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Sample GSM902867 Query DataSets for GSM902867
Status Public on Sep 01, 2014
Title CVL125 Selected sample 1
Sample type RNA
 
Source name CVL125 Selected sample
Organism Arabidopsis thaliana
Characteristics genotype: Recombinant inbred lines CVL125
tissue: Whole above ground plant
age: 25 days
Treatment protocol -
Growth protocol Sterilized seeds were initially sown on MA agar plates and stratified at 4°C for three days. After 12 days seedlings of CVL39 and CVL125 were transferred to pots in a general soil mix and grown under long-day conditions (23°C, 16 h light, 8 h dark). On day 25 the above ground parts of one individual were harvested in an Eppendorf tube containing glass beads and flash frozen in liquid nitrogen for RNA extraction.
Extracted molecule total RNA
Extraction protocol Approximately half of the frozen whole plant tissue from 25-day old plants was used for RNA extractions. Total RNA was isolated with the TRIzol® Reagent (Invitrogen) and treated with DNAse (Applied Biosystems, AM1906) to remove any contaminating DNA. 2 µg of RNA were reverse transcribed using standard Invitrogen reagents and protocols. cDNA samples were subjected to RNAse H digestion to remove any remaining RNA/DNA hybrid complexes (Invitrogen). The quality of RNA (integrity and purity) and cDNA was assessed with the 2100 Bioanalyzer pico Chip (Agilent Technologies). cDNA was quantified with the NanoDrop 1000TM Spectrophotometer (Thermo SCIENTIFIC) and diluted to 100 ng/µl with sterile dH2O.
Label biotin
Label protocol Biotinylated cRNA were prepared according to the standarf Affymetrix protocol from 1 microgram cDNA
 
Hybridization protocol Labeled cDNA was hybridized to AGRONOMICS1 Chips using standardized assays and reagents for Affymetrix Fluidics Station 450
Scan protocol GeneChips were scanned using the Affymetrix Scanner 3000 7G with autoloader
Description gene expression data of 25-day-old plants which experienced 5 generations of selection and 2 generations without selection
Data processing Expression signals were normalized using the Robust Multichip Average (RMA) approach, defined in custom functions for analyzing AGRONOMICS1 Chip data (http://www.agron-omics.eu/index.php/resource_center/tiling-array/tools-and-protocols), implemented in R and bioconductor which also requires the aroma.affymetrix package. Log2 RMA expression values (summarized by gene) were generated using Agronomics R script and are available on associated GSE entry.
 
Submission date Mar 27, 2012
Last update date Sep 01, 2014
Contact name Christian Heichinger
E-mail(s) christian.heichinger@uzh.ch
Phone 41-(0)44-634 8275
Organization name Zürich University
Department Institute of Plant Biology
Lab Developmental Genetics
Street address Zollikerstrasse 107
City Zürich
State/province Zürich
ZIP/Postal code 8008
Country Switzerland
 
Platform ID GPL14926
Series (2)
GSE36844 Selection of epigenetic variation in Arabidopsis [Expression]
GSE36846 Selection of epigenetic variation in Arabidopsis

Supplementary file Size Download File type/resource
GSM902867_CVL125_S2_1.CEL.gz 19.2 Mb (ftp)(http) CEL
Processed data are available on Series record

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