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ERX4089797: NextSeq 500 paired end sequencing; Transcriptomic response of Dickeya dadantii ihfA mutant to DNA relaxation by novobiocin
1 ILLUMINA (NextSeq 500) run: 20.2M spots, 3G bases, 1Gb downloads

Design: Transcriptomic response of Dickeya dadantii ihfA mutant to DNA relaxation by novobiocin
Submitted by: INSA Lyon (INSA LYON)
Study: Transcriptomic response of Dickeya dadantii ihfA mutant to DNA relaxation by novobiocin
PRJEB38153 • ERP121539 • All experiments • All runs
show Abstracthide Abstract
We analyze the transcriptomic response of the phytopathogenic enterobacterium Dickeya dadantii ihfA mutant to a DNA supercoiling relaxation shock using the gyrase inhibitor novobiocin. The shock was applied to Dickeya cells grown in minimal medium supplemented with sucrose, in exponential or transition to stationary phase, and in minimal medium with sucrose + PGA (a pectin derivative) in transition to stationary phase.
Sample: ihfA_stat_nov_1
SAMEA6813498 • ERS4541141 • All experiments • All runs
Organism: Dickeya dadantii
Library:
Name: ihfA_stat_nov_1_p
Instrument: NextSeq 500
Strategy: WGS
Source: TRANSCRIPTOMIC
Selection: RANDOM
Layout: PAIRED
Construction protocol: Cells were collected in exponential phase (OD=0.2 at 600nm) or transition to stationary phase (OD=0.9-1.2 for glucose, OD=1.9-2.2 for glucose+PGA,at 600nm). Growth in minimal medium M63 supplemented with sucrose (0.2% wt/vol) Treated samples were subjected to 15 min novobiocin shock (100 ug/ml) 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 for ribosomal depletion (Illumina RiboZero kit) and RNA fragmentation. Strand-specific cDNA libraries were constructed by Vertis Biotechnologie AG.
Experiment attributes:
Experimental Factor: growth condition: M63+G, transition to stationary phase
Experimental Factor: compound: novobiocin
Experimental Factor: dose: 100
Runs: 1 run, 20.2M spots, 3G bases, 1Gb
Run# of Spots# of BasesSizePublished
ERR409449920,185,7813G1Gb2021-03-15

ID:
13484956

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