Extended Data Fig. 1: Histology showing imaging locations for each animal in the MEC group.
From: Minute-scale oscillatory sequences in medial entorhinal cortex
a. Left: Representative image indicating GCaMP6m expression in the superficial layers of the MEC upon local viral injection at postnatal day P1 (sagittal section). Images were acquired with a 20× objective mounted on a confocal laser scanning microscope LSM 880 (Zeiss), operated by ZEN 3 software (blue edition). Red inset, top right: 60× magnification of the most dorsal portion of the MEC. Bottom right: Fraction of MEC neurons (Nissl +) expressing GCaMP6m; data are shown for all 5 animals with MEC imaging. Data are presented as mean values, error bar indicates the S.D. calculated across multiple (n = 8) adjacent slices. Each dot represents one slice. b. Location of the ventro-lateral edge of the prism in stereotactic coordinates, and area of the FoV occupied by cells expressing GCaMP6m. Data are shown for each MEC-imaged animal. Mouse #59911 had no oscillatory sequences. c. Prism location in mice that underwent calcium imaging in MEC in the left hemisphere. Top: Maximum of 50 μm thick sagittal brain sections. For each of the 5 mice in (b), 3 sections, shown from lateral (left) to medial (right), were acquired with an LSM 880, 20×. A DiI-coated piano wire pin was inserted at the ventrolateral corner of FoV to enable identification of the FoV on histology sections. Green is GCaMP6m signal, red is DiI signal. Scale bar is 400 μm. The white stippled line encapsulates the superficial layers of MEC. The blue dot adjacent to the leftmost image of the series marks the location of the ventro-lateral corner of the prism. Bottom: estimated location of the FoV for two-photon imaging, projected onto a flat map encompassing MEC (brown outline) and parasubiculum (PaS, orange outline). The blue dot marks the location of the pin used to demarcate the most lateral-ventral border of the prism, while the green square inset is the microscope’s FoV. Inset image shows the maximum intensity projections of the FoV. Anteroposterior (AP), Mediolateral (ML), and dorso–ventral (DV) axes are indicated in panels (a) and (c). d. Micrographs of Cresylviolet stained sagittal brain sections from all 2 mice implanted with four-shank Neuropixels 2.0 silicon probes in the left hemisphere. Sections are organised from the most laterally placed shank(s) (left) to the most medially placed shank(s) (right). Mouse ID, shank number, and scale bar (1000 μm) are indicated next to each section. The brain of one mouse (#104638) was damaged during extraction, and parts of the MEC and cortex are missing from the section. Coloured arrows indicate MEC borders (dorsal, ventral) and the identified or estimated probe tip in the section. Black arrows indicate estimated dorsoventral range of the probe’s active recording sites (as indicated by the insert). For each section, inserts show the number of units recorded at each depth of the probe shank (histogram bin size = 60 μm). Note that the anatomical location of probe shanks can only be approximately estimated, and indicated unit locations are subject to measurement error, e.g., due to the shank tips exiting the cortex, the brain shrinking during perfusion and error in estimating the position of the tip of the probe. Stippled lines indicate borders between brain regions (MEC, medial entorhinal cortex; LEC, lateral entorhinal cortex; PaS, parasubiculum, HF, hippocampal formation; PoR, postrhinal cortex; VISpl, posterolateral visual area; TR, postpiriform transition area; CoA, cortical amygdalar area; PA, posterior amygdalar nucleus). D = dorsal; V = ventral; A = anterior; P = posterior.
