Journal: bioRxiv

Article Title: YAP disrupts bile acid homeostasis to drive cancer-associated cachexia

doi: 10.64898/2026.02.01.702698

Figure Lengend Snippet: a , Schematic of the CRISPR–Cas9 knockout strategy targeting slc45a2 , designed to induce a visible pigmentation-loss phenotype for screening. Representative brightfield images of 6 and 21 dpf WT and cr slc45a2 zebrafish show loss of melanin pigmentation in mutants. b , Schematic of CRISPR guide RNA target sites (aa and ab) on the slc45a2 gene with representative Sanger sequencing traces and ICE analysis of indels from 7 dpf larvae injected at the one-cell stage with both guides. c , Indel efficiency rates for each slc45a2 CRISPR target site. d , Schematic of CRISPR guide RNA target sites (aa and ab) on the tgr5 gene with representative Sanger sequencing traces and ICE analysis from 7 dpf larvae co-injected at the one-cell stage with tgr5 and slc45a2 guides (latter not shown). e , Indel efficiency rates for each tgr5 CRISPR target site. f , Schematic of the CRISPR target site (ab) on cyp7a1 with corresponding Sanger sequencing traces and ICE analysis from 7 dpf larvae co-injected at the one-cell stage with cyp7a1 and slc45a2 guides (latter not shown). g , Indel efficiency rates for the cyp7a1 CRISPR target site. h-k , Biometrics of body length ( h , standard length, SL), muscle width ( i ), liver size ( j ) and adipose tissue size ( k ) in WT cr slc45a2 , WT cr tgr5 and WT cr cyp7a1 zebrafish at 21 dpf. l , Heat map of selected adipogenic, lipolytic, myogenic, proteolytic and inflammatory gene expression profiles in pooled WT, crslc45a2 , crtgr5 and crcyp7a1 zebrafish at 21 dpf, determined by bulk RNA-seq (n = 4 samples of 5 fish per condition). All data are mean ± s.e.m. P values were determined by one-way ANOVA with Tukey’s multiple-comparisons test ( h,i ) and Kruskal–Wallis test with Dunn’s multiple-comparisons post hoc adjustment ( j,k ). *P < 0.05, **P < 0.01, ***P < 0.001, ****P < 0.0001.

Article Snippet: Indels in the sequenced data were analysed using the Inference of CRISPR Edits (ICE) web-based platform (Synthego).

Techniques: CRISPR, Knock-Out, Sequencing, Injection, Gene Expression, RNA Sequencing

Journal: Aquaculture

Article Title: CRISPR-Cas9/Cas12a-based genome editing in Atlantic cod (Gadus morhua)

doi: 10.1016/j.aquaculture.2023.740440

Figure Lengend Snippet: Fig. 3. A representation of the outputs from the ICE (Inference of CRISPR Edits) software for a guide RNA targeting the slc45a2 gene in an Atlantic cod larva. (A) Sanger sequencing revealed indels in the Atlantic cod larva (ID = A1) treated with Cas9 mRNA-sg1–1. The target region is shown in green and the PAM site in yellow. (B) The inferred distribution and percentage of indels within the target region. (C) Discordance between the edited (in green) and control (in orange) trace files, illustrating the location and prevalence of editing. (D) Sanger sequencing traces after PCR of both edited and wild-type (control) Atlantic cod larvae in the region surrounding the guide sequence. The guide sequence is highlighted with a black underline, the PAM site with a red dotted underline, and the expected cut site is indicated by a vertical dotted line. (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.)

Article Snippet: Four gRNAs were designed and selected with the webbased Benchling's CRISPR analysis tool (https://benchling.com) and CRISPOR tool (http://crispor.org; Concordet and Haeussler, 2018) with the gadMor3.0 Atlantic cod genome as template.

Techniques: CRISPR, Software, Sequencing, Control