Dnase 1 set

RNA extraction was performed using a Direct-zol RNA MiniPrep and DNAse I Set (Zymo Research, Irvine, CA, USA) according to the manufacturers’ instructions. A NanoDrop ND 8000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA) was used to measure the RNA integrity and quality. One microgram of extracted RNA was applied for cDNA synthesis using the GoScript reverse transcription system (Promega) according to the manufacturer’s protocol. After the reaction, the cDNA was diluted 1:25 for further analysis.

Thirty steroid-starved LCLs with similar expression of GR selected from the 300-LCL panel (Supplementary Table S1) were subjected to the four drug exposure conditions in serum-free media for 9 h. After treatment, cells were pelleted, and total RNA was extracted with the RNAeasy Mini Kit per manufacturer's instruction (Qiagen). DNase on-column treatment was performed with the DNase I set (Zymo). RNA integrity number for all samples was 10. RNA-seq libraries were prepared with the TruSeq RNA Library Prep Kit v2 (Illumina). Paired-end sequencing 2 × 100 bp was conducted on an Illumina HiSeq 4000 with a sequencing depth of ∼25 million paired-end reads per sample. Raw RNA sequencing reads were aligned to the human genome GRCh37 (hg19) using STAR (21 (link)). Raw counts were generated with the Python package ‘HTseq’ (22 (link)) and normalized using conditional quantile normalization method (CQN). Only genes that passed normalized counts of 32 in at least 15 cell lines and one drug condition were retained. Downstream differential expression analysis was conducted with the R package ‘EdgeR’ (23 (link)) using a quasi-likelihood model.

Total RNAs were isolated from a pool of ten live ACPs using ZR Tissue and Insect Microprep^™ (Zymo Research, Irvine, CA, USA, catalogue no. D6015), and the genomic DNA was removed from the samples with a DNAse I Set (Zymo Research, Irvine, CA, USA, catalogue no. E1010) according to the manufacturer’s protocol. The concentration and purity were determined using a NanoDrop ND 8000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA). cDNA synthesis was performed using iScript^™ Reverse Transcription Supermix (Bio-Rad^®, Hercules, CA, USA, catalogue no. 170–8841) according the manufacturer’s protocol.