RNAseq of Pseudomonas extremaustralis treated with GSNO at low oxygen conditions (treated sample and controls)
Ontology highlight
ABSTRACT:
INSTRUMENT(S): NextSeq 550
ORGANISM(S): Pseudomonas extremaustralis
SUBMITTER:
PROVIDER: E-MTAB-11689 | biostudies-arrayexpress |
SECONDARY ACCESSION(S): ERP137354
REPOSITORIES: biostudies-arrayexpress
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Project description:sRNA40 (a novel sRNA) was pulse-expressed and its effects studied by transcriptomic profiling in P. extremaustralis, an Antarctic bacterium. For this approach we built a plasmid-based system, where sRNA40 was cloned under the control of the heterologous araBp promoter, inducible by arabinose (pBAD18-sRNA40). P. extremaustralis carrying the empty plasmid pBAD (pBAD18) was used as a control. Both strains were grown at low oxygen conditions for 24 hours. Cells were harvested after 10 min of induction with 0.1% arabinose. RNA was isolated using the Trizol method. RNA quality was analyzed on the Agilent Bioanalyzer and rRNA depletion was performed using the RiboZERO (Illumina). Samples were validated using an Agilent 2100 Bioanalyzer (Agilent Technologies). Libraries were prepared with TruSeq RNA Library Prep Kit v2 (Illumina) and sequenced with the Illumina NextSeq 550 platform with a single-end protocol.
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Project description:To further study the transcriptome of THP-1 human monocytes after exposure to S-Nitrosoglutathione (GSNO), we investigate whole genome microarray expression to identify genes regulated by exposure or not to GSNO. To further study the transcriptome of THP-1 human monocytes after exposure for 4 h to 50 ug / mL of S-Nitrosoglutathione-loaded polymeric Eudragit RL nanoparticles (GSNO-loaded ENP), we investigate whole genome microarray expression to identify genes regulated by exposure or not to 50 ug / mL of GSNO-loaded ENP. To further study the transcriptome of THP-1 human monocytes after exposure for 4 h to 200 ug / mL of empty polymeric Eudragit RL nanoparticles (empty ENP), we investigate whole genome microarray expression to identify genes regulated by exposure or not to 200 ug / mL of empty ENP. To further study the transcriptome of THP-1 human monocytes after exposure for 24 h to 50 ug / mL of S-Nitrosoglutathione-loaded polymeric Eudragit RL nanoparticles (GSNO-loaded ENP), we investigate whole genome microarray expression to identify genes regulated by exposure or not to 50 ug / mL of GSNO-loaded ENP. To further study the transcriptome of THP-1 human monocytes after exposure for 24 h to 50 ug / mL of empty polymeric Eudragit RL nanoparticles (empty ENP), we investigate whole genome microarray expression to identify genes regulated by exposure or not to 50 ug / mL of empty ENP. To further study the transcriptome of THP-1 human monocytes after exposure for 4 h to 50 ug / mL of empty polymeric Eudragit RL nanoparticles (empty ENP), we investigate whole genome microarray expression to identify genes regulated by exposure or not to 50 ug / mL of empty ENP. To further study the transcriptome of THP-1 human monocytes after exposure for 4 h to 200 ug / mL of S-Nitrosoglutathione-loaded polymeric Eudragit RL nanoparticles (GSNO-loaded ENP), we investigate whole genome microarray expression to identify genes regulated by exposure or not to 200 ug / mL of GSNO-loaded ENP. Changes in gene expression in THP-1 cells incubated without (control) or with 50 uM GSNO for 4 h, were measured. Five biological replicates were performed as controls: F_01; F_07; F_13; S_01; S_02. Four biological replicates were performed in GSNO exposed cells: S_13; S_14; S_15; S_16. Changes in gene expression in THP-1 cells incubated without (control) or with 50 ug / mL of GSNO-loaded ENPs (300 nm) for 4 h were measured. Five biological replicates were performed as controls: F_01; F_07; F_13; S_01; S_02. Three biological replicates were performed in 50 ug / mL of GSNO-loaded ENP exposed cells: S_06; S_07; S_08. Changes in gene expression in THP-1 cells incubated without (control) or with 200 ug / mL of empty ENPs (300 nm) for 4 h were measured. Five biological replicates were performed as controls: F_01; F_07; F_13; S_01; S_02. Three biological replicates were performed in 200 ug / mL of empty ENP exposed cells: S_17; S_19; S_20. Changes in gene expression in THP-1 cells incubated without (control) or with 50 ug / mL of GSNO-loaded ENPs (300 nm) for 24 h were measured. Five biological replicates were performed as controls: F_04; F_10; F_16; S_03; S_04. Four biological replicates were performed in 50 ug / mL of GSNO-loaded ENP exposed cells: S_09; S_10; S_11; S_12. Changes in gene expression in THP-1 cells incubated without (control) or with 50 ug / mL of empty ENPs (300 nm) for 24 h were measured. Five biological replicates were performed as controls: F_04; F_10; F_16; S_03; S_04. Three biological replicates were performed in 50 ug / mL of empty ENP exposed cells: F_05; F_11; F_17. Changes in gene expression in THP-1 cells incubated without (control) or with 50 ug / mL of empty ENPs (300 nm) for 4 h were measured. Five biological replicates were performed as controls: F_01; F_07; F_13; S_01; S_02. Three biological replicates were performed in 50 ug / mL of empty ENP exposed cells: F_02; F_08; F_14. Changes in gene expression in THP-1 cells incubated without (control) or with 200 ug / mL of GSNO-loaded ENPs (300 nm) for 4 h were measured. Five biological replicates were performed as controls: F_01; F_07; F_13; S_01; S_02. Four biological replicates were performed in 200 ug / mL of GSNO-loaded ENP exposed cells: S_21; S_22; S_23; S_24.
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