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| Status |
Public on Mar 13, 2023 |
| Title |
Comparison of the Illumina NextSeq 2000 and GeneMind Genolab M sequencing platforms for spatial transcriptomics |
| Organism |
Homo sapiens |
| Experiment type |
Other
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| Summary |
The Illumina sequencing systems demonstrate high efficiency and power and remain the most popular platforms. Platforms with similar throughput and quality profiles but lower costs are under intensive development. In this study, we compared two platforms Illumina NextSeq 2000 and GeneMind Genolab M for 10x Genomics Visium spatial transcriptomics.
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| Overall design |
We performed comparison of GeneMind Genolab M and Illumina NextSeq 2000 sequencing platforms using three ovarian cancer 10x Genomics Visium libraries. We evaluate performance of both platforms in terms of sequencing quality and detection of UMI, spatial barcode, and probe sequence. We compared raw read mapping and read counting efficiency. Additionally, downstream analysis was performed in order to reveal concordance of dimension reduction, clusterization, and differential gene expression results between the Genolab M and NextSeq 2000 platforms. The study was carried out according to Declaration of Helsinki and was approved by the local committee of Medical Ethics of Tomsk Cancer Research Institute; all patients signed informed consent for the study.
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| Contributor(s) |
Iamshchikov P, Larionova I, Gerashchenko T, Piankov D, Koshkin P, Korostelev S, Denisov E |
| Citation(s) |
36882687 |
| BioProject |
PRJNA894440 |
| Submission date |
Mar 09, 2023 |
| Last update date |
May 24, 2023 |
| Contact name |
Irina Larionova |
| E-mail(s) |
larionova0903irina@mail.ru
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| Organization name |
Tomsk State University
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| Lab |
Laboratory of Translational Cellular and Molecular Biomedicine
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| Street address |
Lenin Ave, 36, Tomsk, Tomsk Oblast, Russia
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| City |
Tomsk |
| State/province |
Tomsk oblast |
| ZIP/Postal code |
634050 |
| Country |
Russia |
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| Platforms (2) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
| GPL30173 |
NextSeq 2000 (Homo sapiens) |
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| Samples (6)
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| Supplementary file |
Size |
Download |
File type/resource |
| GSE227019_RAW.tar |
88.2 Mb |
(http)(custom) |
TAR (of CSV, H5, JSON, PNG) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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