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Sample GSM138481 Query DataSets for GSM138481
Status Public on Jan 29, 2008
Title 2-CH-1-1-12
Sample type RNA
 
Channel 1
Source name Helianthus annuus control leaf two-week seedlings rep. 2
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 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) 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 0.125955200902105 197861 149967.00 78802 124317.00
2 -0.0264717293710534 6179343 182400.00 4146359 146600.00
3 -0.0281661190392357 7216553 206275.00 4879412 164574.00
4 -0.109823897655293 257928 199584.00 160638 163520.00
5 -0.475264435516258 1713663 245072.00 1384657 199648.00
6 0.222339194572084 805052 211265.00 451533 172020.00
7 31909 54720.00 0 0.00
8 0 0.00 0 0.00
9 0.0398529791032325 2754875 194312.00 1710575 157504.00
10 -0.769471155441781 967734 161820.00 976410 131400.00
11 -0.0530995346649471 2833554 172710.00 1915379 139840.00
12 -0.128916619462087 1275754 171456.00 819009 140928.00
13 0.0697649644622606 774599 165232.00 476665 135056.00
14 -0.0102171479310626 117861 139761.00 41266 117342.00
15 0.534691379881666 531511 183752.00 199489 152028.00
16 0.0563262069290814 7520196 218380.00 4754800 180560.00
17 0.0361786276080768 5859788 218550.00 3774851 174605.00
18 -0.114552665965442 9891634 196812.00 7188005 157833.00
19 -0.0425516834717067 5534478 270100.00 3586357 215204.00
20 -0.00993528603284527 555700 224523.00 384266 182286.00

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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