Mus musculus
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1023938 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:NCBI-generated Human raw gene counts from SRA RNA-seq data
| PRJNA1023937 | ENA
Project description:In order to test the global effects of CpG island-centered gene regulation on global gene expression profile, pA+ RNA-seq data of diverse tissues and cell lines were gathered and profiled. All available mouse poly-A positive RNA-seq data (3,818 samples) were summarized and downloaded at May, 5th, 2015. Among them, excluding single cell RNA-seq or experiments whose expression verified gene counts are small (less than 5,000 genes with RPKM 0.5 or higher), 1,524 high quality RNA-seq data were used. Raw data were downloaded from Sequence Read Archive (SRA) in National Center for Biotechnology Information (NCBI) database. FASTQ files were extracted with the SRA Toolkit version 2.5.5 and aligned using STAR 2.4.2 onto the mouse and human genome (mm9 and hg19, respectively). Gene expression was calculated as RPKM values using rpkmforgenes.py (Ramsköld et al., 2009).
2018-02-15 | GSE80797 | GEO
Project description:We reanalyzed published RNA-seq data to study 1) the genomic landscapes near surrounding regions of transcriptional start sites with regard to the gene expression activities and 2) the gene expression change upon transcription factor (MYBL1, ATF4) depletion. Raw data were downloaded from Sequence Read Archive (SRA) in National Center for Biotechnology Information (NCBI) database. FASTQ files were extracted with the SRA Toolkit version 2.5.5 and aligned using STAR 2.4.2 onto the mouse and human genome (mm9 and hg19, respectively). Gene expression was calculated as RPKM values using rpkmforgenes.py (Ramsköld et al., 2009).
2018-02-15 | GSE80793 | GEO
Project description:In order to elucidate the general rules for gene localization and regulation mediated by CpG islands, we reanalyzed published ChIP-seq data of CXXC domain, H3K9me3, KDM2A, SUV39H1, ATF4, MYBL1, MYOD1, SPI1, and CTCF. Raw data were downloaded from Sequence Read Archive (SRA) in National Center for Biotechnology Information (NCBI) database. FASTQ files were extracted with the SRA Toolkit version 2.5.5 and aligned using Bowtie 2.2.5 onto the mouse and human genome (mm9 and hg19, respectively). For the identification of factor binding sites, model-based analysis for ChIP-seq peak caller (MACS 1.4.2) was used with a p-value cutoff of 1e-5.
2018-02-15 | GSE80791 | GEO
Project description: Not available
| S-EPMC8784167 | biostudies-literature
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
2004-01-02 | GSE887 | GEO
Project description:Raw 16S rRNA gene sequencing data generated from mouse fecal samples
| PRJNA1405360 | ENA
Project description:Single-nucleus RNA sequencing (snRNA-seq) was used to profile the transcriptome of 5,264 nuclei in mouse adult testis. This dataset includes two samples from two different individuals. This dataset is part of a larger evolutionary study of adult testis at the single-nucleus level (97,521 single-nuclei in total) across mammals including 10 representatives of the three main mammalian lineages: human, chimpanzee, bonobo, gorilla, gibbon, rhesus macaque, marmoset, mouse (placental mammals); grey short-tailed opossum (marsupials); and platypus (egg-laying monotremes). Corresponding data were generated for a bird (red junglefowl, the progenitor of domestic chicken), to be used as an evolutionary outgroup.
2021-11-08 | E-MTAB-11071 | biostudies-arrayexpress
Project description: Not available
| S-EPMC11335981 | biostudies-literature
Project description:We collected whole genome testis expression data from hybrid zone mice. We integrated GWAS mapping of testis expression traits and low testis weight to gain insight into the genetic basis of hybrid male sterility.
2014-12-04 | GSE61417 | GEO