Mutational analysis of IVT mRNAs
Ontology highlight
ABSTRACT:
ORGANISM(S): synthetic construct
PROVIDER: GSE223044 | GEO | 2023/10/13
REPOSITORIES: GEO
Similar Datasets
Project description:Reading canonical and modified nucleotides in 16S ribosomal RNA using nanopore native RNA sequencing
| PRJEB29728 | ENA
Project description:A unified strategy to clone modified/unmodified small RNAs and mRNAs for high throughput sequencing
| PRJNA532412 | ENA
Project description:Even the latest generation of base editor (BE3) causes unwanted indels and non-C-to-T substitutions, compromising the fidelity of base editing outcome. Here we report a enhanced base editing system. The enhanced base edting system decreased the formation of unintended indels and C-to-A/C-to-G substitutions, and increased the frequency of desired C-to-T substitution, thereby improving both the accuracy and efficiency of base editing.
2017-08-29 | GSE98685 | GEO
Project description:This study looks at gene expression changes in Curvibacter sp. AEP1.3 in the presence of homoserine-lactones modified or unmodified by the host (Hydra)
2017-06-01 | GSE81281 | GEO
Project description:In most eukaryotes and bacteria, queuosine (Q) replaces the guanosine at the wobble position of tRNAs harboring a GUN anticodon. To faithfully detect Q-modification in RNAs from Schizosaccharomyces pombe and Shigella flexneri, Q-MaP-Seq was established and applied to tRNAs from S. pombe WT (AEP1) cells and Shigella flexneri WT cells and tgt∆ cells. Q-modification of in vitro-transcribed RNAs and RNAs isolated from S. pombe and S. flexneri followed by reverse transcription using the RT-active DNA polymerase variant RT-KTq I614Y and sequencing of unmodified compared to modified RNAs allowed identification of Q-sites within tRNAs.
2023-03-15 | GSE216921 | GEO
Project description:SHAPE-MaP structure probing experiment was performed on SARS-CoV-2 infected Vero cells at 4 days post infection with two biological replicates. For each replciate, SHAPE-MaP includes a sample treated with 2-methylnicotinic acid imidazolide acid (modified) or a minue reagent (unmodified). NAI preferentially reacts with unpaired bases in RNA, forming acylated bases. These modifications are encoded as mutation during reverse transcripatse and library preparation. After sequencing and alignment, the reactivity profiles of 'modified' and 'unmodified' samples are used to calculate SHAPE reactivity of each base
2021-01-11 | GSE154171 | GEO
Project description:During HIV-1 assembly, the structural protein Pr55Gag specifically selects viral genomic RNA by interacting with packaging signals present in the 5’ untranslated region (UTR). Despite a large number of studies, Pr55Gag binding to the genomic RNA remains poorly understood. To precisely define the Pr55Gag binding site we performed Mutational Interference Mapping Experiment on the 5’UTR and the beginning of the gag gene. To do this, we first generated mutant RNA libraries by in vitro transcription of PCR products that had been subjected to two or three sequential rounds of mutagenic PCR. Sequencing showed a mutation rate of 0.6% ensuring that the vast majority of molecules contained at least one mutation. RNA was mixed with His-tagged Pr55Gag, and functional selection was performed using magnetic beads to separate the bound and the unbound RNA populations. RNA was then reverse transcribed, converted into double stranded DNA, and sequenced using the Illumina HiSeq 2000 platform. This platform generates a large number of sequencing reads but with a read length that is shorter than our target sequence (100 nucleotides from each end of the DNA versus 532 nucleotides). We overcame this limitation by randomly fragmenting our DNA into fragments ranging from 100 to 500 nucleotides during library preparation. Using this strategy sequencing data was obtained for all positions of the target, whilst also retaining linkage data for all pairs of nucleotides whose distance does not exceed the largest fragment size. We aligned approximately 170 million sequences to the reference genome, comprising ~9x107 mutations over ~3x1010 base pairs, after quality control steps. We also sequenced cDNA from a non-mutated template, which we used in a mathematical analysis to correct for errors introduced during in vitro transcription, library preparation and sequencing. Mutational Interference Mapping Experiment of Pr55Gag binding to RNA in vitro
2015-06-13 | E-GEOD-69805 | biostudies-arrayexpress
Project description:SpCas9 INDEL frequency was evaluated at both the on- and off-target sites of guideRNA targeting either the murine Rhodopsin or Albumin by Next Generation Sequencing. Minimal INDELs were found at the off target sites evaluted, while SpCas9 activity was predominantly on-target.
2021-11-11 | GSE180117 | GEO
Project description:Transcript abundance was measured in whole-body virgin male Drosophila serrata from 41 inbred lines that had diverged through 27 generations of mutation accumulation. Pleiotropic mutations are the ultimate source of genetic variation in complex traits, including many human diseases. However, the nature and extent of mutational pleiotropy remain largely unknown. Here, we investigate the variation in 11,604 gene expression traits among 41 mutation accumulation lines of Drosophila serrata, which had diverged for 27 generations. We detected significant mutational variance in 4.6% of ESTs, but 70% of ESTs were invariant among lines, allowing us to reject a null hypothesis of phenome-wide universal pleiotropy. Mutational covariance among ESTs was detected at a frequency of only 1 in 193 random pairs of variable EST, bu t was detected among random combinations of five ESTs in 1 in 5 cases, revealing that mutational covariance among multiple ESTs was common. The observed frequency of significant multivariate covariance among random ESTs implied that a substantial number of ESTs (>70) must be pleiotropically affected by at least some mutations. We measured gene expression of male Drosophila serrata from 41 mutation accumulation lines (whole-body). Data from two replicates for each line are presented.
2013-09-01 | E-GEOD-49815 | biostudies-arrayexpress
Project description:The high-throughput sequencing has become a standard tool for analyzing gene expression. Usually a cDNA/DNA library is constructed with 5' and 3' linkers and then sequenced. Unlike mRNA, small RNA often contains modifications including 5' cap or triphosphate and 3' methylation, affecting the linker addition during cloning processes. Small RNA is expressed at much lower levels than mRNA, making it more difficult to clone small RNA using a small amount of total RNA. Here we have developed a new strategy to clone modified/unmodified small RNA in an all-liquid-based reaction in a single PCR tube using as little as 20 ng total RNA. The 7-hour cloning process only needs ~1 hour labor time. Moreover, this method can be used to clone mRNA, simplifying the need to prepare two cloning systems for small RNA and mRNA. Since the linkers used are derived from the Illumina Truseq linkers for DNA cloning, the PCR primers based on the linker sequences can be used to obtain amplicons derived from small RNA/mRNA/DNA. Not only is our method more convenient for cloning modified RNA than available methods, but it is also more sensitive, accurate and versatile. Moreover, the all-liquid-based reaction can be performed in an automated manner.
2020-01-24 | GSE129664 | GEO