Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

10 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Microbiota regualtion of miRNA

ABSTRACT: This experiment was investigating how gut commensal bacteria and intestinal inflammation affect miRNA expression. We analyzed miRNA expression of spleen and intestine from specific pathogen free (SPF) B6 mice, germ-free (GF) B6 mice, and IL-10 knockout mice which have severe colitis by microarray. Thus we have total 6 samples: GF spleen; GF intestines; SPF spleen; SPF intestine; IL-10 KO spleen and IL-10 KO intestine. We directly isolated RNA from whole spleens or intestines without any treatments, and then did microarray analysis.

ORGANISM(S): Mus musculus

SUBMITTER: yingzi cong

PROVIDER: E-MEXP-3406 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Effect of Fasting on Hepatic Gene Expression in Postpubertal Holstein Dairy Heifers

Project description:102 postpubertal Holstein dairy heifers were randomly assigned to a fed or fasted treatment. Liver biopsies were performed to obtain tissue from which mRNA was extracted and used for microarray analysis. Transcriptional profiling revealed adaptive mechanisms in response to negative energy balance. Two condition experiment; fed and fasted. Common reference design employed; reference sample consisting of RNA derived from bovine liver, spleen and placental tissue. Biological replicates of 51 Fed (as control) and 51 Fasted (as treatment). One replicate per array. Dye swaps performed on 7 of the 51 fasted treatment group samples, and on 5 of the 51 fed treatment group samples.

2009-05-20 | E-GEOD-16154 | biostudies-arrayexpress

Transcription profiling of wild type and Rad6 or Rad18 knock-out yeast to identify genes regulated by Rad6/Rad18

Project description:To identify the yeast genes whose transcription is regulated by Rad6/Rad18

2008-02-20 | E-MEXP-1463 | biostudies-arrayexpress

Chromatin immunoprecipitation of Zea mays chloroplast extracts using antibodies raised against OE17 and OE23 chloroplast targeted proteins

Project description:OE17 and OE23 are chloroplast targeted proteins. RNA co-immunoprecipitation was performed using antibodies raised against these proteins. RNA from the pellet and from the supernatent for each pulldown was labeled with different fluoro-dyes.

2006-09-01 | E-MEXP-784 | biostudies-arrayexpress

Chromatin immunoprecipitation of Zea mays chloroplast extracts prepared from wild type and PPR4-deficient tissue

Project description:Co-immunoprecipitation of the maize pentatricopeptide protein PPR4 and extraction of bound RNA. RNA is labelled and hybridized to a maize chloroplast genome tiling array in order to identify target RNA species of PPR4.

2022-11-22 | E-MEXP-716 | biostudies-arrayexpress

Chromatin immunoprecipitation of RNA binding protein CFM2 in Zea mays chloroplast extracts

Project description:Identification of target transcripts for the putative chloroplast RNA binding protein CFM2 in Zea mays. CFM2 was immunoprecipitated from a chloroplast extract. Chloroplast extracts were prepared from WT tissue. RNA from the pellet and from the supernatant for each pulldown was labelled with different fluoro-dyes and hybridized onto an array covering the complete maize chloroplast genome. Messages enriched in the immunoprecipitate from WT tissue are likely targets for CFM2.

2006-09-01 | E-MEXP-743 | biostudies-arrayexpress

microRNA expression profile of activated versus non activated primary B cells

Project description:microRNA expression profile in 5 indepent sets of paired samples of LPS+IL-4 activated versus non activated primary mouse spleen B cells Keywords: cell type comparison Activated B cells for miRNA array analysis were obtained after CFSE labelling (Molecular Probes), LPS+IL4 stimulation for 3 days and sorting of cells that had undergone at least 1 cell division. Sortings were performed with a FACSAria cell sorter (BD Biosciences).

2008-08-20 | E-GEOD-12176 | biostudies-arrayexpress

Effect pck or ppc expression on intracellular ATP

Project description:Up-regulation of motility genes and biosynthesis genes were found in the pck expressing high ATP cell by transcriptome analysis while catabolism genes were down-regulated. Keywords: response depends on intracellular ATP concentration derived by pck or ppc overexpression 1. pck or ppc overexpressing E. coli at early log phase using glucose-minimal medium 2. pck or ppc overexpressing E. coli at chemostat culture (D=0.1 h-1)using LB-glucose medium

2010-06-09 | E-GEOD-8532 | biostudies-arrayexpress

Global gene expression profile of small intestine from wild-type and NKCC1 (SLC12A2)-knockout mice.

Project description:The objective of this study was to identify changes in gene expression levels between wild-type and NKCC1-knockout small intestine. 6 wild-type and 6 NKCC1-knockout small intestine RNA samples were compared. Total RNA was collected from both male and female 8-week old wild-type and NKCC1-null mice on an inbred FVB\N background. All comparisons were done between wild-type and NHE4-null samples from age- and gender-matched mice.

2010-11-17 | E-GEOD-19117 | biostudies-arrayexpress

Gene expression patterns of biopsies from a colonoscopy taken in 2009 of an ulcerative colitis patient infected with Trichuris trichiura

Project description:Helminth infection may have the potential to suppress intestinal inflammation in inflammatory bowel diseases. Ulcerative colitis is more common in developed countries than in developing countries endemic for helminth infections. There are animal models, as well as clinical trials, suggesting therapeutic effects of experimental helminth infection. Here, we provide a comprehensive molecular portrait of dynamic changes in the intestinal mucosa of an individual who infected himself with Trichuris trichiura to treat his symptoms of ulcerative colitis. Genes involved in carbohydrate and lipid metabolism were upregulated in helminth-colonized tissue, while tissues with active colitis showed upregulation of proinflammatory genes such as IL-17, IL13RA2, and CHI3L1. T. trichiura colonization of the intestine may reduce symptomatic colitis by promoting goblet cell hyperplasia and mucus production through TH2 cytokines and IL-22. By better understanding the physiological effects of helminth infection, new therapies for ulcerative colitis could be identified. This is the third (out of three) series of arrays from this patient from a colonoscopy in 2009 when the patient was in remission. We analyzed 12 HEEBO arrays on which were hybridized RNA amplified from pinch biopsies collected from different regions of the colon. 4 samples were from the ascending colon, which was colonized by worms at the time. 3 samples were from the transverse colon, which appeared normal at the time. 3 samples were from the recto-sigmoid colon, which had recovered from colitis at the time. 2 samples were from the terminal ileum, which was unaffected by worms or colitis.

2010-11-20 | E-GEOD-25277 | biostudies-arrayexpress

Gene expression patterns of biopsies from a colonoscopy taken in 2008 of an ulcerative colitis patient infected with Trichuris trichiura

Project description:Helminth infection may have the potential to suppress intestinal inflammation in inflammatory bowel diseases. Ulcerative colitis is more common in developed countries than in developing countries endemic for helminth infections. There are animal models, as well as clinical trials, suggesting therapeutic effects of experimental helminth infection. Here, we provide a comprehensive molecular portrait of dynamic changes in the intestinal mucosa of an individual who infected himself with Trichuris trichiura to treat his symptoms of ulcerative colitis. Genes involved in carbohydrate and lipid metabolism were upregulated in helminth-colonized tissue, while tissues with active colitis showed upregulation of proinflammatory genes such as IL-17, IL13RA2, and CHI3L1. T. trichiura colonization of the intestine may reduce symptomatic colitis by promoting goblet cell hyperplasia and mucus production through TH2 cytokines and IL-22. By better understanding the physiological effects of helminth infection, new therapies for ulcerative colitis could be identified. This is the second (out of three) series of arrays from this patient from a colonoscopy in 2008 when the patient was suffering from severe colitis but still had worms in the ascending colon. We analyzed 12 HEEBO arrays on which were hybridized RNA amplified from pinch biopsies collected from different regions of the colon. 4 samples were from the ascending colon, which was colonized by worms at the time. 4 samples were from the transverse colon, which was no longer colonized by worms at the time. 4 samples were from the recto-sigmoid colon, which was suffering from severe colitis at the time.

2010-11-20 | E-GEOD-25276 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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