|
| Status |
Public on Jun 30, 2023 |
| Title |
HEK293_SnxB_Rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Serum-starved HEK293 cells, treated with 1μM Senexin B for 90 min, biological replicate-#2
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HEK293 (ATCC)
treatment: Serum-starved for 48 hours, treated with 1microM Senexin B for 90 minutes
|
| Treatment protocol |
Cells were first pre-treated with 1μM Senexin B or 0.1% DMSO (control) for 1 hour and then treated with or without 10% FBS for 30 minutes.
|
| Growth protocol |
HEK293 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 2x10^5 cells per well. 24 hours post seeding, cells were washed with serum-free media twice and serum-starved in serum-free DMEM (high-glucose) media for 48 hours before the treatment.
|
| 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 NEBNext Ultra II Directional RNA Library prep Kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
S05
|
| 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 |
Mar 24, 2022 |
| Last update date |
Jun 30, 2023 |
| Contact name |
HAO JI |
| E-mail(s) |
ji5@email.sc.edu
|
| 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 (2) |
| GSE199331 |
Effects of Inhibition of CDK8/19 Mediator Kinase on serum-regulated gene expression in 293 cells |
| GSE200754 |
Transcriptomic and Proteomic Effects of CDK8 and CDK19 Mediator Kinases |
|
| Relations |
| BioSample |
SAMN26927221 |
| SRA |
SRX14595823 |
