|
| Status |
Public on Jul 03, 2017 |
| Title |
Oenococcus oeni 217T [OoC1] |
| Sample type |
RNA |
| |
|
| Source name |
Oenococcus oeni 217T
|
| Organism |
Oenococcus oeni |
| Characteristics |
strain: 217T
|
| Treatment protocol |
When cultures reached the late exponential phase (OD600nm ≈ 1) they were collected by centrifugation and inoculated in flasks of 500ml with wine like medium (2 g/L fructose, 2 g/L tartaric acid, 0.5 g/L citric acid, 0.6 g/L L-malic acid, 5 g/L yeast extract, 0.1 g/L acetic acid, 5 g/L glycerol and 12 % ethanol v/v, it was adjusted to a pH 3.4 with NaOH 1N)
|
| Growth protocol |
O. oeni was cultured at 30ºC in MRS broth medium supplemented with L-malic acid (4 g l-1) and fructose (5 g l-1) at pH 5.0.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extractions were performed using the Roche RNeasy kit according to the manufacturer’s instructions (Mannheim, Germany).
|
| Label |
Cy3
|
| Label protocol |
dsDNA was generated from 10 mg RNA following Nimblegen array user's guide protocol. 1mg dsDNA was labeled by Klenow random priming with Cy3 nonamers with Nimblegen One-color DNA labeling kit (cat.# 06370411001) following manufacturer's user's guide
|
| |
|
| Hybridization protocol |
Cy3-labeled DNA was precipitated with 1 volume isopropanol. Hybridization mixture including 2mg labeled DNA was prepared using Nimblegen hybridization kit (cat.#05583683001). 090324_Ooen_exp Nimblegen arrays were hybridized in Nimblegen hybridization system 4 station for 16-18 h at 42ºC, and then washed in 1XWash solution I, II and III (cat.#5584507001).Hybridization buffers and washes were completed according to manufacturer's protocol
|
| Scan protocol |
Arrays were scanned on a Genepix 4000B scanner
|
| Description |
Oenococcus oeni total RNA from cells before inoculation in wine like medium (12% ethanol v/v)
|
| Data processing |
Pair reports (raw data) listing the probe intensities of the arrays were extracted and processed using Nimblescan software v2.6
|
| |
|
| Submission date |
Jul 13, 2015 |
| Last update date |
Jul 03, 2017 |
| Contact name |
Cristina Reguant |
| E-mail(s) |
cristina.reguant@urv.cat
|
| Phone |
+34 977558043
|
| Organization name |
University Rovira i Virgili
|
| Department |
Biochemistry and Biotechnology
|
| Street address |
Marcel·lí Domingo 1
|
| City |
Tarragona |
| State/province |
Tarragona |
| ZIP/Postal code |
43007 |
| Country |
Spain |
| |
|
| Platform ID |
GPL19261 |
| Series (1) |
| GSE70820 |
Transcriptomic analysis of three Oenococcus oeni strains in the early response to stress |
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