MouseHypothalamusMoffitt2018: MERFISH mouse hypothalamus dataset from Moffitt et al., 2018

In ccb-hms/MerfishData: Collection of public MERFISH datasets

MERFISH mouse hypothalamus dataset from Moffitt et al., 2018

Description

Obtain the MERFISH mouse hypothalamic preoptic region dataset from Moffitt et al., 2018

Usage

MouseHypothalamusMoffitt2018(center.coords = TRUE)

Arguments

center.coords

logical. Should spatial x- and y-coordinates be centered for each z-layer (bregma slice)? This is useful for making coordinates comparable between bregma slices for visualization and analysis. Defaults to TRUE. Use FALSE to obtain the coordinates as provided in the data release.

Details

The hypothalamus controls essential social behaviors and homeostatic functions. However, the cellular architecture of hypothalamic nuclei, including the molecular identity, spatial organization, and function of distinct cell types, is not well understood.

Moffitt et al., 2018, developed an imaging-based cell type identification and mapping method and combined it with single-cell RNA-sequencing to create a molecularly annotated and spatially resolved cell atlas of the mouse hypothalamic preoptic region.

The MERFISH measurements were obtained via combinatorial smFISH imaging for 135 genes (main experiment named "smFISH"), followed by sequential rounds of non-combinatorial seqFISH for 20 additional genes (stored as an altExp named "seqFISH"). These genes were considered neuronal markers and important for discriminating neuronal cell populations. For behavioral measurements, cFos was added to the set of genes measured with sequential rounds of FISH.

The barcoding scheme contained 140 possible barcodes; 135 of them were used to code the RNAs of the genes assayed via combinatorial smFISH; 5 of these barcodes were left unassigned ("blank"), providing a direct measure of the false-positive rate in MERFISH. Measurements for these 5 blank barcodes is stored in an altExp named "blank".

Value

An object of class SpatialExperiment.

Source

https://doi.org/10.5061/dryad.8t8s248

References

Moffitt et al. (2018) Molecular, spatial, and functional single-cell profiling of the hypothalamic preoptic region. Science, 362(6416), eaau5324.

Examples

spe <- MouseHypothalamusMoffitt2018()

ccb-hms/MerfishData documentation built on June 30, 2024, 8:14 p.m.