|
| Status |
Public on May 23, 2022 |
| Title |
avrRpm1-OUT-1HPI-A |
| Sample type |
SRA |
| |
|
| Source name |
Leaf
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype: Columbia-0
tissue: Leaf
treatment: Pto AvrRpm1
area: Area surrounding the infiltration zone (OUT)
time: 1 hours post-infiltration
biological replicate: A
|
| Treatment protocol |
Arabidopsis Col-0 leaves were infiltrated locally with Pto DC3000 (avrRpm1) (5*107cfu/mL) or mock in a spatio-temporal manner. The infiltrated cells (IN zone) were harvested in parallel with the immediately adjacent uninfected cells (OUT zone). Samples were taken at 0,1,2,4,6 post-inoculation in three biological replicates.
|
| Growth protocol |
7 days on MS sucrose 1% sucrose : 16h light / 22°C, 3 weeks in short day condition : 9h light / 22°C
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
NucleoSpin RNA Macherey-Nagel
PolyA-mRNA
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Data processing |
Base-calling protocol: RTA2.7.3 bcl2fastQV2.17.1.14
“FastQC” and “TrimGalore!” software was used for raw Illumina reads quality control analysis and trimming of reads containing adaptor- or vector-derived sequences, respectively
rRNA was detected and removed using “SortMeRNA 2.1b” software
Cleaned reads together with the transcriptome of Arabidopsis thaliana (as of 30 August 2018), including ncRNA, were used to quantify gene expression at transcript level using the software “Salmon v0.11.3”
Raw counts aggregated by gene were obtained using “tximport v1.14.2” and the result was used as input to “DESeq2”. Then, genes adding up to less than 10 counts across all 60 samples were removed.
Counts were normalized using size factors calculated by DESeq2.
Genome_build: EnsemblPlants cDNA file Arabidopsis_thaliana.TAIR10.cdna.all.fa.gz as of 30 August 2018
Supplementary_files_format_and_content: Matrix table with normalized gene counts for every gene and every sample
|
| |
|
| Submission date |
Mar 07, 2022 |
| Last update date |
May 23, 2022 |
| Contact name |
Jose Salguero Linares |
| E-mail(s) |
[email protected]
|
| Organization name |
Centre for Research in Agricultural Genomics
|
| Lab |
Bacterial plant diseases and plant cell death
|
| Street address |
Carrer de la Vall Moronta s/n
|
| City |
Bellaterra |
| State/province |
Barcelona |
| ZIP/Postal code |
08193 |
| Country |
Spain |
| |
|
| Platform ID |
GPL21179 |
| Series (1) |
| GSE198022 |
Robust transcriptional indicators of plant immune cell death revealed by spatio-temporal transcriptome analyses |
|
| Relations |
| BioSample |
SAMN26505635 |
| SRA |
SRX14395956 |
