|
| Status |
Public on Feb 26, 2018 |
| Title |
Pto-AvrRpt2_Col_A71 |
| Sample type |
SRA |
| |
|
| Source name |
Bacteria isolated from Arabidopsis thaliana
|
| Organism |
Pseudomonas syringae pv. tomato str. DC3000 |
| Characteristics |
strain: Pto-AvrRpt2
host genotype: Col-0
replicate: A71
|
| Growth protocol |
Arabidopsis plants were grown in a chamber at 22°C with a 10 h light period and 60% relative humidity for 3 weeks and then in another chamber at 22°C with a 12 h light period and 60% relative humidity.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For RNA extraction, the TriFast solution was mixed with 200 μl of chloroform and the aqueous phase was isolated by centrifugation (typically 400 μl). The aqueous phase was mixed with 200 μl (half volume) of ethanol and then applied to the column of RNAqueous kit (Ambion). RNA was eluted in 30 μl of RNase free water following the manufacture’s protocol and treated with 2 U of TURBO DNase (Ambion) for 30 min at 37 ºC. Plant rRNAs were removed using Ribo-Zero plant kit (Epicentre) following the manufacture’s protocol.
cDNA libraries were generated with Ovation Complete Prokaryotic RNA-Seq kit 1-8 (NuGEN)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Data processing |
Illumina CASAVA-1.8.2 software was used for basecalling and Illumina adapter matching reads were removed using cutadapt 1.5
Reads were mapped to the P. syringae pv. tomato DC3000 genome using Bowtie2 (version 2.2.8) with the parameters -p 20 -q --phred33 and transformed into a count per gene per library by using HTSeq (version 0.6.0).
Supplementary_files_format_and_content: Tab-delimited text file including raw read counts per gene for each sample.
|
| |
|
| Submission date |
Sep 05, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Tatsuya Nobori |
| E-mail(s) |
[email protected]
|
| Phone |
+49-(0)221-5062-302
|
| Organization name |
Max-Planck Institute for Plant Breeding Research
|
| Street address |
Carl-von-Linne Weg 10, Max-Planck Institute for Plant Breeding Research
|
| City |
Cologne |
| ZIP/Postal code |
50829 |
| Country |
Germany |
| |
|
| Platform ID |
GPL23983 |
| Series (2) |
| GSE103441 |
In planta bacterial RNA-Seq with bacterial isolation. |
| GSE103442 |
Transcriptome landscape of a bacterial pathogen under plant immunity |
|
| Relations |
| BioSample |
SAMN07604134 |
| SRA |
SRX3159094 |
