GEO series
Programmable transcript-specific enrichment for single-cell sequencing enables profiling of rare cell states
GSE262355
Homo sapiens; Mus musculus
Other; Expression profiling by high throughput sequencing
23 samples
Submitted 2024/03/26
Platform GPL18573Platform GPL24676Platform GPL24247Platform GPL34284
Summary
The widespread application of single-cell genomics technologies has accelerated our understanding of the breadth and depth of heterogeneity of cell states across diverse contexts. As single-cell RNA sequencing (scRNA-seq) has been the most popular modality used for profiling, many populations have been described primarily based on specific marker transcript profiles compared to classical cytometry approaches relying on protein expression. Additionally, many single cell studies require the isolation of nuclei from tissue, eliminating the ability to enrich learned rare cell states based on extranuclear protein markers. To address this limitation, we describe Programmable Enrichment via RNA Flow-FISH by sequencing (PERFF-seq), a scalable assay that enables single cell and single nuclei RNA-seq profiling from subpopulations of complex cellular mixtures solely defined by the abundance of RNA transcripts. Across vignettes of immune cell populations as well as nuclei from fresh frozen and formalin-fixed paraffin-embedded brain tissue, we demonstrate the enrichment of cell populations via RNA-based cytometry upstream of high-throughput scRNA-seq. Together, our approach provides a rational, programmable method for studying cell identities and transcriptional heterogeneity of rare populations identifiable by as few as one marker transcript, advancing the rational study of cellular diversity across fresh and archived tissue materials.
Published in
Abay T, Stickels RR, Takizawa MT et al.
· bioRxiv : the preprint server for biology 2024
· PMID 38586040
· doi:10.1101/2024.03.27.587039
This dataset
Download
Direct links to NCBI, no account and no request form: the whole study as GSE262355_RAW.tar, processed values as the series matrix, the supplementary file directory, and per-sample supplementary files for any of the 23 samples. Raw sequencing reads are also available from ENA.
Also filed as BioProject PRJNA1091573 and SRA study SRP497622. Searching any of these in the dataset finder brings you back here.
Study design
22 conditions, each sampled once — no replicated groups
Loss of Y chromosome, Pool ×2
Read from 23 sample titles: 22 distinct titles with little repetition. Check it against the sample list below before relying on it.
Samples in this study
0 selected
- GSM8163764 Development_A
- GSM8163765 Development_B
- GSM8163766 Development_C
- GSM8163767 Development_D
- GSM8163768 Development_E
- GSM8163769 Development_F
- GSM8163770 Development_G
- GSM8163771 Development_H
- GSM8163772 Development_I
- GSM8163773 Development_J
- GSM8163774 Development_K
- GSM8163775 Development_L
- GSM8163776 Pilot_Flex
- GSM8163777 PERFFseq_TFPool
- GSM8163778 PERFFseq_GBMPool
- GSM8163779 PERFFseq_LogicPool
- GSM8163780 PERFFseq_IL3RAminus
- GSM8163781 PERFFseq_IL3RAplus
- GSM8163782 PERFFseq_Mobpminus
- GSM8163783 PERFFseq_Mobpplus
- GSM8163784 PERFFseq_CD3Pool
- GSM8607450 Loss of Y chromosome, Pool1
- GSM8607451 Loss of Y chromosome, Pool2
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