ABSTRACT: Population genomics of Lepraria finkii, Lepraria lanata, Punctelia appalachensis, Punctelia rudecta, Usnea strigosa, and Usnea subfusca. Raw sequence reads
Project description:Illumina technology was used to generate mRNA profiles of galls from root-knot nematodes infected and corresponding uninfected roots from Poplar CAD and WT lines. RNA was extracted from 3 replicates.TruSeq mRNA Stranded libraries were constructed and after pooling and normalization of libraries, sequencing was done on a NextSeq500 Sequencing System. Raw reads were trimmed for quality and mapped to the substituted genome sequence of P. tremula x P. alba 717-1B4 using CLC Genomics Workbench v9.5.2 and the primary transcripts only.
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:Purpose: The goals of this study are to elucidate the underlying mechanism for the regulation of HSC divisions. Methods: One hundred thousand cells of subfractions within the HSC fraction were sorted. These cells were subjected to ATAC-sequence by using 10X Genomics Chromium Next GEM Single Cell ATAC Reagent Kits v1.1. The sequence reads that passed quality filters were analyzed by FASTX-toolkit.
Project description:Purpose: The goal of this study is to compare the transcriptome profiling of SCF/2i expanded cells to freshly sorted hemtopoietic stem/progenitor cells (HSPCs) at single cell level. Methods: Mouse bone marrow HSPCs (HSC, MEP, CLP, CMP, GMP) and alive SCF/2i expanded cells were sorted by FACS. The FACS-sorted single cell suspensions were washed with ice cold 0.04% BSA in PBS, then loaded onto 3’ library chips as per the manufacturer’s protocol for the Chromium Single Cell 3’ Library (10X Genomics, V2). The 10× Genomics libraries were first sequenced on an Illumina NextSeq 500 aiming at a coverage of 5,000 raw reads per cell to estimate the cell numbers, before being sequenced deeper on an Illumina HiSeq 2500 aiming at a coverage of 50,000 raw reads per cell. (paired-end; read1: 26 cycles; i7 index: 8 cycles; read 2: 98 cycles). Raw sequencing data were pre-processed using the Cell Ranger pipeline (10× Genomics, v 2.1.0). The raw-count datasets from difference cell types were integrated and analyzed by Seurat3 R package. Results: tSNE plot showed that the transcriptome of SCF/2i cells overlapped with that of freshly sorted GMPs. The top 50 highly expressed genes from each comparison were used for analysis by heatmap, which showed that the SCF/2i cells shared a similar gene expression pattern with GMPs, but not other hematopoietic cell lineages. Conclusion: The SCF/2i expanded cells are GMPs.
