Protocols: D. dadantii cells were grown at exponential and stationary phases in four different growth media: M63 supplemented with 0.2% saccharose as carbon source (minimum medium), with or without 0.2% (w/v) polygalacturonate (PGA) and with or without 0.1% Saintpaulia leaf extracts (plant extract- 1 g leaves in 1 L M63). Total RNA from each D. dadantii sample was isolated using the frozen acid phenol method (Maes et Messens 1992), and submitted to Vertis Biotechnologie AG: ribosomal RNA molecules were depleted from the total RNA samples using the Ribo-Zero rRNA Removal Kit for bacteria (Epicentre). From the rRNA depleted RNA samples, the small RNA fractions <200 nt were separated from the large fractions using the RNeasy MinElute Cleanup Kit (Qiagen). TSS cDNA libraries were generated from the rRNA depleted large RNA fractions by Vertis Biotechnologie AG: first, the samples were fragmented using RNase III. Samples were then poly(A)-tailed using poly(A) polymerase, and split into two halves. One half was treated with Terminator exonuclease (+TEX, Epicentre), while the other one was left untreated (-TEX). 5'PPP structures were then converted into 5'P ends using RNA 5' Polyphosphatase (5'PP, Epicentre). Afterwards, an RNA adapter was ligated to the 5'P of the RNA. First-strand cDNA synthesis was performed using an oligo(dT)-adapter primer and the M-MLV reverse transcriptase. The resulting cDNAs were PCR-amplified using a high fidelity DNA polymerase, and purified using the Agencourt AMPure XP kit (Beckman Coulter Genomics).
ENA first public
2022-01-01
ENA last update
2022-01-01
External Id
SAMEA6846198
INSDC center alias
Universite de Lyon, INSA Lyon, Universite Claude Bernard Lyon 1, CNRS UMR5240, Laboratoire de Microbiologie, Adaptation et Pathogenie
INSDC center name
Universite de Lyon, INSA Lyon, Universite Claude Bernard Lyon 1, CNRS UMR5240, Laboratoire de Microbiologie, Adaptation et Pathogenie
INSDC first public
2022-01-01T00:12:24Z
INSDC last update
2022-01-01T00:12:24Z
INSDC status
public
Submitter Id
E-MTAB-9075:S3 -TEX
broker name
ArrayExpress
environmental stress
mixed (pH, NaCl, H2O2)
growth phase
stationary
organism part
whole organism
sample name
E-MTAB-9075:S3 -TEX
strain
3937