Project description:Studies have shown that Respiratory Burst Oxidase Homolog B (RBOHB) are involved in stress response in rice plants. Primers were developed for amplification via Polymerase Chain Reaction (PCR) of a region that contained a simple sequence repeat (SSR) in RBOHB. PCR was performed on 6 different varieties of Oryza sativa. PCR product was sequenced on an ABI 3730 capillary sequence machine. Sequence data was aligned to observe differences in SSR length between each rice variety.
Project description:Studies have shown that Rice Salt Sensitive 1 (RSS1) is involved in stress response in rice plants. Primers were developed for amplification via Polymerase Chain Reaction (PCR) of a region that contained a simple sequence repeat (SSR) in RSS1. PCR was performed on 6 different varieties of Oryza sativa. PCR product was sequenced on an ABI 3730 capillary sequence machine. Sequence data was aligned to observe differences in SSR length between each rice variety.
Project description:Rhododendron hybridum Hort. (Ericaceae) is an important ornamental species with striking continuous flowering feature. However, few genomic resources are currently available in this species, and the breeding programs were handicapped by the lack of basic genetic information. Here, we established a transcriptomic profiling study from four different tissues using RNA-Seq to gain insight on the functional genes and to isolate EST-SSR markers for breeding and conservation purposes. In total 38,050,296 high-quality sequence reads were obtained, and 56,120 unigenes (with N50 = 1,236bp) were assembled. Of which, 32,580 (58.05 %) and 8,788 (15.66 %) were annotated to GO and KEGG database, respectively. Additionally, 38,775 (69.09 %) and 37,409 (66.66 %) R. hybridum unigenes were aligned to the Arabidopsis thaliana and Oryza sativa genome, respectively. A total of 21,103 simple sequence repeat (SSR) motifs were identified in 15,050 contigs. Among them, dinucleotide repeats account for the largest proportion for 49.27%, followed by mono- (35.94%) and trinucleotide (21.5%). This study represents the first transcriptome data of R. hybridum and confirms that the transcriptome assembly data are a useful resource for EST-SSR loci development. Such vast sequence data and markers will be robust tools for genomic research and breeding of R. hybridum and related species.
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:Whole genome sequencing of four Primulina species of P. huaijiensis, P. renifolia, P. luochengensis, P. mollifolia, Primulina linearifolia, and Primulina eburnea Raw sequence reads
| PRJNA552759 | ENA
Project description:Primulina xiuningensis Raw sequences
