FlyPN_development

Analysis workflow for Xie et al. 2021

This repository contains Jupyter Notebooks that were used to analyze the scRNA-seq data of Drosophila Olfactory Projection Neurons (PN) at 4 different developmental stages.

Configuration

Enviroment

Analysis requires Scanpy, anndata, ICIM, and MARS. ICIM was modified to run in Python 3.7 environment.

Notebooks

Code for analyzing the data and reproducing the figures shown in the paper.

Data

Sequencing reads and preprocessed sequence data are available in the NCBI Gene Expression Omnibus (GSE161228, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE161228). Data have been preprocessed to keep only high quality neurons and normalized via the transformation Log2(CPM+1). The expression data and annotations are stored as anndata objects are used as inputs for analysis.

Left: knot+ PNs at three pupal stages. Right: most PNs at four stages.

Contact

Please contact ChiChi at cqxie@stanford.edu for questions.