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Sample GSM138453 Query DataSets for GSM138453
Status Public on Jan 29, 2008
Title 2-CH-1-1-11
Sample type RNA
 
Channel 1
Source name Helianthus annuus control leaf two-week seedlings reference sample (pooled leaves)
Organism Helianthus annuus
Characteristics leaves from two-week seedlings grown under standard conditions in greenhouse (16 h photoperiod and 20-24oC temperature) in pots containing composite soil, reference sample (pooled leaves)
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name Helianthus annuus control leaf two-week seedlings rep. 1
Organism Helianthus annuus
Characteristics leaves from two-week seedlings grown under standard conditions in greenhouse (16 h photoperiod and 20-24oC temperature) in pots containing composite soil
Extracted molecule total RNA
Label Cy5
 
 
Description The RNA (800ng) samples were labeled by using SuperScript Indirect RNA Amplification System Kit (Invitrogen, cat# L1016-02) based on the method designed by Eberwine y col. 1992. Following RNA amplification (with the incorporation of UTP aminoallil), labeled product was achieved by incubating with Cy3 or Cy5 esters in alkaline media.Dye-swaps were used to correct for differences in incorporation and fluorescent properties of both dyes, generating a number of 9 slides per experiment (three slides for control and three slides for each treatment) with a total number of 18 slides considering technical replicates. The microarray slides were prehybridized by incubation in 5X SSC, 0.1% SDS, 1% BSA at 42°C. The next day the cover slip was removed and the slide was washed once in 1X SSC, 0.2% SDS prewarmed to 42°C; once in 0.2X SSC, 0.2% SDS at room temperature; and once in 0.1X SSC at room temperature. The washes were conduced with gentle shaking at 100 rpm for 5 minutes. Slides were subjected to low speed centrifugation for 2 min at 500 rpm to dry. The hybridized slides were scanned using a VersArray Chip Reader (BioRad) scanner (two different channels for the two different dyes were used) at three different detector sensitivities. Images analysis and signal quantification were performed using Spotfinder (free open source software) (www.tm4.org/spotfinder.html), quantifying signal intensity for each spot. Then, data integration from multiple scanning processes were achieved.
Data processing Background subtraction was performed before calculating ratios. The elements with either printing or hybridization artifacts were flagged and discarded before analysis. Only spots with an intensity of at least 1.5 times above the local background in both channels were used for subsequent analysis. The extracted data from each slide were then log transformed (using log base two) and normalized using two different methods: 3-D normalization (normalization intensity and space dependant) (Alvarez y col, unpublished data) using R package (University of Auckland) R 1.9.0 version (http://www.r-project.org). Potential artifacts and false positives were eliminated by selecting for further analysis only those clones that exhibited similar expression patterns between the original hybridization and their dye swaps (Yang y col. 2002). A gene expression matrix was generated and its analysis was focused on genes differentially expressed. The whole analysis related to gene expression matrix was performed using software Infostat 2006® (Infostat Group, FCA, Córdoba, Argentina).
 
Submission date Oct 03, 2006
Last update date Jan 29, 2008
Contact name Paula Fernandez
E-mail(s) pfernandez@cnia.inta.gov.ar
Organization name INTA Castelar
Street address N. Repetto y Los Reseros S/N
City Castelar
State/province Buenos Aires
ZIP/Postal code 1712
Country Argentina
 
Platform ID GPL4366
Series (1)
GSE6201 profiling of an organ-specific sunflower transcriptoma under abiotic stress (salinity and cold conditions)

Data table header descriptions
ID_REF
VALUE normalized log2 ratios CHB/CHA
ChannelA Channel A mean intensity
BackA Channel A mean background intensity
ChannelB Channel B mean intensity
BackB Channel B mean background intensity

Data table
ID_REF VALUE ChannelA BackA ChannelB BackB
1 -0.0346944664717689 125265 139784.00 135458 153722.00
2 -0.0660792524746748 2766494 140494.00 4196881 153031.00
3 0.00202374508525005 5029178 186940.00 8131117 203060.00
4 0.047536713358611 145390 164934.00 190163 183022.00
5 0.106975249092151 1011914 177660.00 1602883 195048.00
6 0.0954159364010165 535539 155722.00 875616 174563.00
7 -0.069725131256386 17145 72710.00 18947 83160.00
8 0 0.00 0 0.00
9 -0.101486619537822 1760127 178416.00 2539693 195048.00
10 -0.352608174031532 870979 140592.00 992364 156146.00
11 0.0827826783162464 1296530 112539.00 2159337 125419.00
12 0.035639583641247 706444 141381.00 1129167 160632.00
13 -0.0387463607469272 477705 132172.00 704091 148598.00
14 -0.0172928741655520 64942 139668.00 75897 159032.00
15 -0.263795274876205 395637 146960.00 409148 169840.00
16 -0.0570397342560265 5479024 140456.00 8202362 152872.00
17 0.0707664200123618 3041019 156981.00 5091150 165501.00
18 0.0686682950221515 5824459 169929.00 9608636 183552.00
19 0.0118124077519214 3078513 175207.00 5054163 187257.00
20 -0.0217950109553545 374452 192622.00 486200 210980.00

Total number of rows: 1536

Table truncated, full table size 81 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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