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Sample GSM21820 Query DataSets for GSM21820
Status Public on Jun 12, 2004
Title EV109, Wild-type seedlings H3mK9
Sample type genomic
 
Channel 1
Source name Total ChIP wild-type DNA
Organism Arabidopsis thaliana
Extracted molecule genomic DNA
 
Channel 2
Source name H3mK9 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-9 (H3mK9) (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 (H3mK9) 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: EV108+109
 
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)
GSE1339 Histone 3 Lysine 9 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 33 51 46 31 32 8 31 17 34 39 18 33 34 15 12 10 1.000 2 1 20 6 -50
pc03b01F.977.4.1409029.F4C21_1 1803 1564 626 31 36 32 100 96 136 133 41 35 41 47 88 57 4.133 1772 101 1533 98 0
pc03b03F.1001.4.1410945.F4C21_1 433 406 163 31 32 8 98 94 90 87 26 34 35 7 96 90 2.844 402 56 375 53 0
pc03b05F.990.4.1413204.F4C21_1 426 440 203 32 34 9 100 100 103 102 33 34 35 7 96 96 2.514 394 69 408 68 0
pc03b07F.983.4.1415196.F4C21_1 656 583 340 33 34 8 100 100 127 116 51 33 34 7 96 84 2.728 623 94 550 83 0
pc03b09F.960.4.1417276.F4C21_1 536 492 179 34 36 15 100 98 145 150 40 33 37 23 98 96 2.164 502 112 458 117 0
pc03b11F.994.4.1419153.F4C21_1 1075 1093 397 34 36 10 100 100 115 118 37 34 36 12 96 92 3.684 1041 81 1059 84 0
pc03d01F.1198.4.1433545.F4C21_1 347 328 106 34 47 70 100 92 103 107 37 34 44 73 48 1 2.181 313 69 294 73 0
pc03d03F.977.4.1435723.F4C21_1 41 67 57 34 39 37 22 17 35 45 25 33 40 45 13 0 1.807 7 2 33 12 -50
pc03d05F.989.4.1437691.F4C21_1 32 33 6 35 38 22 0 0 31 32 6 33 37 23 0 0 0.585 -3 -2 -2 -1 -50
pc03d07F.1091.4.1439632.F4C21_1 66 158 190 35 38 17 60 47 39 51 31 33 38 33 18 15 2.369 31 6 123 18 -50
pc03d09F.908.4.1441784.F4C21_1 90 176 170 33 36 20 73 57 42 73 84 34 36 16 42 36 2.833 57 8 143 39 0
pc03d11F.980.4.1443801.F4C21_1 67 98 77 33 34 10 70 60 45 76 66 33 34 8 58 41 1.503 34 12 65 43 -50
pc03f01F.989.4.1458066.F4C21_1 404 620 521 34 35 9 100 100 314 444 326 33 35 9 100 98 0.397 370 281 586 411 0
pc03f03F.1000.4.1460097.F4C21_1 987 914 509 33 35 8 100 100 675 647 343 33 35 9 100 100 0.571 954 642 881 614 0
pc03f05F.1029.4.1462184.F4C21_1 32 33 6 33 34 8 12 1 32 32 6 32 33 6 15 5 16.610 -1 0 0 0 -50
pc03f07F.939.4.1464333.F4C21_1 33 33 7 32 34 9 20 1 32 32 6 32 33 7 10 3 16.610 1 0 1 0 -50
pc03f09F.1002.4.1466314.F4C21_1 32 32 6 33 34 8 7 1 33 33 6 32 33 7 17 2 0 -1 1 -1 1 -50
pc03f11F.986.4.1468378.F4C21_1 117 181 123 34 35 11 100 96 45 60 35 33 33 7 57 40 2.790 83 12 147 27 0
pc03h01F.909.4.1482593.F4C21_1 37 38 9 36 38 13 15 0 34 35 7 34 35 10 8 0 16.610 1 0 2 1 -50

Total number of rows: 5748

Table truncated, full table size 596 Kbytes.




Supplementary data files not provided
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