|
| Status |
Public on Feb 26, 2018 |
| Title |
Pto_flg22_#1-3 |
| Sample type |
SRA |
| |
|
| Source name |
Bacteria infected to Arabidopsis thaliana
|
| Organism |
Pseudomonas syringae pv. tomato str. DC3000 |
| Characteristics |
strain: Pto
host genotype: Col-0
replicate: #1
agent: 500 nM flg22
|
| Growth protocol |
Plants were grown in a chamber with a 12-h light period, 23 °C temperature at day time and 21 °C at night time.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using the TRIzolTM reagent (Thermo Fisher Scientific) and the Direct-zolTM RNA Miniprep kit (Zymo Research). Purified RNA was treated with 10 U of RNase-free DNase I (Roche Applied Science), after which RNA was purified a second time with the Direct-zolTM RNA Miniprep kit. Non-organellar 18S and 28S rRNAs, and poly(A) mRNAs were depleted using the MICROBEnrichTM kit (Thermo Fisher Scientific).
RNA-Seq libraries were prepared using the Ovation Arabidopsis RNA-Seq system 1–16 (NuGEN) with two modifications to the manufacturer’s protocol. First strand cDNA synthesis used only the first strand primer random mix (the oligo dT primer mix was omitted), while on strand selection II, custom insert dependent adapter cleavage probes (InDA-C; currently referred to as AnyDeplete) with specificity to highly abundant A. thaliana chloroplast and nuclear transcripts (361 probes) and Pto DC3000 rRNAs (65 probes) (1 µL of each 2 µM probe mixture was used) were added to the mixture of A. thaliana cytoplasmic, chloroplast, and mitochondrial rRNA custom probes that are included with the kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Base calling was done by the Illumina Real Time Analysis software (RTA version 1.18.64).
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 01, 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 |
GPL23977 |
| Series (2) |
| GSE103406 |
In planta bacterial RNA-Seq without bacterial isolation |
| GSE103442 |
Transcriptome landscape of a bacterial pathogen under plant immunity |
|
| Relations |
| BioSample |
SAMN07604100 |
| SRA |
SRX3158991 |
