Unique molecular identifiers
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We introduce alevin, a fast end-to-end pipeline to process droplet-based single-cell RNA sequencing data, performing cell barcode detection, read mapping, unique molecular identifier (UMI) deduplication, gene count estimation, and cell barcode whitelisting.
16p vigalileogalilei 27-02-2022 7 1 Download
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The incorporation of unique molecular identifiers (UMIs) in single-cell RNA-seq assays makes possible the identification of duplicated molecules, thereby facilitating the counting of distinct molecules from sequenced reads.
18p viarchimedes 26-01-2022 7 0 Download
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Single-cell RNA-seq (scRNA-seq) profiles gene expression of individual cells. Unique molecular identifiers (UMIs) remove duplicates in read counts resulting from polymerase chain reaction, a major source of noise. For scRNA-seq data lacking UMIs, we propose quasi-UMIs: quantile normalization of read counts to a compound Poisson distribution empirically derived from UMI datasets.
17p viarchimedes 26-01-2022 10 0 Download
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Soft-tissue sarcomas (STS) represent a heterogeneous group of rare tumors including more than 70 different histological subtypes. High throughput molecular analysis (next generation sequencing exome [NGS]) is a unique opportunity to identify driver mutations that can change the usual one-size-fits-all treatment paradigm to a patient-driven therapeutic strategy.
10p vimahuateng 26-11-2021 14 0 Download
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Chondrogenesis is the earliest stage of skeletal development and is a highly dynamic process, integrating the activities and functions of transcription factors, cell signaling molecules and extracellular matrix proteins. The molecular mechanisms underlying chondrogenesis have been extensively studied and multiple key regulators of this process have been identified. However, a genome-wide overview of the gene regulatory network in chondrogenesis has not been achieved.
15p vilarryellison 29-10-2021 7 0 Download
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In this study, we evaluated the performance of 3′ mRNA-Seq using Lexogen QuantSeq 3′ mRNA-Seq Library Prep Kit FWD with UMI, comparing with TruSeq Stranded mRNA-Seq and RNA Exome Capture kit. The fresh-frozen (FF) and FFPE tissues yielded nucleotide sizes range from 13 to > 70% of DV200 values; input amounts ranged from 1 ng to 100 ng for validation.
9p vilarryellison 29-10-2021 10 1 Download
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Nematode sperm have unique and highly diverged morphology and molecular biology. In particular, nematode sperm contain subcellular vesicles known as membranous organelles that are necessary for male fertility, yet play a still unknown role in overall sperm function. Here we take a novel proteomic approach to characterize the functional protein complement of membranous organelles in two Caenorhabditis species: C. elegans and C. remanei.
13p vitzuyu2711 29-09-2021 15 1 Download
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RNA sequencing offers advantages over other quantification methods for microRNA (miRNA), yet numerous biases make reliable quantification challenging. Previous evaluations of these biases have focused on adapter ligation bias with limited evaluation of reverse transcription bias or amplification bias.
21p visilicon2711 20-08-2021 8 1 Download
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Target enrichment is a critical component of targeted deep next-generation sequencing for the costeffective and sensitive detection of mutations, which is predominantly performed by either hybrid selection or PCR.
10p visilicon2711 20-08-2021 19 1 Download
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The yak is a species of livestock which is crucial for local communities of the Qinghai-Tibet Plateau and adjacent regions and naturally owns one more thoracic vertebra than cattle. Recently, a sub-population of yak termed as the Jinchuan yak has been identified with over half its members own a thoracolumbar vertebral formula of T15L5 instead of the natural T14L5 arrangement.
15p vijeeni2711 24-07-2021 14 0 Download
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Gene and protein interaction experiments provide unique opportunities to study the molecular wiring of a cell. Integrating high-throughput functional genomics data with this information can help identifying networks associated with complex diseases and phenotypes.
22p vikentucky2711 24-11-2020 18 3 Download
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The yield obtained from next generation sequencers has increased almost exponentially in recent years, making sample multiplexing common practice. While barcodes (known sequences of fixed length) primarily encode the sample identity of sequenced DNA fragments.
6p vioklahoma2711 19-11-2020 11 1 Download
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Tumour relapse is recognized to be the prime fatal burden in patients affected by head and neck squamous cell carcinoma (HNSCC), but no discrete molecular trait has yet been identified to make reliable early predictions of tumour recurrence.
19p vialabama2711 21-09-2020 12 1 Download
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Phellinus gilvus (Schwein.) Pat, a species of ‘Sanghuang’, has been well-documented for various medicinal uses, but the genome information and active constituents are largely unknown. Here, we sequenced the whole-genome of P. gilvus, identified phenylpropanoids as its key anti-cancer components, and deduced their biosynthesis pathways. A 41.11-Mb genome sequence was assembled and the heatmap created with high-throughput chromosome conformation capture techniques data suggested all bins could be clearly divided into 11 pseudochromosomes. Cellular experiments showed that P.
11p covid19 14-06-2020 26 0 Download
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The complex process of formation of storage roots (SRs) from adventitious roots affects sweetpotato yield. Identifying the genes that are uniquely expressed in the SR forming cultivated species, Ipomoea batatas (Ib), and its immediate ancestral species, Ipomoea trifida (It), which does not form SRs, may provide insights into the molecular mechanisms underlying SR formation in sweetpotato.
14p vihashirama2711 21-05-2020 7 1 Download
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Lichen is a combination of two organisms one is alga and another one is fungus. There is symbiotic relationship between alga and fungus. The algal part provides nutrition to the whole organism and the fungus part provides structural support to the organism.
11p cothumenhmong3 22-02-2020 13 0 Download
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In the present study, sixty four aromatic landraces of rice collected from different districts of Madhya Pradesh were analysed for genetic variation using SSR markers. Specially, the objective of the study was DNA fingerprinting and genetic diversity analysis of aromatic landraces to requisite to study the unique feature and to identify the duplication among them and to assist in broadening the germplasm base of future aromatic rice breeding programs. Very high variation was observed for the trait sterile lemma colour in the classes of straw (76.56%), purple (10.94%), gold (7.81%) and 4.
12p nguaconbaynhay3 07-02-2020 17 0 Download
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Banana bract mosaic disease (BBrMD) is one of the most important viral diseases of banana which leads to a yield reduction. We have identified banana bract mosaic virus (BBrMV) in banana plants growing in the regions of southern India based on symptomatology, sequence homology, and Serodiagnostic assays. The viral sequence encoding the coat protein was specifically amplified by RT-PCR (Reverse Transcriptase – Polymerase chain reaction) using specific primers bordering the Coat Protein (CP) gene.
12p cothumenhmong1 10-12-2019 16 0 Download
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The effects of pesticide contamination on the metabolism of marine mol-luscs are poorly documented. We investigated the response of a marine bivalve, the Pacific oyster,Crassostrea gigas, using a suppression subtrac-tive hybridization method to identify up- and down-regulated genes after a 30-day exposure period to herbicides (a cocktail of atrazine, diuron and isoproturon, and to the single herbicide glyphosate). A total of 137 unique differentially expressed gene sequences was identified, as well as their asso-ciated physiological process....
14p awards 05-04-2013 45 1 Download
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In mammals, cytochrome P450 17a-hydroxylase⁄17–20 lyase (CYP17), which is encoded by a single gene, plays a critical role in the production of mineralocorticoids, glucocorticoids and androgens by the adrenal cortex. Two CYP17 isoforms with unique catalytic properties have been identified in the South African Angora goat (Capra hircus), a subspecies that is susceptible to cold stress because of the inability of the adrenal cortex to produce sufficient levels of cortisol.
10p galaxyss3 07-03-2013 20 2 Download