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Status
Public on Dec 06, 2006
Title
FOS vs. Fructose Rep#1
Sample type
RNA
Channel 1 Source name
1% FOS, 30 min
Organism
Lacticaseibacillus paracasei Characteristics
strain 1195
Extracted molecule
total RNA
Label
Cy5
Channel 2 Source name
1% fructose, 30 min
Organism
Lacticaseibacillus paracasei Characteristics
strain 1195
Extracted molecule
total RNA
Label
Cy3
Description
L. paracasei (2% [v/v] inoculum from overnight culture in MRS broth) were grown in 300 ml of modified MRS basal medium (with no added sugar source) until the cells reached a final OD625 nm of ca. 0.3. The culture was then divided into two 150-ml portions, where FOS or fructose was added to a 1% final concentration. Cells were collected for total RNA isolation after 30 min incubation (OD625 nm 0.3 – 0.4).
Data processing
Hybridized arrays were scanned with ScanArray 5000 (Packard Instrument Co., Downers Grove, IL) at 10 micrometer per pixel resolution. The relative fluorescent intensity of Cy3 and Cy5 for each of the 7,680 features was quantified from TIFF image files (generated by ScanArray 5000) using ImaGene v.4.2 (BioDiscovery, Inc., Marina Del Rey, CA). The fluorescent signal intensities of the array spots for each channel were obtained by subtracting the median intensities of background pixels from the mean pixel intensities. Global mean normalization of the spot intensities from each channel on individual slides was performed using SNOMAD. All array data were composited using a Perl-based program, FormatALL (J. Wise and A. K. Benson, unpublished data), yielding the ratio representing the fold change in genes expression levels in FOS conditions (Cy5) with relative to FOS + glucose (Cy3).
Submission date
Sep 20, 2006
Last update date
Dec 06, 2006
Contact name
Yong Jun Goh
E-mail(s)
[email protected] Organization name
University of Nebraska
Department
Food Science and Technology
Street address
332 Food Industry Complex
City
Lincoln
State/province
NE
ZIP/Postal code
68583-0919
Country
USA
Platform ID
GPL4355 Series (1)
GSE5890 Identification of candidate genes involved in fructooligosaccharides (FOS) utilization by Lactobacillus paracasei
Data table header descriptions ID_REF VALUE log2 of PRE_VALUE
CH1_SIG_MEAN channel 1 mean signal
CH1_BKD_MEAN channel 1 mean background signal
CH1_SIG_MED channel 1 median signal
CH1_BKD_MED channel 1 median backgroud signal
CH1_SIG_ SD channel 1 standard deviation of intensities over local signal region
CH1_BKD_SD channel 1 standard deviation of intensities over local background region
CH2_SIG_MEAN channel 2 mean signal
CH2_BKD_MEAN channel 2 mean background signal
CH2_SIG_MED channel 2 median signal
CH2_BKD_MED channel 2 median backgroud signal
CH2_SIG_ SD channel 2 standard deviation of intensities over local signal region
CH2_BKD_SD channel 2 standard deviation of intensities over local background region
PRE_VALUE normalized Cy5/normalized Cy3 ratio
Data table ID_REF VALUE CH1_SIG_MEAN CH1_BKD_MEAN CH1_SIG_MED CH1_BKD_MED CH1_SIG_ SD CH1_BKD_SD CH2_SIG_MEAN CH2_BKD_MEAN CH2_SIG_MED CH2_BKD_MED CH2_SIG_ SD CH2_BKD_SD PRE_VALUE 1
1.7114
16855.41121
4645.663934
9054
3897.5
15576.99821
3958.543782
5043.093023
1314.76943
3090.5
689.5
4658.294275
2894.353475
3.274862542
2
0.5649
6439.902174
4394.594828
6099
3848
1848.147175
2873.544852
2297.950617
915.3185841
1989
705
1043.740861
965.8818729
1.479285375
3
1.3285
14262.05369
4458.07037
12002
3753.5
9168.693976
3153.754046
5044.629371
1140.888087
4315
789
3486.304346
1301.130505
2.511432651
4
1.6197
11071.63448
4188.552727
10241
3839
4948.61901
1967.101652
3349.041667
1109.19
2898.5
683
2055.411724
1275.791177
3.07300785
5
0.3731
8187.913333
3905.988
7162
3628
4550.143592
1921.451785
4384.632353
1078.469231
3740.5
841.5
2676.308396
1231.196705
1.295134322
6
-0.3026
5917.027027
3365.5
5741
3299.5
1355.106528
567.4007457
4102.817568
955.8219178
3659.5
750.5
1842.695089
788.3733095
0.810781873
7
0.6446
4015.831081
2920.160959
3943
2914
588.2101044
406.8517006
1496.062069
795.2
1428
617
926.2187514
676.8056156
1.563317763
8
-0.4003
4457.372671
2968.894958
4340
3001
691.5129494
475.1608767
2703.028571
738.6160714
2320
551
1662.618394
641.7562781
0.757721565
9
1.7013
3416.093023
2473.302583
3350
2444
520.3250243
432.8883053
1003.365517
713.4527559
849
536
703.9548067
595.6004544
3.251979788
10
-0.4887
3730.951724
2248.220339
3681
2211
644.2716211
392.5621906
2764.430556
683.9594595
2414.5
495.5
1566.464422
588.1332858
0.712690211
11
0.0983
2763.351955
2035.73444
2706
2029
506.3776652
339.6093619
1323.744186
644.0604839
1138.5
504
862.6407291
483.3243422
1.070523706
12
-0.0958
9183.856459
1859
8474
1803
4741.234495
355.3983947
8600.924731
772.9313305
7422.5
561
4994.261801
708.0861799
0.935725937
13
0.2321
2167.031496
1559.265176
2138
1563
326.5255398
292.5516529
1005.201389
487.7525424
806.5
347
747.1087473
404.1568119
1.174543773
14
0.1174
2997.97546
1416.610738
2909
1363
771.3511526
420.1652872
2035.219512
577.4832215
1918
432.5
1091.556201
490.2505195
1.084808502
15
-0.1130
2162.434286
1342.358885
2121
1340
418.6898135
272.6709804
1414.06135
527.1546392
1202
366
824.3662648
452.0094806
0.924646742
16
0.2621
1642.891192
1343.581498
1626
1316
327.0082212
305.6054671
781.7512953
532.1681416
627
374
567.9443163
477.2781494
1.199238368
17
0.1118
2664.878453
1284.231317
2572
1247
865.9060892
295.2856266
1912.25
634.5516129
1811
515.5
1049.224408
490.4034767
1.080573593
18
-0.2503
1722.305785
1187.174545
1667
1144
351.5077052
299.0935009
1213.8
577.3067729
1077
379
751.1036716
585.9869102
0.840749307
19
0.4205
1857.518293
1171.391489
1792
1132
461.9737543
307.5806345
1162.79021
650.1333333
1029
465
838.970055
547.76814
1.33837433
20
0.3464
5786.291005
1174.982456
5457
1142
2430.19563
315.0166518
4499.680982
872.7664975
4147
739
2161.048884
664.5708407
1.271413641
7680 1044 Kbytes .Supplementary data files not provided
