Dataset Information

Differential gene expression of cells located in the top and bottom of yeast colonies

ABSTRACT: Saccharomyces cerevisiae colonies were grown on synthetic minimal media containing 1% glucose. The top layer of cells was scraped off using a custom plastic guide and a cell scraper. The remaining bottom layer of cells was then washed off with water and proteomics samples were prepared from both layers separately. Label-free quantification by DIA-SWATH was used to assess differences in gene expression between top and bottom layers.

INSTRUMENT(S): TripleTOF 6600

ORGANISM(S): Saccharomyces Cerevisiae (baker's Yeast)

SUBMITTER: Stephan Kamrad

LAB HEAD: Markus Ralser

PROVIDER: PXD033395 | Pride | 2023-02-13

REPOSITORIES: Pride

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Source:

			Action	DRS
	20210225_yeastspeclib.tsv.speclib	Tabular
	20210602_colony_12C_TvB_SM_bot_r1.wiff	Wiff
	20210602_colony_12C_TvB_SM_bot_r1.wiff.scan	Wiff
	20210602_colony_12C_TvB_SM_bot_r2.wiff	Wiff
	20210602_colony_12C_TvB_SM_bot_r2.wiff.scan	Wiff

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Project description:Unified visual perception relies on the integration of bottom-up and top-down inputs in the primary visual cortex (V1), with top-down inputs known to provide behavior-related modulation on visual processing. However, the organization of top-down inputs in V1 remains unclear. Here, using optogenetics-assisted circuit mapping, we characterized how multiple top-down inputs from higher-order cortical and thalamic areas engage excitatory and inhibitory neurons in V1. Systematic layer- and cell-type-specific profiling of the innervation properties of top-down inputs ultimately revealed that each top-down input employs a unique laminar profile when innervating V1. These profiles partially overlap in superficial layers, bypass layer 4 (L4), and clearly segregate upon reaching deep layers. Specifically, inputs from the medial secondary visual cortex (V2M) and anterior cingulate cortex (ACA) preferentially activate L6 neurons, while inputs from the ventrolateral orbitofrontal cortex (ORBvl) and lateral posterior thalamic nucleus (LP) activate L5 neurons. Having defined the inputs, we conducted independent optogenetic activation studies and discovered that ORBvl and LP inputs selectively activate two types of pyramidal neurons (Pyrs) in L5: Pyr <-- ORBvl and Pyr <-- LP neurons, each with specific electrophysiological properties and gene expression profiles. Retrograde mapping subsequently revealed that Pyr <-- ORBvl neurons preferentially innervate subcortical areas and Pyr <-- LP neurons innervate cortical areas, indicating parallel processing of ORBvl and LP inputs in Pyr-type-specific subnetworks. Further, we found mutual inhibition between these two subnetworks, as LP inputs indirectly inhibit Pyr <-- ORBvl neurons and ORBvl inputs inhibit Pyr <-- LP neurons through local inhibitory neurons. Our study thus deepens understanding of the neuronal mechanisms involved in top-down modulation of visual processing by providing a valuable resource characterizing the layer- and cell-type-specific organization of top-down inputs in V1 and by revealing that L5 Pyr-type-specific subnetworks engage in parallel processing of corticocortical and thalamocortical top-down inputs.

Dataset Information

Differential gene expression of cells located in the top and bottom of yeast colonies

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