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Sample GSM21811 Query DataSets for GSM21811
Status Public on Jun 12, 2004
Title EV107, WT seedlings H3mK4
Sample type genomic
 
Channel 1
Source name Total ChIP WT DNA
Organism Arabidopsis thaliana
Extracted molecule genomic DNA
 
Channel 2
Source name H3mK4 ChIP WT DNA
Organism Arabidopsis thaliana
Extracted molecule genomic DNA
 
 
Description WT 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 (H3mK4, 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: EV106+107
 
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)
GSE1336 Ev106+107, Histone 3 Lysine 4 methylation in WT 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_1 237 223 96 40 42 9 100 100 68 67 20 35 36 7 93 75 2.578 197 33 183 32 0
pc03b01F.977.4.1409029.F4C21_1 1738 1508 511 42 45 14 100 100 244 230 64 37 38 8 98 98 3.034 1696 207 1466 193 0
pc03b03F.1001.4.1410945.F4C21_1 516 421 190 43 47 19 100 98 127 114 42 37 37 8 94 90 2.394 473 90 378 77 0
pc03b05F.990.4.1413204.F4C21_1 476 441 228 43 44 11 100 100 118 113 46 36 37 7 98 88 2.401 433 82 398 77 0
pc03b07F.983.4.1415196.F4C21_1 824 741 330 44 45 10 100 100 547 511 220 38 38 8 100 100 0.616 780 509 697 473 0
pc03b09F.960.4.1417276.F4C21_1 437 412 151 48 48 11 100 100 138 127 37 39 40 9 100 94 1.974 389 99 364 88 0
pc03b11F.994.4.1419153.F4C21_1 968 955 647 47 48 12 100 100 228 216 117 38 39 9 96 94 2.277 921 190 908 178 0
pc03d01F.1198.4.1433545.F4C21_1 355 337 99 46 48 11 100 100 91 91 24 38 38 7 96 94 2.544 309 53 291 53 0
pc03d03F.977.4.1435723.F4C21_1 58 95 76 46 47 11 52 37 42 46 15 38 38 8 33 25 1.585 12 4 49 8 -50
pc03d05F.989.4.1437691.F4C21_1 42 43 10 46 48 11 10 1 35 35 6 37 39 8 5 0 1.000 -4 -2 -3 -2 -50
pc03d07F.1091.4.1439632.F4C21_1 530 465 177 46 48 13 100 100 209 199 64 38 39 8 100 96 1.501 484 171 419 161 0
pc03d09F.908.4.1441784.F4C21_1 365 346 127 46 48 12 100 100 83 77 20 37 38 8 93 84 2.794 319 46 300 40 0
pc03d11F.980.4.1443801.F4C21_1 316 344 144 47 48 11 100 100 186 195 55 37 39 8 100 100 0.852 269 149 297 158 0
pc03f01F.989.4.1458066.F4C21_1 1081 1071 617 46 47 11 100 100 106 104 42 38 38 7 98 86 3.928 1035 68 1025 66 0
pc03f03F.1000.4.1460097.F4C21_1 1371 1244 562 47 48 11 100 100 126 124 44 36 37 7 96 96 3.879 1324 90 1197 88 0
pc03f05F.1029.4.1462184.F4C21_1 49 48 12 45 47 12 16 3 36 37 7 37 38 12 5 0 0 4 -1 3 0 -50
pc03f07F.939.4.1464333.F4C21_1 48 50 11 45 47 13 18 2 37 38 8 37 38 11 8 0 16.610 3 0 5 1 -50
pc03f09F.1002.4.1466314.F4C21_1 46 46 10 45 46 10 16 2 37 36 7 37 37 7 17 0 16.610 1 0 1 -1 -50
pc03f11F.986.4.1468378.F4C21_1 253 264 137 46 47 11 100 100 120 126 54 38 39 8 98 96 1.336 207 82 218 88 0
pc03h01F.909.4.1482593.F4C21_1 41 43 10 42 44 11 16 6 38 38 7 38 39 8 12 1 16.610 -1 0 1 0 -50

Total number of rows: 5748

Table truncated, full table size 603 Kbytes.




Supplementary data files not provided
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