|
| Status |
Public on Dec 01, 2018 |
| Title |
35S::CLE41 stem rep 2 |
| Sample type |
RNA |
| |
|
| Source name |
35S::CLE41_Inflorescence stem
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype: Columbia
age: 5 week old plants
genotype/variation: 35S::CLE41
tissue: lower third of inflorescence stem exluding 1 cm directly above the rosette
|
| Treatment protocol |
35S::CLE41 lines were generated in the Col background as described in Etchells and Turner (2010) Development 137:767-774.
|
| Growth protocol |
long day growth conditions (16h light, 8 hours dark)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extractions were performed using Trizol according to the manufacturers instructions
|
| Label |
biotin
|
| Label protocol |
Labelling protocol was the Two-cycle Target labelling protocol as described in https://www.thermofisher.com/document-connect/document-connect.html?url=https://assets.thermofisher.com/TFS-Assets/LSG/manuals/expression_analysis_technical_manual.pdf&title=Manuals:%20Expression%20Analysis%20Technical%20Manual,%20with%20Specific%20Protocols%20for%20Use%20with%20the%20Hybridization,%20Wash,%20and%20Stain%20Kit
|
| |
|
| Hybridization protocol |
Hybridization protols was as described in https://www.thermofisher.com/document-connect/document-connect.html?url=https://assets.thermofisher.com/TFS-Assets/LSG/manuals/expression_analysis_technical_manual.pdf&title=Manuals:%20Expression%20Analysis%20Technical%20Manual,%20with%20Specific%20Protocols%20for%20Use%20with%20the%20Hybridization,%20Wash,%20and%20Stain%20Kit using the GeneChip Hybridzation Oven 645 and Fluidics protocol: EukGE-WS2
|
| Scan protocol |
GeneChip Scanner 3000 7G as detailed in the GeneChipTM Expression Wash, Stain and Scan User Manual, P/N 702731 (ThermoFisher)
|
| Description |
PE-41-OX2
|
| Data processing |
Technical quality control was performed with dChip (V2005; www.dchip.org), using the default settings. Background correction, quantile normalization, and gene expression analysis were performed using RMA in Bioconductor. Differential expression analysis was performed using Limma using the functions lmFit and eBayes.
|
| |
|
| Submission date |
Nov 30, 2018 |
| Last update date |
Dec 01, 2018 |
| Contact name |
Peter Etchells |
| E-mail(s) |
[email protected]
|
| Organization name |
Durham University
|
| Department |
Biosciences
|
| Street address |
South Road
|
| City |
Durham |
| ZIP/Postal code |
DH1 3LE |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL198 |
| Series (1) |
| GSE123162 |
Expression differences in wild type and 35S::CLE41 Arabidopsis stems |
|
