|
| Status |
Public on Sep 01, 2023 |
| Title |
R. porcellionis strain 15C, 2 dpi (mid phase), rep2 |
| Sample type |
SRA |
| |
|
| Source name |
15C
|
| Organism |
Candidatus Rhabdochlamydia porcellionis |
| Characteristics |
strain: 15C
host: Spodoptera frugiperda
phase: 2 dpi (mid phase)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted with the All-In-One DNA/RNA/Protein Mini_Prep Kit (Bio Basic) according to the manufacturer's recommendation. Remaining DNA was removed using the GeneJET RNA Cleanup and Concentration Micro Kit (Thermo Scientific) as recommended by the manufacturer.
Chlamydial and host (Spodoptera frugiperda) rRNAs were removed using custom rRNA primers and RNase H and afterwards polyadenylated host mRNAs were depleted using oligo (dT) beads. For strand-specific cDNA library preparation, the NEBNext Ultra directional RNA library prep kit for Illumina (New England Biolabs) and the NEBNext multiplex oligonucleotides (New England Biolabs) were used.
|
| |
|
| Library strategy |
ssRNA-seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
15C_2dpi
|
| Data processing |
The quality of the sequencing reads was checked using fastqc (v.0.11.8)
Sequencing adapters were clipped and sequences shorter than 30 bp were removed with cutadapt (v3.5; “-m 30”)
Reads were mapped to the R. porcellionis genome with bowtie2 (v.2.3.5.1; “-N 1 --very-sensitive-local --reorder --no-unal”) and only unambiguously mapped reads were kept using SAMtools (v1.15.1)
Strand-specific reads were counted for each coding sequence using featureCounts (v.2.0.0; “-p -t CDS -s 2”)
Assembly: Assemblies and genome sequencing data are registered under the NCBI sample accessions: SAMN10089613 (15C), SAMN30436884 (ZGO)
Supplementary files format and content: tab-delimited text files include count values for each sample
|
| |
|
| Submission date |
Aug 25, 2022 |
| Last update date |
Sep 01, 2023 |
| Contact name |
Matthias Horn |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Vienna, Center of Microbiology and Environmental Systems Science
|
| Department |
Division of Microbial Ecology
|
| Street address |
Djerassiplatz 1
|
| City |
Vienna |
| ZIP/Postal code |
1030 |
| Country |
Austria |
| |
|
| Platform ID |
GPL32597 |
| Series (1) |
| GSE212062 |
Molecular basis of strain variations of a chlamydial pathogen of arthropods |
|
| Relations |
| BioSample |
SAMN30499826 |
| SRA |
SRX17215798 |
