GSM4501074: MCF7 TM_6B; Homo sapiens; RNA-Seq
The cells were plated at a density of 8,000 cells per well in a 96 well plate (Greiner Cat. No. 655083) and placed in an incubator.  After 24 hours, the plates were removed from the incubator and treated with drugs using the HP D300 Digital Dispenser. The cells were then collected at the targeted time point by removing the media and pipetting 150uL of Qiagen Buffer RLT into each well.  The plates were then frozen and stored at -80C. For RNA extraction, the Qiagen RNeasy 96 kit (Cat. No. 74181) was used with the Hamilton ML STAR liquid handling machine equipped with a Vacuubrand 96 well plate vacuum manifold. A Sorvall HT 6 floor centrifuge was used to follow the vacuum/spin version of the RNeasy 96 kit protocol. The samples were treated with DNAse (Rnase-Free Dnase Set Qiagen Cat. No. 79254) during RNA isolation.  The RNA samples were then tested for yield and quality with the Bioanalyzer and the Agilent RNA 6000 Pico Kit. The TruSeq Stranded mRNA Library Prep Kit (RS-122-2101/RS-122-2102) was then used to prepare the samples for 30 million reads of single end sequencing (100bp) with the Illumina HiSeq2500. Three replicates were used for the combination experiments and two replicates for the dose experiments. 