|
Status |
Public on Jun 30, 2021 |
Title |
colon Braf on rep2 |
Sample type |
SRA |
|
|
Source name |
colonic organoids
|
Organism |
Mus musculus |
Characteristics |
strain: C57BL/6N tissue: colon genotype: BraffloxV600E/+;Villin::CreERT2 agent: 4-Hydroytamoxifen
|
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 |
4-Hydroytamoxifen treated colon.txt colon_Braf_on_2
|
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 |
SAMN12022592 |
SRA |
SRX6046256 |