GSE184564
GSE GEOSpatial transcriptomic studies of the small intestine from WT and DDX5â³IEC (KO) mice
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Summary
DDX5, a DEAD box containing RNA binding protein, is involved in multiple aspects of RNA metabolism and is abundantly expressed in all subsets of the intestinal epithelial cells (IEC). Here, we characterized the DDX5-dependent transcriptome in the small intestine. In the DDX5â³IEC tissue, we found that secretory IEC lineage progenitor containing spots (Atoh1hi and Sox4hi) had reduced expression of Pou2f3, a master regulator of a subset of IECs called tuft cells. As a result of the loss of Pou2f3 expression in the progenitors, DDX5â³IEC tissue harbored lower number of tuft cell containing spots (Dclk1hi) compare to WT tissues.
Overall Design
One intestine tissue from each genotype were obtained from 8wk old cohoused mice. Results of ileum epithelium from DDX5â³IEC mutant mice were compared to those from WT mice.
Analysis (3 steps)
View Data Processing- Space v3.1.0 to align reads to mouse reference genome (mm10)
- Used Loupe Browser to filter Atoh1, Sox4, Lgr5 high progenitor-containing spots and Dclk1, Klf4, Lyz1, Chga high mature secretory lineage-containing spots (Log2 expression > 0.5)
- Differential gene expression analysis
Supplementary Files (12)
GEO Samples (2)
Dataset Citations (1)
SRA Experiments (2) and Runs (2)
Total: 11996 MBSample attributes
Original files (1)
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR15999537 | 77498423 | 15654681446 | 5889.0 | TL_WT_S8_L002_R1_001.fastq.gz, TL_WT_S8_L002_R2_001.fastq.gz, SRR1599… | SRA |
Sample attributes
Original files (1)
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR15999538 | 81195958 | 16401583516 | 6107.15 | TL_KO_S9_L002_R1_001.fastq, TL_KO_S9_L002_R2_001.fastq.gz, SRR1599953… | SRA |