab. It includes:
Quality control
> Quantification of RNA, DNA and protein
> Quitt 2.0 and Qubos Flex
> Determination of the RIN value (RNA integrity number), shape and average size of libraries
> Shearing of chromatin by sonication
Capturing of single cells
The CF NGS FZI has a total of four devices for single cell capture and provide help and support with capture of single cells and library preparations.
> targeted and whole transcriptome amplification (WTA)
> up to 12 samples tagged by sample tags on one cartridge
> up to 1-3 x 10^4 cells
> 3' prime and full-length
> whole transcriptome amplification (WTA)
> selection of single cells to proceed with
> up to 8 samples per chip
> up to 1800 cells overall
Spatial transcriptomics
The CF NGS offers help and support on your Spatial transcriptomics experiment. A complete pipeline for Visium (10X Genomics) has been set up, which includes the cutting of your FFPE sample, H&E staining, scanning of your sections up to the transfer of the hybridized probes to the capture chip using CytAssist. You will receive support during the preparation of the libraries and the final QC of the samples.
Analysis
In addition, the FZI provides its users the following software licence for evaluation
> Partek Flow Enterprise Edition
> RNA-Seq and Single Cell Toolkit for Partek Flow
> if you would like to use PARTEK please complete this file and send it via e-mail to drmklein@uni-mainz.de
> further information please have a look at: https://www.partek.com
