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| Status |
Public on Sep 01, 2023 |
| Title |
Pg+Fa H2O2-2 |
| Sample type |
SRA |
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| Source name |
culture
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| Organisms |
Porphyromonas gingivalis W83; Filifactor alocis ATCC 35896 |
| Characteristics |
cell type: culture
treatment: 0.25 mM H2O2 stress
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| Treatment protocol |
Treated by 0.25 mM of hydrogen peroxide
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| Growth protocol |
Anaerobic condotions (80% N2, 10% H2, 10%CO2)
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| 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).
cDNA in library were taged by specific barcode sequence and exposed to sequencing.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
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| 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: Porphyromonas gingivalis W83, Filifactor alocis ATCC 35896
Supplementary files format and content: original process to.csv file, with all genes reads in two files, P. gingivalis and F. alocis respectively.
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| Submission date |
Aug 24, 2023 |
| Last update date |
Sep 01, 2023 |
| Contact name |
Yuetan Dou |
| E-mail(s) |
[email protected]
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| Organization name |
Loma Linda University
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| Department |
Microbiology and Molecular Genetics
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| Street address |
11021 Campus Street AH114
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| City |
Loma Linda |
| State/province |
CA |
| ZIP/Postal code |
92354 |
| Country |
USA |
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| Platform ID |
GPL33710 |
| Series (1) |
| GSE241660 |
Transcriptome analyses of Filifactor alocis ATCC35896 and Porphyromonas gingivalis W83 in mono-culture as compared to co-culture under hydrogen peroxide stress conditions |
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| Relations |
| BioSample |
SAMN37145668 |
| SRA |
SRX21480281 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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