This submission contains the following datasets:

1) Mouse colon ENS (plate-based SMART-Seq2):
- 2,657 neurons
- 3,039 glia
- File prefixes: ss2 (all cell types), ss2.neur (neurons), ss2.glia (glia)

2) Mouse full colon (droplet-based MIRACL-Seq)
- 704,314 total nuclei (343,000 highest-quality used for visualization/analyses)
- 1,938 neurons
- 1,690 glia"
- File prefixes: mli (all cell types), mli.neur (neurons), mli.glia (glia)

3) Mouse full ileum (droplet-based MIRACL-Seq)
- 436,202 total nuclei (79,293 highest-quality used for visualization/analyses)
- 473 neurons
- 429 glia
- File prefixes: msi (all cell types), msi.neur (neurons), msi.glia (glia)

4) Human full colon myenteric plexus (droplet-based MIRACL-Seq)
- 436,202 total nuclei (146,442 highest-quality used for visualization/analyses)
- 1,445 neurons
- 6,054 glia
- File prefixes: hli (all cell types), hli.neur (neurons), hli.glia (glia)


Download instructions:

To download a particular dataset, please identify the correct file prefix (see above). Next, click “Download” and download all files with that prefix. For example, to download all human cells, you will need the following files:
- all.meta.txt (metadata for all datasets)
- gene_sorted-hli.matrix.mtx
- hli.barcodes.tsv
- hli.genes.tsv
- hli.tsne2.txt

To download the high resolution sub-clustering of human neurons, you would need the “hli.neur” files.


Raw human FASTQ files:

The raw FASTQ files for human are stored in DUOS, a controlled access repository (because they are sensitive human data). You will need to sign up and apply for access:
Once you have been granted access, you should be able to find the data here:


Study summary:

The enteric nervous system (ENS) coordinates diverse functions in the intestine, but has eluded comprehensive molecular characterization due to the rarity and diversity of cells. Here, we develop two methods to profile the ENS of adult mice and humans at single cell resolution: RAISIN RNA-Seq, for profiling intact nuclei with ribosome-bound mRNA, and MIRACL-Seq, for label-free enrichment of rare cell types by droplet-based profiling. The 1,187,535 nuclei in our mouse atlas include 5,068 neurons from the ileum and colon, revealing extraordinary neuron diversity. We highlight circadian expression changes in enteric neurons, show that disease-related genes are dysregulated with aging, and identify differences between the ileum and proximal/distal colon. In human, we profile 436,202 nuclei recovering 1,445 neurons and identify conserved and species-specific transcriptional programs, and putative neuro-epithelial, neuro-stromal, and neuro-immune interactions. The human ENS expresses risk genes for neuropathic, inflammatory, and extra-intestinal diseases, suggesting neuronal contributions to disease.