Extracellular signal recorded from the silicon probes was amplified (1000×), bandpass-filtered (1 Hz to 5 kHz), and acquired continuously at 20 kHz with a 64-channel DataMax System (RC Electronics or a 258-channel Amplipex) or at 32 kHz with a 64-channel DigitalLynx (NeuraLynx at 16-bit resolution). We preprocessed raw data using a custom-developed suite of programs (31). After recording, the signals were downsampled to 1250 Hz for the LFP analysis. Spike sorting was performed automatically using KLUSTAKWIK [http://klustakwik.sourceforge.net (32)], followed by manual adjustment of the clusters, with the help of autocorrelogram, cross-correlogram (CCG), and spike waveform similarity matrix [KLUSTERS software package; https://klusta.readthedocs.io/en/latest/ (33)]. After spike sorting, we plotted the spike features of units as a function of time and discarded the units with signs of significant drift over the period of recording. Moreover, we included in the analyses only units with clear refractory periods and well-defined clusters. Recording sessions were divided into brain states of THE and SO periods. The epochs of stable theta [THE in anesthesia experiments, REM in natural sleep experiments, or slow oscillations (SO in anesthesia experiments and nonREM in natural sleep experiments)] periods were visually selected from the ratios of the whitened power in the THE band ([3 6] Hz in anesthesia and [6 11] Hz in natural sleep) and the power of the neighboring bands ([1 3] and [7 14] Hz in anesthesia and [12 20] Hz in natural sleep) of EC layer 3 LFP, which was a layer present in all the 18 anesthesia recordings, or layer 5 mPFC recordings in natural sleep recordings, and assisted by visual inspection of the raw traces (fig. S2) (28, 29). We then used band-averaged powers over the same frequency ranges of interest as features for the automated extraction of spectral states via unsupervised clustering, which confirmed our manual classification. We determined the layer assignment of the neurons from the approximate location of their somata relative to the recording sites (with the largest amplitude unit corresponding to the putative location of the soma), the known distances between the recording sites, and the histological reconstruction of the recording electrode tracks.

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