10X Genomics single cell RNA-Seq Gene Expression (GEX) is a 3’ or 5'-mRNA-seq method.
The protocol involves barcoding each cell (10x Barcode) in each sample (i5 & i7 indeces) by reverse transcription using an oligo dT primer, pooling of samples and subsequent molecular reactions for linear amplification and preparation for illumina sequencing. 10X single cell GEX libraries are designed to sequence a tag (short region) near the 3' or 5' end of the gene.
In Read 1 we sequence the cell barcode (16 bases) and a unique molecular identifier (UMIUMI is a random sequence of 10 bases.
Each UMI identifies one mRNA molecule.).
In Read 2 we sequence the tag that will be later aligned to the genome.