NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM27286 Query DataSets for GSM27286
Status Public on Sep 01, 2004
Title Sporulation spoIIID mutant Hour 3.5 exp. 2
Sample type RNA
 
Channel 1
Source name spoIIID mutant (strain PE456)
Organism Bacillus subtilis
Extracted molecule total RNA
 
Channel 2
Source name spoIIID+ (strain PE452)
Organism Bacillus subtilis
Extracted molecule total RNA
 
 
Description Strains PE452 and PE456 were grown in parallel in hydrolysed casein medium at 37°C to an OD600 of 0.6. Sporulation was induced by resuspension in Sterlini-Mandelstam medium at 37C. Three hour and thirty minutes after resuspension, 25 ml of each culture were collected for RNA isolation and immediately mixed with an equal volume of methanol at –20C.
RNA was isolated with a Hot Phenol/Trizol procedure.
cDNA was prepared from 50 ug tot RNA and fluorescently labeled using Superscript Reverse Transcriptase and Cy5-dUTP for the RNA sample from strain PE456 and Cy3-dUTP for the RNA sample from strain PE452.
Protocols for RNA isolation, cDNA preparation and labeling, hybridization to the microarrays and washing procedure can be found at http://mcb.harvard.edu/losick
This is the second repetition of the experiment at this time point (note the dye swap).
 
Submission date Jul 23, 2004
Last update date Oct 28, 2005
Contact name Patrick Yves Eichenberger
E-mail(s) peichenb@mcb.harvard.edu
Phone 617-495-0532
Fax 617-496-4642
URL http://mcb.harvard.edu/losick
Organization name Harvard University
Department Molecular and Cellular Biology
Lab Losick
Street address 16 Divinity Avenue
City Cambridge
State/province MA
ZIP/Postal code 02138
Country USA
 
Platform ID GPL1353
Series (1)
GSE1620 Sporulation in Bacillus subtilis (mother cell)

Data table header descriptions
ID_REF
CH1_MEDIAN channel1 median signal
CH1_MEAN channel1 mean signal
CH1_SD channel1 signal standard deviation
CH1_BKD_MEDIAN channel1 median background
CH1_BKD_MEAN channel1 mean background
CH1_BKD_SD channel1 background standard deviation
CH2_MEDIAN channel2 median signal
CH2_MEAN channel2 mean signal
CH2_SD channel2 signal standard deviation
CH2_BKD_MEDIAN channel2 median background
CH2_BKD_MEAN channel2 mean background
CH2_BKD_SD channel2 background standard deviation
VALUE log ratio (log2 of PRE_VALUE)
FLAGS user defined flag (default=0, bad=-100, empty=-75)
PRE_VALUE ratio channel1 median signal minus median background and channel2 median signal minus median background, not normalized

Data table
ID_REF CH1_MEDIAN CH1_MEAN CH1_SD CH1_BKD_MEDIAN CH1_BKD_MEAN CH1_BKD_SD CH2_MEDIAN CH2_MEAN CH2_SD CH2_BKD_MEDIAN CH2_BKD_MEAN CH2_BKD_SD VALUE FLAGS PRE_VALUE
1 9095 8911 1218 852 873 228 8005 7951 1010 1103 1165 612 0.2558033 0 1.194
2 2923 2995 555 856 870 194 3196 3155 393 1138 1187 593 0.0057593 0 1.004
3 6993 7064 1295 868 883 206 7276 7260 1181 1172 1230 592 0.0043223 0 1.003
4 1583 1624 424 835 853 184 2011 2071 500 1163 1201 280 -0.1811493 0 0.882
5 2676 2672 391 810 816 149 3291 3301 475 1138 1151 166 -0.2058963 0 0.867
6 1669 1791 685 833 843 148 2253 2317 495 1150 1155 151 -0.3997303 0 0.758
7 4886 4780 702 863 879 164 4091 4041 467 1177 1202 240 0.4657133 0 1.381
8 1839 1863 361 886 893 157 2097 2153 282 1196 1205 187 0.0813403 0 1.058
9 1692 1709 305 869 883 153 2074 2132 540 1160 1167 161 -0.1520033 0 0.9
10 5114 4825 1563 831 842 154 6267 5940 1913 1141 1145 154 -0.2584253 0 0.836
11 2781 2861 530 817 821 144 3516 3618 700 1133 1131 149 -0.2792843 0 0.824
12 2784 2671 742 796 798 144 2937 2880 686 1111 1120 148 0.1230043 0 1.089
13 1609 1658 340 809 824 158 2252 2349 384 1129 1143 167 -0.4900513 0 0.712
14 1137 1131 200 804 809 141 1567 1583 207 1136 1137 137 -0.3714603 0 0.773
15 2462 2433 645 802 807 147 2522 2536 497 1129 1135 154 0.2533843 0 1.192
16 1279 1308 344 837 846 161 1739 1751 273 1159 1171 162 -0.3921373 0 0.762
17 3969 3955 521 818 823 156 3589 3562 381 1139 1153 161 0.3628913 0 1.286
18 1585 1699 486 849 848 155 1857 1873 308 1115 1121 148 -0.0115883 0 0.992
19 1298 1359 383 856 855 160 1712 1792 543 1126 1131 182 -0.4073643 0 0.754
20 4081 5402 5062 868 881 182 4383 5418 5309 1174 1186 190 0.0014423 0 1.001

Total number of rows: 4623

Table truncated, full table size 332 Kbytes.




Supplementary file Size Download File type/resource
GSM27286-cy3.tif.gz 5.5 Mb (ftp)(http) TIFF
GSM27286-cy5.tif.gz 5.5 Mb (ftp)(http) TIFF

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap