|
| Status |
Public on Mar 29, 2024 |
| Title |
A. thaliana, control, 0 h, rep1 |
| Sample type |
SRA |
| |
|
| Source name |
root
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: root
ecotype: Col-0
treatment: control
time: 0 h
|
| Treatment protocol |
Trichoderma-Arabidopsis assays involved the sterilization and sowing of seeds as described earlier. Pots containing the seeds were placed at 21 ± 2°C, under a 12 h light (150 µmol m-2 sec-1 light) and 12 h dark photoperiod. Four-day-old seedlings were then transferred to individual inserts with the specified substrate and grown for 0, 24, 48, 72 and 96 h at 21 ± 1°C under a 12/12 h light/dark regime.
|
| Growth protocol |
Arabidopsis seeds underwent surface sterilization with 75% ethanol for 3 minutes, followed by a 7-minute treatment with a 20% (v/v) chlorine solution. After three rinses with sterile distilled water (3 minutes each), the seeds were either placed on plates with 1× Murashige and Skoog (MS) medium (PhytoTech Labs, Lenexa, KS, US; Murashige and Skoog, 1962) or sown in flowerpots with a mixture of sterilized peat moss (LAMBERT™), perlite (Hortipel), and vermiculite (Verlite) in a 3:1:1 ratio. The seeds were stratified by 48 h at 4°C in the dark and were subsequently germinated on MS medium with 0.7% agar or in pots under a 12-hour light (150 µmol m-2 sec-1 light) and 12-hour dark photoperiod. In vitro-grown seedlings were collected for further analyses.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted and sRNA-seq libraries were generated according to the sRNA cloning protocol provided by Solexa.
|
| |
|
| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina MiSeq |
| |
|
| Description |
Ath_R1
|
| Data processing |
Raw reads were quality assessed using cutadapt v1.9.1 and Trimmomatic v0.36 to remove adapter sequences and low-quality reads, respectively.
To identify sRNA source, the sRNA sequences were mapped to the T. atroviride and A. thaliana genomes using standalone BLAST version 2.11.0+ with word length 7 and e-value cut-off of 0.1.
The BLAST hits were then filtered based on their occurrence at only one location and maximum number of mismatches of 1.
Assembly: TAIR10 for A. thaliana, and JGI v2 for T. atroviride
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
|
| |
|
| Submission date |
Jan 26, 2024 |
| Last update date |
Mar 29, 2024 |
| Contact name |
Luis F. Garcia-Ortega |
| E-mail(s) |
[email protected]
|
| Organization name |
Center for Research and Advanced Studies of the National Polytechnic Institute (Cinvestav)
|
| Department |
Department of Genetic Engineering
|
| Lab |
Laboratory for research and learning in biological computing
|
| Street address |
Km 9.6 Libramiento Norte
|
| City |
Irapuato |
| State/province |
Guanajuato |
| ZIP/Postal code |
36824 |
| Country |
Mexico |
| |
|
| Platform ID |
GPL17970 |
| Series (1) |
| GSE254275 |
Trichoderma atroviride small RNA1 targets the Arabidopsis PRIM2 gene to establish a mutualistic relationship |
|
| Relations |
| BioSample |
SAMN39616634 |
| SRA |
SRX23398520 |
