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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-well variability in the differences in behaviour between the two spike-in sets. The data contain four batches of libraries (block), using different batches of cells that were processed and sequenced separately. Each batch contains libraries with all three types of spike-in addition (ERCC+SIRV, SIRV+ERCC or Premixed). The 416B cells also contain a CBFB-MYH11 oncogene, which is expressed in half of the cells (Induced) and silent in the other half (Control).

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

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