DLD1WT18hr2
RNA-sequencing was performed by the Experimental and Computational Genomics Core at Johns Hopkins University. In brief, 1 g of RNA extracted from G3BP1 WT or KO DLD-1 cells treated with or without actinomycin D (ACTD; 10 g/ml for 18 h) were used for library preparation. To better normalize changes in RNA expression between 0 h and 18 h of ACTD treatment, 1 l of 1:100 diluted ERCC RNA Spike-In Mix (Thermo) was added to each sample. Libraries were prepared following manufacturers instructions using the TruSeq Stranded Total RNA Kit (Illumina) with barcoding and sequenced on the HiSeq2500 (Illumina) with 151x151 paired-end reads. Illumina's CASAVA 1.8.4 was used to convert BCL files to FASTQ files using default parameters. rsem-1.3.0 was used for running the alignments as well as generating gene expression levels. The rsem-calculate-expression module was used with the following options: --star, --star-gzipped-read-file, --calc-ci, --star-output-genome-bam, --paired-end, --forward-prob 0. The data were aligned to hg19 reference genome with ERCC spike-in RNA sequences.