|
| 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 (https://vizgen.com/resources/fresh-and-fixed-frozen-tissue-sample-preparation)
|
| Label |
n.a.
|
| Label protocol |
n.a.
|
| |
|
| Hybridization protocol |
n.a.
|
| Scan protocol |
n.a.
|
| Description |
panel of 496 genes was measured by MERFISH
MERFISH_5xFAD_expression.txt
MERFISH_5xFAD_metadata.txt
|
| Data processing |
Brain sections were measured by MERFISH according to the manufacturer's protocol (https://vizgen.com/technology/#merfish)
Encoded MERFISH images were processed according to manufacturer's pipeline (https://vizgen.com/technology/#merfish). 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] |
|
