|
| Status |
Public on Sep 09, 2024 |
| Title |
pH 6.8 treated cells versus pH 7.4, replicate #4 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Mouse B16-BL6 melanoma, cultured at pH 7.4 for 24 h
|
| Organism |
Mus musculus |
| Characteristics |
cell line: B16-BL6
treatment: pH 7.4
time: 24 hour
|
| Treatment protocol |
Serum starved (overnight) cells were further incubated with serum-free growth medium at pH 7.4, 6.8, and 5.9 for 24 hours.
|
| Growth protocol |
Cells were cultured with DMEM/F12 supplemented with 15 mM HEPES, 4 mM phosphoric acid, and 10% fetal bovine serum.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extracted using Isogen (Nippon gene) following manufacturer's instructions.
|
| Label |
Cy3
|
| Label protocol |
cRNA was labeled with Cy3-CTP and Cy5-CTP using Quick Amp Labeling Kit (5190-0444 : Agilent).
|
| |
|
| Channel 2 |
| Source name |
Mouse B16-BL6 melanoma, cultured at pH 6.8 for 24 h
|
| Organism |
Mus musculus |
| Characteristics |
cell line: B16-BL6
treatment: pH 6.8
time: 24 hour
|
| Treatment protocol |
Serum starved (overnight) cells were further incubated with serum-free growth medium at pH 7.4, 6.8, and 5.9 for 24 hours.
|
| Growth protocol |
Cells were cultured with DMEM/F12 supplemented with 15 mM HEPES, 4 mM phosphoric acid, and 10% fetal bovine serum.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extracted using Isogen (Nippon gene) following manufacturer's instructions.
|
| Label |
Cy5
|
| Label protocol |
cRNA was labeled with Cy3-CTP and Cy5-CTP using Quick Amp Labeling Kit (5190-0444 : Agilent).
|
| |
|
| |
| Hybridization protocol |
Hybridization and wash were performed by Gene Expression Hybridization Kit (5188-5242 : Agilent) and Gene Expression Wash Pack (5188-5327 : Agilent), respectively, according to manufacture's protocols.
|
| Scan protocol |
Arrays were scanned with Agilent Technologies Scanner, model G2505B.
|
| Description |
pH 6.8 treated cells versus pH 7.4 (log2), replicate #4 of quadruplicate)
Biological replicate 1 of 4. Control cells at 7.4 (7h) versus acid treatment at pH 6.8 (6d) for 24 h.
|
| Data processing |
The scanned images were analyzed with Feature Extraction Software 9.5.3 (Agilent).
The data are normalized for signal intensity and are presented as the ratio of pH 5.9 to pH 7.4 or pH 6.8 to pH 7.4 (Log2).
|
| |
|
| Submission date |
Aug 31, 2024 |
| Last update date |
Sep 09, 2024 |
| Contact name |
Yasumasa Kato |
| E-mail(s) |
yasumasa_kato@live.jp
|
| Organization name |
Ohu University School of Dentistry
|
| Department |
Department of Oral Function and Molecular Biology
|
| Lab |
Biochemistry
|
| Street address |
31-1 Misumido, Tomitamachi
|
| City |
Koriyama |
| State/province |
Fukushima |
| ZIP/Postal code |
963-8611 |
| Country |
Japan |
| |
|
| Platform ID |
GPL7202 |
| Series (1) |
| GSE276124 |
Identification of acidic extracellular pH-modulated genes |
|
