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
- 1. Bioinformatics and Systems Biology Program, University of California San Diego and Integrative Biology Laboratory, Salk Institute for Biological Studies
- 2. Department of Psychiatry, University of California San Diego
- 3. Integrative Biology Laboratory, Salk Institute for Biological Studies
- 4. Department of Medicine, University of California San Diego
- 5. Department of Psychiatry, University of California San Diego and Department of Integrative Structural and Computational Biology, The Scripps Research Institute
- 6. Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Department of Pediatrics, University of Washington School of Medicine and Department of Genome Sciences, University of Washington
- 7. Department of Psychiatry, University of California San Diego and Institute for Genomic Medicine, University of California San Diego
- 8. Department of Medicine, University of California San Diego and Department of Psychiatry, University of California San Diego
Description
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
Notes
Files
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Additional details
Related works
- Is cited by
- Preprint: https://www.biorxiv.org/content/10.1101/2022.09.08.506493v2 (URL)