long-read sequencing with crispr/cas9-mediated target selection  (Oxford Nanopore)

Journal: bioRxiv

Article Title: FDA-approved drug repurposing in zebrafish identifies thyroid hormone and other compounds as potential antithrombotics

doi: 10.1101/2025.09.23.677920

Figure Lengend Snippet: CRISPR sgRNA/Cas9 complexes were injected into single-cell embryos that were then treated with L-thyroxine (0.6 µM) at 3 dpf and mestranol (25 µM) at 4 dpf. Statistical analyses were performed using proportional odds logistic regression (polr) models with MASS and emmeans libraries in R (v4.3.3). ****: p < 0.0001, ns: not significant. wt: wild-type (uninjected fabp-fgb-egfp control group), - thr : combined knockdown of all thyroid hormone receptor paralogs thraa , thrab , and thrb . Magenta borders indicate mestranol treated groups. All data were collected by an observer blinded to the condition. Sample sizes for each group, corresponding to the thrombosis grades, are indicated within their respective stack.

Article Snippet: CRISPR single-guide RNA (sgRNA) sequences targeting early exons were designed with the Knockout Guide Design Tool ( synthego.com ).

Techniques: CRISPR, Injection, Control, Knockdown

Journal: bioRxiv

Article Title: FDA-approved drug repurposing in zebrafish identifies thyroid hormone and other compounds as potential antithrombotics

doi: 10.1101/2025.09.23.677920

Figure Lengend Snippet: CRISPR sgRNA/Cas9 complexes were injected into single-cell embryos that were then treated with tiratricol (0.1 µM) at 3 dpf and mestranol (25 µM) at 4 dpf. Statistical analyses were performed using proportional odds logistic regression (polr) models with MASS and emmeans libraries in R (v4.3.3). To prevent infinitesimal values that would be generated by the regression models, each thrombosis grade group was incremented by one count across all treatment groups. ****: p < 0.0001, ***: p < 0.001. wt: wild-type (uninjected fabp-fgb-egfp control group), - thr : combined knockdown of all thyroid hormone receptor paralogs thraa , thrab , and thrb . Magenta borders indicate mestranol treated groups. All data were collected by an observer blinded to the condition. Sample sizes for each group, corresponding to the thrombosis grades, are indicated within their respective stack.

Article Snippet: CRISPR single-guide RNA (sgRNA) sequences targeting early exons were designed with the Knockout Guide Design Tool ( synthego.com ).

Techniques: CRISPR, Injection, Generated, Control, Knockdown

Journal: bioRxiv

Article Title: FDA-approved drug repurposing in zebrafish identifies thyroid hormone and other compounds as potential antithrombotics

doi: 10.1101/2025.09.23.677920

Figure Lengend Snippet: CRISPR sgRNA/Cas9 complexes were injected into single-cell embryos that were then treated with L-thyroxine (0.6 µM) at 3 dpf and observed at 5 dpf. Thrombosis grades were collected simultaneously with the TTO evaluations, ensuring consistent sample use as presented in . Statistical analyses were performed using proportional odds logistic regression ( polr ) models with MASS and emmeans libraries in R (v4.3.3). ****: p < 0.0001, *: p < 0.05. - proc : genetic thrombosis line ( proc −/− ::fabp-fgb-egfp control group), - thr : combined knockdown of all thyroid hormone receptor paralogs thraa , thrab , and thrb . All data were collected by an observer blinded to the condition. Sample sizes for each group, corresponding to the thrombosis grades, are indicated within their respective stack.

Article Snippet: CRISPR single-guide RNA (sgRNA) sequences targeting early exons were designed with the Knockout Guide Design Tool ( synthego.com ).

Techniques: CRISPR, Injection, Control, Knockdown

Journal: bioRxiv

Article Title: FDA-approved drug repurposing in zebrafish identifies thyroid hormone and other compounds as potential antithrombotics

doi: 10.1101/2025.09.23.677920

Figure Lengend Snippet: CRISPR sgRNA/Cas9 complexes were injected into single-cell embryos that were then treated with L-thyroxine (0.6 µM) at 3 dpf, and mestranol (25 µM) at 4 dpf, followed by assessment of laser-mediated endothelial injury at 5 dpf. Increased TTO observed in wild-type embryos treated with thyroid hormone was diminished upon thr knockdown, indicating involvement of thyroid receptor signaling. Increased TTO levels were still present in the L-thyroxine-mestranol combination groups. ****: p<0.0001, ***: p<0.001, **: p<0.01, *: p<0.05, ns: not significant. wt: wild-type (uninjected fabp-fgb-egfp control group), - thr : combined knockdown of all thyroid hormone receptor paralogs thraa , thrab , and thrb . All data were collected by an observer blinded to the condition.

Article Snippet: CRISPR single-guide RNA (sgRNA) sequences targeting early exons were designed with the Knockout Guide Design Tool ( synthego.com ).

Techniques: CRISPR, Injection, Knockdown, Control

Journal: bioRxiv

Article Title: FDA-approved drug repurposing in zebrafish identifies thyroid hormone and other compounds as potential antithrombotics

doi: 10.1101/2025.09.23.677920

Figure Lengend Snippet: After CRISPR-mediated individual knockdown of each canonical thyroid hormone receptor (- thraa , - thrab , and - thrb ) or combination (- thr ), embryos were co-treated with L-thyroxine (3 µM) and mestranol (25 µM) at 4 dpf and evaluated 24 hours later. Magenta borders indicate mestranol treated groups. ****: p < 0.0001, *: p < 0.05, ns: not significant. All data were collected by an observer blinded to the condition. Sample sizes for each group, corresponding to the thrombosis grades, are indicated within their respective stack.

Article Snippet: CRISPR single-guide RNA (sgRNA) sequences targeting early exons were designed with the Knockout Guide Design Tool ( synthego.com ).

Techniques: CRISPR, Knockdown