|
| Status |
Public on Sep 02, 2017 |
| Title |
BY4743_YPD_2 |
| Sample type |
RNA |
| |
|
| Source name |
BY4743 strain, YPD culture
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: BY4743
|
| Treatment protocol |
The cell pellets were immediately frozen in liquid nitrogen and stored at - 80°C until RNA extraction.
|
| Growth protocol |
Cultures of each strain were carried out in 50 ml of YPD in a 250 mL shake flasks on a rotary shaker set at 200 rpm at 30°C. Yeast cells (about 10 OD600 units) were collected at OD600=1 by centrifugation (3,000 rpm, 4°C, 2 min).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Frozen cells were mechanically disrupted using a ball mill (MicroDismembrator Braun, Melsungen, Germany). Total RNA was extracted using SV Total RNA Isolation System (Promega) following the protocol of the Manufacturer.
|
| Label |
Cy3
|
| Label protocol |
Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.
|
| |
|
| Hybridization protocol |
0.6 ug of Cy3-labelled cRNA (specific activity > 40 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1 ul Agilent fragmentation buffer and 5 ul Agilent blocking agent following the manufacturers instructions, then hybridized to Agilent Yeast Gene Expression Microarray (V2G4813A-016322) for 12 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed two times for 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 MS200 scanner (NimbleGen Roche Diagnostics, Meylan, France) using one color scan setting for 8x15k array slides.
|
| Data processing |
The scanned images were analyzed with Feature Extraction V.11.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.
|
| |
|
| Submission date |
Sep 01, 2017 |
| Last update date |
Jan 23, 2018 |
| Contact name |
Marion Schiavone |
| E-mail(s) |
schiavon@insa-toulouse.fr
|
| Organization name |
INSA-Toulouse
|
| Department |
LISBP
|
| Street address |
135 avenue de Rangueil
|
| City |
Toulouse |
| ZIP/Postal code |
31077 |
| Country |
France |
| |
|
| Platform ID |
GPL16244 |
| Series (1) |
| GSE103392 |
Integration of biochemical, biophysical and transcriptomics data for investigating the structural and nanomechanical properties of the yeast cell wall |
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