|
| Status |
Public on Mar 13, 2023 |
| Title |
exosomes of EBV-positive cancer cell [SNU-719_exo-2_R1] |
| Sample type |
SRA |
| |
|
| Source name |
exosome
|
| Organism |
Homo sapiens |
| Characteristics |
sample type: exosome
cell line: exosome
cell type: exosomes of EBV-positive cancer cell
|
| Growth protocol |
SNU-719 (EBV-positive gastric cancer cell line), AGS(EBV-negative gastric cancer cell line) were cultured in PMI-1640 and F12, respectively. 5% fetal bovine serum without exosome and penicillin and streptomycin (100U/mL) were added to the medium prior to use. The supernatant was collected when the cells were growing vigorously (up to about 70% fusion).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from cells and exosomes using a high purity RNA extraction kit (TRIzol) according to the manufacturer's protocol. The OD260 and OD280 values and ratios of 1 μl extracted samples were determined by ultraviolet spectrophotometer to determine the concentration and purity of extracted samples.
The miRNA library was prepared using an RNA sample preparation kit (Epicenter, San Diego, CA, USA) according to the manufacturer's instructions. As outlined below, small RNAs were attached to 3 and 5 splices for reverse transcription to produce single-stranded cDNA. Then PCR amplification was performed. The constructed library was tested for quality and yield using the Agilent 2100 bioanalyzer and ABI StepOnePlus real-time fluorescence quantitative PCR system. Four small RNA libraries were constructed from RNA samples extracted from EBV-positive gastric cancer cell lines (SNU-719) and EBV-negative gastric cancer cell lines (AGS) and their exosomes. The library was sequenced on Illumina HiSeq 2500 platform.
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
The raw data (raw reads) obtained by llumina HiSegTM2500 sequencing should be filtered first: remove the connectors at both ends of the reads, remove the reads with fragment length<17nt and low-quality reads, etc., complete the preliminary filtering of the data and obtain high-quality data (clean reads).
The expression of miRNAs can be obtained by comparing the clean reads obtained by sequencing with all EBV miRNA mature body sequences in the miRBase.v22 database.
The expression of miRNAs can be obtained by comparing the clean reads obtained by sequencing with all human miRNA mature body sequences in the miRBase.v22 database.
Assembly: hg18
Supplementary files format and content: miRNA counts
|
| |
|
| Submission date |
Mar 09, 2023 |
| Last update date |
Mar 14, 2023 |
| Contact name |
Shun Hu |
| E-mail(s) |
hush111@fjmu.edu.cn
|
| Phone |
13459484721
|
| Organization name |
The First Affiliated Hospital of Fujian Medical University
|
| Department |
Department of Pathology
|
| Street address |
Chazhong Road
|
| City |
Fuzhou |
| State/province |
Fujian |
| ZIP/Postal code |
350005 |
| Country |
China |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE227017 |
Effects of co-culture EBV-miR-BART1-3p on proliferation and invasion of gastric cancer cells based on exosomes |
|
| Relations |
| BioSample |
SAMN33699275 |
| SRA |
SRX19611862 |
