The ribosomal protein S1-dependent standby site in tisB mRNA consists of a single-stranded region and a 5' structure element

In this study we report here on a detailed characterization of
the standby site in tisB mRNA. 30S
subunits bind to a single-stranded region and a 5'- stem loop structure, as
shown by fluorescence anisotropy experiments and footprint mapping by CLIP
experiments.

The data presented in figshare
includes raw and processed RNA reads obtained from our in vitro CLIP
experiment. Briefly, purified tisB mRNA was incubated with sub-stoichiometric
concentrations of either purified 30S subunits (carrying S1-3xFLAG) or
S1-3xFLAG only, followed by UV-crosslinking (250 mJ/cm2). 30S, S1 and
cross-linked RNAs were isolated by immuno-precipitation using Anti-FLAG coupled
magnetic beads. RNA footprints were generated on the beads with benzonase.
Proteins were digested with proteinase K, and, after labeling with radioactive
gamma-ATP, labeled RNA footprints (25-50 nt) were gel-purified. Eluted RNAs
were converted into cDNA using the CATS RNA-Seq kit v2 (diagenode) and
sequenced on an Illumina Miseq device. Reads were then aligned either to the
tisB sequence or the 16S rRNA sequence (as control).

The files available comprised:

- The raw data from the 30S and S1
CLIP experiments (Romilly_30S.fa and Romilly_S1.fa)

- Bam/bai files of reads mapped to
the tisB mRNA or the 16S rRNA, from the 30S and S1 pulldown assay
(30S_tisB.bam/bai, 30S_16S.bam.bai, S1_tisB.bam/bai, S1_16S.bam/bai)

- The sequence file containing the
tisB sequence and 16S rRNA, respectively (tisB_sequence.fa, 16S_sequence.fa)

- A gff files containing the
postions of the CDS and the standby site for the tisB sequence
(tisB_annotation.gff)

- Files with bowtie 2 summary and
stats for each of the processing step (Bowtie2 sumary, stats.30S.tabular, stats.S1.tabular,
stats.30Svs16SrRNA.tabular, stats.S1vs16SrRNA.tabular)

The figure representing the data
in the paper was generated using the visualization tool IGV 2.3.68

For more information on data
processing, please refer to the paper SI, or contact [e-mail] or
[e-mail].