Project description:Purpose: The goals of this study are to identify the molecular mechanism by which NA improves meat quality and find differentially expressed genes in longissimus muscles between cattle treated with/without dietary NA. Methods: gene expression profiles of longissimus muscle from 4 cattle mRNA pools including 6 control and 6 NA treated cattle were generated by single-end sequencing (50 bp), using Illumina HiSeq™ 2000. The sequence reads that passed quality control were analyzed at the transcript isoform level with TopHat followed by Cufflinks. Results: Using SOAPaligner (V2.21) analysis, we mapped about 23,359,272-25,165,811 clean reads per sample to the bovine reference genome assembly (unmasked genomic DNA sequences: Bos_taurus.UMD3.1.75.dna.chromosome.1-29 and X) (ftp://ftp.ensembl.org/pub/release-75/fasta/bos_taurus/dna/). Our NOISeq analysis identified a list of 124 differentially expressed genes with a probability value ≥ 0.8 and an absolute value of log2 Ratio of NA to Control ≥ 1. Conclusions: In our study, dietary NA increases the IMF content of longissimus muscle may through up-regulating the expressions of genes and pathways related to lipid metabolism.
Project description:Purpose: The paired-end sequencing strategy of RNA-Seq improves sequencing efficiency and extends short read lengths for better understanding pig transcriptome. The goals of this study are to identify whether alternative splicing sites or alternative 3' gene boundary caused by a CNV located in 3' region of MSRB3 gene and find differential expression genes in ear tissue between QQ and qq genotype piglets for QTL of ear size Methods: Ear tissue mRNA profiles of 6 piglets including 3 QQ and 3 qq genotypes responsible for QTL of ear size were generated by deep sequencing, using Illumina HiSeq 2000. The sequence reads that passed quality filters were analyzed at the transcript isoform level with TopHat followed by Cufflinks. Results: Using an optimized data analysis workflow, we mapped about 93.6-95.3 million 2 x 90 bp paired-end clean reads per sample to the pig genome (Sscrofa 10.2) and identify 19,819-20,136 annotated genes in each sample. Our ranking analysis identified a list of 281 differentially expressed genes with a >1 fold change at a false discovery rate lower than 0.001. But we found no alternative transcripts and differential expression of MSRB3 gene. Conclusions: In our study, the expression levels of MSRB3 gene had no significant difference in the ear tissue between QQ and qq individuals, and no alternative splicing was found for MSRB3 gene between QQ and qq individuals.
Project description:The Illumina HiSeq platform has been a commonly used option for bacterial genome sequencing. Now the BGI DNA nanoball (DNB) nanoarrays platform may provide an alternative platform for sequencing of bacterial genomes. To explore the impact of sequencing platforms on bacterial genome assembly, quality assessment, sequence alignment, functional annotation, mutation detection, and metagenome mapping, we compared genome assemblies based on sequencing of cultured bacterial species using the HiSeq 2000 and BGISEQ-500 platforms. In addition, simulated reads were used to evaluate the impact of insert size on genome assembly. Genome assemblies based on BGISEQ-500 sequencing exhibited higher completeness and fewer N bases in high GC genomes, whereas HiSeq 2000 assemblies exhibited higher N50. The majority of assembly assessment parameters, sequences of 16S rRNA genes and genomes, numbers of single nucleotide variants (SNV), and mapping to metagenome data did not differ significantly between platforms. More insertions were detected in HiSeq 2000 genome assemblies, whereas more deletions were detected in BGISEQ-500 genome assemblies. Insert size had no significant impact on genome assembly. Taken together, our results suggest that DNBSEQ platforms would be a valid substitute for HiSeq 2000 for bacterial genome sequencing.
Project description:Currently, Illumina sequencers are the globally leading sequencing platform in the next-generation sequencing market. Recently, MGI Tech launched a series of new sequencers, including the MGISEQ-2000, which promise to deliver high-quality sequencing data faster and at lower prices than Illumina's sequencers. In this study, we compared the performance of two major sequencers (MGISEQ-2000 and HiSeq 4000) to test whether the MGISEQ-2000 sequencer delivers high-quality sequence data as suggested. We performed RNA sequencing of four human colon cancer samples with the two platforms, and compared the sequencing quality and expression values. The data produced from the MGISEQ-2000 and HiSeq 4000 showed high concordance, with Pearson correlation coefficients ranging from 0.98 to 0.99. Various quality control (QC) analyses showed that the MGISEQ-2000 data fulfilled the required QC measures. Our study suggests that the performance of the MGISEQ-2000 is comparable to that of the HiSeq 4000 and that the MGISEQ-2000 can be a useful platform for sequencing.
Project description:The MGISEQ-2000 developed by MGI Tech Co. Ltd. (a subsidiary of the BGI Group) is a new competitor of such next-generation sequencing platforms as NovaSeq and HiSeq (Illumina). Its sequencing principle is based on the DNB and the cPAS technologies, which were also used in the previous version of the BGISEQ-500 device. However, the reagents for MGISEQ-2000 have been refined and the platform utilizes updated software. The cPAS method is an advanced technology based on the cPAL previously created by Complete Genomics. In this paper, the authors compare the results of the whole-genome sequencing of a DNA sample from a Russian female donor performed on MGISEQ-2000 and Illumina HiSeq 2500 (both PE150). Two platforms were compared in terms of sequencing quality, number of errors and performance. Additionally, we performed variant calling using four different software packages: Samtools mpileaup, Strelka2, Sentieon, and GATK. The accuracy of SNP detection was similar in the data generated by MGISEQ-2000 and HiSeq 2500, which was used as a reference. At the same time, a separate indel analysis of the overall error rate revealed similar FPR values and lower sensitivity. It may be concluded with confidence that the data generated by the analyzed sequencing systems is characterized by comparable magnitudes of error and that MGISEQ-2000 and HiSeq 2500 can be used interchangeably for similar tasks like whole genome sequencing.
Project description:RNAseq was done on Breast cancer PDX samples uisng Library protocol =llumina TruSeq Stranded Total RNA Kit with Ribo-Zero Gold , HiSeq 50 Cycle Single-Read Sequencing v4
Project description:BackgroundThe oriental river prawn, Macrobrachium nipponense, is an important aquaculture species in China, even in whole of Asia. The androgenic gland produces hormones that play crucial roles in sexual differentiation to maleness. This study is the first de novo M. nipponense transcriptome analysis using cDNA prepared from mRNA isolated from the androgenic gland. Illumina/Solexa was used for sequencing.Methodology and principal findingThe total volume of RNA sample was more than 5 ug. We generated 70,853,361 high quality reads after eliminating adapter sequences and filtering out low-quality reads. A total of 78,408 isosequences were obtained by clustering and assembly of the clean reads, producing 57,619 non-redundant transcripts with an average length of 1244.19 bp. In total 70,702 isosequences were matched to the Nr database, additional analyses were performed by GO (33,203), KEGG (17,868), and COG analyses (13,817), identifying the potential genes and their functions. A total of 47 sex-determination related gene families were identified from the M. nipponense androgenic gland transcriptome based on the functional annotation of non-redundant transcripts and comparisons with the published literature. Furthermore, a total of 40 candidate novel genes were found, that may contribute to sex-determination based on their extremely high expression levels in the androgenic compared to other sex glands,. Further, 437 SSRs and 65,535 high-confidence SNPs were identified in this EST dataset from which 14 EST-SSR markers have been isolated.ConclusionOur study provides new sequence information for M. nipponense, which will be the basis for further genetic studies on decapods crustaceans. More importantly, this study dramatically improves understanding of sex-determination mechanisms, and advances sex-determination research in all crustacean species. The huge number of potential SSR and SNP markers isolated from the transcriptome may shed the lights on research in many fields, including the evolution and molecular ecology of Macrobrachium species.
Project description:The Malayan pangolin (Manis javanica), an unusual mammal that is a scale-covered, toothless specialist myrmecophage, is maintained primarily through captive breeding in China. Maintaining this species in captivity is a significant challenge partly because little is known about its behavior and reproduction. The molecular mechanisms of its digestive system play a key role in the feeding and dietary husbandry of pangolins in captivity. Here, we performed the first large-scale sequencing of M. javanica transcriptomes from three digestive organs—the salivary glands, liver, and small intestine—by using Illumina HiSeq technology- to provides useful genetic resources for future functional work that may be relevant for the maintenance of captive pangolins.