Project description:The goal of this study was to determine how the method of pooling (combining mutants) for bacteral Tn libraries affected mutant distribution. Previously we generated a pooled version of a~6,800 Tn mutant library in Enterococcus faecalis OG1RF by plating and scraping individual mutants. Here, we combined liquid cultures grown in deep well plates. DNA from the new pooled library was extracted, and TnSeq was used to compare mutant distribution between the old (plate scraping) and new (liquid pooling) Tn library formats. This is important because it will guide best practices for handling large collections of bacterial mutants.

2023-05-22 | GSE233193 | GEO

Transposon-based construction of strand-specific RNA-seq libraries

Project description:We have developed two methods for efficiently consructing RNA-seq libraries using transposition. Each method constructs high quality RNA-seq libraries when compared to standard approaches. One of the methods (Directional Tn-RNA-seq) maintains strand-of-origin information and exhibits strand specificity comparable to current approaches. RNA-seq libraries were constructed from ECC-1, a human cell line, and Universal Human Reference RNA using transposon-based and standard RNA-seq library construciton methods.

2011-10-10 | E-GEOD-32307 | biostudies-arrayexpress

Synthetic lethal siRNA screen for TN-IBC cell line SUM149PT using kinome library with EPA treatment

Project description:Synthetic lethal siRNA screen using a kinome library containing 939 druggable genes in the TN-IBC cell line SUM149PT, in combination with EPA treatment.

2019-01-31 | GSE102057 | GEO

Comparison of methods to generate a pooled Enterococcus faecalis Tn library from arrayed library plates

Project description:Comparison of methods to generate a pooled Enterococcus faecalis Tn library from arrayed library plates

| PRJNA975209 | ENA

Determination of the transposon insertion effect in Tn::Psrg mutant by RNA-seq

Project description:Determination of the effect of transposon insertion in Tn::Psrg mutant by RNA-seq in Pseudomonas aeruginosa IHMA87

2023-01-10 | GSE192761 | GEO

EXoO-Tn: Tag-n-Map the Tn Antigen in the Human Proteome

Project description:Tn antigen (Tn), a single N-acetylgalactosamine (GalNAc) monosaccharide attached to protein Ser and Thr residues, is found on most solid tumors yet rarely detected in adult tissues: featuring it one of the most distinctive signatures of cancers. Although it is prevalent in cancers, Tn-glycosylation sites are not entirely clear owing to the lack of suitable technology. Knowing the Tn-glycosylation sites will spur the development of the new vaccines, diagnostics, and therapeutics of cancers. Here, we report a novel technology named EXoO-Tn for large-scale mapping of Tn-glycosylation sites. EXoO-Tn utilizes glycosyltransferase C1GalT1 and isotopically-labeled UDP-Gal(13C6) to tag and convert Tn to Gal(13C6)-Tn. This exquisite Gal(13C6)-Tn structure is recognized by a human-gut-bacterial enzyme, called OpeRATOR, that specifically cleaves N-termini of the Gal(13C6)-Tn-occupied Ser and Thr residues to yield site-containing glycopeptides. The enzymes C1GalT1 and OpeRATOR could be used concurrently in one-pot. The effectiveness of EXoO-Tn was evaluated by analyzing Jurkat cells, where 947 Tn-glycosylation sites from 480 glycoproteins were mapped. Bioinformatic analysis of the identified site-specific Tn-glycoproteins revealed conserved motif, cellular localization, relative position in proteins, and mapped site-specific Tn-glycoproteome in different studies. Given the significance of Tn in cancers, EXoO-Tn is anticipated to have broad utilities in clinical study of cancers.

2022-02-15 | PXD014390 | Pride

Transposon-based construction of strand-specific RNA-seq libraries

2011-10-10 | GSE32307 | GEO