Additional file 5: Table S4. of Genome-wide transcription start site profiling in biofilm-grown Burkholderia cenocepacia J2315

Additional file 4: of Transcription profiling of butanol producer Clostridium beijerinckii NRRL B-598 using RNA-Seq

Karel Sedlar (607534)
Pavlina Koscova (5315204)
Maryna Vasylkivska (5315201)
Barbora Branska (5315207)
Jan Kolek (712011)
Kristyna Kupkova (5315210)
Petra Patakova (5315213)
Ivo Provaznik (579935)

May 2018

Circular plots showing average coverage of the genome by RNA-Seq reads in all six time points. The o...

Additional file 7: Table S4. of Whole transcriptomic analysis of the plant-beneficial rhizobacterium Bacillus amyloliquefaciens SQR9 during enhanced biofilm formation regulated by maize root exudates

Nan Zhang (46264)
Dongqing Yang (675454)
Dandan Wang (286632)
Youzhi Miao (3480608)
Jiahui Shao (3130440)
Xuan Zhou (329338)
Zhihui Xu (453724)
Qing Li (84975)
Haichao Feng (3480605)
Shuqing Li (1430998)
Qirong Shen (404759)
Ruifu Zhang (331550)

September 2015

Genomic island (GI) prediction of Bacillus amyloliquefaciens SQR9. GIs were predicted by IslandViewe...

Additional file 1: of Transcriptionally promiscuous “blurry” promoters in Tc1/mariner transposons allow transcription in distantly related genomes

Antonio Palazzo (484949)
Patrizio Lorusso (6553208)
Csaba Miskey (466684)
Oliver Walisko (6553211)
Andrea Gerbino (716948)
Carlo Marobbio (6553214)
Zoltán Ivics (196129)
René Marsano (6553217)

April 2019

Table S1. TATA box motif prediction. Pval cutoff 10exp-2; origin = START; only direct strand results...

Additional file 4: Figure S1. of Genome-wide transcription start site profiling in biofilm-grown Burkholderia cenocepacia J2315

Andrea Sass (224214)
Heleen Van Acker (286683)
Konrad Förstner (822551)
Filip Van Nieuwerburgh (20881)
Dieter Deforce (20882)
Jörg Vogel (11205)
Tom Coenye (20880)

October 2015

Transcription start sites confirmed by 5′RACE. dRNA-Seq data are represented as number of read start...

Genome-wide transcription start site profiling in biofilm-grown Burkholderia cenocepacia J2315

Sass, Andrea M.
Van Acker, Heleen
Förstner, Konrad U.
Van Nieuwerburgh, Filip
Deforce, Dieter
Vogel, Jörg
Coenye, Tom

January 2015

Background: Burkholderia cenocepacia is a soil-dwelling Gram-negative Betaproteobacterium with an im...

RESEARCH ARTICLE Open Access Genome-wide transcription start site profiling in biofilm-grown Burkholderia cenocepacia J2315

Andrea M. Sass
Heleen Van Acker
Konrad U. Förstner
Filip Van Nieuwerburgh
Dieter Deforce
Jörg Vogel
Tom Coenye

August 2016

Background: Burkholderia cenocepacia is a soil-dwelling Gram-negative Betaproteobacterium with an im...

Additional file 5: Table S4. of TSS-EMOTE, a refined protocol for a more complete and less biased global mapping of transcription start sites in bacterial pathogens

Julien Prados (743297)
Patrick Linder (7345)
Peter Redder (528225)

November 2016

Predicted operon structure based on TSS-EMOTE experimental data and in silico transcription terminat...

Genome-wide prediction and validation of sigma70 promoters in Lactobacillus plantarum WCFS1

Todt, T.J.
Wels, M.W.
Bongers, R.S.
Siezen, R.S.
van Hijum, S.A.
Kleerebezem, M.

January 2012

Contains fulltext : 108029.pdf (publisher's version ) (Open Access)BACKGROUND: In ...

Additional file 3: of Genome-wide transcription start site mapping of Bradyrhizobium japonicum grown free-living or in symbiosis â a rich resource to identify new transcripts, proteins and to study gene regulation

Jelena Äuklina (3491417)
Julia Hahn (3279486)
Maxim Imakaev (648765)
Ulrich Omasits (119127)
Konrad FĂśrstner (3491414)
Nikolay Ljubimov (3491387)
Melanie Goebel (3491390)
Gabriella Pessi (119095)
Hans-Martin Fischer (143595)
Christian Ahrens (3490766)
Mikhail Gelfand (4027)
Elena Evguenieva-Hackenberg (828729)

April 2016

Table S3 listing all mapped TSSs; Table S4 listing previously published TSSs compared to our TSS map...

Genome-wide determination of transcription start sites reveals new insights into promoter structures in the actinomycete Corynebacterium glutamicum.

Albersmeier, Andreas
Pfeifer-Sancar, Katharina
Rückert, Christian
Kalinowski, Jörn

January 2017

Albersmeier A, Pfeifer-Sancar K, Rückert C, Kalinowski J. Genome-wide determination of transcription...

Global mapping of transcription start sites and promoter motifs in the symbiotic a-proteobacterium Sinorhizobium meliloti 1021

Schlueter, Jan-Philip
Reinkensmeier, Jan
Barnett, Melanie J.
Lang, Claus
Krol, Elizaveta
Giegerich, Robert
Long, Sharon R.
Becker, Anke

January 2013

Schlueter J-P, Reinkensmeier J, Barnett MJ, et al. Global mapping of transcription start sites and p...

Additional file 6: Figure S3. of Global transcriptional landscape and promoter mapping of the gut commensal Bifidobacterium breve UCC2003

Francesca Bottacini (133911)
Aldert Zomer (144349)
Christian Milani (133915)
Chiara Ferrario (504451)
Gabriele Lugli (3522308)
Muireann Egan (4722105)
Marco Ventura (133957)
Douwe van Sinderen (62590)

December 2017

B. breve ribosomal operon and CRISPR-Cas system transcription. Artemis plot showing the level of tra...

Additional file 1: of G4PromFinder: an algorithm for predicting transcription promoters in GC-rich bacterial genomes based on AT-rich elements and G-quadruplex motifs

Marco Di Salvo (4831365)
Eva Pinatel (4431565)
Adelfia TalĂ (4831368)
Marco Fondi (66036)
Clelia Peano (67208)
Pietro Alifano (70214)

February 2018

Statistics of predicted promoters by G4PromFinder, PromPredict, PePPER and bTSSfinder in the whole g...

Additional File 1:

Erin Gill (5023145)
Luisa Chan (5023151)
Geoffrey Winsor (5023139)
Neil Dobson (2715607)
Raymond Lo (57516)
Shannan Ho Sui (5023157)
Bhavjinder Dhillon (5023142)
Patrick Taylor (2673580)
Raunak Shrestha (600729)
Cory Spencer (5023148)
Robert Hancock (3454853)
Peter Unrau (5023154)
Fiona Brinkman (3370223)

March 2018

Supplementary results, figures and methods. Figure S1. Measures of cleavage site motif category sequ...

Genome-wide prediction and validation of sigma70 promoters in Lactobacillus plantarum WCFS1.

Tilman J Todt
Michiel Wels
Roger S Bongers
Roland S Siezen
Sacha A F T van Hijum
Michiel Kleerebezem

BACKGROUND: In prokaryotes, sigma factors are essential for directing the transcription machinery to...

Additional file 4: of Transcription profiling of butanol producer Clostridium beijerinckii NRRL B-598 using RNA-Seq

Karel Sedlar (607534)
Pavlina Koscova (5315204)
Maryna Vasylkivska (5315201)
Barbora Branska (5315207)
Jan Kolek (712011)
Kristyna Kupkova (5315210)
Petra Patakova (5315213)
Ivo Provaznik (579935)

May 2018

Circular plots showing average coverage of the genome by RNA-Seq reads in all six time points. The o...

Additional file 7: Table S4. of Whole transcriptomic analysis of the plant-beneficial rhizobacterium Bacillus amyloliquefaciens SQR9 during enhanced biofilm formation regulated by maize root exudates

Nan Zhang (46264)
Dongqing Yang (675454)
Dandan Wang (286632)
Youzhi Miao (3480608)
Jiahui Shao (3130440)
Xuan Zhou (329338)
Zhihui Xu (453724)
Qing Li (84975)
Haichao Feng (3480605)
Shuqing Li (1430998)
Qirong Shen (404759)
Ruifu Zhang (331550)

September 2015

Genomic island (GI) prediction of Bacillus amyloliquefaciens SQR9. GIs were predicted by IslandViewe...

Additional file 1: of Transcriptionally promiscuous “blurry” promoters in Tc1/mariner transposons allow transcription in distantly related genomes

Antonio Palazzo (484949)
Patrizio Lorusso (6553208)
Csaba Miskey (466684)
Oliver Walisko (6553211)
Andrea Gerbino (716948)
Carlo Marobbio (6553214)
Zoltán Ivics (196129)
René Marsano (6553217)

April 2019

Table S1. TATA box motif prediction. Pval cutoff 10exp-2; origin = START; only direct strand results...

Additional file 4: Figure S1. of Genome-wide transcription start site profiling in biofilm-grown Burkholderia cenocepacia J2315

Andrea Sass (224214)
Heleen Van Acker (286683)
Konrad Förstner (822551)
Filip Van Nieuwerburgh (20881)
Dieter Deforce (20882)
Jörg Vogel (11205)
Tom Coenye (20880)

October 2015

Transcription start sites confirmed by 5′RACE. dRNA-Seq data are represented as number of read start...

Genome-wide transcription start site profiling in biofilm-grown Burkholderia cenocepacia J2315

Sass, Andrea M.
Van Acker, Heleen
Förstner, Konrad U.
Van Nieuwerburgh, Filip
Deforce, Dieter
Vogel, Jörg
Coenye, Tom

January 2015

Background: Burkholderia cenocepacia is a soil-dwelling Gram-negative Betaproteobacterium with an im...

RESEARCH ARTICLE Open Access Genome-wide transcription start site profiling in biofilm-grown Burkholderia cenocepacia J2315

Andrea M. Sass
Heleen Van Acker
Konrad U. Förstner
Filip Van Nieuwerburgh
Dieter Deforce
Jörg Vogel
Tom Coenye

August 2016

Background: Burkholderia cenocepacia is a soil-dwelling Gram-negative Betaproteobacterium with an im...

Additional file 5: Table S4. of TSS-EMOTE, a refined protocol for a more complete and less biased global mapping of transcription start sites in bacterial pathogens

Julien Prados (743297)
Patrick Linder (7345)
Peter Redder (528225)

November 2016

Predicted operon structure based on TSS-EMOTE experimental data and in silico transcription terminat...

Genome-wide prediction and validation of sigma70 promoters in Lactobacillus plantarum WCFS1

Todt, T.J.
Wels, M.W.
Bongers, R.S.
Siezen, R.S.
van Hijum, S.A.
Kleerebezem, M.

January 2012

Contains fulltext : 108029.pdf (publisher's version ) (Open Access)BACKGROUND: In ...

Additional file 3: of Genome-wide transcription start site mapping of Bradyrhizobium japonicum grown free-living or in symbiosis â a rich resource to identify new transcripts, proteins and to study gene regulation

Jelena Äuklina (3491417)
Julia Hahn (3279486)
Maxim Imakaev (648765)
Ulrich Omasits (119127)
Konrad FĂśrstner (3491414)
Nikolay Ljubimov (3491387)
Melanie Goebel (3491390)
Gabriella Pessi (119095)
Hans-Martin Fischer (143595)
Christian Ahrens (3490766)
Mikhail Gelfand (4027)
Elena Evguenieva-Hackenberg (828729)

April 2016

Table S3 listing all mapped TSSs; Table S4 listing previously published TSSs compared to our TSS map...

Genome-wide determination of transcription start sites reveals new insights into promoter structures in the actinomycete Corynebacterium glutamicum.

Albersmeier, Andreas
Pfeifer-Sancar, Katharina
Rückert, Christian
Kalinowski, Jörn

January 2017

Albersmeier A, Pfeifer-Sancar K, Rückert C, Kalinowski J. Genome-wide determination of transcription...

Global mapping of transcription start sites and promoter motifs in the symbiotic a-proteobacterium Sinorhizobium meliloti 1021

Schlueter, Jan-Philip
Reinkensmeier, Jan
Barnett, Melanie J.
Lang, Claus
Krol, Elizaveta
Giegerich, Robert
Long, Sharon R.
Becker, Anke

January 2013

Schlueter J-P, Reinkensmeier J, Barnett MJ, et al. Global mapping of transcription start sites and p...

Additional file 6: Figure S3. of Global transcriptional landscape and promoter mapping of the gut commensal Bifidobacterium breve UCC2003

Francesca Bottacini (133911)
Aldert Zomer (144349)
Christian Milani (133915)
Chiara Ferrario (504451)
Gabriele Lugli (3522308)
Muireann Egan (4722105)
Marco Ventura (133957)
Douwe van Sinderen (62590)

December 2017

B. breve ribosomal operon and CRISPR-Cas system transcription. Artemis plot showing the level of tra...

Additional file 1: of G4PromFinder: an algorithm for predicting transcription promoters in GC-rich bacterial genomes based on AT-rich elements and G-quadruplex motifs

Marco Di Salvo (4831365)
Eva Pinatel (4431565)
Adelfia TalĂ (4831368)
Marco Fondi (66036)
Clelia Peano (67208)
Pietro Alifano (70214)

February 2018

Statistics of predicted promoters by G4PromFinder, PromPredict, PePPER and bTSSfinder in the whole g...

Additional File 1:

Erin Gill (5023145)
Luisa Chan (5023151)
Geoffrey Winsor (5023139)
Neil Dobson (2715607)
Raymond Lo (57516)
Shannan Ho Sui (5023157)
Bhavjinder Dhillon (5023142)
Patrick Taylor (2673580)
Raunak Shrestha (600729)
Cory Spencer (5023148)
Robert Hancock (3454853)
Peter Unrau (5023154)
Fiona Brinkman (3370223)

March 2018

Supplementary results, figures and methods. Figure S1. Measures of cleavage site motif category sequ...

Genome-wide prediction and validation of sigma70 promoters in Lactobacillus plantarum WCFS1.

Tilman J Todt
Michiel Wels
Roger S Bongers
Roland S Siezen
Sacha A F T van Hijum
Michiel Kleerebezem

BACKGROUND: In prokaryotes, sigma factors are essential for directing the transcription machinery to...

Additional file 4: of Transcription profiling of butanol producer Clostridium beijerinckii NRRL B-598 using RNA-Seq

Karel Sedlar (607534)
Pavlina Koscova (5315204)
Maryna Vasylkivska (5315201)
Barbora Branska (5315207)
Jan Kolek (712011)
Kristyna Kupkova (5315210)
Petra Patakova (5315213)
Ivo Provaznik (579935)

May 2018

Circular plots showing average coverage of the genome by RNA-Seq reads in all six time points. The o...

Additional file 7: Table S4. of Whole transcriptomic analysis of the plant-beneficial rhizobacterium Bacillus amyloliquefaciens SQR9 during enhanced biofilm formation regulated by maize root exudates

Nan Zhang (46264)
Dongqing Yang (675454)
Dandan Wang (286632)
Youzhi Miao (3480608)
Jiahui Shao (3130440)
Xuan Zhou (329338)
Zhihui Xu (453724)
Qing Li (84975)
Haichao Feng (3480605)
Shuqing Li (1430998)
Qirong Shen (404759)
Ruifu Zhang (331550)

September 2015

Genomic island (GI) prediction of Bacillus amyloliquefaciens SQR9. GIs were predicted by IslandViewe...

Additional file 1: of Transcriptionally promiscuous “blurry” promoters in Tc1/mariner transposons allow transcription in distantly related genomes

Antonio Palazzo (484949)
Patrizio Lorusso (6553208)
Csaba Miskey (466684)
Oliver Walisko (6553211)
Andrea Gerbino (716948)
Carlo Marobbio (6553214)
Zoltán Ivics (196129)
René Marsano (6553217)

April 2019

Table S1. TATA box motif prediction. Pval cutoff 10exp-2; origin = START; only direct strand results...

Additional file 5: Table S4. of Genome-wide transcription start site profiling in biofilm-grown Burkholderia cenocepacia J2315

Abstract

Extracted data

Additional file 5: Table S4. of Genome-wide transcription start site profiling in biofilm-grown Burkholderia cenocepacia J2315

Abstract

Extracted data

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