Adult Churra sheep abomasal lymphnode transcriptome

In this study, we detected long noncoding RNAs (lncRNAs) in the transcriptome of abomasal lymph node tissue, which was extracted from adult sheep after an experimental infection with T. circumcincta. After a first experimental infection based on the accumulative faecal egg counts, six ewes were classified as 'Susceptible' and six ewes as 'Resistant'. After second experimental infection, these animals were sacrificed and abomasal lymph node tissue samples were collected. The total polyA RNA extracted from these samples was sequenced using an Illumina Hi-SEq 2000 sequencer by generating 'paired-end' reads of 75 bp, with a depth of 30M reads per sample. Using standard pipeline with different bioinformatics tools, initially the quality of raw sequence data was assessed, followed by trimming adapter and low-quality sequences, aligning and sorting the obtained reads against the sheep reference genome (Oar_v.3.1) ensembl release 95. Then we detected potential transcripts by reference-guided transcript assembly, merging and transcript annotation and finally counted the number of transcripts in each sample in the annotated feature file. On average, the data contained 44,203 genes with 77,039 transcripts. This annotated feature file was used to detect the lncRNA with the FEELnc package. In total 9,105 lncRNA were detected. Among them 2,092 were classified as novel with gffcompare tool. After differential gene expression with DESeq2 between susceptible and resistant ewes, we found 440 genes differentially expressed (adj p-value < 0.05) with 158 up-regulated and 282 down regulated in resistant sheep. Out of 440 differentially expressed genes, 44 contain 63 lncRNA transcripts out of these 30 were novel.This study is part of the FAANG project, promoting rapid prepublication of data to support the research community. These data are released under Fort Lauderdale principles, as confirmed in the Toronto Statement (Toronto International Data Release Workshop. Birney et al. 2009. Pre-publication data sharing. Nature 461:168-170). Any use of this dataset must abide by the FAANG data sharing principles. Data producers reserve the right to make the first publication of a global analysis of this data. If you are unsure if you are allowed to publish on this dataset, please contact FAANG consortium to enquire. The full guidelines can be found at http://www.faang.org/data-share-principle."