Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Fine-mapping of DNA modifications in the lactase gene region of mice

ABSTRACT: Transcriptional variation between cells of the same type is a widespread phenomenon which allows for tissues to exhibit regional differences in biological function and disease vulnerability. We analyzed an in vivo transcriptional gradient occurring in enterocytes along the proximal-to-distal axis of the mouse small intestine via bisulfite padlock probe technique. DNA modifications at the lactase gene were investigated in infant and adult mice as well as following lactose-treatment.

ORGANISM(S): Mus musculus

PROVIDER: GSE76373 | GEO | 2017/01/17

SECONDARY ACCESSION(S): PRJNA307112

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Fine-mapping of DNA modifications in the lactase gene region of humans and mice

Project description:Bisulfite padlock probe technique was used to examine DNA modifications at the lactase gene region for human and mouse tissues DNA modifications were investigated in human sperm, blood, jejunal enterocytes and jejunum lacking enterocytes, as well as mouse jejunal enterocytes and jejunum lacking enterocytes. For WGA samples, a genome devoid of DNA modifications was used to verify the efficiency of the bisulfite conversion reactions (the tissue sources were human or mouse intestine).

2016-03-25 | E-GEOD-69977 | biostudies-arrayexpress

Fine-mapping of DNA modifications in the lactase gene region of humans and mice

Project description:Bisulfite padlock probe technique was used to examine DNA modifications at the lactase gene region for human and mouse tissues

2016-03-25 | GSE69977 | GEO

Bovine protein glycation sites in different milk products

Project description:Here we studied the glycation of bovine milk proteins by lactose as dominant sugar in milk and hexoses using tandem mass spectrometry (CID and ETD mode). In a bottom-up proteomics approach after enriching glycated peptides by boronate affinity chromatography, first we could identify 260 lactosylated peptides corresponding to 124 lactosylation sites in 28 bovine milk proteins in raw milk, raw colostrum, three brands of pasteurized milk, three brands of UHT milk, and five brands of infant formula. The same regular and additionally two lactose-free milk products (pasteurized and UHT milk) where lactose is enzymatically cleaved into the more reactive hexoses were analyzed in terms of hexosylation sites that resulted in identification of 124 hexosylated tryptic peptides corresponding to 86 glycation sites in 17 bovine milk proteins. In quantitative terms glycation increased from raw milk to pasteurized milk to UHT milk and infant formula, i.e., with the harsher processing conditions. Lactose-free milk contained significantly higher hexosylation degrees than the corresponding regular milk product.

2016-01-11 | PXD003054 | Pride

Cortical region confers neuron-type-specific vulnerability to human APP expression

Project description:Alzheimer’s Disease is a devastating and an irreversible neurodegenerative disease currently afflicting 50 million individuals worldwide, a number expected to escalate three-fold over the next 25 years. Preventative treatment is of dire importance, and yet, cellular mechanisms underlying early regional vulnerability in Alzheimer’s Disease remain unknown. In human patients with Alzheimer’s Disease, the earliest observed pathophysiological correlate to cognitive decline is hyperexcitability. In mouse models, early hyperexcitability has been shown in the cortical region first impacted by Alzheimer’s Disease. The origin of hyperexcitability in early stage-disease and why it preferentially emerges in specific regions is unclear. Using cortical-region and cell-type- specific proteomics and patch-clamp electrophysiology, we uncovered differential susceptibility to human-specific APP in a model of sporadic Alzheimer’s Disease. Shockingly, our findings reveal that early entorhinal hyperexcitability may result from intrinsic vulnerability of parvalbumin interneurons, prior to changes in surrounding excitatory neurons. This study suggests early disease interventions addressing non-excitatory cell-types may protect regions first vulnerable to pathological symptoms of Alzheimer’s Disease and downstream cognitive decline.

2024-06-28 | PXD053491 | Pride

Epithelial cell diversity in small intestine of pigs

Project description:To establish better understanding of specific epithelial cells found across different regions of the small intestine in pigs, we utilized single-cell RNA sequencing (scRNA-seq) to recover and analyze epithelial cells from duodenum, jejunum, and ileum. Cells identified included crypt cells, enterocytes, BEST4 enterocytes, goblet cells, and enteroendocrine (EE) cells. Overall, results provide new information on regional localization and transcriptional profiles of epithelial cells in the pig small intestine.

2023-01-18 | GSE208613 | GEO

Differential gene expression in mouse retina related to regional differences in vulnerability to hyperoxia

Project description:Purpose: In the C57BL/6J mouse retina, hyperoxia-induced degeneration of photoreceptors shows strong regional variation, beginning at a locus ~0.5mm inferior to the optic disc. To identify gene expression differences that might underlie this variability in vulnerability, we have used microarray techniques to describe regional (superior-inferior) variations in gene expression in the retina. Methods: Young adult C57BL/6J mice raised in dim cyclic illumination (12h 5lux, 12h darkness) were exposed to hyperoxia (75% oxygen for 2w). Retinas were collected from hyperoxia-exposed and control animals without fixation, and divided into superior and inferior halves. RNA was extracted from each sample, purified and hybridised to mouse 1.0 ST arrays (Affymetrix). The consistency of the microarray results was assessed with quantitative PCR for selected genes. Expression data were analysed to identify genes and ncRNAs whose differential expression between superior and inferior retina could be associated with relative vulnerability to hyperoxia.

2010-04-08 | E-GEOD-21246 | biostudies-arrayexpress

Transcription profile of aging and cognitive-related genes in the medial prefrontal cortex and hippocampal region CA1

Project description:This study focused on transcription in the medial PFC (mPFC) as a function of age and cognition. Young and aged F344 rats were characterized on tasks, attentional set shift and spatial memory, which depend on the mPFC and hippocampus, respectively. Differences in transcription associated with age and cognitive function were examined using RNA sequencing to construct transcriptomic profiles for the mPFC, white matter, and region CA1 of the hippocampus. The results indicate regional differences in vulnerability to aging associated with increased expression of immune and defense response genes and a decline in synaptic and neural activity genes. Importantly, we provide evidence for region specific transcription related to behavior. In particular, expression of transcriptional regulators and neural activity-related immediate-early genes (IEGs) are increased in the mPFC of aged animals that exhibit delayed set shift behavior; relative to age-matched animals that exhibit set shift behavior similar to younger animals. The study contains 11 young and 20 aged rats for the mPFC and CA1 samples, which were used to investigate expression patterns associated with aging and behavior. White matter samples were used to investigate an age-related effect with 8 young and 9 aged rats.

2016-05-17 | E-GEOD-75772 | biostudies-arrayexpress

Gene expression in B breve SW1107E in the presence of media containing lactose, BMO and 3SL as carbon sources

Project description:Bifidobacterium species in the infant gut can metabolize intact human milk oligosaccrides. There is species varation in the types of the olgosaccharides that can bedigested by Bifidobacterium species. B. breve strains have shown digestion of LNT and LNnT oligoscchrides. The objective of te current study was idetification of B. breve strains that can digest sialylated oligosacchrides. The currnet study was designed to idetify the genes that show upregulation when grown in lactose, 3'-siallylactose and Bovine Milk Oligosaccharides

2023-07-31 | GSE237076 | GEO

Differential gene expression in mouse retina related to regional differences in vulnerability to hyperoxia

2010-04-08 | GSE21246 | GEO

RNA sequencing of CACO-2 cells incubated with Bifidobacteria breve grown on human milk oligosaccharides.

Project description:Background: Breastfed human infants are predominantly colonized by bifidobacteria that thrive on human milk oligosaccharides (HMO). The two most predominant species of bifidobacteria in infant feces are Bifidobacterium breve (B. breve) and Bifidobacterium longum subsp. infantis (B. infantis), both avid HMO-consumer strains. Our laboratory has previously shown that B. infantis, when grown on HMO, increase adhesion to intestinal cells and increase the expression of the anti-inflammatory cytokine interleukin-10. The purpose of the current study was to investigate the effects of carbon source—glucose, lactose, or HMO—on the ability of B. breve and B. infantis to adhere to and affect the transcription of intestinal epithelial cells on a genome-wide basis. Results: HMO-grown B. infantis had higher percent binding to Caco-2 cell monolayers compared to B. infantis grown on glucose or lactose. B. breve had low adhesive ability regardless of carbon source. Despite differential binding ability, both HMO-grown strains significantly differentially affected the Caco-2 transcriptome compared to their glucose or lactose grown controls. HMO-grown B. breve and B. infantis both down-regulated genes in Caco-2 cells associated with chemokine activity. Conclusion: The choice of carbon source affects the interaction of bifidobacteria with intestinal epithelial cells. HMO-grown bifidobacteria reduce markers of inflammation, compared to glucose or lactose-grown bifidobacteria. In the future, the design of preventative or therapeutic probiotic supplements may need to include appropriately chosen prebiotics.

2017-02-10 | GSE64017 | 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