|
| Status |
Public on Apr 30, 2023 |
| Title |
SGC-R |
| Sample type |
RNA |
| |
|
| Source name |
SGC-R
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: SGC-R
|
| Treatment protocol |
BGC-R and SGC-R cells were changed to no cisplatin medium for one week, and cells were havested together with BGC823 and SGC7901 under normal culture condition.
|
| Growth protocol |
BGC823 and SGC7901 cells are maintained in RPMI1640 plus 10%FBS. BGC-R and SGC-R cells are maintained in RPMI1640 plus 10%FBS and 0.5μg/ml cisplatin
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA quantity and quality were measured by NanoDrop ND-1000. RNA integrity was assessed by standard denaturing agarose gel electrophoresis.
|
| Label |
Cy3
|
| Label protocol |
Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications. Briefly, mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3' bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.
|
| |
|
| Hybridization protocol |
1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60°C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven. The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).
|
| Scan protocol |
Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides.
|
| Description |
Gene expression of SGC-R
|
| Data processing |
Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 3 out of 4 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis. Differentially expressed LncRNAs and mRNAs with statistical significance between the two groups were identified through P-value/FDR filtering. Differentially expressed LncRNAs and mRNAs between the two samples were identified through Fold Change filtering. Hierarchical Clustering and combined analysis were performed using homemade scripts.
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| |
|
| Submission date |
Apr 19, 2021 |
| Last update date |
Apr 30, 2023 |
| Contact name |
Lifeng Feng |
| E-mail(s) |
lffeng@zju.edu.cn
|
| Organization name |
Zhejiang University, School of Medicine, Sir Run Run Shaw Hospital
|
| Street address |
No.3 East Qingchun Road
|
| City |
Hangzhou |
| State/province |
Zhejiang |
| ZIP/Postal code |
310016 |
| Country |
China |
| |
|
| Platform ID |
GPL16956 |
| Series (1) |
| GSE172364 |
Development of gene expression signatures for cisplatin resistance in gastric cancer cells |
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