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Series GSE183590 Query DataSets for GSE183590
Status Public on Sep 14, 2021
Title Single-cell RNA sequencing for the identification of early-stage lung cancer biomarkers from circulating blood
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary To develop biomarkers for diagnosis of early-stage lung adenocarcinoma (LUAD) patients, we set up single-cell RNA sequencing (scRNA-seq) pipeline using Fluidigm C1 systems. Through the scRNA-seq pipeline, we clustered 1,441 single cells from four non-small cell lung cancer (NSCLC) cell lines (A549, H460, H1299 and Calu3) into four groups based on differential gene expression and detected over 2,400 differentially expressed genes (DEGs) from a comparison of four clusters following dimension reduction. We validated fold change values of 120 DEGs selected from three cluster comparisons (top 20 up- and top 20 down-regulated genes per cluster comparison) using qRT-PCR approach. We performed further quantitative validation of chemokine genes (CXCL1 and CXCL2 with corresponding receptor, CXCR2) at mRNA level in tumour and tumour-adjacent normal lung tissues of LUAD patients (16 female and 19 male). Next, we profiled microRNAs epigenetically regulating expression of those chemokine genes in the tumour and normal tissues as well as blood (plasma) samples from corresponding LUAD patients. Finally, we identified relatively high copy number of miR-532-5p regulating those chemokine genes in patient plasma samples.
Overall design We loaded 400 single cells per NSCLC cell lines (A549, H460, H1299 and Calu3) to chambers of high-throughput (HT) scRNA-seq integrated fluidics circuits (IFCs). We generated four hundreds of 3'-end enriched scRNA-seq libraries per NSCLC cell line using in Fluidigm C1 systems (1,600 libraries in total). Those libraries were sequenced using illumina Nextseq 500 systems.
Web link
Contributor(s) Kim J, Xu Z, Marignani PA
Citation(s) 34654834
Submission date Sep 07, 2021
Last update date Oct 21, 2021
Contact name Paola Marignani
Phone 1 902 494 6033
Organization name Dalhousie University
Department Biochemistry & Molecular Biology
Lab 9F1
Street address 5850 College Street, Tupper Medical Building
City Halifax
State/province Nova Scotia
ZIP/Postal code B3H 1X5
Country Canada
Platforms (1)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
Samples (1456)
GSM5561685 A549 1
GSM5561686 A549 2
GSM5561687 A549 3
BioProject PRJNA761375
SRA SRP336022

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Supplementary file Size Download File type/resource
GSE183590_Read_count_matrix_05092021.txt.gz 9.2 Mb (ftp)(http) TXT
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Raw data are available in SRA
Processed data are available on Series record

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