Single-cell transcriptomics allows characterization of cerebrospinal fluid (CSF) cells at an
unprecedented level. Here, we report a robust cryopreservation protocol adapted for the
characterization of fragile CSF cells by single-cell RNA sequencing (RNA-seq) in moderate-
to large-scale studies. Fresh CSF was collected from twenty-one participants at two
independent sites. Each CSF sample was split into two fractions: one was processed fresh,
while the second was cryopreserved for months and profiled after thawing. B and T cell …

Importance: A robust cerebrospinal fluid (CSF) cell cryopreservation protocol using high
resolution single-cell (sc) transcriptomic data would enable the deployment of this important
modality in multi-center translational research studies and clinical trials in which many sites
do not have the expertise or resources to produce data from fresh samples. It would also
serve to reduce technical variability in larger projects. Objective: To test a reliable
cryopreservation protocol adapted for CSF cells, facilitating the characterization of these …