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Sample GSM6125919 Query DataSets for GSM6125919
Status Public on Jun 21, 2023
Title replicate 1, MERFISH
Sample type RNA
 
Source name MERFISH
Organism Mus musculus
Characteristics cell type: brain cells
tissue: Brain
strain: C57BL/6J
age: 18 weeks
molecule: other
instrument model: Vizgen
Treatment protocol Lysophosphatidylcholine (LPC) injections were administered at the age of 16-18 weeks. A solution of 1% LPC (L4129, Sigma) in PBS was mixed with Monastral blue (274011, SigmaAldrich) at a concentration of 0.03% to aid with visualization of the lesion during tissue processing. Mice were anaesthetized with an intraperitoneal injection of MMF solution (0.5 mg medetomidin/kg (body weight), 5.0 mg midazolam/kg (body weight) and 0.05 mg fentanyl/kg (body weight)). Then, head fur was removed, the eyes were treated with bepanthene cream (1578847, Bayer) and a small incision in the skin was performed to expose the skull. The mouse was positioned into a stereotactic injection apparatus and a small hole was drilled at the following injection coordinates (from bregma): X, ± 1.0 mm; Y, −0.1 mm). A glass capillary containing the LPC–monastral blue solution was then lowered to Z: −1.30 mm from bregma, and 1 µL was injected at a rate of 100 nL/minute. Two minutes after the delivery of LPC, the capillary was slowly retracted. The mouse was then injected with 0.05 mg buprenorphin/kg (body weight), and the skin was sutured. Anesthesia was terminated by a subcutaneous injection of AFN solution, containing 2.5 mg/kg (body weight) atipamezol, 1.2 mg/kg (body weight) naloxon and 0.5 mg/kg (body weight) flumazenil.
Extracted molecule total RNA
Extraction protocol 18 days after LPC injection, mice were anaesthetized with an i.p. injection of MMF (fentanyl (0.05 mg/kg)–midazolam (5 mg/kg)–medetomidine (1 mg/kg)) and transcardially perfused with 2 UI/mL Heparin (Heparin-Natrium-25000-ratiopharm®, PZN: 03029843) in HBSS (no calcium, no magnesium, Gibco™, 14175129) for 3 min and 4 % paraformaldehyde (PFA, EM Grade, Electron Microscopy Sciences, Cat. No. 15710, diluted in 10X PBS, Invitrogen™, AM9624 and UltraPure™ Distilled Water, Invitrogen™, 10977-035) for 5 min, before carefully removing the brain from the skull. Afterwards, the brains were fixed by submergingin 4% PFA for 6 hours, followed by 14 hours in 15% sucrose (Sigma-Aldrich, S0389 in UltraPure™ Distilled Water, Invitrogen™, 10977-035) and 5 hours in 30% sucrose. Next, the PFA-fixed brains were simultaneously embedded in Tissue-Tek® O.C.T.™ Compound (Sakura, 4583) and frozen in a plastic mold on dry ice. For the fresh frozen brain samples, the mouse was only perfused with Heparin in HBSS and directly embedded and frozen in Tissue-Tek® O.C.T.™ Compound on dry ice. Brains were stored at -80°C until further processing. Coronal, 10 µm thick brain sections were prepared and collected at a cryotome (CryoStar NX70, Thermo Scientific). Sections determined for MERFISH analysis were placed on round glass slides provided by Vizgen Corp. (Cambridge, MA 02138) and functionalized in-house by coating one side with a 0.1 mg/mL poly-L-ornithine solution (Sigma-Aldrich, P4957 in PBS) for 1 hour, before drying them. Brain sections for MERFISH were subsequently washed two times with PBS and one time with 70 % ethanol (VWR Chemicals, 20.821.310, diluted in UltraPure™ Distilled Water, Invitrogen™) for 5 minutes each. Then samples were individually sealed in bags filled with 70 % ethanol and shipped to Vizgen Corp. (Cambridge, MA 02138) for MERFISH analysis.
MERFISH
Brain sections were measured by MERFISH according to manufacturer's protocol (https://vizgen.com/technology/#merfish)
Label n/a
Label protocol n/a
 
Hybridization protocol n/a
Scan protocol n/a
Description panel of 287 genes was measured by MERFISH
Data processing 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.
Tab-separated single cell expression matrix and cell metadata
 
Submission date May 10, 2022
Last update date Jun 21, 2023
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 (2)
GSE202623 Spatial Transcriptomics correlated Electron Microscopy [MERFISH]
GSE202638 Spatial Transcriptomics correlated Electron Microscopy

Supplementary file Size Download File type/resource
GSM6125919_b2s20_cell_by_gene.csv.gz 11.6 Mb (ftp)(http) CSV
GSM6125919_b2s20_cell_metadata.csv.gz 7.4 Mb (ftp)(http) CSV
GSM6125919_b2s20_detected_transcripts.csv.gz 1.1 Gb (ftp)(http) CSV
Processed data provided as supplementary file

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