|
| Status |
Public on May 20, 2022 |
| Title |
leaf_HYPK-knockout_exon2_rep2 |
| Sample type |
RNA |
| |
|
| Source name |
Arabidopsis leaves
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
genoytpe: knockout of HYPK by T-DNA insertion in the second exon
tissue: leaf
age: 6 weeks
|
| Treatment protocol |
no treatment
|
| Growth protocol |
Plants were grown for 6 weeks on soil under short day conditions (8.5 h day, light intensity: 70 - 100 µmol m-2 s-1, day temperature: 22 °C, night temperature: 18 °C, relative humidity: 50-60%).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total leaf RNA was extracted with the peqGOLD Total RNA Kit (peqlab) according to the manufacturer's instructions followed by DNA digestion with the DNase I Digest Kit (VWR).
|
| Label |
Biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol.
|
| |
|
| Hybridization protocol |
Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.
|
| Scan protocol |
Affymetrix GeneArray Scanner3000
|
| Description |
Gene expression of Arabidopsis leaves of knockout of HYPK by T-DNA insertion in the second exon
|
| Data processing |
The data were analyzed with a commercial software called JMP Genomics, version 6, from SAS. Gene expression profiling was performed using arrays of AraGene-1_0-st type from Affymetrix. A Custom CDF Version 20 with Entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization, RMA background correction and Medianpolish Probeset Summary
|
| |
|
| Submission date |
Sep 25, 2020 |
| Last update date |
May 21, 2022 |
| Contact name |
Carolina Delatorre |
| E-mail(s) |
carolina.delatorre@medma.uni-heidelberg.de
|
| Organization name |
University Heidelberg
|
| Street address |
Theodor-Kutzer-Ufer 1-3
|
| City |
Mannheim |
| ZIP/Postal code |
68167 |
| Country |
Germany |
| |
|
| Platform ID |
GPL23011 |
| Series (1) |
| GSE158586 |
Expression data from Arabidopsis thaliana depleted of HYPK or NAA10 |
|
