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Sample GSM324186 Query DataSets for GSM324186
Status Public on Mar 24, 2009
Title Temporal gene expression and probiotic attributes of Lactobacillus acidophilus during growth in milk [Time 12 h vs. 4 h]
Sample type RNA
 
Channel 1
Source name Time 12h
Organism Lactobacillus acidophilus NCFM
Characteristics RNA samples were obtained from two biological replicates at time 12h (pH= 4.9; ≈ 1.5 X 108 cfu/ml)
Extracted molecule total RNA
Extraction protocol One-hundred ml aliquots of L. acidophilus cells growing in SM were harvested by centrifugation for 10 min at 3,220 x g, and frozen immediately in a dry ice/ethanol bath (the total time of each sampling process was 5 min). RNA isolation was performed as described previously (Azcarate-Peril et al., 2005) with the following modifications: 5 ml Trizol® Reagent (Invitrogen, Carlsband, CA) was added to the cell pellets and they were homogenized in a Mini-Beadbeater-8 cell disruptor (Biospec Products, Bartlesville, OK) for seven 40-sec cycles (and chilled on ice for 40 sec between cycles), the phases were separated by centrifugation (3,220 x g, 20 min, 4º C). The aqueous phase was removed to a fresh tube and 2.1 ml of Trizol and 1 ml of chloroform were added. The mixture was vortexed for 15 s and centrifuged to separate the phases. The Trizol step was repeated twice and RNA was precipitated from the final aqueous phase by adding 1 volume of isopropanol, followed by incubation at room temperature for 10 min and centrifugation (11,600 x g 10 min, 4º C). Purity and quality of RNA samples were determined by electrophoresis on agarose gels. NanoDrop (ND-3300, NanoDrop Technologies, DE) was used as an UV/VIS spectrophotometer for quantification of the RNA samples.
Label Cy3
Label protocol Reverse transcription and labeling of identical amounts (20 µg) of DNAse treated (Invitrogen, Carlsband, CA) RNA was performed with the SuperScript™ Indirect cDNA Labeling System for DNA Microarrays (Invitrogen) according to the manufacturer’s directions. Coupling of the Cy3 and Cy5 dyes (Amersham Biosciences, Piscataway, NJ) to the AA-dUTP labeled cDNA and hybridization of samples to microarrays were performed according to the protocols outlined in the TIGR protocols website (www.tigr.org/tdb/microarray/protocolsTGR.shtml) and described previously (Azcarate-Peril et al., 2005).
 
Channel 2
Source name Time 4h
Organism Lactobacillus acidophilus NCFM
Characteristics RNA samples were obtained from two biological replicates at time 4h (pH= 5.8; ≈ 3.8 X 107 cfu/ml)
Extracted molecule total RNA
Extraction protocol One-hundred ml aliquots of L. acidophilus cells growing in SM were harvested by centrifugation for 10 min at 3,220 x g, and frozen immediately in a dry ice/ethanol bath (the total time of each sampling process was 5 min). RNA isolation was performed as described previously (Azcarate-Peril et al., 2005) with the following modifications: 5 ml Trizol® Reagent (Invitrogen, Carlsband, CA) was added to the cell pellets and they were homogenized in a Mini-Beadbeater-8 cell disruptor (Biospec Products, Bartlesville, OK) for seven 40-sec cycles (and chilled on ice for 40 sec between cycles), the phases were separated by centrifugation (3,220 x g, 20 min, 4º C). The aqueous phase was removed to a fresh tube and 2.1 ml of Trizol and 1 ml of chloroform were added. The mixture was vortexed for 15 s and centrifuged to separate the phases. The Trizol step was repeated twice and RNA was precipitated from the final aqueous phase by adding 1 volume of isopropanol, followed by incubation at room temperature for 10 min and centrifugation (11,600 x g 10 min, 4º C). Purity and quality of RNA samples were determined by electrophoresis on agarose gels. NanoDrop (ND-3300, NanoDrop Technologies, DE) was used as an UV/VIS spectrophotometer for quantification of the RNA samples.
Label Cy5
Label protocol Reverse transcription and labeling of identical amounts (20 µg) of DNAse treated (Invitrogen, Carlsband, CA) RNA was performed with the SuperScript™ Indirect cDNA Labeling System for DNA Microarrays (Invitrogen) according to the manufacturer’s directions. Coupling of the Cy3 and Cy5 dyes (Amersham Biosciences, Piscataway, NJ) to the AA-dUTP labeled cDNA and hybridization of samples to microarrays were performed according to the protocols outlined in the TIGR protocols website (www.tigr.org/tdb/microarray/protocolsTGR.shtml) and described previously (Azcarate-Peril et al., 2005).
 
 
Hybridization protocol Coupling of the Cy3 and Cy5 dyes (Amersham Biosciences, Piscataway, NJ) to the AA-dUTP labeled cDNA and hybridization of samples to microarrays were performed according to the protocols outlined in the TIGR protocols website (www.tigr.org/tdb/microarray/protocolsTGR.shtml) and described previously (Azcarate-Peril et al., 2005).
Scan protocol After acquisition of fluorescence intensities at 10-µm resolution using a ScanArray 4000 Microarray Scanner (Packard Biochip BioScience; Biochip Technologies LLC, Billerica, MA),
Description signal intensities (stored as TIFF files) were quantified, and the local background was subtracted using the QuantArray 3.0 software package (Packard BioScience).
Data processing data was log2 transformed and imported into JMP Genomics (SAS, Cary, NC). Loess normalization was applied to pre-processed data. Following normalization, gene-specific effects were modeled in terms of the residuals. A Mixed Model Analysis was applied to the pre-normalized data (Cui & Churchill, 2003). False discovery rate (FDR) was selected to adjust for the large number of multiple hypothesis tests across all genes. The default value of alpha (0.05) was used. The model-based approach, step-down quadratic regression method was applied to 791 significant genes for pattern recognition (Liu et al., 2005).
 
Submission date Sep 24, 2008
Last update date Oct 06, 2008
Contact name Todd Robert Klaenhammer
E-mail(s) [email protected], [email protected], [email protected]
Phone 919-515-2972
Fax 919 513 0014
Organization name North Carolina State University
Department Department of Food, Bioprocessing, and Nutrition Sciences
Street address
City Raleigh
State/province NC
ZIP/Postal code 27695
Country USA
 
Platform ID GPL1401
Series (1)
GSE12924 Temporal gene expression and probiotic attributes of Lactobacillus acidophilus during growth in milk

Data table header descriptions
ID_REF
RATIO Ratio Cy3 vs. Cy5
VALUE Log2 transformed ratio Cy3/Cy5
ch1 Intensity Cy3 Intensity values
ch1 Background Cy3 Intensity Background values
ch1 Intensity Std Dev Cy3 Intensity Standard deviations
ch1 Background Std Dev Cy3 Background Standard deviations
ch2 Intensity Cy5 Intensity values
ch2 Background Cy5 Intensity Background values
ch2 Intensity Std Dev Cy5 Intensity Standard deviations
ch2 Background Std Dev Cy3 Background Standard deviations

Data table
ID_REF RATIO VALUE ch1 Intensity ch1 Background ch1 Intensity Std Dev ch1 Background Std Dev ch2 Intensity ch2 Background ch2 Intensity Std Dev ch2 Background Std Dev
1 1.281628161 0.357977753 5181.943359 2234.914795 1416.715942 1419.593384 8780.333008 4351.069824 286.986633 1576.073486
2 1.033387326 0.047381096 7087.169922 2885.558105 3280.148926 1912.193604 9386.615234 4294.899414 1168.311401 1559.477783
3 1.514315629 0.598665938 5366.893066 2128.155029 2637.05957 1496.814697 9300 3548.550293 3201.213379 1357.725952
4 0.667223683 -0.583757596 38521.5 3141.860352 22313.7168 3247.008301 32642.71875 4959.922363 20135.58008 1811.304321
5 0.535835065 -0.9001391 24585.34766 3012.852783 17192.49805 1954.69165 18549.02148 4993.488281 11497.30859 1503.862183
6 0.474686441 -1.074953255 25702.42188 3957.434082 16576.23633 4623.157227 17396.99023 5292.37207 7901.635742 3095.969971
7 1.533458772 0.61678938 18362.14453 2006.116333 16905.38086 2550.761475 32518.44727 3105.736328 20280.31641 1100.464111
8 1.688891124 0.756076326 11319.77539 1673.713135 9618.792969 1137.338379 21926.71289 2822.162842 15939.31641 1225.347534
9 1.507836702 0.592480194 16915.00586 2476.961182 12689.97363 1804.696289 29187.0625 3657.240234 17073.33789 1511.912476
10 1.875206015 0.907049102 7696.322754 1519.224854 5370.881836 1205.201172 16483.79297 2900.077637 11509.9668 1117.997559
11 1.7066149 0.771137549 9638.058594 2782.736328 5233.485352 2359.804199 17626.17969 3906.356689 10136.2207 1530.760986
12 1.975036293 0.981879164 7621.196289 2118.775146 4676.037598 5283.501953 14802.47461 2058.232666 9272.483398 812.404114
13 1.487244963 0.572642292 19155.5293 1962.705444 15161.66699 1348.133545 32805.40234 2819.658936 20465.87695 980.583191
14 1.598120528 0.676376218 14502.19922 2017.186035 11305.73145 1500.351318 26367.79102 2969.5271 17487.30469 1372.332397
15 1.51579529 0.600074929 17301.44531 2438.713135 12763.84473 1890.102417 29702.97852 3283.496094 17632.11523 1226.290527
16 1.000906892 0.001307776 36715.80078 1408.651123 24063.95313 979.086182 44432.01563 2989.945801 21411.07422 1198.221436
17 0.957211213 -0.063090798 43812.00391 2880.782959 20735.37891 3164.774414 49958.70703 4012.720947 18425.70508 1496.760376
18 1.045304695 0.063923534 39478.42578 1413.790649 24823.7207 1183.217041 48870.44531 2209.914795 20366.02734 953.075623
19 0.816281911 -0.292860608 50712.75391 2233.038818 23994.2168 2620.512939 49448.3125 3041.116211 24245.83008 1207.621216
20 0.892106729 -0.164711775 47276.71094 2088.418701 25118.02344 1563.937134 50450.11719 3175.519287 23406.66992 1486.562012

Total number of rows: 5685

Table truncated, full table size 681 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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