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Sample GSM347114 Query DataSets for GSM347114
Status Public on Apr 22, 2010
Title Arabidopsis rosette_Light Wounded_Rep2
Sample type RNA
 
Source name Arabidopsis rosette, wounded leaves, 60 min in light
Organism Arabidopsis thaliana
Characteristics Arabidopsis thaliana, ecotype Columbia (Col-0). Age = 4 weeks. Developmental stage = mid rosette growth. Tissue = rosette.
Biomaterial provider M.R. Roberts, Lancaster University, UK
Treatment protocol Plants were left to acclimatise for 30 min in controlled environment growth cabinets at 22º C in the light (PAR - 250 µmol m-2 s-1) with relative humidity between 55-60%. Subsequently, rosette leaves were mechanically wounded using a metal haemostat, once or twice dependent on size, so that a wound site is present at any point on the leaf within a 1cm radius. Leaves were wounded closest to the largest width of the leaf and perpendicular to the mid-vein. Wounded plants were returned to the same controlled environment for a further 60 min in the light, after which whole rosettes were cut off at the base of the stem and frozen in liquid nitrogen.
Growth protocol Surface-sterilised seeds were grown on half-strength Murashige and Skoog basal salt mixture, adjusted to pH 5.8 with 1 M KOH, with 1% sucrose and 0.6% plant cell tissue culture grade agar, in a controlled environment growth room following a 10/14 hour light/dark regime with PAR of 250 µmol m-2 s-1 and temperatures of 20 ± 2º C. Ten-day-old seedlings were subsequently transplanted to a sieved, pre-autoclaved compost and sand mixture (3:1) and plants grown in individual pots (Aracon system) in the same controlled environment growth room. Plants were watered daily by spraying.
Extracted molecule total RNA
Extraction protocol For each treatment, a single RNA extract was made from 15-17 pooled individuals. Frozen plant tissue was ground to a fine powder in a pre-cooled pestle and mortar with liquid nitrogen and acid-washed sand, and transferred to a 15 mL polypropylene centrifuge tube. 2 ml well mixed RNA extraction buffer (1:1 mix of phenol and 0.1 M LiCl, 0.1 M Tris.Cl pH 8.0, 10 mM EDTA and 1% SDS) at 95ºC was added per gram of fresh weight plant material and tubes vortexed until thoroughly mixed. Half a volume of chloroform/isoamyl alcohol (24:1) was added and mixed well by vortexing. After centrifugation in a bench top centrifuge at 3500 x g for 10 min at 4ºC, the upper aqueous phase was removed to a new 15 ml centrifuge tube and re-extracted with chloroform/isoamyl alcohol before centrifugation for a further 10 min as before. The aqueous phase was removed to a new centrifuge tube and mixed with an equal volume of 4 M LiCl and incubated overnight at 4ºC. Tubes were then centrifuged for 15 min at 3500 x g at 4ºC to pellet precipitated RNA. The supernatant was removed and the pellet drained and resuspended in 300 µl 0.3 M NaOAc pH 5.2, before being transferred to an Eppendorf tube. RNA was re-precipitated by the addition of 750 µl cold ethanol, followed by centrifugation in a microcentrifuge for 10 min at 14000 rpm. Pellets were drained and rinsed in 70% ethanol and left to dry on the bench, for ~ 30 min, under a 60 W lamp, after which pellets were resuspended in 50-100 µl ddH2O. 100 µg of RNA was purified using a Qiagen RNeasy kit, using the specified protocol (RNeasy® Mini Handbook, Fourth Edition, April 2006).
Label biotin
Label protocol Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 5 microg total RNA.
 
Hybridization protocol Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C and at 60 rounds/min. The GeneChips were washed and stained in the Affymetrix Fluidics Station 400 and 450.
Scan protocol GeneChips were scanned using the GeneChip Scanner 3000 7G.
Description Arabidopsis rosette_Light Wounded_Rep2
Data processing Normalised using GCRMA with default parameters
 
Submission date Dec 03, 2008
Last update date Aug 15, 2018
Contact name Rekin's Janky
E-mail(s) Nucleomics.Bioinformatics@vib.be
Organization name VIB
Department Nucleomics Core
Street address Herestraat 49 Box 816
City Leuven
ZIP/Postal code B-3000
Country Belgium
 
Platform ID GPL198
Series (1)
GSE13803 Interaction between the light environment and the Arabidopsis wound response
Relations
Reanalyzed by GSE118579

Data table header descriptions
ID_REF
VALUE Normalised using GCRMA with default parameters
ABS_CALL the call in an absolute analysis that indicates if the transcript was present (P), absent (A), marginal (M), or no call (NC)

Data table
ID_REF VALUE ABS_CALL
244901_at 3.153462375 P
244902_at 2.884173501 P
244903_at 3.850904296 P
244904_at 2.519223334 A
244905_at 1.98373095 A
244906_at 2.436439315 A
244907_at 2.472914728 A
244908_at 2.200668647 A
244909_at 2.135740052 A
244910_s_at 2.333470822 P
244911_at 2.686121541 A
244912_at 5.35100828 P
244913_at 1.950352846 A
244914_at 2.706475823 A
244915_s_at 2.052351289 A
244916_at 2.006672148 A
244917_at 2.04208406 A
244918_at 2.201960671 A
244919_at 1.81720781 A
244920_s_at 4.404230914 P

Total number of rows: 22810

Table truncated, full table size 534 Kbytes.




Supplementary file Size Download File type/resource
GSM347114.CEL.gz 2.3 Mb (ftp)(http) CEL
Processed data included within Sample table

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