Mus musculus
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA275943 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR1811710_1.fastq.gz | Fastqsanger.gz | |||
| SRR1811710_2.fastq.gz | Fastqsanger.gz | |||
| SRR1811711_1.fastq.gz | Fastqsanger.gz | |||
| SRR1811711_2.fastq.gz | Fastqsanger.gz | |||
| SRR1811712_1.fastq.gz | Fastqsanger.gz |
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Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived yolk sac transcriptome profiling (RNA-seq) of E16.5 Rsu1-/- mouse embryos to that of the wild-type controls Methods: Yolk sac mRNA profiles of yolk sac isolated from E16.5 wild-type (WT) and ras suppressor 1 (Rsu1−/−) emdbryos were generated by deep sequencing, in triplicate, using Illumina Hiseq 2500 platform. The sequence reads that passed quality filters were were mapped to human reference genome GRCh38 by HISAT2 v2.2.1 with default parameters. Results: Using an optimized data analysis workflow, we mapped about 40 million sequence reads per sample to the mouse genome and identified ___ transcripts in the yolk sacs of E16.5 WT and Rsu1−/− embryos with HISAT2 v2.2.1 workflow . Approximately __ % of the transcripts showed differential expression between the WT and Rsu1−/− yolk sac, with a fold change ≥2.0 and p value <0.05. Altered expression of 12 genes was confirmed with qRT–PCR, demonstrating the high degree of sensitivity of the RNA-seq method. Conclusions: Our study represents the first detailed analysis of E16.5 Rsu1-/- yolk sac transcriptomes, which would expedite genetic network analyses and permit the dissection of complex biologic functions of Rsu1 during late embryogenesis.
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Project description:Comparison of gene expression between wild type, Notch1-activated, and RBPJ loss-of-function embryonic mouse yolk sac tissue at E9.5
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Project description:Tissue-resident macrophages can derive from yolk sac macrophages, fetal liver monocytes or adult bone marrow monocytes. Whether these precursors can give rise to transcriptionally identical alveolar macrophages is unknown. Here, we transferred traceable yolk sac macrophages, fetal liver monocytes, adult bone marrow monocytes or adult alveolar macrophages as a control, into the empty alveolar macrophage niche of neonatal Csf2rb-/- mice. All precursors efficiently colonized the alveolar niche and generated alveolar macrophages that were transcriptionally almost identical, with only 22 genes that could be linked to their origin. Underlining the physiological relevance of our findings, all transfer-derived alveolar macrophages self-maintained within the lungs for up to 1 year and durably prevented alveolar proteinosis. Thus, precursor origin does not affect the development of functional self-maintaining tissue-resident macrophages. CD45.1+CD45.2+ yolk sac macrophages, fetal liver monocytes, adult bone marrow monocytes or adult alveolar macrophages from the bronchoalveolar lavage were sorted from wild type CD45.1+CD45.2+ mice of indicated ages. From part of these samples RNA was isolated. The other part was transferred intranasally into the lungs of neonate Csf2rb-/- mice. 6 weeks post-transfer, transfer-derived CD45.1+CD45.2+ alveolar macrophages were sorted from the bronchoalveolar lavage. Wild type CD45.1+CD45.2 alveolar macrophages from the bronchoalveolar lavage of 6 week old mice were sorted as control. 36 samples (arrays) in total. RNA was isolated, amplified with Nugene pico kit, converted to cDNA and then hybridised on Affymetrix GeneChip Mouse Gene 1.0 ST Arrays.
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