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Sample GSM138529 Query DataSets for GSM138529
Status Public on Jan 29, 2008
Title 2-SH-1-1-20
Sample type RNA
 
Channel 1
Source name Helianthus annuus two-week old seedlings watered with 150 mM salt solution for up to 9 hours, rep. 3 (leaves)
Organism Helianthus annuus
Characteristics leaves from two-week old seedlings watered with 150 mM salt solution for up to 9 hours in pots containing composite soil
Extracted molecule total RNA
Label Cy3
 
Channel 2
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 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) [email protected]
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 0.364001275339494 239532 172716.00 51974 172716.00
2 -0.087690263863552 2174299 147834.00 2183189 148980.00
3 -0.0188518289353090 2765826 201135.00 2636970 199364.00
4 -0.329401717280779 120192 166536.00 73009 169128.00
5 -0.0361977047817035 1343092 172152.00 586861 170208.00
6 0.58697222613467 832591 191590.00 236162 191590.00
7 0 0.00 0 0.00
8 0 0.00 0 0.00
9 0.358609358617582 3084311 195052.00 970323 187550.00
10 -0.0173041912188756 729271 144760.00 402285 145136.00
11 -1.37050224057182 691330 135459.00 808011 133556.00
12 -0.319989275112360 704541 162864.00 497047 160368.00
13 0.566040930443176 1975657 145888.00 384791 144948.00
14 0.116680845198869 63771 118888.00 17619 119042.00
15 0.915485314021672 3004132 158388.00 411550 155172.00
16 0.0292323749738738 3863557 168245.00 3085810 163020.00
17 -0.682925696251457 2360349 213317.00 2162122 210896.00
18 -0.331648544778955 3153322 185640.00 3638216 186592.00
19 0.98311521223933 4381905 238210.00 1642112 226156.00
20 0.593061747698024 720816 200298.00 199647 196533.00

Total number of rows: 1536

Table truncated, full table size 80 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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