|
| Status |
Public on Apr 02, 2024 |
| Title |
D39 CEP:rr01, OD 0.4, Rep3 [RR01-3] |
| Sample type |
SRA |
| |
|
| Source name |
Bacterial cell
|
| Organism |
Streptococcus pneumoniae |
| Characteristics |
strain: D39V
cell type: Bacterial cell
genotype: CEP:rr01
treatment: C+Y media, 37°C, OD 0.4
|
| Growth protocol |
Streptococcus pneumoniae D39V and overexpression mutant derivatives were grown in the rich C+Y medium in triplicate cultures at 37°C with 5% CO2 to an OD600 0.4.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from Streptococcus pneumoniae by a phenol-chloroform extraction.
1 µg RNA was depleted for ribosomal RNA using the NEBNext® rRNA Depletion Kit (Bacteria). RNA libraries were then prepared using the NEBNext® Ultra™ II Directional RNA Library Prep Kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
featureCount_report_TCS.csv
|
| Data processing |
Raw reads from the fastq files were mapped to the genome with bowtie2 using local alignment. Samtools was used for SAM-to-BAM conversion and sorting.
Raw reads were counted at a feature level with featureCounts. Multimapping reads were counted and fractionally assigned to their features. Reads overlapping several features were assigned by largest overlap.
Parameters used with featureCounts (example): featureCounts -p -M --fraction -O --largestOverlap -t gene -f -g Name --extraAttributes locus_tag,gene_biotype -a CP027540.1.gff3 -s 2 -o featureCounts_report FILENAMES
Assembly: CP027540.1 (several sRNA features identified in D39W were manually added to the General Feature Format (GFF)-file)
Supplementary files format and content: File contains read counts for all features of S. pneumoniae D39V in all samples (file format: csv). In addition to feature coordinates, the file also contains locus_tags, names, gene_biotypes.
|
| |
|
| Submission date |
Feb 23, 2023 |
| Last update date |
Apr 02, 2024 |
| Contact name |
Jens Sivkær Pettersen |
| E-mail(s) |
sivkaer@bmb.sdu.dk
|
| Organization name |
University of Southern Denmark
|
| Street address |
Campusvej 55
|
| City |
Odense M |
| State/province |
Danmark |
| ZIP/Postal code |
5230 |
| Country |
Denmark |
| |
|
| Platform ID |
GPL28680 |
| Series (1) |
| GSE225902 |
A comprehensive analysis of pneumcoccal two-component system regulatory networks |
|
| Relations |
| BioSample |
SAMN33422482 |
| SRA |
SRX19481889 |
