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Status
Public on Dec 06, 2006
Title
FOS vs. FOS+glucose Rep#1
Sample type
RNA
Channel 1 Source name
FOS only
Organism
Lacticaseibacillus paracasei Characteristics
strain 1195
Extracted molecule
total RNA
Label
Cy5
Channel 2 Source name
FOS+glucose
Organism
Lacticaseibacillus paracasei Characteristics
strain 1195
Extracted molecule
total RNA
Label
Cy3
Description
Cells (2% inoculum from overnight culture in MRS broth) were grown in 100 ml of modified MRS supplemented with 2% FOS until an OD625nm 0.6. The culture was split into two 50-ml portions, and glucose was added to one of the portions at a 2% final concentration. Both cultures were grown for another 60 min (OD625 ca. 1.0) before harvested for total RNA isolation.
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 All array data were composited using a Perl-based program, FormatALL (J. Wise and A. K. Benson, unpublished data), yielding the ratio representing the fold change in genes expression levels in FOS conditions (Cy5) with relative to FOS + glucose (Cy3).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 21, 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
-0.5506
1093.170455
914.8488746
733.5
786
1019.211786
646.5827757
973.1590909
711.9807074
873.5
504
654.8013385
612.673352
0.682757805
2
-2.1672
1224.601036
1132.569106
1051
981.5
829.4269583
1025.675142
1134.166667
720.805668
962
556
836.2069205
670.148931
0.222642995
3
0.2221
2830.412429
1128.447699
2677
975
1351.293991
816.8245155
2191.595628
732.4894515
2021
585
1150.738247
617.4347545
1.166443373
4
-0.1640
1907.4375
1245.075221
1766.5
963.5
1060.737414
1966.637476
1488.723958
746.6299559
1169.5
540
1256.230137
725.5650052
0.892558458
5
-0.6994
2775.836257
1139.654135
2411
990.5
1733.026649
748.1991969
3404.794737
747.8286853
3043.5
556
1832.517215
619.5291736
0.615808441
6
-1.4366
2228.658333
1043.541176
2103.5
893.5
793.6171463
782.4690605
3983.22293
775.2376238
3629
596
1911.167861
676.3951939
0.36942724
7
-1.3425
1203.113636
1031.773333
986.5
870
705.0451055
784.6737067
1281.577778
847.088
1232
710
739.7411706
657.2820239
0.394348295
8
-0.4975
10892.85714
1163.365217
10017
963.5
6041.54092
886.0351434
14670.39175
934.1869919
13645
714
8066.893992
740.1827323
0.708310053
9
0.2751
1683.36
1062.861017
1409
901
977.1012181
749.9951532
1199.916667
687.1491525
974
510
888.7410532
588.1950312
1.210098078
10
-1.2494
1965.475524
968.9080882
1863
832
775.728873
919.4675623
3130.977143
761.7254098
2913
559
1471.419618
699.4626527
0.420625391
11
-0.6431
1957.303867
875.8210117
1843
760
804.6541424
609.1906213
2326.634921
637.76
2147
480.5
1192.02807
511.5992322
0.640356987
12
-0.8459
7014.653846
922.5436893
6801.5
724
2772.757838
694.0706334
11811.29237
861.7794118
11812
648
5128.382069
729.9103459
0.556381839
13
-0.6464
1193.5
955.3011765
1112
736
483.0121634
1548.57221
1124.0625
751.2164706
1215
516
640.6516671
782.6051248
0.638866462
14
-1.2285
1332.217391
826.0053908
1059
648
874.236095
631.6751869
1970.652174
784.5067385
1795
544
1263.600398
768.9685337
0.426770601
15
-0.5178
2290.59589
954.4966887
2123
837
1004.453641
641.2553693
2639.459627
726.5233333
2564
495.5
1218.075271
639.86106
0.698454625
16
938.5507246
978.5368957
843
850
609.3883257
687.8432453
1023.246377
718.9516539
856
539
741.7455208
624.1306791
0
17
-0.2879
5294.009569
1047.904762
4936
868
2175.955262
718.0788158
6040.033493
856.008658
5724
687
2775.856346
718.2847052
0.819074936
18
2.1471
1311.4375
760.3263708
1255.5
616
610.5212905
567.4247864
814.875
690.4543081
655.5
480
618.6917523
574.1937495
4.429417011
19
-0.7835
1064.680233
850.1013216
1003
702
626.5131887
668.7340287
1035.97093
666.6123348
906
436
732.5028092
809.8464147
0.580950095
20
-0.6509
5103.224359
861.993311
4895.5
767
2167.614018
559.6306952
7373.264706
714.1164384
7327.5
540.5
3864.628725
623.867308
0.636902931
7680 1029 Kbytes .Supplementary data files not provided
