Single-cell and spatial transcriptomics: deciphering brain complexity in health and disease

M Piwecka, N Rajewsky, A Rybak-Wolf - Nature Reviews Neurology, 2023 - nature.com
In the past decade, single-cell technologies have proliferated and improved from their
technically challenging beginnings to become common laboratory methods capable of …

Hippocampal GABAergic interneurons and memory

A Tzilivaki, JJ Tukker, N Maier, P Poirazi, RP Sammons… - Neuron, 2023 - cell.com
One of the most captivating questions in neuroscience revolves around the brain's ability to
efficiently and durably capture and store information. It must process continuous input from …

Molecularly defined and spatially resolved cell atlas of the whole mouse brain

M Zhang, X Pan, W Jung, AR Halpern, SW Eichhorn… - Nature, 2023 - nature.com
In mammalian brains, millions to billions of cells form complex interaction networks to enable
a wide range of functions. The enormous diversity and intricate organization of cells have …

A multimodal cell census and atlas of the mammalian primary motor cortex

Principal manuscript editors, Analysis coordination… - Nature, 2021 - nature.com
Here we report the generation of a multimodal cell census and atlas of the mammalian
primary motor cortex as the initial product of the BRAIN Initiative Cell Census Network …

[HTML][HTML] Spatially resolved cell atlas of the mouse primary motor cortex by MERFISH

M Zhang, SW Eichhorn, B Zingg, Z Yao, K Cotter… - Nature, 2021 - nature.com
A mammalian brain is composed of numerous cell types organized in an intricate manner to
form functional neural circuits. Single-cell RNA sequencing allows systematic identification …

Cell segmentation in imaging-based spatial transcriptomics

V Petukhov, RJ Xu, RA Soldatov, P Cadinu… - Nature …, 2022 - nature.com
Single-molecule spatial transcriptomics protocols based on in situ sequencing or
multiplexed RNA fluorescent hybridization can reveal detailed tissue organization. However …

[HTML][HTML] A taxonomy of transcriptomic cell types across the isocortex and hippocampal formation

Z Yao, CTJ Van Velthoven, TN Nguyen, J Goldy… - Cell, 2021 - cell.com
The isocortex and hippocampal formation (HPF) in the mammalian brain play critical roles in
perception, cognition, emotion, and learning. We profiled∼ 1.3 million cells covering the …

[HTML][HTML] Integrated morphoelectric and transcriptomic classification of cortical GABAergic cells

NW Gouwens, SA Sorensen, F Baftizadeh, A Budzillo… - Cell, 2020 - cell.com
Neurons are frequently classified into distinct types on the basis of structural, physiological,
or genetic attributes. To better constrain the definition of neuronal cell types, we …

The role of inhibitory circuits in hippocampal memory processing

L Topolnik, S Tamboli - Nature Reviews Neuroscience, 2022 - nature.com
GABAergic inhibitory circuits play an essential role in coordinating various hippocampal
functions. Several decades of work dedicated to a thorough characterization of hippocampal …

The art of using t-SNE for single-cell transcriptomics

D Kobak, P Berens - Nature communications, 2019 - nature.com
Single-cell transcriptomics yields ever growing data sets containing RNA expression levels
for thousands of genes from up to millions of cells. Common data analysis pipelines include …