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Project description:Impact of post-lysis stopping point prior to reverse transcription
| PRJNA888144 | ENA
Project description:We used human + mouse cell mixtures to demonstrate the purity of PIP-seq single cell RNA-sequencing
2023-01-12 | GSE215062 | GEO
Project description:We used human + mouse cell mixtures to demonstrate the purity of PIP-seq single cell RNA-sequencing
2023-01-12 | GSE202911 | GEO
Project description:Rapid onsite whole-genome sequencing of two suspected severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) N gene diagnostic escape samples revealed a previously unreported N gene point mutation at genome position 29195. Because the G29195T mutation occurs within a region probed by a commonly referenced U.S. CDC N gene reverse transcription (RT)-PCR assay, we hypothesize that the G29195T mutation rendered the N gene target of a proprietary commercial assay undetectable. The putative diagnostic escape G29195T mutation demonstrates the need for nearly real-time surveillance, as emergence of a novel SARS-CoV-2 variant with the potential to escape diagnostic tests continues to be a threat. IMPORTANCE Accurate diagnostic detection of SARS-CoV-2 currently depends on the large-scale deployment of RT-PCR assays. SARS-CoV-2 RT-PCR assays target predetermined regions in the viral genomes by complementary binding of primers and probes to nucleic acid sequences in the clinical samples. Potential diagnostic escapes, such as those of clinical samples harboring the G29195T mutation, may result in false-negative SARS-CoV-2 RT-PCR results. The rapid detection and sharing of potential diagnostic escapes are essential for diagnostic laboratories and manufacturers around the world, to optimize their assays as SARS-CoV-2 continues to evolve.
| S-EPMC8754125 | biostudies-literature
Project description:Commercially available reverse transcription enzyme and temperature comparison in high throughput sequencing of bacterial ribosomal 16S rRNA.
| PRJEB32237 | ENA
Project description:BackgroundFast, reliable and easy to handle methods are required to facilitate urgently needed point-of-care testing (POCT) in the current coronavirus pandemic. Life-threatening severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has rapidly spread all over the world, infecting more than 33,500,000 people and killing over 1 million of them as of October 2020. Infected individuals without any symptoms might still transfer the virus to others underlining the extraordinary transmissibility of this new coronavirus. In order to identify early infections effectively, treat patients on time and control disease spreading, rapid, accurate and onsite testing methods are urgently required.ResultsHere we report the development of a loop-mediated isothermal amplification (LAMP) based method to detect SARS-CoV-2 genes ORF8 and N directly from pharyngeal swab samples. The established reverse transcription LAMP (RT-LAMP) assay detects SARS-CoV-2 directly from pharyngeal swab samples without previous time-consuming and laborious RNA extraction. The assay is sensitive and highly specific for SARS-CoV-2 detection, showing no cross reactivity when tested on 20 other respiratory pathogens. The assay is 12 times faster and 10 times cheaper than routine reverse transcription real-time polymerase chain reaction, depending on the assay used.ConclusionThe fast and easy to handle RT-LAMP assay amplifying specifically the genomic regions ORF8 and N of SARS-CoV-2 is ideally suited for POCT at e.g. railway stations, airports or hospitals. Given the current pandemic situation, rapid, cost efficient and onsite methods like the here presented RT-LAMP assay are urgently needed to contain the viral spread.
| S-EPMC7576985 | biostudies-literature
Project description:The objective of the study was to utilize DNA methylation to quantify human leukocyte subsets in human blood. This file contains data from an Illumina custom VeraCode GGMA microarray for human leukocyte subtypes (purified from whole blood samples via magnetic activated cell sorting (MACS) and purity confirmed by flourescence activated cell sorting (FACS)) as well as for complex mixtures of DNA from those samples, and for human whole blood samples.
2014-02-04 | GSE54647 | GEO
Project description:IntroductionPost-craniotomy neurosurgical infections (PCNIs) significantly challenge daily neurosurgical practice, affecting patient outcomes and imposing economic burdens on healthcare systems. Despite advances in surgical techniques and infection control protocols, PCNIs still contribute to surgical-related morbidity and mortality.Research questionTo address these unresolved questions through a comprehensive literature review.Material and methodsWe conducted a detailed literature review using the keywords "Infection, Craniotomy, Neurosurgery," on PubMed, which yielded 2330 articles. Out of these, 171 were selected, based on relevance, and rigorously reviewed. The review aimed to answer thirteen major questions stemming from the management of PCNIs.ResultsPCNI incidences range from 0.7% to 8%, predominantly caused by gram-positive bacteria, especially Staphylococcus species. Significant risk factors identified include CSF leakage, emergency surgery, and certain tumour types, with infections typically manifesting post-discharge. Diagnostic approaches integrate clinical, radiological, and laboratory assessments, with advances in molecular diagnostics showing promising precision. While antibiotic prophylaxis remains effective, emerging resistance warrants cautious application. Surgical intervention is often indispensable for managing organ-space infections, with a trend towards bone flap preservation and one-step cranioplasty procedures in certain cases.Discussion and conclusionThe management of PCNIs remains a major challenge. There is a critical need for standardization of definitions and data reporting. Advancements in diagnostic and therapeutic strategies may bring future improvements in clinical outcomes, despite antibiotic resistance phenomena and the complexity of surgical decisions required. Ultimately, major engagement is aimed at refining and updating clinical protocols to improve and standardize the management of PCNIs.
| S-EPMC11814530 | biostudies-literature
Project description:Existing single-cell RNA sequencing (scRNA-seq) methods rely on reverse transcription (RT) and second-strand synthesis (SSS) to convert single-stranded RNA into double-stranded DNA prior to amplification, with the limited RT/SSS efficiency compromising RNA detectability. Here, we develop a new scRNA-seq method, Linearly Amplified Single-stranded-RNA-derived Transcriptome sequencing (LAST-seq), which directly amplifies the original single-stranded RNA molecules without prior RT/SSS. LAST-seq offers a high single-molecule capture efficiency and a low level of technical noise for single-cell transcriptome analyses. Using LAST-seq, we characterize transcriptional bursting kinetics in human cells, revealing a role of topologically associating domains in transcription regulation.
| S-EPMC10413806 | biostudies-literature
Project description:Here we compare the transcriptional profile during the differentiation of hESC into neuroepithelial cells (NSB) (Chambers et. al 2009 Nature Biotechnology) with our new placode differentiation (PIP). Total RNA was isolated at day 1,3, 5 (NSB), 5 (PIP), 7 (NSB), 7 (PIP), 9 (NSB), 9 (PIP), 11 (NSB) and 11 (PIP) of differentiation using Trizol. Samples for each group in triplicate were processed for Illumina bead arrays (Illumina HT-12) by the MSKCC genomics core facility according to the specifications of the manufacturer.
2013-12-04 | E-GEOD-51533 | biostudies-arrayexpress