GSM5627889: PANC-1_sh-Ctrl_acRIP_Rep 1; Homo sapiens; RIP-Seq
The PANC-1 cells were divided in two groups: 1.PANC-1 transfected with short hairpin RNA (shRNA) empty vector; 2.PANC-1 transfected with shRNA vector which could knockdown the expression of NAT10. Lentivirus was used to carry shRNAs, respectively. For RNA-seq, RNA libraries were prepared for sequencing using standard Illumina protocols. For acRIP-seq, fragmented total RNA (Input) and immunoprecipitated RNA (IP) were subjected to library construction by using EpiTM mini longRNA-seq kit(Epibiotek, Cat# E1802) according to the manufacturer's protocols. Breifly, reverse transcription was performed using random primers and the ribosome cDNA (cDNA fragments originating from rRNA molecules) was removed after cDNA synthesis using probes specific to mammalian rRNA. The directionality of the template-switching reaction not only preserves the 5' end sequence information of RNA but the strand orientation of the original RNA. Libraries for immunoprecipitated RNA were PCR amplified for 18 cycles. Libraries quality were determined on Qseq100 Bio-Fragment Analyzer（Bioptic lnc.）.The strand-specific libraries were sequenced on Illumina Novaseq 6000 system with paired-end 2×150 bp read length.