QuickBiology News

CRISPR is a promising tool for correcting genetic defects to prevent or cure genetic disease.  However, gene therapy targeting DNA is irreversible, is potentially damaging to germline cells. Therefore, it has been of great interest to target RNA in somatic cells while avoiding permanent off-target genomic edits.Read More

Next-generation sequencing (NGS) has changed diagnostic workflows and provided an unprecedented, simple way of discovering rare genomic diseases (QB News). Through whole genome sequencing (WGS) or whole exome sequencing (WES), scientists can trace genetic defects to mutations in a single gene. However, as only ~ 1% of the human genome is the coding region, many polymorphisms discovered from patients remain undiagnosed, and such genomic screening diagnostic rates are only 25-30%.Read More

We discussed methods that figure out spatial (location) and temporal resolution in single-cell RNA profiling. ScNT-seq (single-cell metabolically labeled new RNA tagging sequencing) developed by Wu’s Lab as we discussed before, only gives information of newly synthesized transcripts, it lacks the time scale about dynamics of gene expression. To build up a picture of the transcriptional history of a single cell, In Nature Biotechnology, Young scientist Fei Chen at Broad Institute developed RNA timestamps approach for inferring the age of individuals RNAs in RNA profiling by exploiting RNA editing.Read More

Single-cell sequencing is a great method to study cell heterogeneity, track cell lineages. In previous NGS news, we have introduced methods for instances, researchers perform tissue staining combing laser capture microdissection in Geo-seq (Geographical position sequencing) or in situ sequencing in tissue slide sections (slide-seq) to get spatial information of single cells or use metabolically labeled new RNA tagging sequencing to get time-resolved transcripts of single cells. Read More

Cellular hypoxia (low oxygen) is a stress common in the pathological processes, such as cancers (tumor hypoxia), ischemia (ischemic hypoxia), and preeclampsia (placental hypoxia). It affects cell metabolism, apoptosis, proliferation, and differentiation. Importantly, hypoxia in the Tumor Microenvironment (TME) is the negative factor in the efficacy of radio- and chemotherapy, which becomes a big barrier in cancer treatment. Read More

Since the first case of COVID-19 was reported in Dec 2019, a large amount of SARS-CoV-2 strains have been fully sequenced, transcriptome is also being functionally annotated. Such an explosion of omics data of SARS-CoV2 has created a need for storing, analyzing, comparing these data. Read More

Countries across Europe especially France, the UK, and Poland are seeing a resurgence in COVID-19 cases, are likely dealing with the much-feared second wave of SARs-CoV2 recently. Quick Biology previously summarized three methods which used next generation sequencing, to do high throughput diagnostics.
Most of these amplicon NGS libraries are based on RNA extraction followed by PCR; LAMP-seq, although getting rid of RNA extractions, combining isothermal nucleic acid amplification, its dynamic range/quantitative measure is still under evaluation (see News in Quick Biology).
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The cell surface is the crucial interface between cell-cell and cell-environment interactions. These interactions involve extracellular signal sensing, extracellular matrix anchoring, or antigen presentation. The key bioactive molecules in these cell surface functions are transmembrane proteins, glycans, or lipids. In contrast, the contribution of RNAs to the cell functions is largely unknown.Read More

We previously introduced Oxford Nanopore sequencing, a third-generation sequencing that read the nucleotide sequences at a single-molecule level. It has many advantages than the current Illumina sequencing platform, however, its output and reads accuracy so far is far inferior to that of Illumina. Quick Biology believes the products of Illumina and Oxford Nanopore have different applications; both will occupy a certain share in the current high throughput sequencing market.Read More

Single-cell RNA sequencing is a great method to study cell heterogeneity, track cell lineages in developments, but it obscures spatial (location) and temporal resolution. To get spatial information, many other methods are developed such as (1)Geo-seq (Geographical position sequencing) through tissue staining and laser capture microdissection developed by Dr. Han and Dr.Jing’s group in CHINA (Ref1) ; (2) Slide-seq, whereby RNA was spatially resolved from tissue sections by transfer onto a surface covered with DNA-barcoded beads developed by Dr. Chen and Dr. Macosko in Broad Institute in the USA (Ref2).Read More