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
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:Morphological identification of Pedicularis depends on floral characters. However, some important characters may be lost during the process of pressing the specimen. Pedicularis delavayi was described from northwestern Yunnan, and widely adopted as a variety of P. siphonantha. Unfortunately, the name "P. siphonantha var. delavayi' incorrectly referred to P. milliana (a new species described in this study) or P. tenuituba in some herbarium specimens and publications. Moreover, phylogenetic relationships among P. delavayi, P. siphonantha and its allies (P. milliana and P. tenuituba) were not fully resolved. In this study, we sampled 76 individuals representing 56 taxa. Of them, 10 taxa were from P. siphonantha lineage, and 11 individuals of P. delavayi represented 9 populations. These species were named as P. siphonantha group on the basis of morphological similarity. Nuclear ribosomal internal transcribed spacer (nrITS) and four chloroplast genes/regions were used for phylogenetic analyses. Phylogenetic analyses showed that the P. siphonantha group was polyphyletic: P. delavayi was sister to P. obliquigaleata in clade A; and the remaining species of P. siphonantha group were monophyletic in clade B, named as P. siphonantha lineage. In the P. siphonantha lineage, P. milliana, P. siphonantha, and P. tenuituba were well supported as monophyletic, and P. dolichosiphon was sister to P. leptosiphon. Morphologically, P. delavayi differs from species of the P. siphonantha lineage in having a long petiole (~ 50 mm) and pedicel (~ 40 mm), a ridged corolla tube, and a folded lower-lip of the corolla. Therefore, both morphological characters and phylogenetic evidence strongly supported to reinstate P. delavayi as an independent species and describe P. milliana as new species. In addition, P. neolatituba was proposed to reduce as a new synonymy of P. delavayi.
