|
| Status |
Public on Sep 07, 2021 |
| Title |
MDA-MB-231 shS100A10_1 rep1 |
| Sample type |
RNA |
| |
|
| Source name |
MDA-MB-231
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: breast cancer
cell line: MDA-MB-231
treatment: S100A10 knock-downed
|
| Treatment protocol |
none
|
| Growth protocol |
10% FBS RPMI1640 + penicillin/streptomycin + 2.5ug/ml puromycin
|
| Extracted molecule |
total RNA |
| Extraction protocol |
total RNA was extracted using PureLink RNA mini kit (ThermoFisher Scientific) according to the manufacturer's instructions.
|
| Label |
biotin and streptavidin phycoerythrin
|
| Label protocol |
cDNA samples were labeled with a proprietary DNALabeling Reagent that is covalently linked to biotin using GeneChipTM WT Plus Reagent Kit for Cartridge Array (ThermoFisher Scientific) according to the manufacturer's instructions.
|
| |
|
| Hybridization protocol |
cDNA was hybridized to Clarion S array (ThermoFisher Scientific) using the GeneChip WT PLUS Reagent Kit and the GeneChip Hybridization, Wash and Stain Kit (ThermoFisher Scientific).
|
| Scan protocol |
The array chips were scanned immediately after washing with GeneChip Scanner 3000 7G (ThermoFisher Scientific).
|
| Description |
Gene expression of cell
|
| Data processing |
Raw data (CEL files) were processed with Transcriptome Analysis Console (TAC) 4.0.2 (TheromoFisher SCIENTIFIC).
The data (21448 probes) were filtered manually as follow. The probes, which showed values lower than the back-round in all samples were excluded (the number became 19605 probes). Then, one probe was selected among probes which detect expression of same gene by original perl script. Briefly, the values of all samples were averaged, and the one which showed highest value was chosen. If the averages were same, the probe which showed lower coefficient of variance (CV) was chosen (the number of probes became 18130 probes). Thereafter the probes which detect multiple genes were omitted (the number of probes became 18130 probes). Finally the probes which showed CV higher than 50% in any conditions were excluded; as a total, mRNA expression of 16965 genes were obtained.
|
| |
|
| Submission date |
Sep 04, 2020 |
| Last update date |
Sep 07, 2021 |
| Contact name |
Nishimura Tatsunori |
| E-mail(s) |
[email protected]
|
| Organization name |
Nagoya University
|
| Department |
Graduate School of Medicine
|
| Lab |
Division of Cancer Biology
|
| Street address |
65 Tsurumai-cho, Showa-ku
|
| City |
Nagoya |
| State/province |
Aichi |
| ZIP/Postal code |
466-8550 |
| Country |
Japan |
| |
|
| Platform ID |
GPL23159 |
| Series (1) |
| GSE157497 |
Gene expression of S100A10 knocked down human breast cancer cells |
|
