|
| Status |
Public on Apr 15, 2024 |
| Title |
KYSE960 exosome hypoxia |
| Sample type |
RNA |
| |
|
| Source name |
exosomal RNA 48h hypoxia
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: KYSE960
cell type: human esophageal squamous cell carcinoma
sample type: exosome
stress: hypoxia
|
| Treatment protocol |
None
|
| Growth protocol |
Cell lines were grown according to standard conditions up to 80% confluent. After that, the cells were incubated for 48 hours under normoxia (O2: 20%) or hypoxia(O2: 1%).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Exosomes were isolated from 10 ml of culture medium by ultracentrifuge (Optima TLX Ultracentrifuge, Beckman Coulter, CA, USA) at 10,000 g, 4°C for 90 min. Total Exosome RNA & Protein Isolation Kit ( Thermo Fisher Scientific, Inc, cat.#4478545) was used to extract total RNA from exosomes.
|
| Label |
biotin
|
| Label protocol |
Biotin-labeled samples were prepared using the FlashTag™ Biotin HSR RNA Labeling Kit according to the protocol supplied with the kit.
|
| |
|
| Hybridization protocol |
Arrays were incubated with GeneChip™ Hybridization Oven 645 at 48°C for 18 hours (60 rpm) according to the protocol supplied with the kit. The arrays were cleaned using the GeneChip™ Fluidics Station 450 according to the protocol supplied with the kit.
|
| Scan protocol |
Arrays were scanned using the GeneChip™ Scanner 3000 7G according to the accompanying manual <GeneChip™ Command Console (AGCC) 4.0 User Manual>.
|
| Data processing |
Arrays were read using a GeneChip™ Scanner 3000 7G (Thermo Fisher Scientific, Inc.). Images were quantified and corrected using Expression Console™ Software (Thermo Fisher Scientific, Inc.). Normalization was performed by RMA-DABG, and quality flags were calculated by Affymetrix® Expression Console™ Software and are denoted as P: Probes with detectable transcripts and A: Probes with ambiguous transcript detection.
Up regulation (Ratio≥2) is defined when it is more than twice the control, or Down regulation (Ratio≤0.5) when it is less than 1/2 the control. Only data for which both "test,control" in the Quality flag are set to "P" are selected.
|
| |
|
| Submission date |
Apr 14, 2024 |
| Last update date |
Apr 15, 2024 |
| Contact name |
Yasunori Matsumoto |
| E-mail(s) |
ymatsumoto@chiba-u.jp
|
| Organization name |
Chiba University
|
| Department |
Frontier Surgery
|
| Street address |
1-8-1 Inohana, Chuo-Ku
|
| City |
Chiba-Shi |
| State/province |
Chiba |
| ZIP/Postal code |
2608670 |
| Country |
Japan |
| |
|
| Platform ID |
GPL21572 |
| Series (1) |
| GSE263921 |
Profiling of exosomal microRNAs expression in culture medium of human esophageal cancer cell lines under hypoxic conditions |
|
