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BIOINF 16-001: Temperature-responsive in vitro RNA structurome of Yersinia pseudotuberculosis.

Righetti, Francesco and Nuss, Aaron M. and Twittenhoff, Christian and Beele, Sascha and Urban, Kristina and Will, Sebastian and Bernhart, Stephan H. and Stadler, Peter F. and Dersch, Petra and Narberhaus, Franz

Annotation files

Genomic coordinates of the different annnotation sets as gff files referring to the Yersinia pseudotuberculosis genome (NC_010465 and plasmid NC_006153; YPIII [fasta]).

FileDescription
ncRNA.gff Non-coding RNAs
cdRNA_chr.gff Coding RNAs
5UTR_p30.gff 5'-UTR regions extended by 30nt downstream
ICR_m100_p30.gff Intercistronic regions extended by 100nt upstream and 30nt downstream
1stORF.gff First open reading frames
pYV_cdr.gff Coding RNAs (plasmid)
pYV_icr_m100_p30.gff Intercistronic regions (plasmid)
pYV_operons.gff Operons RNAs (plasmid)
pYV_UTR_p30.gff 5UTR regions (plasmid)

PARS Scores

The calculated PARS scores from in vitro structure probing for the annotated regions at the different temperatures 25C, 37C, and 42C.

We provide one file per annotation and temperature. Each line reports the PARS scores for one annotated region in the corresponding gff. Each line starts with the region name, followed by the scores from first to last position (in 5'-3' orientation). The entries of each line are tab-separated (tsv files).

FileAnnotation set at temperature
ncRNA-pars-BC_05_06.tsv Non-coding RNAs at 25C
ncRNA-pars-BC_07_08.tsv Non-coding RNAs at 37C
ncRNA-pars-BC_09_10.tsv Non-coding RNAs at 42C
cdRNA-pars-BC_05_06.tsv Coding RNAs at 25C
cdRNA-pars-BC_07_08.tsv Coding RNAs at 37C
cdRNA-pars-BC_09_10.tsv Coding RNAs at 42C
5UTR_p30-pars-BC_05_06.tsv 5UTRs (+30nt) at 25C
5UTR_p30-pars-BC_07_08.tsv 5UTRs (+30nt) at 37C
5UTR_p30-pars-BC_09_10.tsv 5UTRs (+30nt) at 42C
ICR_m100_p30-pars-BC_05_06.tsv ICRs (-100nt; +30nt) at 25C
ICR_m100_p30-pars-BC_07_08.tsv ICRs (-100nt; +30nt) at 37C
ICR_m100_p30-pars-BC_09_10.tsv ICRs (-100nt; +30nt) at 42C
1stORF-pars-BC_05_06.tsv First ORFs at 25C
1stORF-pars-BC_07_08.tsv First ORFs at 37C
1stORF-pars-BC_09_10.tsv First ORFs at 42C
pYV_cdr-pars-BC_05_06.tsv Coding RNAs (plasmid) at 25C
pYV_cdr-pars-BC_07_08.tsv Coding RNAs (plasmid) at 37C
pYV_cdr-pars-BC_09_10.tsv Coding RNAs (plasmid) at 42C
pYV_icr_m100_p30-pars-BC_05_06.tsv Intercistronic regions (plasmid) at 25C
pYV_icr_m100_p30-pars-BC_07_08.tsv Intercistronic regions (plasmid) at 37C
pYV_icr_m100_p30-pars-BC_09_10.tsv Intercistronic regions (plasmid) at 42C
pYV_operons-pars-BC_05_06.tsv Operons (plasmid) at 25C
pYV_operons-pars-BC_07_08.tsv Operons (plasmid) at 37C
pYV_operons-pars-BC_09_10.tsv Operons (plasmid) at 42C
pYV_UTR_p30-pars-BC_05_06.tsv 5' UTRs (plasmid) at 25C
pYV_UTR_p30-pars-BC_07_08.tsv 5' UTRs (plasmid) at 37C
pYV_UTR_p30-pars-BC_09_10.tsv 5' UTRs (plasmid) at 42C

PARS-guided Predictions of Ensembles and Structures

Predicted secondary structure ensembles of all sequences (length<=400) of the annotation sets. The thermodynamic predictions are guided by the empirically derived PARS scores (applying RNAfold of the Vienna RNA package with the soft-constraint folding method of Washietl et al.). Foreach annotation set and temperature, we provide a zip archive containing 1) the predicted dot plots as postscript files and 2) the mfe secondary structure and ensemble description as text files.

FileAnnotation set at temperature
ncRNA-BC_05_06.zip Non-coding RNAs at 25C
ncRNA-BC_07_08.zip Non-coding RNAs at 37C
ncRNA-BC_09_10.zip Non-coding RNAs at 42C
cdRNA-BC_05_06.zip Coding RNAs at 25C
cdRNA-BC_07_08.zip Coding RNAs at 37C
cdRNA-BC_09_10.zip Coding RNAs at 42C
5UTR_p30-BC_05_06.zip 5UTRs (+30nt) at 25C
5UTR_p30-BC_07_08.zip 5UTRs (+30nt) at 37C
5UTR_p30-BC_09_10.zip 5UTRs (+30nt) at 42C
ICR_m100_p30-BC_05_06.zip ICRs (-100nt; +30nt) at 25C
ICR_m100_p30-BC_07_08.zip ICRs (-100nt; +30nt) at 37C
ICR_m100_p30-BC_09_10.zip ICRs (-100nt; +30nt) at 42C
1stORF-BC_05_06.zip First ORFs at 25C
1stORF-BC_07_08.zip First ORFs at 37C
1stORF-BC_09_10.zip First ORFs at 42C
pYV_cdr-BC_05_06.zip Coding RNAs (plasmid) at 25C
pYV_cdr-BC_07_08.zip Coding RNAs (plasmid) at 37C
pYV_cdr-BC_09_10.zip Coding RNAs (plasmid) at 42C
pYV_icr_m100_p30-BC_05_06.zip Intercistronic regions (plasmid) at 25C
pYV_icr_m100_p30-BC_07_08.zip Intercistronic regions (plasmid) at 37C
pYV_icr_m100_p30-BC_09_10.zip Intercistronic regions (plasmid) at 42C
pYV_operons-BC_05_06.zip Operons (plasmid) at 25C
pYV_operons-BC_07_08.zip Operons (plasmid) at 37C
pYV_operons-BC_09_10.zip Operons (plasmid) at 42C
pYV_UTR_p30-BC_05_06.zip 5' UTRs (plasmid) at 25C
pYV_UTR_p30-BC_07_08.zip 5' UTRs (plasmid) at 37C
pYV_UTR_p30-BC_09_10.zip 5' UTRs (plasmid) at 42C

Raw sequence data

Raw sequence data from the experiments BC_05,...,BC_10 as fastq.gz files.

FileDescription
BC_05.fastq.gz S1 digest (single stranded) at 25C
BC_06.fastq.gz V1 digest (double stranded) at 25C
BC_07.fastq.gz S1 digest (single stranded) at 37C
BC_08.fastq.gz V1 digest (double stranded) at 37C
BC_09.fastq.gz S1 digest (single stranded) at 42C
BC_10.fastq.gz V1 digest (double stranded) at 42C