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

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

PROVIDER: PRJNA421946 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR6366220_1.fastq.gz	Fastqsanger.gz
	SRR6366220_2.fastq.gz	Fastqsanger.gz
	SRR6366230_1.fastq.gz	Fastqsanger.gz
	SRR6366230_2.fastq.gz	Fastqsanger.gz
	SRR6366240_1.fastq.gz	Fastqsanger.gz

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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.

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

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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

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

Transcription profiling of Strongyloides ratti free-living males and females and parastic and free-living females

Project description:This experiment exploits the life-cycle of Strongyloides ratti, which is a parasitic nematode of brown rats that exhibits three adult stages within its life-cycle - parasitic females, freeliving females and free-living males. We use a cDNA microarray to examine patterns of (i) gender-biased gene expression by contrasting free-living females against free-living males, and (ii) parasitic-biased expression by contrasting parasitic females against free-living females. Of the 3688 distinct transcripts represented on our array, 20% exhibited male-biased expression 19% exhibit female-biased expression, 11% exhibit parasitic-biased expression and 8% exhibit free-living-biased expression. Among the top responding genes, an orthologue of major sperm protein is upregulated in males, distinct aspartic protease orthologues are upregulated in either parasitic or in free-living females, and orthologues of hsp-17 chaperone are upregulated in parasitic females. Upon a global analysis of gene expression, we find that female-biased expression is associated with genes involved in reproductive processes and larval development, that male-biased expression is associated with genes involved in metabolism, and that free-living biased expression is associated with genes involved in regulation of body fluids and response to external stimulus. The association of gene ontology with parasite-biased expression is less clear. Our results provide an initial gene expression analysis of gender- and parasite-biased expression in S. ratti, may be more generally applicable to other parasitic nematodes, and may help to refine the search for novel drug or vaccine targets against parasitic nematodes.

2008-01-17 | E-MAXD-37 | biostudies-arrayexpress

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

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

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Gender bias in autoimmunity is influenced by microbiota

Project description:Gender bias and the role of sex hormones in autoimmune diseases are well established. In specific-pathogen free (SPF) non-obese diabetic (NOD) mice females have 1.3-4.4 times higher incidence of Type 1 diabetes (T1D). Germ-free (GF) mice lose the gender bias (female/male ratio 1.1-1.2). Gut microbiota differed in males and females, a trend reversed by male castration, confirming that androgens influence gut microbiota. Colonization of GF NOD mice with defined microbiota revealed that some but not all lineages overrepresented in male mice supported a gender bias in T1D, and protection did not correlate with androgen levels. However, hormone-supported selective microbial lineage variation may work as a positive feedback mechanism contributing to the sexual dimorphism of autoimmune diseases. Gene expression analysis suggested pathways involved in protection of males from T1D by microbiota. We compared gene expression patterns in the pancreatic lymph nodes (PLNs) between four groups of mice (two genders in SPF and GF conditions, respectively). PLNs were isolated from 9-10 week old GF and SPF male and female NOD mice with 3 mice in each group, for a total of 12 samples.

2013-08-02 | E-GEOD-49467 | biostudies-arrayexpress

RNA-seq from the liver, ileum, muscle, fat of SPF or GF mice on ND, WD

Project description:RNA seq from the liver, ileum, muscle, fat of SPF or GF mice on ND, WD. "Microbiota and adipocyte mitochondrial damage in type 2 diabetes are linked by Mmp12+ macrophages"

2022-05-13 | GSE145052 | GEO

RNAseq identifies distinct gene expression profiles in gBT-I isolated from SPF and GF animals.

Project description:Purpose: The aim of this study is to disentangle if microbiota influences the transcriptome of antigen-activated CD8+ T cells. Methods: gBT-I mRNA profiles from SPF and GF mice were generated by deep sequencing, in duplicates, using Illumina GAIIx. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. Results: The analysis of RNAseq data of gBT-I from SPF and GF mice lead to 371 differentially expressed genes (FDR < 0.05; fold change >2). GSEA enrichment analysis revealed depletion of memory T cells signatures in gBT-I from GF mice (Sarkar et al., 2008), and underrepresentation of OXPHOS-related genes. Conclusions: Our data shows that microbiota has an impact on the transcriptome of effector CD8+ T cells, in particular their memory and metabolism signature.

2019-06-07 | GSE132284 | GEO

RNA sequencing of primary isolated unstimulated murine splenic cDC from specific pathogen free (SPF), Germ Free (GF) and Interferon alpha/beta receptor 1 (Ifnar) knock out mice.

Project description:The transcriptome of primary isolated unstimulated murine splenic cDC from specific pathogen free (SPF) was compared to cDC from Germ Free (GF) and Interferon alpha/beta receptor 1 (Ifnar) knock out mice. Cells were isolated and sorted by flow cytometry to high purity. Total RNA was isolated using the RNeasy plus micro kit (Qiagen). Barcoded mRNA seq libraries were prepared from 100 ng of total RNA (RIN>8) using a NEBnext poly(A) mRNA Magnetic Isolation Module and NEBnext UltraII lib prep kit for Illumina (New England Biosciences) according to the manual. Single-end RNA sequencing (59nt) was performed on a HiSeq 2500 (Illumina). Barcoded RNA-seq libraries were onboard clustered using HiSeq® Rapid SR Cluster Kit v2 using 8pM and 59bps were sequenced on the Illumina HiSeq 2500 using HiSeq Rapid SBS Kit v2 (59 Cycle). The raw output data of the HiSeq was preprocessed according to the Illumina standard protocol.

2020-03-30 | E-MTAB-8882 | biostudies-arrayexpress

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