Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ABSTRACT: Long-read sequencing of Escherichia coli mixture

PROVIDER: PRJNA982778 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR24895209_1.fastq.gz	Fastqsanger.gz
	SRR24895210_1.fastq.gz	Fastqsanger.gz
	SRR24895211_1.fastq.gz	Fastqsanger.gz
	SRR24895212_1.fastq.gz	Fastqsanger.gz
	SRR24895213_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 11

Similar Datasets

Escherichia coli DH5alpha Transcriptome Sequencing under Wi-Fi radiofrequency radiation

Project description:Purpose: In this study, Escherichia coli DH5alpha whole transcriptome sequencing was performed in order to compare the different gene expression profiles between control and exposed to Wi-Fi radiofrequency radiations. Methods:Escherichia coli DH5alpha were exposed to Wi-Fi radiations. Total RNA samples( control and exposed ) were extracted by bacteria protect-Rneasy kit,treated with DNAase and subjected to sequnecing using an Illumina-NovaSeq 6000 platform. Library preparation and sequencing were performed by Macrogen (south korea).Trimmed reads are mapped to reference genome with Bowtie. HTseq was used for expression profiling. Expression profile was calculated for each sample and gene as read count.

2019-10-21 | GSE126584 | GEO

Project description:Long Read Sequencing of Escherichia coli from Australian Canine Samples

| PRJNA846578 | ENA

Escherichia coli

Project description:Escherichia coli Genome sequencing and assembly using ONT long-read

| PRJNA1178352 | ENA

Escherichia coli

Project description:Escherichia coli Genome sequencing and assembly using ONT long-read sequencing

| PRJNA1292388 | ENA

Quantitative Genomic Analysis of RecA Protein Binding During DNA Double-Strand Break Repair Reveals RecBCD Action in vivo

Project description:Here we have developed a method that combines chromatin immunoprecipitation with next-generation sequencing (ChIP-Seq) and mathematical modeling to quantify RecA protein binding during the active repair of a single DSB in the chromosome of Escherichia coli. Examination of RecA binding during double-strand break repair in Escherichia coli

2015-08-11 | E-GEOD-71249 | biostudies-arrayexpress

Study for investigating the effects of a probiotic on diarrhea caused by chemotherapy in patients with gastric, colon and rectum cancer

Project description:Primary objectives: The study investigates whether a Escherichia coli Nissle-suspenison has a (preventive) antidiarrheal effect in patients with tumors who are treated with chemotherapeutic schemes which are associated with increased occurances of diarrhea. Diarrhea caused by treatment are thought to be reduced in intensity and/or frequency by the treatment with Escherichia coli Nissle-Suspension. Primary endpoints: Common toxicity criteria (CTC) for diarrhea

| 2534265 | ecrin-mdr-crc

Proteome of the snow alga Chloromonas typhlos

Project description:a chromosome-level nuclear genome and organelle genomes of the alpine snow alga Chloromonas typhlos were sequenced and assembled by integrating short- and long-read sequencing and proteogenomic strategy

2024-10-12 | PXD056928 |

Escherichia coli O157:H7

Project description:Escherichia coli O157:H7 genome sequencing and assembly using long-read sequencing

| PRJNA528413 | ENA

Multi-omic profiling of pathogen-stimulated primary immune cells

Project description:Objectives: To perform long-read transcriptome and proteome profiling of pathogen-stimulated peripheral blood mononuclear cells (PBMCs) from healthy donors. We aim to discover new transcripts and protein isoforms expressed during immune responses to diverse pathogens. Methods: PBMCs were exposed to four microbial stimuli for 24 hours: the TLR4 ligand lipopolysaccharide (LPS), the TLR3 ligand Poly(I:C), heat-inactivated Staphylococcus aureus, Candida albicans, and RPMI medium as negative controls. Long-read sequencing (PacBio) of one donor and secretome proteomics and short-read sequencing of five donors were performed. IsoQuant was used for transcriptome construction, Metamorpheus/FlashLFQ for proteome analysis, and Illumina short-read 3’-end mRNA sequencing for transcript quantification. Results: Long-read transcriptome profiling reveals the expression of novel sequences and isoform switching induced upon pathogen stimulation, including transcripts that are difficult to detect using traditional short-read sequencing. We observe widespread loss of intron retention as a common result of all pathogen stimulations. We highlight novel transcripts of NFKB1 and CASP1 that may indicate novel immunological mechanisms. In general, RNA expression differences did not result in differences in the amounts of secreted proteins. Interindividual differences in the proteome were larger than the differences between stimulated and unstimulated PBMCs. Clustering analysis of secreted proteins revealed a correlation between chemokine (receptor) expression on the RNA and protein levels in C. albicans- and Poly(I:C)-stimulated PBMCs. Conclusion: Isoform aware long-read sequencing of pathogen-stimulated immune cells highlights the potential of these methods to identify novel transcripts, revealing a more complex transcriptome landscape than previously appreciated.

2023-09-16 | PXD045237 | Pride

Aberrant splicing isoforms detected by full-length transcriptome sequencing as transcripts of potential neoantigens in non-small cell lung cancer

Project description:To identify aberrant splicing isoforms and potential neoantigens, we performed full-length cDNA sequencing of lung adenocarcinoma cell lines using a long-read sequencer MinION. We constructed a comprehensive catalog of aberrant splicing isoforms and detected isoform-specific peptides using proteome analysis.

2020-12-09 | PXD019915 | JPOST Repository

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data