GSM7047678: 48_MIBC_HTG; Homo sapiens; RNA-Seq
A 1mm punch was taken from FFPE blocks of a representative tumor area with at least 50% tumor content. RNA was isolated using the “truXTRAC FFPE total NA Kit – Column” (Covaris, Woburn, MA, USA) The mRNA expression was determined using the HTG Transcriptome Panel (HTG Molecular Diagnostics, Tuscon, AZ, USA) as describes before. Briefly, target capture was done by the HTG EdgeSeq chemistry with nuclease protection probes on a 96-well plate. Processed samples were used to set up PCR reactions with specially designed primers, referred to as “tags”. These tags share common sequences that are complementary to 5'-end and 3'-end “wing” sequences of the probes and common adaptors required for cluster generation on an Illumina sequencing platform. In addition, each tag contains a unique barcode that is used for sample identification and multiplexing. The library was prepared using a PCR with OneTaq (New England Biolabs, Ipswich, MA, USA) and EdgeSeq PCR tag primers (HTG Molecular Diagnostics). Sequencing was performed on the Illumina NextSeq 550 system (Illumina, San Diego, CA, USA) in accordance with manufacturer's recommendations but also including two HTG custom sequencing primers.