|
| Status |
Public on Sep 05, 2023 |
| Title |
24h post-infection (hpi) uninduced [UI σ28/σ54 KD 1] |
| Sample type |
SRA |
| |
|
| Source name |
Infected McCoy cell line
|
| Organism |
Chlamydia trachomatis L2/434/Bu |
| Characteristics |
strain: C. trachomatis L2 434/Bu
induction: Uninduced
plasmid: pL12CRia (σ28/σ54)
knockdown/overexpression: Knockdown - dCas12 mediated
|
| Treatment protocol |
Indicated above in the the first characteristics column.
|
| Growth protocol |
McCoy cells were infected with C. trachomatis L2 and induced or not at 4 or 14 hpi with aTc. Samples were collected at 24 or 18 hpi, respectively.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was collected from C. trachomatis infected cell cultures using Trizol. Total RNA was DNased then further purified to remove eukaryotic mRNA and both prokaryotic and eukaryotic rRNA using Oligotex, MicrobEnrich, MicrobExpress, and Ribozero.
Illumina Ribo-Zero plus Microbiome
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
PolyA and rRNA depleted for both human and bacteria
|
| Data processing |
original fastq format reads were trimmed by fqtrim tool (https://ccb.jhu.edu/software/fqtrim) to remove adapters, terminal unknown bases (Ns), and low quality 3’ regions (Phred score < 30)
trimmed fastq files were processed by FastQC
fastq files were mapped to Chlamydia trachomatis 434/Bu by CLC Genomics Workbench 12 for RNAseq analyses
read counts were modeled using Generalized Linear Model (GLM), assuming a negative binomial distribution, and reported as transcripts per million (TPM)
Wald test was used for statistical analysis of two-group comparisons
Assembly: http://bacteria.ensembl.org/Chlamydia_trachomatis_434_bu_gca_000068585/Info/Index
Supplementary files format and content: excel file showing fold changes and statistical significance between strains and treatment conditions
|
| |
|
| Submission date |
Apr 26, 2023 |
| Last update date |
Sep 05, 2023 |
| Contact name |
Scot P. Ouellette |
| E-mail(s) |
Scot.ouellette@unmc.edu
|
| Organization name |
University of Nebraska Medical Center
|
| Department |
Pathology and Microbiology
|
| Lab |
Ouellette
|
| Street address |
985900 Nebraska Medical Center
|
| City |
Omaha |
| State/province |
NE |
| ZIP/Postal code |
68198-5900 |
| Country |
USA |
| |
|
| Platform ID |
GPL33362 |
| Series (1) |
| GSE230645 |
Identification of the alternative sigma factor regulons of Chlamydia trachomatis using multiplexed CRISPR interference |
|
| Relations |
| BioSample |
SAMN34380317 |
| SRA |
SRX20107036 |
