NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM67027 Query DataSets for GSM67027
Status Public on Aug 02, 2006
Title CtrXM_48hr.2_m
Sample type RNA
 
Channel 1
Source name Zebrafish liver tissue
Organism Danio rerio
Characteristics Zebrafish liver tissue exposed to arsenic
Growth protocol Zebrafish were reared at room temperature (27 ± 2°C)
Extracted molecule total RNA
Extraction protocol Total RNA of tissue samples were extracted using Trizol reagent (Invitrogen) according to the manufacturers instructions.
Label Cy5
Label protocol For fluorescence labeling of cDNAs, 20 µg of total RNA from the reference and experimental samples were
reverse transcribed in the presence of Cy3-dUTP and Cy5-dUTP (Amersham Inc.), respectively. Labeled cDNA were pooled, concentrated, and
resuspended in DIG EasyHyb (Roche Applied Science) buffer for hybridization.
 
Channel 2
Source name Zebrafish liver tissue
Organism Danio rerio
Characteristics Reference RNA was obtained by pooling equal amount of male and female total RNA extracted from liver tissues
of wild-type zebrafish.
Extracted molecule total RNA
Extraction protocol Total RNA of tissue samples were extracted using Trizol reagent (Invitrogen) according to the manufacturers instructions.
Label Cy3
Label protocol For fluorescence labeling of cDNAs, 20 µg of total RNA from the reference and experimental samples were reverse
transcribed in the presence of Cy3-dUTP and Cy5-dUTP (Amersham Inc.), respectively. Labeled cDNA were pooled, concentrated, and resuspended in
DIG EasyHyb (Roche Applied Science) buffer for hybridization.
 
 
Scan protocol The arrays were scanned using the GenePix 4000B microarray scanner (Axon Instruments, USA) and the generated images with their fluorescence signal intensities were analyzed using GenePix Pro 4.0 image analysis software (Axon Instruments, USA).
Description Fish were treated with arsenic [As(V)] acid (Na2HAsO4.7H2O; Sigma, USA) at 60 mg/L in a static condition for 96 hours (h) whereby less than 10% mortality occurred in arsenic-treated group within the experiment duration. No mortality was observed in the control group. The concentration was chosen based on an initial survival versus concentration experiment. Fish livers were sampled at 8 h, 24 h, 48 h and 96 h, and 12 fish livers were separated into 3 pooled-samples (each pooled samples consist of 4 livers) at each time point.
Three biological replicates are performed for each time point (8,24,48,96 hrs). Test and control samples are hybridized against a reference. No dye swap experiment has been performed.
Data processing The data were global median normalized.Normalized ratio of means defined by CH1/CH2
 
Submission date Aug 03, 2005
Last update date Aug 03, 2005
Contact name Siew Hong Lam
E-mail(s) [email protected]
Phone (65)- 68742860
Fax (65)-67792486
Organization name National University of Singapore
Department Biological Sciences
Street address 14 Science Drive 4
City Singapore
ZIP/Postal code 117543
Country Singapore
 
Platform ID GPL2715
Series (1)
GSE3048 Trancriptome Kinetics of Arsenic-induced Adaptive Response in Zebrafish Liver.

Data table header descriptions
ID_REF Unique ID
VALUE log2 of PRE_VALUE
CH1_Median CH1(F635) median fluorescence intensity
CH1_MEAN CH1 (F635) mean fluorescence intensity
CH1_SD CH1 (F635) fluorescence intensity standard deviation
CH1_BKD_Median CH1 (F635) background median fluorescence intensity
CH1_BKD_MEAN CH1 (F635) background mean fluorescence intensity
CH1_BKD_SD CH1 (F635) background fluorescence intensity standard deviation
%>CH1_BKD_+2SD % of feature pixels greater than two standard deviations over the background
CH2_Median CH2(F532) median fluorescence intensity
CH2_MEAN CH2 (F532) mean fluorescence intensity
CH2_SD CH2 (F532) fluorescence intensity standard deviation
CH2_BKD_Median CH2 (F532) background median fluorescence intensity
CH2_BKD_MEAN CH2 (F532) background mean fluorescence intensity
CH2_BKD_SD CH2 (F532) background fluorescence intensity standard deviation
%>CH2_BKD_+2SD % of feature pixels greater than two standard deviations over the background
Ratio_of_Means Unnormalized ratio of means defined by CH1/CH2
AREA Number of feature pixels
BKD_AREA Number of feature background pixels
CH1_Median-CH1_BKD Channel 1 median signal
CH2_Median-CH2_BKD Channel 2 median signal
CH1_Mean-CH1_BKD Channel 1 mean signal
CH2_Mean-CH2_BKD Channel 2 mean signal
PRE_VALUE Normalized ratio of means defined by CH1/CH2

Data table
ID_REF VALUE CH1_Median CH1_MEAN CH1_SD CH1_BKD_Median CH1_BKD_MEAN CH1_BKD_SD %>CH1_BKD_+2SD CH2_Median CH2_MEAN CH2_SD CH2_BKD_Median CH2_BKD_MEAN CH2_BKD_SD %>CH2_BKD_+2SD Ratio_of_Means AREA BKD_AREA CH1_Median-CH1_BKD CH2_Median-CH2_BKD CH1_Mean-CH1_BKD CH2_Mean-CH2_BKD PRE_VALUE
5269516 -1.5992 1058 998 425 136 145 70 90 2757 2400 1049 97 101 34 95 .374 120 678 922 2660 853 2299 .33006560724030709
5269517 -1.6238 2415 2423 551 145 160 84 100 6197 6306 835 115 123 52 100 .36799999999999999 52 420 2270 6082 2263 6183 .32447396901173908
5269518 -0.4028 329 359 123 160 173 83 50 338 333 83 101 107 36 96 .85799999999999998 52 420 169 237 186 226 .75640090007906136
5269519 -0.7210 332 332 111 149 161 73 61 375 374 105 108 114 49 96 .68799999999999994 52 420 183 267 171 260 .60667541870549424
5269520 -0.3548 758 768 191 173 182 79 98 768 772 180 101 106 36 100 .88700000000000001 80 560 585 667 586 666 .78195433386690261
5269521 -1.6762 166 184 111 173 186 85 3 122 126 43 95 100 35 16 .35499999999999998 156 1096 -7 27 -2 26 .3129089150594529
5269522 0.7410 298 308 109 145 159 77 48 188 197 59 111 116 43 38 1.895 52 340 153 77 149 81 1.6713834543291917
5269523 -0.6639 283 296 96 155 166 71 48 290 293 74 96 103 37 96 .71599999999999997 52 420 128 194 130 190 .63116052963768743
5269524 0.4824 294 303 112 162 171 87 38 183 187 65 98 103 38 57 1.5840000000000001 52 340 132 85 132 84 1.3970631948160046
5269525 -0.9605 209 206 83 125 145 84 15 218 240 119 101 106 43 65 .58299999999999996 32 236 84 117 61 134 .51387461459403938
5269526 -0.2073 665 650 214 152 164 80 95 619 601 181 94 100 37 98 .98199999999999998 80 650 513 525 486 501 .866180353359841
5269527 0.1665 127 137 67 123 136 71 5 96 101 37 90 94 34 7 1.2729999999999999 156 1203 4 6 1 7 1.1223344556677897
5269528 -0.7527 286 305 124 128 137 63 58 338 356 103 93 98 34 100 .67300000000000004 80 516 158 245 168 258 .59347777978956717
5269529 -1.0181 394 420 147 135 150 70 84 619 611 117 102 105 36 100 .56000000000000005 52 420 259 517 270 506 .49375786114489489
5269530 0.6675 1335 1340 256 153 178 141 100 743 759 176 100 111 52 100 1.8009999999999999 80 628 1182 643 1162 648 1.5883720992471635
5269531 0.9371 1188 1180 327 153 160 72 100 601 585 172 112 116 39 100 2.1709999999999998 52 340 1035 489 1020 469 1.9146802092538537
5269532 -0.3392 580 609 177 185 198 84 93 565 573 128 100 105 36 100 .89600000000000002 80 560 395 465 411 468 .79048141063644994
5269533 -4.7050 155 171 79 171 182 83 3 113 120 41 97 101 34 12 0 156 975 -16 16 -11 19 .038340618050762998
5269534 -0.6144 162 170 74 150 163 76 5 136 145 56 118 131 62 5 .74099999999999999 156 975 12 18 7 14 .65321052975373994
5269535 -1.1110 149 165 74 144 154 71 5 129 135 50 95 100 36 21 .52500000000000002 156 1034 5 34 11 35 .46296296296296324

Total number of rows: 16512

Table truncated, full table size 1982 Kbytes.




Supplementary data files not provided
| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap