Journal: Immunity

Article Title: The cytokine TNF promotes transcription factor SREBP activity and binding to inflammatory genes to activate macrophages and limit tissue repair

doi: 10.1016/j.immuni.2019.06.005

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: SureCell WTA 3′ Library Prep Kit for the ddSeq System , Illumina , Cat# 200142780.

Techniques: Purification, Control, Virus, Plasmid Preparation, Recombinant, Amplex Red Cholesterol Assay, cDNA Synthesis, SYBR Green Assay, Multiplex Assay, RNA Library Preparation, Microarray, Software

Journal: Nature Communications

Article Title: Cell type-dependent differential activation of ERK by oncogenic KRAS in colon cancer and intestinal epithelium

doi: 10.1038/s41467-019-10954-y

Figure Lengend Snippet: Differential effects of BRAF V600E or KRAS G12V on gene expression and intestinal cell hierarchies. All panels: t-SNE visualisations and clustering of organoid single-cell transcriptomes clustered with k-means, 24 h after induction of FLUC control, BRAF V600E or KRAS G12V transgenes. a Colour code for six k-means clusters, and inferred differentiation trajectories starting at cluster 1 shown as grey overlay. b Colour code for transgene and CD44 positivity, as inferred from flow cytometry. CD44 positivity was used to direct cell selection, and thus relative fractions of CD44-high and -low cells are not representative. For CD44 status of the cell populations, see Supplementary Fig. . c Mapping of cell- and pathway-specific differentiation signatures. Numbers of signature genes detected are given per single-cell transcriptome

Article Snippet: Single-cell RNA-sequencing data were pre-processed using the BD Precise Whole Transcriptome Assay Analysis Pipeline v2.0 .

Techniques: Expressing, Flow Cytometry, Selection

Journal: Mutagenesis

Article Title: Towards an advanced testing strategy for genotoxicity using image-based 2D and 3D HepG2 DNA damage response fluorescent protein reporters

doi: 10.1093/mutage/geab031

Figure Lengend Snippet: Hepatocyte maturation status of four different HepG2 models. (A) Bright field pictures showing morphological differences between the different models; HepG2 cultured in 2D and normal DMEM medium, HepG2 cultured in 2D and AAGLY medium, HepG2 cultured in 3D and normal DMEM medium, HepG2 cultured in 3D and AAGLY medium from left to right. (B) Gene expression profiles of some hepatocyte markers ( SERPINA1 and ALB ), CYP enzymes ( 3A4 , 3A7 and 1B1 ) and transporters ( UGT1A1 and SLC10A1 ) and the housekeeping genes ( GAPDH ). Gene expression values are relative to model 1 (HepG2 cultured in 2D and normal DMEM medium) and benchmarked to a pool of 10 different donors of cryopreserved PHHs (10×). N = 6; error bars represent SD; significance levels represented as * P adj < 0.05, ** P adj < 0.01 and *** P adj < 0.001.

Article Snippet: Samples were lysed for 15 min at room temperature, stored at −80°C and shipped for transcriptome analysis by BioSpyder.

Techniques: Cell Culture, Gene Expression

Journal: Advanced Science

Article Title: Highly Accurate Estimation of Cell Type Abundance in Bulk Tissues Based on Single‐Cell Reference and Domain Adaptive Matching

doi: 10.1002/advs.202306329

Figure Lengend Snippet: Overview of SCROAM. a) The deconvolution model that uses a reference requires two input datasets: bulk RNA‐seq count and a reference containing counts of scRNA‐seq reads. Additionally, the single‐cell transcriptome data must label the cell type to be quantified. b) SCROAM learns gene‐specific transformations of bulk data by utilizing the reference sequences observed in single‐cell data. This allows us to account for potential technical bias between sequencing technologies used in single‐cell and bulk RNA‐seq data. c) SCROAM begins with scRNA‐seq data and classifies the cells into different cell types, which were represented by different colors in the analysis. By calculating gene specificity in a given cell type, an expression matrix reflecting cell type specificity was constructed. d) SCROAM employs single‐cell reference data to estimate the cell type ratio in transformed bulk data.

Article Snippet: The raw sequencing reads from a cDNA library using the BD Rhapsody Whole Transcriptome Assay Analysis Pipeline (v1.8) were processed.

Techniques: RNA Sequencing Assay, Sequencing, Expressing, Construct, Transformation Assay