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Status |
Public on Apr 21, 2024 |
Title |
Treated_1 |
Sample type |
SRA |
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Source name |
MHCC97H Hepatoma Cancers Cells
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Organism |
Homo sapiens |
Characteristics |
treatment: Xanthatin treatment cell line: MHCC97H molecule subtype: exosomal miRNA
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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.
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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
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|
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Library strategy |
miRNA-Seq |
Library source |
transcriptomic |
Library selection |
size fractionation |
Instrument model |
Illumina HiSeq 4000 |
|
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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
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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 |
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Relations |
BioSample |
SAMN18824019 |
SRA |
SRX10654439 |