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

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Villanueva Verdejo, Eneko 


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 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 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 (, these are sets of genes that are inferred to have descended from a common ancestral gene.


Software / Usage instructions

No specific software required


Proteomics, Transcriptomics


Wellcome Trust (110170/Z/15/Z)
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