|
| Status |
Public on Aug 02, 2024 |
| Title |
HEK293T, DZNep Rep 2 |
| Sample type |
SRA |
| |
|
| Source name |
HEK293T
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HEK293T
cell type: human embryonic kidney
treatment: 100 uM DZNep
|
| Treatment protocol |
HEK293T cells were treated with either 100 uM DZNep (ApexBio) or vehicle control for 48 hrs.
|
| Growth protocol |
HEK293T cells were grown in DMEM media supplemented with 10% Fetal Bovine Serum and antibiotics in 5% CO2 and 37 C
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Performed by Azenta
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Azenta Life sciences
Sequences were trimmed to remove adapter sequences and nucelotides with poor read quality using Trimmomatic v.0.36
Readers were mapped to the Homo sapiens GRCh38 reference genome using STAR v.2.5.2b
BAM files were generated using Star v.2.5.2b. Unique gene hit counts were calculated using featureCounts from Subread v.1.5.2
Read counts were normalized using deseq2
Assembly: GRCh38
Supplementary files format and content: tab deliminated file includes raw counts for each sample
Supplementary files format and content: tab deliminated file includes normalized counts for each sample
|
| |
|
| Submission date |
May 29, 2024 |
| Last update date |
Aug 02, 2024 |
| Contact name |
Evan Cornett |
| E-mail(s) |
evcorn@iu.edu
|
| Organization name |
Indiana University
|
| Street address |
635 Barnhill Drive
|
| City |
Indianapolis |
| State/province |
Indiana |
| ZIP/Postal code |
46202 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE268629 |
Protein Thermal Stability Changes Induced by the Global Methylation Inhibitor 3-deazaneplanocin A (DZNep) |
|
| Relations |
| BioSample |
SAMN41593959 |
| SRA |
SRX24744836 |
