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Abstract Alternative splicing (AS) is a fundamental regulatory process in all higher eukaryotes. However, AS landscapes for a number of animals, including goats, have not been explored to date. Here, we sequenced 60 samples representing 5 tissues from 4 developmental stages in triplicate using RNA-seq to elucidate the goat AS landscape. In total, 1...
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... We identified DASE across tissues at the same development stage, and across developmental stages for the same tissue using a likelihood-ratio test in the rMATS package 16 followed by GO term functional enrichment analysis. DASE across tissues at the same developmental stage were found to be involved in the functional maintenance of organs ( Fig. 5 and Supplementary Table S7). For example, DASE between heart and leg muscle at the adult timepoint were mainly enriched in positive regulation of heart rate or heart contraction. DASE between leg muscle and liver, and between leg muscle and spleen at the fetal timepoint were mainly enriched in regulation of muscle cell apoptosis or ...
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... The TruSeq Stranded mRNA LT Sample Prep Kit (Illumina, RS-122-2101) was used for the construction of 18 cDNA libraries [24], and the Illumina sequencing platform (HiSeqTM 2500) was used to sequence these libraries, generating 125 bp paired-end reads [25,26]. Raw data underwent recognition analysis to obtain original sequencing. ...
Weighted gene coexpression network analysis (WGCNA) is a novel approach that can quickly analyze the relationships between genes and traits. In this study, the milk yield, lactose, fat, and protein of Holstein dairy cows were detected in a lactation cycle. Meanwhile, a total of 18 gene expression profiles were detected using mammary glands from six lactation stages (day 7 to calving, −7 d; day 30 post-calving, 30 d; day 90 post-calving, 90 d; day 180 post-calving, 180 d; day 270 post-calving, 270 d; day 315 post-calving, 315 d). On the basis of the 18 profiles, WGCNA identified for the first time 10 significant modules that may be related to lactation stage, milk yield, and the main milk composition content. Genes in the 10 significant modules were examined with gene ontology (GO) annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. The results revealed that the galactose metabolism pathway was a potential candidate for milk yield and milk lactose synthesis. In −7 d, ion transportation was more frequent and cell proliferation related terms became active. In late lactation, the suppressor of cytokine signaling 3 (SOCS3) might play a role in apoptosis. The sphingolipid signaling pathway was a potential candidate for milk fat synthesis. Dairy cows at 315 d were in a period of cell proliferation. Another notable phenomenon was that nonlactating dairy cows had a more regular circadian rhythm after a cycle of lactation. The results provide an important theoretical basis for the further molecular breeding of dairy cows.
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