Spatial Total RNA-Sequencing: STRS

Suite of molecular and computational workflows for Spatial Total RNA-Sequencing (STRS)

This repository has all the protocols, pipelines, and scripts you will need to run and analyze STRS on almost any sample!

Check out txg_snake, a work-in-progress pipeline for 10x libraries, especially STRS datasets!

Manuscript links:

• McKellar et al, Nature Biotechnology, 2022
• bioRxiv preprint link

Subdirectory descriptions:

• manuscripts: .pdf files of the preprint and subsequent manuscript (hopefully!)
• protocols: Microsoft word and .pdf documents of the protocols used here
• pipelines: Snakemake workflows used in our study. These include alignment pipelines for STRS data (kallisto, STARsolo, & miRge3.0), small RNAseq data (STAR & miRge3.0), SmartSeqTotal (kallisto), and VASAdrop (kallisto)
• scripts: All the other code we used! Mostly contains R scripts and utility functions used in our spatial analyses.
• references: info & scripts on reference genomes & annotations used in this study
• resources: assorted metadata, gene lists, and other information that we used to analyze our data see README files in each subdirectory for more details

Data generated for this paper:

• STRS datasets: GSE200481
• SkM/heart small RNAseq data: GSE200480
• single-nucleus total RNAseq data (C2C12 cell line): GSE209780

Additional data analyzed:

• Small RNA Atlas data (Isakova et al, PNAS, 2020): GSE119661
• SmartSeqTotal data (Isakova et al, PNAS, 2021): GSE151334
• VASAdrop data (Salmen et al, Nature Biotechnology, 2022): GSE176588

Contact:

• Iwijn De Vlaminck (id93@cornell.edu)
• Benjamin D. Cosgrove (bdc68@cornell.edu)
• David W. McKellar (dwm269@cornell.edu)