|
| Status |
Public on Jul 28, 2021 |
| Title |
dd_3 [111171_R] |
| Sample type |
SRA |
| |
|
| Source name |
mutant ΔΔ162/163_not induced
|
| Organism |
Neisseria gonorrhoeae |
| Characteristics |
strain: MS11
genotype: mutant: {delta}{delta}162/163
induction: not induced
|
| Treatment protocol |
200 ng/ml anhydrous tetracycline were added to WT, sRNA deletion mutants and the sRNA overexpressing strains and incubation was continued for 30 min.
|
| Growth protocol |
Bacteria were grown to an OD550 = 0.4 in PPM containing 1% vitamin mix and 0.04% (w/v) NaHCO3.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Bacteria were harvested by centrifugation and RNA was isolated using the miRNeasy Micro Kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Description |
111171_R_combined
|
| Data processing |
Adapters were removed using cutadapt.
Reads were mapped using Bowtie2, and were indexed with Samtools.
bedtools and featureCount was used to generate gene coverages.
DEseq2 was used to identify differentially expressed genes.
Genome_build: ASM15685v2;RefSeq assembly accession: GCF_000156855.2
Supplementary_files_format_and_content: tab-delimited text files include Reads for each annotation.
|
| |
|
| Submission date |
Jun 11, 2021 |
| Last update date |
Jul 28, 2021 |
| Contact name |
Dagmar Hannelore Irmgard Beier |
| E-mail(s) |
[email protected]
|
| Organization name |
Biocenter, University of Würzburg
|
| Department |
Chair of Microbiology
|
| Street address |
Am Hubland
|
| City |
Würzburg |
| ZIP/Postal code |
97074 |
| Country |
Germany |
| |
|
| Platform ID |
GPL30262 |
| Series (1) |
| GSE177032 |
Identification of target genes differentially expressed after pulse expression of Neisseria gonorrhoeae sRNAs |
|
| Relations |
| BioSample |
SAMN19667779 |
| SRA |
SRX11118845 |
