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Sample GSM5820588 Query DataSets for GSM5820588
Status Public on Apr 26, 2022
Title MERFISH_9
Sample type RNA
 
Source name P14_MERFISH_S1_cortex
Organism Mus musculus
Characteristics genotype: Cx3cr1 GFP tg/+
tissue: S1 cortex
strain: C57Bl/6
age: P14
Treatment protocol Cx3cr1-GFP heterozgous mice were used to genetically label microglia. Genotypes were obtained through standard breeding.
Growth protocol Standard mouse housing conditions
Extracted molecule total RNA
Extraction protocol Brains were flash frozen in LN, then mounted in OCT. 10 micron-thick sections were mounted on pre-treated coverslips, fixed with 4% PFA, washed with PBS, then stored in ethanol. Coverslips were then processed via manufacturer's protocol.
Label n/a
Label protocol https://vizgen.com/technology/#merfish
 
Hybridization protocol not applicable
Scan protocol not applicable
Description Transcripts were selected for their specificity to cell types, or enrichment for microglia states.
Data processing Encoded MERFISH images of RNA spots were de-multiplexed using MERlin https://github.com/emanuega/MERlin), using the codebook provided by Vizgen. This pipeline outputs a table with the coordinates and identity of all detected transcripts. Decoded data were used to generate binary mosaics of the tissue in which transcripts represented a single pixel. Microglia were segmented using methods similar to those described by Favuzzi et al. Images of binary DAPI-identified nuclei were used to segment all other cell types. Counts tables were produced by summing the number of each transcript inside the area of segmented cells (Mg and DAPI-identified nuclei). Mg- and DAPI-segmentation counts were combined by concatenating their respective counts tables.
 
Submission date Jan 15, 2022
Last update date Sep 13, 2023
Contact name Paola Arlotta
E-mail(s) paola_arlotta@harvard.edu
Organization name Harvard University
Department Stem Cell and Regenerative Biology
Lab Arlotta
Street address 7 Divinity Ave
City Cambridge
State/province MA
ZIP/Postal code 02138
Country USA
 
Platform ID GPL31217
Series (1)
GSE193760 Pyramidal neuron subtype diversity governs microglia states in the neocortex [MERFISH]

Supplementary data files not provided
Processed data are available on Series record

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