|
| Status |
Public on Jun 07, 2023 |
| Title |
AGS cells, 1 [miRNA-seq] |
| Sample type |
SRA |
| |
|
| Source name |
AGS
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: AGS
cell type: gastric cancer cells
condition: exosomes from control MKN-28 cells (GCEx)
|
| Treatment protocol |
After the MKN-28 cells were incubated with Fn49256-GCEx or GCEx in an anaerobic environment for another 24 hours, exosomes were extracted from the collected supernatant and added to the RPMI-1640 medium of AGS cells for co-culture.
|
| Growth protocol |
AGS cells were cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum in a humidified atmosphere containing 5% CO2 at 37°C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from cell or animal tissue by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Bioanalyzer 2200 (Agilent) and kept at -80℃. The RNA with RIN >8.0 is right for miRNA purification. miRNA was purified by miRNeasy Mini Kit (Qiagen) and the purification result was validated by gel electrophoresis.
RNA libraries were prepared for sequencing using standard Illumina protocols.
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
HiSeq X Ten |
| |
|
| Description |
G1
|
| Data processing |
We applied the reads filtering towards the raw reads after sequencing to achieve the clean data following the criteria: a) 10% base quality <15, b) 13% base quality <20, and c) 15bp < read length < 30bp.
Utilizing the BWA software, we mapped the clean data to miRBase 22.0 Homo sapiens miRNA database and GRCh38 genome.
Count counting.
Assembly: GRCh38 / miRBase 22.0
Supplementary files format and content: process_data_file.txt: Tab-delimited text file contains counts for each sample.
|
| |
|
| Submission date |
Sep 20, 2022 |
| Last update date |
Jun 07, 2023 |
| Contact name |
Xin Zhang |
| E-mail(s) |
zhangxin_21@126.com
|
| Organization name |
Qilu Hospital, Shandong University
|
| Street address |
107 Wenhua Xi Road
|
| City |
Jinan |
| State/province |
Shandong |
| ZIP/Postal code |
250012 |
| Country |
China |
| |
|
| Platform ID |
GPL20795 |
| Series (2) |
| GSE213833 |
Gastric cancer cells treated with exosomes derived from Fusobacterium nucleatum infected MKN-28 cells [miRNA-seq] |
| GSE214818 |
Gastric cancer cells treated with exosomes derived from Fusobacterium nucleatum infected MKN-28 cells |
|
| Relations |
| BioSample |
SAMN30942132 |
| SRA |
SRX17650513 |
