To mul iplex, o no o mul iplex
S e en Mo gan1
1 Melbou ne Bioin o ma ics, The Uni e si y o Melbou ne
Single-cell sequencing is now a mains ay o genomics esea ch, and al hough he e a e a
mul i ude o expe imen al designs o ma ch a wide a ay o esea ch ques ions, op imal
s a egies o mul iplexing emain unclea . Sample mul iplexing in ol es pooling mul iple
samples oge he , sequencing hem, and subsequen ly decon olu ing hem compu a ionally.
The high- h oughpu o mode n single-cell echnologies makes mul iplexing ealis ic o many
applica ions.
Deciding whe he o mul iplex samples is a key conside a ion in he planning o single-cell
expe imen s. We ocus on publicly a ailable ansc ip omics da a om he 10X Genomics
pla o m o explo e how bes o apply sample mul iplexing. We expand on he consequences
o choosing whe he o no o mul iplex on downs eam analysis, and p o ide
ecommenda ions o esea che s depending on key expe imen al ac o s. In pa icula , his
choice impac s impo an s eps in single-cell wo k lows including duplica e de ec ion and ba ch
e ec co ec ion. The e is a ade-o be ween he minimisa ion o ba ch e ec s ha sample
pooling p o ides, and he educed h oughpu o sequencing samples oge he , as opposed o
c ea ing sepa a e lib a ies. I choosing o p oceed wi h a mul iplexed app oach, esea che s
a e also aced wi h a decision as o how o demul iplex hei samples based on hei chosen
design. Ou esul s p o ide ac ionable insigh s ha can assis esea che s in imp o ing cos -
e ec i eness and e iciency, o make he mos o single-cell genomics echnologies.
