U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

SRX8449846: GSM4585934: SBW25_noplasmid_d4242_BR02; Pseudomonas fluorescens SBW25; RNA-Seq
2 ILLUMINA (Illumina HiSeq 4000) runs: 20.4M spots, 6G bases, 2.1Gb downloads

Submitted by: NCBI (GEO)
Study: Convergent transcriptional responses to acquisition and amelioration of different conjugative plasmids
show Abstracthide Abstract
Aim: to identify the transcriptional responses to acquisition of conjugative megaplasmids by Pseudomonas fluorescens, and how these effects are impacted by known compensatory mutations. Full abstract TBC. Overall design: Examination of effects of megaplasmid acqusition, compensatory mutations, and their combination. Ten treatments in triplicate (30 samples overall). The overall design is broadly factorial, but for some treatments design was nested. Treatments include a no-plasmid baseline control, megaplasmids alone, compensatory mutations alone (where available), and all combinations (where available). Definitions: dPFLU4242 is a deletion of the gene PFLU4242 (?PFLU4242) PQBR57_0059_V100A is a single basepair mutation in the plasmid pQBR57 causing a V100A mutation in PQBR57_0059 (T299>C) dgacS is a deletion of the gene gacS (PFLU3777, ?gacS) pQBR57 is a mercury resistance plasmid (see Hall et al. 2015 doi: 10.1111/1462-2920.12901) pQBR103 is a mercury resistance plasmid
Sample: SBW25_noplasmid_d4242_BR02
SAMN15075940 • SRS6752036 • All experiments • All runs
Library:
Instrument: Illumina HiSeq 4000
Strategy: RNA-Seq
Source: TRANSCRIPTOMIC
Selection: cDNA
Layout: PAIRED
Construction protocol: Samples were harvested at 4.5 G for 10 minutes, resuspended in 1 ml TRI reagent, and incubated at room temperate for 5 minutes. Amylene-stabilised chloroform (400 µl, Sigma-Aldrich 34854-M) was added to each tube, and incubated for 2-15 minutes at room temperature. Samples were then transferred to 5Prime Phase Lock Gel 'Heavy' tubes (VWR 733-2478) and centrifuged at 17 G for 15 minutes at room temperature. The aqueous phase was collected into a fresh microfuge tube and 450 µl isopropanol was added to precipitate RNA. Samples were incubated at room temperature for 30 minutes before pelleting at 17 G for 30 minutes. The pellet was rinsed by gently adding 1 ml of 70% ethanol and pelleting at 7.5 G for 5 minutes. The supernatant was carefully removed and the pellet allowed to air dry before resuspension in RNase-free water at 65°C. To remove any residual contaminating DNA, RNA was diluted to ≤200 ng/µl and treated with TURBO DNA-free RNase-free DNase (Invitrogen AM1907) according to the manufacturer's instructions. Reaction products were purified with Agencourt RNAClean XP beads. Ribosomal RNA was removed using the Bacterial RiboZero rRNA depletion kit (Illumina). NEBNext Ultra-Directional RNA library preparation kit (Illumina). Sequencing is 'reverse-stranded'.
Experiment attributes:
GEO Accession: GSM4585934
Links:
Runs: 2 runs, 20.4M spots, 6G bases, 2.1Gb
Run# of Spots# of BasesSizePublished
SRR1190287910,021,8802.9G1.1Gb2021-04-18
SRR1190288010,418,7193.1G1.1Gb2021-04-18

ID:
10985573

Supplemental Content

Search details

See more...

Recent activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...