Comparative functional genomics identifies unique molecular features of EPSCs

Malik, Vikas; Zang, Ruge; Fuentes-Iglesias, Alejandro; Huang, Xin; Li, Dan; Fidalgo, Miguel; Zhou, Hongwei; Wang, Jianlong

doi:10.26508/lsa.202201608

Cited by 3 publications

(2 citation statements)

References 64 publications

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“…In parallel with the cross-platform comparison, we also analyzed the genomic impact of the RUNX3 and ZBTB46 on the global gene expression profile of ESCs. The transcriptional landscape of the murine ESCs has been intensively studied using bulk or single-cell mRNA sequencing (Lienert et al, 2011;Kumar et al, 2014;Kolodziejczyk et al, 2015;Malik et al, 2022). Interestingly, it was observed that the gene expression pattern of the murine ESCs is heterogeneous and stochastic; moreover, it is depending on the cell culture conditions (Kumar et al, 2014;Torres-Padilla and Chambers, 2014).…”

Section: Discussionmentioning

confidence: 99%

Comparative transcriptomic analysis of Illumina and MGI next-generation sequencing platforms using RUNX3- and ZBTB46-instructed embryonic stem cells

Póliska,

Fareh,

Lengyel

et al. 2024

Front. Genet.

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Introduction: We have previously observed phenotypic and developmental changes upon the ectopic expression of the RUNX3 or the ZBTB46 transcription factors in mouse embryonic stem cell (ESC) derived progenitors. In this study, we evaluated the gene expression profiles of the RUNX3- and the ZBTB46-instructed murine ESCs with RNA-seq testing two next-generation sequencing technologies.Methods: We compared the DNA nanoball-based DNBSEQ G400 sequencer (MGI) with the bridge-PCR-based NextSeq 500 instrument (Illumina) for RNA sequencing. Moreover, we also compared two types of MGI sequencing reagents (Standard versus Hot-massive parallel sequencing (MPS)) with the DNBSEQ G400.Results: We observed that both sequencing platforms showed comparable levels of quality, sequencing uniformity, and gene expression profiles. For example, highly overlapping RUNX3- and ZBTB46-regulated gene lists were obtained from both sequencing datasets. Moreover, we observed that the Standard and the Hot-MPS-derived RUNX3- and ZBTB46-regulated gene lists were also considerably overlapped. This transcriptome analysis also helped us to identify differently expressed genes in the presence of the transgenic RUNX3 or ZBTB46. For example, we found that Gzmb, Gzmd, Gzme, Gdf6, and Ccr7 genes were robustly upregulated upon the forced expression of Runx3; on the other hand, Gpx2, Tdpoz4, and Arg2 were induced alongside the ectopic expression of Zbtb46.Discussion: Similar gene expression profile and greatly overlapping RUNX3- and ZBTB46-regulated gene sets were detected with both DNA sequencing platforms. Our analyses demonstrate that both sequencing technologies are suitable for transcriptome profiling and target gene selection. These findings suggest that DNBSEQ G400 represents a cost-effective alternative sequencing platform for gene expression monitoring. Moreover, this analysis provides a resource for exploration of the RUNX3- and ZBTB46-dependent gene regulatory networks.

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Section: Discussionmentioning

confidence: 99%

Comparative transcriptomic analysis of Illumina and MGI next-generation sequencing platforms using RUNX3- and ZBTB46-instructed embryonic stem cells

Póliska,

Fareh,

Lengyel

et al. 2024

Front. Genet.

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show abstract

“…In parallel with the cross-platform comparison, we also analyzed the genomic impact of the RUNX3 and ZBTB46 on the global gene expression pro le of ESCs. The transcriptional landscape of the murine ESCs has been intensively studied using bulk or single cell mRNA sequencing [27][28][29][30] . Interestingly, it was observed that the gene expression pattern of the murine ESCs is heterogeneous and stochastic, moreover, it is depending on the cell culture conditions 27,31 .…”

Section: Discussionmentioning

confidence: 99%

Comparative transcriptomic analysis of Illumina and MGI next generation sequencing platforms using RUNX3- and ZBTB46-instructed embryonic stem cells

Póliska

Fareh

Lengyel

et al. 2023

Preprint

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We have previously observed phenotypic and developmental changes upon the ectopic expression of the RUNX3 or the ZBTB46 transcription factors in mouse embryonic stem cell (ESC) derived progenitors. In this study we evaluated the gene expression profiles of the RUNX3- and the ZBTB46-instructed murine ESCs with RNA-Seq testing two next generation sequencing (NGS) technologies. We compared the DNA nanoball (DNB) based MGI DNBSEQ G400 sequencer with the bridge-PCR based Illumina NextSeq 500 instrument. Moreover, we also compared two types of MGI sequencing reagents (Standard- versus Hot-MPS) with the DNBSEQ G400. Importantly, very similar gene expression profile and greatly overlapping RUNX3 and ZBTB46 regulated gene sets were detected with both platforms. Moreover, almost identical gene expression pattern was obtained with the Hot-MPS reagent compared to the Standard-MPS chemistry. This transcriptomic analysis also facilitated the identification of RUNX3 and ZBTB46 regulated genes. For example, we found that Gzmd, Gdf6 and Ccr7 genes were robustly upregulated upon the forced expression of Runx3, on the other hand, Gpx2, Tdpoz4 and Arg2 were induced upon the ectopic expression of Zbtb46. Together these findings demonstrate that the DNBSEQ G400 system is also suitable for global transcript profiling and target gene selection with lower cost.

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Recapitulating primary immunodeficiencies with expanded potential stem cells: Proof of concept with STAT1 gain of function

Liu,

Chan,

Smith

et al. 2024

Journal of Allergy and Clinical Immunology

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Comparative functional genomics identifies unique molecular features of EPSCs

Cited by 3 publications

References 64 publications

Comparative transcriptomic analysis of Illumina and MGI next-generation sequencing platforms using RUNX3- and ZBTB46-instructed embryonic stem cells

Comparative transcriptomic analysis of Illumina and MGI next-generation sequencing platforms using RUNX3- and ZBTB46-instructed embryonic stem cells

Comparative transcriptomic analysis of Illumina and MGI next generation sequencing platforms using RUNX3- and ZBTB46-instructed embryonic stem cells

Recapitulating primary immunodeficiencies with expanded potential stem cells: Proof of concept with STAT1 gain of function

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