A online interactive website for browsing multi-omics data of mouse brain, which including Brain cell type specific RNA-seq, scRNAseq, scATACseq, brain spatial transcriptome, brain spatial metabolome. Detailed gene information, protein domain, related publications are included.

References

Brain Atlas

  1. Mouse brain atlas, Adult, Male, C57BL/6J [PDF]
  2. Rat brain atlas, v5.0 [PDF]
  3. Developing Rat brain atlas

Spatial transcriptomics(ST) datasets

  1. Human Breast Cancer dataset (10X Genomics)
  2. Human Cortex dataset (10X Genomics)
  3. Mouse Embryo dataset (Slide-seq)
  4. Mouse Brain dataset (Allen Brain Atlas)

sc-RNAseq datasets

  1. Brain vasculature system, Mouse, Adult

  2. Developing brain, Mouse, E8-E16

    • La Manno, Gioele, et al. “Molecular architecture of the developing mouse brain.” Nature 596.7870 (2021): 92-96. [PDF | PMID: 34321664 | DOI Link]

  3. Developing Cortex, Mouse

    • Di Bella, Daniela J., et al. “Molecular logic of cellular diversification in the mouse cerebral cortex.” Nature 595.7868 (2021): 554-559. [PDF | PMID: 34163074 | DOI Link]

  4. 9 Brain regions, Mouse, Adult

    • Saunders, Arpiar, et al. “Molecular diversity and specializations among the cells of the adult mouse brain.” Cell 174.4 (2018): 1015-1030. [PDF | PMID: 30096314 | DOI Link]

  5. 11 Brain regions, Mouse, Adolescent

    • Zeisel, Amit, et al. “Molecular architecture of the mouse nervous system.” Cell 174.4 (2018): 999-1014. [PDF | PMID: 30096314 | DOI Link]

  6. 2021-Cell-Allen brain-HPF and isocortex

    • Yao, Zizhen, et al. “A taxonomy of transcriptomic cell types across the isocortex and hippocampal formation.” Cell 184.12 (2021): 3222-3241. [PDF | PMID: 34004146 | DOI Link]

  7. Aging mouse brain[8 young (2–3 months) and 8 old (21–23 months) mice], 50,212 cells(24,401 young and 25,811 old)

    • Ximerakis, Methodios, et al. “Single-cell transcriptomic profiling of the aging mouse brain.” Nature neuroscience 22.10 (2019): 1696-1708. [PDF | PMID: 31551601 | DOI Link]

  8. scRNAseq profiling of mouse retinal bipolar cells (BCs), ~25,000 BCs.

    • Shekhar, Karthik, et al. “Comprehensive classification of retinal bipolar neurons by single-cell transcriptomics.” Cell 166.5 (2016): 1308-1323. [PDF | PMID: 27565351 | DOI Link]

sc-ATACseq datasets

  1. Developing mouse cerebellum, 11 stages, ~90,000 cells, snATAC-seq

    • Sarropoulos, Ioannis, et al. “Developmental and evolutionary dynamics of cis-regulatory elements in mouse cerebellar cells.” Science 373.6558 (2021): eabg4696. [PDF | PMID: 34446581 | DOI Link]

  2. 45 regions of mouse cerebrum, Adult, 800,000 nuclei, snATAC-seq

    • Li, Yang Eric, et al. “An atlas of gene regulatory elements in adult mouse cerebrum.” Nature 598.7879 (2021): 129-136. [PDF | PMID: 34616068 | DOI Link]