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Sample GSM5258577 Query DataSets for GSM5258577
Status Public on Apr 21, 2024
Title Treated_3
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
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
BioSample SAMN18824017
SRA SRX10654441

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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