Importance of experimental information (metadata) for archived sequence data: case of specific gene bias due to lag time between sample harvest and RNA protection in RNA sequencing

Large volumes of high-throughput sequencing data have been submitted to the Sequencing Read Archive (SRA). The lack experimental metadata associated with makes reuse and understanding quality very difficult. In case RNA (RNA-Seq), which reveals presence quantity in a biological sample at any moment, it is necessary consider that gene expression responds over short time interval (several seconds few minutes) many organisms. Therefore, isolate accurately reflects transcriptome point harvest, raw samples should be processed by freezing liquid nitrogen, immersing stabilization reagent or lysing homogenizing lysis buffer containing guanidine thiocyanate as soon possible. As number handled simultaneously increases, until protected can increase. Here, evaluate effect different lag times protection on RNA-Seq data, we harvested CHO-S cells after 3, 5, 6, 7 days cultivation, added course 15, 30, 45, 60 min conducted RNA-Seq. These showed high integrity (RIN) values indicating non-degraded RNA, sequence from libraries prepared these was according FastQC. We observed that, same cultivation day, global trends were similar across addition buffer; however, some genes significantly between time-course day; most differentially expressed related apoptosis. conclude harvest influences specific genes. It is, therefore, know not only RIN but also how experiment performed when acquiring database.