|
| Status |
Public on Jul 26, 2023 |
| Title |
Col-0 t6HL, rep3 |
| Sample type |
SRA |
| |
|
| Source name |
7 day old seedlings (1 replicate = 30 seedlings)
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
age: 7 day old
tissue: seedlings
genotype: Col-0 (WT)
treatment: t6HL
|
| Treatment protocol |
The light treatments consisted of either six hours of high-light (HL) with 1200 µmol m-2 s-1 at 20-22°C (t6HL) or a six hour mock treatment under constant light with 60-70 µmol m-2 s-1 at 20-22°C (t6GL). One third of the plants were harvested and immediately frozen in liquid nitrogen each before the shift to high-light (t0), after six hours of high-light (t6HL) or six hours of mock (t6G¬L).
|
| Growth protocol |
Arabidopsis thaliana lines Col-0, hex (gnc gnl gata15 gata16 gata17 gata17l) and GNLox were grown on 1/2 MS medium in constant light at 60 µmol m-2 s-1 and 22°C for seven days.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using a NucleoSpin RNA kit (Macherey-Nagel).
Illumina stranded mRNA Kit (Illumina, San Diego, USA) with IDT for Illumina RNA UD Indexes Set A and protocol 1000000124518v01 with 11 cycles of enrichment
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
1x100bp, dual index
|
| Data processing |
CLC Genomics Workbench v20.0.2
Sequence reads were trimmed using CLC Genomics Workbench - Quality limit: 0.05.
Trimmed sequence reads were mapped to the TAIR10 release of the Arabidopsis thaliana Col-0 genome using CLC Genomics Workbench - Mismatch cost: 2, Insertion cost: 3, Deletion cost: 3, Length fraction: 0.5, Similarity fraction: 0.8.
Read count extraction and normalization were performed using CLC Genomics Workbench.
Assembly: TAIR10 release of Arabidopsis thaliana Col-0.
Supplementary files format and content: Tab-delimited text files, including TPM.
|
| |
|
| Submission date |
Jul 19, 2022 |
| Last update date |
Jul 26, 2023 |
| Contact name |
Peter Michael Schröder |
| E-mail(s) |
p.schroeder@tum.de
|
| Organization name |
Technical University of Munich
|
| Department |
School of Life Sciences
|
| Lab |
Plant Systems Biology
|
| Street address |
Emil-Ramann-Straße 8, Gebäude 4223
|
| City |
Freising |
| State/province |
Bavaria |
| ZIP/Postal code |
85354 |
| Country |
Germany |
| |
|
| Platform ID |
GPL26208 |
| Series (2) |
| GSE208555 |
High-light stress RNA-seq Arabidopsis thaliana |
| GSE208563 |
Conserved roles of B-GATAs in the regulation of photosynthesis and high-light stress response |
|
| Relations |
| BioSample |
SAMN29828221 |
| SRA |
SRX16342091 |
