|
| Status |
Public on Nov 18, 2022 |
| Title |
ApoYap ctrl 3 |
| Sample type |
SRA |
| |
|
| Source name |
Liver
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Liver
cell type: Hepatocyte
strain: ApoE-rtTA, TRE-hYAP
treatment: -
effective genotype: WT
group: ApoYap ctrl
|
| Treatment protocol |
-
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Mice were anesthetized by intraperitoneal injection of sodium pentobarbital (Nembutal, 50mg/kg). Livers were perfused for 5min with 40ml of perfusion medium SC-1 to remove the blood and for rapid destruction of intercellular junctions, followed by perfusion with 40ml of SC-2 medium containing 10mg collagenase for 5min to break up the supporting extracellular matrix. Each lobe was dissected off, and the tissue was disrupted inside of a beaker containing 50ml of SC-2 with 20mg collagenase (Roche) and 1ml DNase I (Sigma) followed by rotating incubation for 20min at 37°C. Cells were then filtered through a 100μm strainer and centrifuged at 50g for 2min at room temperature. Hepatocytes were washed once with 1X PBS and centrifuged again at 50g for 2min. Pellet was resuspend with 2ml of 1X PBS containing 0.04% BSA, filtered through a 70µm strainer and FACS sorted. 500,000 sorted cells were collected and lysed for RNA extraction.
RNA was extracted immediately using the RNAeasy mini spin kit (Qiagen) and stored at -80°C.
Library preparation was performed according to the QuantSeq 3’ mRNA-Seq Library Prep kit FWD (Lexogen).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Quality control and trimming of the sequencing reads was performed using FastQC and Cutadapt (-q 15 --minmum-length 60, -a AGATCGGAAGAG)
Trimmed sequence reads were mapped to mm10 using STAR v2.6.1d (with default mapping parameters).
Reads were counted with STAR --quantMode GeneCounts
Assembly: GRCm38/mm10
Supplementary files format and content: Tab-delimited text file with raw gene counts for every gene and every sample
|
| |
|
| Submission date |
Aug 17, 2022 |
| Last update date |
Nov 18, 2022 |
| Contact name |
Georg Halder |
| E-mail(s) |
[email protected]
|
| Organization name |
VIB-KU Leuven
|
| Department |
VIB-KU Leuven Center for Cancer Biology
|
| Lab |
Laboratory of Growth Control
|
| Street address |
Herestraat 49
|
| City |
Leuven |
| ZIP/Postal code |
3000 |
| Country |
Belgium |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE211459 |
Hippo signaling instructs ectopic but not normal organ growth [Liver YapHyper] |
| GSE211461 |
Hippo signaling instructs ectopic but not normal organ growth |
|
| Relations |
| BioSample |
SAMN30370846 |
| SRA |
SRX17116915 |
