|
| Status |
Public on Apr 21, 2024 |
| Title |
Treated_2 |
| Sample type |
SRA |
| |
|
| Source name |
MHCC97H Hepatoma Cancers Cells
|
| Organism |
Homo sapiens |
| Characteristics |
treatment: Xanthatin treatment
cell line: MHCC97H
molecule subtype: exosomal miRNA
|
| Treatment protocol |
Xanthatin was dissolved in dimethylsulfoxide (DMSO) and with a final concentration of 0.5% in all experiments. Cells were treated with xanthatin (final concentration of 4 μmol/L) for 24h.
|
| Growth protocol |
The human high metastatic liver cells line MHCC97H was purchased from Wuhan University. Cells were cultured in DMEM medium supplemented with 5%fetal bovine serum (FBS) and 5% fetal bovine serum without exosomes (Gibco A2720801), 100 U/ml penicillin, 100 g/ml streptomycin (Life Technologies, Inc., Rockville, MD) in a humidified incubator under 5% CO2 at 37◦C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cell culture supernatant was collected from the control group and the xanthatin group. Supernatant were collected by differential centrifugation (500xg at 4℃ for 5min, 2000xg at 4℃ for 30min, 10000xg at 4℃ for 60min). Filtrated with a 0.22um sterile filter, added into the ultra-high speed centrifuge tube, centrifuged at 4℃ for 70min at 120000xg and discarded the supernatant. Finally, depending on the amount of precipitation, 200-400 L of pre-cooled sterile PBS was added for resuspended suspension, which was high purity EVs. Total RNA was extracted by TRIzol reagent, and the RNA molecules in a size range of 18–30 nt were enriched by poly-acrylamide gel electrophoresis.
The 3'adapters were added and the 36–44 nt RNAs were enriched. The 5'adapters were then ligated to the RNAs as well. The ligation products were reverse-transcribed by PCR amplification, and the 140–160 bp size PCR products were enriched to generate a cDNA library. The cDNA fragments were purified with PCR extraction kit, poly(A) added and ligated to Illumina sequencing adapters
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
The raw data were quality controlled by removing adapters, Q20 less than 80% to obtain clean reads.
The clean reads were aligned to miRBase (version 22.0). The expression of miRNAs were estimated using transcript per million (TPM).
The miRNAs with |log2FoldChange|≥0.58 and p<0.05 were regarded as differences miRNAs.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include count and TPM values for each Sample
|
| |
|
| Submission date |
Apr 21, 2021 |
| Last update date |
Apr 21, 2024 |
| Contact name |
YU WU |
| E-mail(s) |
wylucky@njucm.edu.cn
|
| Phone |
15862715062
|
| Organization name |
Nantong Hospital of Traditional Chinese Medicine
|
| Street address |
Nantong, 226001, PR China;
|
| City |
Nantong |
| ZIP/Postal code |
226000 |
| Country |
China |
| |
|
| Platform ID |
GPL20301 |
| Series (1) |
| GSE172654 |
MiRNA sequencing revealed differentially expressed miRNAs in MHCC97H Hepatoma Cancers Cells exosomes Co-cultured with Xanthatin |
|
| Relations |
| BioSample |
SAMN18824018 |
| SRA |
SRX10654440 |
