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Series GSE168626 Query DataSets for GSE168626
Status Public on Mar 10, 2021
Title Targeted single cell RNA-sequencing of transcription factors facilitates biological insights from human cell experimental models [intestinal stromal cells pre-capture]
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Single cell RNA sequencing (scRNA-seq) is a widely used method for identifying cell types and trajectories in biologically heterogeneous samples, but is limited in its detection and quantification of lowly expressed genes. This results in missing important biological signals, such as the expression of key transcription factors (TFs) driving cellular differentiation. We show that targeted sequencing of ~1000 TFs (scCapture-seq) in iPSC-derived neuronal cultures greatly improves the biological information garnered from scRNA-seq. Increased TF resolution enhanced cell-type identification, developmental trajectories and gene regulatory networks. This allowed us to resolve differences amongst neuronal populations, which were generated in two different labs using the same differentiation protocol. ScCapture-seq improved TF gene-regulatory network inference and thus identified divergent patterns of neurogenesis into either excitatory cortical neurons or inhibitory interneurons. Furthermore, scCapture-seq revealed a role for of retinoic acid signalling in the developmental divergence between these different neuronal populations. Our results demonstrate that TF targeting improves the characterization of human cellular models and allows identification of the essential differences between cellular populations, which would otherwise be missed in traditional scRNA-seq. scCapture-seq TF targeting represents a cost-effective enhancement of scRNA-seq, which could be broadly applied to any cellular models to improve scRNA-seq resolution
 
Overall design RNAseq profiles of 188 intestinal stromal cells from UC patients made using the 10x droplet-based protocol (Kinchen et.al., Cell, 2018; PMID: 30270042). Post-capture libraries were sequenced on 1 lane of a HiSeq 4000 at 75 bp paired end. RNA from each cell was sequenced twice: the PRE-capture libraries have all human genome sequenced, while only chosen set of transcription factors was sequenced in POST-capture libraries
 
Contributor(s) Pokhilko A, Handel AE, Curion F, Volpato V, Whiteley ES, Bøstrand S, Newey SE, Akerman CJ, Webber C, Clark MB, Bowden R, Cader Z
Citation(s) 34011578
Submission date Mar 10, 2021
Last update date Jun 13, 2021
Contact name Alexandra Pokhilko
Organization name University of Oxford
Department Nuffield Department of Clinical Neurosciences
Street address John Radcliffe Hospital, Headington
City Oxford
ZIP/Postal code OX3 9DS
Country United Kingdom
 
Platforms (1)
GPL20301 Illumina HiSeq 4000 (Homo sapiens)
Samples (252)
GSM5151438 intestinal stromal cells pre-capture [WTCHG_288196_201201]
GSM5151439 intestinal stromal cells pre-capture [WTCHG_288196_201202]
GSM5151440 intestinal stromal cells pre-capture [WTCHG_288196_201203]
This SubSeries is part of SuperSeries:
GSE168634 Targeted single-cell RNA sequencing of transcription factors facilitates biological insights from human cell experimental models
Relations
BioProject PRJNA713312
SRA SRP310097

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SOFT formatted family file(s) SOFTHelp
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Supplementary file Size Download File type/resource
GSE168626_counts_genes_symbols_POSTcapture_GI.csv.gz 64.1 Kb (ftp)(http) CSV
GSE168626_counts_genes_symbols_PREcapture_GI.csv.gz 561.3 Kb (ftp)(http) CSV
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Raw data are available in SRA
Processed data are available on Series record

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