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| Status |
Public on Oct 09, 2021 |
| Title |
Spatial discordances between mRNAs and proteins in the intestinal epithelium |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
A cell’s proteome is an important determinant of its functional state, however the use of transcriptomes as reliable proxies for cellular proteomes is debatable. In the small intestine, nutrient absorbing enterocytes operate for four days as they migrate along villi, highly graded microenvironments. Spatial transcriptomics demonstrated profound zonation in enterocyte gene expression, but how this variability translates to protein content is unclear. Here, we used spatial sorting to generate global spatial maps of enterocyte proteins and mRNAs along the villus axis. We found that both were zonated, yet often spatially anti-correlated. We developed a Bayesian approach to infer protein translation and degradation rates from the combined spatial profiles, and demonstrate that space-independent protein-synthesis delays can explain the mRNA-protein discordances. Our work provides a proteomic spatial blueprint of the intestinal epithelium and highlights the importance of protein measurements for inferring states of tissue cells that operate outside of steady state.
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| Overall design |
mRNA profiles of enterocytes from spatially stratified villi zones, EDTA isolated jejunum epithelial cells from mouse jejunum were sequenced in several batches in an Illumina NextSeq.
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| Contributor(s) |
Harnik Y, Buchauer L, Ben-Moshe S, Levine Y, Savidor A, Eilam R, Moor A, Itzkovitz S |
| Citation(s) |
34931081 |
| Submission date |
Jan 13, 2021 |
| Last update date |
Jan 09, 2022 |
| Contact name |
Keren Bahar-Halpern |
| Organization name |
Weizmann Institute
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| Lab |
Itzkovitz
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| Street address |
Herzl St 234
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| City |
Rehovot |
| ZIP/Postal code |
7610001 |
| Country |
Israel |
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| Platforms (1) |
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| Samples (24)
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| Relations |
| BioProject |
PRJNA691886 |
| SRA |
SRP301595 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE164746_sample_sheet_SST_WT_M1-M4_barcodes.txt.gz |
297 b |
(ftp)(http) |
TXT |
| GSE164746_zUMIs_Table_SST_WT_M1-M4_GEO.txt.gz |
519.9 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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