|
| Status |
Public on Sep 01, 2014 |
| Title |
CVL125 Ancestral sample 3 |
| Sample type |
RNA |
| |
|
| Source name |
CVL125 Ancestral 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 did not undergo 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 |
|
