Salient experiences are represented by unique transcriptional signatures in the mouse brain
- The Hebrew University, Israel
- Weizmann Institute of Science, Israel
- Ben-Gurion University of the Negev, Israel
- Vanderbilt University School of Medicine, United States
- Canadian Institute for Advanced Research, Canada
Figures
Figure 1 with 6 supplements
Transcriptional signatures representing recent experience.
(A) Schematic of experimental paradigm for cocaine sensitization. Mice were exposed to cocaine (i.p., 20 mg/kg) or saline, either acutely, repeatedly or re-exposed following abstinence (challenge), …
Figure 1—figure supplement 1
Boundaries of dissected structures.
Shaded regions in blue represent areas cut out from 400 µm slices for LCtx (limbic cortex), NAc (nucleus accumbens), DS (dorsal striatum), Amy (amygdala), LH (lateral hypothalamus), and Hipp …
Figure 1—figure supplement 2
Acute, repeated and challenge cocaine experiences induce distinct transcriptional programs across brain structures.
(A) Schematic of the experimental paradigm. (B) Average transcriptional induction of 78 genes one hour following acute, repeated or challenge cocaine experiences in six brain nuclei [LCtx: limbic …
Figure 1—figure supplement 3
Time course of transcriptional induction of a minimal set of markers representing cocaine-induced transcriptional dynamics.
(A) Schematic of the experimental paradigms. (B) Arc, Egr2, Egr4, Fos and Fosb induction (0, 1, 2, 4 hr) following acute, repeated and challenge cocaine in seven brain nuclei (LCtx: limbic cortex, …
Figure 1—figure supplement 4
Transcriptional representation of LiCl experience.
(A) Schematic of experimental paradigm. (B) Comparison of average transcriptional induction of 78 genes following acute LiCl (n = 5) or repeated LiCl (n = 4) at 1 hr time point, in limbic cortex …
Figure 1—figure supplement 5
Characterization of repeated saline exposures illustrates the effect of habituation on induced transcription.
(A) Experimental paradigm for i.p. saline injections. (B) Bar graphs demonstrating the transcriptional induction of Arc, Egr2, Egr4 and Fos in the LCtx, NAc, and DS (limbic cortex, nucleus …
Figure 1—figure supplement 6
Characterization of the transcription induced by acute and repeated saline experiences.
(A) Schematic of the experimental paradigm of i.p. injections of saline. (B) Expression matrix of the transcriptional induction of IEGs following acute or repeated saline experiences. Each column …
Figure 2 with 5 supplements
Salient experiences are represented by unique transcriptional signatures.
(A) Schematic of experimental paradigms. Experiences analyzed include saline (acute and repeated); foot shock (acute shock and no-shock controls exposed to the same environment); LiCl (acute and …
Figure 2—figure supplement 1
Low variability of the individual transcriptional representations of recent experience.
Radar plots representing the transcriptional induction of Arc, Egr2, Egr4 and Fos, in seven brain nuclei [LCtx: limbic cortex (n = 4–14), NAc: nucleus accumbens (n = 4–14), DS: dorsal striatum (n = 4…
Figure 2—figure supplement 2
Transcriptional representation of negative valence in the amygdala.
Comparison of average transcriptional induction of Arc, Egr2, Egr4 and Fos in the LCtx, NAc, DS, Amy, LH and Hipp, 1 hr following acute exposure to the fear-conditioning chamber (no shock) or brief …
Figure 2—figure supplement 3
Transcriptional representation of habituation and reinforcement.
Comparison of the transcriptional profiles induced by acute and repeated aversive (LiCl) and rewarding (cocaine and sucrose) experiences reveal distinctions and commonalities in the encoding of an …
Figure 2—figure supplement 4
Reinstatement of feeding is represented by robust transcriptional dynamics.
(A) Schematic of experimental paradigm for reinstatement of feeding. Mice were continuously fed or food deprived for 18 hr, followed by analysis of transcription at 0, 1, 2, 4 hr after reinstatement …
Figure 2—figure supplement 5
Reinstatement of feeding is represented by robust transcriptional dynamics.
Comparison of transcriptional induction of Arc, Egr2, Egr4 and Fos, at 0 (deprived) and 1 hr following reinstatement of feeding (re-fed), and continuously fed mice (fed control) across five brain …
Figure 3 with 2 supplements
Decoding the recent experience of individual mice from minimal transcriptional signatures.
(A) Confusion matrix representing the classification accuracy (90.7%) of decoding the recent experience of individual mice based on 25 features. Efficiency is scaled from blue to green, with bright …
Figure 3—figure supplement 1
Decoding the recent experience of individual mice from averaged gene expression across different brain regions.
Confusion matrix representing the classification accuracy (55.6%) of decoding the recent experience of individual mice based on averaged transcriptional induction of Arc, Egr2, Egr4, Fos and Fosb) …
Figure 3—figure supplement 2
Feature selection to identify the features contributing most significantly to decoding.
(A, E) Selection of features (expression of IEG in a brain structure) with the highest potential to contribute to the classification of recent experiences (‘support’). Support was defined by running …
Additional files
-
Source Code 1
Classfication Tests_averageGenes
- https://doi.org/10.7554/eLife.31220.019
-
Source Code 2
Classfication Tests_averageRegions
- https://doi.org/10.7554/eLife.31220.020
-
Source Code 3
Classfication Tests_pcaOverRegions
- https://doi.org/10.7554/eLife.31220.021
-
Source Code 4
ClassificationAndConfusionMatrices_confMat
- https://doi.org/10.7554/eLife.31220.022
-
Source Code 5
Classification And Confusion Matrices_knnEvaluate
- https://doi.org/10.7554/eLife.31220.023
-
Source Code 6
Feature Selection RKNN_find Features
- https://doi.org/10.7554/eLife.31220.024
-
Source Code 7
Feature Selection RKNN_find Interesting Genes
- https://doi.org/10.7554/eLife.31220.025
-
Source Code 8
Features Selection Random Forest_DecisionTree
- https://doi.org/10.7554/eLife.31220.026
-
Source Code 9
Linear Projections_RegionsScatter
- https://doi.org/10.7554/eLife.31220.027
-
Source Code 10
Linear Projections
- https://doi.org/10.7554/eLife.31220.028
-
Source Code 11
Randomization_permTest
- https://doi.org/10.7554/eLife.31220.029
-
Supplementary file 1
Primer sequences and efficiency calculations.
- https://doi.org/10.7554/eLife.31220.030
-
Supplementary file 2
Raw data.
- https://doi.org/10.7554/eLife.31220.031
-
Supplementary file 3
Statistics.
- https://doi.org/10.7554/eLife.31220.032
-
Supplementary file 4
Animal numbers
- https://doi.org/10.7554/eLife.31220.033
-
Transparent reporting form
- https://doi.org/10.7554/eLife.31220.034
