Fluidigm C1 for Illumina Seq

[SDGenomics]

Our core has been using the Fluidigm C1 Single Cell Analyzer for generating cDNA for Illumina seq with the NEXTera kits. Do any other cores offer this service? I was trying to establish a fair price and looking to see what kind of issues others have encountered? So far, the biggest problem we have encountered is capture inefficiency on the C1 chip. However, with certain cultured cells we have gotten great capture. We normally run into problems with primary cells dying in the chip. Anyone have any troubleshooting advice?

[kwaraska]

I wish I had advice but we are having the same issue.

The only thing we have discovered is that even though they tell you that you can run the capture up to 3X to increase the capture number on the small cells, it isn't worth the time and effort-you might get 2 more.

[SDGenomics]

Kwaraska-
Thanks for the reply. I know this is a relatively new instrument, so we are trying to work out all the kinks. Please keep me updated if you have any new tips or tricks and I will do the same.

[genlyai]

We're interested in trying single-cell RNA seq as well. Does anyone know of a core or service provider currently offering this as a service?

Can those of you who have the fluidigm system in hand give any info as to the price? In this thread, $23/sample was mentioned as the library cost. Does that seem right?

Thanks for any help or additional thoughts. I'm very interested to see whether this is feasible for us!

[kwaraska]

You mention you are in Boston.

The BPF at Harvard Medical School has a C1.

Here is a link to the website www.genome.med.harvard.edu