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| Status |
Public on Mar 29, 2022 |
| Title |
Multi-omic analysis defines the first microRNA atlas across all small intestinal epithelial lineages and reveals microRNA markers of almost all major cell types |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
Non-coding RNA profiling by high throughput sequencing
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| Summary |
MicroRNA-mediated regulation is critical for the proper development and function of the small intestinal epithelium. However, it is not yet known which microRNAs are expressed in which cell types of the small intestinal epithelium. To bridge this important knowledge gap, in this study we performed a comprehensive profiling analysis of microRNAs in all major epithelial cell types of the mouse small intestine. We first used flow cytometry and fluorescence activated cell sorting with multiple different reporter mouse models to isolate intestinal stem cells (ISCs), enterocytes, goblet cells, Paneth cells, enteroendocrine cells (EECs), tuft cells and secretory progenitor cells. We then subjected these cell populations to small RNA-seq. We identified highly enriched microRNA markers for every major small intestinal epithelial cell type except goblet cells. Interestingly, one of the secretory progenitor cell enriched microRNAs, miR-672, is deleted in hominin species. Several of these lineage-enriched microRNAs (LEMs) were observed to be embedded in annotated host genes. We used chromatin run-on sequencing (ChRO-seq) to determine which of these LEMs are likely co-transcribed with their host genes. We then employed single cell RNA-sequencing (scRNA-seq) in order to define the cell type specificity of the host genes, and by proxy, the LEMs as well. Finally, using four additional in vivo models, we validated that miR-375 is highly enriched in secretory progenitor cells that give rise to enteroendocrine and tuft cells and that miR-152 is a Paneth cell-specific microRNA.
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| Overall design |
Small RNAseq of sorted populations of the small intestiinal epithelium cell lineages.
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| Contributor(s) |
Sethupathy P, Kanke M |
| Citation(s) |
34643097, 37884859 |
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| Submission date |
Jun 24, 2021 |
| Last update date |
Nov 09, 2023 |
| Contact name |
Praveen Sethupathy |
| Organization name |
Cornell University
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| Lab |
Dr. Sethupathy Lab
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| Street address |
Cornell University College of Veterinary Medicine, Box 17
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| City |
Ithica |
| State/province |
NY |
| ZIP/Postal code |
14853 |
| Country |
USA |
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| Platforms (2) |
| GPL17021 |
Illumina HiSeq 2500 (Mus musculus) |
| GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
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| Samples (36)
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| Relations |
| BioProject |
PRJNA741197 |
| SRA |
SRP325482 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE178826_12M_WT_metadata.csv.gz |
17.2 Kb |
(ftp)(http) |
CSV |
| GSE178826_RAW.tar |
54.7 Mb |
(http)(custom) |
TAR (of MTX, TSV) |
| GSE178826_SI_ISC-types_normalized_miR_counts.csv.gz |
188.9 Kb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Processed data are available on Series record |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
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