Project description:Gene expression was measured on the Affymetrix platform in primary xenografts, xenograft-derived cell lines, secondary xenografts, normal lung, and primary tumors obtained from chemotherapy naive Small Cell Lung Cancer (SCLC). The SCLC primary xenografts were serially propagated in vivo in immunodeficient mice. Cell lines were derived from each xenograft and grown for 6 months using conventional tissue culture conditions. Secondary xenografts were obtained from cell cultures by re-implantation in immunodeficient mice. Such SCLC laboratory models were analyzed along with conventional SCLC cell lines and the derivative secondary xenografts, with normal lung and primary tumors, to assess irreversible gene expression changes induced by culturing conditions. Experiment Overall Design: SCLC primary xenografts were compared to the corresponding xenograft-derived cell lines, and to the secondary xenografts established from the cell lines using the Affymetrix GeneChip Human Genome U133 Plus 2.0 Array. Gene expression from SCLC primary tumors was measured using the Affymetrix GeneChip Human Genome U133A 2.0 Array. 3 datasets: GSM380476-GSM380512, GSM380513-GSM380516, and GSM380517-GSM380520
Project description:In order to study the mechanism of co-inactivation of RB1 and TP53 in the transformation of lung adenocarcinoma to small cell lung cancer, we established the NCI-H1975 cell line with RB1 knockdown.NCI-H1975 cells were cultured and infected with lentivirus expressing RB1-shRNA (n=3) or pLKO.1-shRNA (n=3), We then performed transcriptome sequencing (RNA-seq) on the above cells.
Project description:Gene expression was measured on the Affymetrix platform in primary xenografts, xenograft-derived cell lines, secondary xenografts, normal lung, and primary tumors obtained from chemotherapy naive Small Cell Lung Cancer (SCLC). The SCLC primary xenografts were serially propagated in vivo in immunodeficient mice. Cell lines were derived from each xenograft and grown for 6 months using conventional tissue culture conditions. Secondary xenografts were obtained from cell cultures by re-implantation in immunodeficient mice. Such SCLC laboratory models were analyzed along with conventional SCLC cell lines and the derivative secondary xenografts, with normal lung and primary tumors, to assess irreversible gene expression changes induced by culturing conditions.
Project description:Genome-wide DNA methylation profiling of non-small cell lung cancer (NSCLC) cell line A549 and breast cancer cell line MDA-MB-231 stably expressing hSTELLA and mSTELLA, as well as the HCT116 xenograft tumor tissues from the mice treated by the indicated LNP formulations. The Infinium MethylationEPIC v2.0 array was used to obtain DNA methylation profiles across more than 935,000 CpGs in 15 samples. Samples included 3 stable NSCLC cells and 3 stable breast cancer cells expressing the STELLA orthologs, and 9 xenograft tumors from the mice with the indicated treatments.