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Series GSE249416 Query DataSets for GSE249416
Status Public on Dec 05, 2023
Title Massively parallel in vivo Perturb-seq reveals cell type-specific transcriptional networks in cortical development
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary Leveraging AAV's versatile tropism and labeling capacity, we expanded the scale of in vivo CRISPR screen with single-cell transcriptomic phenotyping across embryonic to adult brains and peripheral nervous systems. Through extensive tests of 86 AAV serotypes, combined with transposon systems, we substantially amplified labeling and accelerated in vivo gene delivery from weeks to days. Our proof-of-principle in utero screen identified the pleiotropic effects of Foxg1, highlighting its tight regulation of distinct networks essential for cell fate specification of Layer 6 corticothalamic neurons. Notably, our platform can label >6% of cerebral cells, surpassing the current state-of-the-art efficacy at <0.1% by lentivirus, to achieve analysis of over 30,000 cells in one experiment and enable massively parallel in vivo Perturb-seq. Compatible with various phenotypic measurements (single-cell or spatial multi-omics), it presents a flexible approach to interrogate gene function across cell types in vivo, translating gene variants to their causal function.
 
Overall design AAV transduced cells were dissociated and Fluorescent-activated sorted (FACS) to analyze the AAV transduction efficiency, gRNA capturing efficiency or perturbation effects with scRNA-seq
Please note that the Perturb_* samples are the standard scRNA-seq sample, while the Perturb_*_Foxgdialout samples are enriched library on Foxg1 only with a separate library prep and sequencing.
 
Contributor(s) Zheng X, Simmons SK, Kim K, Park J, Levin JZ, Jin X
Citation missing Has this study been published? Please login to update or notify GEO.
Submission date Dec 05, 2023
Last update date Dec 05, 2023
Contact name Xinhe Zheng
E-mail(s) xzheng@scripps.edu
Organization name The Scripps Research Institute
Department Neuroscience
Lab Xin Jin
Street address 3528 General Atomics Court
City San Diego
State/province California
ZIP/Postal code 92121
Country USA
 
Platforms (2)
GPL19057 Illumina NextSeq 500 (Mus musculus)
GPL32071 Illumina iSeq 100 (Mus musculus)
Samples (14)
GSM7946926 AAVlib2_E15_unsort
GSM7946927 AAVlib2_E15_sort
GSM7946928 SCH9_P9_3p
Relations
BioProject PRJNA1049003

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE249416_3p5p_all.Robj.gz 281.4 Mb (ftp)(http) ROBJ
GSE249416_3p5p_ctxobj.Robj.gz 235.4 Mb (ftp)(http) ROBJ
GSE249416_AAV_all.Robj.gz 502.6 Mb (ftp)(http) ROBJ
GSE249416_AAV_ctxobj.Robj.gz 408.6 Mb (ftp)(http) ROBJ
GSE249416_Perturb_all.qs.gz 1.5 Gb (ftp)(http) QS
GSE249416_Perturb_sg.qs.gz 464.8 Mb (ftp)(http) QS
Raw data are available in SRA

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