|
| Status |
Public on May 12, 2024 |
| Title |
HCC+ EVs treatment3 replicate2 |
| Sample type |
SRA |
| |
|
| Source name |
HCT-116
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HCT-116
cell type: epithelial-like cell
treatment: 0.048 mg/mL
|
| Treatment protocol |
HCT-116 cells were treated with different concerntrations of EVs from HCC patients serum or healthy peopele serum.
|
| Growth protocol |
HCT-116 cells were maintained in DMEM supplemented with 10% exosome-depleted serum and 1% antibiotics in humidified atmosphere with 5% CO2 at 37 ℃.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was extracted using RNeasy Mini Kit (Qiagen).
RNA libraries for RNA-seq were prepared using NEBNext Ultra II RNA Library reagent kit following manufacturer's protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
| |
|
| Description |
3-2-2_R1
|
| Data processing |
Sequence reads were trimmed adaptor/low-quality sequences using cutadapt v3.4
Trimmed sequence reads were mapped to Grch38/hg38 using HISAT2 v2.2.1 (parameters-mismath cost:1)
Read count extraction were performed using featureCounts v2.0.1
Assembly: Grch38
Supplementary files format and content: Comma separator csv file includes raw counts for all samples
|
| |
|
| Submission date |
May 05, 2024 |
| Last update date |
May 12, 2024 |
| Contact name |
Boan Li |
| E-mail(s) |
yue_zhao20@mails.jlu.edu.cn
|
| Phone |
010-66933114
|
| Organization name |
the Fifth medical center of Chinese PLA General Hospital
|
| Street address |
Baili Street and Qingfeng West Road in Tiangongyuan Street
|
| City |
Beijing |
| ZIP/Postal code |
100039 |
| Country |
China |
| |
|
| Platform ID |
GPL20795 |
| Series (1) |
| GSE266634 |
Gene expression of HCT-116 cell lines treated with EVs isolated using GlyExo-Capture method |
|
| Relations |
| BioSample |
SAMN41219933 |
| SRA |
SRX24459939 |
