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Sample GSM590053 Query DataSets for GSM590053
Status Public on Aug 01, 2011
Title 5131
Sample type RNA
 
Channel 1
Source name 293 L plantarum G6 pH5.0
Organism Lactiplantibacillus plantarum
Characteristics bacterial strain: IMDO 130201
flour type: wheat
depositor: 13
sampling time: 240h
ph: 5.0
repeat: 1
Extracted molecule total RNA
Extraction protocol To obtain total RNA from L. plantarum IMDO 130201, 5 mL of fermentation medium of a mid-exponential growth phase culture, was collected in 10 mL RNAprotect (Qiagen, Hilden, Germany), mixed, and kept at room temperature for minimum 5 min. Subsequently, the sample was centrifuged at 5,000 Í g for 15 min and the RNA was isolated from the resulting cell pellet by applying an enzymatic lysis using mutanolysin and lysozyme, after which the RNA was extracted from the resulting mixture by using an RNeasy minikit (Qiagen) following standard instructions and including mechanical disruption of the cells using glass beads, as described previously (Weckx et al., 2009). As the RNA profiles, obtained after capillary electrophoresis using the Bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA) showed an unexpected peak at the lower size range, possibly due to the presence of small RNA molecules (e.g., tRNA), an additional RNA clean-up step was performed. To remove the small RNA molecules, the Microcon YM-50 (Millipore, Bedford, MA) was used according to the Manufacturer’s standard instructions. Sampling was performed in duplicate, resulting in two technical repeat samples for each pH value.
Label Cy5
Label protocol RNA was linearly amplified using Genisphere SensAmp kit (Genisphere, Hatfield, Pennsylvania, USA) using 200 ng of total RNA. The protocol was followed according to manufacturer's instructions. The amplified RNA (aRNA) was purified using the RNeasy Mini Kit (Qiagen), and the purified aRNA was Cy5 labeled by a reverse transcription reaction as earlier described by Puskas LG, Zvara A, Hackler L, Van Hummelen P: RNA amplification results in reproducible microarray data with slight ratio bias. Biotechniques 2002, 32(6):1330-1340.
 
Channel 2
Source name 295 L plantarum G7 pH5.5
Organism Lactiplantibacillus plantarum
Characteristics bacterial strain: IMDO 130201
flour type: wheat
depositor: 13
sampling time: 240h
ph: 5.5
repeat: 1
Extracted molecule total RNA
Extraction protocol To obtain total RNA from L. plantarum IMDO 130201, 5 mL of fermentation medium of a mid-exponential growth phase culture, was collected in 10 mL RNAprotect (Qiagen, Hilden, Germany), mixed, and kept at room temperature for minimum 5 min. Subsequently, the sample was centrifuged at 5,000 Í g for 15 min and the RNA was isolated from the resulting cell pellet by applying an enzymatic lysis using mutanolysin and lysozyme, after which the RNA was extracted from the resulting mixture by using an RNeasy minikit (Qiagen) following standard instructions and including mechanical disruption of the cells using glass beads, as described previously (Weckx et al., 2009). As the RNA profiles, obtained after capillary electrophoresis using the Bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA) showed an unexpected peak at the lower size range, possibly due to the presence of small RNA molecules (e.g., tRNA), an additional RNA clean-up step was performed. To remove the small RNA molecules, the Microcon YM-50 (Millipore, Bedford, MA) was used according to the Manufacturer’s standard instructions. Sampling was performed in duplicate, resulting in two technical repeat samples for each pH value.
Label Cy3
Label protocol RNA was linearly amplified using Genisphere SensAmp kit (Genisphere, Hatfield, Pennsylvania, USA) using 200 ng of total RNA. The protocol was followed according to manufacturer's instructions. The amplified RNA (aRNA) was purified using the RNeasy Mini Kit (Qiagen), and the purified aRNA was Cy3 labeled by a reverse transcription reaction as earlier described by Puskas LG, Zvara A, Hackler L, Van Hummelen P: RNA amplification results in reproducible microarray data with slight ratio bias. Biotechniques 2002, 32(6):1330-1340.
 
 
Hybridization protocol Samples were hybridized for 16 h using a HS 4800 Pro automated hybridization station (Tecan Systems Inc., San Jose, CA), as described previously (Weckx et al., 2009), except that with the only difference that 130 µL hybridization mixture was used instead of 210 µL.
Scan protocol Slides were scanned using the Agilent scanner (Agilent) and images were analysed using ArrayVision v7 (GE Healthcare).
Description The bacterial strain used throughout this study was L. plantarum IMDO 130201, an isolate obtained from a 10-day laboratory wheat sourdough fermentation performed through back-slopping (Van der Meulen et al., 2007). The strain was stored at –80°C in wheat sourdough simulation medium (W-SSM; Vrancken et al., 2008), supplemented with 25 % (vol/vol) glycerol as cryoprotectant. W-SSM was also used as the medium to perform simulated wheat sourdough fermentations.
Data processing We apply a background correction, i.e. we subtract the local background for the local foreground intensities. We compute the base 2 log-ratios (ratio of Cy5/Cy3). Per slide, a Loess correction per print tip on the average log-ratios was applied, to remove non-linear dye effects and print-tip effects per array. We average the log-ratios over the replicates (# = 3) on the array.
 
Submission date Sep 02, 2010
Last update date Aug 01, 2011
Contact name Rekin's Janky
E-mail(s) Nucleomics.Bioinformatics@vib.be
Organization name VIB
Department Nucleomics Core
Street address Herestraat 49 Box 816
City Leuven
ZIP/Postal code B-3000
Country Belgium
 
Platform ID GPL10874
Series (1)
GSE23945 Lactobacillus plantarum IMDO 130201, a wheat sourdough isolate, adapts to growth in wheat sourdough simulation medium at different pH values through differential gene expression

Data table header descriptions
ID_REF
VALUE log2 ratio Cy5/Cy3)

Data table
ID_REF VALUE
F000001 0.481562227016838
F000010 -1.20946124931913
F000012 -0.458815281687714
F000014 0.0114516255297912
F000015 -0.118417366577569
F000021 0.15409700246693
F000023 0.751097781161617
F000025 -0.376065705862261
F000027 0.145626715647009
F000029 -0.7317927546744
F000031 0.567079217568513
F000032 -1.17024551817884
F000033 0.279061520151799
F000034 -2.0860914540883
F000035 -0.0600416198247304
F000045 0.306417541979894
F000048 1.33450842088814
F000063 -0.346251813087295
F000065 0.153790457570686
F000070 -1.04531493400193

Total number of rows: 6209

Table truncated, full table size 158 Kbytes.




Supplementary file Size Download File type/resource
GSM590053.txt.gz 667.5 Kb (ftp)(http) TXT
Processed data included within Sample table

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