Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR28810954_1.fastq.gz | Fastqsanger.gz | |||
| SRR28810954_2.fastq.gz | Fastqsanger.gz | |||
| SRR28810955_1.fastq.gz | Fastqsanger.gz | |||
| SRR28810955_2.fastq.gz | Fastqsanger.gz | |||
| SRR28810956_1.fastq.gz | Fastqsanger.gz |
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Project description:Neurons in posterior parietal cortex contribute to the execution of goal-directed navigation and other decision-making tasks. Although molecular studies have catalogued over fifty cortical cell types, it remains unknown what distinct functions they serve during goal-directed navigation. Here, we identified a molecularly defined subset of somatostatin (Sst) inhibitory neurons that, in mouse posterior parietal cortex, carry a novel cell type-specific error correction signal for navigation. We obtained repeatable experimental access to these cells using an adeno-associated virus (AAV) in which gene expression is driven by an enhancer that functions specifically in a subset of Sst cells. We found that during goal-directed navigation in a virtual environment, this subset of Sst neurons activates in a synchronous pattern that is distinct from the activity of surrounding neurons, including other Sst neurons. Using in vivo two-photon photostimulation and ex vivo paired patch clamp recordings, we show that nearby cells of this Sst subtype excite each other through gap junctions, revealing a self-excitation circuit motif that contributes to the synchronous activity of this cell type. Remarkably, these cells selectively activate as mice execute course corrections for deviations in their virtual heading during navigation toward a reward location, both for self- and experimentally-induced deviations. We propose that this subtype of Sst neurons provides a self-reinforcing and cell type-specific error-correction signal in posterior parietal cortex that may aid the execution and learning of accurate goal-directed navigation trajectories.
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Project description:The goal of this study was to assay the extent of variation in chromatin organization between 3 ant castes (major and minor female workers and males) in one colony of Camponotus floridanus carpenter ant using ChIPseq. 45 samples total: 30 ChIP samples and 3 inputs for total histone H3, 7 histone H3 PTMs and RNA Pol II in major, minor, and male ants; CBP in major and minor ants; the major H3K27ac sample was replicated. 4 ChIP samples for H3 and H3K27ac in brains of majors and minors, and 2 inputs. 2 RNAseq samples for major and minor ants head+thorax; 4 RNAseq samples for brain (majors and minors with 2 replicates each).
2012-11-26 | E-GEOD-37523 | biostudies-arrayexpress
Project description:Gene deserts spanning more than 500kb of non-protein coding genomic sequence are considered evolutionarily ancient and stable and are enriched in the vicinity of developmental regulator genes (Ovcharenko 2005). These extensive genomic regions typically harbor numerous conserved elements with predicted gene regulatory potential pointing to critical tissue-specific functions during development. Nevertheless, the biological necessity and underlying funtional enhancer landscapes of most gene deserts near developmental transcription factors (TFs) remain unknown, and it is unclear how precise pleiotropic expression patterns emerge from gene desert sequence. Here, we investigated the cis-regulatory architecture and function of a gene desert flanking the mouse Shox2 transcriptional regulator which itself is essential for embryonic limb, craniofacial, and cardiac pacemaker development. By combining epigenomic enhancer prediction, transgenic reporter validation and region-specific chromatin capture (C-HiC), we define the embryonic in vivo enhancer landscape and chromatin topology of the Shox2 gene desert. Targeted and context-specific genomic deletions uncover the gene desert not only as a regulator of embryonic survival through enhancer-mediated control of cardiac Shox2 expression, but also link distinct subsets of tissue-specific gene desert enhancers to the regulation of craniofacial patterning and proximal limb development. Our results hence identify the Shox2 gene desert as a fundamental genomic unit indispensable for pleiotropic patterning, robust organ morphogenesis and embryonic development progression by serving as a dynamic hub for tissue-specific developmental enhancers.
2024-06-01 | GSE232883 | GEO
Project description:Gene deserts spanning more than 500kb of non-protein coding genomic sequence are considered evolutionarily ancient and stable and are enriched in the vicinity of developmental regulator genes (Ovcharenko 2005). These extensive genomic regions typically harbor numerous conserved elements with predicted gene regulatory potential pointing to critical tissue-specific functions during development. Nevertheless, the biological necessity and underlying funtional enhancer landscapes of most gene deserts near developmental transcription factors (TFs) remain unknown, and it is unclear how precise pleiotropic expression patterns emerge from gene desert sequence. Here, we investigated the cis-regulatory architecture and function of a gene desert flanking the mouse Shox2 transcriptional regulator which itself is essential for embryonic limb, craniofacial, and cardiac pacemaker development. By combining epigenomic enhancer prediction, transgenic reporter validation and region-specific chromatin capture (C-HiC), we define the embryonic in vivo enhancer landscape and chromatin topology of the Shox2 gene desert. Targeted and context-specific genomic deletions uncover the gene desert not only as a regulator of embryonic survival through enhancer-mediated control of cardiac Shox2 expression, but also link distinct subsets of tissue-specific gene desert enhancers to the regulation of craniofacial patterning and proximal limb development. Our results hence identify the Shox2 gene desert as a fundamental genomic unit indispensable for pleiotropic patterning, robust organ morphogenesis and embryonic development progression by serving as a dynamic hub for tissue-specific developmental enhancers.
2024-06-01 | GSE232882 | GEO
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2012-11-26 | GSE37523 | GEO
Project description:The study evaluated the differential gene expression in control Antibody or Ant-CXCL10 antibody injected mouse when compared to EZH2 inhibitor GSK343 treated mice tumors Briefly, control Antibody or Ant-CXCL10 antibody injected C57BL/6 mouse were treated with or without GSK343were analyzed for RNA-seq
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Project description:We used whole-genome fire ant microarrays to examine the molecular basis for division of labor in fire ant workers by comparing foraging and non-foraging workers from monogyne colonies. Fire ant colonies were collected in the field and transported into the lab were they were reared in standard conditions. We created a nesting chamber containing the queen, the brood and workers performing nursing tasks and a foraging area, separated from the nesting chamber and provided with food and water sources. Foraging workers were collected in the foraging area while non-foraging workers were collected in the nesting chamber. Total RNA was isolated from pools of whole workers and processed for microarrays.
2014-01-08 | E-MTAB-2094 | biostudies-arrayexpress