|
| Status |
Public on Jul 31, 2022 |
| Title |
RC1 |
| Sample type |
SRA |
| |
|
| Source name |
Roots
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype: Col-0
developmental stage: Aprox. 9-days-old plants (3 days post infection)
agent: Non-infected
|
| Treatment protocol |
Arabidopsis plants were inoculated at 5 days post germination at the root tip with approximately 20 freshly-hatched Meloidogyne J2 each plant. The inoculated and non-inoculated plants were then kept in the dark for 2 days. During the first 48 hours, the infections and control roots growth were accessed. After 2 days, the plates containing both inoculated and non-inoculated plants were maintained in the light, covered by a gauze. For more details concerning this protocol please see Olmo et al. (2017; doi: 10.1007/978-1-4939-6831-2_5).
|
| Growth protocol |
Arabidopsis thaliana plants were were grown in controlled environment chambers under 16 h/8 h of light/dark at 23ºC
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Galls and control roots were collected at 3 days post infection and frozen on liquid nitrogen. Total RNA was extracted using the AllPrep DNA/RNA/miRNA Universal Kit from Qiagen with several adaptations (Silva et al., 2019; doi: 10.3389/fpls.2019.00657)
Illumina's TruSeq Stranded mRNA Library Prep Kit was used to prepare the libraries, strictly following the manufacturer's instructions. The fragment size distribution of the libraries were checked in the Agilent 2100 Bioanalyzer using the Agilent High Sensitivity DNA Kit. The libraries were then sequenced in a fraction of an Illumina HiSeq X PE150. Both steps were performed by the company AllGenetics & Biology SL.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Control (non-infected roots)
|
| Data processing |
The reads were firstly checked for quality using FastQC (version 0.11.8). Trimming was then performed using BBDuk (version 38.39).
Trimmed reads were mapped to the combined A. thaliana (TAIR10) and M. javanica (Assembly GCA_900003945.1; Blanc-Mathieu et al., 2017) using STAR (version 2.7.0d; Dobin et al., 2013) and the following parameters: --outFilterMismatchNmax 7, --outFilterMultimapNmax 5.
The BAM files produced with STAR where then used by HTSeq (version 0.11.2), in order to produce the count tables used for the differentially expressed analysis.
The normalized count tables and the posterior differentially expression analysis were performed with DESeq2 (version 1.20.0; Love et al., 2014) using R (version 3.5.2) and RStudio (version 1.1.463).
Genome_build: A. thaliana (TAIR10) and M. javanica (Assembly GCA_900003945.1; Blanc-Mathieu et al., 2017)
Supplementary_files_format_and_content: Matrix table with normalized counts for each A. thaliana gene and sample
Supplementary_files_format_and_content: Text file including pvalue and padjusted value for each A.thaliana gene
Supplementary_files_format_and_content: normalized counts (.txt)
Supplementary_files_format_and_content: DEseq analysis output (.txt)
|
| |
|
| Submission date |
Jul 27, 2020 |
| Last update date |
Jul 31, 2022 |
| Contact name |
Carolina Escobar |
| E-mail(s) |
carolina.escobar@uclm.es
|
| Organization name |
University of Castilla-La Mancha
|
| Street address |
Avenida Carlos III, s/n
|
| City |
Toledo |
| ZIP/Postal code |
45071 |
| Country |
Spain |
| |
|
| Platform ID |
GPL13222 |
| Series (1) |
| GSE155171 |
Transcriptome of galls formed by Meloidogyne javanica in Arabidopsis thaliana at 3 days post infection |
|
| Relations |
| BioSample |
SAMN15650411 |
| SRA |
SRX8830924 |
