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RNA-Seq data of Dictyostelium lacteum cell types and P. pallidum encystation time series

ABSTRACT: RNA-Seq data of Dictyostelium lacteum cell types and P. pallidum encystation time series

PROVIDER: PRJEB31876 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR3252990_1.fastq.gz	Fastqsanger.gz
	ERR3252990_2.fastq.gz	Fastqsanger.gz
	ERR3252991_1.fastq.gz	Fastqsanger.gz
	ERR3252991_2.fastq.gz	Fastqsanger.gz
	ERR3252992_1.fastq.gz	Fastqsanger.gz

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RNA-Seq data of Dictyostelium lacteum cell types and P. pallidum encystation time series

Project description:The experiment was performed with the intention of collecting transcriptomic data from isolated cell types (spore, stalk and vegetative cells) in Dictyostelium lacteum as well as from cysts in Polyshpondlyium pallidum. By combining these data with similar cell-type specific RNA-Seq data from other organisms, and by examining the expression patterns of transcription factor genes, we tried to characterize how gene regulation for cell differentiation evolved in Dictyostelia. Specifically ,we dissociated and collected spore and stalk from the fruiting bodies of D. lacteum at 24 hours of development. We also collected exponentially growing vegetative cells of D. lacteum. For collecting P. pallidum cyst samples, cells were induced to encyst with sorbitol, and samples were collected at 0, 8, 16, and 24 h of incubation. RNA was extracted using the RNeasy kit (QIAGEN), and cDNA libraries were made using the Illumina TruSeq kit. The Illumina sequencing platforms (NextSeq500 for D. lacteum samples, and Hi-seq 2000 for P. pallidum samples) were used for sequencing.

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Project description:Treponema pallidum ssp. pallidum, the causative agent of syphilis, can now be cultured continuously in vitro utilizing a tissue culture system, and the multiplication rates are similar to those obtained in experimental infection of rabbits. In this study, the RNA transcript profiles of the T. pallidum Nichols during in vitro culture and rabbit infection were compared to examine whether gene expression patterns differed in these two environments. To this end, RNA preparations were converted to cDNA and subjected to RNA-seq using high throughput Illumina sequencing; reverse transcriptase quantitative PCR was also performed on selected genes for validation of results. The transcript profiles in the in vivo and in vitro environments were remarkably similar, exhibiting a high degree of concordance overall. However, transcript levels of 94 genes (9%) out of the 1,063 predicted genes in the T. pallidum genome were significantly different during rabbit infection versus in vitro culture, varying by up to 8-fold in the two environments. Genes that exhibited significantly higher transcript levels during rabbit infection included those encoding multiple ribosomal proteins, several prominent membrane proteins, glycolysis-associated enzymes, replication initiator DnaA, rubredoxin, thioredoxin, two putative regulatory proteins, and proteins associated with solute transport. In vitro cultured T. pallidum had higher transcript levels of DNA repair proteins, cofactor synthesis enzymes, and several hypothetical proteins. The overall concordance of the transcript profiles may indicate that these environments are highly similar in terms of their effects on T. pallidum physiology and growth, and may also reflect a relatively low level of transcriptional regulation in this reduced genome organism.

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Project description:We performed a comprehensive miRNA profiling analysis of exosomes by Treponema pallidum-stimulated microarrays. A total of 2×106 macrophages were obtained by THP-1 differentiation and grown in RPMI-1640 containing 10% exosome-free FBS. Exosomes were acquired from macrophage culture supernatants with (n = 7) or without (n = 3) T. pallidum. Briefly, macrophages were washed in PBS twice and further grown in fresh medium for 12 h (n = 2), 24 h (n = 2) and 48 h (n = 3) to collect exosomes. Exosomal miRNA microarray assays were carried out with Agilent Human miRNA (8*60K) array.

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