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Sample GSM5258574 Query DataSets for GSM5258574
Status Public on Apr 21, 2024
Title Blank_3
Sample type SRA
 
Source name MHCC97H Hepatoma Cancers Cells
Organism Homo sapiens
Characteristics treatment: Control
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 SAMN18824020
SRA SRX10654438

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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