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| Status |
Public on Sep 17, 2021 |
| Title |
Next Generation Sequencing Facilitates Quantitative Analysis of P. gingivalis and HUVEC Transcriptomes |
| Organisms |
Homo sapiens; Porphyromonas gingivalis ATCC 33277 |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Purpose: This study provides the transcriptional landscape of intracellular P. gingivalis as well as that of endothelial cells infected by this bacteria based on dual RNA sequencing.
Methods: HUVECs were seeded in 6-well plates and cultured to 80% confluence. After washing with phosphate-buffered saline (PBS), cell were infected with P. gingivalis at a multiplicity of infection (MOI) of 100 for 2 h at 37 °C in 5% CO2, unless otherwise stated. Non-adherent bacteria were removed by washing with PBS, and the cell-adherent bacteria were killed using gentamicin (300 μg/mL) and metronidazole (200 μg/mL) for 1 h at 37 °C in 5% CO2.Total RNA was isolated from the samples using TRIzol® reagent.cDNA libraries for Illumina® sequencing were generated using the KC-DigitalTM Stranded mRNA Library Prep Kit (Illumina, San Diego, CA, USA). The library products corresponding to 200–250 bps were then enriched, quantified, and sequenced using a Nova-seq 6000 sequencer (Illumina, San Diego, CA, USA).
Results: Using an optimized data analysis workflow, intracellular P. gingivalis showed a total of 573 DEGs compared with the control bacteria, and of these DEGs, 304 and 269 were upregulated and downregulated, respectively. A total of 838 DEGs were detected in P. gingivalis-infected HUVECs compared with their uninfected counterparts, and of these, 297 and 541 genes were upregulated and downregulated, respectively.
Conclusions: This study firstly provides the transcriptional landscape of intracellular P. gingivalis as well as that of endothelial cells infected by this bacteria based on dual RNA sequencing.
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| Overall design |
P. gingivalis cultured in the miedum; intracellular P. gingivlais; HUVEC cultured in the medium; HUVEC infected with P. gingivalis
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| Contributor(s) |
Liu C |
| Citation(s) |
35360107 |
| Submission date |
Sep 14, 2021 |
| Last update date |
Apr 07, 2022 |
| Contact name |
CHENGCHENG LIU |
| E-mail(s) |
liuchengchengsc@gmail.com
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| Organization name |
Sichuan University
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| Street address |
No. 14, Section 3, Renminnan Road
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| City |
CHENGDU |
| State/province |
SICHUAN |
| ZIP/Postal code |
610041 |
| Country |
China |
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| Platforms (2) |
| GPL11154 |
Illumina HiSeq 2000 (Homo sapiens) |
| GPL18306 |
Illumina HiSeq 2000 (Porphyromonas gingivalis ATCC 33277) |
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| Samples (12)
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| Relations |
| BioProject |
PRJNA763155 |
| SRA |
SRP336996 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE184085_9-14-2021-Matrix_table-HUVEC.txt.gz |
34.1 Kb |
(ftp)(http) |
TXT |
| GSE184085_9-14-2021-Matrix_table-Pg.txt.gz |
20.9 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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