NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM21786 Query DataSets for GSM21786
Status Public on Jun 12, 2004
Title VC1110, Wild-type versus ddm1 Arabidopsis thaliana
Sample type RNA
 
Channel 1
Source name ddm1 poly(A)+ mRNA
Organism Arabidopsis thaliana
Extracted molecule total RNA
 
Channel 2
Source name Wild-type poly(A)+ mRNA
Organism Arabidopsis thaliana
Extracted molecule total RNA
 
 
Description Wild-type and ddm1 bolting plants
Total RNA was extracted with Trizol (Invitrogen) from bolting plants, following the manufacturer's instructions. Polyadenylated RNA were then extracted from total RNA with either the MicroPoly(A)purist (Ambion) or the Dynabeads kit (oligo(dT)25, Dynal). For each hybridization experiment, 1ug of poly(A)+ WT and ddm1 RNA were labeled using an indirect labeling procedure. The probes were synthesized from poly(A)+ RNA using random and oligodT primers and Superscript II reverse transcriptase (Invitrogen) to incorporate amine-modified nucleotides (amino allyl-dUTP; Sigma). cDNA samples were purified, concentrated using Microcon 30 spin columns (Millipore) and dried.
Dried cDNA were resuspended in Sodium Bicarbonate buffer 0.05M, pH 9.0 and coupled with Cy3 (Wild-type) or Cy5 (ddm1) amine reactive dyes (Amersham). The labeled cDNA were purified using the Qiagen Qiaquick PCR purification kit and concentrated with Microcon 30 spin columns.
For hybridization, the sample volume was brought to 25ul with a final concentration of 4X SSC, 0.2% SDS. Microarrays were hybridized at 65°C, for approximately 15 hr and washed once in 1XSSC, 0.2%SDS and twice in 0.2XSSC.
Slides were pre-hybridized in BSA 1%, SDS 0.1% for 1 hour before hybridization.
Slides were then scanned with a GenePix 4000A scanner (Axon Instruments). We quantified the fluorescence with the GenePix Pro software.
Sample_series_id: VC110+112
 
Submission date Apr 21, 2004
Last update date Oct 28, 2005
Contact name Matthew Wayne Vaughn
E-mail(s) vaughn@tacc.utexas.edu
Phone (512) 232-7124
Organization name University of Texas at Austin
Department Texas Advanced Computing Center
Lab Vaughn
Street address 10100 Burnet Rd
City Austin
State/province TX
ZIP/Postal code 78758
Country USA
 
Platform ID GPL785
Series (2)
GSE1328 VC110+112 mRNA levels in Wild-type versus ddm1 bolting Arabidopsis thaliana plants
GSE1354 mRNA levels in Wild-type versus ddm1 Arabidopsis thaliana

Data table header descriptions
ID_REF Spot name
F635_MEDIAN Cy5 channel foreground median
F635_MEAN Cy5 channel foreground mean
F635_SD Cy5 channel foreground stdev
B635_MEDIAN Cy5 channel background median
B635_MEAN Cy5 channel background mean
B635_SD Cy5 channel background stdev
PCT_GT_B635+1SD Percent Cy5 channel background > 1 stdev
PCT_GT_B635+2SD Percent Cy5 channel background > 2 stdev
F532_MEDIAN Cy3 channel foreground median
F532_MEAN Cy3 channel foreground mean
F532_SD Cy3 channel foreground stdev
B532_MED Cy3 channel background median
B532_MEAN Cy3 channel background mean
B532_SD Cy3 channel background stdev
PCT_GT_B532+1SD Percent Cy3 channel background > 1 stdev
PCT_GT_B532+2SD Percent Cy3 channel background > 2 stdev
VALUE Natural log of ratio of means
F635_MEDIAN-B635 Foreground median Cy5 - Background Cy5
F532_MEDIAN-B532 Foreground median Cy3 - Background Cy3
F635_MEAN-B635 Foreground mean Cy5 - Background Cy5
F532_MEAN-B532 Foreground mean Cy3 - Background Cy3
FLAGS Present:0, Absent:-50

Data table
ID_REF F635_MEDIAN F635_MEAN F635_SD B635_MEDIAN B635_MEAN B635_SD PCT_GT_B635+1SD PCT_GT_B635+2SD F532_MEDIAN F532_MEAN F532_SD B532_MED B532_MEAN B532_SD PCT_GT_B532+1SD PCT_GT_B532+2SD VALUE F635_MEDIAN-B635 F532_MEDIAN-B532 F635_MEAN-B635 F532_MEAN-B532 FLAGS
pc13a09F.1044.4.2387459.T4B21_1 51 57 22 47 51 18 26 10 70 81 35 65 67 19 33 20 -0.322 4 5 10 16 -50
pc03b01F.977.4.1409029.F4C21_1 169 173 42 47 49 14 100 100 386 379 88 64 65 19 100 100 -1.400 122 322 126 315 0
pc03b03F.1001.4.1410945.F4C21_1 305 287 100 48 50 15 100 96 490 449 165 67 69 18 100 100 -0.719 257 423 239 382 0
pc03b05F.990.4.1413204.F4C21_1 146 143 38 48 51 17 100 90 262 254 58 62 66 20 100 100 -1.029 98 200 95 192 0
pc03b07F.983.4.1415196.F4C21_1 1150 1110 610 46 49 16 100 98 1671 1820 1054 62 65 18 100 100 -0.543 1104 1609 1064 1758 0
pc03b09F.960.4.1417276.F4C21_1 50 52 15 46 50 21 15 1 72 77 25 60 63 23 33 9 -1.585 4 12 6 17 -50
pc03b11F.994.4.1419153.F4C21_1 57 63 20 43 46 17 46 25 134 129 27 60 61 14 96 90 -2.402 14 74 20 69 0
pc03d01F.1198.4.1433545.F4C21_1 38 39 10 44 47 34 0 0 65 70 24 59 61 16 31 20 0 -6 6 -5 11 -50
pc03d03F.977.4.1435723.F4C21_1 132 136 31 46 49 19 96 96 154 152 38 60 63 26 96 87 -0.128 86 94 90 92 0
pc03d05F.989.4.1437691.F4C21_1 75 82 29 46 48 15 71 46 110 121 44 62 67 28 71 37 -0.727 29 48 36 59 0
pc03d07F.1091.4.1439632.F4C21_1 1354 2156 2115 43 45 15 96 92 1107 2279 2236 59 62 17 98 98 0.323 1311 1048 2113 2220 0
pc03d09F.908.4.1441784.F4C21_1 252 232 99 42 46 19 100 94 277 260 108 59 64 27 98 86 -0.054 210 218 190 201 0
pc03d11F.980.4.1443801.F4C21_1 49 59 28 42 44 15 35 20 63 72 27 57 60 19 30 16 0.222 7 6 17 15 -50
pc03f01F.989.4.1458066.F4C21_1 254 256 84 42 43 10 100 100 83 80 22 55 56 14 71 46 2.921 212 28 214 25 0
pc03f03F.1000.4.1460097.F4C21_1 1281 1174 472 43 45 13 100 100 93 95 28 57 59 19 73 46 5.104 1238 36 1131 38 0
pc03f05F.1029.4.1462184.F4C21_1 108 114 41 46 53 27 85 55 151 156 65 62 77 47 77 43 -0.522 62 89 68 94 -100
pc03f07F.939.4.1464333.F4C21_1 57 60 20 42 49 25 30 9 77 82 28 57 71 43 28 0 -0.415 15 20 18 25 -50
pc03f09F.1002.4.1466314.F4C21_1 62 61 14 39 39 10 78 53 109 109 22 53 55 13 96 90 -1.284 23 56 22 56 0
pc03f11F.986.4.1468378.F4C21_1 43 45 12 39 41 11 23 10 60 61 17 51 54 15 30 10 -1.170 4 9 6 10 -50
pc03h01F.909.4.1482593.F4C21_1 188 206 65 38 40 10 100 100 247 257 73 50 52 13 100 100 -0.393 150 197 168 207 0

Total number of rows: 3822

Table truncated, full table size 380 Kbytes.




Supplementary data files not provided
| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap