Sci-Plex

Sci-Plex is a labeling sampling that enables sample labeling within sci-RNA-seq. This github repository documents processing pipelines, primary and secondary analyses, and other files used in the generation, analysis and interpretation of the data.

Contents

Primary Analysis and data

Our data derive primarily from 4 sequencing experiments. Which are all available on GEO both in their raw and processed forms.

Name	Experiment	GEO Accession	Analysis Scripts
sciPlex1	Barnyard Experiment	GSM4150376	barnyard_experiment
sciPlex2	Small Screen	GSM4150377	small_screen
sciPlex3	Large Screen	GSM4150378	large_screen
sciPlex4	HDACi Phenocopy Rescue	GSM4150379	large_screen

Processing the raw data

The scripts and code used to process the data can be accessed within the process_from_raw folder. This code was used to process the data from a demulitplexed sequencing run to a gene expression matrix.

Ordering Reagents for Hashing

As highlighted by the paper, oligo-hashing is an simple procedure employing off the shelf reagents. To make this more accessible we have included 96-well format IDT order forms for the hash-oligo sequences used in this study. These excel files can be found in the reagents folder in this github repository. A single plate of 40nmols of hash-oligos from IDT should be sufficient for up to 800 labeling reactions per well.

We are currently working on a protocols.io page for both sci-RNA-seq and sci-plex. As soon as this is ready we will update with a link here and advertise it more broadly.