Journal: bioRxiv

Article Title: Flexiplex: A versatile demultiplexer and search tool for omics data

doi: 10.1101/2023.08.21.554084

Figure Lengend Snippet: (A) The demultiplexing approach used by Flexiplex. The right and left flank are first searched for within a read. The barcode and UMI regions are then extracted from the intermediate sequence, with barcode error correction if known barcodes are provided. (B) UMAP of the short-read single cell dataset of 8 pooled cells lines. Cells positive for BCAS4-BCAS3 (orange) and Adenovirus 5 EA1 (red) are indicated. (C) The number of cells identified with grep, seqkit grep, ugrep and Flexiplex that express sequence from BCAS4-BCAS3 (SNP - using an MCF-7 specific variant or Reference - using the reference allele) and Adenovirus 5 EA1 in a short-read single cell dataset of 8 pooled cells lines. Cells which cluster away from the presumed cluster (hatched) are likely to be false positives, whereas those falling within the presumed cluster are true positives (values on bars) (D) The accuracy of barcode demultiplexing on a simulated set of 5 million single cell RNA-seq long-reads for Flexiplex, scTagger and FLAMES, varying the maximum allowed edit distance to known barcodes between 0 to 3. (E) The estimated accuracy of barcode demultiplexing on a real dataset of 248 cells sequenced with ONT for Flexiplex (with and without chimeric read splitting), scTagger and FLAMES, varying the maximum allowed edit distance to known barcodes between 0 to 3. (F) The number of barcodes recovered across four datasets when no known barcode list was provided, but the number of expected cells was given (orange dashed lines). As Flexiplex does not filter empty drops, we evaluated its performance for two estimated cell numbers: determined manually via knee plot, and using the same number of estimated cells as provided to BLAZE and sockeye. (G) The run-time (log scale, four threads) of Flexiplex, BLAZE and sockeye as a function of the number of reads processed from the four datasets used for barcode discovery evaluation.

Article Snippet: We demonstrate Flexiplex’s application on three use cases, identifying cell line specific sequences in Illumina short read single cell data, and discovering and demultiplexing cellular barcodes from noisy long-read single cell RNA-seq data.

Techniques: Sequencing, Variant Assay, RNA Sequencing

Journal: Frontiers in Immunology

Article Title: Single-Cell Profiling to Explore Immunological Heterogeneity of Tumor Microenvironment in Breast Cancer

doi: 10.3389/fimmu.2021.643692

Figure Lengend Snippet: Summary table for the hallmark breast cancer studies using single-cell technologies.

Article Snippet: Spatial mapping of single-cell RNA-seq data , Spatial Transcriptomics (in-house) , Tumor tissue sections from BRCA patients diagnosed with HER2+ subtype , Demonstration of the heterogeneous nature of tumor-immune interactions and reveal interpatient differences in immune cell infiltration patterns , Potential for an improved stratification and description of the tumor-immune interplay, which is likely to be essential in treatment decisions , ( , ) .

Techniques: Biomarker Discovery, Sequencing, Activation Assay, Mass Cytometry, Clinical Proteomics, Imaging, Single-cell Analysis