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Hi all,
we are designing an experiment to compare a control vs. condition (diet based) in rats to trial the new BioRad/Illumina single cell RNAseq protocol. I am interested to know if there are any pitfalls to first running FACS on samples, and sorting into 4 cell types (likely epithelial, keratinocytes, CD9+, CD45+). The protocol requires ~12,000 cell input, but only sequences 300 of these I know...). Therefore splitting into 3,000 x 4 populations in equal amount makes sense. Concern with taking 12,000 of total cell pop. is that with max. 300 cells, we may get swamped by a single cell type (we expect more immune in condition) in some samples.
Am I missing anything WRT sub-sampling and sequencing those. Seems like a neat experiment but we have not done this before and I am not finding much in literature. Appreciate all and any ideas,
Bruce.
we are designing an experiment to compare a control vs. condition (diet based) in rats to trial the new BioRad/Illumina single cell RNAseq protocol. I am interested to know if there are any pitfalls to first running FACS on samples, and sorting into 4 cell types (likely epithelial, keratinocytes, CD9+, CD45+). The protocol requires ~12,000 cell input, but only sequences 300 of these I know...). Therefore splitting into 3,000 x 4 populations in equal amount makes sense. Concern with taking 12,000 of total cell pop. is that with max. 300 cells, we may get swamped by a single cell type (we expect more immune in condition) in some samples.
Am I missing anything WRT sub-sampling and sequencing those. Seems like a neat experiment but we have not done this before and I am not finding much in literature. Appreciate all and any ideas,
Bruce.