Expression data from lncRNA AL078604.2 and LINC01269 knockdown in MDA-MB-231, MDA-MB-468 and SKBR3 breast cancer cell lines

Breast cancer subtype-specific lncRNAs AL078604.2 and LINC01269 were knockdown in breast cancer cell lines LncRNA AL078604.2 was knockdown by an anti-AL076804.2 antisense oligonucleotides (ASOs) in triple-negative breast cancer cell lines MDA-MB-231 and MDA-MB-468 breast cancer cells. LncRNA LINC01269 was knockdown by an anti-LINC01269 ASOs in HER2+ SKBR3 breast cancer cells. To ensure the initial presence of AL078604.2 and LINC01269 in their respective cell lines, qPCR analysis was performed to confirm their expression levels prior to knockdown experiments. The effectiveness of knockdown was confirmed by qPCR analysis, which validated the reduction in AL078604.2 and LNC01269 expression in their corresponding cell lines following ASO treatment. To investigate the impact of lncRNA AL078604.2 on the transcriptome of triple-negative breast cancer, microarray analyses were conducted on MDA-MB-231 and MDA-MB-468 cell lines. Cells were treated with either control ASO or anti-AL078604.2 ASO1 for 48 hours. A parallel investigation was carried out to evaluate the effect of lncRNA LINC01269 on gene expression in HER2+ breast cancer cells. SKBR3 cells were treated with control ASO and anti-LINC01269 ASO for 48 hours. Following the ASO treatment, the cells were collected and preserved in TRIzol reagent for subsequent RNA purification. The purified RNA samples were then sent to The Centre for Applied Genomics (TCAG), located at The Hospital for Sick Children in Toronto, Canada. The RNA samples underwent reverse transcription into complementary DNA (cDNA) and were subsequently hybridized to the Affymetrix Human Gene 2.0 ST microarray platform. The collected data was initially obtained in raw CEL format and subsequently processed using the Transcriptome Analysis Console (Affymetrix).