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Structured Review

10X Genomics single nucleus barcoded cdna libraries
a Schematic representation of experimental workflow <t>for</t> <t>single-nucleus</t> short-read RNA-sequencing and Kinnex long-read RNA-sequencing. Figure 1a. was partially created with BioRender. https://BioRender.com/c44n540 . b UMAP plot colored by cell type assignments. c Bar plot showing the proportions of each cell type in AD and ND samples (ns: not significant; Two-sided t-test). d Differentially expressed genes (DEGs) identified across different cell types in AD and ND samples (absolute log2 fold change > 0.25 and adjusted p -value < 0.05, Wilcoxon Rank Sum test with Bonferroni correction). e–h Circos plots of five selected Gene Ontology (GO) terms for excitatory neurons, microglia, oligodendrocytes, and astrocytes with associated genes (false discovery rate (FDR) of <0.05 with the Benjamini-Hochberg (BH) test). Conserved GO terms are shown in the same color.
Single Nucleus Barcoded Cdna Libraries, supplied by 10X Genomics, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/barcoded+libraries/cdna+libraries/pmc13065774-26-0-8
Average 86 stars, based on 1 article reviews
single nucleus barcoded cdna libraries - by Bioz Stars, 2026-10
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Images

1) Product Images from "RNA isoform diversity, splicing variants and switching in single cells of the Alzheimer’s disease brain"

Article Title: RNA isoform diversity, splicing variants and switching in single cells of the Alzheimer’s disease brain

Journal: Communications Biology

doi: 10.1038/s42003-026-09759-9

a Schematic representation of experimental workflow for single-nucleus short-read RNA-sequencing and Kinnex long-read RNA-sequencing. Figure 1a. was partially created with BioRender. https://BioRender.com/c44n540 . b UMAP plot colored by cell type assignments. c Bar plot showing the proportions of each cell type in AD and ND samples (ns: not significant; Two-sided t-test). d Differentially expressed genes (DEGs) identified across different cell types in AD and ND samples (absolute log2 fold change > 0.25 and adjusted p -value < 0.05, Wilcoxon Rank Sum test with Bonferroni correction). e–h Circos plots of five selected Gene Ontology (GO) terms for excitatory neurons, microglia, oligodendrocytes, and astrocytes with associated genes (false discovery rate (FDR) of <0.05 with the Benjamini-Hochberg (BH) test). Conserved GO terms are shown in the same color.
Figure Legend Snippet: a Schematic representation of experimental workflow for single-nucleus short-read RNA-sequencing and Kinnex long-read RNA-sequencing. Figure 1a. was partially created with BioRender. https://BioRender.com/c44n540 . b UMAP plot colored by cell type assignments. c Bar plot showing the proportions of each cell type in AD and ND samples (ns: not significant; Two-sided t-test). d Differentially expressed genes (DEGs) identified across different cell types in AD and ND samples (absolute log2 fold change > 0.25 and adjusted p -value < 0.05, Wilcoxon Rank Sum test with Bonferroni correction). e–h Circos plots of five selected Gene Ontology (GO) terms for excitatory neurons, microglia, oligodendrocytes, and astrocytes with associated genes (false discovery rate (FDR) of <0.05 with the Benjamini-Hochberg (BH) test). Conserved GO terms are shown in the same color.

Techniques Used: RNA Sequencing

Related Articles

Generated:

Article Title: RNA isoform diversity, splicing variants and switching in single cells of the Alzheimer’s disease brain
Article Snippet: .. Single-nucleus barcoded cDNA libraries were generated using the 10X Genomics Single Cell 3’ v3.1 kit. ..

Article Title: A CD4 + T cell-fibroblast crosstalk exacerbates autoimmunity in a mouse model of primary Sjögren disease.
Article Snippet: Single-cell T-cell receptor repertoire sequencing Total CD4+ T cells from the cervical lymph nodes (cLN) of Ctrl and pSjD model mice were purified with CD4 (L3T4) MicroBeads (Miltenyii BioThech, Cat# 130-117-043). .. The cDNA libraries were generated using the Chromium Next GEM Single Cell 5' Reagent Kit v2 (Dual Index) (10x Genomics, Cat# PN-1000265). .. Single-cell T-cell receptor repertoire sequencing Total CD4+ T cells from the cervical lymph nodes (cLN) of Ctrl and pSjD model mice were purified with CD4 (L3T4) MicroBeads (Miltenyii BioThech, Cat# 130-117-043).

Article Title: Early sex-related transcriptional differences in CD8 + T cells responding to chronic viral infection reveal a sex bias in exhaustion
Article Snippet: .. Barcoded single-cell (sc) cDNA libraries were generated (10X Genomics) from inactivated naïve and antigen-specific CD8 + T cells harvested at 7 dpi with LCMV-Armstrong or LCMV-clone 13 viruses. ..

Article Title: A Multi-Step Immune-Competent Genetically Engineered Mouse Model Reveals Phenotypic Plasticity in Uveal Melanoma
Article Snippet: Single cells, reagents, and 10X Genomics gel beads were encapsulated into individual nanoliter-sized Gelbeads in Emulsion (GEMs), and reverse transcription of polyadenylated mRNA was performed in each droplet at 53°C. .. The cDNA libraries were then completed in a single bulk reaction by following the 10X Genomics Chromium GEM-X Single Cell 3’ Reagent Kit v4 user guide, and 50,000 sequencing reads per cell were generated on the Illumina NovaSeq6000 instrument (RRID:SCR_016387). .. Demultiplexing, barcode processing, alignment, and gene counting were performed using the 10X Genomics CellRanger v8 software (RRID:SCR_023221).

Article Title: T cell populations are negatively correlated with natural killer and macrophage cell populations in aspirate samples of peripheral lymphadenopathies.
Article Snippet: .. 10X Genomics generated cDNA libraries will be sequenced on NovaSeq 6000 instruments using 150 cycle paired-end sequencing at a depth of 10K reads per cell. ..

Single Cell:

Article Title: RNA isoform diversity, splicing variants and switching in single cells of the Alzheimer’s disease brain
Article Snippet: .. Single-nucleus barcoded cDNA libraries were generated using the 10X Genomics Single Cell 3’ v3.1 kit. ..

Article Title: A CD4 + T cell-fibroblast crosstalk exacerbates autoimmunity in a mouse model of primary Sjögren disease.
Article Snippet: Single-cell T-cell receptor repertoire sequencing Total CD4+ T cells from the cervical lymph nodes (cLN) of Ctrl and pSjD model mice were purified with CD4 (L3T4) MicroBeads (Miltenyii BioThech, Cat# 130-117-043). .. The cDNA libraries were generated using the Chromium Next GEM Single Cell 5' Reagent Kit v2 (Dual Index) (10x Genomics, Cat# PN-1000265). .. Single-cell T-cell receptor repertoire sequencing Total CD4+ T cells from the cervical lymph nodes (cLN) of Ctrl and pSjD model mice were purified with CD4 (L3T4) MicroBeads (Miltenyii BioThech, Cat# 130-117-043).

Article Title: Early sex-related transcriptional differences in CD8 + T cells responding to chronic viral infection reveal a sex bias in exhaustion
Article Snippet: .. Barcoded single-cell (sc) cDNA libraries were generated (10X Genomics) from inactivated naïve and antigen-specific CD8 + T cells harvested at 7 dpi with LCMV-Armstrong or LCMV-clone 13 viruses. ..

Article Title: A Multi-Step Immune-Competent Genetically Engineered Mouse Model Reveals Phenotypic Plasticity in Uveal Melanoma
Article Snippet: Single cells, reagents, and 10X Genomics gel beads were encapsulated into individual nanoliter-sized Gelbeads in Emulsion (GEMs), and reverse transcription of polyadenylated mRNA was performed in each droplet at 53°C. .. The cDNA libraries were then completed in a single bulk reaction by following the 10X Genomics Chromium GEM-X Single Cell 3’ Reagent Kit v4 user guide, and 50,000 sequencing reads per cell were generated on the Illumina NovaSeq6000 instrument (RRID:SCR_016387). .. Demultiplexing, barcode processing, alignment, and gene counting were performed using the 10X Genomics CellRanger v8 software (RRID:SCR_023221).

Sequencing:

Article Title: Mapping glioblastoma's isoform diversity using long-read single-cell analysis.
Article Snippet: .. Among these, 19 were male (70.4%; median age: 63 years) and 8 were female (29.6%; median age: 57 years). cDNA libraries were prepared using the 10x Genomics droplet-based platform and subjected to both Illumina short-read and Oxford Nanopore Technologies (ONT) long-read sequencing (Fig. 1a). ..

Article Title: A Multi-Step Immune-Competent Genetically Engineered Mouse Model Reveals Phenotypic Plasticity in Uveal Melanoma
Article Snippet: Single cells, reagents, and 10X Genomics gel beads were encapsulated into individual nanoliter-sized Gelbeads in Emulsion (GEMs), and reverse transcription of polyadenylated mRNA was performed in each droplet at 53°C. .. The cDNA libraries were then completed in a single bulk reaction by following the 10X Genomics Chromium GEM-X Single Cell 3’ Reagent Kit v4 user guide, and 50,000 sequencing reads per cell were generated on the Illumina NovaSeq6000 instrument (RRID:SCR_016387). .. Demultiplexing, barcode processing, alignment, and gene counting were performed using the 10X Genomics CellRanger v8 software (RRID:SCR_023221).

Article Title: T cell populations are negatively correlated with natural killer and macrophage cell populations in aspirate samples of peripheral lymphadenopathies.
Article Snippet: .. 10X Genomics generated cDNA libraries will be sequenced on NovaSeq 6000 instruments using 150 cycle paired-end sequencing at a depth of 10K reads per cell. ..

other:

Article Title: YAP/TAZ-VGLL3 governs adipocyte fate via epigenetic reprogramming of PPARγ and its target enhancers.
Article Snippet: The quality of each library was determined with an Agilent Bioanalyzer, and the libraries were sequenced with a NovaSeq 6000 system (Illumina).

Mouse Assay:

Article Title: ACNP 64 th Annual Meeting: Panels, Mini-Panels and Study Groups.
Article Snippet: .. Methods: snRNA-Seq: Mice (60) self-administered OXY (12 days) prior to introducing air-puff paired to drug intake; following classification as punishment sensitive (PS) or resistant (PR), the VP was collected and cDNA libraries from individuals were sequenced (10X Genomics 3’ V3.1). ..



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Image Search Results


a) Schematic overview of the experimental design. Mouse PDAC cell lines were clonally barcoded using a lentiviral library (1), expanded and orthotopically transplanted into syngeneic immunocompetent mice (2–3), followed by scRNA-seq profiling of resultant tumours (4). Expressed barcode tracing enabled unambiguous separation of malignant (TAG⁺) from host-derived non-malignant cells (right panel, UMAPs depicting barcoded (TAG + ) (top) and malignant (bottom) cells). b-e) UMAPs of the integrated Mouse PDAC Atlas coloured by dataset (b), sex (c), treatment type (d), and model (orthotopic syngeneic immunocompetent allografts vs. autochthonous GEMMs (e). f) Sample-wise cell-type composition across treatment types, datasets, and models. Autochthonous tumours were dominated by classical epithelial-like malignant states, whereas orthotopic allografts displayed greater heterogeneity with an enrichment of EMT, hypoxic, and mesenchymal programs. g ) Level 3 hierarchical annotation of the Mouse Atlas using the same multi-tiered scheme as the Human Atlas, resolving lymphoid, myeloid, stromal, endocrine, exocrine, endothelial, and malignant compartments. h-j) Substate resolution of major immune and stromal lineages: CD4⁺ T cells (h), CD8⁺ T cells (i), and macrophages (j), showing distinct regulatory, effector, angiogenic, and lipid-processing programs. k) Validation of double-positive (DP) CD4⁺CD8⁺ T cells at the transcriptomics level (transcription density plots, left panel) and at the protein level by flow cytometry (right panel). l) UMAP showing DP T cells coloured by species (left) and Pearson correlation of mouse DP T cell gene expression against the human DP T cell archetype (right).

Journal: bioRxiv

Article Title: Cross-species single-cell atlases chart progression, therapy-driven remodelling and immune evasion in pancreatic cancer

doi: 10.64898/2026.03.19.712924

Figure Lengend Snippet: a) Schematic overview of the experimental design. Mouse PDAC cell lines were clonally barcoded using a lentiviral library (1), expanded and orthotopically transplanted into syngeneic immunocompetent mice (2–3), followed by scRNA-seq profiling of resultant tumours (4). Expressed barcode tracing enabled unambiguous separation of malignant (TAG⁺) from host-derived non-malignant cells (right panel, UMAPs depicting barcoded (TAG + ) (top) and malignant (bottom) cells). b-e) UMAPs of the integrated Mouse PDAC Atlas coloured by dataset (b), sex (c), treatment type (d), and model (orthotopic syngeneic immunocompetent allografts vs. autochthonous GEMMs (e). f) Sample-wise cell-type composition across treatment types, datasets, and models. Autochthonous tumours were dominated by classical epithelial-like malignant states, whereas orthotopic allografts displayed greater heterogeneity with an enrichment of EMT, hypoxic, and mesenchymal programs. g ) Level 3 hierarchical annotation of the Mouse Atlas using the same multi-tiered scheme as the Human Atlas, resolving lymphoid, myeloid, stromal, endocrine, exocrine, endothelial, and malignant compartments. h-j) Substate resolution of major immune and stromal lineages: CD4⁺ T cells (h), CD8⁺ T cells (i), and macrophages (j), showing distinct regulatory, effector, angiogenic, and lipid-processing programs. k) Validation of double-positive (DP) CD4⁺CD8⁺ T cells at the transcriptomics level (transcription density plots, left panel) and at the protein level by flow cytometry (right panel). l) UMAP showing DP T cells coloured by species (left) and Pearson correlation of mouse DP T cell gene expression against the human DP T cell archetype (right).

Article Snippet: For clonal and state-fate analysis by single-cell RNA-seq, primary mouse PDAC cells were clonally tagged with expressed DNA barcodes using the LARRY Barcode Library (Addgene #140024; RRID: Addgene 140024) .

Techniques: Derivative Assay, Biomarker Discovery, Transcriptomics, Flow Cytometry, Gene Expression

a Schematic representation of experimental workflow for single-nucleus short-read RNA-sequencing and Kinnex long-read RNA-sequencing. Figure 1a. was partially created with BioRender. https://BioRender.com/c44n540 . b UMAP plot colored by cell type assignments. c Bar plot showing the proportions of each cell type in AD and ND samples (ns: not significant; Two-sided t-test). d Differentially expressed genes (DEGs) identified across different cell types in AD and ND samples (absolute log2 fold change > 0.25 and adjusted p -value < 0.05, Wilcoxon Rank Sum test with Bonferroni correction). e–h Circos plots of five selected Gene Ontology (GO) terms for excitatory neurons, microglia, oligodendrocytes, and astrocytes with associated genes (false discovery rate (FDR) of <0.05 with the Benjamini-Hochberg (BH) test). Conserved GO terms are shown in the same color.

Journal: Communications Biology

Article Title: RNA isoform diversity, splicing variants and switching in single cells of the Alzheimer’s disease brain

doi: 10.1038/s42003-026-09759-9

Figure Lengend Snippet: a Schematic representation of experimental workflow for single-nucleus short-read RNA-sequencing and Kinnex long-read RNA-sequencing. Figure 1a. was partially created with BioRender. https://BioRender.com/c44n540 . b UMAP plot colored by cell type assignments. c Bar plot showing the proportions of each cell type in AD and ND samples (ns: not significant; Two-sided t-test). d Differentially expressed genes (DEGs) identified across different cell types in AD and ND samples (absolute log2 fold change > 0.25 and adjusted p -value < 0.05, Wilcoxon Rank Sum test with Bonferroni correction). e–h Circos plots of five selected Gene Ontology (GO) terms for excitatory neurons, microglia, oligodendrocytes, and astrocytes with associated genes (false discovery rate (FDR) of <0.05 with the Benjamini-Hochberg (BH) test). Conserved GO terms are shown in the same color.

Article Snippet: Single-nucleus barcoded cDNA libraries were generated using the 10X Genomics Single Cell 3’ v3.1 kit.

Techniques: RNA Sequencing