|
| Status |
Public on Sep 27, 2022 |
| Title |
A549_Smp2_Vehicle_Repeat2 |
| Sample type |
RNA |
| |
|
| Source name |
Lung cancer cell line A549
|
| Organism |
Homo sapiens |
| Characteristics |
disease state: Non-small cell lung carcinoma (A549) cell line
treatment: vehicle
|
| Treatment protocol |
TGFb was disolved in 4 mM HCl, Crizotinib was dissolved in DMSO and treated in A549 cells.
|
| Growth protocol |
The cells were maintained under RPMI1640 medium containing 10% FBS.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from the cells and processed according to the manufacturer’s guideline (Affymetrix).
|
| Label |
biotin
|
| Label protocol |
The Affymetrix GeneChip® procedure for generation of the biotin-labeled single-stranded cDNA by in vitro transcription were performed according to the manufacturer's instructions from 300ng total RNA(GeneChip® Whole Transcript (WT) Sense Target Labeling Assay Rev.5). Protocol performed using the Whole Transcript Sense Target Labeling and Control Reagents (Affymetrix 900652).
|
| |
|
| Hybridization protocol |
Following fragmentation, 5.5 ug of framented cDNA were hybridized for about 17 hr at 45℃ on Human Gene 2.0 ST array. The hybridized probe arrays were stained and washed with GeneChip® Hybridization, Wash and Stain Kit using the Fluidics Station 450(Affymetrix).
|
| Scan protocol |
The stained GeneChips were scanned with a GeneChip® Scanner 3000+ 7G(Affymetrix) a 570 nm.
|
| Description |
Gene expression profile in A549 cells vehicle treated
|
| Data processing |
Raw data were normalized using the Single Channel Array Normalization (Piccolo et al. 2012, PMID: 22959562) method. As part of the normalization process, a custom chip-definition file (hugene20sthsentrezgprobe_25.0.0.tar.gz) from the BrainArray resource was used to map genes based on updated genome mappings and excludes inaccurate or wrongly annotated probes. The microarray probests were mapped to 18,549 of protein coding genes.
|
| |
|
| Submission date |
Nov 17, 2021 |
| Last update date |
Sep 27, 2022 |
| Contact name |
Ju-Hong Jeon |
| E-mail(s) |
jhjeon2@snu.ac.kr
|
| Organization name |
Seoul National University College of Medicine
|
| Department |
Department of Physiology and Biomedical Sciences
|
| Lab |
Smooth muscle lab
|
| Street address |
28 Yongon-Dong, Chongno-Gu
|
| City |
Seoul |
| State/province |
Seoul |
| ZIP/Postal code |
110-799 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL30971 |
| Series (1) |
| GSE189047 |
The effect of crizotinib in A549 lung cancer cell |
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