Muraro, M. J. | Search bioRxiv

bioRxiv2018

Combined quantification of intracellular (phospho-)proteins and transcriptomics from fixed single cells.

Environmental stimuli often lead to heterogeneous cellular responses and transcriptional output. We developed single-cell RNA and Immunodetection (RAID) to allow combined analysis the transcriptome and intracellular (phospho-)proteins from fixed single cells. RAID successfully recapitulated differentiation-state changes at the protein and mRNA level in human keratinocytes. Furthermore, we show that differentiated keratinocytes that retain high phosphorylated FAK levels, a feature associated with stem cells, also express a selection of stem cell associated transcripts. Our data demonstrates that RAID allows investigation of heterogenenous cellular responses to environmental signals at the mRNA and phospho-proteome level.

genomics↗

bioRxiv2018

Sharq, a versatile preprocessing and QC pipeline for Single Cell RNA-seq

Despite the meteoric rise of single cell RNA-seq, only a few preprocessing pipelines exist that are able to perform all steps from the original fastq files to a gene expression table ready for further analysis. Here we present Sharq, a versatile preprocessing pipeline designed to work with plate-based 3-end protocols that include Unique Molecular Identifiers (UMIs). Sharq performs stringent step-wise trimming of reads, assigns them to features according to a flexible hierarchical model, and uses the barcode and UMI information to avoid amplification biases and produce gene expression tables. Additionally, Sharq provides an extensive plate diagnostics report for quality control and troubleshooting, including that of spatial artefacts. The diagnostics report includes measures of the quality of the individual plate wells as well as a robust assessment which of them contain material from live cells. Collectively, the innovative approaches presented here provide a valuable tool for processing and quality control of single cell RNA-seq data.

bioinformatics↗