Journal: bioRxiv

Article Title: Interface-guided phenotyping of coding variants in the transcription factor RUNX1 with SEUSS

doi: 10.1101/2023.08.03.551876

Figure Lengend Snippet: An interface-guided Perturb-seq assay for coding variant phenotyping of RUNX1. a. 3D crystal structure of transcription factor CBF, consisting of RUNX1 Runt domain (purple) and CBFB (blue), interacting with DNA (yellow and pink strands) (PDB: 1h9d). b. Amino acid residue map of the RUNX1 Runt domain. Columns represent amino acid residues, while rows represent interaction partners of RUNX1. At each row, interface residues involved in interaction to the partner are highlighted black. Rows are hierarchically clustered. On top: 3D location annotations of each residue (core, intermediate, and surface), followed by VEST and FoldX scores of most damaging mutations targeting the residue. The darker the color, the more damaging (VEST) or destabilizing (FoldX) the mutation is. c. Schematic of lentiviral ORF vector containing the RUNX1 variant (WT, mutated, or GFP) and a 12 base pair barcode sequence unique to each variant for identification during single cell transcriptome sequencing. d. Experimental and computational overview: ORF variant library design, transduction, single cell RNA-sequencing of all 117 library elements, bulk RNA and ATAC-sequencing of 12 selected library elements, and computational analysis.

Article Snippet: The gene overexpression vector was generated from a modified lentiviral vector (Addgene #120426).

Techniques: Variant Assay, Mutagenesis, Plasmid Preparation, Sequencing, Transduction, RNA Sequencing Assay

Journal: Cell reports

Article Title: High-Throughput Screens of PAM-Flexible Cas9 Variants for Gene Knockout and Transcriptional Modulation

doi: 10.1016/j.celrep.2020.02.010

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: pCC_01 - lenti-hU6-sgRNA{F+E)-EFS-Gas9-NLS-2A-Puro , This study , Addgene, plasmid #139086.

Techniques: Virus, Recombinant, DNA Extraction, DNA Purification, Staining, Plasmid Preparation, Software

Journal: Cell reports

Article Title: High-Throughput Screens of PAM-Flexible Cas9 Variants for Gene Knockout and Transcriptional Modulation

doi: 10.1016/j.celrep.2020.02.010

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: pCC_07 - lenti-hU6-sgRNA(F+E)-EFS-dxCas9-NLS-VPR-2A-Puro , This study , Addgene, plasmid #139092.

Techniques: Virus, Recombinant, DNA Extraction, DNA Purification, Staining, Plasmid Preparation, Software

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