Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA-seq of coding RNA of Streptococcus pneumoniae D39 after FCS addition

ABSTRACT: RNA-seq of coding RNA of Streptococcus pneumoniae D39 after FCS addition

PROVIDER: PRJEB69532 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	ERR12267754_1.fastq.gz	Fastqsanger.gz
	ERR12267754_2.fastq.gz	Fastqsanger.gz
	ERR12267755_1.fastq.gz	Fastqsanger.gz
	ERR12267755_2.fastq.gz	Fastqsanger.gz
	ERR12267756_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 72

Similar Datasets

RNA-seq of coding RNA of Streptococcus pneumoniae D39 after FCS addition

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

Fucose-mediated transcriptional activation of the fcs operon by FcsR in Streptococcus pneumoniae

Project description:In this study, we explore the impact of fucose on the transcriptome of S. pneumoniae D39. The expression of various genes and operons, including the fucose uptake PTS and utilization operon (fcs operon), was altered in the presence of fucose. By means of quantitative RT-PCR and β-galactosidase analysis, we demonstrate the role of the transcriptional regulator FcsR, present upstream of the fcs operon, as a transcriptional activator of the fcs operon. We also predict a 19-bp putative FcsR regulatory site (5’-ATTTGAACATTATTCAAGT-3’) in the promoter region of the fcs operon. The functionality of this predicted FcsR regulatory site was further confirmed by promoter-truncation experiments, where deletion of half of the FscR regulatory site or full deletion led to the abolition of expression of the fcs operon.

2015-04-23 | GSE65673 | GEO

Fucose-mediated transcriptional activation of the fcs operon by FcsR in Streptococcus pneumoniae

2015-04-23 | E-GEOD-65673 | biostudies-arrayexpress

Streptococcus pneumoniae D39 spxB- mutant vs. D39 wild-type

Project description:Comparison of the Streptococcus pneumoniae D39 spxB- mutant vs D39. For DNA microarray analysis, D39 wild-type and two independently obtained D39spxB- mutants were grown as four, two and two biological replicates, respectively, in Glc-M17 under semi-aerobic conditions and harvested at an OD595 of approximately 0.25 (mid-exponential). The RNA of both D39spxB- strains was compared to D39 and the combined data was analyzed. All other procedures regarding microarray analyses were done as described before. A gene was considered differentially expressed when the fold change was ≥ 2, ≤ 0.5, with a Bayes p ≤ 0.00001 and when at least 7 measurements were available.

2013-08-08 | GSE45971 | GEO

Long non-coding RNA pull down-MS

Project description:long non-coding RNA pull down-MS and protein candidates bind to LRTOR

2024-09-06 | PXD055610 |

Study on expression of long non-coding RNA in colorectal cancer tissues and adjacent tissues

Project description:Interventions: Case series:No Primary outcome(s): long non-coding Ribonucleic Acid Study Design: Sequential

| 2725570 | ecrin-mdr-crc

Deep analysis of FCS used in cell culture experiment

Project description:roteome analysis of commercially available foetal calf serum (FCS) for background correction. Commercially available FCS was depleted of high abundant and enriched for low abundant proteins with commercially available equalizer beads (BioRad) to create a background list of potential contaminates.

2025-11-17 | PXD062778 | Pride

Study on the expression of long-chain non coding RNA and coding gene in patients with colorectal cancer

Project description:Interventions: lesion tissues vs. adjacent tissues of colorectal cancer patients:nil Primary outcome(s): RNA Study Design: Factorial

| 2693518 | ecrin-mdr-crc

Luteimonas sp. FCS-9

Project description:Luteiomonas oceanisediminis (strain FCS-9) sp.nov. Genome sequencing and assembly

| PRJNA280025 | ENA

Streptococcus pneumoniae D39 spxB- mutant vs. D39 wild-type

Project description:Comparison of the Streptococcus pneumoniae D39 spxB- mutant vs D39. For DNA microarray analysis, D39 wild-type and two independently obtained D39spxB- mutants were grown as four, two and two biological replicates, respectively, in Glc-M17 under semi-aerobic conditions and harvested at an OD595 of approximately 0.25 (mid-exponential). The RNA of both D39spxB- strains was compared to D39 and the combined data was analyzed. All other procedures regarding microarray analyses were done as described before. A gene was considered differentially expressed when the fold change was M-bM-^IM-% 2, M-bM-^IM-$ 0.5, with a Bayes p M-bM-^IM-$ 0.00001 and when at least 7 measurements were available. One condition design comparision of two strains including a dye swap.

2013-08-08 | E-GEOD-45971 | biostudies-arrayexpress

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