|
| Status |
Public on Jul 24, 2024 |
| Title |
Col-0 normoxia/flg22 rep1 [3Col-0NF-1] |
| Sample type |
SRA |
| |
|
| Source name |
whole seedlings
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: whole seedlings
accession: Col-0
genotype: wild type
treatment: normoxia/flg22
|
| Treatment protocol |
Five 9-day old seedlings per genotype per treatment were transferred to 35 mm x 10 mm dishes, each containing 4 mL of 0.5xMS liquid medium and placed on a shaker at 120 rpm overnight in continuous light conditions, 20°C. On day 10, seedlings were treated simultaneously with 100 nM flg22, or equivalent volume of water (mock), and hypoxia in anaerojars or normoxia at ambient oxygen levels. After 1 hr, the seedlings were harvested in liquid nitrogen and stored at -80°C for total RNA extraction.
|
| Growth protocol |
Arabidopsis seedlings were sown and grown on 0.5xMS agar with 0.5% (w/v) sucrose plates in continuous light at 20°C.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was extracted using Spectrum Plant Total RNA extraction kit (Merck)
Libraries were prepared by BGI Genomics (Hong Kong)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
BGISEQ-500 |
| |
|
| Description |
Col-0_NF_1
|
| Data processing |
Data processing was carried out by BGI using the filtering software SOAPnuke (including removal of reads containing the adaptor; removal of reads whose N content is greater than 5%; and removal of low-quality reads).
The Hierarchical Indexing for Spliced Alignment of Transcripts (HISAT) software was then used for mapping clean reads to the reference genome.
Differential gene expression was determined using DESeq2.
Assembly: Reference Genome Version: GCF_000001735.4_TAIR10.1
Supplementary files format and content: Tab-delimited file including gene counts for each sample
|
| |
|
| Submission date |
Nov 02, 2023 |
| Last update date |
Jul 24, 2024 |
| Contact name |
Emmanuelle Graciet |
| E-mail(s) |
[email protected]
|
| Organization name |
Maynooth University
|
| Department |
Biology
|
| Lab |
Graciet Lab
|
| Street address |
Biology Department
|
| City |
Maynooth |
| State/province |
Kildare |
| ZIP/Postal code |
W23 C2N1 |
| Country |
Ireland |
| |
|
| Platform ID |
GPL24025 |
| Series (1) |
| GSE246848 |
Analysis of the transcriptional effect of hypoxia on flg22 response |
|
| Relations |
| BioSample |
SAMN38080477 |
| SRA |
SRX22339536 |
