|
| Status |
Public on Sep 26, 2024 |
| Title |
LNCaP spheroids, siCtrl, rep1 |
| Sample type |
SRA |
| |
|
| Source name |
spheroids
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: spheroids
cell line: LNCaP
treatment: siCtrl
|
| Treatment protocol |
Cells were seeded in 6-well plates and incubated for 24 h. Cells were transfected with 25pmol ON-TARGETplus SMARTpools (siCtrl: non-targeting pool, #D-001810-10-05; siMED12: human MED12 siRNA, #L-009092-00-0005) using Lipofectamine RNAiMAX. The medium was changed after 6 h and the cells were cultivated in 2D for 3 days after transfection. Subsequently, the cells were trypsinized and re-seeded in ultra low attachment plates to induce spheroid formation. The spheroids were harvested 4 days after reseeding.
|
| Growth protocol |
All cells were acquired from the American Type Culture Collection (ATCC) and cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum (FBS), 1% penicillin/streptomycin, and 1% GlutaMAX.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from spheroids was extracted using the Quick-RNA MagBead kit from Zymo Research.
Library prep was performed with the high throughput 3’ tag BRB-seq kit from Alithea genomics using early barcoding RT primers.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq X Plus |
| |
|
| Description |
LNCaP_siCtrl_rep1
|
| Data processing |
The multiplexed fastq file was split into individual per sample fastq files with STARsolo using the cellular barcodes and PCR duplicates were removed using the UMIs. Read alignment and counting of the individual fastq files were performed in R using the Rsubread package and the Gencode Release 43 (GRCh38.p13)
Assembly: GRCh38
Supplementary files format and content: count_file.txt: Tab-delimited text file with ensemble gene ID, gene symbol and gene counts for each sample
Supplementary files format and content: log2CPM_expression.txt: Tab-delimited text file with ensemble gene ID, gene symbol and log2 transformed CPM gene expression values for each sample
|
| |
|
| Submission date |
Jun 04, 2024 |
| Last update date |
Sep 26, 2024 |
| Contact name |
Florian Handle |
| E-mail(s) |
[email protected]
|
| Organization name |
Medical University of Innsbruck
|
| Department |
Institute of Pathology, Neuropathology and Molecular Pathology
|
| Street address |
Müllerstrasse 44
|
| City |
Innsbruck |
| ZIP/Postal code |
6020 |
| Country |
Austria |
| |
|
| Platform ID |
GPL34284 |
| Series (1) |
| GSE269073 |
Downregulation of MED12 via siRNA in SPHEROIDS derived from prostate cancer cell lines (3’ tag DGE) |
|
| Relations |
| BioSample |
SAMN41675409 |
| SRA |
SRX24802460 |
