Streptococcus
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1082471 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| SRR29837587_1.fastq.gz | Fastqsanger.gz | |||
| SRR29837588_1.fastq.gz | Fastqsanger.gz | |||
| SRR29837589_1.fastq.gz | Fastqsanger.gz | |||
| SRR29837590_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 14 |
Similar Datasets
Project description:Streptococcus suis Genome sequencing and assembly with short-read (illumina) and long-read (MinION) hybrid method
| PRJNA547793 | ENA
Project description:Formalin-fixed paraffin-embedded (FFPE) samples represent the gold standard for archiving pathology samples, and thus FFPE samples are a major resource of samples in clinical research. However, chromatin-based epigenetic assays in the clinical settings are limited to fresh or frozen samples, and are hampered by low chromatin yield in FFPE samples due to the lack of a reliable and efficient chromatin preparation method. Here, we introduce a new chromatin extraction method from FFPE tissues (Chrom-EX PE) for chromatin-based epigenetic assays.This study provided a new method that achieves efficient extraction of high-quality chromatin suitable for chromatin-based epigenetic assays with less damage on chromatin.
2019-03-18 | GSE128202 | GEO
Project description:Streptococcus pyogenes (Group A Streptococcus: GAS) is a major human pathogen that causes streptococcal pharyngitis, skin and soft-tissue infections, and life-threatening conditions such as streptococcal toxic shock syndrome (STSS). A large number of virulence-related genes are encoded on GAS genomes, which are involved in host-pathogen interaction, colonization, immune invasion, and long-term survival within hosts, causing the diverse symptoms. Here, we investigated the interaction between GAS-derived extracellular vesicles and host cells in order to reveal pathogenicity mechanisms induced by GAS infection.
2021-05-17 | PXD026040 | JPOST Repository
Project description:Long-read sequencing has become a powerful tool for alternative splicing analysis. However, technical and computational challenges have limited our ability to couple long-read sequencing with single cell and spatial barcoding to explore alternative splicing in the single cell and spatial setting. Though Nanopore-based long reads sequencing are widelyhave been adopted applied to explore single cell alternative and spatially barcoded librariessplicing in recent research, there still exist technical issues have problems which could bias the hindered accurate single cell isoform-level quantification, which are not well addressed in such settings. First, Tthe relatively higher sequencing error of Nanopore long reads, despite the recent improvements, has limited the accuracy ofhinder cell barcode and unique molecular identifier (UMI) recovery, a necessary first step in the analysis of single cell/spatial sequencing data. Then Rread truncation and mapping errors, the latter exacerbated by the higher sequencing error rates, further leads to the false detection of spurious new isoformsdegrade quantification accuracy. We show that these technical issues persist despite the recent improvements in long read sequencing accuracy. Beyond the initial data pre-processing, in downstream analysis we are lacking a statistical framework to quantify splicing variation within and between cells/spots. In light of these multiple challenges, we developed Longcell, a statistical framework and computational pipeline for isoform quantification using single cell and spatial spot barcoded Nanopore long read sequencing data. Longcell performs computationally efficient cell/spot barcode extraction, UMI recovery, and UMI-based truncation- and mapping-error correction. Through a statistical model that accounts for varying read coverage across cells/spots, Longcell rigorously quantifies the level of inter-cell/spot versus intra-cell/ spot diversity in exon-usage and detects changes in splicing distributions between cell populations. Applying Longcell to single cell long-read data from multiple contexts, we found that intra-cell splicing heterogeneity, where multiple isoforms co-exist within the same cell, is ubiquitous for highly expressed genes. On matched single cell and Visium long read sequencing for a tissue of colorectal cancer metastasis to the liver, Longcell found concordant signals between the single cell and spatial data modalities. On Visium long read sequencing data for multiple tissues, Longcell allows accurate identification of spatial isoform switching. Finally, on a perturbation experiment for 9 splicing factors, Longcell identified regulatory targets that are validated by targeted sequencing.
2025-05-23 | GSE295932 | GEO
Project description:Long-read RNA sequencing (RNA-seq) is a powerful technology for transcriptome analysis, but the relatively low throughput of current long-read sequencing platforms limits transcript coverage. We present TEQUILA-seq, a versatile, easy-to-implement, and low-cost method for targeted long-read RNA-seq. TEQUILA-seq can be broadly used for targeted sequencing of full-length transcripts in diverse biomedical research settings.
2023-06-06 | GSE213984 | GEO
Project description:Whole genone expression profile comparing wild-type NZ131 to serR deletion mutant, grown in C-medium Mutants and interpretation are described further in the manuscript to be submitted: LaSarre and Federle, 2010. Title: Regulation and Consequence of Serine Catabolism in Streptococcus pyogenes. A two chip study using total RNA recovered from three separate wild-type cultures of Streptococcus pyogenes NZ131 and three separate mutant cultures of Streptococcus pyogenes NZ131 seR-, pooled following RNA extraction
2010-11-15 | E-GEOD-24860 | biostudies-arrayexpress
Project description:Streptococcus spp., Staphylococcus spp., Escherichia spp. Raw sequence reads
| PRJNA1081048 | ENA
Project description:Streptococcus pneumoniae (S.p.) is the most common causative agent of community-acquired pneumonia worldwide. A key pathogenic mechanism that exacerbates severity of disease is the disruption of the alveolo-capillary barrier. However, the specific virulence mechanisms responsible for this in the human lung are not yet fully understood. RNA sequencing of Streptococcus pneumoniae transcriptome under infection media conditions, but without the presence of lung tissue, representing anon-host-infection scenario FCS+/- was analyzed,. RNA isolation was performed using an acidic phenol-chloroform extraction protocol (Wetzstein et al., 1992). After DNase-I treatment (Zymo Research, Germany), the RNA quality was checked by Trinean Xpose (Gentbrugge, Belgium) and the Agilent RNA Nano 6000 kit using an Agilent 2100 Bioanalyzer (Agilent Technologies, Böblingen, Germany). For RNA-seq transcriptomics, Ribo-Zero rRNA Removal Kit (Bacteria) from Illumina (San Diego, CA, USA) was used to remove the rRNA. TruSeq Stranded mRNA Library Prep Kit from Illumina (San Diego, CA, United States) was applied to prepare the cDNA libraries. The cDNAs were sequenced paired end on an Illumina HiSeq 1500 (San Diego, CA, United States) using 70 and 75 bp read length and a minimum sequencing depth of 10 million reads per library.
2023-11-30 | E-MTAB-13533 | biostudies-arrayexpress