Assessing the reliability of spike-in normalization for analyses of single-cell RNA sequencing data

ABSTRACT: This study aims to assess the reliability of spike-in normalization for analyzing single-cell RNA sequencing data. This is done by performing mixture experiments where two different sets of spike-in RNA (ERCC and SIRV) are added separately to a single mouse cell (416B or trophoblast stem cells (TSCs)), followed by generation of sequencing libraries using a modified version of the Smart-seq2 protocol. The aim is to measure the variance of the log-ratio of the total counts between the two spike-in sets. This will quantify how precisely the spike-in RNA was added to each well. As a control, addition was also performed with a premixed solution of both spike-ins, to quantify the variability in the log-ratios due to the experimental protocol. The same data can also be used to measure the well-to

INSTRUMENT(S): Illumina HiSeq 2500, BD Fortessa, Illumina HiSeq 4000

ORGANISM(S): Mus musculus

SUBMITTER: Aaron Lun 

PROVIDER: E-MTAB-5522 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress