title: GSM2652427: VN25065; Homo sapiens; RNA-Seq
library_construction_protocol: For each FFPE sample, 6 pieces of 10 μm thick sections were used. RNA was extracted with PureLink FFPE Total RNA Isolation Kit from Invitrogen (Invitrogen Corporation, Carlsbad, CA, USA). For all samples (fresh and FFPE) osteosarcoma was confirmed samples by two independent pathologists 50 ng of total RNA was amplified by applying Ovation RNA-Seq System V2 (NuGen, Emeryville, CA, USA) after which the resulting cDNAs were pooled in equal amount and the pool was used to prepare the DNA fragment library with SOLiD System chemistry (Life Technologies Corp., Carlsbad, CA, USA). Sequencing was performed using SOLiD 5500W platform and DNA sequencing chemistry (Life Technologies Corp., Carlsbad, CA, USA). Raw reads (75 bp) were color-space mapped to the human genome hg19 reference using Maxmapper algorithm implemented in the Lifescope software (Life Technologies, Ltd). Mapping to multiple locations was permitted. The quality threshold was set to 10 giving the mapping confidence more than 90. Reads with score less than 10 were filtered out. Average mapping quality was 30. Analysis of the RNA content and gene-based annotation was done within whole transcriptome workflow implemented in Lifescope.
attributes.tag: GEO Accession
attributes.value: GSM2652427