This repository contains count matrices of published RNA-seq experiments (xx_cnts.rda) and estimated negative binomial parameters as exemplaric input to powsim (xx_estparam.rda). For the Kolodziejczk data set we also included simulation results.
The following published data sets are available:
Islam et al. 2011 GSE29087
The 48 mouse embryonic stem cells were prepared with the STRT-seq protocol.
Islam et al. 2014 GSE46980
The 96 mouse embryonic stem cells were prepared with the improved STRT-seq protocol, i.e. including unique molecular identifiers (UMI).
Buettner et al. 2014 E-MTAB-2805
288 mouse embryonic stem cells were stained with Hoechst and sorted by FACS into three different cell cycle stages (G1, G2M, S1). Single cell RNA-Seq was performed using Fluidigm C1 system and libraries were generated using Nextera XT (Illumina) kit.
Kolodziejczk et al. 2015 E-MTAB-2600
869 mouse embryonic stem cells under three different conditions: serum + LIF (242 cells), 2i + LIF (433 cells) and alternative 2i + LIF (194 cells). Single cell RNA-Seq was performed using Fluidigm C1 system and libraries were generated using Nextera XT (Illumina) kit. We reduced the data set to standard serum + LIF cultured cells for parameter estimation.
Soumillon et al. 2014 GSE53638
Directed adipogenic differentiation of human cells in vitro over time. We have included the transcriptomic profiling of approx. 12000 cells collected over the differentiation of human adipose-derived stem/stromal cells. Library protocol is Single Cell RNA Barcoding and Sequencing (SCRB-Seq) with unique molecular identifiers (UMI).