|
| Status |
Public on Apr 21, 2020 |
| Title |
D164A1 |
| Sample type |
SRA |
| |
|
| Source name |
Intestinal epithelium
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Intestinal epithelium
strain/genotype: Tg(Vil1-cre/ERT2); Ctnnb1-D164A/flox
days post cre induction: 2
background strain: C57BL/6
|
| Treatment protocol |
To induce Cre-ERT2-mediated recombination, tamoxifen (Sigma, 80 mg/kg) was injected intraperitoneally on two consecutive days. Mice were sacrificed 48 hours after the first tamoxifen injection.
|
| Growth protocol |
All animals were kept on a C57BL/6 background. Mice were 8-12 weeks old at the time of treatments and cell isolations. Mice of both sexes were used in all experiments and littermates were used as controls.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Control (n=3), KO (n=2), dm (n=3), ∆C (n=2) and D164A (n=3) mice were sacrificed 2d pi and the duodenal epithelial RNA isolation was performed as described (Gracz et al., 2012). Briefly, dissected duodenum was flushed thoroughly in ice-cold PBS, then opened longitudinally and incubated for 20 min on ice in dissociation buffer 1 (30 mM EDTA, 1.5 mM DTT in PBS), followed by 10 min incubation in dissociation buffer 2 (30 mM EDTA in PBS) at 37 °C under gentle agitation. The epithelium was released by vortexing, pelleted by centrifugation at 4 °C for 5 min at 1000g, and resuspended in 500 mL TRI Reagent (Sigma). RNA was extracted by phenol-chloroform precipitation. DNAse treatment was carried out with DNA-free DNA Removal Kit (Invitrogen) according to the manufacturer’s instructions.
Library preparation was performed with the Illumina TruSeq RNA Kit. RNA sequencing was performed on the Illumina NextSeq500 by the Functional Genomics Centre Zurich (FGCZ).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
FastQC, alignment and counting on RSEMApp supported by SUSHI.
Pairwise comparisons were performed with the SUSHI application EdgeRApp
Genome_build: Mus_musculus.GRCm38.95
Supplementary_files_format_and_content: normalized counts and FPKM values from EdgeR
|
| |
|
| Submission date |
Apr 20, 2020 |
| Last update date |
Apr 22, 2020 |
| Contact name |
Tomas Valenta |
| E-mail(s) |
tomas.valenta@mls.uzh.ch
|
| Organization name |
University of Zurich
|
| Department |
Institute of Molecular Life Sciences
|
| Street address |
Winterthurerstrasse 190
|
| City |
Zurich |
| ZIP/Postal code |
CH-8057 Zurich |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE148941 |
Discrete regulation of β-catenin-mediated transcription governs identity of intestinal epithelial stem cells [RNA-Seq] |
| GSE148943 |
Discrete regulation of β-catenin-mediated transcription governs identity of intestinal epithelial stem cells |
|
| Relations |
| BioSample |
SAMN14645603 |
| SRA |
SRX8142705 |
