Epigenetics via ChIP-Seq (Chromatin Immunoprecipitation Sequencing)
As technology progresses, so does the curiosity of scientific minds around the globe. As more and more scientists shift from traditional DNA sequencing methods to massively parallel DNA sequencing, the new discoveries are increasing at an exponential rate. Such discoveries come with the popularization of chromatin immunoprecipitation sequencing or ChIP-Seq. ChIP sequencing is able to take scientists who were once excited to decipher the genomic code and stimulate new discoveries by determining how those genes are expressed. Laboratories, such as MR DNA, are assisting researchers from universities around the world to pinpoint how DNA and/or RNA are interacting with certain proteins by employing the ChIP-Seq protocol on a routine basis. Contact the highly experienced team at MR DNA in order to take advantage of their affordable cost and rapid turnaround time for your next epigenetic study.
Illumina HiSeq 2500/200, MiSeq – The HiSeq 2500/2000 sequencing systems offer the … Metagenomics and amplicon sequencing; ChIP–Seq …
MR DNA offers library prep, sequencing, and basic data analysis services for …Simple ChIP–Seq … hiSeq2500, …., sequence the samples
We provide services for high-throughput next-generation sequencing using the … (ChIP–SEQ), RNA discovery and Multiplex sequencing … Pricing forHiSeq 2500 sequencing is based on ……..sequencing run, …
Services. Transcriptomics. mRNA-Seq: Stranded and non-stranded, high levels of multiplexing … ChIP–Seq. Transcription factor analysis; Histone modifications
21. Genome Med. 2016 Jul 1;8(1):72. doi: 10.1186/s13073-016-0327-7.
Lau JT(1), Whelan FJ(1), Herath I(1), Lee CH(2,)(3), Collins SM(4), Bercik P(4),
(1)Department of Biochemistry and Biomedical Sciences, McMaster University,
Hamilton, ON, L8S 4K1, Canada. (2)Department of Medicine, Division of Infectious
Diseases, McMaster University, Hamilton, ON, L8S 4K1, Canada. (3)Hamilton
Regional Laboratory Medicine Program, Hamilton, ON, L8N 4A6, Canada.
(4)Department of Medicine, Farncombe Family Digestive Health Research Institute,
McMaster University, 1280 Main St W, HSC 3N-9, Hamilton, ON, L8S 4K1, Canada.
(5)Department of Biochemistry and Biomedical Sciences, McMaster University,
Hamilton, ON, L8S 4K1, Canada. email@example.com. (6)Department of Medicine,
Farncombe Family Digestive Health Research Institute, McMaster University, 1280
Main St W, HSC 3N-9, Hamilton, ON, L8S 4K1, Canada. firstname.lastname@example.org.
BACKGROUND: The human gut microbiota has been implicated in most aspects of
health and disease; however, most of the bacteria in this community are
considered unculturable, so studies have relied on molecular-based methods. These
methods generally do not permit the isolation of organisms, which is required to
fully explore the functional roles of bacteria for definitive association with
host phenotypes. Using a combination of culture and 16S rRNA gene sequencing,
referred to as culture-enriched molecular profiling, we show that the majority of
the bacteria identified by 16S sequencing of the human gut microbiota can be
METHODS: Five fresh, anaerobic fecal samples were cultured using 33 media and
incubation of plates anaerobically and aerobically resulted in 66 culture
conditions for culture-enriched molecular profiling. The cultivable portion of
the fecal microbiota was determined by comparing the operational taxonomic units
(OTUs) recovered by 16S sequencing of the culture plates to OTUs from
culture-independent sequencing of the fecal sample. Targeted isolation of
Lachnospiraceae strains using conditions defined by culture-enriched molecular
profiling was carried out on two fresh stool samples.
RESULTS: We show that culture-enriched molecular profiling, utilizing 66 culture
conditions combined with 16S rRNA gene sequencing, allowed for the culturing of
an average of 95 % of the OTUs present at greater than 0.1 % abundance in fecal
samples. Uncultured OTUs were low abundance in stool. Importantly, comparing
culture-enrichment to culture-independent sequencing revealed that the majority
of OTUs were detected only by culture, highlighting the advantage of culture for
studying the diversity of the gut microbiota. Applying culture-enriched molecular
profiling to target Lachnospiraceae strains resulted in the recovery of 79
isolates, 12 of which are on the Human Microbiome Project's "Most Wanted" list.
CONCLUSIONS: We show that, through culture-enriched molecular profiling, the
majority of the bacteria in the human gut microbiota can be cultured and this
method revealed greater bacterial diversity compared to culture-independent
sequencing. Additionally, this method could be applied for the targeted recovery
of a specific bacterial group. This approach allows for the isolation of bacteria
of interest from the gut microbiota, providing new opportunities to explore
mechanisms of microbiota-host interactions and the diversity of the human
PMID: 27363992 [PubMed - in process]
22. World J Gastroenterol. 2015 Jan 21;21(3):803-14. doi: 10.3748/wjg.v21.i3.803.
Wang WL(1), Xu SY(1), Ren ZG(1), Tao L(1), Jiang JW(1), Zheng SS(1).
(1)Wei-Lin Wang, Shao-Yan Xu, Zhi-Gang Ren, Liang Tao, Jian-Wen Jiang, Shu-Sen
Zheng, Department of Hepatobiliary and Pancreatic Surgery, First Affiliated
Hospital, Zhejiang University School of Medicine, Hangzhou 310003, Zhejiang
There are more than 1000 microbial species living in the complex human intestine.
The gut microbial community plays an important role in protecting the host
against pathogenic microbes, modulating immunity, regulating metabolic processes,
and is even regarded as an endocrine organ. However, traditional culture methods
are very limited for identifying microbes. With the application of molecular
biologic technology in the field of the intestinal microbiome, especially
metagenomic sequencing of the next-generation sequencing technology, progress has
been made in the study of the human intestinal microbiome. Metagenomics can be
used to study intestinal microbiome diversity and dysbiosis, as well as its
relationship to health and disease. Moreover, functional metagenomics can
identify novel functional genes, microbial pathways, antibiotic resistance genes,
functional dysbiosis of the intestinal microbiome, and determine interactions and
co-evolution between microbiota and host, though there are still some
limitations. Metatranscriptomics, metaproteomics and metabolomics represent
enormous complements to the understanding of the human gut microbiome. This
review aims to demonstrate that metagenomics can be a powerful tool in studying
the human gut microbiome with encouraging prospects. The limitations of
metagenomics to be overcome are also discussed. Metatranscriptomics,
metaproteomics and metabolomics in relation to the study of the human gut
microbiome are also briefly discussed.
PMID: 25624713 [PubMed - indexed for MEDLINE]
23. Environ Health Perspect. 2015 Jul;123(7):679-88. doi: 10.1289/ehp.1409055. Epub
2015 Mar 13.
Zhang L(1), Nichols RG, Correll J, Murray IA, Tanaka N, Smith PB, Hubbard TD,
Sebastian A, Albert I, Hatzakis E, Gonzalez FJ, Perdew GH, Patterson AD.
(1)Center for Molecular Toxicology and Carcinogenesis, Department of Veterinary
and Biomedical Sciences, The Pennsylvania State University, University Park,
Environ Health Perspect. 2015 Jul;123(7):A187.
BACKGROUND: Alteration of the gut microbiota through diet and environmental
contaminants may disturb physiological homeostasis, leading to various diseases
including obesity and type 2 diabetes. Because most exposure to environmentally
persistent organic pollutants (POPs) occurs through the diet, the host
gastrointestinal tract and commensal gut microbiota are likely to be exposed to
OBJECTIVES: We examined the effect of 2,3,7,8-tetrachlorodibenzofuran (TCDF), a
persistent environmental contaminant, on gut microbiota and host metabolism, and
we examined correlations between gut microbiota composition and signaling
METHODS: Six-week-old male wild-type and Ahr-/- mice on the C57BL/6J background
were treated with 24 μg/kg TCDF in the diet for 5 days. We used 16S rRNA gene
sequencing, 1H nuclear magnetic resonance (NMR) metabolomics, targeted
ultra-performance liquid chromatography coupled with triplequadrupole mass
spectrometry, and biochemical assays to determine the microbiota compositions and
the physiological and metabolic effects of TCDF.
RESULTS: Dietary TCDF altered the gut microbiota by shifting the ratio of
Firmicutes to Bacteroidetes. TCDF-treated mouse cecal contents were enriched with
Butyrivibrio spp. but depleted in Oscillobacter spp. compared with
vehicle-treated mice. These changes in the gut microbiota were associated with
altered bile acid metabolism. Further, dietary TCDF inhibited the farnesoid X
receptor (FXR) signaling pathway, triggered significant inflammation and host
metabolic disorders as a result of activation of bacterial fermentation, and
altered hepatic lipogenesis, gluconeogenesis, and glycogenolysis in an
CONCLUSION: These findings provide new insights into the biochemical consequences
of TCDF exposure involving the alteration of the gut microbiota, modulation of
nuclear receptor signaling, and disruption of host metabolism.
PMID: 25768209 [PubMed - indexed for MEDLINE]