|
| Status |
Public on Feb 12, 2024 |
| Title |
001-0min-3 |
| Sample type |
SRA |
| |
|
| Source name |
HepG2 cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HepG2 cells
treatment: untreated
|
| Treatment protocol |
About 5×10^7 HepG2 cells were treated in triplicates using 0.001 μM of 2,4-D treated for 0, 10, 30 and 360 min.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
After the culture medium with 2,4-D was removed, the cells were harvested by digestion of trypsin-EDTA solution and washed with ice-cold PBS twice and then centrifuged at 12,000 g for 15 min at 4 °C. RNAs were then purified by Trizol reagent. RNAs were quantified by a NanoPhotometer.
The RNA samples were purified by poly (dT) beads, converted to cDNA using SmartScribe Rtase kit according to manufacturer’s protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
DNBSEQ-T7 |
| |
|
| Description |
DNBSEQ-TR7S
|
| Data processing |
Cleaned reads were aligned to the genome reference of Ensembl GRCh38 with Hisat2 using strand specific parameters.
For RNAseq data, a stringent pre-filtering criterion of median counts over all samples < 5 was carried out. The normalization and analysis of differentially expressed genes (DEGs) were conducted by using DESeq2
Assembly: genome reference of Ensembl GRCh38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
|
| |
|
| Submission date |
Dec 20, 2022 |
| Last update date |
Feb 12, 2024 |
| Contact name |
Yuan Li |
| E-mail(s) |
vivian_liyuan@outlook.com
|
| Organization name |
Beijing Proteome Research Center
|
| Department |
Post-translational modification
|
| Lab |
Post-translational modification
|
| Street address |
38 Science Park Road, National Center for Protein Sciences (Beijing), Changping District, Beijing
|
| City |
Beijing |
| ZIP/Postal code |
102206 |
| Country |
China |
| |
|
| Platform ID |
GPL29480 |
| Series (1) |
| GSE221407 |
Transcriptomics study on HepG2 cells treated with 0.001 μM 2,4-D for 0, 10, 30, 360 min |
|
| Relations |
| BioSample |
SAMN32330028 |
| SRA |
SRX18787323 |
