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Validation of single-cell transcriptomic profiles from Illumina and MGI Tech sequencing platforms.

ABSTRACT: Validation of single-cell transcriptomic profiles from Illumina and MGI Tech sequencing platforms.

PROVIDER: PRJNA1149090 | ENA |

REPOSITORIES: ENA

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Validation of single-cell transcriptomic profiles from Illumina and MGI Tech sequencing platforms.

Project description:Different companies have developed sequencing platforms with a wide variety of strengths and drawbacks. Illumina is currently used for high-throughput and highly accurate short-read sequencing, however, other companies, such as MGI Tech, have developed a similar sequencing method at a lower cost. The accuracy, sensitivity, and reproducibility of Illumina and MGI Tech have been compared, showing high similarity. While many comparisons exist, the performance of MGI on gene expression and cell clustering for single-cell applications is unknown. In this study, we performed single-cell RNA sequencing on three human breast cancer samples to compare the cell clustering or average gene expressions for the reads generated by Illumina and MGI sequencing. We observed unique platform-specific cells detected and show that these low-quality cells appear randomly and could only affect minor cell populations.

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Highly comparable metabarcoding results from MGI-Tech and Illumina sequencing platforms.

Project description:With the developments in DNA nanoball sequencing technologies and the emergence of new platforms, there is an increasing interest in their performance in comparison with the widely used sequencing-by-synthesis methods. Here, we test the consistency of metabarcoding results from DNBSEQ-G400RS (DNA nanoball sequencing platform by MGI-Tech) and NovaSeq 6000 (sequencing-by-synthesis platform by Illumina) platforms using technical replicates of DNA libraries that consist of COI gene amplicons from 120 soil DNA samples. By subjecting raw sequencing data from both platforms to a uniform bioinformatics processing, we found that the proportion of high-quality reads passing through the filtering steps was similar in both datasets. Per-sample operational taxonomic unit (OTU) and amplicon sequence variant (ASV) richness patterns were highly correlated, but sequencing data from DNBSEQ-G400RS harbored a higher number of OTUs. This may be related to the lower dominance of most common OTUs in DNBSEQ data set (thus revealing higher richness by detecting rare taxa) and/or to a lower effective read quality leading to generation of spurious OTUs. However, there was no statistical difference in the ASV and post-clustered ASV richness between platforms, suggesting that additional denoising step in the ASV workflow had effectively removed the 'noisy' reads. Both OTU-based and ASV-based composition were strongly correlated between the sequencing platforms, with essentially interchangeable results. Therefore, we conclude that DNBSEQ-G400RS and NovaSeq 6000 are both equally efficient high-throughput sequencing platforms to be utilized in studies aiming to apply the metabarcoding approach, but the main benefit of the former is related to lower sequencing cost.

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Dillution series comparison of Affymetrix and Illumina Expression Platforms

Project description:The growth in popularity of RNA expression microarrays has been accompanied by concerns about the reliability of the data especially when comparing between different platforms. Here we present an evaluation of the reproducibility of microarray results using two platforms, Affymetrix GeneChips and Illumina BeadArrays. The study design is based on a dilution series of two human tissues (blood and placenta), tested in duplicate on each platform. By a variety of measures the two platforms yielded data of similar quality and properties. The results of a comparison between the platforms indicate very high agreement, particularly for genes which are predicted to be differentially expressed between the two tissues. Agreement was strongly correlated with the level of expression of a gene. Concordance was also improved when probes on the two platforms could be identified as being likely to target the same set of transcripts of a given gene. These results shed light on the causes or failures of agreement across microarray platforms. The set of probes we found to be most highly reproducible can be used by others to help increase confidence in analyses of other data sets using these platforms. Keywords: Dilution series, platform comparison, Affymetrix, Illumina

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Comparison of the Illumina NextSeq 2000 and GeneMind Genolab M sequencing platforms for spatial transcriptomics

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