|
| Status |
Public on Mar 15, 2024 |
| Title |
bep.hypo_1401_3 |
| Sample type |
SRA |
| |
|
| Source name |
bacterial cell
|
| Organism |
Pseudomonas aeruginosa UCBPP-PA14 |
| Characteristics |
strain: oprL-hypomorph
cell type: bacterial cell
treatment: 0.5% NaCl + 256 µM BRD1401
replicate: replicate 3
|
| Treatment protocol |
LB medium with appropriate drugs such as BRD1401 or inducers such as arabinose was prepared at 2X final concentration and dispensed into 384 well plates. Diluted bacterial suspensions were added on top to achieve a final bacterial density of 0.1-0.2 OD600nm and incubated at 37ºC for 120 minutes. Three biological replicates were included.
|
| Growth protocol |
Bacterial cultures were inoculated from glycerol stocks, grown overnight with appropriate selection antibiotics at 37ºC with shaking and sub-cultured at 37ºC with shaking until log-phase growth. Cultures were diluted to an OD600nm of 0.2-0.4.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
At the end of the incubation period, samples were mixed with 30uL of 3X RNAgem Blue Buffer (Zygem, Charlottesville VA), and chemically lysed by incubation in a thermocycler at 75°C for 10 minutes. Total RNA was then extracted using the Direct-zol kit (Zymo Research, Irvin CA), and RNA quality and quantity were analyzed using the RNA ScreenTape with the 2200 TapeStation (Agilent, Santa Clara CA).
RNA-Seq libraries were prepared using the RNA TagSeq protocol previously described (Shishkin, A. et al. Nature methods. 2015. https://doi.org/10.1038/nmeth.3313)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
BWA to align reads to reference and read counts generated using custom scripts.
DESeq2 (1.28.1) package in R was used to obtain fold changes in gene expression across multiple conditions
Assembly: NC_0088463.1 (UCBPP-PA14)
Supplementary files format and content: comma separated file with counts for each sample for each gene
|
| |
|
| Submission date |
Jan 24, 2024 |
| Last update date |
Mar 15, 2024 |
| Contact name |
Thulasi Warrier |
| E-mail(s) |
twarrier@broadinstitute.org
|
| Organization name |
Broad Institute
|
| Department |
IDMP
|
| Lab |
Hung Lab
|
| Street address |
415 Main Street
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02142 |
| Country |
USA |
| |
|
| Platform ID |
GPL27892 |
| Series (1) |
| GSE254108 |
A multiplexed chemical screen identifies a novel, species-specific Pseudomonas aeruginosa inhibitor that targets LPS interaction with the outer membrane protein, OprH [1401_dataset2] |
|
| Relations |
| BioSample |
SAMN39596607 |
| SRA |
SRX23385094 |
