GSM7688817: ∆vtlR/lsrB, 24h, biol rep1; Agrobacterium fabrum; RNA-Seq - SRA

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SRX21286622: GSM7688817: ∆vtlR/lsrB, 24h, biol rep1; Agrobacterium fabrum; RNA-Seq
1 ILLUMINA (Illumina NovaSeq 6000) run: 8.2M spots, 2.5G bases, 755.5Mb downloads

External Id: GSM7688817_r1

Submitted by: Microbial Biology, Ruhr University Bochum

Study: The LysR-type transcription factor LsrB regulates beta-lactam resistance in Agrobacterium tumefaciens

PRJNA1003054 • SRP453881 • All experiments • All runs

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We investigated the role of the LysR-type transcriptional regulator LsrB (Atu2186) from Agrobacterium tumefaciens C58 (alias A. fabrum C58), which regulates the expression of small-regulatory-RNA (sRNA) and several protein-coding genes, such as ampD (atu2113). In our current study we invesigated the role of LsrB in beta-lactam resistance. For this purpose, we constructed a vtlR/lsrB deletion mutant. Total RNA was isolated from this mutant. Sequencing was done on the Illumina NovaSeq 6000 platform. Wild-type samples that derived from the same experiment were published previously (Kraus et al., 2020) (GEO accession: GSE150941). In the vtlR/lsrB mutant around 800 protein coding genes and around 80 sRNA coding genes were downregulated or upregulated at least three-fold (p value = 0.05). Overall, the results demonstrate the huge regulatory effect of LsrB on the transcriptome of A. tumefaciens. Kraus, A., Weskamp, M., Zierles, J., Balzer, M., Busch, R., Eisfeld, J., et al. (2020) Arginine-rich small proteins with a domain of unknown function DUF1127 play a role in phosphate and carbon metabolism of Agrobacterium tumefaciens. J Bacteriol 202: e00309-20. Overall design: Illumina RNA sequencing of the transcriptomes of Agrobacterium fabrum C58 wild type, a vtlR/lsrB deletion mutant (?atu2186). Re-analysed Samples: GSM4561620 SAMN14984052 SRX8370442 GSM4561621 SAMN14984051 SRX8370443 GSM4561622 SAMN14984050 SRX8370444

Sample: ∆vtlR/lsrB, 24h, biol rep1

SAMN36877827 • SRS18536735 • All experiments • All runs

Organism: Agrobacterium fabrum

Library:

Name: GSM7688817

Instrument: Illumina NovaSeq 6000

Strategy: RNA-Seq

Source: TRANSCRIPTOMIC

Selection: cDNA

Layout: PAIRED

Construction protocol: RNA was extracted via hot-phenol method as described in Wilms et al. (2012, DOI: 10.4161/rna.17212). Samples were treated with RNase-free DNase. RNA libraries were prepared by Novogene using 1 µg of RNA and the NEBNext® Ultra™ RNA Library Prep Kit for Illumina®. Index codes were added to attribute sequences to each sample. The RNA was fragmented with divalent cations in NEBNext First Strand Synthesis Reaction Buffer (5x) at elevated temperature. Then, first strand synthesis was carried out with random hexamer primers and M-MuLV reverse transcriptase. Second strand synthesis was performed with DNA polymerase I and RNase H. Blunt ends were created from overhangs via exonuclease/polymerase activities. DNA 3' ends were adenylated and NEBNext Adaptors with hairpin loop were ligated. Fragments were purified with the AMPure XP system. The cDNA was then incubated at 37 °C for 15 minutes with 3 µl USER Enzyme and then at 95 °C for 5 minutes. The subsequent PCR was performed with Phusion High-Fidelity DNA polymerase, Universail PCR primers, and Index (X) Primer. The PCR products were purified via AMPure XP system and the quality was assured via Agilent Bioanalyzer 2100.

Runs: 1 run, 8.2M spots, 2.5G bases, 755.5Mb

Run	# of Spots	# of Bases	Size	Published
SRR25557697	8,233,796	2.5G	755.5Mb	2023-08-12

ID:: 28723582

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