NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM21787 Query DataSets for GSM21787
Status Public on Jun 12, 2004
Title VC112, Wild-type versus ddm1 Arabidopsis thaliana
Sample type RNA
 
Channel 1
Source name Wild-type poly(A)+ mRNA
Organism Arabidopsis thaliana
Extracted molecule total RNA
 
Channel 2
Source name ddm1 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 Cy5 (Wild-type) or Cy3 (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 50 57 25 49 54 63 3 0 55 64 31 51 55 20 23 10 -2.000 1 4 8 13 -50
pc03b01F.977.4.1409029.F4C21_1 357 344 132 48 50 13 100 100 186 188 71 50 53 15 100 99 1.184 309 136 296 138 0
pc03b03F.1001.4.1410945.F4C21_1 392 378 170 49 51 15 100 100 282 258 94 52 54 17 98 96 0.577 343 230 329 206 0
pc03b05F.990.4.1413204.F4C21_1 206 210 48 48 50 10 100 100 128 130 34 50 50 12 96 96 1.018 158 78 162 80 0
pc03b07F.983.4.1415196.F4C21_1 1243 1514 865 48 49 11 100 100 667 741 419 49 51 14 100 100 0.951 1195 618 1466 692 0
pc03b09F.960.4.1417276.F4C21_1 61 62 17 47 48 11 55 30 57 58 16 49 50 13 29 11 0.807 14 8 15 9 -50
pc03b11F.994.4.1419153.F4C21_1 93 96 25 44 46 10 100 90 64 65 16 47 48 12 62 34 1.527 49 17 52 18 0
pc03d01F.1198.4.1433545.F4C21_1 41 43 11 45 54 111 0 0 53 55 18 49 61 120 0 0 0 -4 4 -2 6 -50
pc03d03F.977.4.1435723.F4C21_1 48 50 12 45 53 110 0 0 51 54 15 48 60 119 0 0 0.000 3 3 5 6 -50
pc03d05F.989.4.1437691.F4C21_1 74 75 21 46 48 11 78 56 72 73 18 50 52 12 78 40 0.348 28 22 29 23 0
pc03d07F.1091.4.1439632.F4C21_1 915 1515 1278 46 48 14 98 98 652 1060 844 48 50 12 100 100 0.525 869 604 1469 1012 0
pc03d09F.908.4.1441784.F4C21_1 51 57 21 43 46 17 26 13 52 53 14 46 48 14 26 7 0.415 8 6 14 7 -50
pc03d11F.980.4.1443801.F4C21_1 49 52 14 43 45 11 32 13 54 57 18 46 48 15 30 13 -0.415 6 8 9 11 -50
pc03f01F.989.4.1458066.F4C21_1 62 68 26 43 44 12 62 37 203 224 105 45 47 12 100 100 -3.056 19 158 25 179 0
pc03f03F.1000.4.1460097.F4C21_1 59 60 18 42 44 10 60 40 709 646 420 46 47 13 100 100 -5.285 17 663 18 600 0
pc03f05F.1029.4.1462184.F4C21_1 41 42 8 42 43 10 8 1 47 49 16 45 46 11 20 9 0 -1 2 0 4 -50
pc03f07F.939.4.1464333.F4C21_1 71 71 18 42 43 10 87 75 64 67 17 45 46 12 68 34 0.610 29 19 29 22 0
pc03f09F.1002.4.1466314.F4C21_1 53 57 16 42 44 11 46 26 51 53 13 46 48 14 21 7 1.138 11 5 15 7 -50
pc03f11F.986.4.1468378.F4C21_1 41 42 9 42 44 10 9 2 41 45 15 43 46 14 15 5 -1.000 -1 -2 0 2 -50
pc03h01F.909.4.1482593.F4C21_1 45 50 17 39 41 9 40 25 53 54 14 43 45 11 44 15 -0.737 6 10 11 11 -50

Total number of rows: 3822

Table truncated, full table size 372 Kbytes.




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