Joseph Replogle
@josephmreplogle
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MD PhD, PGY1 at @MGHMedicine/@HarvardMed
Joined October 2021
Our genome-scale Perturb-seq paper is out today in Cell! @CellCellPress @JswLab . Thanks to all the authors and reviewers for their contributions. See the thread below for key findings.
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Congrats @NadigAjay on TRADE out now in @NatureGenet: These statistical metrics enable more meaningful comparisons in Perturb-seq atlases. Also, now find the HepG2 and Jurkat Perturb-seq datasets on GEO GSE264667!.
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Even while in residency and with infants at home, I find it hard not to put everything down to read this new analysis of our data by @jkpritch and team! . And in the same week others are working toward optimizing large-scale Perturb-seq in cardiomyocytes
Modern GWAS can identify 1000s of hits but it can be hard to turn this into biological insight. What key cellular functions link genetic variation to disease? . I'm excited to present our new work combining associations + Perturb-seq to build interpretable causal graphs! Aš§µ
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The Norman lab's new large-scale CRISPRa Perturb-seq is a beautiful combination of question driven biology with single cell tech/analytic developments. I would expect nothing less from the lab!.
Can we recreate the transcriptional states seen in single-cell atlas projects? In our new preprint we try to do this using large-scale Perturb-seq experiments. Along the way we discuss off-target effects of CRISPR epigenetic editors and identify drivers of key fibroblast states.
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RT @thenormanlab: Can we recreate the transcriptional states seen in single-cell atlas projects? In our new preprint we try to do this usinā¦.
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RT @thenormanlab: Excited to share our preprint "Multiome Perturb-seq unlocks scalable discovery of integrated perturbation effects on theā¦.
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RT @NadigAjay: Just how impactful are large-scale perturbational data in single cell genomics?. In the last two weeks, there have been *thrā¦.
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RT @NadigAjay: How do genetic perturbations change cells? How are these effects shaped by cell type and dosage? How do we best extract insiā¦.
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Check out our latest large-scale Perturb-seq on biorxiv! A new stat gen/GWAS-inspired analytic framework + large-scale screens in an expanded range of cell types. Thanks @NadigAjay and @Luke0connor for involving us!
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From @russelltwalton @BlaineyLab , a very useful vector for those interested in taking advantage of sgRNA multiplexing for single cell CRISPR screens!.
Our new preprint describes āCROPseq-multiā: a versatile solution for multiplexed perturbation and decoding in pooled CRISPR screens Reagents on Addgene:
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RT @BryanDChoi: Today, @NEJM published our clinical study of a novel #CARTCell in patients with #Glioblastoma. Early results with CARv3-TEAā¦.
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RT @Dr_RajatGupta: Our study is out @Nature. We identify non-lipid risk pathways for coronary artery disease using pooled CRISPR-interferenā¦.
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Our latest CRISPRi screening tools + tips w/ @JSWlab and @MarcoJost_:. (1) dual-sgRNA libraries ā¬ knockdown while decreasing library size. (2) comparison of CRISPRi effectors finds that Zim3-dCas9 offers ā¬ knockdown with minimal toxicity. (3) validated Zim3-dCas9 cell lines
Maximizing CRISPRi efficacy and accessibility with dual-sgRNA libraries and optimal effectors #bioRxiv.
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Dreaming of a day when you won't need pipette arm PT after doing a genome-scale Perturb-seq experiment š.
New preprint out! We present a rapid and highly scalable scRNA-seq method. Thousands of samples or millions of cells with only a vortexer. Microfluidics-free single-cell genomics with templated emulsification
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1. While traditional genetic screens study simple, predefined phenotypes, Perturb-seq enables the construction of information-rich genotype-phenotype maps using single-cell RNA-sequencing (scRNA-seq) phenotypes. However, to date, Perturb-seq has been used at limited scales.
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I also shared 3' scRNA-seq data (~1500 K562 cells profiled on @10xGenomics 3' v3) deeply sequenced on Illumina and Ultima sequencers: Enjoy!.
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Open fluidics and less labeled nucleotides = cost-efficient, ultra-high throughput sequencing ideal for single-cell screens and atlases! Here are a few more Ultima papers:.
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$1/Gb? I had a great experience collaborating w/ Ultima genomics to sequence genome-scale Perturb-seq libraries on their new open fluidics sequencing platform: (see Figure S13 for comparison).
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Fun to see the Perturb-seq toolbox continue to expand from @satijalab @nevillesanjana. Cas13 Perturb-seq has been on the tech with list! Capture of barcode gRNA at 3' end of tandem Cas13 guide array = less sgrna recombination and higher lenti titers.
We are excited to introduce CaRPool-seq, a new technology that utilizes Cas13 to perform combinatorial single-cell perturbation screens! Check it out, esp. if you're interested in simultaneously perturbing multiple genes and exploring genetic interactions:
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7. We hope this is just the beginning of building comprehensive genotype-phenotype maps w/ Perturb-seq to discover gene function and cellular phenomena! New sequencing, single-cell tech, and disease-relevant cell models ā much more to come here : ).
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