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Sample GSM21779 Query DataSets for GSM21779
Status Public on Jun 12, 2004
Title EV39, Wild-type versus ddm1 seedlings
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 9 day-old seedlings
Total RNA was extracted with Trizol (Invitrogen) from 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 (ddm1) or Cy5 (wild-type) 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 18 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: EV39+40
 
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)
GSE1327 EV39+40 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
pd03a02F.988.5.4725940_1 792 1001 659 164 174 55 98 96 618 826 634 140 149 78 98 91 0.394 628 478 837 686 0
pd03c02F.997.1.5775600_1 2585 2641 1939 163 185 244 88 82 1656 1905 1518 143 164 260 85 75 0.679 2422 1513 2478 1762 0
pd03e03F.957.4.7348959_1 159 157 27 155 165 86 0 0 164 161 39 140 151 108 1 0 -2.585 4 24 2 21 -50
pd03g03F.1002.1.2504335_1 361 371 116 154 156 38 96 91 283 298 100 141 144 40 91 80 0.544 207 142 217 157 0
pd03a04F.992.5.4728124_1 659 813 528 158 171 143 97 87 524 642 419 152 170 146 91 67 0.430 501 372 655 490 0
pd03c04F.1005.1.5773598_1 2032 3006 2715 153 167 129 97 90 1419 2043 1935 144 158 128 94 81 0.559 1879 1275 2853 1899 0
pd03e05F.992.4.7350939_1 148 147 38 144 148 34 11 2 163 175 106 133 137 39 37 18 -2.907 4 30 3 42 -50
pd03g05F.984.1.2506342_1 212 214 47 140 144 38 76 46 204 201 51 139 144 40 63 36 0.148 72 65 74 62 0
pd03a06F.992.5.4730182_1 141 140 32 141 145 37 10 0 164 160 47 141 147 37 38 8 0 0 23 -1 19 -50
pd03c07F.1078.1.549731_1 152 153 42 141 148 48 20 2 167 170 36 146 155 61 18 0 -0.933 11 21 12 24 -50
pd03e07F.990.4.7352999_1 141 144 29 141 143 31 16 3 173 170 42 146 149 40 36 5 0 0 27 3 24 -50
pd03g07F.988.1.2508376_1 143 144 29 136 140 38 16 1 169 167 42 144 146 39 33 12 -1.837 7 25 8 23 -50
pd03a08F.1029.5.4732110_1 247 263 116 138 143 42 76 61 220 250 121 142 146 39 69 50 0.483 109 78 125 108 0
pd03c09F.1001.1.547605_1 141 147 29 136 151 165 0 0 167 168 44 137 141 60 20 5 -2.585 5 30 11 31 -50
pd03e09F.1021.4.7354943_1 156 157 37 136 139 31 38 15 166 167 46 135 139 37 42 17 -0.632 20 31 21 32 -50
pd03g09F.984.5.19519390_1 154 154 36 140 148 94 2 0 161 166 37 147 151 44 28 3 0.000 14 14 14 19 -50
pd03a10F.1005.5.4734240_1 741 817 304 139 148 94 100 97 735 797 348 149 156 47 98 98 0.039 602 586 678 648 0
pd03c11F.955.1.545657_1 146 150 41 136 141 38 18 7 167 173 62 148 154 43 35 7 -0.926 10 19 14 25 -50
pd03e11F.992.4.7357000_1 151 154 39 132 135 30 40 20 166 175 43 144 147 36 38 16 -0.212 19 22 22 31 -50
pd03g11F.1020.5.19521453_1 130 130 28 135 137 31 11 1 161 165 40 144 147 36 27 13 0 -5 17 -5 21 -50

Total number of rows: 5748

Table truncated, full table size 615 Kbytes.




Supplementary data files not provided
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