|
| Status |
Public on Jun 30, 2021 |
| Title |
small intestine p53 off rep1 |
| Sample type |
SRA |
| |
|
| Source name |
small intestinal organoids
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6N
tissue: small intestine
genotype: Trp53LSL-R172H/+;Villin::CreERT2
agent: Ethanol control
|
| Treatment protocol |
Cre recombination was induced in vitro with 4-Hydroxytamoxifen (0.5 µM for SI organoids, 3.5 µM for COL organoids) or organoids were treated with ethanol as controls for 24 hours. SI organoid RNA was isolated 8 days, and COL organoid RNA was isolated 3 days after Cre recombination.
|
| Growth protocol |
Organoids were generated and propagated as described before (Sato and Clevers, 2013; Sato et al., 2009; Yui et al., 2012)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated according to manufacturer's protocol (Roboklon, Cat#E3598)
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
Ethanol treated control
small_intestine.txt
small_intestine_p53_off_1
|
| Data processing |
Basecalls performed using RTA 2.7.3
Bad quality reads were filtered out using Trimmomatic (v 0.36) with the following paramters: HEADCROP:5 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:25
paired-end reads were aligned to the mm9 genome assembly using STAR (v2.5.2b), and read count per gene was subsequently estimated with the following parameters: --outFilterType BySJout --outFilterMultimapNmax 10 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.05 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outFilterMatchNmin 16 --quantMode GeneCounts
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited txt file including read count per gene for each sample
|
| |
|
| Submission date |
Jun 11, 2019 |
| Last update date |
Jun 30, 2021 |
| Contact name |
Geoffroy Andrieux |
| Organization name |
University clinics Freiburg
|
| Street address |
Breisacherstr 153
|
| City |
Freiburg |
| ZIP/Postal code |
79110 |
| Country |
Germany |
| |
|
| Platform ID |
GPL21103 |
| Series (1) |
| GSE132551 |
Analysis of the transcriptomic changes in murine small and large intestinal organoids after the sudden expression of BRAFV600E and/or p53R172H |
|
| Relations |
| BioSample |
SAMN12022600 |
| SRA |
SRX6046273 |
