Journal: iScience

Article Title: Single-cell RNA-Seq reveals intracellular microbial diversity within immune cells during SARS-CoV-2 infection and recovery

doi: 10.1016/j.isci.2023.108357

Figure Lengend Snippet: Validation of scRNAseq-based findings using a complementary technique in a different cohort (A) Although the disease, sample source, sequencing platform, and analysis methods are constant between the two cohorts used for detection of microbial reads, they differ only with respect to the underlying capturing technique. (B) The comparison of alpha diversity between scRNAseq and bulk RNAseq cohorts. (C) The alluvial plot represents the top genus and their corresponding phyla in the bulk RNA-Seq data. (D) The Venn diagram shows unique bacterial species found in the bulk and scRNA-Seq as well as overlap between the two. The violin plot represents the comparison of abundances proportion between scRNAseq and bulk RNAseq COVID-19-positive cohort of the 8 common species: (E) Bacillus cereus , (F) Bacillus thuringiensis , (G) Clostridium botulinum , (H) Klebsiella pneumoniae , (I) Polynucleobacter necessarius , (J) Staphylococcus aureus , (K) Staphylococcus cohnii , and (L) Staphylococcus simulans.

Article Snippet: Oxford Nanopore sequencing was used to identify the SARS-CoV-2 variant that was causing infection (Ligation sequencing kit, catalog no SQK-LSK109, Native barcoding expansion kit, EXP-NBD104).

Techniques: Biomarker Discovery, Sequencing, Comparison, RNA Sequencing

Journal: iScience

Article Title: Single-cell RNA-Seq reveals intracellular microbial diversity within immune cells during SARS-CoV-2 infection and recovery

doi: 10.1016/j.isci.2023.108357

Figure Lengend Snippet:

Article Snippet: Oxford Nanopore sequencing was used to identify the SARS-CoV-2 variant that was causing infection (Ligation sequencing kit, catalog no SQK-LSK109, Native barcoding expansion kit, EXP-NBD104).

Techniques: Quantitative RT-PCR, Ligation, Sequencing, Multiplexing, Amplification, Software

Journal: bioRxiv

Article Title: Environmental radiation exposure at Chornobyl has not systematically affected the genomes or mutagen tolerance phenotypes of local worms

doi: 10.1101/2023.05.28.542665

Figure Lengend Snippet: Assembly contiguity can be partially explained by coverage of long-read (Oxford Nanopore Technology MinION) sequences ( p = 0.019). Higher-contiguity assemblies (towards the left, with fewer and larger contigs) correlate with deeper Oxford Nanopore sequencing. Only contigs larger than 200K were counted, disregarding small pieces that did not assemble well.

Article Snippet: Purified DNA was prepared and sequenced using the Oxford Nanopore Technology MinION device (Ligation Sequencing Kit SQK-LSK110, Spot on flow cell Mk1 FLO-MIN106D, and Native Barcoding Expansion EXP-NBD104) according to the manufacturer’s instructions.

Techniques: Nanopore Sequencing

Journal: Cell reports

Article Title: Parallel Single-Cell RNA-Seq and Genetic Recording Reveals Lineage Decisions in Developing Embryoid Bodies

doi: 10.1016/j.celrep.2020.108222

Figure Lengend Snippet: (A) Illustration depicting procedures for acquiring the transcriptome and timestamp barcode information from each single cell. ESCs are engineered to express an inducible Cre (Cre-ERT2-T2A-BFP), a Cre reporter (lox-RFP-STOP-lox-GFP), and a timestamp barcoding system containing a static barcode (N 10 nucleotides) and an inducible tandem-loxP barcode (E2-crimson-tandem-loxp-UCI). ESCs are sorted into culture plates based on reporter expression (RFP, BFP, and E2-crimson) (as in ). Recombination of the tandem-loxP sequence is induced by addition of Cre-ERT2. At the end of the 14-day time course, cells are harvested. The timestamp barcode is amplified using targeted primers and sequenced using Oxford Nanopore long-read sequencing. The transcriptome is profiled as before . (B) The black histogram shows barcode distribution calculated from NGS data. The red cumulative frequency plot on the same plot shows that that 95% of barcodes are detected with 50 sequencing reads per UCI, consistent with observations from other barcoding studies . (C) Barplot showing the length distribution of long sequencing reads after Cre-ERT2 induction. The tandem-loxP sequence contains 5 converging pairs of loxP sites with 9 spacer sequences, making an intact total of 2,317 bp. The full recombined product yields a 621-bp fragment. (D) Pie charts displaying the number of unique loxp recombined barcodes (left) and the number of unique loxP recombined barcodes+UCI (right). 5,000 static UCIs and a total of 155 achievable, temporally controlled tandem-loxP barcodes yield 514 unique barcodes in EBs after applying strict filtering criteria ( – ; ). See also and and .

Article Snippet: 1D Native barcoding kit , Oxford Nanopore Technologies , EXP-NBD104, EXP-NBD114.

Techniques: Expressing, Sequencing, Amplification

Journal: Cell reports

Article Title: Parallel Single-Cell RNA-Seq and Genetic Recording Reveals Lineage Decisions in Developing Embryoid Bodies

doi: 10.1016/j.celrep.2020.108222

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: 1D Native barcoding kit , Oxford Nanopore Technologies , EXP-NBD104, EXP-NBD114.

Techniques: Recombinant, Staining, Ligation, Sequencing, Software