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Series GSE236936 Query DataSets for GSE236936
Status Public on Jul 01, 2024
Title Genome editing by dual nucleases records deep lineage hierarchy with high fidelity.
Organisms Homo sapiens; Mus musculus
Experiment type Expression profiling by high throughput sequencing
Other
Summary Single-cell lineage tracing based on CRISPR/Cas9 gene editing tracks both cell states and genetic lineages at a single-cell resolution. We developed DuTracer, a single-cell lineage tracing method, to avoid rapid target exhaustion and barcode information dropout. Firstly, we introduced this system into HEK293T cells and initiated DuTracer for tracing. We collected single-cell transcriptome and barcode amplicon, demonstrating that this system could record more hierarchical information with minimal inter-site deletions. Subsequently, we applied DuTracer to a mouse embryoid body differentiation model to track lineage transitions of different cell types. We revealed cell potency hierarchy during the stochastic differentiation process of mES cells.
 
Overall design For HEK293T cells, we sequentially induced the gene editing of Cas12a and Cas9 and harvested the cells at D22. For embryoid body (EB) differentiation, we designed six induction strategies. We sampled cells at different time points between D8 and D14 to capture potential differentiation cascades. Single cell RNA-seq was performed using BGI DNBelab C4 kits. For all seven libraries, the obtained cDNAs were split into two halves. One half was used to generate the RNA-seq libraries and the other half was used to make amplicon libraries.
 
Contributor(s) Liao Y, Chen C
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Submission date Jul 10, 2023
Last update date Jul 01, 2024
Contact name Cheng Chen
E-mail(s) chen_cheng1@gibh.ac.cn
Organization name Guangzhou Institute of Biomedicine and Health, Chinese Academy of Science
Street address Kaiyuan Ave 190
City Guangzhou
State/province Guangdong
ZIP/Postal code 510530
Country China
 
Platforms (4)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
GPL30209 MGISEQ-2000RS (Homo sapiens)
Samples (14)
GSM7586135 EBD8a scRNA-seq
GSM7586136 EBD10a scRNA-seq
GSM7586137 EBD8b scRNA-seq
Relations
BioProject PRJNA993155

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Supplementary file Size Download File type/resource
GSE236936_RAW.tar 436.7 Mb (http)(custom) TAR (of CSV, MTX, TSV)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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