10X Genomics - Single Cell CNV analysis

The 10X Genomics Single Cell CNV Workflow is a single-cell copy number variation (CNV) analysis workflow. First, a suspension of isolated cells is packed into tiny water-in-oil droplets using the undefinedChromium Controller. In this reaction volume of about 1 nl, the cells are lysed and enzymatically treated to remove all proteins present. The generated droplets are then in turn packaged with the help of the Chromium Controller together with Gel Beads, which contain a mixture of different barcodes, into new larger droplets where they are provided with barcodes and amplified. Thereafter, the resulting emulsion is chemically broken and the amplified DNA serves as input material for the creation of an Illumina-compatible library.

This workflow allows CNV analysis with a resolution of 2 Mb in a single cell or of a few hundred Kb when analysing cell clusters. Between 250 and 5,000 cells can be analysed per sample.

Sample Requirements

As input material, a single cell suspension is required. This suspension has to meet two key criteria in order to deliver high-quality data.

On the one hand only truly single cells may be present in the suspension. If cell aggregates are present in the suspension, they have to be removed. On the other hand, the cells should have the highest possible vitality. The suspension should not contain more than about 20% of dead cells. An excessive amount of dead cells leads to a high background signal. If your samples does contain a higher proportion of dead cells it may be necessary to remove the dead cells.

After receiving the samples in our laboratory, a quality control is routinely performed determining both cell count and vitality of your sample.

Since for this type of analysis the input material is cell material, please clarify in advance with us whether your material may be processed in our laboratory!

Head of GTL

Prof. Dr. Karl Köhrer

Biologisch-Medizinisches Forschungszentrum (BMFZ) Heinrich-Heine-Universität Düsseldorf Universitätsstr. 1 40225 Düsseldorf
Phone +49 211 81-13165
Fax +49 211 81-11922
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