Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Investigation of spatial vulnerabilities of Bacterium Escherichia coli genome to spontaneous mutations by molecularly barcoded deep Sequencing

ABSTRACT: Investigation of spatial vulnerabilities of Bacterium Escherichia coli genome to spontaneous mutations by molecularly barcoded deep Sequencing

PROVIDER: PRJNA478517 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR7454859_1.fastq.gz	Fastqsanger.gz
	SRR7454859_2.fastq.gz	Fastqsanger.gz

Items per page:

1 - 2 of 2

Similar Datasets

Investigation of spatial vulnerabilities of Bacterium Escherichia coli genome to spontaneous mutations by molecularly barcoded deep Sequencing

Project description:Investigation of spontaneous mutations by Next-Generation Sequencing technology has attracted extensive attention lately due to the fundamental roles of spontaneous mutations in evolution and pathological processes. However, these studies only focused on the mutations accumulated through many generations during long term --could be years of-- culturing, but not the freshly-generated spontaneous mutations that occurs at very low frequencies. In this study, we established a molecularly-barcoded deep sequencing strategy to detect low abundant spontaneous mutations in genomes of bacteria cell cultures. Genome-wide spontaneous mutations in 15 E. coli cell culture samples were defined with a high confidence (P < 0.01). We also developed a hotspot region-calling approach based on Run-Length Encoding algorithm to find the genomic regions that are vulnerable to the spontaneous mutations. The hotspots for the mutations appeared to be highly conserved across the bacteria samples. Further biological annotation of these regions indicated that most of the spontaneous mutations were located at the repeat domains or nonfunctional domains of the genomes, suggesting the existence of mechanisms that could somehow prevent the occurrence of mutations in crucial genic areas. This study provides a more faithful picture of mutation occurrence and spectra without the distortion of long term culturing.

2018-10-08 | GSE116453 | GEO

Escherichia coli strain:ATCC 8739

Project description:Investigation of spatial vulnerabilities of Bacterium Escherichia coli genome to spontaneous mutations by molecularly barcoded deep Sequencing

| PRJNA476837 | ENA

Three-dimensional molecular cartography of human cerebral organoids revealed by double-barcoded spatial transcriptomics

Project description:Spatially-resolved transcriptomics methodologies are revolutionizing our understanding of complex tissues, but their elevated costs represent still a bottle-neck for their democratization. In this work we present a low-cost strategy for manufacturing molecularly double-barcoded DNA arrays, enabling large-scale spatially-resolved transcriptomics studies. We applied this technique to spatially resolve gene expression in several human brain organoids, including the reconstruction of a 3-dimensional view from multiple consecutive sections, revealing gene expression divergencies throughout the tissue.

2023-07-01 | GSE223020 | GEO

Clinical drug response and proteotype profiling elucidates targetable vulnerabilities of myelofibrosis

Project description:Myelofibrosis (MF) is a hematopoietic stem cell disorder belonging to the myeloproliferative neoplasms. MF patients frequently carry driver mutations in JAK2 and Calreticulin (CALR) and have limited therapeutic options. Here, we integrate ex vivo drug response and proteotype analyses across MF patient cohorts to discover targetable vulnerabilities and associated therapeutic strategies. Drug sensitivities of mutated and progenitor cells were measured in patient blood using high-content imaging and single-cell deep learning-based analyses. Integration with matched molecular profiling revealed three therapeutic vulnerabilities. First, CALR mutations drive BET and HDAC inhibitor sensitivity, particularly in the absence of high MAPK-Ras pathway protein levels. Second, an MCM complex-high proliferative signature corresponds to advanced disease and sensitivity to drugs targeting pro-survival signaling and DNA replication. Third, homozygous CALR mutations result in high ER stress, responding to ER stressors and UPR inhibition. Overall, our integrated analyses provide a molecularly-motivated roadmap for individualized MF patient treatment.

2023-10-12 | PXD036075 | Pride

Targeted DNA sequencing of barcoded SUM159PT cells

Project description:Cancer is a heterogeneous disease, where multiple, phenotypically distinct subpopulations co-exist. Tumour evolution is a result of a complex interplay of genetic and epigenetic factors. To predict the molecular drivers of distinct cancer responses, we apply single-cell lineage tracing (scRNA-Seq of barcoded cells) on a triple-negative breast cancer model. We propose GALILEO, a framework providing lineage tracing, transcriptomic, and chromatin accessibility information simultaneously at single-cell resolution (Multiome ATAC + gene expression on barcoded cells). The combination of single-cell lineage tracing with phenotypic assays allows to link a cell state with its fate.

2024-05-31 | GSE221495 | GEO

Transcription profling of a yeast molecular barcoded ORF library

Project description:I used Affy Tag4 array as a readout of the molecular barcoded yeast orf library<br>

2009-07-02 | E-MEXP-2077 | biostudies-arrayexpress

Molecularly barcoded Zika virus libraries to probe in vivo evolutionary dynamics.

Project description:Defining the complex dynamics of Zika virus (ZIKV) infection in pregnancy and during transmission between vertebrate hosts and mosquito vectors is critical for a thorough understanding of viral transmission, pathogenesis, immune evasion, and potential reservoir establishment. Within-host viral diversity in ZIKV infection is low, which makes it difficult to evaluate infection dynamics. To overcome this biological hurdle, we constructed a molecularly barcoded ZIKV. This virus stock consists of a "synthetic swarm" whose members are genetically identical except for a run of eight consecutive degenerate codons, which creates approximately 64,000 theoretical nucleotide combinations that all encode the same amino acids. Deep sequencing this region of the ZIKV genome enables counting of individual barcodes to quantify the number and relative proportions of viral lineages present within a host. Here we used these molecularly barcoded ZIKV variants to study the dynamics of ZIKV infection in pregnant and non-pregnant macaques as well as during mosquito infection/transmission. The barcoded virus had no discernible fitness defects in vivo, and the proportions of individual barcoded virus templates remained stable throughout the duration of acute plasma viremia. ZIKV RNA also was detected in maternal plasma from a pregnant animal infected with barcoded virus for 67 days. The complexity of the virus population declined precipitously 8 days following infection of the dam, consistent with the timing of typical resolution of ZIKV in non-pregnant macaques and remained low for the subsequent duration of viremia. Our approach showed that synthetic swarm viruses can be used to probe the composition of ZIKV populations over time in vivo to understand vertical transmission, persistent reservoirs, bottlenecks, and evolutionary dynamics.

| S-EPMC5891079 | biostudies-literature

Targeted DNA sequencing of barcoded SUM159PT cells

Project description:Targeted DNA sequencing of barcoded SUM159PT cells

| PRJNA914689 | ENA

Analysis of diversity in barcoded virus library

Project description:Analysis of diversity in barcoded virus library

| PRJNA630756 | ENA

Analysis of diversity in barcoded plasmid library

Project description:Analysis of diversity in barcoded plasmid library

| PRJNA630750 | ENA