Project description:We present a draft genome assembly that includes 200 Gb of Illumina reads, 4 Gb of Moleculo synthetic long-reads and 108 Gb of Chicago libraries, with a final size matching the estimated genome size of 2.7 Gb, and a scaffold N50 of 4.8 Mb. We also present an alternative assembly including 27 Gb raw reads generated using the Pacific Biosciences platform. In addition, we sequenced the proteome of the same individual and RNA from three different tissue types from three other species of squid species (Onychoteuthis banksii, Dosidicus gigas, and Sthenoteuthis oualaniensis) to assist genome annotation. We annotated 33,406 protein coding genes supported by evidence and the genome completeness estimated by BUSCO reached 92%. Repetitive regions cover 49.17% of the genome.
Project description:Purpose: The goal of this study is to compare endothelial small RNA transcriptome to identify the target of OASL under basal or stimulated conditions by utilizing miRNA-seq. Methods: Endothelial miRNA profilies of siCTL or siOASL transfected HUVECs were generated by illumina sequencing method, in duplicate. After sequencing, the raw sequence reads are filtered based on quality. The adapter sequences are also trimmed off the raw sequence reads. rRNA removed reads are sequentially aligned to reference genome (GRCh38) and miRNA prediction is performed by miRDeep2. Results: We identified known miRNA in species (miRDeep2) in the HUVECs transfected with siCTL or siOASL. The expression profile of mature miRNA is used to analyze differentially expressed miRNA(DE miRNA). Conclusions: Our study represents the first analysis of endothelial miRNA profiles affected by OASL knockdown with biologic replicates.
Project description:A cDNA library was constructed by Novogene (CA, USA) using a Small RNA Sample Pre Kit, and Illumina sequencing was conducted according to company workflow, using 20 million reads. Raw data were filtered for quality as determined by reads with a quality score > 5, reads containing N < 10%, no 5' primer contaminants, and reads with a 3' primer and insert tag. The 3' primer sequence was trimmed and reads with a poly A/T/G/C were removed
2021-07-21 | GSE180131 | GEO
Project description:Microbial community characteristics of the intestine and gills of medium-form populations of Sthenoteuthis oualaniensis
Project description:Sthenoteuthis oualaniensis (SA) is an important squid species in the South China Sea. Based on SA samples collected in 2016, SA was divided into the “dwarf” form (DF) and “medium” form (MF). To understand the changes in gastrointestinal function in SA during sexual maturation, we undertook transcriptomic analyses of the stomach and intestine tissues of the DF and MF of SA using the deep-sequencing platform Illumina HiSeq™. We exploited a high-throughput method to delineate differentially expressed genes (DEGs) in the DF and MF of SA. A total of 135,464 unigenes (68627 unigenes of the DG and 66837 unigenes of the MF) were generated. We identified 7965 and 4051 relative DEGs in the intestine and stomach tissue of the mature DF of SA compared with those of the immature DF of SA; and 22138 and 18460 DEGs in the intestine and stomach of the mature MF of SA compared with those of the immature MF of SA. Functional categorization and pathway analyses of these DEGs with regard to the metabolism of differentially expressed genes were noted. This work is the first to identify a set of genes associated with gastrointestinal function during the sexual maturation of SA.
Project description:Whole exome sequencing of 5 HCLc tumor-germline pairs. Genomic DNA from HCLc tumor cells and T-cells for germline was used. Whole exome enrichment was performed with either Agilent SureSelect (50Mb, samples S3G/T, S5G/T, S9G/T) or Roche Nimblegen (44.1Mb, samples S4G/T and S6G/T). The resulting exome libraries were sequenced on the Illumina HiSeq platform with paired-end 100bp reads to an average depth of 120-134x. Bam files were generated using NovoalignMPI (v3.0) to align the raw fastq files to the reference genome sequence (hg19) and picard tools (v1.34) to flag duplicate reads (optical or pcr), unmapped reads, reads mapping to more than one location, and reads failing vendor QC.
Project description:Transcriptomic analyses of gastrointestinal function in the “dwarf” and “medium” forms of Sthenoteuthis oualaniensis during sexual maturation
