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Sample GSM1949714 Query DataSets for GSM1949714
Status Public on Feb 29, 2016
Title KO-6
Sample type RNA
 
Source name Arabidopsis thaliana 96-hours old etiolated hypocotyls, pme3 loss-of- function mutant
Organism Arabidopsis thaliana
Characteristics ecotype: Columbia
genotype: atpme3-1 loss-of-function mutant
Treatment protocol Arabidopsis thaliana (Columbia ecotype): wild type/atpme3-1 loss-of-function mutant
Growth protocol Etiolated 96-hour-old hypocotyls from wild type and atpme3-1 of Arabidopsis thaliana were used. Sterilized seeds were laid on 9 % agar, incubated for 3 days in the dark at 4°C, then transferred for 6 hours at 20°C in a phytotron with white light (200 µm.m-2.s-1). Finally, petri dishes were kept in the dark for 4 days.
Extracted molecule total RNA
Extraction protocol total RNA was extract using Ambion RNAqueous kit and DNA was removed using the Ambion TURBO-DNAfree kit. RNA was quantified using Nanodrop 1000 spectrophotometer (thermo scientific) and RNA quality was assessed using Eukaryote total RNA Standard Sensitivity chips on the Experion system (Biorad). All extract protocols were performed at the Centre de Ressources Régionales en Biologie Moléculaire 5Université de picardie Jules Verne, Amiens). RNA concentration was determined using Nanodrop 1000 and RNA quality was assessed using Eukaryote Total RNA standard Sensitivity on the Experion (Biorad) .
Label Cy3
Label protocol Labeling was performed following NimbleGen One-color labeling kit instructions (Roche)
 
Hybridization protocol Hybridization was performed overnight at 42°C using a 4-position NimbleGen hybridization system 4
Scan protocol Slides were scanned using an Axon GenePix 4400 A scanner (molecular Devices Corporatiion, Sunnyvale, CA, USA) piloted by GenePiix pro software (Axon). Scanned images were then imported into Nimblescan software (NimbleGen Systems, Inc. Madison, WI, USA) for grid alignment and expression data analyses.
Description This sample is of mutant Arabidopsis thaliana. It is the sixth of five mutant biological replicates used in this experiment. Each replicate was obtained separately from the others and each replicate represents about 300 hypocotyles.
Data processing Raw data (.par files) were normalized using intra-array (RMA background correction) and inter-array (quantile) normalizations using ANAIS software (Simon & Biot, 2010, ANAIS: Analysis of NimbleGen Arrays Interface. Bioinformatics 2010 Oct; 26(19):2468-9).
 
Submission date Nov 24, 2015
Last update date Feb 29, 2016
Contact name Alain Mareck
E-mail(s) alain.mareck@univ-rouen.fr
Organization name université de rouen Haute Normandie
Department departement de biologie glycobiologie et matrice extracellulaire végétale
Street address 2 rue tenieres
City Mont-Saint-Aignan
ZIP/Postal code 76821
Country France
 
Platform ID GPL13697
Series (1)
GSE75326 Expression analysis of Arabidopsis thaliana mutant atpme3-1

Data table header descriptions
ID_REF
VALUE RMA-normalized, averaged gene-level signal intensity

Data table
ID_REF VALUE
AT1G01010_1 12372.0414
AT1G01020_1 587.1013
AT1G01020_2 353.0520
AT1G01030_1 3621.1344
AT1G01040_1 11552.6674
AT1G01046_1 4354.8732
AT1G01050_1 15729.8442
AT1G01060_1 18738.1943
AT1G01060_3 590.7518
AT1G01070_1 6867.9737
AT1G01070_2 624.1912
AT1G01073_1 220.9113
AT1G01080_1 13102.9531
AT1G01080_2 11413.8778
AT1G01090_1 30417.1660
AT1G01100_1 12403.6894
AT1G01100_2 14117.9449
AT1G01100_3 17481.7762
AT1G01110_1 6971.4177
AT1G01110_2 8531.1154

Total number of rows: 37118

Table truncated, full table size 795 Kbytes.




Supplementary file Size Download File type/resource
GSM1949714_A12-KO6-532-grid.pair.gz 2.3 Mb (ftp)(http) PAIR
GSM1949714_A12-KO6-532-grid_RMA.calls.gz 409.3 Kb (ftp)(http) CALLS
GSM1949714_A12-KO6-532-grid_norm_RMA.pair.gz 2.3 Mb (ftp)(http) PAIR
Processed data included within Sample table
Processed data provided as supplementary file

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