How does Fluidigm C1 Single Cell RNA-seq workflow allow the quantification of mRNA transcripts in the cell?
From what I know, there are protocols that include ERCC RNA spike-ins as well as UMI tag on the sequencing fragments to exclude the technical variation (PCR, reverse-transcription) from the true biological variation.
Are the single cell cDNA samples not multiplexed and sequenced individually for each cells?
If so, would you tell me why this protocol multiplexed their sample?
And are there any important steps missed below for my understanding of the workflow of Fluidigm C1 Single Cell RNA-seq?
*Workflow of Fluidigm C1 Single Cell RNA-seq: Microfluidics separation into single cell -> mRNA library preparation -> reverse transcription -> cDNA library preparation -> NGS sequencing (BCL into Fastq.gz)
If the samples are not multiplexed, then would each of the Fastq files in the Fastq.gz file represent a single cell?
I really appreciate any help and expertise given on this topic!