Project description:Single-cell genomics encompasses a set of methods whereby hundreds to millions of cells are individually subjected to multiplexed assays including sequencing DNA, chromatin accessibility or modification, RNA, or combinations thereof 1,2. These methods enable unbiased, systematic discovery of cellular phenotypes and their dynamics 1–3. Many functional genomic methods, however, require multiple steps that cannot be easily scaled to high throughput, including assays on living cells. Here we develop capsules with amphiphilic gel envelopes (CAGEs), which selectively retain cells, mRNA, and gDNA, while allowing free diffusion of media, enzymes and reagents. CAGEs enable carrying out high-throughput assays that require multiple steps, including combining genomics with live-cell assays. We establish methods for barcoding CAGE DNA and RNA libraries, and apply them to measure persistence of gene expression programs by capturing the transcriptomes of tens of thousands of expanding clones in CAGEs. The compatibility of CAGEs with diverse enzymatic reactions will facilitate the expansion of the current repertoire of single-cell, high-throughput measurements and extend them to live-cell assays.
Project description:Male C57BL/6J mice were housed in cages and maintained on a 12-hour light-dark cycle. STD (NMF; Oriental Yeast) and HFHS chow (D12331; Research Diet, New Brunswick, NJ) were used, the mice were sacrificed at 20 weeks of age.
Project description:We aimed to address the challenge of accommodating an increasing demand for aged laboratory animals in the context of rising elderly population and research on aging-related diseases. We developed a cost-effective environmental enrichment method and assessed its impact on metabolic changes in Sprague Dawley rats' livers as a proof-of-concept organ. Twenty-four male rats were divided into four groups, with two kept in standard cages and two in modified rabbit cages. Half of each type of cage group received additional enrichment through weekly playtime in a larger cage. Over six months, the rats' weight gain was consistent across all groups, and corticosterone levels did not significantly differ. However, the control group had significantly lower DHEA and Testosterone levels at the study's end. Rats in enriched environments exhibited less distress during inspections and were more resistant to accepting treats. Animals accustomed to playpen time left their cages more easily. Overall, the study demonstrated that refining husbandry for aging rats is both simple and cost-effective, without detrimental effects on stress levels, development, or liver metabolism.
2024-01-22 | PXD046110 | Pride
Project description:Hypothalamic transcriptome of bird raised in different-sized cages
| PRJNA1184358 | ENA
Project description:Separating the grouped middle-aged monkeys to single cages
Project description:Wildtype Swiss webster mice were exposed to four weeks of either standard housing (SH) or environmental enrichment (EE) starting at one month of age. EE chambers were large mouse cages containing two nesting/burrowing materials, a running wheel, and toys that were changed every 3-4 days for novelty and exploration. By contrast, SH control mice were housed with an equal number of littermates in smaller, standard cages containing only one nesting material and no toys or running wheel. We used an antibody for Rbfox3 (NeuN) to sort neuronal nuclei from the dissociated frontal cortices of male mice reared in EE and SH conditions. Isolated neuronal nuclei were then subjected to ATAC-seq or nuclear RNA isolation (random hexamer priming) as per published protocols.