title: GSM5233229: bulk-RNAseq ZHBTc4 -2i/LIF rep 1; Mus musculus; RNA-Seq
library_construction_protocol: Single cells and single clone transcriptomes were extracted in microfluidic droplets. For scRNA-seq experiments, cells were loaded at 200,000 cells/ml in PBS containing 10% v/v OptiPrep and maintained in suspension using a magnetic micro-stirrer bar placed within the tube. For CloneSeq experiments, around 20,000 clones were resuspended in 900 μl PBS and 100 μl OptiPrep and maintained in suspension using a magnetic micro-stirrer bar placed within the tube. The device generates monodispersed droplets with volumes in the range of 2 nl for scRNA-seq and around 4-5 nl for CloneSeq. Single cell/clone lysates were subject to reverse transcription at 50°C without purification of RNA. Cells were barcoded using the using inDrops platform (Klein AM et al., Cell. 2015), which makes use of the CEL-Seq protocol for library construction (Hashimshony et al., Cell Reports 2011).