scScreens_ADARs

Investigating ADAR mediated A-to-I editing in fetal and fetal-like tissue such as organoids and teratoma

Code to reproduce the analysis seen in manuscript: Charting and probing the activity of ADARs in human development and cell-fate specification (Dailamy, Lyu et al.)

Referenced Packages

1. scRNA seq on Teratoma: https://github.com/yanwu2014/teratoma-analysis-code
2. Alu Ediitng Index: https://github.com/a2iEditing/RNAEditingIndexer
3. Site Specific Ediitng Level: https://github.com/BreenMS/Quantify-RNA-editing-from-bam-file
4. Counts to TPM: https://gist.github.com/slowkow/c6ab0348747f86e2748b
5. ivPerturb Seq: https://github.com/klarman-cell-observatory/ivPerturbSeq
6. Seurat: https://github.com/satijalab/seurat

Data Availability

The raw and processed data generated from this study are available at Gene Expression Omnibus with accession code GSE248941. [https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE248941]

General Instructions

Please refer to correspondent folders for reproducing figures of interest. Scripts ordered by numbers should be run in orders, e.g. please run "F01_01_xxx" before "F01_02_xxxx". Some output tables for Alu Editing Index and expression of ADARs are included in relevant folders and can be readily used.