|
| Status |
Public on Jun 30, 2023 |
| Title |
293-WT_SnxB_24h_Rep3 [Batch 3] |
| Sample type |
SRA |
| |
|
| Source name |
Parental HEK293 (WT) cells, treated with 1μM Senexin B for 24 hrs, Experiment 2, biological replicate-#3
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HEK293
genotype: 293-WT cells
agent: 1microM Senexin B
time point: 24 hours
|
| Treatment protocol |
Cells were treated with vehicle control (0.1% DMSO) or 1 μM Senexin B for 24 or 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 |
Total RNA was extracted using RNAeasy Mini Kit (Qiagen) and RNA quality was validated on RNA-1000 chip using Bioanalyzer (Agilent)
Sequencing libraries were generated using Illumina TruSeq Stranded mRNA prep kit or NEBNext Ultra II Directional RNA Library prep Kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
S18
|
| 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 2.7.2 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 |
Dec 16, 2022 |
| Last update date |
Jun 30, 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 |
GPL11154 |
| Series (1) |
| GSE221160 |
Effects of CDK8/19 Mediator Kinase inhibition by Senexin B on gene expression in HEK293 cells |
|
| Relations |
| BioSample |
SAMN32275769 |
| SRA |
SRX18727158 |
