Table 1. Microfluidic-Based Approaches Applied to Single-Cell and Single-Nucleus Sequencing and Preparation of Cell Atlases from Different Brain Regions.

cell source (brain region or organoid)	species (sample)	microfluidic platform	cells or nuclei (number)	sequencing depth (reads/cell)	results (types and number of detected cell clusters and subclusters)
whole brain	human healthy brain during surgery	Fluidigm	466 cells	2.83 million	Oligodendrocyte precursor cells (OPCs), oligodendrocytes, astrocytes, microglia, neurons (excitatory and inhibitory subclusters), endothelial cells, neuronal progenitors, and quiescent newly born neurons were identified.165
whole brain	post-mortem human	Fluidigm	3227 nuclei	8.34 million	Single-nucleus RNA sequencing showed 16 neuronal clusters with 16 neuronal subtypes annotated on the basis of cortical cytoarchitecture.128
telencephalon (cortex and MGEa): germinal zone, cortical plate, prefrontal cortex, and primary visual cortex	human developing brain	Fluidigm	4261 cells		11 classes including astrocytes, OPCs,b microglia, radial glia, intermediate progenitor cells, excitatory cortical neurons, ventral MGE progenitors, inhibitory cortical interneurons, choroid plexus cells, mural cells, and endothelial cells (plus temporal and spatial trajectories of radial glia maturation and neurogenesis).138
whole brain	23–25 dpfc zebrafish	Drop-Seq	58 492 cells	22 500	Simultaneous extraction of cell type and lineage information. More than 100 cell types and marker genes were identified, including 45 neuronal subtypes, 9 neuronal progenitor subtypes, and 3 oligodendrocyte subtypes.80
telencephalon, diencephalon, midbrain, hindbrain, and cerebellum	first trimester human	10× Chromium	289 000 cells		Nine progenitor populations were detected proximal to the telencephalon.140
cortex	P10 to P89d mouse	Fluidigm	50 cells	qPCR	Three subgroups of astrocytes were detected from P10 to P50.178
cortex	mouse	sNucDrop-Seqe	18 194 nuclei	15 471	40 clusters were identified, including 27 excitatory, 7 inhibitory, and 6 non-neuronal cells.121
cortex: germinal zone	16 wpcf human	Fluidigm	65 cells	5000	Four major groups of cells were identified including multiple progenitor and neuronal subtypes.179
cortex: VZg and OSVZh	16–18 wpc human	Fluidigm	393 cells	2.9 million	Transcriptional state associated with neuronal differentiation: radial glia, intermediate neuronal progenitor cells (INPCs), neuronal progenitor cells (NPCs), and excitatory and inhibitory neurons.167
cortex: primary motor cortex	mouse	10× Chromium and Smart-Seq4	175 000 and 6300 cells	1–2.1 million	59 GABAergic inhibitory neurons, 31 glutamatergic excitatory neurons, and 26 non-neurons were detected.142
cortex: primary motor cortex	mouse	SMART-Seq and 10× Chromium	280 327 and 94 162 cells	2.5 million 120 000	Linked the SMART-Seq resolved isoforms to the cell types defined by 10× Chromium. Spatially resolved isoform atlas of the mouse primary motor cortex was generated.155
cortex: primary motor cortex	post-mortem human monkey	SMART-Seq and 10× Chromium	>450 000 nuclei	17 576 and 77 816	Around 100 cell types were detected in each species, with distinct marker-gene expression and accessible chromatin sites.180
cortex: somatosensory S1 and hippocampus CA1	mouse	Fluidigm	3005 cells	500 000	47 molecularly distinct subclasses of cells: 7 S1 pyramidal neurons, 2 CA1 glutamatergic cells, 16 interneurons, 2 astrocytes, 2 immune cells, and 6 oligodendrocytes.120
cortex: primary visual cortex	mouse	Fluidigm	1679 cells	>5 million	49 transcriptomic cell types: 23 GABAergic, 19 glutamatergic, and 7 non-neuronal types.181
visual system	drosophila: multiple stages of neuronal development: over 100 h	10× Chromium	208 976 cells	176 636	Transcriptional atlas generated across multiple stages of visual system development (162 distinct neuronal populations were detected at 7 time points: prior to, during, and after synaptogenesis).182
olfactory epithelium	P4–P10 and P30–P90 mouse	Fluidigm	178 cells	1.06–4.52 million	Classified based on specific olfactory receptor expression in newborn and adult mouse.183
lateral ganglionic eminence (LGE)i	7–20 wpc human embryo	10× Chromium	96 789 cells	80 million	Fifteen different cell states were detected. A common progenitor generates medium spiny neurons with D1 or D2j receptors.141
striatum neurons	mouse	Fluidigm	1208 cells	1–5 million	Ten clusters of cells were detected, including neurons, astrocytes, oligodendrocytes, vascular, and 2 ependymal, 2 immune, and 2 stem cell types.184
striatum	P22–P28, P21–P26, and P55–P76 mouse	Fluidigm	1135 cells and 3417 cells	800–1500	529 cells identified as neurons. Seven interneuron classes (6 subclasses of GABAergic interneurons) were identified.185
substantia nigra (SN) and cortex	human	10× Chromium	2455 nuclei and 690 nuclei	46 598–59 513 and 18 377–44 710	SNk cell-type atlas together with a matching cortical atlas were extracted. Genetic risk in Parkinson’s disease is associated with dopaminergic neurons and oligodendrocytes.186
thalamic reticular nucleus (TRN)l	mouse	Smart-Seq2 and 10× Chromium	1687 nuclei	1.3 million	Two neuronal populations expressing different genes were detected. Each population was connected to distinct thalamus nuclei and formed molecularly specific subnetworks.187
hypothalamus	mouse	Drop-Seq	3131 cells	>1500	Seven cell types were distinguished, including neurons. Neurons were further classified into 62 clusters of glutamatergic, dopaminergic, and GABAergic subclasses.188
hypothalamus	mouse	Drop-Seq	14 437 cells	>800	45 cell clusters were identified, including 34 neuronal and 11 non-neuronal. Neuronal clusters further divided into 15 glutamatergic, 18 GABAergic, and 1 histamatergic subclasses.35
hypothalamus: preoptic region	mouse	10× Chromium	31 299 cells	101 771	23 excitatory neuron subclasses and 43 inhibitory neuron subclasses were identified.189
hypothalamus: ventral posterior hypothalamus (VPH)m	mouse	10× Chromium	16 000 cells	50 000	Twenty neuronal (excitatory and inhibitory) and 18 non-neuronal cell clusters were identified in VPH.190
hypothalamus: lateral hypothalamic neurons	P21–P23 mouse	Fluidigm	89 and 69 cells	qPCR	Both excitatory (glutamate) and inhibitory (GABA) neurons were identified.191
midbrain: dopaminergic neuron	mouse	Fluidigm	159 cells	qPCR	Simultaneous expression of 96 genes in single neuron. Six different subtypes of dopaminergic neurons were distinguished.192
midbrain: ventral midbrain	human embryos (6–11 week) E11.5–E18.5n mouse postnatal mouse	Fluidigm	1977 cells, 1907 cells, 245 cells	1200–24 000 2000–26 000 2000–30 000	25 human and 26 mouse clusters were identified. Human: 5 subtypes of radial glia-like cells and 4 of progenitors. Mouse embryo: 2 dopaminergic neuron subtypes. Mouse postnatal: 5 dopaminergic neuron subtypes. Clear differences in cell proliferation, developmental timing, and dopaminergic neuron development between species.166
midbrain: dopaminergic neurons	mouse	Fluidigm	111 cells	Single-cell qRT-PCR	Co-varying gene modules that link neurotransmitter identity and electrical phenotype.193
midbrain	Drosophila	Drop-Seq	10 286 cells	>800	Cell atlas of the fly brain provides a unique resource of gene expression across many cell types and regions of the visual neuropil. Twenty-nine cell clusters were identified.194
suprachiasmatic nucleus (SCN)	mouse	Fluidigm	352 cells	qRT-PCR	Five subtypes of mammalian SCNo neurons were distinguished.195
suprachiasmatic nucleus	mouse	10× Chromium and Drop-Seq	62 083 cells and 16 004 cells	1 million	Based on combinations of markers and their spatial distribution, circadian rhythmicity and light responsiveness, 5 SCN neuronal subtypes were identified.196
geniculate ganglion	mouse	Fluidigm	96 cells	1 million	Two main groups of gustatory and somatosensory neurons were detected. Gustatory neurons included 3 subclasses.197
trigeminal ganglion neurons	mouse	Drop-Seq	6998 cells		13 genetically defined classes of sensory neurons were identified.198
DRG sensory neurons	mouse	Fluidigm	334 cells	qRT-PCR	Six distinct subgroups of DRGp populations were identified.199
spinal cord	postnatal mouse	10× Chromium	19 353 nuclei	50 000	Unifying the previously published data sets137,145,200−202 into a common reference framework.203 Validated combinatory marker codes for 84 types of spinal-cord cells and mapped their spatial distributions.
retina	mouse	Drop-Seq	44 808 cells	>100 000	39 transcriptionally distinct clusters in 6 classes: photoreceptor, bipolar, horizontal, amacrine, and ganglion cells, and other cell types.33
retina	E18 chicken	droplet-based scRNA-Seq platform160	30 022 cells		Five neuronal classes (PRs,q HCs,r BCs,s ACs,t and RGCsu) as well as 2 glial types, Müller glia and oligodendrocytes were identified.204
retina: bipolar cells	mouse	Drop-Seq	27 499 cells	8200	26 cell classes identified: 14 bipolar, Müller glia, 11 rods and cones, and amacrine cells. These data were validated by in vivo matching of gene expression to bipolar cell morphology.136
retina: fovea and peripheral retina	human	10× Chromium	85 000 cells	4062–550 895	58 cell types were identified in following cell classes: photoreceptor, horizontal, bipolar, amacrine, retinal ganglion and non-neuronal cells.205
retina: amacrine cells (ACs)	P19 mouse	10× Chromium	32 000 cells		63 types of ACs were identified in mice retina.206
cerebral organoids vs fetal neocortex	hiPSC-derived organoids, 12–13 wpc human	Fluidigm	333 + 175 cells, 226 cells	2–5 million	Similar genetic features responsible for human cortical development between in vivo fetal brain and in vitro organoid culture were identified.34
cerebral organoids	hiPSC lines, chimpanzee iPSC lines, fetal human cortex	Fluidigm	52 cells, 344 cells, 220 cells		Transcriptomic similarities between human and chimpanzee neuronal stem and progenitor cells were highlighted.132
brain organoid	hiPSC lines, 3–6 month old organoids	Drop-Seq	82 291 cells		Beyond similarities between 3- and 6-month-old organoids, mature photoreceptors and mature astrocytes only presented in 6-month-old organoids.168 Despite the differences in the profiling methods used (Drop-Seq and Fluidigm C1v), preferential correlation between corresponding cell types for radial glia, interneurons, projection neurons, and induced pluripotent stem cells were detected.

^aMedial ganglionic eminence.

^bOligodendrocyte precursor cells.

^cDays postfertilization.

^dPostnatal day.

^eSingle-nucleus RNA-Seq approach.

^fWeeks post conception.

^gVentricular zone.

^hOuter subventricular zone.

ⁱLateral ganglionic eminence.

^jDopamine receptor 1 and 2.

^kSubstantia nigra.

^lThalamic reticular nucleus.

^mVentral posterior hypothalamus.

ⁿEmbryonic day.

^oSuprachiasmatic nucleus.

^pDorsal root ganglion.

^qPhotoreceptors.

^rHorizontal cells.

^sBipolar cells.

^tAmacrine cells.

^uRetinal ganglion cells.

^vC1TM single-cell auto prep integrated fluidic circuit (IFC).