Journal: medRxiv

Article Title: A multi-omics resource of B cell activation reveals genetic mechanisms for immune-mediated diseases

doi: 10.1101/2025.05.22.25328104

Figure Lengend Snippet: (a) GWAS data from Langefeld et al. rs2205960 is the most likely causal variant. PIP: posterior inclusion probability from SuSiE. (b) Chromatin peaks at the genomic region in (a). (c) TNFSF4 gene expression in the same conditions shown in (b). TPM: transcripts per million. (d) CRISPRi shows that inhibiting the region containing the putative causal variant leads to downregulation of TNFSF4 RNA expression.

Article Snippet: To generate GM12878 cells stably expressing the CRISPR interference (CRISPRi) system, we produced lentiviral particles using either the lentiCRISPRi(v1)-Blast plasmid (Addgene #170067, expressing dCas9-KRAB) or lentiCRISPRi(v2)-Blast, according to previously published protocols.

Techniques: Variant Assay, Gene Expression, RNA Expression

Journal: Nature Communications

Article Title: A searchable atlas of pathogen-sensitive lncRNA networks in human macrophages

doi: 10.1038/s41467-025-60084-x

Figure Lengend Snippet: A Left: Evolutionary tree of selected mammalian species. Right: Percent base conservation of human LPS-inducible macrophage lncRNA sequences across the genomes of indicated species, sorted by evolutionary distance; top panel includes all 24 lncRNAs from Fig. and data are shown as box plots (median and 75th-25th percentile interquartile range, whiskers indicate minimum and maximum data values), with species generation time overlayed; bottom panel focuses on specific lncRNAs. B Illustration of genomic locations of specified lncRNAs relative to nearest neighboring genes (distance in kilobases [kb] provided). Red triangles indicate transcriptional start site positions targeted by CRISPRi for lncRNA silencing. C Volcano plots from CRISPRi-based lncRNA loss-of-function experiments in THP1 cells stimulated with LPS for 8 h. Fold-changes (fc) compare lncRNA-knockdown cells to empty vector control cells. Results from three independent experiments. Two-tailed Student’s t-test p -values are shown. D Cytoscape network of lncRNAs (blue) and mRNAs from panel C , regulated upon lncRNA silencing (≥2-fold up or down, p ≤ 0.05, two-tailed Student’s t-test). E Pie charts showing proportions of all expressed mRNAs or LPS-responsive mRNAs (≥2-fold up or down, p ≤ 0.05, two-tailed Student’s t-test) affected by silencing of one or more lncRNAs. C – E: 8 h LPS-stimulated THP1 cells and three independent replicates.

Article Snippet: Stable knockdown cell lines were generated using the CRISPR interference (CRISPRi) vector pLV-hU6-sgRNA-hUbC-dCas9-KRAB-T2a-GFP (Addgene #71237).

Techniques: Knockdown, Plasmid Preparation, Control, Two Tailed Test