|
| Status |
Public on May 01, 2024 |
| Title |
siPC1_A2_S9 |
| Sample type |
SRA |
| |
|
| Source name |
kidney
|
| Organism |
Sus scrofa |
| Characteristics |
tissue: kidney
cell line: LLC-PK1 porcine proximal tubule cell line
cell type: Epithelial cell
genotype: LLC-PK1 porcine proximal tubule cell line
treatment: siPC1
|
| Treatment protocol |
Cells were transfected at 30-40% confluency and with siRNA(siNR, siPC1,siPC2, siPC1 & siMRTFA (aka siPC1siMRTFA), siPC2 & siMRTFA (aka siPC2siMRTFA) respectively using RNAiMax, following the manufacturer’s protocol.
|
| Growth protocol |
LLC-PK1 porcine proximal tubule cell line were cultured in DMEM, supplemented with 10% FBS and penicillin-streptomycin in humidified environment with 5% CO2 at 37 degree centigrade.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated with RNeasy® Plus Mini (Qiagen, Venlo, Netherlands), following the manufacturer’s protocol.
mRNA libraries were prepared using the NEBNext® Poly(A) mRNA Magnetic Isolation Module, NEBNext® Ultra™
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
FastQC v0.11.8 for quality control assessment and Trimgalore_v0.6.3_dev to eliminate low-quality reads.
A quasi-mapping Salmon 0.14.1 1 was used mapping to the pig reference transcriptome (Ensembl: Sus_scrofa.Sscrofa11.1.cds.all 2023-04-22 ) and with HISAT2 (Sus scrofa 11.1, http://asia.ensembl.org/Sus_scrofa/Info/Index) aligner using default parameters.
Transcript abundance was calculated using bioconductor Rsubread package.
Assembly: Sus scrofa 11.1
Supplementary files format and content: LLC-PK1_siPC_count
|
| |
|
| Submission date |
Jan 08, 2024 |
| Last update date |
May 01, 2024 |
| Contact name |
Andras Kapus |
| E-mail(s) |
Andras.Kapus@unityhealth.to
|
| Organization name |
St. Michael's Hospital
|
| Department |
Keenan Research Centre for Biomedical Science
|
| Lab |
Kapus Lab
|
| Street address |
209 Victoria Street
|
| City |
Toronto |
| State/province |
Ontario |
| ZIP/Postal code |
M5B 1T8 |
| Country |
Canada |
| |
|
| Platform ID |
GPL26351 |
| Series (1) |
| GSE252716 |
Myocardin-related transcription factor (MRTF) mediates epithelial fibrogenesis in polycystic kidney disease |
|
| Relations |
| BioSample |
SAMN39298958 |
| SRA |
SRX23132848 |
