Data Sharing

Interactive Borrelia (Borreliella) burgdorferi B31 Genome Browsers 

RNA 5' and 3' end mapping (logarithmic phase cells):

https://www.nichd.nih.gov/about/org/dir/other-facilities/cores/bioinformatics/data/adams-borrelia-RNA-mapping-log

5'RNA-seq, total RNA-seq, and 3'RNA-seq was performed using total RNA isolated from logarithmic grown spirochetes (3-5x107 cells/ml), in BSKII culture media, at 35°C. Transcription start sites (TSSs) are indicated for each DNA strand and were determined based on a 2-fold enrichment of a 5' end in the TAP+ tracks (RNA samples incubated with pyrophosphatase) compared to the TAP- tracks. 3'ends were determined by identify peaks using a statistically-informed method and multiple replicates. Browser assembled by C. Esnault.

 

RNA 3' end mapping (logarithmic and TS-stationary phase cells):

https://www.nichd.nih.gov/about/org/dir/other-facilities/cores/bioinformatics/data/adams-borrelia-three-prime

3'RNA-seq was performed using total RNA isolated from either logarithmic grown spirochetes (3-5x107 cells/ml) at 35°C or temperature-shifted (TS) stationary phase spirochetes in BSKII culture media. Temperature-shifted stationary cultures were grown to mid-logarithmic phase (3-5x107 cells/ml) at 35°C, temperature shifted to the bench (~23°C) for 48 hours, and then temperature shifted back to 35°C for 48 hours resulting in a stationary culture (2-3x108 cells/ml). 3' ends were determined by identify peaks using a statistically-informed method and multiple replicates. Browser assembled by C. Esnault.

 

B. burgdorferi Rho-dependent 3' ends (logarithmic phase cells):

https://www.nichd.nih.gov/about/org/dir/other-facilities/cores/bioinformatics/data/adams-borrelia-rho-dependent

Total RNA-seq was performed using total RNA isolated from logarithmic grown spirochetes (3-5x107 cells/ml) in the presence or absence of bicyclomycin (BCM) – the selective inhibitor of Rho. Rho regions were determined by calculating the degree of transcriptional readthrough when Rho-activity is inhibited, for each biological replicate. 

 

B. burgdorferi ±spermidine total RNA-seq (stationary phase cells):

https://www.nichd.nih.gov/about/org/dir/other-facilities/cores/bioinformatics/data/adams-borrelia-spermidine

Total RNA-seq was performed using total RNA isolated from stationary phase spirochetes (1-2x108 cells/ml) in the presence or absence of 10 mM spermidine.

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