E. coli TSS

• Thomason, M. K., Bischler, T., Eisenbart, S. K., Förstner, K. U., Zhang, A., Herbig, A., Nieselt, K., Sharma, C. M. and Storz, G. (2014) Global transcriptional start site mapping using dRNA-seq reveals novel antisense RNAs in Escherichia coli. J. Bacteriol. 197, 18-28.
  
  We had previously provided a link to GenomeView to view the data from the above paper, but the link no longer seems to work for most people. We are now providing access to the dRNA-seq data in the UCSC browser in two different track hubs:

  1. Data mapped to E. coli genome NC_000913.2. This displays the same tracks that were used in GenomeView, as used in the paper:
  https://genome.ucsc.edu/cgi-bin/hgTracks?hubUrl=https://hpc.nih.gov/~NICHD-core0/storz/trackhubs/ecoli_drnaseqV2/hub.hub.txt&hgS_loadUrlName=https://hpc.nih.gov/~NICHD-core0/storz/trackhubs/ecoli_drnaseqV2/session.txt&hgS_doLoadUrl=submit 

  2. Data mapped to E. coli genome NC_000913.3. These tracks represent a re-alignment of the raw data to the new assembly using a standard tool set (bwa followed by deepTools bamCoverage) and as such does not identically match the methods in the paper. There are also no TSSs called on these data. We are providing these data as a convenience to those using the updated E. coli assembly:
  https://genome.ucsc.edu/cgi-bin/hgTracks?hubUrl=https://hpc.nih.gov/~NICHD-core0/storz/trackhubs/ecoli_tss/hub.hub.txt&hgS_loadUrlName=https://hpc.nih.gov/~NICHD-core0/storz/trackhubs/ecoli_tss/session.txt&hgS_doLoadUrl=submit 

E. coli Term-seq (and combined TSS, TTS and total RNA data)

• Adams, P. P., Baniulyte, G., Esnault, C., Chegireddy, K., Singh, N., Monge, M., Dale, R. K., Storz, G. and Wade, J. T. (2020) Regulatory roles of 5’ UTR and ORF-internal RNA detected by 3’ end mapping. bioRxiv 2020.07.18.207399.
  
  E. coli Term-seq.
  https://genome.ucsc.edu/cgi-bin/hgTracks?hubUrl=https://hpc.nih.gov/~NICHD-core0/storz/trackhubs/ecoli_all_Feb2019/hub.hub.txt&hgS_loadUrlName=https://hpc.nih.gov/~NICHD-core0/storz/trackhubs/ecoli_all_Feb2019/session.txt&hgS_doLoadUrl=submit
  
  E. coli Rho-dependent 3` ends (Term-seq LB 0.4 and DirectRNA-seq).
  https://genome.ucsc.edu/cgi-bin/hgTracks?hubUrl=https://hpc.nih.gov/~NICHD-core0/storz/trackhubs/ecoli_rho/hub.hub.txt&hgS_loadUrlName=https://hpc.nih.gov/~NICHD-core0/storz/trackhubs/ecoli_rho/session.txt&hgS_doLoadUrl=submit
  
  E. coli combined TSS, TTS and total RNA data.
  https://genome.ucsc.edu/cgi-bin/hgTracks?hubUrl=https://hpc.nih.gov/~NICHD-core0/storz/trackhubs/ecoli_dRNAseq/hub.hub.txt&hgS_loadUrlName=https://hpc.nih.gov/~NICHD-core0/storz/trackhubs/ecoli_dRNAseq/session.txt&hgS_doLoadUrl=submit

E. coli RIL-seq for ProQ and Hfq (and comparison to previous E. coli RIL-seq and E. coli CLASH data for Hfq)

• Melamed, S., Adams, P.P., Zhang, A., Zhang, H. and Storz, G. (2020) RNA-RNA interactomes of ProQ and Hfq reveal overlapping and competing roles. Mol. Cell, 77:411-425.e7.
  
  Two independent datasets.
  RIL-seq experiment 1:
  https://genome.ucsc.edu/cgi-bin/hgTracks?hubUrl=https://hpc.nih.gov/~NICHD-core0/storz/trackhubs/ecoli_rilseq/hub.hub.txt&hgS_loadUrlName=https://hpc.nih.gov/~NICHD-core0/storz/trackhubs/ecoli_rilseq/session.txt&hgS_doLoadUrl=submit
  RIL-seq experiment 2:
  https://genome.ucsc.edu/cgi-bin/hgTracks?hubUrl=https://hpc.nih.gov/~NICHD-core0/storz/trackhubs/ecoli_rilseq2/hub.hub.txt&hgS_loadUrlName=https://hpc.nih.gov/~NICHD-core0/storz/trackhubs/ecoli_rilseq2/session.txt&hgS_doLoadUrl=submit

  E. coli RIL-seq data for Hfq from Melamed, S., Peer, A., Faigenbaum-Romm, R., Gatt, Y.E., Reiss, N., Bar, A., Altuvia, Y., Argaman, L. and Margalit, H. (2016) Global mapping of small RNA-target interactions in bacteria. Mol. Cell 63:884-897. (These data a mapped to E. coli genome NC_000913.2)
  RIL-seq single fragments:
  http://microbes.ucsc.edu/cgi-bin/hgTracks?db=eschColi_K12&hgt.customText=http://www.cs.huji.ac.il/~asafp5/RILseq/RILseq_coverage.wig.gz
  RIL-seq chimeric fragments:
  http://microbes.ucsc.edu/cgi-bin/hgTracks?db=eschColi_K12&hgt.customText=http://www.cs.huji.ac.il/~asafp5/RILseq/RILseq_interactions.bed.gz

  E. coli CLASH data for Hfq from Iosub, I. A., van Nues, R. W., McKellar, S. W., Nieken, K. J., Marchioretto, M., Sy, B., Tree, J. J., Viero, G., and Granneman, S. (2020) Hfq CLASH uncovers sRNA-target interaction networks linked to nutrient availability adaptation. eLife 9:e54655.
  https://genome.ucsc.edu/cgi-bin/hgTracks?hubUrl=https://hpc.nih.gov/~NICHD-core0/storz/trackhubs/CLASH_trackhub/CLASH_assembly_hub.hub.txt&hgS_loadUrlName=https://hpc.nih.gov/~NICHD-core0/storz/trackhubs/CLASH_trackhub/session.txt&hgS_doLoadUrl=submit

E. coli ribosome profiling with stalled initiation complexes

• Weaver, J., Mohammad, F., Buskirk, A.R. and Storz, G. (2019) Identifying small proteins by ribosome profiling with stalled initiation complexes. mBio, 10:e02819-18.
  
  Onc112 data from this paper together with the retapamulin data from Meydan S, Marks J, Klepacki D, Sharma V, Baranov PV, Firth AE, Margus T, Kefi A, Vázquez-Laslop N, Mankin AS. (2019) Retapamulin-Assisted Ribosome Profiling Reveals the Alternative Bacterial Proteome. Mol Cell, 74:481-493 can be found in the UCSC browser: https://genome.ucsc.edu/cgi-bin/hgTracks?hubUrl=https://hpc.nih.gov/~NICHD-core0/storz/trackhubs/ecoli_ribo/hub.hub.txt&hgS_loadUrlName=https://hpc.nih.gov/~NICHD-core0/storz/trackhubs/ecoli_ribo/session.txt&hgS_doLoadUrl=submit 

E. coli RNA-RNA interactome data for Hfq mutants

• Luo, X., Zhang, A., Esnault, C., De Mets, F., Adams, P.P., Dale, R.K., Storz, G. and Gottesman, S. (2025) RNA-RNA interactome approaches provide in vivo evidence for a critical role of the Hfq rim face in sRNA-mRNA pairing. bioRxiv 2025.06.26.660752.
  
  Two different datasets: 
  E. coli RIL-seq (anti-Flag) for wild type Hfq and D9A, R16A, Y25D and K31A mutants (two replicate datasets)
  https://www.nichd.nih.gov/about/org/dir/other-facilities/cores/bioinformatics/data/luo-RILSeq_antiFlag_rep1
  https://www.nichd.nih.gov/about/org/dir/other-facilities/cores/bioinformatics/data/luo-RILSeq_antiFlag_rep2 

  E. coli RIL-seq and iRIL-seq (anti-Hfq) for wild type Hfq and R16A mutant (two replicate datasets)
  https://www.nichd.nih.gov/about/org/dir/other-facilities/cores/bioinformatics/data/luo-RILSeq_antiHfq_and_iRILseq_rep1
  https://www.nichd.nih.gov/about/org/dir/other-facilities/cores/bioinformatics/data/luo-RILSeq_antiHfq_and_iRILseq_rep2