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Sample GSM1518780 Query DataSets for GSM1518780
Status Public on Oct 01, 2015
Title OoB2
Sample type RNA
 
Source name Oenococcus oeni total RNA from cells after 1 hour of ethanol shock
Organism Oenococcus oeni PSU-1
Characteristics strain: PSU-1
Treatment protocol When cultures reached the late exponential phase (OD600nm ≈ 1) they were divided into two sterile flasks. Immediately, 12% (v/v) of ethanol was added to one flask and 12% (v/v) of water was added to the other (control).
Growth protocol O. oeni PSU-1 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
Data processing Pair reports (raw data) listing the probe intensities of the arrays were extracted and processed using Nimblescan software v2.6
 
Submission date Oct 03, 2014
Last update date Oct 01, 2015
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)
GSE62036 Transcriptomic analysis of Oenococcus oenos response to ethanol shock

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 11.91084
OEOE_0002071000000002 13.98736
OEOE_0003071000000003 13.35438
OEOE_0004071000000004 12.83294
OEOE_0005071000000005 14.25908
OEOE_0006071000000006 14.34798
OEOE_0007071000000007 8.54304
OEOE_0008071000000008 11.92976
OEOE_0009071000000009 13.51966
OEOE_0010071000000010 15.11002
OEOE_0011071000000011 15.59422
OEOE_0012071000000012 14.05152
OEOE_0013071000000013 13.44936
OEOE_0014071000000014 12.45012
OEOE_0015071000000015 13.01108
OEOE_0017071000000016 12.57358
OEOE_0018071000000017 12.70944
OEOE_0019071000000018 11.64584
OEOE_0020071000000019 11.77064
OEOE_0021071000000020 11.6834

Total number of rows: 1611

Table truncated, full table size 48 Kbytes.




Supplementary file Size Download File type/resource
GSM1518780_091127A02_313179_933-2009_OoB2.pair.gz 1.0 Mb (ftp)(http) PAIR
Processed data included within Sample table

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