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About bst-3

Description of dataset bst-3 (Brainstem, dataset 3).

Summary of the data

These data were collected using chronically implanted Neuropixels probes from 10 Long Evans rats (4 females) during a fear discrimination procedure. 1812 Single units were recorded from 21 brainstem regions: deep gray layer superior colliculus (DPG). Deep white layer superior colliculus (DpWh). Dorsolateral periaqueductal gray (DLPAG). Lateral periaqueductal gray (LPAG). Ventrolateral periaqueductal gray (VLPAG). Mesencephalic trigeminal tract (me5). Dorsal raphe nucleus, lateral part (DRL). Dorsal raphe nuclues, dorsal part (DRD). Dorsal raphe nucleus ventral part (DRV). Posterodorsal raphe nucleus (PDR). Medial longitudinal fasciculus (mlf). Isthmic reticular formation (isRt). Paratrochlear nucleus (pa4). Decussation/superior cerebellar peduncle (x/scp). Subpenduncular tegmental nucleus (SPTg). Pontine reticular nucleus, oral part (PnO). Ventral tegmental nucleus (VTg). Dorsomedial tegmental area (DMTg). Tectospinal tract (ts). Paramedian raphe nucleus (PMnR). Median raphe nuclues (MnR).

Fear discrimination sessions consisted of three auditory cues that predicted a unique shock probability (0.5 mA, 0.5 s): danger, p=1.00; uncertainty, p=0.25; and safety, p=0.00. Shock was administered two seconds following the termination of the cue on danger and uncertainty-shock trials. A single session consisted of 4 danger, 2 uncertainty-shock, 6 uncertainty-no shock, and 4 safety trials with a mean inter-trial interval of 3 min. Trial order was randomly determined by the behavioural program and differed for each rat, every session. The physical identities of the auditory cues were counterbalanced across individuals. Following 12 discrimination training sessions rats were implanted at coordinates -8.00 AP, -2.80 ML, -7 to -7.5 DV, with a 15⁰ angle. After recovery recording sessions were carried out during a maximum of 10 further recording sessions per rat.

Data included are the result of spike sorting using Kilosort 2/2.5 (, manual curation in phy (, and final screening in Matlab. These data have been published in Nature Communications where the complete methods are analysis carried out are available.

Format of the data

The data is stored in Matlab files. Details about the format are given in the document linked to at the bottom of this page. Total size of the data set is about 352 MB.

Conditions for using the data

Publications created through usage of the data should cite the paper in which they are first reported:

Strickland, J. A., & McDannald, M. A. (2022). Brainstem networks construct threat probability and prediction error from neuronal building blocks. Nature communications, 13(1), 1-10.

And also cite the dataset using:

Strickland, J. A., & McDannald, M. A. (2022). Neuropixels recordings from 21 brainstem regions in rats during fear discrimination.

The above citation uses a Digital Object Identifier (DOI) which is assigned to the data set.  The DOI was created using DataCite ( and the California Digital Library, "EZID" system (

How to download the data

Data may be downloaded from:
A account is required. See the download link for more instructions.

Getting help using the data

If you have questions about using the data, please post them on the forum for using data sets.

Documentation file

crcns_bst-3_data_description.pdf - (Data description)

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