cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.28074446
title: MJG2402_LB

description: Time-lapse microscopy of MJG2402 grown on LBl media at 37°C.Strains of interest were grown overnight in 5 mL of LB liquid broth shaking at 37°C to obtain a saturated culture. Cultures were back diluted 1,000-fold and grown to an early exponential phase (approximately 3 hours). Cells were concentrated by centrifugation, when necessary, at 5,000 <i>g </i>for 1 minute, before being resuspended in 100 μL of media. Cells were immobilized on agarose pads by spotting 0.5 μL of concentrated culture on the pad, then inverting the pad onto a glass bottom petri dish for imaging. Agarose pads for microscopy were constructed out of LB or MOPS minimal medium containing 1.5% agarose (Thermo Fisher cat. #16500500). Imaging was performed using equipment available at the University of Alabama at Birmingham High-Resolution Imaging Facility (HRIF); a Nikon Ti2 inverted fluorescencemicroscope with a tandem galvano and Nikon A1R-HD25 resonance scanner up to 30 1,024 × 1,024 images/s.Tokai Hit incubation stage chamber was used to heat samples and objectives to 37°C to facilitate the growth of bacteria for live imaging. Images were captured at 60× or 100× magnificationin both transmitted light differentialinterference contrast image and GFP or appropriate fluorescentchannels as needed. Automated time-lapse imaging was performed at 37°C, and motorized x, y, and z tracking was controlled and automated by acquisition software Nis Elements 5.0 Imaging Software available in the HRIF at UAB.
DOI: 10.6084/m9.figshare.28074446.v1
title: MJG2402_LB

description: Time-lapse microscopy of MJG2402 grown on LBl media at 37°C.Strains of interest were grown overnight in 5 mL of LB liquid broth shaking at 37°C to obtain a saturated culture. Cultures were back diluted 1,000-fold and grown to an early exponential phase (approximately 3 hours). Cells were concentrated by centrifugation, when necessary, at 5,000 <i>g </i>for 1 minute, before being resuspended in 100 μL of media. Cells were immobilized on agarose pads by spotting 0.5 μL of concentrated culture on the pad, then inverting the pad onto a glass bottom petri dish for imaging. Agarose pads for microscopy were constructed out of LB or MOPS minimal medium containing 1.5% agarose (Thermo Fisher cat. #16500500). Imaging was performed using equipment available at the University of Alabama at Birmingham High-Resolution Imaging Facility (HRIF); a Nikon Ti2 inverted fluorescencemicroscope with a tandem galvano and Nikon A1R-HD25 resonance scanner up to 30 1,024 × 1,024 images/s.Tokai Hit incubation stage chamber was used to heat samples and objectives to 37°C to facilitate the growth of bacteria for live imaging. Images were captured at 60× or 100× magnificationin both transmitted light differentialinterference contrast image and GFP or appropriate fluorescentchannels as needed. Automated time-lapse imaging was performed at 37°C, and motorized x, y, and z tracking was controlled and automated by acquisition software Nis Elements 5.0 Imaging Software available in the HRIF at UAB.
DOI: 10.6084/m9.figshare.28074458
title: MJG2401_LB

description: Time-lapse microscopy of MJG2401 grown on LB media at 37°C.Strains of interest were grown overnight in 5 mL of LB liquid broth shaking at 37°C to obtain a saturated culture. Cultures were back diluted 1,000-fold and grown to an early exponential phase (approximately 3 hours). Cells were concentrated by centrifugation, when necessary, at 5,000 <i>g </i>for 1 minute, before being resuspended in 100 μL of media. Cells were immobilized on agarose pads by spotting 0.5 μL of concentrated culture on the pad, then inverting the pad onto a glass bottom petri dish for imaging. Agarose pads for microscopy were constructed out of LB or MOPS minimal medium containing 1.5% agarose (Thermo Fisher cat. #16500500). Imaging was performed using equipment available at the University of Alabama at Birmingham High-Resolution Imaging Facility (HRIF); a Nikon Ti2 inverted fluorescencemicroscope with a tandem galvano and Nikon A1R-HD25 resonance scanner up to 30 1,024 × 1,024 images/s.Tokai Hit incubation stage chamber was used to heat samples and objectives to 37°C to facilitate the growth of bacteria for live imaging. Images were captured at 60× or 100× magnificationin both transmitted light differentialinterference contrast image and GFP or appropriate fluorescentchannels as needed. Automated time-lapse imaging was performed at 37°C, and motorized x, y, and z tracking was controlled and automated by acquisition software Nis Elements 5.0 Imaging Software available in the HRIF at UAB.
DOI: 10.6084/m9.figshare.28074467
title: Cryo-Electron Microscopy

description: Cryo-electron microscopy was performed with the help of the UAB institutional Research Core Program with the help of Dr. Terje Dokland and Dr. James Kizziah (University of Alabama at Birmingham). A Thermo Fisher Scientific(TFS) Glacios 2 equipped with a Falcon 4i direct electron detector is optimized for high-throughput cryo-EM and ease of use <i>via </i>the TFS EPU and Tomography software. It has demonstrated data collection speeds up to ~500 images/hour and a capability of 2.2 Å resolution <i>via </i>single particle analysis with apoferritin. A TFS Talos F200C equipped with a Ceta-S CMOS camera and a Direct Electron Apollo direct electron detector is used for imaging of negatively stained samples and specialized cryo-EM applications.For sample preparation, a Pelco EasiGlow glow discharge machine, a PIE ScientificTergeoEM plasma cleaner, and FEI Vitrobot Mark IV sample vitrificationrobot were used. Gatan 626 and 698 “Elsa” cryo-holders are used for cryo-EM on the Talos F200C. An in-house GPU-accelerated computing workstation is used for on-the-flyprocessing of single particle cryo-EM data with CryoSPARC Live, and the CEMF has a direct 10Gbps fiberlink to the UAB supercomputer for offloadingand distribution of data to users. Cells were grown overnight until the morning when they were back diluted and grown for 3 hours until an OD600 of 0.1 was reached, and cells were centrifuged at 8,000 <i>g </i>for 2 minutes and resuspended in PBS for CEM sample prep.
DOI: 10.6084/m9.figshare.28074458.v1
title: MJG2401_LB

description: Time-lapse microscopy of MJG2401 grown on LB media at 37°C.Strains of interest were grown overnight in 5 mL of LB liquid broth shaking at 37°C to obtain a saturated culture. Cultures were back diluted 1,000-fold and grown to an early exponential phase (approximately 3 hours). Cells were concentrated by centrifugation, when necessary, at 5,000 <i>g </i>for 1 minute, before being resuspended in 100 μL of media. Cells were immobilized on agarose pads by spotting 0.5 μL of concentrated culture on the pad, then inverting the pad onto a glass bottom petri dish for imaging. Agarose pads for microscopy were constructed out of LB or MOPS minimal medium containing 1.5% agarose (Thermo Fisher cat. #16500500). Imaging was performed using equipment available at the University of Alabama at Birmingham High-Resolution Imaging Facility (HRIF); a Nikon Ti2 inverted fluorescencemicroscope with a tandem galvano and Nikon A1R-HD25 resonance scanner up to 30 1,024 × 1,024 images/s.Tokai Hit incubation stage chamber was used to heat samples and objectives to 37°C to facilitate the growth of bacteria for live imaging. Images were captured at 60× or 100× magnificationin both transmitted light differentialinterference contrast image and GFP or appropriate fluorescentchannels as needed. Automated time-lapse imaging was performed at 37°C, and motorized x, y, and z tracking was controlled and automated by acquisition software Nis Elements 5.0 Imaging Software available in the HRIF at UAB.
DOI: 10.6084/m9.figshare.28074467.v1
title: Cryo-Electron Microscopy

description: Cryo-electron microscopy was performed with the help of the UAB institutional Research Core Program with the help of Dr. Terje Dokland and Dr. James Kizziah (University of Alabama at Birmingham). A Thermo Fisher Scientific(TFS) Glacios 2 equipped with a Falcon 4i direct electron detector is optimized for high-throughput cryo-EM and ease of use <i>via </i>the TFS EPU and Tomography software. It has demonstrated data collection speeds up to ~500 images/hour and a capability of 2.2 Å resolution <i>via </i>single particle analysis with apoferritin. A TFS Talos F200C equipped with a Ceta-S CMOS camera and a Direct Electron Apollo direct electron detector is used for imaging of negatively stained samples and specialized cryo-EM applications.For sample preparation, a Pelco EasiGlow glow discharge machine, a PIE ScientificTergeoEM plasma cleaner, and FEI Vitrobot Mark IV sample vitrificationrobot were used. Gatan 626 and 698 “Elsa” cryo-holders are used for cryo-EM on the Talos F200C. An in-house GPU-accelerated computing workstation is used for on-the-flyprocessing of single particle cryo-EM data with CryoSPARC Live, and the CEMF has a direct 10Gbps fiberlink to the UAB supercomputer for offloadingand distribution of data to users. Cells were grown overnight until the morning when they were back diluted and grown for 3 hours until an OD600 of 0.1 was reached, and cells were centrifuged at 8,000 <i>g </i>for 2 minutes and resuspended in PBS for CEM sample prep.
DOI: 10.6084/m9.figshare.28074407
title: MJG2403_Mops Minimal Media

description: Time-lapse microscopy of MJG2403 grown on MOPS minimal media at 37°C.Strains of interest were grown overnight in 5 mL of LB liquid broth shaking at 37°C to obtain a saturated culture. Cultures were back diluted 1,000-fold and grown to an early exponential phase (approximately 3 hours). Cells were concentrated by centrifugation, when necessary, at 5,000 <i>g </i>for 1 minute, before being resuspended in 100 μL of media. Cells were immobilized on agarose pads by spotting 0.5 μL of concentrated culture on the pad, then inverting the pad onto a glass bottom petri dish for imaging. Agarose pads for microscopy were constructed out of LB or MOPS minimal medium containing 1.5% agarose (Thermo Fisher cat. #16500500). Imaging was performed using equipment available at the University of Alabama at Birmingham High-Resolution Imaging Facility (HRIF); a Nikon Ti2 inverted fluorescencemicroscope with a tandem galvano and Nikon A1R-HD25 resonance scanner up to 30 1,024 × 1,024 images/s.Tokai Hit incubation stage chamber was used to heat samples and objectives to 37°C to facilitate the growth of bacteria for live imaging. Images were captured at 60× or 100× magnificationin both transmitted light differentialinterference contrast image and GFP or appropriate fluorescentchannels as needed. Automated time-lapse imaging was performed at 37°C, and motorized x, y, and z tracking was controlled and automated by acquisition software Nis Elements 5.0 Imaging Software available in the HRIF at UAB.
DOI: 10.6084/m9.figshare.28074413.v1
title: MJG2405_MOPS Minimal Media

description: Time-lapse microscopy of MJG2405 grown on MOPS minimal media at 37°C.Strains of interest were grown overnight in 5 mL of LB liquid broth shaking at 37°C to obtain a saturated culture. Cultures were back diluted 1,000-fold and grown to an early exponential phase (approximately 3 hours). Cells were concentrated by centrifugation, when necessary, at 5,000 <i>g </i>for 1 minute, before being resuspended in 100 μL of media. Cells were immobilized on agarose pads by spotting 0.5 μL of concentrated culture on the pad, then inverting the pad onto a glass bottom petri dish for imaging. Agarose pads for microscopy were constructed out of LB or MOPS minimal medium containing 1.5% agarose (Thermo Fisher cat. #16500500). Imaging was performed using equipment available at the University of Alabama at Birmingham High-Resolution Imaging Facility (HRIF); a Nikon Ti2 inverted fluorescencemicroscope with a tandem galvano and Nikon A1R-HD25 resonance scanner up to 30 1,024 × 1,024 images/s.Tokai Hit incubation stage chamber was used to heat samples and objectives to 37°C to facilitate the growth of bacteria for live imaging. Images were captured at 60× or 100× magnificationin both transmitted light differentialinterference contrast image and GFP or appropriate fluorescentchannels as needed. Automated time-lapse imaging was performed at 37°C, and motorized x, y, and z tracking was controlled and automated by acquisition software Nis Elements 5.0 Imaging Software available in the HRIF at UAB.
DOI: 10.6084/m9.figshare.28074404.v1
title: MJG2405_LB media

description: Time-lapse microscopy of MJG2405 <i>∆ppk ∆relA ∆spoT </i>grown on LB agarose pads at 37°C.Strains of interest were grown overnight in 5 mL of LB liquid broth shaking at 37°C to obtain a saturated culture. Cultures were back diluted 1,000-fold and grown to an early exponential phase (approximately 3 hours). Cells were concentrated by centrifugation, when necessary, at 5,000 <i>g </i>for 1 minute, before being resuspended in 100 μL of media. Cells were immobilized on agarose pads by spotting 0.5 μL of concentrated culture on the pad, then inverting the pad onto a glass bottom petri dish for imaging. Agarose pads for microscopy were constructed out of LB or MOPS minimal medium containing 1.5% agarose (Thermo Fisher cat. #16500500). Imaging was performed using equipment available at the University of Alabama at Birmingham High-Resolution Imaging Facility (HRIF); a Nikon Ti2 inverted fluorescencemicroscope with a tandem galvano and Nikon A1R-HD25 resonance scanner up to 30 1,024 × 1,024 images/s.Tokai Hit incubation stage chamber was used to heat samples and objectives to 37°C to facilitate the growth of bacteria for live imaging. Images were captured at 60× or 100× magnificationin both transmitted light differentialinterference contrast image and GFP or appropriate fluorescentchannels as needed. Automated time-lapse imaging was performed at 37°C, and motorized x, y, and z tracking was controlled and automated by acquisition software Nis Elements 5.0 Imaging Software available in the HRIF at UAB.
DOI: 10.6084/m9.figshare.28074413
title: MJG2405_MOPS Minimal Media

description: Time-lapse microscopy of MJG2405 grown on MOPS minimal media at 37°C.Strains of interest were grown overnight in 5 mL of LB liquid broth shaking at 37°C to obtain a saturated culture. Cultures were back diluted 1,000-fold and grown to an early exponential phase (approximately 3 hours). Cells were concentrated by centrifugation, when necessary, at 5,000 <i>g </i>for 1 minute, before being resuspended in 100 μL of media. Cells were immobilized on agarose pads by spotting 0.5 μL of concentrated culture on the pad, then inverting the pad onto a glass bottom petri dish for imaging. Agarose pads for microscopy were constructed out of LB or MOPS minimal medium containing 1.5% agarose (Thermo Fisher cat. #16500500). Imaging was performed using equipment available at the University of Alabama at Birmingham High-Resolution Imaging Facility (HRIF); a Nikon Ti2 inverted fluorescencemicroscope with a tandem galvano and Nikon A1R-HD25 resonance scanner up to 30 1,024 × 1,024 images/s.Tokai Hit incubation stage chamber was used to heat samples and objectives to 37°C to facilitate the growth of bacteria for live imaging. Images were captured at 60× or 100× magnificationin both transmitted light differentialinterference contrast image and GFP or appropriate fluorescentchannels as needed. Automated time-lapse imaging was performed at 37°C, and motorized x, y, and z tracking was controlled and automated by acquisition software Nis Elements 5.0 Imaging Software available in the HRIF at UAB.
DOI: 10.6084/m9.figshare.28074428
title: MJG2404_LB

description: Time-lapse microscopy of MJG2404 grown on LB media at 37°C.Strains of interest were grown overnight in 5 mL of LB liquid broth shaking at 37°C to obtain a saturated culture. Cultures were back diluted 1,000-fold and grown to an early exponential phase (approximately 3 hours). Cells were concentrated by centrifugation, when necessary, at 5,000 <i>g </i>for 1 minute, before being resuspended in 100 μL of media. Cells were immobilized on agarose pads by spotting 0.5 μL of concentrated culture on the pad, then inverting the pad onto a glass bottom petri dish for imaging. Agarose pads for microscopy were constructed out of LB or MOPS minimal medium containing 1.5% agarose (Thermo Fisher cat. #16500500). Imaging was performed using equipment available at the University of Alabama at Birmingham High-Resolution Imaging Facility (HRIF); a Nikon Ti2 inverted fluorescencemicroscope with a tandem galvano and Nikon A1R-HD25 resonance scanner up to 30 1,024 × 1,024 images/s.Tokai Hit incubation stage chamber was used to heat samples and objectives to 37°C to facilitate the growth of bacteria for live imaging. Images were captured at 60× or 100× magnificationin both transmitted light differentialinterference contrast image and GFP or appropriate fluorescentchannels as needed. Automated time-lapse imaging was performed at 37°C, and motorized x, y, and z tracking was controlled and automated by acquisition software Nis Elements 5.0 Imaging Software available in the HRIF at UAB.
DOI: 10.6084/m9.figshare.28074428.v1
title: MJG2404_LB

description: Time-lapse microscopy of MJG2404 grown on LB media at 37°C.Strains of interest were grown overnight in 5 mL of LB liquid broth shaking at 37°C to obtain a saturated culture. Cultures were back diluted 1,000-fold and grown to an early exponential phase (approximately 3 hours). Cells were concentrated by centrifugation, when necessary, at 5,000 <i>g </i>for 1 minute, before being resuspended in 100 μL of media. Cells were immobilized on agarose pads by spotting 0.5 μL of concentrated culture on the pad, then inverting the pad onto a glass bottom petri dish for imaging. Agarose pads for microscopy were constructed out of LB or MOPS minimal medium containing 1.5% agarose (Thermo Fisher cat. #16500500). Imaging was performed using equipment available at the University of Alabama at Birmingham High-Resolution Imaging Facility (HRIF); a Nikon Ti2 inverted fluorescencemicroscope with a tandem galvano and Nikon A1R-HD25 resonance scanner up to 30 1,024 × 1,024 images/s.Tokai Hit incubation stage chamber was used to heat samples and objectives to 37°C to facilitate the growth of bacteria for live imaging. Images were captured at 60× or 100× magnificationin both transmitted light differentialinterference contrast image and GFP or appropriate fluorescentchannels as needed. Automated time-lapse imaging was performed at 37°C, and motorized x, y, and z tracking was controlled and automated by acquisition software Nis Elements 5.0 Imaging Software available in the HRIF at UAB.
DOI: 10.6084/m9.figshare.28074440
title: MJG2403_LB

description: Time-lapse microscopy of MJG2403 grown on LB media at 37°C.Strains of interest were grown overnight in 5 mL of LB liquid broth shaking at 37°C to obtain a saturated culture. Cultures were back diluted 1,000-fold and grown to an early exponential phase (approximately 3 hours). Cells were concentrated by centrifugation, when necessary, at 5,000 <i>g </i>for 1 minute, before being resuspended in 100 μL of media. Cells were immobilized on agarose pads by spotting 0.5 μL of concentrated culture on the pad, then inverting the pad onto a glass bottom petri dish for imaging. Agarose pads for microscopy were constructed out of LB or MOPS minimal medium containing 1.5% agarose (Thermo Fisher cat. #16500500). Imaging was performed using equipment available at the University of Alabama at Birmingham High-Resolution Imaging Facility (HRIF); a Nikon Ti2 inverted fluorescencemicroscope with a tandem galvano and Nikon A1R-HD25 resonance scanner up to 30 1,024 × 1,024 images/s.Tokai Hit incubation stage chamber was used to heat samples and objectives to 37°C to facilitate the growth of bacteria for live imaging. Images were captured at 60× or 100× magnificationin both transmitted light differentialinterference contrast image and GFP or appropriate fluorescentchannels as needed. Automated time-lapse imaging was performed at 37°C, and motorized x, y, and z tracking was controlled and automated by acquisition software Nis Elements 5.0 Imaging Software available in the HRIF at UAB.
DOI: 10.6084/m9.figshare.28074440.v1
title: MJG2403_LB

description: Time-lapse microscopy of MJG2403 grown on LB media at 37°C.Strains of interest were grown overnight in 5 mL of LB liquid broth shaking at 37°C to obtain a saturated culture. Cultures were back diluted 1,000-fold and grown to an early exponential phase (approximately 3 hours). Cells were concentrated by centrifugation, when necessary, at 5,000 <i>g </i>for 1 minute, before being resuspended in 100 μL of media. Cells were immobilized on agarose pads by spotting 0.5 μL of concentrated culture on the pad, then inverting the pad onto a glass bottom petri dish for imaging. Agarose pads for microscopy were constructed out of LB or MOPS minimal medium containing 1.5% agarose (Thermo Fisher cat. #16500500). Imaging was performed using equipment available at the University of Alabama at Birmingham High-Resolution Imaging Facility (HRIF); a Nikon Ti2 inverted fluorescencemicroscope with a tandem galvano and Nikon A1R-HD25 resonance scanner up to 30 1,024 × 1,024 images/s.Tokai Hit incubation stage chamber was used to heat samples and objectives to 37°C to facilitate the growth of bacteria for live imaging. Images were captured at 60× or 100× magnificationin both transmitted light differentialinterference contrast image and GFP or appropriate fluorescentchannels as needed. Automated time-lapse imaging was performed at 37°C, and motorized x, y, and z tracking was controlled and automated by acquisition software Nis Elements 5.0 Imaging Software available in the HRIF at UAB.
DOI: 10.6084/m9.figshare.28072667
title: MJG0001_MOPS Minimal Media

description: Time-lapse microscopy of MJG2403 grown on MOPS minimal media at 37°C. Strains of interest were grown overnight in 5 mL of LB liquid broth shaking at 37°C to obtain a saturated culture. Cultures were back diluted 1,000-fold and grown to an early exponential phase (approximately 3 hours). Cells were concentrated by centrifugation, when necessary, at 5,000 <i>g </i>for 1 minute, before being resuspended in 100 μL of media. Cells were immobilized on agarose pads by spotting 0.5 μL of concentrated culture on the pad, then inverting the pad onto a glass bottom petri dish for imaging. Agarose pads for microscopy were constructed out of LB or MOPS minimal medium containing 1.5% agarose (Thermo Fisher cat. #16500500). Imaging was performed using equipment available at the University of Alabama at Birmingham High-Resolution Imaging Facility (HRIF); a Nikon Ti2 inverted fluorescencemicroscope with a tandem galvano and Nikon A1R-HD25 resonance scanner up to 30 1,024 × 1,024 images/s.Tokai Hit incubation stage chamber was used to heat samples and objectives to 37°C to facilitate the growth of bacteria for live imaging. Images were captured at 60× or 100× magnificationin both transmitted light differentialinterference contrast image and GFP or appropriate fluorescentchannels as needed. Automated time-lapse imaging was performed at 37°C, and motorized x, y, and z tracking was controlled and automated by acquisition software Nis Elements 5.0 Imaging Software available in the HRIF at UAB.