GSM5227570: MCF10A_p53-KO_MMC_r2; Homo sapiens; RNA-Seq
Total RNA was extracted from cell pellets with the miRNeasy Kit (Qiagen, cat#217504). cDNAs were reverse-transcribed, DNA sequencing adapters were ligated, and fragments were PCR-amplified. Resultant fragments were then read in triplicate on an Illumina HiSeq 2500 system (24 total samples including the replicates). Reads were assembled and splice junctions were aligned to the genome using existing data, and using the TopHat software (Open source, Haas and Zody 2010, Nature Biotechnology 28,421–423), which can align short fragment reads across exon-exonjunctions and without a reference genome.