Mus musculus
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA295013 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR2295930.fastq.gz | Fastqsanger.gz | |||
| SRR2295931.fastq.gz | Fastqsanger.gz | |||
| SRR2295926.fastq.gz | Fastqsanger.gz | |||
| SRR2295927.fastq.gz | Fastqsanger.gz | |||
| SRR2295928.fastq.gz | Fastqsanger.gz |
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Project description:Aim: Transcriptional analysis of the duodenum of adult Nkx2.2flox/TN;Villin-Cre (TNint) mice versus control Methods: 2 cm of the duodenum (as measured from the stomach) of 6 week old control and mutant mice were dissected and total RNA extracted. Libraries were prepared from total RNA (RIN>8) with the TruSeq RNA prep kit (Illumina) and sequenced using the HiSeq2000 (Illumina) instrument. More than 20 million reads were mapped to the mouse genome (UCSC/mm9) using Tophat (version 2.0.4) with 4 mismatches and 10 maximum multiple hits. Significantly differentially expressed genes were calculated using DEseq. Results: 299 genes with a p-value <0.05 were significantly changed. Among these are some enteroendocrine hormones. Conclusion: The TN domain of Nkx2.2 regulates specification of some enteroendocrine cells mRNA profiles of the duodenum of 6 week old control and TNint mice were generated by deep sequencing, in triplicate, using Illumina HiSeq2000.
2016-07-28 | E-GEOD-72764 | biostudies-arrayexpress
Project description:Aim: Transcriptional analysis of the duodenum of adult Nkx2.2flox/TN;Villin-Cre (TNint) mice versus control Methods: 2 cm of the duodenum (as measured from the stomach) of 6 week old control and mutant mice were dissected and total RNA extracted. Libraries were prepared from total RNA (RIN>8) with the TruSeq RNA prep kit (Illumina) and sequenced using the HiSeq2000 (Illumina) instrument. More than 20 million reads were mapped to the mouse genome (UCSC/mm9) using Tophat (version 2.0.4) with 4 mismatches and 10 maximum multiple hits. Significantly differentially expressed genes were calculated using DEseq. Results: 299 genes with a p-value <0.05 were significantly changed. Among these are some enteroendocrine hormones. Conclusion: The TN domain of Nkx2.2 regulates specification of some enteroendocrine cells
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Project description:Unpublished single cell RNAseq data from pan-GI integration study from healthy adult donors (20-70 years old; stomach, duodenum, ileum) and control samples from preterm infants (23-31 PCW; small intestine and colon). Details for sample processing can be found in the manuscript.
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Project description:Introgressed variants from other species can be an important source of genetic variation because they may arise rapidly, can include multiple mutations on a single haplotype, and have often been pretested by selection in the species of origin. Although introgressed alleles are generally deleterious, several studies have reported introgression as the source of adaptive alleles-including the rodenticide-resistant variant of Vkorc1 that introgressed from Mus spretus into European populations of Mus musculus domesticus. Here, we conducted bidirectional genome scans to characterize introgressed regions into one wild population of M. spretus from Spain and three wild populations of M. m. domesticus from France, Germany, and Iran. Despite the fact that these species show considerable intrinsic postzygotic reproductive isolation, introgression was observed in all individuals, including in the M. musculus reference genome (GRCm38). Mus spretus individuals had a greater proportion of introgression compared with M. m. domesticus, and within M. m. domesticus, the proportion of introgression decreased with geographic distance from the area of sympatry. Introgression was observed on all autosomes for both species, but not on the X-chromosome in M. m. domesticus, consistent with known X-linked hybrid sterility and inviability genes that have been mapped to the M. spretus X-chromosome. Tract lengths were generally short with a few outliers of up to 2.7 Mb. Interestingly, the longest introgressed tracts were in olfactory receptor regions, and introgressed tracts were significantly enriched for olfactory receptor genes in both species, suggesting that introgression may be a source of functional novelty even between species with high barriers to gene flow.
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Project description:PURPOSE: To provide a detailed gene expression profile of the normal postnatal mouse cornea. METHODS: Serial analysis of gene expression (SAGE) was performed on postnatal day (PN)9 and adult mouse (6 week) total corneas. The expression of selected genes was analyzed by in situ hybridization. RESULTS: A total of 64,272 PN9 and 62,206 adult tags were sequenced. Mouse corneal transcriptomes are composed of at least 19,544 and 18,509 unique mRNAs, respectively. One third of the unique tags were expressed at both stages, whereas a third was identified exclusively in PN9 or adult corneas. Three hundred thirty-four PN9 and 339 adult tags were enriched more than fivefold over other published nonocular libraries. Abundant transcripts were associated with metabolic functions, redox activities, and barrier integrity. Three members of the Ly-6/uPAR family whose functions are unknown in the cornea constitute more than 1% of the total mRNA. Aquaporin 5, epithelial membrane protein and glutathione-S-transferase (GST) omega-1, and GST alpha-4 mRNAs were preferentially expressed in distinct corneal epithelial layers, providing new markers for stratification. More than 200 tags were differentially expressed, of which 25 mediate transcription. CONCLUSIONS: In addition to providing a detailed profile of expressed genes in the PN9 and mature mouse cornea, the present SAGE data demonstrate dynamic changes in gene expression after eye opening and provide new probes for exploring corneal epithelial cell stratification, development, and function and for exploring the intricate relationship between programmed and environmentally induced gene expression in the cornea. Keywords: other
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Project description:The goal of this study was to compare global RNA expression data obtained from: i) duodenal organoids cultured in conventional plastic-adherent Matrigel drop overlaid with growth medium; ii) Duodenum Intestine-Chips derived from organoids in the presence of constant flow and stretch; iii) human adult duodenum tissue and to verify whether Duodenum Intestine-Chip faithfully recapitulates human adult duodenum tissue and to better understand how much it differs from the organoids from which it’s derived.
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