Data from: Single-nucleus RNA-seq and ATAC-seq in outbred rats with divergent cocaine addiction behaviors reveal long-term changes in gene regulation and GABAergic inhibition in the amygdala

This dataset accompanies our publication titled: "Single-nucleus RNA-seq and ATAC-seq in outbred rats with divergent cocaine addiction behaviors reveal long-term changes in gene regulation and GABAergic inhibition in the amygdala."

Files Included:

1. geno.N26.vcf.gz
    - Description: Contains genotypes for 26 Heterogeneous Stock rats whose gene expression was predicted.

2. pred_expr.Brain.N26.tsv
    - Description: This tab-delimited table contains predicted relative gene expression in the brain for 26 Heterogeneous Stock rats. 
    - Details: Predictions were made for 8,997 genes from linear models based on cis-eQTLs from whole brain hemisphere tissue downloaded from the RatGTEx Portal. A gene is included in the table if it had at least one significant cis-eQTL, and if its predicted expression in these 26 animals had nonzero variance. The values in the table give the predicted log2(relative expression), where log2(2) = 1 is the baseline expression from the two haplotypes of the gene if it had only reference alleles at all its regulatory loci.
    - Additional Info: Predictions were generated using gene_expr_pred.py available at https://github.com/PejLab/gene_expr_pred
An explanation of the prediction model is given in https://doi.org/10.1101/2022.01.28.478116

3. Behavioral data.xlsx
    - Description: Contains behavioral data for the Heterogeneous Stock (HS) rats.
    - Organization: Each sheet in the file corresponds to data for a specific figure.

Additional Dataset Locations:

The primary datasets generated during this study can be found on the Gene Expression Omnibus under accession number GSE212417

Publicly Available Datasets Utilized:

- Rattus norvegicus Ensembl v98 reference genome and genome assembly: Rnor_6.0
- JASPAR2022 transcription factor binding profiles for vertebrates: JASPAR
- ENCODE Honeybadger 2 ChIP-seq: Broad Institute
- Liu et al. 2019106 GWAS for tobacco and nicotine addiction summary statistics: PubMed
- RatGTEx Portal tissue-specific cis-eQTLs: RatGTEx Portal 
- 1000 Genomes European reference panel: Alkes Group
- KEGG pathways: KEGG API