|
| Status |
Public on Mar 17, 2017 |
| Title |
GQD treated sample 2 |
| Sample type |
RNA |
| |
|
| Source name |
GQD treated HET-1A
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HET-1A
cell type: Esophageal epithelial cells
treatment: hydroxyl-modified graphene quantum dots (GQD)
|
| Treatment protocol |
HET-1A cells were seeded in 6-cm dishes and treated with 50 μg/mL hydroxyl-modified Graphene quantum dots (GQD) in triplicate. After 24 hours of incubation, cells were harvested with RNAiso Plus (TAKARA). Equivalent volume of ddH2O treated cells were served as controls.
|
| Growth protocol |
HET-1A cells were maintained in RPMI 1640 medium (Hyclone) supplemented with 10% heat-inactivated fetal calf serum (Gibco), containing 100 U/mL penicillin and 100 U/mL streptomycin and were incubated in a 5% CO2 humidified incubator at 37°C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted by mirVanaTM RNA Isolation Kit (Applied Biosystem p/n AM1561) following the manufacturer's instructions.
|
| Label |
Cy3
|
| Label protocol |
Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 μg RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.
|
| |
|
| Hybridization protocol |
0.6 μg of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/μg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 22.5μl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers' instructions. On completion of the fragmentation reaction, 22.5μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human Gene Expression v3 Microarray (8*60K) 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 brief centrifugation.
|
| Scan protocol |
Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x180k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).
|
| Description |
Gene expression of 50 μg/mL GQD-treated HET-1A cells, replicate 2.
|
| Data processing |
The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities as the raw data. Raw data were normalized in quantile algorithm with GeneSpring 13.1(Agilent). Probes that had at least 1 out of 2 samples flagged as Detected were maintained.
|
| |
|
| Submission date |
Mar 16, 2017 |
| Last update date |
Mar 17, 2017 |
| Contact name |
Ming Li |
| E-mail(s) |
lim1984@suda.edu.cn
|
| Organization name |
Soochow University
|
| Street address |
No. 199 Ren'ai Road
|
| City |
Suzhou |
| ZIP/Postal code |
215123 |
| Country |
China |
| |
|
| Platform ID |
GPL21185 |
| Series (1) |
| GSE96720 |
Genome-wide analysis of the toxic effect of hydroxyl-modified Graphene quantum dots (GQD) on normal human esophageal epithelial cells |
|
