Research data supporting: Interrogation of RNA-protein interaction dynamics in bacterial growth

This record containts mass spectrometry analysis of total proteome and RBPs dynamics in E coli growth and iCLIP analysis of Yfif and HtpG. This records contains 10 datasets, EV 1 - 10. The description for each dataset is: Dataset EV1: MS LFQ quantification of protein abudance across E. coli growth curve. For the growth curve experiments (n = 5 for each phase), the protein abundance was quantified by label-free quantification (LFQ) and data analysis was performed using the pRoloc R package. Category refers to 'Group' label in Figure 1. Dataset EV2: GO term annotations for proteins identified across E. coli growth curve by LFQ MS. Annotations of the 2360 proteins identified in LFQ assay and categorised into 6 groups. Dataset EV3: MS OOPS output RNase +/- assay normalized by trypsin amount along cell growth Dataset EV4: TMT quantification of protein abudance across E. coli growth curve. Data rendered in Figure 2 of the manuscript. Samples were takan a the lag (n=4), exponential (n=3) and stationary (n=3) phases and both the total proteome and the RBPome were subimitted for MS analyisis. Values were normalised acorss protein values for total protein and RBP separately. Extended EV5: STREME analysis YFIF table Completed at MEMESuite interface https://meme-suite.org/meme/doc/streme.html YFIF CL peaks against the control NC peaks. Extended EV6: Supplementary tables to phylogenetic analyses. Sheet 1: Whole Tree of Life (Binary columns indicating the presence/absence of ortholog for a given protein across the nodes of the tree of life). Sheet 2: Proteobacteria annot. Name of species and whether or not pathogenic (data represented in Fig. 4b) Extended EV7: STREME analysis HtpG table. Completed at MEMESuite interface https://meme-suite.org/meme/doc/streme.html HtpG CL peaks against the control NC peaks. Extended EV8: Additional information on proteomic data. Tags split to label total proteome and OOPS separately. Same tags used for each sample. Extended EV9: Primer information for iCLIP experiment. 3′ infrared adaptor (IDT, HPLC purified DNA with 5’ phosphate), RT primers (IDT, HPLC-purified), cDNA elution oligo, PCR primers (HPLC purified) Extended EV10: Orthologue reference table. The hierarchical orthologous groups (HOGs) for each candidate protein (i.e. experimentally uncharacterised RBPs) were retrieved from the OMA browser (https://omabrowser.org/oma/home/), these are sets of genes that are inferred to have descended from a common ancestral gene.