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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.

 

Genomic analysis of host - Peste des petits ruminants vaccine viral transcriptome

uncovers transcription factors modulating immune regulatory pathways.

 

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.

 

DOI: 10.1186/s13567-015-0153-8

PMCID: PMC4337102

PMID: 25827022  [PubMed - indexed for MEDLINE]

 

 

122. PLoS One. 2015 Aug 19;10(8):e0134837. doi: 10.1371/journal.pone.0134837.

eCollection 2015.

 

Assembly and Analysis of Differential Transcriptome Responses of Hevea

brasiliensis on Interaction with Microcyclus ulei.

 

Hurtado Páez UA(1), García Romero IA(1), Restrepo Restrepo S(2), Aristizábal

Gutiérrez FA(1), Montoya Castaño D(3).

 

Author information:

(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.

 

DOI: 10.1371/journal.pone.0134837

PMCID: PMC4564276

PMID: 26287380  [PubMed - indexed for MEDLINE]

 

 

123. PLoS Pathog. 2015 Nov 12;11(11):e1005262. doi: 10.1371/journal.ppat.1005262.

eCollection 2015.

 

RNA-seq Brings New Insights to the Intra-Macrophage Transcriptome of Salmonella

Typhimurium.

 

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).

 

Author information:

(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.

 

DOI: 10.1371/journal.ppat.1005262

PMCID: PMC4643027

PMID: 26561851  [PubMed - indexed for MEDLINE]

 

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