Pectobacterium carotovorum subsp. carotovorum
Protocols: Potato minitubers (cv. 'Asterix') were inoculated with bacterial suspension (30 µL, OD600=0.8 in PBS), in vitro control was bacteria on solid M9 minimal medium (70 µL, OD600=0.8 in PBS). Infected potato tissue was harvested at 24, 48 and 72 hpi, and M9 control was harvested at 24 hpi. Samples were frozen in liquid N2 an stored at -80 °C. Macerated potato tissue and bacteria grown on M9 were homogenized in liquid N2 using pestle and mortar. RNA was isolated from the homogenized samples using the Spectrum Plant Total RNA kit (Sigma Aldrich) with the optional on-column DNase digestion (On-Column DNase I Digestion Set, Sigma-Aldrich). Ribosomal RNA was depleted using the RiboMinus Transcriptome Isolation Kit for bacteria (ThermoFisher). Libraries were prepared by the Norwegian Sequencing Centre (NSC). RiboZero ribosome depletion was done before delivery of the samples and NSC performed the remaining library preparation steps using the TruSeq Stranded RNA HT kit (Illumina).
ENA-FIRST-PUBLIC
2020-03-19T04:03:10Z
ENA-LAST-UPDATE
2019-04-30T14:36:44Z
External Id
SAMEA5585412
INSDC center name
Norwegian Institute for Bioeconomy Research (NIBIO)
INSDC first public
2020-03-19T04:03:10Z
INSDC last update
2019-04-30T14:36:44Z
INSDC status
public
Submitter Id
E-MTAB-7921:PccPot72hpi-rep2
broker name
ArrayExpress
genotype
wild type genotype
growth condition
grown on Potato minituber (cv. 'Asterix')
sample name
E-MTAB-7921:PccPot72hpi-rep2
scientific_name
Pectobacterium carotovorum subsp. carotovorum
strain
PK1045-1-2-13