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| Status |
Public on Jun 23, 2016 |
| Title |
Single-cell RNA-seq reveals distinct maturation stages of the Paneth cell lineage |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Paneth cells (PCs) are long-lived secretory cells that reside at the bottoms of small intestinal crypts. Besides serving as niche cells for the neighboring Lgr5-positive stem cells, PCs secrete granules containing a broad spectrum of antimicrobial proteins, including lysozymes and defensins1. Here, we have used single-cell RNA sequencing to explore PC differentiation. We found a maturation gradient from early secretory progenitors to mature PCs, capturing the full maturation path of PCs. Moreover, differential expression of a subset of defensin genes in lysozyme-high PCs, e.g. Defa20, reveals at least two distinct stages of maturation.
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| Overall design |
We traced Lgr5+ stem cells from Lgr5-CreERT2 C57Bl6/J mice bred to a Rosa26LSL-YFP reporter mice and sorted YFP+ cells 5 days, 3 weeks and 8 weeks after tamoxifen injection.
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| Contributor(s) |
Wiebrands K, Grün D, Lyubimova A, van Oudenaarden A |
| Citation(s) |
27345837 |
| Submission date |
Dec 29, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Kay Wiebrands |
| E-mail(s) |
k.wiebrands@hubrecht.eu
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| Organization name |
Hubrecht Institute
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| Street address |
Uppsalalaan 8
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| City |
Utrecht |
| ZIP/Postal code |
3584CT |
| Country |
Netherlands |
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| Platforms (2) |
| GPL17021 |
Illumina HiSeq 2500 (Mus musculus) |
| GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
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| Samples (13)
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| GSM1987570 |
Extracted RNA 5-day traced Lgr5+ cells replicate 1 |
| GSM1987571 |
Extracted RNA 5-day traced Lgr5+ cells replicate 2 |
| GSM1987573 |
Extracted RNA 5-day traced Lgr5+ cells replicate 3 |
| GSM1987574 |
Extracted RNA 5-day traced Lgr5+ cells replicate 4 |
| GSM1987575 |
Extracted RNA 5-day traced Lgr5+ cells replicate 5 |
| GSM1987576 |
Extracted RNA 3-week traced Lgr5+ cells, CD24+ fraction |
| GSM1987577 |
Extracted RNA 3-week CD24+ control cells, non-traced |
| GSM1987578 |
Extracted RNA 8-week traced Lgr5+ cells, CD24+ fraction replicate 1 |
| GSM1987579 |
Extracted RNA 8-week traced Lgr5+ cells |
| GSM1987581 |
Extracted RNA 8-week traced Lgr5+ cells, CD24+ fraction replicate 2 |
| GSM1987582 |
Extracted RNA 8-week traced Lgr5+ cells, CD24+ fraction replicate 3 |
| GSM1987583 |
Extracted RNA 8-week CD24+ control cells, non-traced replicate 1 |
| GSM1987584 |
Extracted RNA 8-week CD24+ control cells, non-traced replicate 2 |
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| Relations |
| BioProject |
PRJNA307195 |
| SRA |
SRP067892 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE76408_RAW.tar |
5.4 Mb |
(http)(custom) |
TAR (of CSV) |
| GSE76408_cel-seq_barcodes.txt.gz |
427 b |
(ftp)(http) |
TXT |
| GSE76408_expdata.txt.gz |
2.5 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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