|
| Status |
Public on Oct 28, 2020 |
| Title |
RL-04-Control-WT-6_S4 |
| Sample type |
SRA |
| |
|
| Source name |
Culture
|
| Organism |
Porphyromonas gingivalis |
| Characteristics |
genotype: WT
strain: ATCC 33277
|
| Treatment protocol |
NA
|
| Growth protocol |
Porphyromonas gingivalis ATCC 33277 and isogenic mutants were cultured anaerobically at 37℃ in trypticase soy broth (TSB) supplemented with 1 mg/mL yeast extract, 5 µg/mL hemin, and 1 µg/mL menadione.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from the cells using the Qiagen RNAeasy kit (Qiagen) with DNase treatment.
Ribosomal RNA depletion and library construction were performed using the Universal Prokaryotic RNA-Seq kit (Tecan).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Fastq files were downloaded from Illumina's BaseSpace for analysis.
Quality control was perfomed using FastQC (version 0.10.1). After examining the results of QC it was determined that no sequence trimming was required due to the sequences having a sufficiently high enough quality.
Reads were mapped to the P. gingivalis ATCC 33277 genome (NCBI accession # AP009380) using STAR (version 2.6) to generate alignment files in bam format.
HTSeq was used to generate raw gene counts for every sample from aligned bam files produced from STAR. HTSeq was set to include reads aligned to up to ten locations.
DESeq2 was used to perform differential gene expression analysis using the recommened guidelines.
Performed a regularized log transformation on raw count data as outlined in Love et al. 2014 (DOI: 10.1186/s13059-014-0550-8) for principal component analysis.
Genome_build: NCBI Accession AP009380
Supplementary_files_format_and_content: Matrix tables with raw gene counts for every gene and every sample
|
| |
|
| Submission date |
May 27, 2020 |
| Last update date |
Oct 29, 2020 |
| Contact name |
Richard Lamont |
| E-mail(s) |
rich.lamont@louisville.edu
|
| Organization name |
University of Louisville
|
| Department |
Oral Immunology and Infectious Diseases
|
| Street address |
501 S. Preston St
|
| City |
Louisville |
| State/province |
Kentucky |
| ZIP/Postal code |
40292 |
| Country |
USA |
| |
|
| Platform ID |
GPL28580 |
| Series (1) |
| GSE151241 |
Role of the RprY Response Regulator in P. gingivalis Community Development and Virulence |
|
| Relations |
| BioSample |
SAMN15030563 |
| SRA |
SRX8403835 |
