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Sample GSM773054 Query DataSets for GSM773054
Status Public on Aug 04, 2011
Title M5-K6-DSRep2
Sample type RNA
 
Channel 1
Source name Tall Mokka shoot tip including first unopened leaf pair
Organism Coffea arabica
Characteristics cultivar: Tall Mokka
Treatment protocol Shoot tips including unopened leaves were collected from all trees.
Growth protocol Tall Mokka and Typica trees were clonally propagated and maintained under similar environmental conditions in the fields at the Kunia experimental station of Hawaii Agriculture Research Center (HARC) on Oahu.
Extracted molecule total RNA
Extraction protocol Total RNA extracted using RNeasy Plant mini kit following manufacturers instructions.
Label Alexa 555
Label protocol Total RNA was used to synthesize fluorescently labeled (Alexa Fluor 555 & Alexa Fluor 647) cDNA probes using the SuperScript Indirect cDNA Labeling System (Invitrogen Corporation, Carlsbad, CA) following manufacturers instructions.
 
Channel 2
Source name Typica shoot tip
Organism Coffea arabica
Characteristics cultivar: Typica
Treatment protocol Shoot tips including unopened leaves were collected from all trees.
Growth protocol Tall Mokka and Typica trees were clonally propagated and maintained under similar environmental conditions in the fields at the Kunia experimental station of Hawaii Agriculture Research Center (HARC) on Oahu.
Extracted molecule total RNA
Extraction protocol Total RNA extracted using RNeasy Plant mini kit following manufacturers instructions.
Label Alexa 647
Label protocol Total RNA was used to synthesize fluorescently labeled (Alexa Fluor 555 & Alexa Fluor 647) cDNA probes using the SuperScript Indirect cDNA Labeling System (Invitrogen Corporation, Carlsbad, CA) following manufacturers instructions.
 
 
Hybridization protocol Potato cDNA microarrays were prehybridized for 45 min in prehybridization buffer (5X SSC, 0.1% SDS, 1% BSA) preheated at 42°C. Prehybridized slides were washed twice in miliQ water for 5 min each, then washed for 2 min in isopropanol and air dried. Labelled cDNA probes were dissolved in 45 µl of 1X hybridization buffer (50% formamide, 5X SSC, and 0.1% SDS). 2 µl of EDTA (from 0.5M stock), 2 µl of polyA DNA (from 10 µg/ µl stock) and 0.75 µl of salmon sperm DNA (from 10 µg/µl stock) were added into the probe mix. Heat denatured probes were carefully applied to the microarray slides and incubated in hybridization chamber at 42°C for 16-20h. Hybridized slides were washed for 5 min in a low stringency wash buffer (2X SSC and 0.1% SDS) preheated to 42°C, followed by 10 min wash in a high-stringency wash buffer (0.05X SSC and 0.1% SDS) at room temperature. Slides were washed four times for one min each in 0.05X SSC, and dried using centrifuge.
Scan protocol Scanned on GenePix Personal 4100A scanner (Molecular Devices Corporation, Sunnyvale, CA). Images were quantified using using GenePix Pro 6.0 (Molecular Devices Corporation, Sunnyvale, CA).
Description 65_MA5-KA6
Dye swap Replicate of 66_KA5-MA6, Total RNA from shoot tip including first unopened leaf of Tall Mokka and Typica.
Data processing Per spot and per chip normalization based on the Lowess method was implemented using GeneSpring 7.0 (Agilent Technologies, Santa Clara, CA). Statistically significant differentially expressed genes were identified by applying one-way ANOVA analysis.
 
Submission date Aug 03, 2011
Last update date Aug 04, 2011
Contact name Ratnesh Singh
E-mail(s) ratnesh@hawaii.edu
Phone 808-621-1279
Fax 808-621-1399
Organization name Hawaii Agriculture Research Center
Street address 94-340 Kunia Rd
City Waipahu
State/province HI
ZIP/Postal code 96797
Country USA
 
Platform ID GPL14110
Series (1)
GSE31179 Shoot tip tissue: Tall Mokka vs Typica.

Data table header descriptions
ID_REF
VALUE -[INV_VALUE]
INV_VALUE normalized log2 ratio (Alexa647/Alexa555)

Data table
ID_REF VALUE INV_VALUE
STMIR33 -0.104337 0.10433666
STMIR34 0.139236 -0.139235797
STMJN90 0.0908029 -0.090802937
STMIR35 -0.588805 0.588804567
STMJN91 -0.0143553 0.014355293
STMIR36 1.35845 -1.358453971
STMJN92 -0.0398403 0.039840265
STMJN93 -0.728574 0.728573603
STMIR37 0.0320936 -0.03209363
STMJN94 -0.557778 0.557777671
STMIR38 -0.0100637 0.010063683
STMJN95 0.0320936 -0.03209363
STMIR39 0.0454314 -0.045431429
STMDH10 -0.0328061 0.032806145
STMJN96 null null
STMDH11 0.21424 -0.214240226
STMDH12 0.694321 -0.694321257
STMDH13 -0.0607392 0.060739158
STMED70 -1.08542 1.085424656
STMDH14 null null

Total number of rows: 15264

Table truncated, full table size 417 Kbytes.




Supplementary file Size Download File type/resource
GSM773054.gpr.gz 4.7 Mb (ftp)(http) GPR
Processed data included within Sample table

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