Commit a14e0010 authored by Robert Phillips's avatar Robert Phillips
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Update README.md

parent 9ba7d239
...@@ -4,13 +4,9 @@ ...@@ -4,13 +4,9 @@
This page contains bash and R code, as well as SeqMonk workflow information, for the enhancer identification pipeline used in "Enhancer RNAs predict enhancer-gene regulatory links and are critical for enhancer function in neuronal systems" This page contains bash and R code, as well as SeqMonk workflow information, for the enhancer identification pipeline used in "Enhancer RNAs predict enhancer-gene regulatory links and are critical for enhancer function in neuronal systems"
```mermaid ## **General Enhancer Identification Workflow**
graph TD;
A-->B; The diagram below outlines a general workflow for the identifcation of enhancers. Code corresponding to each step can be found within the repository.
A-->C;
B-->D;
C-->D;
```
## **Study design** ## **Study design**
...@@ -33,25 +29,16 @@ Datasets in this manuscript used the 10X Genomics Chromium Single Cell 3’ libr ...@@ -33,25 +29,16 @@ Datasets in this manuscript used the 10X Genomics Chromium Single Cell 3’ libr
## **Citation** ## **Citation**
Savell, K.E.*, Tuscher, J.J.*, Zipperly, M.E.*, Duke, C.G.*, Phillips III, R.A.*, Bauman, A.J., Thukral, S., Sultan, F.A., Goska, N.A., Ianov, L., & Day, J.J. (2020). A dopamine-induced gene expression signature regulates neuronal function and cocaine response. *Science Advances* 6(26): eaba4221.
[Link](https://advances.sciencemag.org/content/6/26/eaba4221)
## **Links** ## **Links**
All Day lab resources may be found at the [Day Lab website](http://day-lab.org/resources) 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/) [BioRxiv preprint](https://www.biorxiv.org/content/10.1101/270967v3)
[Published manuscript](https://advances.sciencemag.org/content/6/26/eaba4221)
[BioRxiv preprint](https://www.biorxiv.org/content/10.1101/781872v1)
## **Raw data** ## **Raw data**
Primary striatal neuron culture snRNA-seq - GEO accession [GSE137759](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE137759) Will be added once deposited on GEO
Adult NAc snRNA-seq - GEO accession [GSE137763](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE137763)
## **Source code**
[Manifold Enhancement of Latent Dimensions (MELD)](https://github.com/KrishnaswamyLab/MELD)
[Seurat v3](https://github.com/satijalab/seurat)
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