Effect of TIMP1 depletion on gene expression in MIA PaCa-2 cell line by CRISPR/Cas9-based targeting of exon 4
This is a bulk RNA sequencing dataset of MIA PaCa-2 cells with or without genetic manipulation of the TIMP1 gene. A two-guide RNA system was used and designed to target two sites of exon 4, introducing a 64-bp deletion, leading to a frameshift and premature stop-codon. This led to the generation of two TIMP1 KO cell lines, as well as a CRISPR control cell line that acquired only a silent point mutation (g.64C>T) without altering the amino acid sequence. To measure the impact of TIMP1 on MIA PaCa-2 gene expression, bulk RNAseq was performed for all four cell lines (WT, CRISPR Control, KO 1, and KO 2) in triplicates. Overall design: All four cell lines were culltured to 70% confluency. Total RNA was isolated using the RNeasy Plus Mini Kit (Qiagen) and RNAseq was performed on a NovaSeq X Plus platform (Illumina).