|
| Status |
Public on Apr 01, 2024 |
| Title |
8wLD_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
main stem
|
| Organism |
Arabis alpina |
| Characteristics |
arabis alpina ecotype: Pajares
duration of cold exposure: 0 weeks
days in ld after cold exposure: 0
position of tissue collection: 2 cm of the main stem below the rosette
|
| Treatment protocol |
After 8 weeks in LD (16h light at 20°C, 8h dark at 18°C) conditions, plants were exposed to 4, 8, 12, 16 and 21 weeks of cold (4°C). After cold exposure, plants were transfered to LD conditions.
|
| Growth protocol |
Plants were grown for 8 weeks in long day conditions (LD, 16h light at 20°C, 8h dark at 18°C) followed by extended exposure to cold (4°C) in LD conditions for different durations. The plants were then shifted back to greenhouse LD conditions.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was isolated using RNeasy Plant RNA isolation kit (Qiagen) according to the manufacturer's instructions.
The libraries were prepared from 1 µg total RNA with RNA integrity number >8 (Bioanalyzer; Agilent) using the NEBNext Ultra Directional II RNA Library Prep Kit for Illumina (New England Biolabs) at the Cologne Genome Centre and sequencing was carried out using a HiSeq3000 (Illumina) generating 1 x 150 bp single reads.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Description |
Mishra_RNA-Seq_GEO_Count.xlsx
Mishra_RNA-Seq_GEO_Comparison.xlsx
|
| Data processing |
The reads were mapped to the Arabis alpina reference genome (Assembly Version 5) using HISAT2 package with default settings. The SAM files obtained after mapping were converted into BAM files.
Genes were assembled and quantified in each sample using StringTie package. The raw gene count was obtained by feeding the .gtf file to a python script (prepDE.py) obtained from http://ccb.jhu.edu/software/stringtie/index.shtml?t=manual.
The raw gene counts table was further analysed with DESeq2 to obtain differentially expressed genes.
Differentially expressed genes within 2 conditions with a fold change of 2 and a p-value significance <0.05 were analysed further.
Genome_build: Arabis alpina ( NCBI ID: 17813)
Supplementary_files_format_and_content: Excel sheets containing the count of each gene in each replicate of each sample and the normalised abundance measurement from DESeq2.
|
| |
|
| Submission date |
Jun 02, 2021 |
| Last update date |
Apr 01, 2024 |
| Contact name |
Maria Albani |
| Organization name |
University of Cologne
|
| Department |
Botanical institute
|
| Street address |
Carl-von-Linné-Weg 10
|
| City |
Köln |
| ZIP/Postal code |
50829 |
| Country |
Germany |
| |
|
| Platform ID |
GPL26216 |
| Series (1) |
| GSE176054 |
RNA-Seq analysis of adventitious rooting zone of Arabis alpina main stem during extended cold exposure. |
|
| Relations |
| BioSample |
SAMN19515891 |
| SRA |
SRX11051672 |
