Transcription Factor RFX3 Stabilizes Mammary Basal Cell Identity

We report the role of RFX3 in the stabilization of the basal cell lineages Bulk RNA seq Total RNA (50-200ng) isolation was performed using either TRIzol (Life Technologies) or the RNeasy Mini Kit (Qiagen, Hilden, Germany). 5 samples of myoepithelial cells and 5 samples of s-SHIP GFP+ cap cells from 5-week-old female Tg11.5kb-GFP mice were submitted and subjected to quality analysis using a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA). All Samples had an average RNA integrity number (RIN) value ∼8. Libraries for whole transcriptome analysis were generated following Illumina’s TruSeq RNA v2 sample preparation protocol. Libraries were sequenced on an Illumina HiSeq 3000. 150 million reads at 75 basepairs were obtained for each of the samples. Single-Cell RNA seq After 96 hrs cultivation, myoepitheial cells were dissociated using TrypLE and cell viability was determined using Trypan Blue. The control sample (fresh s-SHIP GFP+ cap cells, myoepithelial cells and luminal cells) and cultivated cells were encapsulated and barcoded using the inDrop platform (1CellBio) with an in vitro transcription library preparation protocol (Klein et al., 2015).