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Sample GSM21781 Query DataSets for GSM21781
Status Public on Jun 12, 2004
Title VC109, 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 eight day-old seedlings
Total RNA was extracted with Trizol (Invitrogen) from seedlings, 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: VC109+111
 
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)
GSE1326 VC109+111 mRNA levels in Wild-type versus ddm1 Arabidopsis thaliana seedlings
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 60 62 18 60 63 19 18 1 75 74 20 80 82 19 10 3 0 0 -5 2 -6 -50
pc03b01F.977.4.1409029.F4C21_1 243 240 55 69 71 22 100 100 152 153 28 85 87 18 96 85 1.377 174 67 171 68 0
pc03b03F.1001.4.1410945.F4C21_1 306 299 58 66 71 24 100 100 227 227 49 86 90 20 100 100 0.767 240 141 233 141 0
pc03b05F.990.4.1413204.F4C21_1 71 76 27 65 68 21 29 15 76 80 20 81 83 18 16 4 0 6 -5 11 -1 -50
pc03b07F.983.4.1415196.F4C21_1 1061 1097 504 60 64 22 100 100 983 959 473 79 80 17 100 97 0.147 1001 904 1037 880 0
pc03b09F.960.4.1417276.F4C21_1 56 60 20 59 62 21 14 2 67 69 16 74 76 16 10 1 -1.222 -3 -7 1 -5 -50
pc03b11F.994.4.1419153.F4C21_1 62 67 23 56 59 17 29 16 68 69 17 72 73 15 14 4 0 6 -4 11 -3 -50
pc03d01F.1198.4.1433545.F4C21_1 47 48 16 57 59 18 6 0 61 64 17 74 75 16 9 2 -0.379 -10 -13 -9 -10 -50
pc03d03F.977.4.1435723.F4C21_1 53 55 17 57 60 22 11 0 68 67 14 73 73 14 6 0 -0.322 -4 -5 -2 -6 -50
pc03d05F.989.4.1437691.F4C21_1 67 70 22 57 61 21 31 6 69 71 16 73 74 15 15 4 0 10 -4 13 -2 -50
pc03d07F.1091.4.1439632.F4C21_1 2671 2604 1366 59 67 48 100 100 1870 1892 1058 74 78 28 100 100 0.540 2612 1796 2545 1818 0
pc03d09F.908.4.1441784.F4C21_1 60 66 26 57 63 40 11 2 66 67 14 72 76 25 1 0 0 3 -6 9 -5 -50
pc03d11F.980.4.1443801.F4C21_1 60 64 23 55 57 17 33 15 71 73 15 68 70 14 21 9 0.737 5 3 9 5 -50
pc03f01F.989.4.1458066.F4C21_1 315 305 109 57 59 18 100 96 61 62 14 67 69 13 9 0 0 258 -6 248 -5 0
pc03f03F.1000.4.1460097.F4C21_1 758 690 285 54 56 16 100 100 59 61 12 68 68 13 7 0 0 704 -9 636 -7 0
pc03f05F.1029.4.1462184.F4C21_1 55 56 17 54 56 17 19 3 62 62 15 69 69 13 9 3 0 1 -7 2 -7 -50
pc03f07F.939.4.1464333.F4C21_1 101 101 22 50 53 14 96 84 100 102 18 63 65 13 96 71 0.463 51 37 51 39 0
pc03f09F.1002.4.1466314.F4C21_1 59 62 21 51 53 15 37 17 66 67 13 66 67 14 15 3 16.610 8 0 11 1 -50
pc03f11F.986.4.1468378.F4C21_1 55 60 23 54 60 39 6 0 62 64 18 67 68 15 9 2 0 1 -5 6 -3 -50
pc03h01F.909.4.1482593.F4C21_1 65 68 23 52 58 39 15 0 64 65 16 68 70 15 14 2 0 13 -4 16 -3 -50

Total number of rows: 3822

Table truncated, full table size 372 Kbytes.




Supplementary data files not provided

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