|
| Status |
Public on Aug 03, 2023 |
| Title |
Exp2_halfparS25_Rep2 |
| Sample type |
SRA |
| |
|
| Source name |
bacterial cell
|
| Organism |
Pseudomonas aeruginosa |
| Characteristics |
strain: PAO1161 leu-
genotype: half-parS25
growth phase: LB 37oC log phase of culture growth
cell type: bacterial cell
|
| Growth protocol |
P. aeruginosa PAO1161 (WT) as well as half-parS25 strains were grown overnight in LB broth (DifcoTM L Broth, Lennox, BD), diluted 1:200 in fresh medium and cells were harvested at logarithmic phase of growth (OD 600nm of 0.5). Culturing was performed in 20ml of medium in 100ml flask, closed with a cotton plug with shaking 200 rpm, at 37oC.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from three independent replicates of each strain. 2 ml of cultures which reached optical density 0.4-0.6 at 600 nm were mixed with 4 ml of RNAprotect Bacteria Reagent (Qiagen). RNA was isolated with an RNeasy mini-kit (Qiagen) according to the manufacturer’s protocol. Total RNA was digested with DNase (TURBO DNA-free Kit, Ambion) to eliminate genomic DNA.
rRNA was depleted using Ribo-Zero rRNA Removal Kit (Bacteria) (MRZMB126, Illumina) according to manufacturer instructions. Libraries were prepared according to instructions accompanying the NEBNext Ultra DirectionalRNA Library Prep Kit for Illumina (NEB, E7420). Libraries were sequenced using standard Illumina protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
RNAseq_WT_halfparS25_raw_counts.csv
Exp2_halfparS25_vs_WT_gene_expression_changes_All.csv
|
| Data processing |
base calling: bcl2fastq v2.20 (Illumina)
Sequencing data were quality-checked and filtered using FASTP version 0.22.0.
Reads were mapped to P. aeruginosa PAO11161 genome (CP032126) using Bowtie2 version 2.2.5 using default settings.
The number of reads mapping to individual genes was counted using FeatureCounts v 2.0.3 (with the -s2 option).
Differential expression analysis was conducted using edgeR ver 3.40.2.
Assembly: CP032126
Supplementary files format and content: Raw counts of sequencing (FeatureCounts output summarized for all samples) (RNAseq_WT_halfparS25_raw_counts.csv).
Supplementary files format and content: A table with DE data for all genes and normalized abundance measurements (EdgeR output, separately for the two experiments) (Exp1_halfparS25_vs_WT_gene_expression_changes_All.csv and Exp2_halfparS25_vs_WT_gene_expression_changes_All.csv).
|
| |
|
| Submission date |
May 23, 2023 |
| Last update date |
Aug 03, 2023 |
| Contact name |
Adam Kawałek |
| E-mail(s) |
a.kawalek@ibb.waw.pl
|
| Phone |
+48225921216
|
| Organization name |
Institute of Biochemistry and Biophysics, PAS
|
| Department |
Department of Microbial Biochemistry
|
| Street address |
Pawinskiego 5A
|
| City |
Warszawa |
| ZIP/Postal code |
02-106 |
| Country |
Poland |
| |
|
| Platform ID |
GPL26913 |
| Series (2) |
| GSE233235 |
Transcriptome analysis of Pseudomonas aeruginosa strain, with 25 mutated half-parSs (ParB binding sites) |
| GSE233379 |
ChIPseq analysis of ParB binding to parSs and half-parSs in Pseudomonas aeruginosa under different environmental conditions and RNAseq analysis of selected half-parS removal on transcriptome |
|
| Relations |
| BioSample |
SAMN35329716 |
| SRA |
SRX20484644 |
