STORM-seq protocols for library preparation and analysis

This repository contains the current and archived STORM-seq protocols for library construction and analysis.

Library construction

You can expect this process to take approximately ~8 hours to go from single cells to prepared library. Please feel free to open an issue if you encounter any sort of problem, have a question, 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-seq protocol and is functional with tooling that supports this kind of input. Additionally, we recommend and support analysis using kallisto|bustools and STARsolo. The required software and scripts to run these tools are found in the 'analysis' folder/directory. Additionally, we are working on producing docker and singularity containers for distribution as well. As with the library prep documentation, please feel free to open an issue if you encounter a problem or have suggestions for feature development.

Manuscript analysis

STORM-seq analyses found in the manuscript can be found in the analysis directory. This is currently under construction with scripts being updated daily. We will update this README once it is complete!

Data location

STORM-seq data found in the manuscript can be found at GSE296406. This super series contains all data found in each iteration of the manuscript.

# Data generated for the paper

## STORM-seq
K-562 - GSM8969807
HEK293T - GSM8969808
RMG-2 - GSM8969809

## Smart-seq3xpress
K-562 unmapped BAM - GSM8969813
K-562 remux'd from uBAM FASTQs - GSM8969812

## VASA-seq
K-562 and HEK293T plate 1 - GSM8969810
K-562 and HEK293T plate 2 - GSM8969811

## Bulk total RNA-seq
K-562 rep 1 - GSM5505429
K-562 rep 2 - GSM5505430

## Fallopian tube epithelium
Donor 1 - GSM5505431
Donor 2 - GSM5505432

Other data present in this super series is from previous iterations of the paper and method. The rationale to include it is some of it has been cited as part of other manuscripts. NOTE: any other STORM-seq data not noted above 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

STORM-seq workflow diagram