{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Léon-Charles Tranchevent"],"organism":["Sus scrofa"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-15113"],"description":["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."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sequencing - Libraries were sequenced on an Illumina NovaSeqX platform, relying on services from the iGenSeq core facility, at ICM (Paris, France). The following settings were used: paired end sequencing with 150nt reads (2x150bp), 7Gbp data/sample (depth of coverage).","Nucleic Acid Extraction - The total RNA of jejunum crypts, 3D organoids, 2D organoids, piglet jejunums and ST cells were extracted with Trizol Reagent, according to the supplier’s recommendations. After Turbo DNAse treatment and validation of RNA quality, 500ng of RNA were used to build the sequencing librairies.","Sample Treatment - After two washes with EMEM but without FBS, ST cells (after 1 day of plating) were inoculated with TGEV at multiplicity of infection of 0.06. The cells were washed twice after 1 hour of inoculation and EMEM,1% Penicilinn/Streptomycin and 1% Glutamax was added. The corresponding controls were mock-infected with ST cells supernatant.","Sample Treatment - This represents a control sample, and as such no treatment was applied.","Sample Collection - Crypts were isolated from jejunum of stillborn piglets.","Sample Collection - Crypts were isolated from jejunum of stillborn piglets and put in culture in matrigel (Corning) and Organoid Growth Medium with a ratio 1:1 of Supplement and basal mediums (Stem Cell Technology). After 8 days of culture, 3D organoids were formed. To maintain the 3D organoids culture, the cells were dissociated and diluted in 1:4 to add matrigel and Organoid Growth Medium with a ratio 1:1 of basal and Supplement mediums (Stem Cell Technology). This protocol was maintained during 5, 14 and 25 passages. At passage 25, 3D organoids were dissociated and transfered in matrigel coated plated to spread the cells and produced 2D organoids cultivated in Organoid Growth Medium with a ratio 1:0.8 of basal and Supplement mediums (Stem Cell Technology).","Sample Treatment - 2D organoids (after 3 days of plating) were washed twice with DMEM F12 and were inoculated with TGEV at multiplicity of infection of 0.06 and 1. The cells were washed twice after 1 hour of inoculation and Organoid Growth Medium with a ratio 1:0.8 of basal and Supplement mediums (Stem Cell Technology) was added. The corresponding controls were mock-infected with ST cells supernatant.","Sample Treatment - Specific Pathogen-Free (SPF) piglets were oro-nasally inoculated with 7 mL of EMEM (2 mL nasal and 5mL in the oral route) for the control piglets or with 10^4.75 TCID50 per piglet, corresponding to 10^8 copies of viral N gene per pig for the infected piglets.","Sample Collection - Each experimental group of Specific Pathogen-Free (SPF) piglets was housed in a separate room in a ABSL3 facility. After 24hpi and 48hpi, different organs from the piglets, including the jejunum, duodenum, ileum, colon, lung, trachea, bronchi, trachea-bronchial and mesenteric lymph node, were harvested and placed in RNAlatter (ThermoFisher) to preserve RNA quality.","Library Construction - Libraries were generated with the Illumina Stranded mRNA Kit, according to the supplier’s recommendations. Essentially, the mRNA were first enriched by the capture of polyA tails via oligoDT. After enzymatic fragmentation, the cDNA were synthetized and the protruding ends of the cDNA were converted into blunt ends by exonuclease/polymerase activities. The 3' ends were adenilated and the adaptators were ligated. The libraries were amplified by PCR reactions and sequenced.","Sample Collection - ST cells were cultivated in EMEM (Lonza), 10% FBS, 1% Penicilinn/Streptomycin and 1% Glutamax (ThermoFisher).","Sequencing - Libraries were sequenced on an Illumina NovaSeq6000 platform from Novogene service (London, United Kingdom). The following settings were used: paired end sequencing with 150nt reads (2x150bp), 8Gbp data/sample (depth of coverage).","Sample Collection - Crypts were isolated from jejunum of stillborn piglets and put in culture in matrigel (Corning) and Organoid Growth Medium with a ratio 1:1 of Supplement and basal mediums (Stem Cell Technology). After 8 days of culture, 3D organoids were formed. To maintain the 3D organoids culture, the cells were dissociated and diluted in 1:4 to add matrigel and Organoid Growth Medium with a ratio 1:1 of basal and Supplement mediums (Stem Cell Technology). This protocol was maintained during 5, 14 and 25 passages.","Library Construction - Libraries were generated with the Total RNA Library Prep Set Kit, according to the supplier’s recommendations. Essentially, the mRNA were first enriched by the capture of polyA tails via oligoDT. After fragmentation per sonication, the cDNA were synthetized and the protruding ends of the cDNA were converted into blunt ends by exonuclease/polymerase activities. The 3' ends were adenilated and the adaptators were ligated. The libraries were amplified by PCR reactions and sequenced."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Sequence Alignment - The RNA sequencing data were processed and cleaned with fastp (version 0.23.2). The reads were then mapped on the pig transcriptome (Sus scrofa v11.1) and counted with RasFlow (relying on Salmon version 0.14.1).","Data Transformation - The normalized read count for each gene was calculated with DESeq2 (version 1.42.0) and converted to base 2 logarithm. The FPKM (Fragment Per Kilobase Million) have been calculated with the edgeR package (version 4.0.9) and also converted to base 2 logarithm. Differential expression was achieved using DESeq2 (version 1.42.0). All analyses were performed in R (version 4.3.1)"],"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq 6000","Illumina NovaSeq X"],"study_type":["RNA-seq of total RNA"],"species":["Sus scrofa"],"pubmed_authors":["Léon-Charles Tranchevent","Ludivine Percevault","Maud Contrant"],"additional_accession":[]},"is_claimable":false,"name":"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)","description":"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.","dates":{"release":"2025-10-10T00:00:00Z","modification":"2025-10-10T09:28:02.213Z","creation":"2025-05-02T13:40:06.575Z"},"accession":"E-MTAB-15113","cross_references":{"ENA":["ERP172212"],"EFO":["EFO_0002944","EFO_0004170","EFO_0009653","EFO_0004917","EFO_0005518","EFO_0003816","EFO_0004184","EFO_0003969"]}}