deep-sequencing raw data  (Illumina Inc)

Journal: Cell reports

Article Title: Viral Fitness Landscapes in Diverse Host Species Reveal Multiple Evolutionary Lines for the NS1 Gene of Influenza A Viruses

doi: 10.1016/j.celrep.2019.11.070

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: Illumina deep-sequencing raw data , This manuscript , https://data.mendeley.com/datasets/77x6pyfk79/1 https://data.mendeley.com/datasets/ryr859j6pr/1.

Techniques: Virus, Recombinant, Purification, One Step RT-PCR, Reverse Transcription, Gel Extraction, Library Quantification, DNA Library Preparation, Sample Prep, Software

Journal: Journal of Virology

Article Title: Single-Cell Virus Sequencing of Influenza Infections That Trigger Innate Immunity

doi: 10.1128/JVI.00500-19

Figure Lengend Snippet: Approach for combined transcriptomics and viral sequencing of single influenza virus-infected cells that express IFN. (A) IFN reporter A549 cells are infected with a mix of wild-type and synonymously barcoded viruses. IFN + cells are enriched by MACS and pooled with nonenriched cells and uninfected canine cells that serve as controls for multiplets and mRNA leakage. (B) The mRNAs from individual cells are converted to cDNAs tagged with cell-specific barcodes. (C) Cellular transcriptomes are quantified using standard single-cell 3′-end Illumina sequencing, and (D) viral genes are enriched by influenza virus-specific PCR and fully sequenced by PacBio (in this schematic, only the cell labeled by the red barcode is infected and has viral transcripts that are sequenced by PacBio). (E) The result is a matrix giving the expression of each gene in each cell, as well as the full sequences of the viral genes in infected cells.

Article Snippet: Briefly, the raw deep-sequencing data from the Illumina 3′-end sequencing were processed using the 10x Genomics software package cellranger (version 2.2.0).

Techniques: Sequencing, Infection, Labeling, Expressing