NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM6008666 Query DataSets for GSM6008666
Status Public on Apr 09, 2022
Title WT-control-2
Sample type RNA
 
Source name whole seedling
Organism Arabidopsis thaliana
Characteristics tissue: whole seedling
genotype/variation: WT
treatment: control
age: 10-day old
Treatment protocol Plant samples were divided into two groups and each group contained three trays. One group set were subjected to continuous 40°C heat stress, while control group was grown at 23°C using growth chamber
Growth protocol 10-day-old plants (45 plants from each genotype per tray) were grown on plastic trays ((21×30×5 cm in width, length and height, respectively) containing dry soil and saturated with water
Extracted molecule total RNA
Extraction protocol Aerial tissues of 10-day-old WT and kai2-2 mutant plants grown on soil under control and 6h and 24h heat stress conditions were detached and collected in four biological replicates for transcriptome analysis
Label Cy3
Label protocol Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions,
 
Hybridization protocol 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized for 17 hours at 65C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.
Scan protocol ly after washing on the Agilent DNA Microarray Scanner G2505C using one color scan setting
Description Gene expression inWT-control-2
Data processing The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
 
Submission date Apr 04, 2022
Last update date Apr 10, 2022
Contact name MOSTAFA ABDELWAHED Abdelrahman
E-mail(s) meettoo2000@yahoo.com
Phone +201095725679
Organization name GALALA UNNIVERSITY
Street address Suze
City El Sokhna
State/province SUZE
ZIP/Postal code 43511
Country Egypt
 
Platform ID GPL12621
Series (1)
GSE200100 Karrikin Receptor KARRIKIN INSENSITIVE2 Positively Regulates Heat Stress Tolerance in Arabidopsis thaliana

Data table header descriptions
ID_REF
VALUE Normalized signal intensity

Data table
ID_REF VALUE
A_84_P800302 2.638710475
A_84_P20838 2.902156214
A_84_P13493 2.678170575
A_84_P759826 2.9268245
A_84_P14691 3.218640345
A_84_P51360 3.343189761
A_84_P12037 3.235461488
A_84_P225689 3.157313355
A_84_P229159 3.444996983
A_84_P23129 3.307751421
A_84_P11290 3.607706637
A_84_P859330 3.338193136
A_84_P218478 3.319000903
A_84_P14283 3.086891925
A_84_P12356 3.644925639
A_84_P125381 2.789775197
A_84_P89749 3.482902182
A_84_P752993 3.063290109
A_84_P505397 3.890463652
A_84_P23645 3.098165684

Total number of rows: 9999

Table truncated, full table size 237 Kbytes.




Supplementary file Size Download File type/resource
GSM6008666_US45103077_252116915408_S01_GE1_107_Sep09_1_2.txt.gz 8.6 Mb (ftp)(http) TXT
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap