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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.

ABSTRACT: 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.

PROVIDER: PRJEB37203 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR3987190.fastq.gz	Fastqsanger.gz
	ERR3987191.fastq.gz	Fastqsanger.gz
	ERR3987192.fastq.gz	Fastqsanger.gz
	ERR3987184.fastq.gz	Fastqsanger.gz
	ERR3987185.fastq.gz	Fastqsanger.gz

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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

RNA sequencing of primary isolated unstimulated murine splenic DC1 and DC2 from specific pathogen free (SPF), Germ free (GF) and Interferon alpha/beta receptor 1 (Ifnar) knock out mice

Project description:The transcriptomes of primary isolated unstimulated murine splenic cDC1 and cDC2 from specific pathogen free (SPF) were compared to cDC1 and cDC2 from Germ Free (GF) and Interferon alpha/beta receptor 1 (Ifnar) knock out mice. Total RNA was prepared from sort-purified cDC1 and cDC2 (for each sample 3 individual mice were pooled) using Trizol reagent (Invitrogen) in combination with the miRNeasy Micro Kit (Qiagen) according to the manufacturer’s instructions. For poly-A-dependent cDNA synthesis and a first amplification step 10 ng of total RNA was used as input in the Smart-Seq v4 mRNA Ultra Low Input RNA Kit (Clontech) and processed according to the manufacturer’s instructions. 1 ng of the purified cDNA was used for tagmentation and library completion with the Nextera XT library preparation kit (Illumina). In the following, 2x75nt paired-end sequencing was performed on a NextSeq 500.

2020-03-30 | E-MTAB-8883 | biostudies-arrayexpress

RNA sequencing of primary isolated unstimulated murine splenic DC1 and DC2 from specific pathogen free (SPF), Germ free (GF) and Interferon alpha/beta receptor 1 (Ifnar) knock out mice

Project description:RNA sequencing of primary isolated unstimulated murine splenic DC1 and DC2 from specific pathogen free (SPF), Germ free (GF) and Interferon alpha/beta receptor 1 (Ifnar) knock out mice

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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.

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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.

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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)

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2018-06-30 | E-MTAB-5190 | biostudies-arrayexpress

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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.

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