Global transcriptome profiling of the 889PF mouse pleural fluid disseminating tumour cell-derived cell line, with or without Cd109 knockdown

In order to determine the role of Cd109 in regulating metastatic ability and identify Cd109-dependent transcriptonal targets in metastatic lung adenocarcinoma, we sequenced the mRNA from 3 mouse metastasis cell lines. Each of these cell lines (889PF-shGFP, 889PF-shCd109#1, and 889PF-shCd109#2) were derived from the same parental cell line 889PF. 889PF was derived from the pleural fluid of a Kras LSL G12D, p53 flox/flox 129S1/SvlmJ mouse model of metastatic lung adenocarcinoma. A comparison of shGFP and shCd109 cell lines reveals Cd109-dependent changes in the metastatic transcriptome. Overall design: This study includes 6 samples: 2 biological replicates of 889PF shGFP, 2 biological replicates of 889PF shCd109#1, and 2 biological replicates of 889PFshCd109#2. Poly-A RNA was isolated and prepared for sequencing using the Illumina TruSeq RNA kit (v2) to generate 100bp paired end reads. Reads were aligned to mm10.