Chromatin immunoprecipitation (ChIP) is a powerful method for investigating interactions between specific proteins, genomic DNA, and RNA. Recent advancement in Next Generation Sequencing (NGS) technique allows us to sequence the ChIP DNA with high resolution, enabling us to perform unbiased and genome-wide mapping of epigenetic changes. Scientists at MR DNA are proficient in ChIP-Seq using NGS technology, and routinely provide this service to the researchers around the world at competitive cost. In addition to the sequencing service, MR DNA also provides bioinformatics service to analyze the ChIP-Seq data. For more information please visit https://www.mrdnalab.com.
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Services. Transcriptomics. mRNA-Seq: Stranded and non-stranded, high levels of multiplexing … ChIP–Seq sequencing. Transcription factor analysis; Histone modifications
121. Vet Res. 2015 Feb 24;46:15. doi: 10.1186/s13567-015-0153-8.
Manjunath S, Kumar GR, Mishra BP, Mishra B, Sahoo AP, Joshi CG, Tiwari AK, Rajak
KK, Janga SC.
Peste des petits ruminants (PPR), is an acute transboundary viral disease of
economic importance, affecting goats and sheep. Mass vaccination programs around
the world resulted in the decline of PPR outbreaks. Sungri 96 is a live
attenuated vaccine, widely used in Northern India against PPR. This vaccine
virus, isolated from goat works efficiently both in sheep and goat. Global gene
expression changes under PPR vaccine virus infection are not yet well defined.
Therefore, in this study we investigated the host-vaccine virus interactions by
infecting the peripheral blood mononuclear cells isolated from goat with PPRV
(Sungri 96 vaccine virus), to quantify the global changes in the transcriptomic
signature by RNA-sequencing. Viral genome of Sungri 96 vaccine virus was
assembled from the PPRV infected transcriptome confirming the infection and
demonstrating the feasibility of building a complete non-host genome from the
blood transcriptome. Comparison of infected transcriptome with control
transcriptome revealed 985 differentially expressed genes. Functional analysis
showed enrichment of immune regulatory pathways under PPRV infection. Key genes
involved in immune system regulation, spliceosomal and apoptotic pathways were
identified to be dysregulated. Network analysis revealed that the protein -
protein interaction network among differentially expressed genes is significantly
disrupted in infected state. Several genes encoding TFs that govern immune
regulatory pathways were identified to co-regulate the differentially expressed
genes. These data provide insights into the host - PPRV vaccine virus interactome
for the first time. Our findings suggested dysregulation of immune regulatory
pathways and genes encoding Transcription Factors (TFs) that govern these
pathways in response to viral infection.
PMID: 25827022 [PubMed - indexed for MEDLINE]
122. PLoS One. 2015 Aug 19;10(8):e0134837. doi: 10.1371/journal.pone.0134837.
Hurtado Páez UA(1), García Romero IA(1), Restrepo Restrepo S(2), Aristizábal
Gutiérrez FA(1), Montoya Castaño D(3).
(1)Laboratorio de Caracterización Molecular, Instituto de Biotecnología,
Universidad Nacional de Colombia, Bogotá, Colombia; Grupo de Bioprocesos y
Bioprospección, Instituto de Biotecnología, Universidad Nacional de Colombia,
Bogotá, Colombia. (2)Laboratorio de Micología y Fitopatología, Universidad de los
Andes, Bogotá, Colombia. (3)Grupo de Bioprocesos y Bioprospección, Instituto de
Biotecnología, Universidad Nacional de Colombia, Bogotá, Colombia.
Natural rubber (Hevea brasiliensis) is a tropical tree used commercially for the
production of latex, from which 40,000 products are generated. The fungus
Microcyclus ulei infects this tree, causing South American leaf blight (SALB)
disease. This disease causes developmental delays and significant crop losses,
thereby decreasing the production of latex. Currently several groups are working
on obtaining clones of rubber tree with durable resistance to SALB through the
use of extensive molecular biology techniques. In this study, we used a secondary
clone that was resistant to M. ulei isolate GCL012. This clone, FX 3864 was
obtained by crossing between clones PB 86 and B 38 (H. brasiliensis x H.
brasiliensis). RNA-Seq high-throughput sequencing technology was used to analyze
the differential expression of the FX 3864 clone transcriptome at 0 and 48 h post
infection (hpi) with the M. ulei isolate GCL012. A total of 158,134,220 reads
were assembled using the de novo assembly strategy to generate 90,775 contigs
with an N50 of 1672. Using a reference-based assembly, 76,278 contigs were
generated with an N50 of 1324. We identified 86 differentially expressed genes
associated with the defense response of FX 3864 to GCL012. Seven putative genes
members of the AP2/ERF ethylene (ET)-dependent superfamily were found to be
down-regulated. An increase in salicylic acid (SA) was associated with the
up-regulation of three genes involved in cell wall synthesis and remodeling, as
well as in the down-regulation of the putative gene CPR5. The defense response of
FX 3864 against the GCL012 isolate was associated with the antagonistic SA, ET
and jasmonic acid (JA) pathways. These responses are characteristic of plant
resistance to biotrophic pathogens.
PMID: 26287380 [PubMed - indexed for MEDLINE]
123. PLoS Pathog. 2015 Nov 12;11(11):e1005262. doi: 10.1371/journal.ppat.1005262.
Srikumar S(1,)(2), Kröger C(1,)(2), Hébrard M(1), Colgan A(1), Owen SV(2),
Sivasankaran SK(1), Cameron AD(3), Hokamp K(4), Hinton JC(1,)(2).
(1)Department of Microbiology, School of Genetics and Microbiology, Moyne
Institute of Preventive Medicine, Trinity College, Dublin, Ireland. (2)Institute
of Integrative Biology, University of Liverpool, Liverpool, United Kingdom.
(3)Department of Biology, University of Regina, Regina, Saskatchewan, Canada.
(4)Department of Genetics, School of Genetics and Microbiology, Smurfit Institute
of Genetics, Trinity College, Dublin, Ireland.
Salmonella enterica serovar Typhimurium is arguably the world's best-understood
bacterial pathogen. However, crucial details about the genetic programs used by
the bacterium to survive and replicate in macrophages have remained obscure
because of the challenge of studying gene expression of intracellular pathogens
during infection. Here, we report the use of deep sequencing (RNA-seq) to reveal
the transcriptional architecture and gene activity of Salmonella during infection
of murine macrophages, providing new insights into the strategies used by the
pathogen to survive in a bactericidal immune cell. We characterized 3583
transcriptional start sites that are active within macrophages, and highlight 11
of these as candidates for the delivery of heterologous antigens from Salmonella
vaccine strains. A majority (88%) of the 280 S. Typhimurium sRNAs were expressed
inside macrophages, and SPI13 and SPI2 were the most highly expressed
pathogenicity islands. We identified 31 S. Typhimurium genes that were strongly
up-regulated inside macrophages but expressed at very low levels during in vitro
growth. The SalComMac online resource allows the visualisation of every
transcript expressed during bacterial replication within mammalian cells. This
primary transcriptome of intra-macrophage S.-Typhimurium describes the
transcriptional start sites and the transcripts responsible for virulence traits,
and catalogues the sRNAs that may play a role in the regulation of gene
expression during infection.
PMID: 26561851 [PubMed - indexed for MEDLINE]