|
| Status |
Public on Sep 14, 2017 |
| Title |
W83 H2O2-1 |
| Sample type |
SRA |
| |
|
| Source name |
W83 H2O2
|
| Organism |
Porphyromonas gingivalis W83 |
| Characteristics |
genotype/variation: wild-type
treatment: H2O2
|
| Treatment protocol |
Porphyromonas gingivalis were grown to mid-log phase (O.D.600nm 0.8) anerobically (80% N2, 10% CO2, 10% H2) at 37°C in BHI media. The culture was stressed by 0.25 mM of hydrogen peroxide for 15 min . McKenzie et al., Microbiology, 158(Pt 10):2465-79.
|
| Growth protocol |
Porphyromonas gingivalis cultures were grown to mid-log phase (O.D.600nm 0.8) anerobically (80% N2, 10% CO2, 10% H2) at 37°C in BHI media (Dou et al. FEMS Micro Lett. 312(1):24-32).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted by using SV Total RNA Isolation system (Promega)Dou et al., Journal of Bacteriology, 196(23):4057-70. ribosomal RNA was removed from 2 µg of total RNA by using RiboMinus Transcriptome Isolation Kit (Life Technologies, Carlsbad, CA).
The library construction, the first- and the second- strand cDNA synthesis, and the RNA-seq barcode ligation were performed by using Nextflex RNA-Seq kit (Bioo Scientific, Austin, TX)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
| |
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed and filtered by Trimmomatic 0.35, and then mapped to Porphyromonas gingivalis W83 genome by Tophat v2.1.1
Reads Per Kilobase per Megabase of library size (RPKM) was calculated by Cufflinks v2.2.1and differential expression analyses was performed by Cuffdiff v2.2.1
Genome_build: ASM758v1
Supplementary_files_format_and_content: RPKMs
|
| |
|
| Submission date |
Sep 12, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Yuetan Dou |
| E-mail(s) |
[email protected]
|
| 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 |
GPL24003 |
| Series (2) |
| GSE103739 |
Expression profiling analyses of ECF sigma factor PG0162-PG1660 mutant of Porphyromonas gingivalis W83 [RNA-Seq] |
| GSE103839 |
Expression profiling analyses of ECF sigma factor of Porphyromonas gingivalis W83 |
|
| Relations |
| BioSample |
SAMN07634092 |
| SRA |
SRX3179091 |
