Project description:The catfish (Silurus lanzhouensis), a popular scaleless fish, is highly nutritious and of great commercial importance. However, transcriptome information related to growth traits in S.lanzhouensis are still unknown. In this study, muscle transcriptome data was used to study this issue by RNA-Seq. In total 44,176,578 to 52,345,588 raw reads were generated for each sample, 163,949 transcripts and 89,579 genes were obtained from the two groups. 843 DEGs showed significant differential expression among 89579 unigenes between two groups, of these, 366 DEGs were up-regulated while 477 DEGs were down-regulated.
2019-11-24 | GSE108573 | GEO
Project description:Skin microbiome of European catfish (Silurus glanis)
Project description:Channel catfish, Ictalurus punctatus, is an important model U.S. aquaculutre species. Given its role in food production, the catfish immune response to industry-relevant pathogens has been extensively studied and has provided crucial information on innate and adaptive immune function during disease progression. To further examine the channel catfish immune system, single-nuclei RNA sequencing on whole spleens from three adult individuals was performed. Spleen cell suspensions were prepared by passing tissues through cell sieves. Single-cell RNAseq libraries were then prepared using the 10X Genomics Chromium X with the Next GEM Single Cell 3’ Reagents and sequenced 2x150bp on an Illumina sequencer. Each demultiplexed library was aligned to the CoCo_2.0 channel catfish reference assembly, filtered, and counted to generate feature-barcode matrices. Cluster analysis allowed for the identification of multiple cell types including erythrocytes, hematopoietic stem cells, B cells, T/NK cells, myeloid lineage derivatives, plasma cells and endothelial cells. The majority of cells detected were erythrocytes, which are nucleated in teleost fish.
