|
| Status |
Public on Sep 22, 2017 |
| Title |
A549_DPF3_CT1_p |
| Sample type |
RNA |
| |
|
| Source name |
A549, DPF3, CT1, TNF+
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: A549
|
| Treatment protocol |
Cells transduced with a dominant negative mutant of d4-family protein (CT1) or empty vector (Control) were grown in the absence or presence (10 ng/ml) of TNF-alpha for 1 hour at 37 ºC in a humidified incubator with 5% CO2.
|
| Growth protocol |
Cells were grown in Dulbeco's modified Eagle`s mudium containing 10% fetal calf serum.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was prepared using a mirVana miRNA isolation kit (Ambion) and DNA was removed by a TURBO DNA-free™ kit (Ambion) according to the manufacturer’s instructions. The quality of all RNA samples was measured using a 2200 TapeStation (Agilent). RNA samples with RNA integrity numbers higher than 9.0 were used for gene expression analysis.
|
| Label |
Cy3
|
| Label protocol |
cRNA was amplified and labelled using a Low input Quick Amp Labelling Kit (Agilent Technologies).
|
| |
|
| Hybridization protocol |
cRNA was hybridized to a 60K 60-mer oligomicroarray (SurePrint G3 Human Gene Expression Microarray 8x60K v3; Agilent Technologies) according to the manufacturer's instructions.
|
| Scan protocol |
The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).
|
| Data processing |
The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. The raw signal intensities of all samples were normalized by the quantile algorithm with the Bioconductor.
|
| |
|
| Submission date |
Jan 18, 2017 |
| Last update date |
Sep 22, 2017 |
| Contact name |
Kazuyoshi Kobayashi |
| E-mail(s) |
jgdfd547@gmail.com
|
| Organization name |
Chiba University
|
| Department |
Medical Mycology Research Center (MMRC)
|
| Street address |
1-8-1 Inohana, Chuo-ku
|
| City |
Chiba |
| ZIP/Postal code |
260-8673 |
| Country |
Japan |
| |
|
| Platform ID |
GPL21185 |
| Series (2) |
| GSE93768 |
Tumor suppression via inhibition of SWI/SNF complex-dependent NF-kappaB activation [A549 subset] |
| GSE93770 |
Tumor suppression via inhibition of SWI/SNF complex-dependent NF-kappaB activation |
|
