cell barcodes  (10X Genomics)

Journal: Frontiers in Genetics

Article Title: Decoding the human PBMC isonome: isoform-level resolution with single-cell long-read transcriptomics

doi: 10.3389/fgene.2026.1782221

Figure Lengend Snippet: Adapted PIPseq protocol enables bench-top long-read single-cell sequencing. (a) Buffy coat from whole blood was processed and 30k cells per replicate were targeted for capture. (b) Single cells were encapsulated in lipid droplets with barcoded templates, lysed, and mRNA was captured for reverse transcription. Resulting barcoded cDNA preserved cell-of-origin information during subsequent whole-transcriptome amplification. (c) Barcoded cDNA underwent quality assurance, adapter addition, biotin-mediated enrichment of long fragments, and preparation for PromethION sequencing. (d) Reads underwent quality filtering, barcodes were rescued, and reads were processed with PIPseeker and fed into pipelines for bulk-level isoform discovery and single-cell isoform quantification. Clustering and cell-type analyses were then performed. Figure created at BioRender.com .

Article Snippet: The ONT single-cell method was designed to be used with single-cell barcoded cDNA produced with the 10X Genomics Next GEM Single Cell 3′ Kit (V3.1).

Techniques: Single Cell, Sequencing, Reverse Transcription, Amplification

Journal: Frontiers in Genetics

Article Title: Decoding the human PBMC isonome: isoform-level resolution with single-cell long-read transcriptomics

doi: 10.3389/fgene.2026.1782221

Figure Lengend Snippet: Bulk-level characterization of transcripts from long-read single-cell PBMC data after QC. (a) Number of gene bodies expressing more than one isoform. (b) Transcript length distribution (nt) for new isoforms found in known genes (median = 453 nt, range = 142–1300). (c) Exon number distribution for new isoforms from known genes. (d) Bar plot demonstrating genomic position of new transcripts in relation to known genes and transcripts. (e) Transcript length distribution for new isoforms from new genes (median = 506 nt, range = 204–1504). (f) Exon number distribution for new isoforms from new genes. (g) Bar plot of gene bodies by isoform number, as in 2a, subdivided by transcript biotype. The “Other” Category includes biotypes such as long non-coding RNAs and pseudogenes.

Article Snippet: The ONT single-cell method was designed to be used with single-cell barcoded cDNA produced with the 10X Genomics Next GEM Single Cell 3′ Kit (V3.1).

Techniques: Single Cell, Expressing

Journal: Frontiers in Genetics

Article Title: Decoding the human PBMC isonome: isoform-level resolution with single-cell long-read transcriptomics

doi: 10.3389/fgene.2026.1782221

Figure Lengend Snippet: T cell subtype clustering by canonical markers at the gene- and isoform-level. (a) Gene-level UMAP projection of T cell subtype clusters. (b) Isoform-level UMAP projection of T cell subtype clusters. (c–e) Dot plots of up to three representative isoforms per gene, selected as the most highly expressed isoforms by raw counts , and including any isoforms enriched in a non-canonical cell-type. X axis represents isoform transcript ID (ENST00000xxxxxx) with the last 6 digits of the isoform ID printed to differentiate isoforms and their respective dot. See for all isoforms expressed. Colored boxes correspond to cluster-defining markers. Genes marked with an asterisk (*) indicate isoforms not recovered in unique-count analysis alone, which may reflect read counts split between multiple similar isoforms or insufficient full-length reads to resolve isoform ambiguity. Circle size indicates the percentage of cells in each cluster expressing the marker; circle color indicates fold change relative to average expression. Transcript type is indicated above each transcript (C, Canonical Protein; P, Alternative Protein; N, nonsense-mediated decay; RI, Retained intron, noncoding; U, Unknown coding sequence). Plots are split up by (c) Main T cell sub-type markers (Memory T cells, Effector CD4 and CD8 T cells), (d) markers specific to effector-memory transition T cells, and (e) general T cell markers. (f–i) Gene-level expression aggregation on the single-cell level in (f) CD4 + effector T cells, (g) cytotoxic/effector CD8 + T cells, (h) memory T cells, and (i) effector-memory transition T cells. (j–m) Isoform-level expression aggregation on the single-cell level in (j) CD4 + effector T cells, (k) cytotoxic/CD8 + effector T cells, (l) memory T cells, and (m) effector-memory transition T cells.

Article Snippet: The ONT single-cell method was designed to be used with single-cell barcoded cDNA produced with the 10X Genomics Next GEM Single Cell 3′ Kit (V3.1).

Techniques: Expressing, Marker, Sequencing, Single Cell