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Sample GSM21802 Query DataSets for GSM21802
Status Public on Jun 12, 2004
Title EV50, Wild-type seedlings H3mK4
Sample type genomic
 
Channel 1
Source name Total ChIP wild-type DNA
Organism Arabidopsis thaliana
Extracted molecule genomic DNA
 
Channel 2
Source name H3mK4 ChIP wild-type DNA
Organism Arabidopsis thaliana
Extracted molecule genomic DNA
 
 
Description Wild-type seedlings, 9 days
Chromatin immunoprecipitation with antibodies raised against dimethyl histone-H3 lysine-4 (H3mK4) (Upstate Biotechnology) was performed as previously described in Gendrel et al. (2002) on material from nine-day-old seedlings, except that the immunoprecipitated (IP) DNA was resuspended in 15ul H20. Seven l from each sample (H3mK9, no antibody control, and input DNA) was used for random amplification. The DNA amplification was performed as described at <http://www.microarrays.org>, except that after Round A (Sequenase step), we carried out only a single Round B of 35 cycles. The DNA obtained was quantified and resolved on a 1.5% agarose gel to check that the range of sizes was between 500bp and ~1.5kb.
1.5ug from each sample was labeled with Cy3 (H3mK4) and Cy5 (Total) using the Megaprime DNA labeling kit (Amersham Pharmacia). Labeled DNA samples were then mixed, purified, and concentrated using Microcon YM-30 columns. The volume was brought to 25ul in a final concentration of 4X SSC, 0.2% SDS.
Hybridizations were carried out at 65C for approximately 15 hrs. Slides were washed in 1X SSC, 0.2% SDS once and 0.2X SSC twice.
Slides were scanned with a GenePix 4000A scanner (Axon Instruments). We quantified the fluorescence with the GenePix Pro software.
Sample_series_id: EV49+50
 
Submission date Apr 21, 2004
Last update date May 27, 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)
GSE1333 EV49+50, Histone 3 Lysine 4 methylation in wild-type Arabidopsis thaliana seedlings
GSE1356 Histone methylation in wild type and ddm1 Arabidopsis thaliana seedlings

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_1 123 144 76 38 39 9 98 92 102 118 54 41 43 10 97 86 0.479 85 61 106 77 0
pc03b01F.977.4.1409029.F4C21_1 531 483 269 41 46 18 100 100 352 380 179 44 50 20 100 98 0.670 490 308 442 336 0
pc03b03F.1001.4.1410945.F4C21_1 292 289 127 43 52 23 100 98 226 231 80 45 51 21 100 100 0.460 249 181 246 186 0
pc03b05F.990.4.1413204.F4C21_1 302 278 90 42 44 11 100 100 175 168 47 43 45 12 100 100 0.978 260 132 236 125 0
pc03b07F.983.4.1415196.F4C21_1 569 504 202 43 45 10 100 100 540 495 161 46 49 14 100 100 0.091 526 494 461 449 0
pc03b09F.960.4.1417276.F4C21_1 167 201 120 41 53 51 78 53 148 152 61 45 50 24 96 84 0.291 126 103 160 107 0
pc03b11F.994.4.1419153.F4C21_1 181 368 378 42 57 56 66 53 158 290 263 42 46 22 85 74 0.261 139 116 326 248 0
pc03d01F.1198.4.1433545.F4C21_1 70 105 71 39 42 15 73 50 55 67 31 40 41 8 60 47 1.047 31 15 66 27 0
pc03d03F.977.4.1435723.F4C21_1 92 112 62 38 39 8 90 78 52 57 18 39 40 7 65 46 2.054 54 13 74 18 0
pc03d05F.989.4.1437691.F4C21_1 35 35 4 37 41 16 0 0 39 39 7 40 41 9 8 0 1.000 -2 -1 -2 -1 -50
pc03d07F.1091.4.1439632.F4C21_1 100 145 96 37 38 7 95 87 108 121 54 40 42 9 91 87 -0.110 63 68 108 81 0
pc03d09F.908.4.1441784.F4C21_1 87 128 86 38 39 8 100 86 63 70 27 40 42 9 78 65 1.091 49 23 90 30 0
pc03d11F.980.4.1443801.F4C21_1 182 182 102 37 38 8 100 94 131 130 59 41 42 8 92 84 0.688 145 90 145 89 0
pc03f01F.989.4.1458066.F4C21_1 237 379 323 38 39 8 100 100 87 108 58 41 41 7 94 90 2.113 199 46 341 67 0
pc03f03F.1000.4.1460097.F4C21_1 350 481 347 41 44 15 100 100 102 113 50 41 42 9 98 85 2.341 309 61 440 72 0
pc03f05F.1029.4.1462184.F4C21_1 35 36 6 38 42 15 1 0 40 41 12 40 41 9 10 2 16.610 -3 0 -2 1 -50
pc03f07F.939.4.1464333.F4C21_1 37 36 6 35 35 5 18 2 39 39 7 38 39 7 17 4 1.000 2 1 1 1 -50
pc03f09F.1002.4.1466314.F4C21_1 35 35 5 36 37 8 7 0 38 38 7 40 41 10 5 0 -1.000 -1 -2 -1 -2 -50
pc03f11F.986.4.1468378.F4C21_1 166 161 71 41 43 11 98 98 128 134 29 45 48 15 100 100 0.591 125 83 120 89 0
pc03h01F.909.4.1482593.F4C21_1 39 40 7 40 45 26 0 0 44 45 9 43 46 14 9 0 0 -1 1 0 2 -50

Total number of rows: 5748

Table truncated, full table size 602 Kbytes.




Supplementary data files not provided
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