|
| Status |
Public on Sep 01, 2021 |
| Title |
LW45 DKO 1 |
| Sample type |
SRA |
| |
|
| Source name |
Intestinal organoid
|
| Organism |
Mus musculus |
| Characteristics |
genotype: H2b/Xbp1[delta]IEC
|
| Growth protocol |
Small intestinal organoids were derived following standard protocols from healthy tissue of 8-12 weeks old mice (n = 3) of the strains Rnaseh2b_Xbp1fl/fl and ΔIEC, Rnaseh2bVilCreΔIEC, Xbp1VilCreΔIEC and Rnaseh2b_p53VilCreΔIEC. Cells were grown on 24-well plates in a combination of Matrigel and IntestiCult™ Organoid Growth Medium (STEMCELL Technologies).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Organoids were washed in PBS and RNA was extracted following the RNeasy Kit (Qiagen) according to manufacturer's protocol.
RNA libraries were prepared using TruSeq stranded mRNA Kit (Illumina) according to manufacturer’s instructions. All samples were sequenced using an Illumina HiSeq 4000 with single-end sequencing of 50bp reads
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Adapters and low-quality bases from the RNA-seq reads were removed using Cutadapt
The filtered reads were mapped to the mouse genome (GRCm38) using TopHat2
htseq was used to estimate the expression counts of the genes
Genome_build: GRCm38
Supplementary_files_format_and_content: Gene expression counts in tabular format
|
| |
|
| Submission date |
Aug 18, 2021 |
| Last update date |
Sep 01, 2021 |
| Contact name |
Neha Mishra |
| E-mail(s) |
n.mishra@ikmb.uni-kiel.de
|
| Organization name |
Institute of Clinical Molecular Biology
|
| Lab |
Cell biology Lab
|
| Street address |
Rosalind-Franklin-Str. 12
|
| City |
Kiel |
| ZIP/Postal code |
24105 |
| Country |
Germany |
| |
|
| Platform ID |
GPL21103 |
| Series (1) |
| GSE182353 |
Epithelial XBP1 coordinates TP53-driven DNA damage responses and suppression of intestinal carcinogenesis |
|
| Relations |
| BioSample |
SAMN20848392 |
| SRA |
SRX11809407 |
