GEO DataSets

(Submitter supplied) We develop So-Smart-seq to interrogate a comprehensive transcriptome inclusive of coding, noncoding, and repetitive element transcription. We reveal that, surprisingly, de novo silencing pertains only to a subset of paternal X (Xp) genes. In contrast, a set of evolutionarily older genes and LINEs demonstrate constitutive Xp silencing, adopt epigenetically distinct signatures, and do not require Xist to initiate silencing. more...

Organism:

Mus musculus castaneus; Mus musculus

Type:

Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing; Other

Platforms:

GPL33198 GPL33196 GPL33197

235 Samples

Download data: TAR, TXT

(Submitter supplied) The mammalian genome is constantly exposed to genotoxins that can lead to mutations and ultimately tumorigenesis. Despite cancer being recognized as a genetic disease, much is still unknown regarding tumor induction and evolution of the cancer genome. To study gradual (reactive oxygen species, ROS) and acute (ultraviolet radiation, UV) mutagenic processes both in vitro and then in vivo, we first use microfluidic separation of cells after a single mitosis following pulse mutagenesis. more...

Organism:

Mus musculus; Mus musculus castaneus

Type:

Other; Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platforms:

GPL30172 GPL24247 GPL33115

32 Samples

Download data: RDS

(Submitter supplied) The laboratory mouse (Mus musculus domesticus) has long been used in biomedical research due to its easy maintenance and availability of abundant genetic information. However, laboratory mice have an inherent disadvantage of low genetic diversity caused by their origin from a relatively small colony of “fancy mice” in western Europe. Recently captured wild mice (wild-derived mice) are expected to compensate for this shortcoming because of their greater genetic diversity. more...

Organism:

Mus musculus domesticus; Mus musculus castaneus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL29744 GPL33115

13 Samples

Download data: XLSX

(Submitter supplied) Recent advances in transcriptome sequencing have enabled the discovery of thousands of long non-coding RNAs (lncRNAs) across many species. Though several lncRNAs have been shown to play important roles in diverse biological processes, the functions and mechanisms of most lncRNAs remain unknown. Two significant obstacles lie between transcriptome sequencing and functional characterization of lncRNAs: identifying truly non-coding genes from de novo reconstructed transcriptomes, and prioritizing the hundreds of resulting putative lncRNAs for downstream experimental interrogation. more...

Organism:

Homo sapiens; Mus musculus castaneus; Rattus norvegicus; Mus musculus

Type:

Expression profiling by high throughput sequencing

4 related Platforms

9 Samples

Download data: TXT, WIG

(Submitter supplied) We studied the evolution of alternative splicing in the early stages of species divergence in the house mouse.

Organism:

Mus musculus castaneus; Mus spretus; Mus musculus domesticus; Mus musculus musculus

Type:

Expression profiling by high throughput sequencing

4 related Platforms

7 Samples

Download data: SAM

(Submitter supplied) We have studied different subspecies of the house mouse (M. m. musculus, M. m. domesticus and M. m. castaneus) and their reciprocal F1 hybrids to estimate the within-locus mode of inheritance for subspecies differences in gene expression in three tissues (brain, liver, testis) of male mice. This study investigates mode of inheritance in crosses at a larger taxonomic distance than have been previously systematically investigated. more...

Organism:

Mus musculus castaneus; Mus musculus; Mus musculus musculus x M. m. domesticus; Mus musculus musculus x Mus musculus castaneus; Mus musculus domesticus; Mus musculus musculus

Type:

Expression profiling by array

Platform:

GPL1261

42 Samples

Download data: CEL