|
| Status |
Public on Jun 20, 2024 |
| Title |
RNA-Seq of HEK293T:B2_Taqtth_NT |
| Sample type |
SRA |
| |
|
| Source name |
cell line
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: cell line
cell line: HEK295T cell
cell type: Human Embryonic Kidney 293 Cells
genotype: TaqTth-KRASknockdown-control
treatment: TransIntro EL Transfection Reagent
|
| Treatment protocol |
Cells were transfected by using TransIntro EL Transfection Reagent following the manufacturer’s recommended protocol. For each well of a 6-well plate, 4 μg plasmids were transfected and 500 pmoL of DNA probes were transfected 24 h later.
|
| Growth protocol |
Cells were maintained in Dulbecco’s modified Eagle’s Medium (DMEM) supplemented with 10% fetal bovine serum (HyClone), 100 U/mL penicillin, and 100 µg/mL streptomycin at 37 °C with 5% CO2 incubation. Cells were seeded into 6-well plates (Corning) 24 h prior to transfection at a density of 200,000 cells per well.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was prepared from transfection experiments after 72 h using a RNA Isolation Reagent (R701-01, Vazyme). A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations
Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
Assembly: After cluster generation, the library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated.
Supplementary files format and content: FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
|
| |
|
| Submission date |
Jun 11, 2024 |
| Last update date |
Jun 20, 2024 |
| Contact name |
Shu Xu |
| E-mail(s) |
shuxu@cpu.edu.cn
|
| Organization name |
China Pharmaceutical University
|
| Street address |
China Pharmaceutical University
|
| City |
Nanjing |
| State/province |
Jiangsu Province |
| ZIP/Postal code |
210009 |
| Country |
China |
| |
|
| Platform ID |
GPL20301 |
| Series (1) |
| GSE269592 |
Specific silencing of pathogenic mRNA by a novel compact RNA-targeting tool TaqTth-hpRNA [RNA-seq] |
|
| Relations |
| BioSample |
SAMN41753815 |
| SRA |
SRX24845368 |
