Malwina Prater

Comparative Single-Cell Profiling of CRISPR Knockout and Interference Defines Modality-Specific Strengths in Functional Genomics

Nikhil Gupta, Andy Sayer, Malwina Prater, Chara Mastrokalou et autres

Abstract Pooled CRISPR screens coupled with single-cell RNA sequencing enable high-throughput functional interrogation of gene regulatory networks, yet systematic comparisons of CRISPR knockout (CRISPRko) and CRISPR interference (CRISPRi) remain limited. We established a single-cell CRISPRko workflow and benchmarked it against CRISPRi using …

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MitoPerturb-Seq identifies gene-specific single-cell responses to mitochondrial DNA depletion and heteroplasmy

Stephen P. Burr, Kathryn Auckland, Angelos Glynos, Abhilesh S Dhawanjewar et autres

Mitochondria contain their own genome, mitochondrial DNA (mtDNA), which is under strict control by the cell nucleus. mtDNA occurs in many copies per cell and mutations often only affect a proportion of them, giving rise to heteroplasmy. mtDNA copy number and heteroplasmy …

gb (code pays fourni par la source)

MitoPerturb-Seq: Analysis code for 'MitoPerturb-Seq identifies gene-specific single-cell responses to mitochondrial DNA depletion and heteroplasmy'

Stephen P. Burr, Kathryn Auckland, Angelos Glynos, Abhilesh S Dhawanjewar et autres

Computational pipelines for the MitoPerturb-Seq study: single-cell multiome (scRNA-seq + scATAC-seq) with CRISPR perturbation screening across 13 mitochondrial target genes, mitochondrial heteroplasmy calling and variance modelling, and ATF4 chromatin binding analysis using DamID-seq. ~6,500 mouse embryonic fibroblasts (MEFs) from the m.5024C>T heteroplasmic …

gb (code pays fourni par la source)

MitoPerturb-Seq: Analysis code for 'MitoPerturb-Seq identifies gene-specific single-cell responses to mitochondrial DNA depletion and heteroplasmy'

Stephen P. Burr, Kathryn Auckland, Angelos Glynos, Abhilesh S Dhawanjewar et autres

Computational pipelines for the MitoPerturb-Seq study: single-cell multiome (scRNA-seq + scATAC-seq) with CRISPR perturbation screening across 13 mitochondrial target genes, mitochondrial heteroplasmy calling and variance modelling, and ATF4 chromatin binding analysis using DamID-seq. ~6,500 mouse embryonic fibroblasts (MEFs) from the m.5024C>T heteroplasmic …

gb (code pays fourni par la source)

MitoPerturb-Seq: Analysis code for 'MitoPerturb-Seq identifies gene-specific single-cell responses to mitochondrial DNA depletion and heteroplasmy'

Stephen P. Burr, Kathryn Auckland, Angelos Glynos, Abhilesh S Dhawanjewar et autres

Computational pipelines for the MitoPerturb-Seq study: single-cell multiome (scRNA-seq + scATAC-seq) with CRISPR perturbation screening across 13 mitochondrial target genes, mitochondrial heteroplasmy calling and variance modelling, and ATF4 chromatin binding analysis using DamID-seq. ~6,500 mouse embryonic fibroblasts (MEFs) from the m.5024C>T heteroplasmic …

gb (code pays fourni par la source)

MitoPerturb-Seq identifies gene-specific single-cell responses to mitochondrial DNA depletion and heteroplasmy.

Stephen P. Burr, Kathryn Auckland, Angelos Glynos, Abhilesh S Dhawanjewar et autres

Ubiquitin-mediated mitophagy regulates the inheritance of mitochondrial DNA mutations

Michele Frison, Brandon S. Lockey, Yu Nie, Zoe J. Golder et autres

Mitochondrial synthesis of adenosine triphosphate is essential for eukaryotic life but is dependent on the cooperation of two genomes: nuclear and mitochondrial DNA (mtDNA). mtDNA mutates ~15 times as fast as the nuclear genome, challenging this symbiotic relationship. Mechanisms must have evolved …

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MitoPerturb-Seq identifies common and gene-specific single-cell responses to mitochondrial DNA depletion and heteroplasmy

Stephen P. Burr, Kathryn Auckland, Angelos Glynos, Abhilesh S Dhawanjewar et autres

Summary Mitochondria contain their own genome, the mitochondrial DNA (mtDNA), which is under strict control of the cell nucleus. mtDNA occurs in many copies in each cell, and mutations often only affect a proportion of them, giving rise to heteroplasmy. mtDNA copy …

gb (code pays fourni par la source)

Single-cell RNA sequencing identifies CXADR as a fate determinant of the placental exchange surface

Dafina M. Angelova, Aleksandra O Tsolova, Malwina Prater, Noura Ballasy et autres

The placenta is the critical interface between mother and fetus, and consequently, placental dysfunction underlies many pregnancy complications. Placental formation requires an adequate expansion of trophoblast stem and progenitor cells followed by finely tuned lineage specification events. Here, using single-cell RNA sequencing …

gb, ca, fr, cn (code pays fourni par la source)

Transcriptional profiling of Kiss1 neurons from arcuate and rostral periventricular hypothalamic regions in female mice

Stephen M. Manchishi, Malwina Prater, William Henry Colledge

In brief: The transcriptional profiles of Kiss1 neurons from the arcuate and the rostral periventricular region of the third ventricle of the hypothalamus have been directly compared in diestrous female mice. Differentially expressed genes provide molecular signatures for these two populations of …

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Alternative splicing in the transitional period underpinning the onset of maternal blood flow in the human early placenta.

Cherlyn Tan, Malwina Prater, Xiaohui Zhao, Hung Wa Yung et autres

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One-carbon metabolism is required for epigenetic stability in the mouse placenta

Claire E. Senner, Ziqi Dong, Malwina Prater, Miguel Ramos Branco et autres

One-carbon metabolism, including the folate cycle, has a crucial role in fetal development though its molecular function is complex and unclear. The hypomorphic Mtrr gt allele is known to disrupt one-carbon metabolism, and thus methyl group availability, leading to several developmental phenotypes …

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