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Series GSE254034 Query DataSets for GSE254034
Status Public on Feb 05, 2024
Title Integration of hyperspectral imaging and transcriptomics from individual cells with HyperSeq
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Microscopy and omics are complementary approaches to probe the molecular state of cells in health and disease, combining granularity with scalability. While important advances have been achieved over the last decade in each area, integrating both imaging- and sequencing-based assays on the same cell has proven challenging. In this study, a new approach called HyperSeq that combines hyperspectral autofluorescence imaging with transcriptomics on the same cell is demonstrated. HyperSeq was applied to Michigan Cancer Foundation 7 (MCF-7) breast cancer cells and identified a subpopulation of cells exhibiting bright autofluorescence rings at the plasma membrane in optical channel 13 (ex = 431 nm, em = 594 nm). Correlating the presence of a ring with the gene expression in the same cell indicated that ringed cells are more likely to express hallmark genes of apoptosis and gene silencing and less likely to express genes associated with ATP production. Further, correlation of cell morphology with gene expression suggested that multiple members of the spliceosome were upregulated in larger cells. A number of genes, albeit evenly expressed across cell sizes, exhibited higher usage of specific exons in larger or smaller cells. Finally, correlation between gene expression and fluorescence within the spectral range of Nicotinamide adenine dinucleotide hydrogen (NADH) provided preliminary insight into the metabolic states of cells. These observations provided a link between the cell’s optical spectrum and its internal molecular state, demonstrating the utility of HyperSeq to study cell biology at single cell resolution by integrating spectral, morphological and transcriptomic analyses into a single, streamlined workflow.
 
Overall design MCF-7 cells were imaged by a Hyperspectral microscope and then captured by CellCelector to 384-well PCR plates for subsequent SmartSeq2 library preparation
 
Contributor(s) Xie Y, Habibalahi A, Anwer AG, Wahi K, Gatt C, Johansson EM, Holst J, Goldys E, Zanini F
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Submission date Jan 23, 2024
Last update date Feb 05, 2024
Contact name Yike Xie
E-mail(s) yike.echo.xie@gmail.com
Organization name UNSW Sydney
Street address Lowy 2, Cnr High and Botany St
City Kensington
State/province NSW
ZIP/Postal code 2052
Country Australia
 
Platforms (3)
GPL15520 Illumina MiSeq (Homo sapiens)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
GPL30882 NextSeq 1000 (Homo sapiens)
Samples (204)
GSM8032143 1-1_C3_S1,HyperSeq, scRNASeq
GSM8032144 1-1_H3_S6,HyperSeq, scRNASeq
GSM8032145 1-1_I3_S7,HyperSeq, scRNASeq
Relations
BioProject PRJNA1068168

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
GSE254034_HyperSeq_cell_images.h5 1004.9 Mb (ftp)(http) H5
GSE254034_HyperSeq_exon_with_spectra.h5ad.gz 68.3 Mb (ftp)(http) H5AD
GSE254034_HyperSeq_gene_with_spectra.h5ad.gz 2.6 Mb (ftp)(http) H5AD
GSE254034_pilot_experiment_without_spectra.h5ad.gz 756.2 Kb (ftp)(http) H5AD
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Raw data are available in SRA
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