|
| Status |
Public on Jun 11, 2020 |
| Title |
D2_A: Double deficiency replicate 1 |
| Sample type |
SRA |
| |
|
| Source name |
Rossete leafs
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype: Col0
Stage: 20-d-old plants
treatment lenght: 10 d
tissue: rosette leaves
|
| Treatment protocol |
After 10 d of adaptation, plants were kept under the same (control) conditions or under copper deficiency (no CuSO4 and Bathocuproinedisulfonic acid disodium salt 10 µM), iron deficiency (no FeEDTA) or both deficiencies for 10 additional days.
|
| Growth protocol |
Arabidopsis plants were grown on soil for 12 d before been transferred to hydroponic systems and cultivated for 10 d under 1/10 Hoagland as in Hermans and Verbruggen (2005; J Exp Botany) with modifications for copper (CuSO4 1 µM). Long day conditions (diurnal phase: 22 h; 23°C; 120 µmols m-2 s-1 and night phase: 8 h; 18°C) were applied and all samples were harvested 4 h after the light onset.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Rosette leaves were flash frozen in liquid nitrogen and total RNA prepared using Trizol according to the manufacturer's instructions.
RNA libraries were prepared by Novogene (Beijing, China) for sequencing using standard Illumina protocols (HiSeq 2500 platform).
RNA-Seq for First Read unstranded libraries
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Illumina sequencing reads were generated using HiSeq 2500 platform by Novogene (Beijing, China)
Reads were treated with Trimmomatic to remove adapter sequences, aligned to the Araport11 genome reference with Tophat 2.1.1 and the counts and differential expression files generated with Cufflinks/Cuffdiff.
Genome_build: Araport11
Supplementary_files_format_and_content: tab-delimited text files including FPKM values for each sample according to Cufflinks
|
| |
|
| Submission date |
Jan 30, 2019 |
| Last update date |
Jun 11, 2020 |
| Contact name |
ANTONI GARCIA-MOLINA |
| E-mail(s) |
[email protected]
|
| Phone |
0034 686672735
|
| Organization name |
Centre for Research in Agrigenomics
|
| Department |
Plant Development and Signal Transduction
|
| Lab |
Gene regulatory networks in plant development
|
| Street address |
Campus UAB - CRAG Building
|
| City |
Cerdanyola del Vallès |
| State/province |
Barcelona |
| ZIP/Postal code |
08193 |
| Country |
Spain |
| |
|
| Platform ID |
GPL17639 |
| Series (1) |
| GSE125894 |
Comparison of transcriptomic responses to individual and combinatorial copper and iron deficiencies in Arabidopsis thaliana rosettes. |
|
| Relations |
| BioSample |
SAMN10847096 |
| SRA |
SRX5310902 |
