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Series GSE124703 Query DataSets for GSE124703
Status Public on Jan 07, 2019
Title CRISPR-based multimodal genetic screens in human iPSC-derived neurons
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary CRISPR/Cas9-based functional genomics have transformed our ability to elucidate mammalian cell biology. Most previous CRISPR-based screens were implemented in cancer cell lines, rather than healthy, differentiated cells. Here, we describe a CRISPR interference (CRISPRi)-based platform for genetic screens in human neurons derived from induced pluripotent stem cells (iPSCs). We demonstrate robust and durable knockdown of endogenous genes in such neurons, and present results from three complementary genetic screens. A survival-based screen revealed neuron-specific essential genes and a small number of genes that improved neuronal survival upon knockdown. A screen with a single-cell transcriptomic readout uncovered several examples for genes knockdown of which had dramatically different cell-type specific consequences. A longitudinal imaging screen detected distinct consequences of gene knockdown on neuronal morphology. Our results highlight the potential of interrogating cell biology in iPSC-derived differentiated cell types and provide a platform for the systematic dissection of normal and disease states of neurons.
Overall design The Quant-seq experiments were performed using iPSC-derived neurons at Day 14, Day 21 and Day 28 of differentiation with 2 replicates for each sample. The CROP-seq experiments were performed using iPSCs and Day 7 neurons infected by a library of sgRNAs. Two lanes of 10X platform were used for each CROP-seq sample.
Contributor(s) Tian R, Ludwig C, Kampmann M
Citation(s) 31422865
Submission date Jan 06, 2019
Last update date Jun 19, 2020
Contact name Ruilin Tian
Organization name University of California, San Francisco
Department Institute for Neurodegenerative Diseases
Lab Martin Kampmann
Street address 675 Nelson Rising Lane, 3rd Floor
City San Francisco
State/province CA
ZIP/Postal code 94158
Country USA
Platforms (2)
GPL20301 Illumina HiSeq 4000 (Homo sapiens)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Samples (14)
GSM3543612 Quant-seq_Day 14_neuron_rep1
GSM3543613 Quant-seq_Day 14_neuron_rep2
GSM3543614 Quant-seq_Day 21_neuron_rep1
BioProject PRJNA513160
SRA SRP176013

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Supplementary file Size Download File type/resource
GSE124703_RAW.tar 1.0 Gb (http)(custom) TAR (of MTX, TSV, TXT)
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Raw data are available in SRA
Processed data provided as supplementary file

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