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

ABSTRACT: 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.

ORGANISM(S): Homo sapiens

PROVIDER: GSE275090 | GEO | 2025/06/04

REPOSITORIES: GEO

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Project description:The tracks show enrichment of RNA sequence tags generated by high throughput sequencing (RNA-seq) and mapped to the human genome. Double stranded cDNA was synthesized from polyadenylated RNA (polyA+) . PCR amplified, adapter ligated cDNA, 150-300nt long, was sequenced on an Illumina GA sequencer. Where designated, cell lines received specific treatments prior to RNA isolation. As indicated, K562 cells were treated with either interferon-a or interferon-g for 30 minutes or 6 hours. These experiments were carried out in conjunction with ChIP-Seq experiments on the transcription factors STAT1 and STAT2 in order to examine the effects that inducers of a specific transcriptional response might have on gene expression and on transcription factor binding site discovery. K562 cells were treated with a-amanitin in order to examine the effects of RNA polymerase II inhibition on RNA polymerase III-mediated transcription. This track shows expression data generated as confirmation of the SYDH TFBS (http://genome-preview.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeSydhTfbs) tracks currently available on genome-preview. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Cells were grown according to the approved ENCODE cell culture protocols (http://hgwdev.cse.ucsc.edu/ENCODE/protocols/cell). Total RNA was extracted using TRIzol reagents (15596-018, Life Tech), following the manufacturer's protocol. For polyA+ samples, polyadenylated RNA was purified using the MicroPoly(A) Purist kit (AM1919, Life Tech) and fragmented using RNA Fragmentation Reagent (AM8740, Life Tech). Illumina adapters were ligated to double stranded cDNA which was synthesized using reagents from Life Tech (11917-010). PCR amplified adapter ligated cDNA (150-300 bp) was sequenced using Illumina GA. Sequence reads of 27-33nt long with 0-2 mismatches were mapped to the genome. The signal height corresponds to the number of overlapping fragments at each nucleotide position in the genome. Samples originally mapped to the hg18 version of the human genome were remapped to hg19 using the BWA aligner, version 0.5.7.

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

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