NextSeq 500 paired end sequencing; RNA-seq of human breast cancer cell lines: CAL120; MDAMB468 and BT549 incubated in DMEM-F12 and Plasmax in normoxia (21%O2) and hypoxia (0.1% O2)
RNA-seq of human breast cancer cell lines: CAL120; MDAMB468 and BT549 incubated in DMEM-F12 and Plasmax in normoxia (21%O2) and hypoxia (0.1% O2)
Cell lines were grown either in normoxia (21 percent oxygen) or in hypoxia (0.1 percent oxygen). Cells were cultured in 6-well plates, harvested in 600 uL RLT buffer (RNeasy Mini Kit, Qiagen) and homogenized (QIAshredder, Qiagen). Plasmax cell culture medium which is the subject of this study is produced in house and it is not commercially available. However the precise formulation as well as other relevant information on its production are provided in the manuscript. RNA was extracted using the RNease Mini kit (Qiagen) and processed with on column DNAse digestion (Qiagen). Libraries for cluster generation and DNA sequencing were prepared following an adapted method from Fisher et al. (Genome Biol 12, R1, 2011) using Illumina TruSeq RNA Library Preparation Kit v2. Quality and quantity of the DNA libraries were assessed on an Agilent 2200 Tapestation (D1000 screentape) and Qubit (Thermo Fisher Scientific), respectively.
Experimental Factor: growth condition
DMEM-F12 media
Experimental Factor: cell line
BT549