Transcriptome and translatome of ribosomal protein-deficient human cells

Human ribosomes are made of around 80 ribosomal proteins (RPs) and four ribosomal RNAs. To explore gene expression regulation by RPs at the transcriptional and translational levels, parallel RNA-seq and Ribo-seq were conducted in A549 cells after knockdown of individual RP. 75 human RPs were knocked-down by specific siRNAs one-by-one in A549 cells, and the RP-deficient cells were subjected to parallel RNA-seq and Ribo-seq. Gene expression in RP-deficient cells was compared with that in the control cells treated by non-targeting siRNAs. In total, we prepared 105 Ribo-seq libraries, with 105 paired RNA-seq libraries, for 78 human RPs as well as 8 control samples, where biological replicates were performed for 16 RPs and for 3 control samples.