GSM9143706: Breast CAFs DDR1 Knockdown RNA Replicate 2; Homo sapiens; RNA-Seq
Total RNA from CAFs was isolated using the GenCatch Total RNA mini prep kit (Epoch Life Science, Inc. Missouri City, TX, USA). Total RNA from control and doramapimod-treated tumors was isolated using Trizol (Invitrogen) according to the manufacturer's instructions. Library preparation, sequencing, and alignment were conducted by the Novogene. Pair-end sequencing was performed on an Illumina HiSeq 2500 machine using the poly-A capturing protocol with a read length of 43 base pairs. Libraries were prepared with the TruSeq Stranded Sample Preparation Kit (Illumina, RS-122-2201) starting from 1000 ng of total RNA. cDNA libraries were amplified and sequenced on the HiSeq2500. RNA-Seq data were filtered and normalized using the edgeR Bioconductor package in R. Differentially expressed genes (DEGs) were identified between the two cell-line groups using edgeR with parameters: log fold change > 1 (absolute fold change > 2) and P < 0.05. RNA libraries for RNA sequencing were prepared using Novogene and following the Illumina manufacturer's protocol.