|
| Status |
Public on Aug 21, 2023 |
| Title |
293-WT_Ctrl_3d_Rep1 |
| Sample type |
SRA |
| |
|
| Source name |
HEK293
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HEK293
cell type: immortalized human embryonic kidney cells
genotype: WT
treatment: 0.1percent DMSO (vehicle control) for 72 hours
time: 3 days
|
| Treatment protocol |
Cells were treated with vehicle control (0.1% DMSO) or 200nM BI1347 or 200nM SNX7886 for 72 hours.
|
| Growth protocol |
293-WT and 293-dKO cells were grown in DMEM (High-glucose) media with 10% FBS, 1% penicillin-streptomycin and 2 mM L-glutamine. The cells were plated in 12-well plate at the density of 5x10^4 cells per well. 24 hours post seeding, cells were treated as indicated.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using RNeasy Mini Kit (Qiagen) and RNA quality was validated on RNA-1000 chip using Bioanalyzer (Agilent). 1.0 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext Ultra II Directional RNA Library prep Kit following manufacturer's protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Indexed sequences were checked quality by Fastqc
Indexed sequences were trimmed adaptor sequence by TrimGalore-0.4.5
Reads were mapped to the hg38 reference genome using STAR | version 2.7.2b with default parameters (generation of sam files)
Convert .sam files to .bam files using samtools | version: 1.5 with parameters -bh -F 3840 -q 255
Read counts over annotated genes were obtained using featureCount (subreads | version: 1.5.3) with parameters -p -B -M -O --fraction -T 10
Assembly: GRCh38.98
Supplementary files format and content: tab-delimited text files include gene counts for each sample
|
| |
|
| Submission date |
May 08, 2023 |
| Last update date |
Aug 21, 2023 |
| Contact name |
HAO JI |
| E-mail(s) |
[email protected]
|
| Phone |
8037774689
|
| Organization name |
University of South Carolina
|
| Department |
College of Pharmacy
|
| Street address |
715 SUMTER ST CLS RM 109
|
| City |
COLUMBIA |
| State/province |
SC |
| ZIP/Postal code |
29208 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE231891 |
Effects of CDK8/19 Mediator Kinase inhibition by BI1347 and depletion by SNX7886 on gene expression in HEK293 cells |
|
| Relations |
| BioSample |
SAMN34995254 |
| SRA |
SRX20250333 |
