|
| Status |
Public on Jul 01, 2024 |
| Title |
D39_D-pptAB_planktonic_biol-rep-1 |
| Sample type |
SRA |
| |
|
| Source name |
D39
|
| Organism |
Streptococcus pneumoniae |
| Characteristics |
strain: D39
genotype: pptAB deletion
|
| Treatment protocol |
No treatments were added to the cultures, the collected culture were mixed 1:1 with in-house RNA-later, spun down for 5 min at max speed.
|
| Growth protocol |
Spn strains were grown in chemically-defined media supplemented with 55mM final concentration glucose at 37C, 5%CO2 until OD600 reached 0.3, 2mL cultures were collected.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Pelleted samples were treated with proteinase K, lysozyme and mutanulysin and samples were extracted using Quick-RNA™ MiniPrep Kit (Zymo Research Cooperation Cat. no. R1055).
Using manufacturer's protocol, RNA libraries for RNA-seq were prepared with NEB E7770 (NEBNext® Ultra™ II RNA Library Prep Kit for Illumina) on ribosomal RNA (rRNA) depleted RNA.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
D39 D-pptAB biol-rep-1
|
| Data processing |
Data processing performed on Galaxy platform
Sequence reads were mapped to Spn D39 genome using bowtie2 on Galaxy (version 2.5.3) with default parameters
Read count extraction was performed using featureCounts on Galaxy (version 2.0.3) (parameters - GFF feature type filter: gene)
Read count normalization was performed using DESeq2 on Galaxy
Assembly: GCF_000014365.2
Supplementary files format and content: Comma separated CSV file includes raw counts for each sample. Rows are genes that can be identified by a new gene ID, corresponding old gene ID or a locus tag. Some old gene IDs have no corresponding new gene ID, hence they are identified solely by their locus tag (genome accession and coordinates).
|
| |
|
| Submission date |
May 29, 2024 |
| Last update date |
Jul 01, 2024 |
| Contact name |
N. Luisa Hiller |
| E-mail(s) |
[email protected]
|
| Phone |
412-268-5994
|
| Organization name |
Carnegie Mellon University
|
| Department |
Biological Sciences
|
| Street address |
4400 Fifth Ave
|
| City |
Pittsburgh |
| State/province |
PA |
| ZIP/Postal code |
15213 |
| Country |
USA |
| |
|
| Platform ID |
GPL28680 |
| Series (1) |
| GSE268602 |
Molecular gatekeepers: how peptide maturation molecules coordinate cell-cell communication in Streptococcus pneumoniae |
|
| Relations |
| BioSample |
SAMN41589777 |
| SRA |
SRX24740612 |
