Drop-seq and 10X Genomics Chromium 3’ sequencing (V3)
Anna, Axelle, Michela, Galina, Hanja, Petra
CSAMA 2019
Drop-Seq
Macosko et al., 2015
Droplets are pooled
Illumina bridge Amplification
Similarities
Droplet Generation
Barcoded primer bead
Differences
Drop-seq
10X Genomics
Emulsion
Reaction after demulsification
Reaction in droplets
Experimental design
2 blood samples from 5 donors -> 10 samples
Investigation: which activated lymphocyte populations appear in the peripheral blood after the vaccination and how they differ from one donor to the other
4000 cells each sample (2000 T + 2000 B cells)
Use 2 chips, 8 wells each (6+4 paired patients, 2+4 remain empty)
Batch effect between chips and wells -> design avoiding chip batch effect
Price: $2300x10(wells)=$23000 (library prep)
Advantages/disadvantages
High number of cells
Low coverage
No information about isoforms
Details:
UMI
3’end
cells/expression
duration