|
| Status |
Public on Jun 04, 2024 |
| Title |
Col-0, cold (4°C), 12h, Bio Replicate 2 |
| Sample type |
SRA |
| |
|
| Source name |
10-day seedling
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: 10-day seedling
genotype: WT
treatment: Cold
time: 12h
|
| Treatment protocol |
12 day old seedlings were subjected to 4°C cold stress and samples were collected after 12h.
|
| Growth protocol |
Seeds were surface sterilized and stratified at 4°C for 48-72h in the dark. Growth media constituted of 1/2 MS media.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated using RNeasy Plant mini kit (Qiagen). Isolated RNA was treated with TURBO DNAse to remove DNA contamination.
Strand specific libraries were prepared by Novogene Europe.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
UPSC pipeline was used to generare salmon files. More information can be found at doi: 10.5281/zenodo.4001773.
Trimmmomatic was used to trim adapter sequences and SortMeRNA was used to remove rRNA contamination.
FastQC was used to monitor the quality of reads at each step. Salmon was used to determine the read counts with AtRTD2 as reference.
Salmon files generated above were used for differential gene expression analysis using Deseq2
Assembly: Araport11
Supplementary files format and content: Salmon files
|
| |
|
| Submission date |
Jan 09, 2024 |
| Last update date |
Jun 04, 2024 |
| Contact name |
Peter Kindgren |
| E-mail(s) |
peter.kindgren@slu.se
|
| Organization name |
Swedish University of Agricultural Sciences
|
| Department |
Department of Forest Genetics and Plant Physiology
|
| Street address |
KB5C5, KBC building, Linnaeus väg 6
|
| City |
Umea |
| State/province |
Vasterbotten |
| ZIP/Postal code |
90736 |
| Country |
Sweden |
| |
|
| Platform ID |
GPL26208 |
| Series (1) |
| GSE252832 |
Antisense transcription from stress-responsive transcription factors fine-tunes the cold response in Arabidopsis |
|
| Relations |
| BioSample |
SAMN39324644 |
| SRA |
SRX23145992 |
