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| Status |
Public on Jul 21, 2016 |
| Title |
MFI |
| Sample type |
SRA |
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| Source name |
Monocyte-derived dendritic cells (MoDCs)_MFI
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| Organism |
Homo sapiens |
| Characteristics |
cell type: Monocyte-derived dendritic cells (MoDCs)
pathogen strain: MFI
pathogen genotype: Mfa1-/fimA+
incubation duration: 12h
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| Treatment protocol |
DC infection with Porphyromonas gingivalis:- Bacterial suspensions were washed five times in PBS and re-suspended for spectrophotometer reading at OD 660 nm of 0.11, which previously determined to be equal to 5 x 107 CFU. For bacterial CFSE staining, the suspension were washed (3 times) and re-suspended in 5 μM of CFSE in PBS. The bacteria were incubated for 30 min at 37°C in the dark. MoDCs were pulsed with Pg381, DPG3, MFI and MFB at 10 MOI and incubated with the MoDCs for 12 hours.
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| Growth protocol |
Porphyromonas gingivalis strains:- Four P. gingivalis strains were used in this study; 1) Pg381, which expresses both minor (Mfa1) and major (FimA) fimbriae, 2) isogenic minor fimbria-deficient mutant (FimA+Pg), which expresses only the major fimbriae, 3) isogenic major fimbria-deficient mutant (Mfa1+Pg), which expresses only the minor fimbriae and 4) the double fimbriae mutant (MFB). P. gingivalis strains were maintained anaerobically in (10% H2, 10% CO2, and 80% N2) in a Forma Scientific anaerobic system glove box model 1025/1029 at 37°C in Difco anaerobe broth MIC. Mutant strains were maintained using erythromycin (5 μg/ml) for mutant Mfa1+Pg, tetracycline (2 μg/ml) for mutant FimA+Pg and both erythromycin and tetracycline for double fimbriae mutant MFB.
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| Extracted molecule |
total RNA |
| Extraction protocol |
For RNA isolation:- Total RNA was isolated using RNeasy kit (Cat. no. 74104) according to the manufacturer’s instruction (Qiagen, Valencia, CA). Illumina TruSeq RNA Sample Prep Kit (Cat# FC-122-1001) was used with 800 ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
Isogenic minor fimbria-deficient mutant (FimA+Pg), which expresses only the major fimbriae.
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| Data processing |
Illumina Casava1.8 software used for base-calling and demultiplexing
Genome_build: Ensembl70
Supplementary_files_format_and_content: cuffdiff.txt, including values of rpkm, log2foldchage, p-value
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| Submission date |
Mar 21, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Pachiappan Arjunan |
| Organization name |
NUS, NIH, GRU
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| Department |
Anatomy, Unit on Retinal Vascular Neurobiology, BMB
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| Lab |
VTRP, URVN, BMB
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| Street address |
1120 15th ST, Laney walker Blvd,
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| City |
Augusta |
| State/province |
Georgia |
| ZIP/Postal code |
30904 |
| Country |
USA |
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| Platform ID |
GPL16791 |
| Series (1) |
| GSE67141 |
High-throughput sequencing reveals key genes and immune homeostatic pathways activated in myeloid dendritic cells by Porphyromonas gingivalis 381 and its fimbrial mutants |
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| Relations |
| BioSample |
SAMN03436882 |
| SRA |
SRX963974 |
| 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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