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Sample GSM138451 Query DataSets for GSM138451
Status Public on Jan 29, 2008
Title 2-CH-1-1-10
Sample type RNA
 
Channel 1
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 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 -0.0594924535577032 145378 126276.00 123578 147900.00
2 0.0756704479278829 4546745 138866.00 3958217 159358.00
3 -0.121864858110003 7403701 189295.00 7250461 212993.00
4 -0.257219117957482 218413 156736.00 213130 181288.00
5 -0.183172858755402 1796078 167700.00 1780224 189630.00
6 0.00703225815502337 777244 149457.00 708928 169785.00
7 -0.116558745477578 22060 69597.00 17629 80919.00
8 10734 18088.00 3672 20356.00
9 0.600506414082742 5219070 187050.00 3028871 216050.00
10 -0.360538564628372 1078243 135300.00 1171215 161480.00
11 -0.178943446820869 2051827 105952.00 2124658 127452.00
12 0.107349570641423 1362626 140850.00 1076520 165825.00
13 0.847637157187584 1745075 125442.00 759399 148672.00
14 0.160681537419802 138187 148800.00 87052 177840.00
15 1.29189062392348 2749796 158500.00 839666 186000.00
16 0 0.00 0 0.00
17 -0.0797574696675475 5995423 203896.00 5757140 229152.00
18 -0.220582592027429 8312107 187144.00 9011998 219626.00
19 0.0495298553608214 6120621 197639.00 5388398 220961.00
20 0.366167938759612 984438 204638.00 655501 240499.00

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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