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| Status |
Public on Sep 13, 2021 |
| Title |
Drosophila S2R+ cells_11°C_Rep 1 |
| Sample type |
RNA |
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| Source name |
Drosophila S2R+ cells_11°C_24 hrs
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| Organism |
Drosophila melanogaster |
| Characteristics |
cell line: S2R+ cells
treatment: 11°C, 24 hours
|
| Treatment protocol |
S2R+ cells were plated in 60 mm culture dishes in 2.5 ml medium. The numbers of cells that were plated were adjusted to the temperature, to which they were shifted eventually (30°C: 1.5x106; 25°C: 1.7x106; 14°C: 3.5x106; 11°C: 4.5x106) so that comparable cell densities were present at the end of the temperature treatment. Twenty-four hours after plating, cells were shifted to different temperatures (11, 14, 25 or 30°C) for 24 hours before isolation of total RNA. Three biological replicates were performed.
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| Growth protocol |
S2R+ cells were cultured in Schneider’s medium (Gibco, cat# 21720, Thermo Fisher Scientific, Waltham, MA), supplemented with 10% fetal bovine serum (Gibco, cat# 10500-064) and 1% Penicillin-Streptomycin (Gibco, cat# 15140).
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated with the NucleoSpin RNAII kit (Macherey-Nagel, Oensingen, Switzerland)
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| Label |
Cy3
|
| Label protocol |
For generation of Cyanine 3 (Cy3)-labelled complementary RNA (cRNA) probes, we used the Low-Input QuickAmp kit (Agilent, Santa Clara, CA, USA). The resulting cRNA was purified using the Absolute RNA Nanoprep kit (Agilent).
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| Hybridization protocol |
The hybridization mix (55 µl) contained 1.65 µg of fragmented cRNA, 2.2 µl of 25x hybridization buffer, 11 µl of 10x blocking agent and RNase-free water. For hybridization, we used single-color gene-expression microarrays purchased from Agilent.
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| Scan protocol |
After microarray hybridization and washing, signal intensities were recorded with Agilent Feature Extraction Software
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| Description |
Gene expression after 24 hours at 11°C
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| Data processing |
Raw data was processed with GeneSpringGX11.0 (Agilent). Inter array differences were corrected using the option “median scaling to a control sample” of this software and the three replicates obtained after incubation at 25°C as control samples.
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| Submission date |
Oct 07, 2020 |
| Last update date |
Sep 13, 2021 |
| Contact name |
Christian F. Lehner |
| Organization name |
University of Zurich
|
| Department |
DMLS
|
| Street address |
Winterthurerstrasse 190
|
| City |
Zurich |
| ZIP/Postal code |
8057 |
| Country |
Switzerland |
| |
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| Platform ID |
GPL7300 |
| Series (2) |
| GSE159170 |
Temperature dependence of the transcriptome in cultured Drosophila S2R+ cells |
| GSE159174 |
Effects of temperature change within the readily tolerated range on transcription and DNA accessibility in the Drosophila S2R+ cell line |
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