Unknown,Transcriptomics,Genomics,Proteomics

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Transcriptomics analysis of different porcine intestinal models (piglet jejunums, jejunum crypts, and organoids) and conventional cell line models upon infection with the transmissible gastroenteritis virus (TGEV)

ABSTRACT: The objective is to study the relevance of porcine intestinal models (incl. piglet jejunums, 2D and 3D organoids derived from piglet jejunums and swine testicular cells) to study intestinal functions and to decipher the host-virus interactions during viral porcine coronavirus infection. This dataset includes RNA-seq profiling of 54 samples covering the four experimental models mentioned above, uninfected or infected with the Purdue P115 strain of the transmissible gastroenteritis virus (TGEV). Details about the experimental models: - For the in vivo model, jejunums of five week old piglets were extracted. - For the organoid model, first jejunum crypts of newborn piglets were extracted and profiled. Then, 3D organoids derived from these crypts were profiled after 5, 14 and 25 passages. Last, 2D organoids derived from 3D organoids at passage 25 were also included. - For the cellular model, we relied on swine testicular cells (ST cells) at passage 53. Samples were either mock-infected or infected with TGEV (Purdue P115 strain) at MOI 0.06 (ST cells), 0.06 and 1 (2D organoids), and 10^4.75 TCID50 (piglets). For ST cells and organoids, the total RNA was recovered at 9hpi (hours post-infection) and 24hpi. For piglets jejunums, only the latest time point was included (24hpi). For each model and each condition (control / infected), three replicates were performed.

INSTRUMENT(S): Illumina NovaSeq 6000, Illumina NovaSeq X

ORGANISM(S): Sus scrofa

SUBMITTER: Léon-Charles Tranchevent

PROVIDER: E-MTAB-15113 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Genetically engineered human pluripotent stem cells (hPSCs) have been proposed as a source for transplantation therapies and are rapidly becoming valuable tools for human disease modeling. However, many of the potential applications are still limited by the lack of robust differentiation paradigms that allow for the isolation of defined functional tissues. These challenges could be overcome by the use of adult tissue stem cells derived from hPSCs, as their restricted potential could limit the differentiation towards other undesired linages, and allow in vitro expansion and long- term propagation of fully differentiated tissue. To isolate adult stem cells from hPSCs, we applied genome-editing to generate an LGR5-GFP reporter system and subsequently developed a differentiation protocol for human intestinal tissue comprising an adult stem cell niche and all major cell types of the adult intestine. This novel derivation protocol is highly robust and even permits the isolation of intestinal organoids without the LGR5 reporter. Transcriptional profiling, electron microscopy and functional analysis revealed that such human organoid cultures could be derived with high purity, and a composition and morphology similar to that of cultures obtained from human biopsies. Importantly, hPSC-derived organoids responded to the canonical signaling pathways that control self-renewal and differentiation in the adult human intestinal stem cell compartment. With our ability to genetically engineer hPSCs using site-specific nucleases, this adult stem cell system provides a novel platform by which to study human intestinal disease in vitro. RNA from primary organoid samples was isolated from organoid lines that were both cultured for 1-6 months and derived from duodenum, ileum, or rectum biopsies of human subjects as described previously (Sato et al., Gastroenterology 2011) grown in media called WENR+inhibitors. RNA was also isolated from various steps in the culturing and differentiation protocol.

Dataset Information

Transcriptomics analysis of different porcine intestinal models (piglet jejunums, jejunum crypts, and organoids) and conventional cell line models upon infection with the transmissible gastroenteritis virus (TGEV)

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