GSM6807933: Control: Dendritic cells without collagen matrix_biol rep 1; Mus musculus; RNA-Seq
Five hours after introduction of the CCL19 chemokine gradient, the gel was isolated from the chamber and immediately bathed in Trizol. Subsequently, RNA extraction was performed following the 'Total RNA extraction' protocol of the 'Immunological Genome Project' (ImmGen.org). The amount of total RNA was quantified using the Qubit 2.0 Fluorometric Quantitation system (Thermo Fisher Scientific, Waltham, MA, USA) and the RNA integrity number (RIN) was determined using the Experion Automated Electrophoresis System (Bio-Rad, Hercules, CA, USA). RNA-seq libraries were prepared with the TruSeq Stranded mRNA LT sample preparation kit (Illumina, San Diego, CA, USA) using Sciclone and Zephyr liquid handling workstations (PerkinElmer, Waltham, MA, USA) for pre- and post-PCR steps, respectively. Library concentrations were quantified with the Qubit 2.0 Fluorometric Quantitation system (Life Technologies, Carlsbad, CA, USA) and the size distribution was assessed using the Experion Automated Electrophoresis System (Bio-Rad, Hercules, CA, USA). Before sequencing on an Illumina HiSeq 2000 instrument following a 50 base single end protocol, samples were diluted and pooled into NGS libraries in equimolar amounts. 50 base single end protocol