|
| Status |
Public on Jan 23, 2023 |
| Title |
PgW83-H2O2-2 |
| Sample type |
SRA |
| |
|
| Source name |
Wild-type strain Pg W87
|
| Organism |
Porphyromonas gingivalis |
| Characteristics |
strain: Key stone oral pathogen Porphyromonas gingivalis W83
growing condition: anaerobic
treatment: hydrogen peroxide stress
|
| Treatment protocol |
Treatment group treated by 0.25 mM of hydrogen peroxide
|
| Growth protocol |
Anaerobic condotions (80% N2, 10% H2, 10%CO2)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Briefly, RNA were harvested by Qiagen RNA kit. ribosomal RNA was removed from 2 µg of total RNA by using RiboMinus Transcriptome Isolation Kit (Life Technologies, Carlsbad, CA).
The first- and the second- strand cDNA synthesis, the RNA-seq barcode ligation, and other steps of libraries construction were performed by using Nextflex RNA-Seq kit according to the protocol of manufacturer (Bioo Scientific, Austin, TX).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
| |
|
| Description |
H2O2
0.25 mM of hydrogen peroxide stressed for 15 min
|
| Data processing |
NextSeq 550 onboard basecalling, fastq files were generated using Illumina bcl2fastq package v1.8.4 with default settings.
RNA-seq fastq files were trimmed with trimmomatic, aligned to P. gingivalis W83 genome, and reads were qunatified with cutfflinks. Gene differential expression was analyzed using cuffdiff with FPKM threshold of 1.
Assembly: P. gingivalis W83
Supplementary files format and content: .csv file, with all genes reads in one file, includes FPKM values.
|
| |
|
| Submission date |
Aug 31, 2022 |
| Last update date |
Aug 25, 2023 |
| Contact name |
Yuetan Dou |
| E-mail(s) |
ydou@llu.edu
|
| Organization name |
Loma Linda University
|
| Department |
Microbiology and Molecular Genetics
|
| Street address |
11021 Campus Street AH114
|
| City |
Loma Linda |
| State/province |
CA |
| ZIP/Postal code |
92354 |
| Country |
USA |
| |
|
| Platform ID |
GPL32620 |
| Series (1) |
| GSE212414 |
Transcriptome analysis of PG0686 mutant in co-culture with Porphyromonas gingivalis II |
|
| Relations |
| BioSample |
SAMN30616134 |
| SRA |
SRX17382533 |
