GSM9196826: Isogenic SW48 cell line (parental, wild-type for KRAS) - low nutrient conditions - DMSO control; Homo sapiens; RNA-Seq
SW48 isogenic cells were thawed and cultured for 3 passages before sample preparation. 5 replicates from 3 different batches of each cell line were used for the RNAseq experiment. Briefly, 1.5 million cells were seeded on a 6 cm dish in full media conditions. 48 hours later, cells were washed once with cold PBS and collected by scraping with 1 ml PBS into 1.5 ml Eppendorf tubes. Samples were centrifuged for 3 minutes at 1,000 rpm and 4 °C. Pellets were stored at -80 °C until shipment. RNA extraction, library preparation and sequencing (20 million reads per sample) was performed by BGI Genomics (BGI Hong Kong Company Limited). Libraries were prepared by BGI. 1)mRNA enrichment and purification: rRNA depletion or Oligo dT Selection to enrich the mRNA 2)RNA fragment and reverse transcription 3)End repair, add A and adaptor ligation 4)RCR amplification 5)Single strand separation and cyclization 6)DNA nanoball synthesis 7)Sequencing on BGISEQ platform