|
| Status |
Public on Mar 08, 2023 |
| Title |
siRNA13D_drought_biol_rep_1 |
| Sample type |
SRA |
| |
|
| Source name |
second leaf
|
| Organism |
Triticum aestivum |
| Characteristics |
cultivar: Atlas66
developmental stage: 21 days post-germination
tissue: second leaf
genotype: Under-expressing TaZFP13D
treatment: well-watered 14 days and 7 days drought
|
| Treatment protocol |
Control well-watered wheat plants were grown for 21 days and watered every day, while drought-treated plants were watered daily for 14 days, then, drought was initiated by withholding water for 7 days.
|
| Growth protocol |
Wheat seeds were inoculated with the 4RNAs Barley stripe mosaic virus using the previously described seed imbibition method (Cheuk and Houde 2017 Plant Methods (2017) 13:24 DOI 10.1186/s13007-017-0175-5). Wild-type plants (WT) without BSMV, were germinated in the same conditions with distilled water only. After 4 days of germination, wheat seedlings were potted in soil mix with a density of 10 plants per pot (13.5-13.5-13 cm; length-width-height).Plants were grown in a mixture of black earth, perlite, and peat moss (2:1:1, v:v:v) in E15 Conviron growth cabinets at 22 °C and 70% relative humidity, under a photon flux density of 100 µmol m-2 s-1 (fluorescent and incandescent lighting) and a 16 h / 8 h (day/night) photoperiod.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Samples are composed of complete second leaves from three different 21-days old wheat seedlings, harvested at the same time of day and flash-frozen in liquid nitrogen. Total RNA was extracted from plant tissues using the Monarch Total RNA Miniprep Kit (New England Biolabs).
RNA libraries were prepared for sequencing using standard Illumina protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
The wrapper script Trim-galore (version 0.6.3) was used to remove sequencing adapters (Illumina universal) and four additional bases at the 5’ and 3’ ends of each read, retained reads with a Phred quality score exceeding 30, and discarded reads shorter than 20 nucleotides.
Sequencing artifacts were filtered from the remaining reads using the Fastx_toolkit (version 0.0.14) and reads quality was verified with the FastQC tool (version 0.11.9).
Triticum aestivum reference transcriptome (release 52) was retrieved on Ensembl Plants and used for transcripts abundances quantification using Salmon (version 1.5.1) in quasi-mapping mode, with Kmer size set to 31.
Transcripts-levels count tables obtained with Salmon and the Triticum aestivum gff3-type annotation file (release 52 from Ensembl Plants) were used to determine differentially expressed genes in TaZFP13D OEX and TaZFP13DsiRNA samples with the DESeq2 software (version 2.11.40.7).
Assembly: triticum aestivum release 52 from Enesembl plant.
Supplementary files format and content: The processed data file is a matrix (.xlsx) containing gene-level normalized abundance measurements provided by the DESeq2 software (a mean value was calculated if different biological replicates were available).
|
| |
|
| Submission date |
Mar 07, 2023 |
| Last update date |
Mar 08, 2023 |
| Contact name |
William BOUARD |
| E-mail(s) |
william.bouard@gmail.com
|
| Phone |
514-978-3000
|
| Organization name |
UQAM
|
| Department |
sciences biologiques
|
| Lab |
Mario Houde
|
| Street address |
141 Av. du Président-Kennedy
|
| City |
Montreal |
| State/province |
QC |
| ZIP/Postal code |
H2X 1Y4 |
| Country |
Canada |
| |
|
| Platform ID |
GPL25409 |
| Series (1) |
| GSE226842 |
The wheat C2H2 zinc finger protein TaZFP13D modulates the expression of chloroplast-related genes, improves growth and drought stress tolerance. |
|
| Relations |
| BioSample |
SAMN33614580 |
| SRA |
SRX19580845 |
