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# **VTA snRNA-seq**


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This page contains R code for analysis of single-nucleus RNA-seq (snRNA-seq) datasets from "_An atlas of transcriptionally defined cell populations in the rat ventral tegmental area_".  R objects containg UMAP coordindates and other metadata characteristics for the complete dataset and neuronal subclustering are available upon request. 
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## **Study design**

This snRNA-seq dataset was generated from VTA punches from naive adult male and female Sprague Dawley rats.  

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Datasets in this preprint used the 10X Genomics Chromium Single Cell Next GEM 3’ library construction kit to generate barcoded libraries for Illumina sequencing. For each dataset, we provide R Markdown and Word documents containing analysis parameters and code.  
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## **Citation**

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Phillips III, R.A.* Tuscher, J.J.*, Black, S.L., Ianov, L., & Day, J.J. (2021). An atlas of transcriptionally defined cell populations in the rat ventral tegmental area. *bioRxiv* DOI: 10.1101/2021.06.02.446737
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[Link](https://www.biorxiv.org/content/10.1101/2021.06.02.446737v1)
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## **Links**

All Day lab resources may be found at the [Day Lab website](http://day-lab.org/resources)  
[Ratlas Shiny App](https://day-lab.shinyapps.io/ratlas/)  
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[BioRxiv preprint](https://www.biorxiv.org/content/10.1101/2021.06.02.446737v1)  
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## **Raw data**

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GEO accession [GSE168156](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE168156)  
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## **Source code**
All packages required for reproduction of this analysis are included in the session info section of the word doc included in this repository.
[Seurat v3.2.2](https://github.com/satijalab/seurat)  
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## **Docker image**
A Docker image containing all depedencies needed to reproduce the analysis from the code present in this repository: [Day lab VTA Docker image](https://hub.docker.com/r/daylabprojects/daylab_rat_vta_snrna)