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Sample GSM2258285 Query DataSets for GSM2258285
Status Public on Feb 12, 2017
Title OoT1
Sample type RNA
 
Source name Oenococcus oeni PSU-1
Organism Oenococcus oeni
Characteristics strain: PSU-1
Treatment protocol When cultures reached the late exponential phase (OD600nm ≈ 1,6) they were collected by centrifugation and inoculated in flasks of 5L 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 PSU-1 was cultured at 28ºC 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 after 1 hour after 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 Aug 03, 2016
Last update date Feb 12, 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)
GSE85137 Transcriptomic and proteomic analysis of Oenococcus oeni adaptation to wine stress conditions

Data table header descriptions
ID_REF
VALUE RMA normalized with NimbleGen software. Mean value of five analysis replicates has been log2 transformed.

Data table
ID_REF VALUE
OEOE_0001071000000001 11.8164
OEOE_0002071000000002 11.0465
OEOE_0003071000000003 12.7587
OEOE_0004071000000004 11.3105
OEOE_0005071000000005 13.3493
OEOE_0006071000000006 12.5833
OEOE_0007071000000007 6.23175
OEOE_0008071000000008 12.3374
OEOE_0009071000000009 13.8968
OEOE_0010071000000010 14.5588
OEOE_0011071000000011 14.9881
OEOE_0012071000000012 13.7097
OEOE_0013071000000013 13.6078
OEOE_0014071000000014 9.81237
OEOE_0015071000000015 11.113
OEOE_0017071000000016 8.92354
OEOE_0018071000000017 9.92184
OEOE_0019071000000018 8.97332
OEOE_0020071000000019 10.4891
OEOE_0021071000000020 10.7686

Total number of rows: 1611

Table truncated, full table size 47 Kbytes.




Supplementary file Size Download File type/resource
GSM2258285_415324_393_gridded.pair.gz 1.0 Mb (ftp)(http) PAIR
Processed data included within Sample table

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