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Sample GSM109328 Query DataSets for GSM109328
Status Public on May 22, 2006
Title H3K4Me3_gastrula_2_Slide2
Sample type genomic
 
Channel 1
Source name IP H3K4Me3
Organism Danio rerio
Characteristics Zebrafish Gastrula
Extracted molecule genomic DNA
Label Cy3
 
Channel 2
Source name Whole Cell Extract
Organism Danio rerio
Characteristics Control Whole Cell Extract
Extracted molecule genomic DNA
Label Cy5
 
 
Description IPed H3K4Me3 versus Control Whole Cell Extract Replicate 2
Data processing None; Raw Data files
 
Submission date May 18, 2006
Last update date May 22, 2006
Contact name Elizabeth Herbolsheimer
E-mail(s) herbolsheimer@wi.mit.edu
Organization name Whitehead Institute
Lab Young Lab
Street address 9 Cambridge Center
City Cambridge
State/province MA
ZIP/Postal code 02140
Country USA
 
Platform ID GPL3767
Series (1)
GSE4863 Zebrafish promoter microarrays identify actively transcribed embryonic genes

Data table header descriptions
ID_REF ID reference to platfrom
VALUE raw data files; no processed value (dummy Column)
MetaColumn placement on array MetaColumn
MetaRow Placement on array MetaRow
Column Placement on array Column
Row Placement on array Row
Name Name of Probe
AID Agilent ID
B635 B635
B635 Median B635 Median
B635 Mean B635 Mean
B635 SD B635 SD
F532 Median F532 Median
F532 Mean F532 Mean
F532 SD F532 SD
Ratio of Medians (635/532) Ratio of Medians (635/532)
Ratio of Means (635/532) Ratio of Means (635/532)
Median of Ratios (635/532) Median of Ratios (635/532)
Mean of Ratios (635/532) Mean of Ratios (635/532)
Ratios SD (635/532) Ratios SD (635/532)
Sum of Medians (635/532) Sum of Medians (635/532)
Sum of Means (635/532) Sum of Means (635/532)
Log Ratio (635/532) Log Ratio (635/532)
F635 Median - B635 F635 Median - B635
F532 Median - B532 F532 Median - B532
F635 Mean - B635 F635 Mean - B635
F532 Mean - B532 F532 Mean - B532
F635 Total Intensity F635 Total Intensity
F532 Total Intensity F532 Total Intensity
Flags Flags

Data table
ID_REF VALUE MetaColumn MetaRow Column Row Name AID B635 B635 Median B635 Mean B635 SD F532 Median F532 Mean F532 SD Ratio of Medians (635/532) Ratio of Means (635/532) Median of Ratios (635/532) Mean of Ratios (635/532) Ratios SD (635/532) Sum of Medians (635/532) Sum of Means (635/532) Log Ratio (635/532) F635 Median - B635 F532 Median - B532 F635 Mean - B635 F532 Mean - B532 F635 Total Intensity F532 Total Intensity Flags
1 null 1 1 430 103 BrightCorner Pro25G_T10_Pro25G 34 34 35 5 102 99 27 0.231 0.258 0.262 0.246 2.235 80 78 -2.115 15 65 16 62 4005 7948 0
2 null 1 1 430 102 BrightCorner Pro25G_T10_Pro25G 34 34 34 5 116 113 17 0.266 0.276 0.309 0.249 2.1 100 97 -1.911 21 79 21 76 2872 5871 0
3 null 1 1 430 101 3xSLv1 (-)3xSLv1 34 34 34 5 75 77 14 0.081 0.077 0.172 0.141 2.283 40 42 -3.624 3 37 3 39 1933 3990 0
4 null 1 1 430 100 Dr_0604_4_8299601+60 WH_07_P0060909 34 34 34 5 83 81 20 0.217 0.25 0.259 0.239 3.062 56 55 -2.202 10 46 11 44 3576 6519 0
5 null 1 1 430 99 Dr_0604_Un_19520004-60 WH_07_P0050678 34 34 34 5 180 167 49 0.42 0.454 0.445 0.441 2.261 203 189 -1.253 60 143 59 130 7450 13398 0
6 null 1 1 430 98 Dr_0604_5_38199913+60 WH_07_P0067569 34 34 34 5 293 261 88 0.523 0.549 0.543 0.547 2.04 390 347 -0.934 134 256 123 224 12527 20862 0
7 null 1 1 430 97 Dr_0604_NA_227407957+60 WH_07_P0078407 34 34 34 5 144 138 40 0.421 0.416 0.408 0.377 2.464 152 143 -1.25 45 107 42 101 6088 11042 0
8 null 1 1 430 96 Dr_0604_5_21232891+60 WH_07_P0066809 34 34 35 6 101 103 17 0.813 0.818 0.813 0.797 1.613 116 120 -0.3 52 64 54 66 4584 5380 0
9 null 1 1 430 95 Dr_0604_9_32119804+60 WH_07_P0065203 35 35 35 6 76 78 16 0.105 0.125 0.19 0.164 2.895 42 45 -3.248 4 38 5 40 2061 4077 0
10 null 1 1 430 94 Dr_0604_NA_35611477-60 WH_07_P0070238 35 35 35 6 101 97 21 0.238 0.254 0.27 0.258 2.242 78 74 -2.07 15 63 15 59 4009 7768 0
11 null 1 1 430 93 Dr_0604_Un_50230764-60 WH_07_P0052074 35 35 35 5 120 119 27 5.976 5.988 5.684 6.208 1.399 572 566 2.579 490 82 485 81 27041 6168 0
12 null 1 1 430 92 Dr_0604_NA_40599708-60 WH_07_P0070438 35 35 35 5 249 228 76 0.872 0.842 0.873 0.809 1.821 395 350 -0.198 184 211 160 190 15565 18247 0
13 null 1 1 430 91 3xSLv1 (-)3xSLv1 35 35 36 5 77 77 12 0.154 0.154 0.256 0.19 2.379 45 45 -2.7 6 39 6 39 2151 3984 0
14 null 1 1 430 90 Dr_0604_2_12186747+60 WH_07_P0047471 35 35 35 5 623 612 67 1.01 1.04 1.016 1.043 1.192 1176 1171 0.015 591 585 597 574 32882 31838 0
15 null 1 1 430 89 Dr_0604_5_40971371-60 WH_07_P0067818 36 36 36 5 653 586 190 1.021 1.026 1.002 0.828 2.486 1241 1108 0.03 627 614 561 547 47732 46859 0
16 null 1 1 430 88 Gene_desert_5-39 WH_07_P8000557 36 36 36 5 183 183 27 0.389 0.403 0.385 0.374 1.579 200 202 -1.363 56 144 58 144 4867 9535 0
17 null 1 1 430 87 Dr_0604_2_40726050+60 WH_07_P0049061 36 36 36 6 74 78 15 0.143 0.128 0.194 0.174 2.559 40 44 -2.807 5 35 5 39 2137 4045 0
18 null 1 1 430 86 Dr_0604_NA_227237000-60 WH_07_P0078400 36 36 36 6 361 357 68 0.537 0.525 0.509 0.529 1.45 495 485 -0.896 173 322 167 318 10556 18569 0
19 null 1 1 430 85 Dr_0604_3_26570052+60 WH_07_P0043703 36 36 36 6 219 195 71 7.838 7.948 7.893 8.589 1.894 1582 1387 2.97 1403 179 1232 155 101400 15620 0
20 null 1 1 430 84 Dr_0604_Un_161187278-60 WH_07_P0056182 36 36 36 5 268 267 42 0.445 0.452 0.447 0.449 1.371 331 331 -1.167 102 229 103 228 7250 13879 0

Total number of rows: 44290

Table truncated, full table size 6438 Kbytes.




Supplementary data files not provided

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