Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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ScRNA-seq of sheep abomasal epithelial tissue post-nematode infection

ABSTRACT: Tuft cells are required for an effective immune response to gastrointestinal parasitic nematodes in mice, but little is known about tuft cells in other animals. Using scRNA-seq, we profiled the transcriptome of tuft cells and other mucosal cell types from the sheep abomasal epithelium following nematode infection. Cells were isolated from abomasum mucosal tissue of two sheep and processed using 10x Genomics Chromium Single Cell 3’ Reagent kit (v.3) using a total of 20,000 input cells. cDNA libraries were sequenced on an Illumina NextSeq 500 system to a depth of 50,000 read pairs per cell. Sequences were mapped to the genomes for ovine (Ovis aries Oar_v3.1; https://www.ensembl.org/Ovis_aries/Info/Index) and bovine (Bos taurus ARS-UCD1.2; https://www.ensembl.org/Bos_taurus/Info/Index) and gene count matrices generated using the Cell Ranger software (v.3.1.0) and analysed using Seurat package (v.3.1) with R version 3.6.0. The “Find Markers” function identified a tuft cell cluster and other distinct epithelial (Epcam+) and immune (Ptprc+) cell clusters.

INSTRUMENT(S): NextSeq 500, 10X chromium

ORGANISM(S): Ovis aries

SUBMITTER: Thomas Otto

PROVIDER: E-MTAB-10231 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:The Bashbay sheep (Ovis aries), an indigenous breed of Xinjiang, China, has many excellent characteristics. However, hybrids of Argali sheep and Bashbay sheep are susceptible to Mycoplasma ovipneumoniae infection, the causative agent of mycoplasma ovipneumonia, a chronic respiratory disease that is harmful to the sheep industry. To date, knowledge regarding the mechanisms responsible for M. ovipneumoniae pathogenesis is in scant. Herein, we report the results of transcriptome profiling of lung tissues from Argali hybrid sheep experimentally infected with an M. ovipneumoniae strain at 4 and 14 days post-infection, in comparison to mock-infected animals (0 d). Transcriptome profiling was performed by deep RNA sequencing, using the Illumina platform. The analysis of differentially expressed genes was performed to determine concomitant gene-specific temporal patterns of mRNA expression in the lungs after M. ovipneumoniae infection. We found 156 differentially expressed genes (44 up-regulated, 112 down-regulated) when comparing transcriptomic data at 4 and 0 days post-infection, and 367 (35 up-regulated, 332 down-regulated) when comparing 14 versus 0 days post-infection. Kyoto Encyclopedia of Genes and Genomes pathway analysis showed that the differentially expressed genes at 4 and 14 versus 0 days post-infection were enriched in 109 and 150 pathways, respectively, and the Primary immunodeficiency pathway was considered most closely related to MO infection (p < 0.01). Hyper-IgM syndrome was identified based on the B-cell immunodeficiency signaling pathway from differentially expressed genes related M. ovipneumoniae infection. Gene Ontology analysis showed that differentially expressed genes in different groups were enriched for 497 and 928 terms, where those most closely related to M. ovipneumoniae infection are ciliated motor damage (p < 0.01). These results could aid in understanding why the Argali hybrid sheep are susceptible to MO as well as how M. ovipneumoniae infection progresses in the lungs and may provide useful information regarding key regulatory pathways.

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ScRNA-seq of sheep abomasal epithelial tissue post-nematode infection

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