|
| Status |
Public on Mar 13, 2021 |
| Title |
SS5_2_1 |
| Sample type |
SRA |
| |
|
| Source name |
KHM-5M thyroid cancer cell
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: KHM-5M
tumor: anaplastic thyroid cancer
treatment group: Treated with sodium selenite
|
| Treatment protocol |
Thyroid cancer cells(KHM-5M) were treated with sodium selenite or PBS (negative control). Cells were harvested and Total RNA was extracted.
|
| Growth protocol |
KHM-5M cells were cultured in RPMI-1640 (Gibco) with 10% fetal bovine serum (FBS, Gibco).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Trizol reagent.
Total RNA was purified by Oligo(dT)-attached magnetic beads. Purified RNA was fragmented into small pieces, and the first-strand cDNA was generated using random priming, followed with second-strand cDNA synthesis. After end repairing, the cDNA was amplified by PCR and the products were validated on the Agilent Technologies. The final library was generated after heated denature and circularization of the PCR products. Then the single end 50 bases reads were generated on BGIseq500 platform (BGI-Shenzhen, China).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
BGISEQ-500 |
| |
|
| Description |
core_table_gene.xls
|
| Data processing |
The sequencing data was filtered with SOAPnuke (v1.5.2) by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format.
The clean reads were mapped to the reference genome using HISAT2 (v2.0.4).
Bowtie2 (v2.2.5) was applied to align the clean reads to the reference coding gene set, then expression level of gene was calculated by RSEM (v1.2.12).
Supplementary_files_format_and_content: core_table_gene.xls
|
| |
|
| Submission date |
Mar 12, 2021 |
| Last update date |
Mar 15, 2021 |
| Contact name |
Zhen Cheng |
| E-mail(s) |
[email protected]
|
| Phone |
+8613602263913
|
| Organization name |
The First Affiliated Hospital of Sun Yat-Sen University
|
| Street address |
58 Zhongshan Er Road, Guangzhou
|
| City |
Guangzhou |
| State/province |
China |
| ZIP/Postal code |
510080 |
| Country |
China |
| |
|
| Platform ID |
GPL23227 |
| Series (1) |
| GSE168843 |
Selenite induces cell cycle arrest and apoptosis through ROS-dependent inhibition of the AKT/mTOR pathway in thyroid cancer |
|
| Relations |
| BioSample |
SAMN18290573 |
| SRA |
SRX10335525 |
