Dear Allen Institute team,
I am analyzing spatial expression patterns of immediate-early genes (IEGs) in the olfactory tubercle using the adult mouse whole-brain MERFISH dataset. Because IEG expression can change rapidly in response to handling, environmental changes, stress, and anesthesia, I would like to better understand the conditions experienced by the mice before tissue collection.
Could you please provide information about the approximately two hours preceding euthanasia, including:
- Whether the mice remained in their home cages and usual housing room
- Whether they were handled, transported, transferred to another cage, or moved to a different room
- Whether they were exposed to a novel environment or other experimental procedures
- The anesthesia and euthanasia methods used
- The approximate interval between initial handling, euthanasia, and tissue preservation
- The time of day or light-cycle phase at which tissue collection was performed
If these procedures differed among individual animals, specimen-specific information—particularly for specimens C57BL6J-638850 and C57BL6J-638851—would be especially helpful.
A detailed protocol, standard operating procedure, or reference describing these conditions would also be greatly appreciated. This information would help us distinguish biologically organized spatial IEG patterns from possible procedure-related activation.
Thank you very much for your assistance.