|
| Status |
Public on Aug 01, 2011 |
| Title |
pH 5.8 12h rep. D / pH 5.8 20h rep. D |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Total RNA at pH 5.8 time point 20h replicate D
|
| Organism |
Lacticaseibacillus rhamnosus GG |
| Characteristics |
strain: GG
medium ph: 5.8
time: 20h
|
| Growth protocol |
Bacterial cells were grown in whey medium in bioreactor at 37 °C. pH was maintained constant either at 5.8 or 4.8.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
One to four milliliters of bacterial culture were mixed with 2–8 mL of RNAprotect Bacteria reagent (Qiagen) and handled according to the manufacturer’s instructions. The cell pellets were stored at –70°C for subsequent RNA extraction. Cells were lysed with 10 mg/mL lysozyme (Amresco), 3 mg/mL proteinase K (Sigma-Aldrich), and 100 U of mutanolysin (Sigma-Aldrich) at 37°C for 30 minutes. The suspension was supplemented with 1 mL of preheated (65°C) TRIzol reagent (Invitrogen) and vortexed for 3 minutes. After incubation at RT for 5 minutes, the cell lysate was homogenized in a MagNA Lyser instrument (Roche) with <106 µm glass beads (Sigma-Aldrich) for four 30 s cycles at 6000 rpm. Between each cycle, the cells were chilled on ice for 1 minute. Cell debris was removed by centrifugation (12000 × g at 4°C for 15 min), and the lysate was extracted with 200 µl of chloroform by vortexing for 15 s. After incubation at RT for 3 min, the phases were separated by centrifugation (12000 × g at 4°C for 15 min). The aqueous phase was mixed with 500 µl of 80% ethanol for total RNA purification with an RNeasy Mini Kit (Qiagen). During RNA purification, DNA was removed using RNase-Free DNase (Qiagen) as described in the manual.
|
| Label |
Cy3
|
| Label protocol |
Five micrograms of RNA were reverse transcribed to cDNA with the SuperScript Indirect cDNA Labeling System (Invitrogen) according to the manufacturer’s protocol except that 6 µg of random primers (Invitrogen, 48190-011) were used instead of anchored oligo(dT)20 primers and random hexamers. The cDNA was fluorescently labeled using Cy3 or Cy5 mono-reactive dyes (Amersham Biosciences) and purified with a column included in the SuperScript Indirect cDNA Labeling System kit.
|
| |
|
| Channel 2 |
| Source name |
Total RNA at pH 5.8 time point 12h replicate D
|
| Organism |
Lacticaseibacillus rhamnosus GG |
| Characteristics |
strain: GG
medium ph: 5.8
time: 12h
|
| Growth protocol |
Bacterial cells were grown in whey medium in bioreactor at 37 °C. pH was maintained constant either at 5.8 or 4.8.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
One to four milliliters of bacterial culture were mixed with 2–8 mL of RNAprotect Bacteria reagent (Qiagen) and handled according to the manufacturer’s instructions. The cell pellets were stored at –70°C for subsequent RNA extraction. Cells were lysed with 10 mg/mL lysozyme (Amresco), 3 mg/mL proteinase K (Sigma-Aldrich), and 100 U of mutanolysin (Sigma-Aldrich) at 37°C for 30 minutes. The suspension was supplemented with 1 mL of preheated (65°C) TRIzol reagent (Invitrogen) and vortexed for 3 minutes. After incubation at RT for 5 minutes, the cell lysate was homogenized in a MagNA Lyser instrument (Roche) with <106 µm glass beads (Sigma-Aldrich) for four 30 s cycles at 6000 rpm. Between each cycle, the cells were chilled on ice for 1 minute. Cell debris was removed by centrifugation (12000 × g at 4°C for 15 min), and the lysate was extracted with 200 µl of chloroform by vortexing for 15 s. After incubation at RT for 3 min, the phases were separated by centrifugation (12000 × g at 4°C for 15 min). The aqueous phase was mixed with 500 µl of 80% ethanol for total RNA purification with an RNeasy Mini Kit (Qiagen). During RNA purification, DNA was removed using RNase-Free DNase (Qiagen) as described in the manual.
|
| Label |
Cy5
|
| Label protocol |
Five micrograms of RNA were reverse transcribed to cDNA with the SuperScript Indirect cDNA Labeling System (Invitrogen) according to the manufacturer’s protocol except that 6 µg of random primers (Invitrogen, 48190-011) were used instead of anchored oligo(dT)20 primers and random hexamers. The cDNA was fluorescently labeled using Cy3 or Cy5 mono-reactive dyes (Amersham Biosciences) and purified with a column included in the SuperScript Indirect cDNA Labeling System kit.
|
| |
|
| |
| Hybridization protocol |
The labeled cDNA samples were hybridized to microarrays following Agilent’s procedure titled “Two-Color Microarray-Based Gene Expression Analysis.” For each microarray, 825 ng of cyanine 3-labeled cDNA and 825 ng of cyanine 5-labeled cDNA were mixed with 11 µl of 10X GE Blocking Agent and 2.2 µl of 25X Fragmentation Buffer. Volume of this fragmentation mix was brought to 55 µl with nuclease-free water and mix was incubated at 60°C for exactly 30 minutes. After incubation, fragmentation reaction was stopped by adding 55 µl of 2X Hi-RPM Hybridization Buffer, mixed gently and centrifuged for one minute at RT at 15800 × g. 100 µl of hybridization sample was loaded onto an array and hybridized at 65°C for 17 hours at 10 rpm with Agilent hybridization oven. Microarrays were washed twice with GE Wash Buffer 1 for one minute at RT and once with prewarmed (37°C) GE Wash Buffer 2 for one minute.
|
| Scan protocol |
Immediately after washing, microarrays were scanned at 5 µm resolution with a GenePix 4200 AL scanner (Axon Instruments) and stored as TIFF images. The fluorescence intensities were quantified and addressed to genomic ORFs with GenePix Pro 6.0 software (Axon Instruments / Molecular Devices Corp.). Microarray image analysis and feature detection were performed using GenePix Pro 6.0 software with default parameters, and results were further improved manually.
|
| Description |
PH58_D12_Cy5_D20_Cy3
|
| Data processing |
Analyses were performed with the Bioconductor package for statistical analysis using the R programming language (Gentleman et al. 2004). The data were preprocessed with limma (Smyth and Speed 2003). The foreground and background median intensity estimates were corrected for the background using the normexp-function (offset set to 50) (Ritchie et al. 2007), normalized within arrays using loess (100 iterations, suspicious spots and probe sequences matching multiple hits or borders of the coding regions were down weight to zero, and intergenic probe sequences were down weight to 0.1) (Smyth and Speed 2003) and normalized between arrays using quantile normalization (Yang and Thorne 2003). Gene expression ratios were obtained by taking the average over the log2-transformed expression ratios of features describing the same gene and matching a single genetic coding locus. Expression ratios between conditions were calculated using linear models implemented in limma (Smyth 2004). Gene expression ratios were calculated for 2798 genes out of the total 2944 genes predicted to be encoded by the genome (95% coverage).
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| |
|
| Submission date |
Apr 28, 2011 |
| Last update date |
Aug 01, 2011 |
| Contact name |
Kati Laakso |
| E-mail(s) |
kati.laakso@valio.fi
|
| Organization name |
Valio Ltd
|
| Department |
R&D
|
| Street address |
Meijeritie 4
|
| City |
Helsinki |
| ZIP/Postal code |
00370 |
| Country |
Finland |
| |
|
| Platform ID |
GPL10580 |
| Series (1) |
| GSE28903 |
Growth phase-associated changes in Lactobacillus rhamnosus GG |
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