HeLa cells RNA-seq following heat shock, geldanamycin and radicicol treatments

Culture of cell lines and stress treatment. HeLa (ovary) cells were cultured in Dulbecco's modified Eagle's medium (DMEM) supplemented with 10% foetal bovine serum (SVF). Each stress treatment was monitored 24 hours after to have seeded 2.5x106 cells in each well of a 6-well plates of plaque assays that was maintained at 37°C and with 5% CO2. For the heat shock, cells were incubated for 3 hours at 42°C and with 5% CO2. For the chemical treatment, the medium was adjusted at 500 nM in geldanamycine and 100 nM radicicol (ENZO Life Sciences, Villeurbanne, France) and the cells were maintained for 1 hour at 37°C and with 5% CO2. At the end of each of these treatments, cells were trypsinized, washed twice with 1XPBS and total RNA were finally purified using the NucleoSpin Extract RNA kit (Macherey Nagel, Hœrdt, France). Illumina library and sequencing. Libraries for Illumina sequencing were made using NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® (New England Biolabs, Ipswich, MA, USA). DNA quantities were monitored at various steps in the procedure with the Qubit® dsDNA HS Assay Kit (Molecular Probes, Eugene, USA). Fragment size selection, library quality control and Illumina sequencing (HiSeq 51 and 76 nucleotides, TruSeq SBS Kit v3) were achieved at the Plateforme de Séquençage Haut Débit I2BC (Gif-sur-Yvette, France), following published quality recommendations [doi: 10.1371/journal.pcbi.1003326]. Data published in this paper are based on two biological replicates