Methods: Yao et al 2020 “AllenBrainMap”

Cell-types: Neurons (plus small sample of non-neuronal cells)

Brain regions: Cerebral cortex (frontal pole (FRP), primary motor (MOp), secondary motor (MOs), primary somatosensory (SSp), supplemental somatosensory (SSs), gustatory (GU), visceral (VISC), auditory (AUD), primary visual (VISp), anterolateral visual (VISal), anteromedial visual (VISam), lateral visual (VISl), posterolateral visual (VISpl), posteromedial (VISpm), laterointermediate (VISli), postrhinal (VISpor), anterior cingulate (ACA), prelimbic (PL), infralimbic (ILA), orbital (ORB), agranular insular (AI), retrosplenial (RSP), posterior parietal association (PTLp), temporal association (TEa), perirhinal (PERI), and ectorhinal (ECT) areas); Hippocampal region (CA1, CA2, CA3, and dentate gyrus (DG), and the retrohippocampal region (RHP) which includes lateral entorhinal area (ENTl), medial entorhinal area (ENTm), parasubiculum (PAR), postsubiculum (POST), presubiculum (PRE), subiculum (SUB), and prosubiculum (ProS)).

Techniques: Genetic neuronal labeling with CreER transgenic mice; retrograde labeling; fluorescence-activated cell sorting (FACS). Single-cell RNAseq using droplet microfluidics (10X Genomics Chromium). A total of 1,138,179  single-cells (including 12,513 non-neuronal cells) were assigned to 379 cell-type (metacell) clusters (e.g.110 Pvalb)

Details of mice: Male and female; C57BL/6J background; P53-56.

Data processing for BrainPalmSeq: Expression data were downloaded from and were not further processed.

Heatmap units: Trimmed Mean (25%-75%) Log2(CPM+1)

References: Yao Z, van Velthoven CTJ, Nguyen TN, Goldy J, Sedeno-Cortes AE, Baftizadeh F, Bertagnolli D, Casper T, Chiang M, Crichton K, Ding SL, Fong O, Garren E, Glandon A, Gouwens NW, Gray J, Graybuck LT, Hawrylycz MJ, Hirschstein D, Kroll M, Lathia K, Lee C, Levi B, McMillen D, Mok S, Pham T, Ren Q, Rimorin C, Shapovalova N, Sulc J, Sunkin SM, Tieu M, Torkelson A, Tung H, Ward K, Dee N, Smith KA, Tasic B, Zeng H. A taxonomy of transcriptomic cell types across the isocortex and hippocampal formation. Cell. 2021 Jun 10;184(12):3222-3241.e26. doi: 10.1016/j.cell.2021.04.021.PMID: 34004146.


Original data availability: