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larry barcode library  (Addgene inc)


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    Addgene inc larry barcode library
    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 <t>barcode</t> 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).
    Larry Barcode Library, supplied by Addgene inc, used in various techniques. Bioz Stars score: 93/100, based on 13 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/barcoded+libraries/Camargo+Lab+LARRY+Barcode+Library+Version+1+(Pooled+Library+%23140024)/bio_rxiv__64898__2026__03__19__712924-300-21-24
    Average 93 stars, based on 13 article reviews
    larry barcode library - by Bioz Stars, 2026-10
    93/100 stars

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    1) Product Images from "Cross-species single-cell atlases chart progression, therapy-driven remodelling and immune evasion in pancreatic cancer"

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

    Journal: bioRxiv

    doi: 10.64898/2026.03.19.712924

    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).
    Figure Legend 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).

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

    Related Articles

    Generated:

    Article Title: High-Complexity Barcoded Rabies Virus for Scalable Circuit Mapping Using Single-Cell and Single-Nucleus Sequencing
    Article Snippet: To generate the backbone for the barcoded plasmid library, 10 μg of pSADdeltaG-dTomato was digested using SacII (NEB, R0157) overnight and purified using the Zymo DNA Clean and Concentrator-5 kit (Zymo, D4004). .. The insert containing the barcode library was generated by performing PCR on the STICR barcoded lentiviral plasmid library (Addgene 180483) using primers flanking the barcode sequences and containing overhangs matching the SacII-digested pSADdeltaG-dTomato plasmid (Primers 1 and 2, Table S2). .. Similarly, to prepare a CVS-N2c strain rabies genome plasmid for barcoding and nuclear capture, the RabV CVS-N2c(deltaG)-mCherry plasmid (Addgene #73464) was digested with SmaI (NEB, R0141) and NheII-HF (NEB, R3131) to replace the gene encoding mCherry with a gblock (IDT) encoding a fusion protein consisting of the MS2 coat protein MCP, the fluorescent protein oScarlet, and the KASH nuclear localization signal.

    Article Title: High-Complexity Barcoded Rabies Virus for Scalable Circuit Mapping Using Single-Cell and Single-Nucleus Sequencing
    Article Snippet: 10 μg of the resulting plasmid was digested using SacII (NEB, R0157) overnight and purified using the Zymo DNA Clean and Concentrator-5 kit (Zymo, D4004). .. The insert containing the barcode library was generated by performing PCR on the STICR barcoded lentiviral plasmid library (Addgene 180483), with overhangs matching the SacII digested plasmid (Primers 1 and 2, Table S2). .. Based on our initial qPCR optimization (Figure S1C), 10 cycles of PCR were performed on 25 ng of plasmid DNA in 50 μL total volume using KAPA HotStart PCR ReadyMix (Roche KK2601), with the following parameters: Initial denaturation: 95C for 3 min, Denaturation: 98C for 20 s, Annealing: 62C for 15 s, Extension: 72C for 10 s. A total of 5 PCR reactions was performed, which represents a starting amount of approximately 1.3×10 molecules of DNA, or ∼100-fold excess of the theoretical diversity of the plasmid library.

    Article Title: High-throughput sequencing of single neuron projections reveals spatial organization in the olfactory cortex.
    Article Snippet: .. Barcoded Sindbis viral library Abarcoded Sindbis virus library (JK100L2, Addgene plasmid #79785) was generated and used forMAPseq andBARseq experiments as described previously (Chen et al., 2019; Han et al., 2018; Huang et al., 2020; Kebschull et al., 2016). ..

    Polymerase Chain Reaction:

    Article Title: High-Complexity Barcoded Rabies Virus for Scalable Circuit Mapping Using Single-Cell and Single-Nucleus Sequencing
    Article Snippet: To generate the backbone for the barcoded plasmid library, 10 μg of pSADdeltaG-dTomato was digested using SacII (NEB, R0157) overnight and purified using the Zymo DNA Clean and Concentrator-5 kit (Zymo, D4004). .. The insert containing the barcode library was generated by performing PCR on the STICR barcoded lentiviral plasmid library (Addgene 180483) using primers flanking the barcode sequences and containing overhangs matching the SacII-digested pSADdeltaG-dTomato plasmid (Primers 1 and 2, Table S2). .. Similarly, to prepare a CVS-N2c strain rabies genome plasmid for barcoding and nuclear capture, the RabV CVS-N2c(deltaG)-mCherry plasmid (Addgene #73464) was digested with SmaI (NEB, R0141) and NheII-HF (NEB, R3131) to replace the gene encoding mCherry with a gblock (IDT) encoding a fusion protein consisting of the MS2 coat protein MCP, the fluorescent protein oScarlet, and the KASH nuclear localization signal.

    Article Title: High-Complexity Barcoded Rabies Virus for Scalable Circuit Mapping Using Single-Cell and Single-Nucleus Sequencing
    Article Snippet: 10 μg of the resulting plasmid was digested using SacII (NEB, R0157) overnight and purified using the Zymo DNA Clean and Concentrator-5 kit (Zymo, D4004). .. The insert containing the barcode library was generated by performing PCR on the STICR barcoded lentiviral plasmid library (Addgene 180483), with overhangs matching the SacII digested plasmid (Primers 1 and 2, Table S2). .. Based on our initial qPCR optimization (Figure S1C), 10 cycles of PCR were performed on 25 ng of plasmid DNA in 50 μL total volume using KAPA HotStart PCR ReadyMix (Roche KK2601), with the following parameters: Initial denaturation: 95C for 3 min, Denaturation: 98C for 20 s, Annealing: 62C for 15 s, Extension: 72C for 10 s. A total of 5 PCR reactions was performed, which represents a starting amount of approximately 1.3×10 molecules of DNA, or ∼100-fold excess of the theoretical diversity of the plasmid library.

    Plasmid Preparation:

    Article Title: High-Complexity Barcoded Rabies Virus for Scalable Circuit Mapping Using Single-Cell and Single-Nucleus Sequencing
    Article Snippet: To generate the backbone for the barcoded plasmid library, 10 μg of pSADdeltaG-dTomato was digested using SacII (NEB, R0157) overnight and purified using the Zymo DNA Clean and Concentrator-5 kit (Zymo, D4004). .. The insert containing the barcode library was generated by performing PCR on the STICR barcoded lentiviral plasmid library (Addgene 180483) using primers flanking the barcode sequences and containing overhangs matching the SacII-digested pSADdeltaG-dTomato plasmid (Primers 1 and 2, Table S2). .. Similarly, to prepare a CVS-N2c strain rabies genome plasmid for barcoding and nuclear capture, the RabV CVS-N2c(deltaG)-mCherry plasmid (Addgene #73464) was digested with SmaI (NEB, R0141) and NheII-HF (NEB, R3131) to replace the gene encoding mCherry with a gblock (IDT) encoding a fusion protein consisting of the MS2 coat protein MCP, the fluorescent protein oScarlet, and the KASH nuclear localization signal.

    Article Title: Ascertaining cells’ synaptic connections and RNA expression simultaneously with barcoded rabies virus libraries
    Article Snippet: .. Specifically, poly-L-lysine (Sigma-Aldrich, P4707) coated T-225 flasks containing 85–95% confluent HEK-293T/17 cells (ATCC, CRL-11268) were each transfected (Xfect, Takara #631318) with a DNA cocktail containing (1) the barcoded rabies virus plasmid library (131.36 μg) and CAG-promoter driven plasmids for T7 polymerase (23.66 mg, Addgene 59926) and SAD-B19 helper proteins (N, 52.11 μg, Addgene 59924; P, 30.15 μg, Addgene 59925; L, 23.70 μg, Addgene 59922; G, 20.26 μg, Addgene 59921). .. Cells were maintained with DMEM with GlutaMAX supplement, pyruvate, high glucose media (Thermo Fisher Scientific, 10569010) supplemented with 5% fetal bovine serum (Thermo Fisher Scientific, 10082147) and 1x antibiotic-antimycotic (Thermo Fisher Scientific, 15240062) and incubated at 35 °C with 5% CO 2 .

    Article Title: High-Complexity Barcoded Rabies Virus for Scalable Circuit Mapping Using Single-Cell and Single-Nucleus Sequencing
    Article Snippet: 10 μg of the resulting plasmid was digested using SacII (NEB, R0157) overnight and purified using the Zymo DNA Clean and Concentrator-5 kit (Zymo, D4004). .. The insert containing the barcode library was generated by performing PCR on the STICR barcoded lentiviral plasmid library (Addgene 180483), with overhangs matching the SacII digested plasmid (Primers 1 and 2, Table S2). .. Based on our initial qPCR optimization (Figure S1C), 10 cycles of PCR were performed on 25 ng of plasmid DNA in 50 μL total volume using KAPA HotStart PCR ReadyMix (Roche KK2601), with the following parameters: Initial denaturation: 95C for 3 min, Denaturation: 98C for 20 s, Annealing: 62C for 15 s, Extension: 72C for 10 s. A total of 5 PCR reactions was performed, which represents a starting amount of approximately 1.3×10 molecules of DNA, or ∼100-fold excess of the theoretical diversity of the plasmid library.

    Article Title: Therapeutic targeting nudix hydrolase 1 creates a MYC-driven metabolic vulnerability.
    Article Snippet: The designed 20-nt target-specific sgRNA sequences were synthesized as a pool on microarray surfaces (Genscript). .. Overhangs compatible with Gibson Assembly were added to the sequences, which were inserted into the pSico-based barcoded sgLenti sgRNA library vector (Addgene) kindly provided by Dr Haopeng Wang (School of Life Science and Technology, ShanghaiTech University, China). ..

    Article Title: Therapeutic targeting nudix hydrolase 1 creates a MYC-driven metabolic vulnerability
    Article Snippet: The designed 20-nt target-specific sgRNA sequences were synthesized as a pool on microarray surfaces (Genscript). .. Overhangs compatible with Gibson Assembly were added to the sequences, which were inserted into the pSico-based barcoded sgLenti sgRNA library vector (Addgene) kindly provided by Dr Haopeng Wang (School of Life Science and Technology, ShanghaiTech University, China). ..

    Article Title: High-throughput sequencing of single neuron projections reveals spatial organization in the olfactory cortex.
    Article Snippet: .. Barcoded Sindbis viral library Abarcoded Sindbis virus library (JK100L2, Addgene plasmid #79785) was generated and used forMAPseq andBARseq experiments as described previously (Chen et al., 2019; Han et al., 2018; Huang et al., 2020; Kebschull et al., 2016). ..

    Transfection:

    Article Title: Ascertaining cells’ synaptic connections and RNA expression simultaneously with barcoded rabies virus libraries
    Article Snippet: .. Specifically, poly-L-lysine (Sigma-Aldrich, P4707) coated T-225 flasks containing 85–95% confluent HEK-293T/17 cells (ATCC, CRL-11268) were each transfected (Xfect, Takara #631318) with a DNA cocktail containing (1) the barcoded rabies virus plasmid library (131.36 μg) and CAG-promoter driven plasmids for T7 polymerase (23.66 mg, Addgene 59926) and SAD-B19 helper proteins (N, 52.11 μg, Addgene 59924; P, 30.15 μg, Addgene 59925; L, 23.70 μg, Addgene 59922; G, 20.26 μg, Addgene 59921). .. Cells were maintained with DMEM with GlutaMAX supplement, pyruvate, high glucose media (Thermo Fisher Scientific, 10569010) supplemented with 5% fetal bovine serum (Thermo Fisher Scientific, 10082147) and 1x antibiotic-antimycotic (Thermo Fisher Scientific, 15240062) and incubated at 35 °C with 5% CO 2 .

    Article Title: Rabies virus-based barcoded neuroanatomy resolved by single-cell RNA and in situ sequencing
    Article Snippet: For SAD B19 viruses, HEK-293T cells were transfected with the respective genome library along with helper plasmids pCAG-B19N (Addgene cat. # 59924), pCAG-B19P (Addgene cat. # 59925), pCAG-B19G (Addgene cat. # 59921), pCAG-B19L (Addgene cat. # 59922), and pCAG-T7pol (Addgene cat. # 59926), were used for rescue transfections, using Lipofectamine 2000 (Thermo Fisher). .. For CVS-N2c virus, Neuro2a cells stably expressing the CVS-N2c glycoprotein (N2A-N2cG_02 cells) were transfected with the barcoded N2c library along with helper plasmids pCAG-N2cN (Addgene cat. # 100801), pCAG N2cP (Addgene cat. # 100808), pCAG-N2cG (Addgene cat. # 100811), pCAG-N2cL (Addgene cat. # 100812), and pCAG-T7pol. ..

    Article Title: Rabies virus-based barcoded neuroanatomy resolved by single-cell RNA and in situ sequencing
    Article Snippet: For SAD B19 viruses, HEK-293T cells were transfected with the respective genome library along with helper plasmids pCAG-B19N (Addgene cat. # 59924), pCAG-B19P (Addgene cat. # 59925), pCAG-B19G (Addgene cat. # 59921), pCAG-B19L (Addgene cat. # 59922), and pCAG-T7pol (Addgene cat. # 59926), were used for rescue transfections, using Lipofectamine 2000 (Thermo Fisher). .. For CVS-N2c virus, Neuro2a cells stably expressing the CVS-N2c glycoprotein (N2A-N2cG_02 cells) were transfected with the barcoded N2c library along with helper plasmids pCAG-N2cN (Addgene cat. # 100801), pCAG N2cP (Addgene cat. # 100808), pCAG-N2cG (Addgene cat. # 100811), pCAG-N2cL (Addgene cat. # 100812), and pCAG-T7pol. ..

    Virus:

    Article Title: Ascertaining cells’ synaptic connections and RNA expression simultaneously with barcoded rabies virus libraries
    Article Snippet: .. Specifically, poly-L-lysine (Sigma-Aldrich, P4707) coated T-225 flasks containing 85–95% confluent HEK-293T/17 cells (ATCC, CRL-11268) were each transfected (Xfect, Takara #631318) with a DNA cocktail containing (1) the barcoded rabies virus plasmid library (131.36 μg) and CAG-promoter driven plasmids for T7 polymerase (23.66 mg, Addgene 59926) and SAD-B19 helper proteins (N, 52.11 μg, Addgene 59924; P, 30.15 μg, Addgene 59925; L, 23.70 μg, Addgene 59922; G, 20.26 μg, Addgene 59921). .. Cells were maintained with DMEM with GlutaMAX supplement, pyruvate, high glucose media (Thermo Fisher Scientific, 10569010) supplemented with 5% fetal bovine serum (Thermo Fisher Scientific, 10082147) and 1x antibiotic-antimycotic (Thermo Fisher Scientific, 15240062) and incubated at 35 °C with 5% CO 2 .

    Article Title: High-throughput sequencing of single neuron projections reveals spatial organization in the olfactory cortex.
    Article Snippet: .. Barcoded Sindbis viral library Abarcoded Sindbis virus library (JK100L2, Addgene plasmid #79785) was generated and used forMAPseq andBARseq experiments as described previously (Chen et al., 2019; Han et al., 2018; Huang et al., 2020; Kebschull et al., 2016). ..

    Article Title: Rabies virus-based barcoded neuroanatomy resolved by single-cell RNA and in situ sequencing
    Article Snippet: For SAD B19 viruses, HEK-293T cells were transfected with the respective genome library along with helper plasmids pCAG-B19N (Addgene cat. # 59924), pCAG-B19P (Addgene cat. # 59925), pCAG-B19G (Addgene cat. # 59921), pCAG-B19L (Addgene cat. # 59922), and pCAG-T7pol (Addgene cat. # 59926), were used for rescue transfections, using Lipofectamine 2000 (Thermo Fisher). .. For CVS-N2c virus, Neuro2a cells stably expressing the CVS-N2c glycoprotein (N2A-N2cG_02 cells) were transfected with the barcoded N2c library along with helper plasmids pCAG-N2cN (Addgene cat. # 100801), pCAG N2cP (Addgene cat. # 100808), pCAG-N2cG (Addgene cat. # 100811), pCAG-N2cL (Addgene cat. # 100812), and pCAG-T7pol. ..

    Article Title: Rabies virus-based barcoded neuroanatomy resolved by single-cell RNA and in situ sequencing
    Article Snippet: For SAD B19 viruses, HEK-293T cells were transfected with the respective genome library along with helper plasmids pCAG-B19N (Addgene cat. # 59924), pCAG-B19P (Addgene cat. # 59925), pCAG-B19G (Addgene cat. # 59921), pCAG-B19L (Addgene cat. # 59922), and pCAG-T7pol (Addgene cat. # 59926), were used for rescue transfections, using Lipofectamine 2000 (Thermo Fisher). .. For CVS-N2c virus, Neuro2a cells stably expressing the CVS-N2c glycoprotein (N2A-N2cG_02 cells) were transfected with the barcoded N2c library along with helper plasmids pCAG-N2cN (Addgene cat. # 100801), pCAG N2cP (Addgene cat. # 100808), pCAG-N2cG (Addgene cat. # 100811), pCAG-N2cL (Addgene cat. # 100812), and pCAG-T7pol. ..

    Stable Transfection:

    Article Title: Rabies virus-based barcoded neuroanatomy resolved by single-cell RNA and in situ sequencing
    Article Snippet: For SAD B19 viruses, HEK-293T cells were transfected with the respective genome library along with helper plasmids pCAG-B19N (Addgene cat. # 59924), pCAG-B19P (Addgene cat. # 59925), pCAG-B19G (Addgene cat. # 59921), pCAG-B19L (Addgene cat. # 59922), and pCAG-T7pol (Addgene cat. # 59926), were used for rescue transfections, using Lipofectamine 2000 (Thermo Fisher). .. For CVS-N2c virus, Neuro2a cells stably expressing the CVS-N2c glycoprotein (N2A-N2cG_02 cells) were transfected with the barcoded N2c library along with helper plasmids pCAG-N2cN (Addgene cat. # 100801), pCAG N2cP (Addgene cat. # 100808), pCAG-N2cG (Addgene cat. # 100811), pCAG-N2cL (Addgene cat. # 100812), and pCAG-T7pol. ..

    Article Title: Rabies virus-based barcoded neuroanatomy resolved by single-cell RNA and in situ sequencing
    Article Snippet: For SAD B19 viruses, HEK-293T cells were transfected with the respective genome library along with helper plasmids pCAG-B19N (Addgene cat. # 59924), pCAG-B19P (Addgene cat. # 59925), pCAG-B19G (Addgene cat. # 59921), pCAG-B19L (Addgene cat. # 59922), and pCAG-T7pol (Addgene cat. # 59926), were used for rescue transfections, using Lipofectamine 2000 (Thermo Fisher). .. For CVS-N2c virus, Neuro2a cells stably expressing the CVS-N2c glycoprotein (N2A-N2cG_02 cells) were transfected with the barcoded N2c library along with helper plasmids pCAG-N2cN (Addgene cat. # 100801), pCAG N2cP (Addgene cat. # 100808), pCAG-N2cG (Addgene cat. # 100811), pCAG-N2cL (Addgene cat. # 100812), and pCAG-T7pol. ..

    Expressing:

    Article Title: Rabies virus-based barcoded neuroanatomy resolved by single-cell RNA and in situ sequencing
    Article Snippet: For SAD B19 viruses, HEK-293T cells were transfected with the respective genome library along with helper plasmids pCAG-B19N (Addgene cat. # 59924), pCAG-B19P (Addgene cat. # 59925), pCAG-B19G (Addgene cat. # 59921), pCAG-B19L (Addgene cat. # 59922), and pCAG-T7pol (Addgene cat. # 59926), were used for rescue transfections, using Lipofectamine 2000 (Thermo Fisher). .. For CVS-N2c virus, Neuro2a cells stably expressing the CVS-N2c glycoprotein (N2A-N2cG_02 cells) were transfected with the barcoded N2c library along with helper plasmids pCAG-N2cN (Addgene cat. # 100801), pCAG N2cP (Addgene cat. # 100808), pCAG-N2cG (Addgene cat. # 100811), pCAG-N2cL (Addgene cat. # 100812), and pCAG-T7pol. ..

    Article Title: Rabies virus-based barcoded neuroanatomy resolved by single-cell RNA and in situ sequencing
    Article Snippet: For SAD B19 viruses, HEK-293T cells were transfected with the respective genome library along with helper plasmids pCAG-B19N (Addgene cat. # 59924), pCAG-B19P (Addgene cat. # 59925), pCAG-B19G (Addgene cat. # 59921), pCAG-B19L (Addgene cat. # 59922), and pCAG-T7pol (Addgene cat. # 59926), were used for rescue transfections, using Lipofectamine 2000 (Thermo Fisher). .. For CVS-N2c virus, Neuro2a cells stably expressing the CVS-N2c glycoprotein (N2A-N2cG_02 cells) were transfected with the barcoded N2c library along with helper plasmids pCAG-N2cN (Addgene cat. # 100801), pCAG N2cP (Addgene cat. # 100808), pCAG-N2cG (Addgene cat. # 100811), pCAG-N2cL (Addgene cat. # 100812), and pCAG-T7pol. ..



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    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 <t>barcode</t> 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).
    Larry Barcode Library, supplied by Addgene inc, used in various techniques. Bioz Stars score: 93/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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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