Journal: iScience

Article Title: Comparison of different sequencing strategies for assembling chromosome-level genomes of extremophiles with variable GC content

doi: 10.1016/j.isci.2021.102219

Figure Lengend Snippet: The five different enzyme concentrations/ng DNA using stLFR sequencing of D. wulumuqiensis R12 (A) The barcode frequency distribution of five conditions. (B) The Supernova-assembled statistics of five conditions.

Article Snippet: Different from previous studies, in which stLFR was applied for animal or plant genomics, our method allowed the pooling and parallel sequencing of a large number of samples, which cannot be achieved by 10X Genomics read cloud sequencing technology ( ).

Techniques: Sequencing

Journal: iScience

Article Title: Comparison of different sequencing strategies for assembling chromosome-level genomes of extremophiles with variable GC content

doi: 10.1016/j.isci.2021.102219

Figure Lengend Snippet: Statistics of three sequencing strategies assembly genomes

Article Snippet: Different from previous studies, in which stLFR was applied for animal or plant genomics, our method allowed the pooling and parallel sequencing of a large number of samples, which cannot be achieved by 10X Genomics read cloud sequencing technology ( ).

Techniques: Sequencing

Journal: iScience

Article Title: Comparison of different sequencing strategies for assembling chromosome-level genomes of extremophiles with variable GC content

doi: 10.1016/j.isci.2021.102219

Figure Lengend Snippet: The three sequencing strategies-assembled genome statistics of the six bacterial strains The total assembly genome length (bottom), N50 length (middle), and maximum scaffold length (top) by using different algorithms are shown. The assembly algorithms of each sample from left to right are NGS draft genome, stLFR chromosome scaffolds, stLFR + ONT complete genome, ONT complete genome assembled by Canu, and Hybrid complete genome assembled by Unicycler using ONT reads and NGS reads.

Article Snippet: Different from previous studies, in which stLFR was applied for animal or plant genomics, our method allowed the pooling and parallel sequencing of a large number of samples, which cannot be achieved by 10X Genomics read cloud sequencing technology ( ).

Techniques: Sequencing

Journal: iScience

Article Title: Comparison of different sequencing strategies for assembling chromosome-level genomes of extremophiles with variable GC content

doi: 10.1016/j.isci.2021.102219

Figure Lengend Snippet: The longest chromosome sequence comparisons for strains (A–D) (A) E. coli K-12 using stLFR-assembled genome and the third-generation sequencing-assembled genome, (B) Rufibacter sp. LB8, (C) D. wulumuqiensis R12, and (D) J. melonis M714 using stLFR-assembled genomes, stLFR + ONT-assembled genomes, ONT + NGS Unicycler-assembled genomes, and ONT Canu-assembled genomes. The outermost circle is GC heatmap, the next circle is the histogram of GC (red: G > C; blue: G < (C), and the middle circle is gene density in chromosomes. The last two circles are the COG positive/negative annotation heatmaps, and the legend is shown at the bottom.

Article Snippet: Different from previous studies, in which stLFR was applied for animal or plant genomics, our method allowed the pooling and parallel sequencing of a large number of samples, which cannot be achieved by 10X Genomics read cloud sequencing technology ( ).

Techniques: Sequencing

Journal: iScience

Article Title: Comparison of different sequencing strategies for assembling chromosome-level genomes of extremophiles with variable GC content

doi: 10.1016/j.isci.2021.102219

Figure Lengend Snippet: The longest chromosome sequence comparison (A and B) (A) Sequences alignment viewer and (B) accuracy evaluation of stLFR genomes, stLFR + ONT genomes, Canu-assembled genomes, and NGS genomes when compared with the complete genomes assembled by Unicycler using NGS and ONT reads for the strains E. coli K-12, Rufibacter sp. LB8, D. wulumuqiensis R12, and J. melonis M714.

Article Snippet: Different from previous studies, in which stLFR was applied for animal or plant genomics, our method allowed the pooling and parallel sequencing of a large number of samples, which cannot be achieved by 10X Genomics read cloud sequencing technology ( ).

Techniques: Sequencing, Comparison

Journal: Bioinformatics

Article Title: AsaruSim: a single-cell and spatial RNA-Seq Nanopore long-reads simulation workflow

doi: 10.1093/bioinformatics/btaf087

Figure Lengend Snippet: Summary of the AsaruSim workflow. It takes as input a real UMI count matrix and (1) trains the count simulator SPARSim to generate the corresponding synthetic UMI count matrix, serving as ground truth. It then (2) generates perfect reads (FASTA file) based on this synthetic UMI count matrix and a reference transcriptome. (3) It can optionally simulate bias introduced by PCR cycles. (4) It generates more realistic synthetic reads from the previous read templates (perfect or post-PCR) using a Badread simulator with a pre-trained error model on real Nanopore reads. (5) It outputs an HTML report presenting quality control plots that enable the user to assess the simulated reads, before using them to evaluate tools dedicated to analyze scRNAseq long-read data.

Article Snippet: The final construction corresponds to a 10X Genomics coupled with Nanopore sequencing library ( Lebrigand et al. 2020 ): an adaptor sequence composed of 10× and Nanopore adaptors, a CB, UMI sequences at the same frequencies as in the synthetic count matrix, a 20-bp oligo(dT), the feature-corresponding cDNA sequence from the reference transcriptome, and a template switch oligo (TSO) at the end.

Techniques: Control

Journal: bioRxiv

Article Title: Single-nucleus transcriptome analysis provides new insights into B chromosome elimination in sorghum

doi: 10.1101/2025.10.07.680864

Figure Lengend Snippet: A . Developing seed of wild sorghum approx. 21DAP. Embryo position is indicated by red-dashed line. B . Intact isolated embryo of 21 DAP (ventral side) and its transversal section stained with toluidine blue illuminating embryo organogenesis. C. Distribution of the B chromosome in developing embryo visualized using FISH with B-specific probe cocktail on embryo cryo-sections; DAPI counterstaining (left) and signal from B-repeat cocktail (right). D. Chimeric composition of embryonic tissue consisting of three types of nuclei – harbouring B chromosomes (positive for B-repeat signal), undergoing B chromosome elimination (B chromosome located in micronucleus) and yet free from B chromosome (nuclei absent for specific signal). B chromosome is detected using FISH with B-repeat cocktail (red). E. Nuclei isolation for snRNA-seq using flow cytometry. Green-marked populations represent the mix of +B and 0B embryonic nuclei in G1/S/G2 phase used as input DNA for sequencing library.

Article Snippet: Sequencing library was prepared using Chromium Next GEM Single Cell 3’v3.1. (10x Genomics, Pleasanton, CA, USA) according to manufactureŕs instructions with minor modification.

Techniques: Isolation, Staining, Flow Cytometry, Sequencing