Massively parallel signature sequencing is an ultra-high throughput sequencing technology. It can simultaneously sequence millions of sequence tags, and, therefore, is ideal for whole genome analysis. When applied to expression profiling, it reveals almost every transcript in the sample and provides its accurate expression level. This chapter describes the technology and its application in establishing stem cell transcriptome databases.
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Illuminating the dark mess of fibers: Application of circular cross polarized light in unravelling the bone tissue structure of the dermal pectoral girdle of Metoposaurus krasiejowensis.
J Anat
January 2025
Bonn Institute of Organismal Biology, Paleontology, University of Bonn, Bonn, Germany.
Current understanding of the histology of the dermoskeleton of tetrapods comes from fossilized and recent remains of skulls, osteoderms, carapace, plastron and other postcranial material which were always investigated using linear cross polarized light (LCPL) microscopy. The pectoral girdle of vast majority of non-amniote tetrapods, including temnospondyls evolved large ventrally located dermal bones- the interclavicle and a pair of clavicles. Despite that, there is a lack of information about the bone tissue structure from these postcranial dermal bones.
View Article and Find Full Text PDFThe regulatory landscape of 5' UTRs in translational control during zebrafish embryogenesis.
Dev Cell
January 2025
Biozentrum, University of Basel, 4056 Basel, Switzerland; Allen Discovery Center for Cell Lineage Tracing, Seattle, WA 98195, USA. Electronic address:
The 5' UTRs of mRNAs are critical for translation regulation during development, but their in vivo regulatory features are poorly characterized. Here, we report the regulatory landscape of 5' UTRs during early zebrafish embryogenesis using a massively parallel reporter assay of 18,154 sequences coupled to polysome profiling. We found that the 5' UTR suffices to confer temporal dynamics to translation initiation and identified 86 motifs enriched in 5' UTRs with distinct ribosome recruitment capabilities.
View Article and Find Full Text PDFApplication of a new composite genetic marker semen-specific methylation-microhaplotype in the analysis of semen-vaginal fluid mixtures.
R Soc Open Sci
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Department of Forensic Medicine, School of Basic Medical Sciences, Central South University, No172. Tongzipo Road, Changsha, Hunan 410013, People's Republic of China.
DNA mixtures containing semen and vaginal fluid are common biological samples in forensic analysis. However, the analysis of semen-vaginal fluid mixtures remains challenging. In this study, to solve these problems, it is proposed to combine semen-specific CpG sites and closely related microhaplotype sites to form a new composite genetic marker (semen-specific methylation-microhaplotype).
View Article and Find Full Text PDFMassively parallel characterization of transcriptional regulatory elements.
Nature
January 2025
Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA.
The human genome contains millions of candidate cis-regulatory elements (cCREs) with cell-type-specific activities that shape both health and many disease states. However, we lack a functional understanding of the sequence features that control the activity and cell-type-specific features of these cCREs. Here we used lentivirus-based massively parallel reporter assays (lentiMPRAs) to test the regulatory activity of more than 680,000 sequences, representing an extensive set of annotated cCREs among three cell types (HepG2, K562 and WTC11), and found that 41.
View Article and Find Full Text PDFMassively parallel homogeneous amplification of chip-scale DNA for DNA information storage (MPHAC-DIS).
Nat Commun
January 2025
School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules, National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, China.
Chip scale DNA synthesis offers a high-throughput and cost-effective method for large-scale DNA-based information storage. Nevertheless, unbiased information retrieval from low-copy-number sequences remains a barricade that largely arises from the indispensable DNA amplification. Here, we devise a simulation-guided quantitative primer-template hybridization strategy to realize massively parallel homogeneous amplification of chip-scale DNA for DNA information storage (MPHAC-DIS).
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