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Category:Papers with tracks in Gbrowse

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EcoliWiki strives to make all E. coli data available, in the long run. We are working on putting the data from many papers into our genome browser, available here. This category might be called "Papers we want to put into Gbrowse" instead. For more information, see each paper's page.

To add papers to this list, add the tag:

Category:Papers with tracks in Gbrowse

If you would like to see your data as a viewable track in Gbrowse, feel free to contact us at ecoliwiki@gmail.com.

To access datasets:

  • Select desired dataset(s) by clicking on checkboxes in the table below, or the "Check all" box at the top of the table.
    • You can filter the table entries first by typing a keyword in the search box below.
  • Once you have selected at least one dataset, buttons will appear to allow you to view the data in the context of the relevant genome assembly. Just click on one of these buttons.

Check all strain experiment Analyte Reference Variable Conditions Notes Links

MG1655

ChIP-chip

RNAP

PMID:16109958[1]

Track is for both strands.

MG1655

ChIP-chip

FIS

PMID:16963779[2]

MG1655

ChIP-chip

H-NS

PMID:16963779[2]

MG1655

ChIP-chip

IHF

PMID:16963779[2]

MG1655

ChIP-chip

FNR

PMID:17164287[3]

MG1655

ChIP-chip

IHF

PMID:17164287[3]

MG1655

ChIP-chip

RNAP

PMID:17164287[3]

MG1655

ChIP-chip

Lrp

PMID:19052235[4]

Exponential phase w/ and w/o Rifampicin

Rifampicin effects are shown as subtracks

MG1655

ChIP-chip

Lrp

PMID:19052235[4]

Stationary phase w/and w/o Rifampicin

Rifampicin effects shown as subtracks.

MG1655

ChIP-chip

NusA

PMID:19150431[5]

MG1655

ChIP-chip

NusG

PMID:19150431[5]

MG1655

ChIP-chip

Rho

PMID:19150431[5]

MG1655

ChIP-chip

RNAP

PMID:19150431[5]

MG1655

ChIP-chip

RpoD (Sigma70)

PMID:19150431[5]

MG1655

ChIP-chip

RpoC RNAP beta prime

PMID:19706412[6]

RNAP in response to the Rho-specific inhibitor bicyclomycin (BCM)

MG1655

ChIP-chip

RpoB RNAP beta

PMID:19706412[6]

RNAP in response to the Rho-specific inhibitor bicyclomycin (BCM)

MG1655

ChIP-chip

RpoB RNAP beta

PMID:19706412[6]

Untreated

MG1655

ChIP-chip

RpoC RNAP beta prime

PMID:19706412[6]

Untreated

MG1655

ChIP-chip

SeqA

PMID:20689753[7]

dnaC(ts) at 30°ree;C

MG1655

ChIP-chip

SeqA

PMID:20689753[7]

dnaC(ts) at 42°ree;C for 1 hour; replication ceased

MG1655

ChIP-chip

SeqA

PMID:20689753[7]

dnaC(ts) at 42°ree;C for 1 hour; shifted back to 30°ree;C for 6 min; synchronized initiation of replication

MG1655

ChIP-chip

RNAP

PMID:20689753[7]

dnaC(ts) at 30°C for 1 hour; shifted back to 30°C for 6 min; synchronized initiation of replication

MG1655

ChIP-seq

Fis

PMID:21097887[8]

early and mid exponential phase.

MG1655

ChIP-seq

H-NS

PMID:21097887[8]

Early exponential, mid exponential, stationary, transition-to-stationary

MG1655

ChIP-seq

RNAP

PMID:21097887[8]

Deletion Fis mid-exponential phase, deletion Hns mid-exponential phase, wildtype mid-exponential phase.

BW25113

ChIP-chip

MntR

PMID:21239586[9]

This track is for E. coli strain BW25113 but is found under MG1655 since the array used was intended for MG1655.

MG1655

ChIP-chip

SlmA

PMID:21321206[10]

MG1655

ChIP-chip

PurR

PMID:21572102[11]

Adenine, Glucose

BW2952

Ribosome Profiling

Ribosomes

PMID:22153074[12]

dithiobis succinimidyl propionate (DSP) total and 1-ethyl 3-[3-dimethylaminopropyl]carbodiimide (EDC) total

2 crosslinkers, forward and reverse strands

BW2952

Ribosome Profiling

Trigger Factor (tig)

PMID:22153074[12]

dithiobis succinimidyl propionate (DSP) affinity purified (AP), 1-ethyl 3-[3-dimethylaminopropyl]carbodiimide (EDC) AP

Ribosomes crosslinked to trigger factor were affinity purified

MG1655

Ribosome Profiling

ribosomes

PMID:22456704[13]

MG1655

Ribosome Profiling

Ribosomes

PMID:23812753[14]

lambda induction timecourse

phage lambda

Ribosome Profiling

Ribosomes

PMID:23812753[14]

lambda induction timecourse

MG1655

ChIP-chip

FNR

PMID:23818864[15]

negative control (fnr deletion) and titration of Ptac-fnr

MG1655

ChIP-seq

FNR

PMID:23818864[15]

Anaerobic

MG1655

ChIP-chip

FNR

PMID:23818864[15]

negative control (fnr deletion) vs anaerobic vs hns stp double mutant

MG1655

ChIP-chip

H-NS

PMID:23818864[15]

aerobic vs anaerobic

MG1655

ChIP-chip

IHF

PMID:23818864[15]

Anaerobic

MG1655

ChIP-chip

RpoD RNAP sigma70

PMID:23818864[15]

aerobic vs anaerobic

MG1655

ChIP-chip

RpoB RNAP beta

PMID:23818864[15]

aerobic vs anaerobic

MG1655

RNA-seq

total RNA

PMID:23899370[16]

Heat shock

MG1655

RNA-seq

total RNA

PMID:23899370[16]

phosphorus starvation



  • Cho, BK, Barrett, CL, Knight, EM, Park, YS, Palsson, BØ (2008) Genome-scale reconstruction of the Lrp regulatory network in Escherichia coli. Proc. Natl. Acad. Sci. U.S.A. 105 19462-7 PMID:19052235
  • Cho, BK, Federowicz, SA, Embree, M, Park, YS, Kim, D, Palsson, BØ (2011) The PurR regulon in Escherichia coli K-12 MG1655. Nucleic Acids Res. 39 6456-64 PMID:21572102
  • Cho, H, McManus, HR, Dove, SL, Bernhardt, TG (2011) Nucleoid occlusion factor SlmA is a DNA-activated FtsZ polymerization antagonist. Proc. Natl. Acad. Sci. U.S.A. 108 3773-8 PMID:21321206
  • Grainger, DC, Aiba, H, Hurd, D, Browning, DF, Busby, SJ (2007) Transcription factor distribution in Escherichia coli: studies with FNR protein. Nucleic Acids Res. 35 269-78 PMID:17164287
  • Grainger, DC, Hurd, D, Goldberg, MD, Busby, SJ (2006) Association of nucleoid proteins with coding and non-coding segments of the Escherichia coli genome. Nucleic Acids Res. 34 4642-52 PMID:16963779
  • Herring, CD, Raffaelle, M, Allen, TE, Kanin, EI, Landick, R, Ansari, AZ, Palsson, BØ (2005) Immobilization of Escherichia coli RNA polymerase and location of binding sites by use of chromatin immunoprecipitation and microarrays. J. Bacteriol. 187 6166-74 PMID:16109958
  • Kahramanoglou, C, Seshasayee, AS, Prieto, AI, Ibberson, D, Schmidt, S, Zimmermann, J, Benes, V, Fraser, GM, Luscombe, NM (2011) Direct and indirect effects of H-NS and Fis on global gene expression control in Escherichia coli. Nucleic Acids Res. 39 2073-91 PMID:21097887
  • Li, GW, Oh, E, Weissman, JS (2012) The anti-Shine-Dalgarno sequence drives translational pausing and codon choice in bacteria. Nature 484 538-41 PMID:22456704
  • Li, S, Dong, X, Su, Z (2013) Directional RNA-seq reveals highly complex condition-dependent transcriptomes in E. coli K12 through accurate full-length transcripts assembling. BMC Genomics 14 520 PMID:23899370
  • Liu, X, Jiang, H, Gu, Z, Roberts, JW (2013) High-resolution view of bacteriophage lambda gene expression by ribosome profiling. Proc. Natl. Acad. Sci. U.S.A. PMID:23812753
  • Mooney, RA, Davis, SE, Peters, JM, Rowland, JL, Ansari, AZ, Landick, R (2009) Regulator trafficking on bacterial transcription units in vivo. Mol. Cell 33 97-108 PMID:19150431
  • Myers, KS, Yan, H, Ong, IM, Chung, D, Liang, K, Tran, F, Keleş, S, Landick, R, Kiley, PJ (2013) Genome-scale Analysis of Escherichia coli FNR Reveals Complex Features of Transcription Factor Binding. PLoS Genet. 9 e1003565 PMID:23818864
  • Oh, E, Becker, AH, Sandikci, A, Huber, D, Chaba, R, Gloge, F, Nichols, RJ, Typas, A, Gross, CA, Kramer, G, Weissman, JS, Bukau, B (2011) Selective ribosome profiling reveals the cotranslational chaperone action of trigger factor in vivo. Cell 147 1295-308 PMID:22153074
  • Peters, JM, Mooney, RA, Kuan, PF, Rowland, JL, Keles, S, Landick, R (2009) Rho directs widespread termination of intragenic and stable RNA transcription. Proc. Natl. Acad. Sci. U.S.A. 106 15406-11 PMID:19706412
  • Sánchez-Romero, MA, Busby, SJ, Dyer, NP, Ott, S, Millard, AD, Grainger, DC (2010) Dynamic distribution of seqa protein across the chromosome of escherichia coli K-12. MBio 1 PMID:20689753
  • Yamamoto, K, Ishihama, A, Busby, SJ, Grainger, DC (2011) The Escherichia coli K-12 MntR miniregulon includes dps, which encodes the major stationary-phase DNA-binding protein. J. Bacteriol. 193 1477-80 PMID:21239586

See also

References

See Help:References for how to manage references in EcoliWiki.
  1. Herring, CD et al. (2005) Immobilization of Escherichia coli RNA polymerase and location of binding sites by use of chromatin immunoprecipitation and microarrays. J. Bacteriol. 187 6166-74 PubMed EcoliWiki page
  2. 2.0 2.1 2.2 Grainger, DC et al. (2006) Association of nucleoid proteins with coding and non-coding segments of the Escherichia coli genome. Nucleic Acids Res. 34 4642-52 PubMed EcoliWiki page
  3. 3.0 3.1 3.2 Grainger, DC et al. (2007) Transcription factor distribution in Escherichia coli: studies with FNR protein. Nucleic Acids Res. 35 269-78 PubMed EcoliWiki page
  4. 4.0 4.1 Cho, BK et al. (2008) Genome-scale reconstruction of the Lrp regulatory network in Escherichia coli. Proc. Natl. Acad. Sci. U.S.A. 105 19462-7 PubMed EcoliWiki page
  5. 5.0 5.1 5.2 5.3 5.4 Mooney, RA et al. (2009) Regulator trafficking on bacterial transcription units in vivo. Mol. Cell 33 97-108 PubMed EcoliWiki page
  6. 6.0 6.1 6.2 6.3 Peters, JM et al. (2009) Rho directs widespread termination of intragenic and stable RNA transcription. Proc. Natl. Acad. Sci. U.S.A. 106 15406-11 PubMed EcoliWiki page
  7. 7.0 7.1 7.2 7.3 Sánchez-Romero, MA et al. (2010) Dynamic distribution of seqa protein across the chromosome of escherichia coli K-12. MBio 1 PubMed EcoliWiki page
  8. 8.0 8.1 8.2 Kahramanoglou, C et al. (2011) Direct and indirect effects of H-NS and Fis on global gene expression control in Escherichia coli. Nucleic Acids Res. 39 2073-91 PubMed EcoliWiki page
  9. Yamamoto, K et al. (2011) The Escherichia coli K-12 MntR miniregulon includes dps, which encodes the major stationary-phase DNA-binding protein. J. Bacteriol. 193 1477-80 PubMed EcoliWiki page
  10. Cho, H et al. (2011) Nucleoid occlusion factor SlmA is a DNA-activated FtsZ polymerization antagonist. Proc. Natl. Acad. Sci. U.S.A. 108 3773-8 PubMed EcoliWiki page
  11. Cho, BK et al. (2011) The PurR regulon in Escherichia coli K-12 MG1655. Nucleic Acids Res. 39 6456-64 PubMed EcoliWiki page
  12. 12.0 12.1 Oh, E et al. (2011) Selective ribosome profiling reveals the cotranslational chaperone action of trigger factor in vivo. Cell 147 1295-308 PubMed EcoliWiki page
  13. Li, GW et al. (2012) The anti-Shine-Dalgarno sequence drives translational pausing and codon choice in bacteria. Nature 484 538-41 PubMed EcoliWiki page
  14. 14.0 14.1 Liu, X et al. (2013) High-resolution view of bacteriophage lambda gene expression by ribosome profiling. Proc. Natl. Acad. Sci. U.S.A. PubMed EcoliWiki page
  15. 15.0 15.1 15.2 15.3 15.4 15.5 15.6 Myers, KS et al. (2013) Genome-scale Analysis of Escherichia coli FNR Reveals Complex Features of Transcription Factor Binding. PLoS Genet. 9 e1003565 PubMed EcoliWiki page
  16. 16.0 16.1 Li, S et al. (2013) Directional RNA-seq reveals highly complex condition-dependent transcriptomes in E. coli K12 through accurate full-length transcripts assembling. BMC Genomics 14 520 PubMed EcoliWiki page

Subcategories

This category has only the following subcategory.

Pages in category "Papers with tracks in Gbrowse"

The following 16 pages are in this category, out of 16 total.