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| Status |
Public on Jan 08, 2022 |
| Title |
RNA-seq of Paneth cells |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
The impact of removal of Mll1 in intestinal Paneth cells expressing an constitutively active form of beta-catenin (beta-cateninGOF) was analysed in 4 pairs of sorted Paneth cells of Lgr5-CreERT2; beta-cateninGOF;Mll1+/- (control) and Lgr5-CreERT2; beta-cateninGOF;Mll1-/- (knockout) mice at 10 days after tamoxifen-induced mutagenesis. Using 75-base-pair reads, around 30 million reads per sample with comparable unique mapped reads (52-93%) were obtained. To analyze differentially expressed genes, we applied DESeq2 analysis to the RNA-seq dataset. Differentially expressed genes in beta-cateninGOF; Mll1-/- versus beta-cateninGOF; Mll1+/- Paneth cells showed both up- and downregulation of genes at a false discovery rate (FDR) of 10%. This included a global increase in the expression of goblet cell-specific genes. Downregulated genes included specific markers of Paneth cells, indicating that ablation of Mll1 in Paneth cells shifted their identity towards a mixed Paneth-goblet cell fate.
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| Overall design |
mRNA profiles of beta-cateninGOF; Mll1+/- (control) and beta-cateninGOF; Mll1-/- (knockout) Paneth cells were generated by deep sequencing in quadruplicates.
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| Contributor(s) |
Grinat J, Kosel F, Goveas N, Kranz A, Sigal M, Rajewsky K, Stewart F, Birchmeier W, Heuberger J, Alexopoulou D |
| Citation(s) |
35064075 |
| Submission date |
Jun 11, 2021 |
| Last update date |
Jan 24, 2022 |
| Contact name |
Francis Stewart |
| E-mail(s) |
francis.stewart@biotec.tu-dresden.de
|
| Organization name |
BIOTEChnology Center TU Dresden
|
| Lab |
Stewart
|
| Street address |
Tatzberg 47-49
|
| City |
Dresden |
| ZIP/Postal code |
01307 |
| Country |
Germany |
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| Platforms (1) |
| GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
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| Samples (8)
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| Relations |
| BioProject |
PRJNA736960 |
| SRA |
SRP323731 |
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