|
| Status |
Public on Sep 23, 2024 |
| Title |
SPN_D39_3_BHI |
| Sample type |
SRA |
| |
|
| Source name |
bacterial cell
|
| Organism |
Streptococcus pneumoniae D39 |
| Characteristics |
cell type: bacterial cell
genotype: rpsL1
treatment: BHI
|
| Treatment protocol |
BHI Broth at 37 degrees celsius under atmosphere of 5% carbon dioxide
|
| Growth protocol |
Strains were grown in Difco Brain Heart Infusion Broth alone or supplmented with 0.2 mM zinc sulfate at 37oC in atmosphere of 5% CO2 to an OD620 of 0.2
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated from cells via the Fastprep blue kit (MPBiomedicals)
Library was generated with NEBNext Ultra II RNA Library Prep Kit for library preparation after removing DNA by DNase treatment and depleting rRNA with FastSelect Bacteria kit for rRNA depletion.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
rRNA depleted
|
| Data processing |
Adapters and low quality bases were trimmed using Cutadapt
Trimmed reads were mapped on the Streptococcus pneumoniae D39 using Bowtie2
Read counting was performed with HTSeq
Differential Gene expression analysis performed with DESeq2
Assembly: Streptococcus pneumoniae D39 (Genbank CP000410.1) genome and Streptococcus pneumoniae TIGR4 (Genbank AE005672.3) genome
Supplementary files format and content: WT_vs_ccn_DESeq2.xlsx: differentially expressed genes
|
| |
|
| Submission date |
Oct 31, 2023 |
| Last update date |
Sep 23, 2024 |
| Contact name |
Nicholas De Lay |
| E-mail(s) |
nicholas.r.delay@uth.tmc.edu
|
| Phone |
713-500-6293
|
| Organization name |
University of Texas Health Science Center
|
| Department |
Microbiology and Molecular Genetics
|
| Street address |
6431 Fannin St
|
| City |
Houston |
| State/province |
Texas |
| ZIP/Postal code |
77030 |
| Country |
USA |
| |
|
| Platform ID |
GPL33901 |
| Series (1) |
| GSE246655 |
The five homologous CiaR-controlled sRNAs modulate Streptococcus pneumoniae Zn-resistance |
|
| Relations |
| BioSample |
SAMN38051227 |
| SRA |
SRX22318712 |
