Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Sorted HSCs from aged Specific Pathogen Free and germ free mice

ABSTRACT: To begin to explore mechanisms by which microbiota signals regulate HSC lineage bias, gene expression profiling was performed on sorted LSK-SLAM cells from aged SPF and aged GF mice.

ORGANISM(S): Mus musculus

PROVIDER: GSE183138 | GEO | 2021/11/10

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Global hepatic gene expression data from germ free and specific pathogen free male mice.

Project description:Liver clock regulates transcription of hepatic genes in response to feeding. To explore the possibility that the microbiome influences this process, we measured the liver transcriptome in normal mice (Specific Pathogen Free or SPF mice) and compared it to the transcriptome in mice lacking microbiota (Germ Free or GF mice) at different time points over 24h. We used microarrays to detail the global programme of gene expression in liver of GF and SPF 10-12 weeks-old male C57Bl/6 male mice. There are 40 liver samples, each from an individual mouse. The samples are from germ free mice (GF) and specific pathogen free mice (SPF). Mice of both types were sacrificed at four time points: Zeitgeber Time 0, 6, 12, and 18. There are five replicates per condition.

2016-02-20 | E-GEOD-71628 | biostudies-arrayexpress

Global hepatic gene expression data from germ free and specific pathogen free male mice.

2016-02-20 | GSE71628 | GEO

RNA-seq of fetal murine intestine, brain and placenta from germ-free vs specific pathogen free dams

Project description:The effects of maternal microbiota on the fetal development was investigated by comparing tissues of fetuses from germ-free (GF) and normal (SPF) murine dams using RNA-seq and non-targeted metabolomics (for metabolomics data, see: https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-022-02457-6). For RNA-seq, two E18.5 fetuses were collected from 6 GF dams and 6 SPF dams, and transcriptomes analyzed by QuantSeq in whole intestine, brain and placenta.

2022-12-17 | E-MTAB-12442 | biostudies-arrayexpress

Arthritic KRN T cells and wild type T cells from germ free and specific pathogen free mice

Project description:A general defect of GF K/BxN T cell proliferation response toward antigen motivated us to look for the impairment in GF K/BxN T cells that might leads to the low Ab production and reduced disease phenotype seen in GF K/BxN mice. To find the difference between GF and SPF K/BxN T cells in a broad and non-biased fashion, we performed gene-expression profiling of these cells using microarrays.

2010-06-05 | GSE22140 | GEO

Genome wide study of microglia in Specific-pathogen-free (SPF) and Germ-free (GF) mice at different stages in males and females.

Project description:ATACseq was performed on microglia from male and female, SPF or GF mice to elucidate the chromatin accessibility implicated by microbiota and gender. Differential accessible regions (DARs) between the various groups gave some ideas on what different pathways or functions might be affected due to the different factors.

2017-12-06 | GSE107757 | GEO

Genome wide study of microglia in Specific-pathogen-free (SPF) and Germ-free (GF) mice at different stages in males and females (RNA-Seq)

Project description:RNAseq was performed on microglia from male and female, SPF or GF mice to elucidate the genetic differences implicated by microbiota and gender. DEGs between the various groups gave some ideas on what different pathways or functions might be affected due to the different factors.

2017-12-12 | GSE107925 | GEO

Sorted HSCs from aged Specific Pathogen Free and germ free mice

Project description:Sorted HSCs from aged Specific Pathogen Free and germ free mice

| PRJNA759251 | ENA

mRNA expression from wild type and gp130F/F mice antrum at 4 weeks of age in specific pathogen free (SPF) and germ free (GF) conditions

Project description:The role of microbe in promoting the initiation of gastric cancer (GC), the third most lethal cancer worldwide, are ill-defined. Here, we found that tumor size and weight in gp130F/F mouse stomach at condition were significantly reduced compared to those of at SPF condition. To investigate the underlying mechanism and how host genes were regulated in the presence/absence of microbe, arrays were performed in stomach tissue from gp130F/F and WT at 4 week old at SPF and GF conditions. The onset of gastric inflammation-associated adenomatous hyperplasia in gp130F/F mice occurs at ~6 weeks of age, with established intestinal-type tumors (3 months of age) progressively growing until a maximum size is reached at 6 months of age, with some evidence of carcinoma in situ. Since this phenotype histologically mimics early stage human GC, we therefore utilized gp130F/F mice as a model to identify miRNAs involved in the initiating molecular events leading to early stage GC. For this purpose, we performed miRNA microarrays on mouse gastric antrum tissue from gp130F/F and sex-matched littermate wild-type (gp130+/+) control mice aged 4 weeks; this age was chosen since antrum tissue from 4 week old (wo) gp130F/F mice is devoid of any histological signs of inflammation or hyperplasia, and is thus comparable to wild-type gastric antrum tissue.

2017-12-01 | GSE93173 | GEO

Small RNA sequencing of lipoproteins (HDL) obtained from germ-free mice and facility matched specific-pathogen free mice.

Project description:Plasma was harvested from two cohorts of facility-matched germ free (GF) and specific-pathogen free (SPF) mice at the National Gnotobiotic Rodent Resource Center (NGRRC; North Carolina, USA). Plasma was then fractionated by size-exclusion chromatography using three tandem Superdex200 increase columns (Cytiva). Fractions corresponding with HDL were then pooled and concentrated prior to RNA isolation. Small RNA libraries were generated from total RNA using NextFlex V3 Small RNA Seq-kit (Perkin Elmer) according to manufacturer’s instructions. Equimolar amounts of each library were then pooled and sequenced on the NextSeq500 platform (Illumina). Individual libraries were then demultiplexed and analyzed with the TIGER analytical pipeline.

2022-06-29 | GSE206857 | GEO

Expression data from germ free (GF) and specific pathogen free (SPF) mouse wound bed

Project description:Environmental factors that enhance regeneration are largely unknown. We hypothesized that skin bacteria modulate regeneration. Here, we assessed low, medium, and high levels of bacterial burden in Wound Induced Hair follicle Neogenesis (WIHN), a rare adult organogenesis model. WIHN levels and stem cell markers indeed correlated with bacterial counts, being lowest in germ free (GF), intermediate in conventional specific pathogen free (SPF), and highest even in mice infected with pathogenic Staphylococcus aureus. We identified IL-1β and keratinocyte-dependent IL-1R-MyD88 signaling as necessary and sufficient for bacteria to promote regeneration. Finally, in a small clinical trial, we found that a topical broad-spectrum antibiotic slowed skin wound healing. These results counter conventional notions that infection inhibits regeneration and the need for full sterility of small wounds.

2021-04-01 | GSE158613 | GEO

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