Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

44 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcription profiling by array to investigate the response of mice colon samples when infected by a H3N2 influenza virus.

ABSTRACT: To study the impact of influenza infection on gene expression changes in the colon, mice were intra-nasally infected with 30 plaque forming units of the mouse-adapted H3N2 IAV strain Scotland/20/1974. PBS-treated mice served as controls. The colons were collected 7 days post-infection.

ORGANISM(S): Mus musculus

SUBMITTER: Ronan Le Goffic

PROVIDER: E-MTAB-6707 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

RNA-seq of mouse colon to investigate how influenza infection leads to intestinal disorders

Project description:To study the impact of influenza infection on gene expression changes in the colon, mice were intra-nasally infected with 30 plaque forming units of the mouse-adapted H3N2 IAV strain Scotland/20/1974. PBS-treated mice served as controls. The colons were collected 7 days post-infection. The 4 samples presented here are \\"pair feed\\" controls of the samples presented in E-MTAB-6707. To provide the pair-fed group with only as much food daily as is consumed by IAV-infected mice, we restricted the food access during the last three days for 15% (day 4), 35% (day 5) and 85% (day 6), respectively (sacrifice at day 7). Mice were anesthetized at day 0. Food was supplied twice a day to pair-fed animals and water was available at all times. The ad libitum (normally nourished) group mice were allowed unrestricted access to food and water. At the sacrifice, paired-fed mice lost ~15% of body mass.

2021-04-21 | E-MTAB-10036 | biostudies-arrayexpress

Analyses of lung early responses to RSV in the neonatal environment reveal key roles for DC and type I IFN in controlling immunopathologic imprinting.

Project description:The gene expression profile of neonatal versus adult lung, 2 days after an RSV or mock infection was analyzed using whole mouse genome agilent microarrays. Total lung RNA were extracted, labeled with Cy3 and hybridized on Agilent G4122F slides. We used 4 biological replicates per condition.

2015-12-21 | E-GEOD-42759 | biostudies-arrayexpress

mRNA-seq of intestinal epithelial cells isolated from Rnf20 and Rnf40 knockout mice

Project description:Intestinal epithelial cells (IECs) were isolated from the colon of Villin-CreERT2, Rnf20-flox and Rnf40-flox mice two weeks upon the Tamoxifen-induced, intestinal knockout of Rnf20 and Rnf40. RNA was isolated from snap-frozen IECs to perform mRNA-seq.

2021-06-16 | E-MTAB-9405 | biostudies-arrayexpress

Anti-influenza activity of succinate

Project description:In the present study, we discovered an unexpected interplay between immunometabolism and antiviral immunity. Profiling of human bronchial epithelial BEAS-2B cells was performed using Agilent’s SurePrint G3 human gene expression microarray kit. A single-color design provided two types of comparison: (i) IAV-infected versus mock-infected cells, and (ii) succinate-treated infected cells versus mock-infected cells.

2022-02-17 | E-MTAB-10031 | biostudies-arrayexpress

Identification of potential visceral pain biomarkers in colon exudates from mice with experimental colitis: an exploratory in vitro study

Project description:Chronic visceral pain (CVP) is extremely difficult to diagnose, and available analgesic treatment options are quite limited. Identifying the proteins secreted from the colonic nociceptors, or their neighbor cells within the tube walls, in the context of disorders that course with visceral pain, might be useful to decipher the mechanism involved in the establishment of CVP. Addressing this question in patients with gastrointestinal disorders entails multiple difficulties, as there is not a clear classification of disease severity, and colonic secretion is not easy to manage.We propose using of a murine model of colitis to identify new algesic molecules and pathways that could be explored as pain biomarkers or analgesia targets.Descending colons from naïve and colitis mice with visceral hyperalgesia were excised and maintained ex vivo. The proteins secreted in the perfusion fluid before and during acute noxious distension were evaluated using high-resolution mass spectrometry (MS). Haptoglobin (Hp), PZD and LIM domain protein 3 (Pdlim3), NADP-dependent malic enzyme (Me1), and Apolipoprotein A-I (Apoa1) were increased during visceral insult, whilst Triosephosphate isomerase (Tpi1), Glucose-6-phosphate isomerase (Gpi1), Alpha-enolase (Eno1), and Isoform 2 of Tropomyosin alpha-1 chain (Tpm1) were decreased.Most identified proteins have been described in the context of different chronic pain conditions and, according to gene ontology analysis, they are also involved in diverse biological processes of relevance.Thus, animal models that mimic human conditions in combination with unbiased omics approaches will ultimately help to identify new pathophysiological mechanisms underlying pain that might be useful in diagnosing and treating pain.

2023-01-11 | PXD033902 | Pride

DOCK8 regulates protective immunity by controlling the function and survival of RORγt+ ILCs

Project description:Retinoic-acid receptor-related orphan receptor-γt-positive (RORγt+) innate lymphoid cells (ILCs) produce interleukin (IL)-22 and IL-17, which are critical for protective immunity against enteric pathogens. The molecular mechanism underlying the development and survival of RORγt+ ILCs is not thoroughly understood. Here we show that Dedicator of cytokinesis 8 (DOCK8), a scaffolding protein involved in cytoskeletal rearrangement and cell migration, is essential for the protective immunity against Citrobacter rodentium. A comparative RNA sequencing-based analysis reveals an impaired induction of antimicrobial peptides in the colon of DOCK8-deficient mice, which correlates with high susceptibility to infection and a very low number of IL-22-producing RORγt+ ILCs in their GI tract. Furthermore, DOCK8-deficient RORγt+ ILCs are less responsive to IL-7 mediated signaling, more prone to apoptosis and produce less IL-22 due to a defect in IL-23-mediated STAT3 phosphorylation. Our studies reveal an unsuspected role of DOCK8 for the function, generation and survival of RORγt+ ILCs. Control and DOCK8 KO mice were infected with 2X109 CFU of Citrobacter rodentium and day 8 post infection mice were sacrificed and their colons were harvested (n=5) . Total RNA was purified from the infected colons with RNeasy mini kit (Qiagen). RNA sequencing was performed (pooled RNA sample from five mice in each group) at Genomic Core Facility Southwestern Medical Center, University of Texas.

2014-06-25 | E-GEOD-58765 | biostudies-arrayexpress

Mthfd1 is a modifier of intestinal carcinogenesis

Project description:The metabolic pathways that underlie the association between folate deficiency and increased risk for colorectal cancer (CRC) remain unclear. We have studied the effect of C1THF synthase (encoded by the Mthfd1 gene) and dietary folate and choline on intestinal tumor development in Apcmin/+ mice and azoxymethane (AOM)-induced colon cancer in mice. Mthfd1 deficiency did not alter tumor number or load in Apcmin/+ mice, but did result in a decreased incidence of colon tumors. Conversely, Mthfd1 deficiency increased tumor number 3.5-fold and tumor load 2-fold in AOM-treated mice. Here we tested colons isolated from wildtype and Mthfd1-deficient animals for alterations in gene expression. Keywords: genetic modification RNA was isolated from proximal colons of MTHFD heterozygous and wild-type mice raised on a control diet. Three colon samples were isolated from each genotype to provide biological replication.

2010-03-20 | E-GEOD-15419 | biostudies-arrayexpress

The lipid metabolism enzyme DGAT1 mediates Treg control of type 2 immunity at barrier sites

Project description:Regulatory T cells were sorted from the colon of mice under steady state conditions from mice that were either wild type or Dgat1 knockout. To gain enough cells for sequencing samples from the same group were pooled (n=5/pool).

2023-01-01 | E-MTAB-9477 | biostudies-arrayexpress

Gene expression data of cSHMT mutant, heterozygous, and wild-type mouse colons

Project description:Folate-mediated one-carbon metabolism is required for purine, thymidylate, and S-adenosylmethionine synthesis. Impairments in folate metabolism diminish cellular methylation potential and genome stability. Cytoplasmic serine hydroxymethyl transferase (cSHMT) regulates partitioning between thymidylate and SAM biosynthesis. These experiments were designed to determine if mutations in cSHMT led to alterations in gene expression. Keywords: genetic modification RNA was isolated from proximal colons of cSHMT mutant, heterozygous, and wild-type mice raised on a folate-deficient diet. Three colon samples were isolated from each genotype to provide biological replication. Mutant and heterozygous data were then compared pair-wise against wild-type expression data.

2010-03-03 | E-GEOD-14645 | biostudies-arrayexpress

Study of the host response to an influenza virus infection in a mouse model

Project description:Mice were infected intranasally with 1.5x10E5 PFU and total RNA were extracted from mice lungs at day 3. RNA samples were extracted from mice lung infected or not by influenza virus.

2016-10-19 | E-MTAB-4891 | biostudies-arrayexpress

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