Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

58 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Changes in cellular microRNA expression induced by porcine circovirus type 2-encoded proteins.

ABSTRACT: We employed deep sequencing technology to uncover cellular miRNAs differentially regulated after expression of each of three PCV2-encoded open reading frames (ORFs) in porcine kidney epithelial PK15 cells. Control PK15 vs. PCV2 ORF1, ORF2, ORF3-expressing PK15.

ORGANISM(S): Sus scrofa

SUBMITTER: Jae-Sang Hong

PROVIDER: E-GEOD-60206 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Changes in cellular microRNA expression induced by porcine circovirus type 2-encoded proteins.

Project description:We employed deep sequencing technology to uncover cellular miRNAs differentially regulated after expression of each of three PCV2-encoded open reading frames (ORFs) in porcine kidney epithelial PK15 cells.

2014-08-08 | GSE60206 | GEO

Genome-wide transcriptional response of primary alveolar macrophages (PAMs) following infection with porcine circovirus type 2

2011-07-27 | GSE30918 | GEO

Genome-wide transcriptional response of primary alveolar macrophages (PAMs) following infection with porcine circovirus type 2

Project description:Porcine alveolar macrophages (PAMs) play impoartant role in innate immunity. Porcine circovirus type 2 (PCV2) has been identified as the causal agent of postweaning multisystemic wasting syndrome, an economically important multifactorial disease of the swine industry worldwide. We used microarrays to study the transcriptome of PAMs infection with PCV2. PAMs were collected by bronchoalveolar lavage from health piglets (free of PCV2, PRRSV, PRV, CSFV, PPV), and PAMs were cultured for 48 hours and inoculated with 5 moi of PCV2.

2011-07-26 | E-GEOD-30918 | biostudies-arrayexpress

Identification of microproteins in Mycobacterium smegmatis by proteogenomics

Project description:We employed a proteogenomics workflow to identify microproteins encoded by small Open Reading Frames (ORFs) in the genome of Mycobacterium smegmatis strain mc²155.

2022-04-21 | PXD025604 | JPOST Repository

Expression data from blood samples of piglets experimentally infected with porcine circovirus type 2 (PCV2)

2009-12-31 | GSE14790 | GEO

Expression data from mediastinal lymph nodes of piglets experimentally infected with porcine circovirus type 2 (PCV2)

2009-11-04 | GSE14758 | GEO

Expression data from blood samples of piglets experimentally infected with porcine circovirus type 2 (PCV2)

Project description:This study aimed to characterize differences in gene expression in piglets inoculated with porcine circovirus type 2 (PCV2), the essential causative agent of postweaning multisystemic wasting syndrome (PMWS). Comparisons between control and PCV2-inoculated pigs were done at five different time points: 0, 7, 14, 21 and 29 days post-inoculation. Keywords: time course Seven-day-old caesarean-derived, colostrum-deprived piglets were distributed into two groups: control (n=4) and inoculated with 105.2 TCID50 of the Burgos PCV2 isolate (n=4). Pigs were bled at 0, 7, 14, 21, and 29 days post-inoculation.

2009-12-31 | E-GEOD-14790 | biostudies-arrayexpress

Pervasive, non-functional translation in mycobacterium tuberculosis

Project description:Open reading frame (ORF) boundaries in bacterial genomes have largely been drawn by gene prediction algorithms. However, these algorithms often fail to predict ORFs with non-canonical features, including those that are short, overlapping, or lack 5’ UTRs. Recent developments in genome-scale mapping of translation have facilitated the empirical identification of open reading frames (ORFs). Here, we use ribosome profiling approaches to map initiating and elongating ribosomes in Mycobacterium tuberculosis. Thus, we identify over 1,000 novel ORFs, revealing that much of the M. tuberculosis genome encodes proteins in overlapping reading frames, and/or on both strands. Most of the novel ORFs are short (sORFs), impeding their identification by traditional methods. The strong codon bias that characterizes annotated mycobacterial ORFs is not evident in the aggregate novel sORFs, and hence most are unlikely to encode functional proteins. Thus, our data suggest that bacterial transcriptomes are subject to pervasive translation that occurs as a result of the relatively low specificity requirements of initiating ribosomes. We speculate that the inefficiency of expressing spurious sORFs may be offset by positive contributions to M. tuberculosis biology through cis and trans regulatory activities of a small subset.

2019-06-20 | E-MTAB-8039 | biostudies-arrayexpress

Rhesus macaque rhadinovirus (RRV) gene expression in vivo

Project description:Viral gene expression profiling in a rhesus macaque rhadinovirus positive B cell lymphoma obtained from a rhesus macaque experimentally infected with simian immunodeficiency virus and rhesus macaque rhadinovirus strain 17577. The experiment identified two viral open reading frames (ORFs) that were expressed in the lymphoma. Expression of these viral ORFs were confirmed by reverse transcriptase-PCR.

2008-08-29 | GSE12608 | GEO

RNAs associated with Upf1, Pab1, Rpl16a, Lsm1 proteins in yeast

Project description:Nonsense mediated mRNA decay (NMD) is a translation-dependent surveillance pathway that eliminates RNAs with short open reading frames (ORFs) and long 3' untranslated regions (UTRs). Upf1 is the key protein of this degradation pathway and we were interested to purify the associated RNAs. Moreover we have done purifications of two proteins from the general mRNA turnover in yeast : Pab1 and Lsm1 that both bind RNAs poly(A) tails. We have also done a purification with a protein from the small ribosomal subunit (40S) in order to have a look at the translated RNAs.

2022-10-01 | GSE160642 | GEO

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