Chongyi Chen

2 months ago | biorxiv.org | Jun Lyu |Xiaoyan Xu |Chongyi Chen

AbstractSequencing newly synthesized transcriptome alongside regular transcriptome in single cells enables the study of gene expression temporal dynamics during rapid chromatin and gene regulation processes. Existing assays for profiling single-cell newly synthesized transcriptome often require specialized technical expertise to achieve high cellular throughput, limiting their accessibility.

Nov 29, 2024 | mdpi.com | Jun Lyu |Chongyi Chen

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Aug 23, 2024 | biorxiv.org | Jun Lyu |Xiaoyan Xu |Chongyi Chen

AbstractSequencing newly synthesized transcriptome alongside regular transcriptome in single cells enables the study of gene expression temporal dynamics during rapid chromatin and gene regulation processes. However, existing assays to profile single-cell newly synthesized transcriptome require in-house technical expertise to achieve high cellular throughput, limiting their widespread application.

Aug 16, 2024 | nature.com | Chongyi Chen

AbstractDNA supercoiling is a biophysical feature of the double helix with a pivotal role in biological processes. However, understanding of DNA supercoiling in the chromatin remains limited. Here, we developed azide-trimethylpsoralen sequencing (ATMP-seq), a DNA supercoiling assay offering quantitative accuracy while minimizing genomic bias and background noise.

Aug 9, 2023 | genomebiology.biomedcentral.com | Jun Lyu |Chongyi Chen

Results Efficient T7 in vitro transcription of single-stranded RNA templates T7 in vitro transcription (IVT) of double-stranded DNA (dsDNA) templates to generate antisense RNA (aRNA) [24] has been widely used to achieve linear amplification in single-cell assays [4, 7, 25]. Here, we tested the efficiency of T7 IVT with a 20-nt ssRNA template as compared to a dsDNA template of the same sequence.