GSM2970293: MEFs transduced 4 foctors (Nkx2-1, Foxa1, Foxa2, Gata6) [MY-5]; Mus musculus; RNA-Seq
For total RNA extraction of MEFs (iPUL cells), matrigel blocks containing differentiated cells and fibroblasts were digested using dispase (Corning) at 37°C for 120 minutes. The clusters of the cells were separated using 70 μm cell strainer and lysed and total RNA was harvested using RNA easy kit (Quiagen).For total RNA extraction of adult lung, lungs  were removed, flash frozen on dry ice, and total RNA was harvested using RNA easy kit (Quiagen). For total RNA extraction of SP-C+ cells in 3D culture, matrigel blocks containing differentiated cells and fibroblasts were digested using dispase (Corning) at 37°C for 120 minutes. To prepare the single cell suspension of iPUL cells, cells were incubated in 0.25% Tripsin/EDTA at 37°C for 5 min. GFP+/SP-C+ cells were sorted by flow cytometry. The sorted GFP+/SP-C+ cells were lysed and total RNA was harvested using RNA easy kit (Quiagen). Total RNA obtained from each sample was subjected to a sequencing library construction using NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs, MA) with NEBNext Poly(A) mRNA Magnetic Isolation Module according to the manufacturer's protocols.   The quality of the libraries was assessed with an Agilent 2200 TapeStation High Sensitivity D1000 (Agilent Technologies, Santa Clara, CA).   The pooled libraries of the samples were sequenced using the illumina HiSeq 1500 system (Illumina, Inc., San Diego, CA) in 50-base-pair (bp) single-end reads.