varshneylab.social
Assoc. Prof. Interested in CRISPR, Zebrafish, Disease Modeling, Rare Diseases, and Neurodevelopmental Disorders. The opinions expressed here are my own.
51 posts
1,237 followers
539 following
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What! That's where I worked. So many fond memories. ðŸ˜
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Terrible! What building is it? I spent a year in this amazing campus.
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Congrats Ben and team!
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My lab contributed to functional data showing zebrafish trmt1 knockouts recapitulated patient phenotypes: abnormal brain morphology, altered behavior, and dysregulated gene expression linked to [email protected]
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@varshneylab.social‬ @sheng-jia.bsky.social (gRNA selection/ Phenotypic penetrance/ Neurodevelopmental disorders)
https://doi.org/10.1093/nar/gkaf180
‪@jutfelt.bsky.social Version 2 Husmorph (Image Analysis/ Landmarking)Â
https://github.com/HenHus/Husmorph (32/34)
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We validated 37 candidate disease genes across 8 tissues and screened 63 hearing-related genes, identifying 52 with hearing defects. Also, we identified 10 new neurodevelopmental disorder (NDD) genes in zebrafish.
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Transcriptomic analysis revealed that gene expression patterns in F0 knockouts closely mimic those in stable knockout lines.
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Our data shows that targeting the N-terminal half of a functional protein domain significantly increases phenotypic penetrance compared to targeting other regions of the gene. Selecting gRNAs with high Lindel scores (>75) substantially improved knockout efficiency.
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We utilized indel prediction models such as Lindel (or inDelphi/ForeCast and others) to design gRNAs with high predicted success.
Targeting the N-terminal half of functional domains worked best. We tested 324 gRNAs across 125 genes, targeting key protein domains with just 1-2 gRNAs.
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Several papers on F0 mutagenesis have been published, including those by Jao et al., Burger et al., Wu et al., Kroll et al., and others—all methods work well. We set out to test and compare strategies to achieve the highest phenotype penetrance using minimal resources.
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Our data shows that targeting the N-terminal half of a functional protein domain significantly increases phenotypic penetrance compared to targeting other regions of the gene. Selecting gRNAs with high Lindel scores (>75) substantially improved knockout efficiency.
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We utilized indel prediction models such as Lindel (or inDelphi/ForeCast and others) to design gRNAs with high predicted success.
Targeting the N-terminal half of functional domains worked best. We tested 324 gRNAs across 125 genes, targeting key protein domains with just 1-2 gRNAs.
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Several papers on F0 mutagenesis have been published, including those by Jao et al., Burger et al., Wu et al., Kroll et al., and others—all methods work well. We set out to test and compare strategies to achieve the highest phenotype penetrance using minimal resources.
comment in response to
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Our data shows that targeting the N-terminal half of a functional protein domain significantly increases phenotypic penetrance compared to targeting other regions of the gene. Selecting gRNAs with high Lindel scores (>75) substantially improved knockout efficiency.
comment in response to
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We utilized indel prediction models such as Lindel (or inDelphi/ForeCast and others) to design gRNAs with high predicted success.
Targeting the N-terminal half of functional domains worked best. We tested 324 gRNAs across 125 genes, targeting key protein domains with just 1-2 gRNAs.
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Several papers on F0 mutagenesis have been published, including those by Jao et al., Burger et al., Wu et al., Kroll et al., and others—all methods work well. We set out to test and compare strategies to achieve the highest phenotype penetrance using minimal resources.
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* Our data shows that targeting the N-terminal half of a functional protein domain significantly increases phenotypic penetrance compared to targeting other regions of the gene. Selecting gRNAs with high Lindel scores (>75) substantially improved knockout efficiency.
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* We utilized indel prediction models such as Lindel (or inDelphi/ForeCast and others) to design gRNAs with high predicted success.
* Targeting the N-terminal half of functional domains worked best. We tested 324 gRNAs across 125 genes, targeting key protein domains with just 1-2 gRNAs.
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* Several papers on F0 mutagenesis have been published, including those by Jao et al., Burger et al., Wu et al., Kroll et al., and others—all methods work well. We set out to test and compare strategies to achieve the highest phenotype penetrance using minimal resources.
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My panel TAG that was scheduled for 2/26-27 is also cancelled.
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MNG study section scheduled in person for 2/20-2/21. Put together in Dec, assignments out 1/14, travel arrangements made mid-Jan. Was NOT posted to Fed Reg. Critiques due 2/14. All normal to that point. Moved to zoom 2/18 in am, discussion order posted 2/18 pm. CANCELLED just now.
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MNG
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Congratulations 🎉!
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It is hilarious to watch that guy ranting. It seems like a study section rejected him as he was calling SS members mediocre people😀