|
| Status |
Public on Jul 16, 2024 |
| Title |
AS2-Vec cells, deNG-IL6, 3h, replicate 1 |
| Sample type |
RNA |
| |
|
| Source name |
AS2-Vec cells, deNG-IL6, 3h
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: AS2-vec
cell type: lung adenocarcinoma cell
treatment: deNG-IL6, 3h
|
| Treatment protocol |
AS2-Vec cells were treated with NG-IL6-containing or deNG-IL6-containing conditioned medium for 3 h.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from the examined cells and tissues with TRIzolTM Reagent (Invitrogen, 15596026) following the manufacturer’s protocol. The integrity of all the RNA samples was evaluated using a Bioanalyzer 2100 (Agilent Technologies) according to the manufacturer’s protocol.
|
| Label |
Cy3
|
| Label protocol |
Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.
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| |
|
| Hybridization protocol |
0.6 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented to an average size of about 50-100 nucleotides by incubation with fragmentation buffer at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human GE 8x60K Microarrays for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by nitrogen gun blowing.
|
| Scan protocol |
Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) at 535 nm for Cy3 using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 3 um, Dye channel is set to Green and Green PMT is set to 100%).
|
| Description |
Gene expression after 3h in deNG-IL6-treated AS2-Vec cells
|
| Data processing |
The scanned images were analyzed with Feature Extraction Software 10.5.1.1 (Agilent) using default parameters to obtain background subtracted (Saptial Detrend Surface Value) and spatially detrended Processed Signal intensities (Density-Mean background). Number of rows:384; number of columns:164. Normalization by quantile. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
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| |
|
| Submission date |
Jun 13, 2024 |
| Last update date |
Jul 16, 2024 |
| Contact name |
Chun-Hua Hung |
| E-mail(s) |
[email protected]
|
| Organization name |
National Cheng Kung University
|
| Department |
Department of Oncology
|
| Street address |
No. 138, Sheng-Li Rd., North Dist.
|
| City |
Tainan |
| ZIP/Postal code |
704 |
| Country |
Taiwan |
| |
|
| Platform ID |
GPL14550 |
| Series (1) |
| GSE269782 |
Defective N-Glycosylation of IL6 Induces Metastasis and Tyrosine Kinase Inhibitor Resistance in Lung Cancer |
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