|
| Status |
Public on Dec 21, 2020 |
| Title |
sg-CTRL r3 |
| Sample type |
SRA |
| |
|
| Source name |
total cell lysate
|
| Organism |
Pseudomonas aeruginosa |
| Characteristics |
strain: PAO1
growth phase: exponential
guide rna target: CTRL
|
| Growth protocol |
over night cultures were grown in LB + 5 ug/ml irgasan & 30 ug/ml gentamycin at 37°C shaking, cultures were backdiluted to fresh LB + antibiotics and 0.2% arabinose to an OD of 0.05 and cultured for 3h. 2 ml of culture were harvested.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
bacterial pellets were resuspended in 1ml Tri Reagent (Sigma Aldrich T9424) and incubated for 5 min. 200 ul Chloroform were added, vortexed and incubated for 5 min. Samples were centrifuged for 10 min at 4°C and the aqueous phase was mixed with 200 ul 100% EtOH and transferred to PureLink RNAMini Columns (Invitrogen). Subsequent washing and elution was performed following manufactorer's instructions. Contaminating DNA was removed using DNA-free kit (Apllied Bioystems). RNA was stored at -80 °C.
Libraries were constructed using NuGEN Ovation Complete Prokaryotic RNA-Seq DR Multiplex Systems kit. Preparation was performed following manufactorer's instructions
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
CTRL r3
|
| Data processing |
Sequncing of the Illumina cDNA libraries was performed by Biopolymers facility at Harvard Medical School. RNA-sequencing was performed on NextSeq Mid Output by 100 bp single end high-throughput sequencing.
The raw reads in FastQ format were aligned to P. aeruginosa PAO1 genome (RefSeq accession number NC_002516) using the bowtie2 algorithm on Geneious 10.0 (http://www.geneious.com).
Differential expression analysis was performed on Geneious using Deseq2
Genome_build: NC_002516
Supplementary_files_format_and_content: RPKM and TPM values of each sample
Supplementary_files_format_and_content: differential expression analysis compared to sg-CTRL
|
| |
|
| Submission date |
Oct 09, 2020 |
| Last update date |
Dec 21, 2020 |
| Contact name |
Anne-Sophie Stolle |
| Organization name |
Institut für Infektiologie
|
| Street address |
Von-Esmarch-Str. 56
|
| City |
Muenster |
| ZIP/Postal code |
48149 |
| Country |
Germany |
| |
|
| Platform ID |
GPL21297 |
| Series (1) |
| GSE159327 |
CRISPRi knockdown of essential genes in Pseudomonas aeruginosa |
|
| Relations |
| BioSample |
SAMN16407323 |
| SRA |
SRX9272857 |
