|
| Status |
Public on Jul 24, 2024 |
| Title |
10-day old Col-0 (wild type) seedlings mock-treated (1 hour)_rep3 |
| Sample type |
SRA |
| |
|
| Source name |
Whole seedlings
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: Whole seedlings
ecotype: Col-0
genotype: wildtype
treatment: mock
|
| Treatment protocol |
Fifty 9-day old seedlings per genotype per treatment were transferred to 2 wells of a 6-well plate, each containing 6 mL of 0.5xMS with 0.5% sucrose liquid medium and returned to the growth room in continuous light with gentle agitation at 120 rpm. 24 hrs after transfer, 1 µM flg22 or an equivalent volume of water (mock treatment) was added to each well for 1 hr, after which seedlings were collected and frozen in liquid nitrogen 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 |
320_CM
|
| 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 |
Oct 25, 2023 |
| Last update date |
Jul 24, 2024 |
| Contact name |
Emmanuelle Graciet |
| E-mail(s) |
emmanuelle.graciet@mu.ie
|
| 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) |
| GSE246173 |
Comparison of the response of Col-0 and ate1 ate2 N-degron mutant to flg22 |
|
| Relations |
| BioSample |
SAMN37976885 |
| SRA |
SRX22215240 |
