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Sample GSM7779548 Query DataSets for GSM7779548
Status Public on May 14, 2024
Title Animal 3, section 1, MERFISH
Sample type other
Source name brain cells
Organism Mus musculus
Characteristics tissue: Brain
strain: C57BL/6J, 5xFAD
age: 9.5 months
Treatment protocol Male 5xFAD and litter-mate mice at 9.5 months old were anesthetized using an Isoflurane chamber and filmcontainer filled with Isoflurane-soaked cotton fibers and perfused with RNase-free PBS (Sigma, D8537). Next, the brains were carefully extracted, cut in half and and frozen in isopentane on dry ice. The brains were then stored at −80 °C until further processing.
Extracted molecule other
Extraction protocol Brain sections, 10 μm in thickness, were cut coronally using a cryotome (CryoStar NX70, Thermo Scientific) and collected onto glass slides supplied by Vizgen Corp. (Cambridge, MA 02138; MERSCOPE slide part number 20400001). To ensure proper adhesion, the glass slides were coated with a solution of 0.1 mg/mL poly-D-lysine bromide (Sigma, P7886) and left to incubate at room temperature for 1 hour and dried before starting the sectioning.
MERFISH sample preparation was performed according to manufacturer's protocol (
Label n.a.
Label protocol n.a.
Hybridization protocol n.a.
Scan protocol n.a.
Description panel of 496 genes was measured by MERFISH
Data processing Brain sections were measured by MERFISH according to the manufacturer's protocol (
Encoded MERFISH images were processed according to manufacturer's pipeline ( The output of this pipeline are spatial positions of individual transcripts and segmented single cells based on DAPI and poly-A stainings. Single cell expression tables are produced by counting individual transcripts within segmented cell boundaries.
Submission date Sep 13, 2023
Last update date May 14, 2024
Contact name Peter Androvic
Organization name LMU Hospital, Institute for Stroke and Dementia Research
Lab Gokce Lab
Street address Feodor-Lynen-Strasse 17
City Munich
State/province Bavaria
ZIP/Postal code 81377
Country Germany
Platform ID GPL31217
Series (1)
GSE243120 T cell mediated microglia activation triggers myelin pathology in a model of amyloidosis [MERFISH]

Supplementary file Size Download File type/resource
GSM7779548_AD_3_1_cell_by_gene.csv.gz 8.4 Mb (ftp)(http) CSV
GSM7779548_AD_3_1_metadata.csv.gz 11.8 Mb (ftp)(http) CSV
GSM7779548_AD_3_1_transcripts.csv.gz 903.5 Mb (ftp)(http) CSV

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