Code supporting "Efficient profiling of total RNA in single cells with STORM-seq"

STORM-seq protocols for library preparation and analysis https://github.com/biobenkj/stormseq_protocols Library construction You can expect this process to take approximately~8 hours to go from single cells to prepared library. Please feelfree to open an issue if you encounter any sort of problem, have aquestion, or have a tip/trick that you'd like to share/see implemented. Analysis STORM-seq can ultimately be analyzed as if it were a "bulk" RNA-seqprotocol and is functional with tooling that supports this kind of input. Additionally, we recommend and support analysis using kallisto|bustoolsand STARsolo. The required software and scripts to run these tools arefound in the 'analysis' folder/directory. Additionally, we are workingon producing docker and singularity containers for distribution as well.As with the library prep documentation, please feel free to open an issueif you encounter a problem or have suggestions for feature development. Manuscript analysis STORM-seq analysis scripts are part of this Zenodo repository, but may continue to be updated at the github repo Data location STORM-seq data found in the manuscript can be found at GSE296406. This superseries contains all data found in each iteration of the manuscript. ```# Data generated for the paper ## STORM-seqK-562 - GSM8969807HEK293T - GSM8969808RMG-2 - GSM8969809 ## Smart-seq3xpressK-562 unmapped BAM - GSM8969813K-562 remux'd from uBAM FASTQs - GSM8969812 ## VASA-seqK-562 and HEK293T plate 1 - GSM8969810K-562 and HEK293T plate 2 - GSM8969811 ## Bulk total RNA-seqK-562 rep 1 - GSM5505429K-562 rep 2 - GSM5505430 ## Fallopian tube epitheliumDonor 1 - GSM5505431Donor 2 - GSM5505432 ``` Other data present in this super series is from previous iterations ofthe paper and method. The rationale to include it is some of it has beencited as part of other manuscripts. NOTE: any other STORM-seq data not notedabove in this GEO super series does _not_ have UMIs added. *Thanks for trying out STORM-seq!* Key kit components to purchase: * STORM-seq kit: Takara Bio cat: 634751 * Takara Bio UDI sets A-D: Takara Bio cats: 634752, 634753, 634754, 634755 * ERCC spike-in mix: Thermo Fisher cat: 4456740 Plate types to purchase: * Eppendorf twin-tec lobind skirted 384-well plates: Eppendorf cat: 0030129547 * Eppendorf twin-tec lobind skirted 96-well plates: Eppendorf cat: 0030129512 * If using SPT Mosquito as automation: SPT 384 LVST plate cat: 4150-05829 Please refer to the latest protocol for remaining reagents needed