cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.22002/faan1-5ws34
title: EPEC_8770_U2OS

description: EPEC cells strain 8770 incubated with U2OS. The aim is to see bacterial nanotubes connected  .  to the eukaryotic cell.
description: <strong>Tilt Series Date:</strong> 2020-02-15</p>
<strong>Data Taken By:</strong> Mohammed Kaplan</p>
<strong>Species / Specimen:</strong> Escherichia coli</p>
<strong>Strain:</strong> 8770, EPEC 8612 + Δbfp ΔtraD-ygeB ΔfinO-traI</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 3°, constant angular increment, dosage: 100.0 eV/Å²,  defocus: -6.0 μm,  magnification: 19500x. </p>
<strong>Microscope:</strong> Caltech Titan Krios</p>
<strong>Acquisition Software:</strong> Serial EM</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> Raptor</p>
<strong>Collaborators and Roles:</strong> The strain EPEC 8770 is obtained from Ritesh (Ilan Rosenshine lab, the Hebrew university) and . Amit (Sigal ben Yehuda lab). U2OS was obtained from Wei Zhao in the Jensen lab.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> U2OS were grown on gold finders grids overnight in DMEM medium at 37 C. next day the grids were washed with PBS and incubated with DMEM+FCS and bacteria were added . (1:100)  and the grids were cultured for 3.5 hours at 37C. Then the grids were washed twice with PBS and incubated with starvation buffer for 1 hour. The samples were plunge . frozen.</p>
<strong>Sample Preparation:</strong> Samples were blotted manually.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2020-02-15-28/rawdata/</p>EPEC_8770_U2OS_029_af.mrc,  Tilt Series (Pixel Size 0.449 nm), 1.9 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2020-02-15-28/rawdata/EPEC_8770_U2OS_029_af.mrc"
        > <i class="download icon"></i> Download </a></p>

        EPEC_8770_U2OS_029_af_full.rec,  Reconstruction (Pixel Size 1.796 nm), 737.3 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2020-02-15-28/3dimage_111350/EPEC_8770_U2OS_029_af_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/5xrgv-kjd69
title: Hpylori_dFliF_FISE

description: These are H_pylori cells that are lacking FliP protein. In these cells, FliF protein was knocked out  .  to examine its relation to the hat-like complex.
description: <strong>Tilt Series Date:</strong> 2020-10-08</p>
<strong>Data Taken By:</strong> Mohammed Kaplan</p>
<strong>Species / Specimen:</strong> Helicobacter pylori</p>
<strong>Strain:</strong> 26695</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 3°, constant angular increment, dosage: 120.0 eV/Å²,  defocus: -8.0 μm,  magnification: 19500x. </p>
<strong>Microscope:</strong> Caltech Titan Krios</p>
<strong>Acquisition Software:</strong> Serial EM</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> Raptor</p>
<strong>Collaborators and Roles:</strong> The cells were prepared and sent by Carrie Schaffer from the university of Kentucky.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> The cells were grown at 37C with 5% CO2 on sheep blood agar plates for 2 days from a -80C . stock. No growth was seen on the plates after 24 hr therefore the plates were kept in the . incubator for another 24Hr.</p>
<strong>Sample Preparation:</strong> The samples were prepared with Vitrobot IV. Blotting conditions were either: blot force 6, blot . time 3, drain time 1 OR blot force -3, blot time 4, drain time 1, 100%  humidity. Cu grids. 20 nm . gold.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2020-10-08-25/rawdata/</p>Hpylori_DFliF_FISE_059.mrc,  Tilt Series (Pixel Size 0.452 nm), 1.9 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2020-10-08-25/rawdata/Hpylori_DFliF_FISE_059.mrc"
        > <i class="download icon"></i> Download </a></p>

        Hpylori_DFliF_FISE_059_full.rec,  Reconstruction (Pixel Size 1.808 nm), 737.3 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2020-10-08-25/3dimage_113534/Hpylori_DFliF_FISE_059_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/gsy9t-59x43
title: Hpylori_dFliF_FISE

description: These are H_pylori cells that are lacking FliP protein. In these cells, FliF protein was knocked out  .  to examine its relation to the hat-like complex.
description: <strong>Tilt Series Date:</strong> 2020-10-08</p>
<strong>Data Taken By:</strong> Mohammed Kaplan</p>
<strong>Species / Specimen:</strong> Helicobacter pylori</p>
<strong>Strain:</strong> 26695</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 3°, constant angular increment, dosage: 120.0 eV/Å²,  defocus: -8.0 μm,  magnification: 19500x. </p>
<strong>Microscope:</strong> Caltech Titan Krios</p>
<strong>Acquisition Software:</strong> Serial EM</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> Raptor</p>
<strong>Collaborators and Roles:</strong> The cells were prepared and sent by Carrie Schaffer from the university of Kentucky.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> The cells were grown at 37C with 5% CO2 on sheep blood agar plates for 2 days from a -80C . stock. No growth was seen on the plates after 24 hr therefore the plates were kept in the . incubator for another 24Hr.</p>
<strong>Sample Preparation:</strong> The samples were prepared with Vitrobot IV. Blotting conditions were either: blot force 6, blot . time 3, drain time 1 OR blot force -3, blot time 4, drain time 1, 100%  humidity. Cu grids. 20 nm . gold.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2020-10-08-189/rawdata/</p>Hpylori_DFliF_FISE_193.mrc,  Tilt Series (Pixel Size 0.452 nm), 1.9 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2020-10-08-189/rawdata/Hpylori_DFliF_FISE_193.mrc"
        > <i class="download icon"></i> Download </a></p>

        Hpylori_DFliF_FISE_193_part41_1.rec,  Reconstruction (Pixel Size 1.808 nm), 737.3 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2020-10-08-189/3dimage_113848/Hpylori_DFliF_FISE_193_part41_1.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/qvsf3-13p38
title: Vibrio cholerae SAD2095 induced

description: SAD2095 (T2SS and T4 competence pili) = rpoS*, pilA S81C, lacZ::lacIq, comEA-mCherry, ΔluxO, Ptac-tfoX, Ptac- recA, ∆TCP::ZeoR, ∆MSHA::CarbR, ∆CTX::KanR, ∆pilT::TmRAnkur: "For the taxonomy ID - unfortunately the strain we sent does not have a taxonomy ID. So, you can use the generic one for V. cholerae which is "666". The strain we are working with is related to N16961, but is certainly not the same strain, so not sure if you would want to indicate that somehow? Just for reference - the strain we sent is E7946 (although it is obviously heavily modified with a number of mutations). "
description: <strong>Tilt Series Date:</strong> 2018-07-18</p>
<strong>Data Taken By:</strong> Sara Weaver</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1°, constant angular increment, dosage: 180.0 eV/Å²,  defocus: -6.0 μm,  magnification: 27500x. </p>
<strong>Microscope:</strong> Caltech Polara</p>
<strong>Acquisition Software:</strong> SerialEM</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> Raptor</p>
<strong>Collaborators and Roles:</strong> Strain from Ankur B Dalia ankdalia@indiana.edu, PhD, Assistant Professor, Indiana University. Cells grown, data collected by Sara Weaver</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Streaked stock on a plate. Grew up a single colony in 3 mL LB with shaking at 37˚C. The next day, subcultured 50uL of this overnight culture into 3mL of fresh LB+100uM IPTG + 20mM MgCl2 + 10mM CaCl2 and grow at 30˚C shaking for ~4 hours.</p>
<strong>Sample Preparation:</strong> spun gold (100 µL 10 nm gold + 25 µL 5% BSA) at 15,000rpm for 20 minutes, removed supernatant.  Resuspended gold beads in 20 µL liquid culture.  Vitrobot RT and 95% humidity, 3µL of gold/sample slurry on carbon/copper Quantifoil Finder grids R2/2 (EmiTech glow discharge 50 mA 120 s)  Blot force -6, blot time 3 s, no waiting time, no drain time.  Plunged into ethane/propane mix.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/swj2018-07-18-36/rawdata/</p>20180718_tiltseries_7.mrc,  Tilt Series (Pixel Size 0.39 nm), 2.9 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/swj2018-07-18-36/rawdata/20180718_tiltseries_7.mrc"
        > <i class="download icon"></i> Download </a></p>

        20180718_tiltseries_7_part103_8.rec,  Reconstruction (Pixel Size 1.56 nm), 444.5 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/swj2018-07-18-36/3dimage_93530/20180718_tiltseries_7_part103_8.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/82rh5-6vm43
title: Shewanella MR1_Iron cores_Chemos

description: Raw data files of Shewanella MR1_Iron cores_Chemos
description: <strong>Tilt Series Date:</strong> 2018-08-09</p>
<strong>Data Taken By:</strong> Mohammed Kaplan</p>
<strong>Species / Specimen:</strong> Shewanella oneidensis</p>
<strong>Strain:</strong> MR-1</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-50.0°, 50.0°), step: 2°, constant angular increment, dosage: 150.0 eV/Å²,  defocus: -9.0 μm,  magnification: 27500x. </p>
<strong>Microscope:</strong> Caltech Polara</p>
<strong>Acquisition Software:</strong> Serial EM</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> Batchruntomo</p>
<strong>Collaborators and Roles:</strong> These are Shewanella oneidensis MR1 prepared by Sahand (USC) by Chemostat method grown for 2 days and chemically fixed. I (Mohammed) imaged these cells on the Polara to see if the have the iron cores in order to send them to Israel (Sharon Wolf) to perform EDX and confirm the components of the iron cores.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Chemostat 2 days growth and chemically fixed. The samples were prepared by Sahand (USC).</p>
<strong>Sample Preparation:</strong> I prepared these samples by blot force 6, blot time 3s and drain time 1. I also used the Bdellovibrio conditions (force -5, time 4 s). 10 nm Gold nanoparticles were added.</p>
description: Files available via S3 at ps://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2018-08-09-59/rawdata/</p>SheweTilt23.mrc,  Tilt Series (Pixel Size 0.39 nm), 1.4 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2018-08-09-59/rawdata/SheweTilt23.mrc"
        > <i class="download icon"></i> Download </a></p>

        SheweTilt23.rec,  Reconstruction (Pixel Size 1.56 nm), 888.1 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2018-08-09-59/3dimage_94137/SheweTilt23.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/nzjaj-2dm94
title: BacillusSubtilis_293

description: Bacterial nanotubes (like what is described in Sigal ben Yehuda and Ilan Rosenshine work).
description: <strong>Tilt Series Date:</strong> 2020-02-16</p>
<strong>Data Taken By:</strong> Mohammed Kaplan</p>
<strong>Species / Specimen:</strong> Bacillus subtilis</p>
<strong>Strain:</strong> AB293, ΔponA amyE::fliP-2XHA sacA::ymdB Δmbl</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 3°, constant angular increment, dosage: 150.0 eV/Å²,  defocus: -6.0 μm,  magnification: 19500x. </p>
<strong>Microscope:</strong> Caltech Titan Krios</p>
<strong>Acquisition Software:</strong> Serial EM</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> Raptor</p>
<strong>Collaborators and Roles:</strong> The samples were prepared with Amit and Ritesh (from Sigal Ben Yehuda and Ilan Rosenshine . labs at the Hebrew University). These Samples were incubated for four hours on grids on plates</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Cells were streaked on an agar plate from a -80C stock and incubated at 37C. Next day, the . cells were inoculated in 3 ml of LB and grown at 37C to OD 0.8-1. Cells were then added to . grids on agar plates and incubated for 4 hours at 37 C. The grids were washed with PBS and . then blotted and plunge frozen.</p>
<strong>Sample Preparation:</strong> The sample was manually blotted to increase the chance of finding an intercellular nanotube.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2020-02-16-78/rawdata/</p>Bsubtilis_293_039_af.mrc,  Tilt Series (Pixel Size 0.449 nm), 1.9 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2020-02-16-78/rawdata/Bsubtilis_293_039_af.mrc"
        > <i class="download icon"></i> Download </a></p>

        Bsubtilis_293_039_af_full.rec,  Reconstruction (Pixel Size 1.796 nm), 737.3 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2020-02-16-78/3dimage_111525/Bsubtilis_293_039_af_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.15468/dl.c2z53h
title: Occurrence Download

description: A dataset containing 9334 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Observation, Human Observation, Specimen, Material sample)",
 "TaxonKey is Quercus variabilis"
 ]
}

 The dataset includes 9334 records from 201 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0006216-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.22002/ydh9a-ps234
title: Shewanella MR1_Iron cores_Chemos

description: Raw data files of Shewanella MR1_Iron cores_Chemos
description: <strong>Tilt Series Date:</strong> 2018-08-09</p>
<strong>Data Taken By:</strong> Mohammed Kaplan</p>
<strong>Species / Specimen:</strong> Shewanella oneidensis</p>
<strong>Strain:</strong> MR-1</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-50.0°, 50.0°), step: 2°, constant angular increment, dosage: 150.0 eV/Å²,  defocus: -9.0 μm,  magnification: 27500x. </p>
<strong>Microscope:</strong> Caltech Polara</p>
<strong>Acquisition Software:</strong> Serial EM</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> Raptor</p>
<strong>Collaborators and Roles:</strong> These are Shewanella oneidensis MR1 prepared by Sahand (USC) by Chemostat method grown for 2 days and chemically fixed. I (Mohammed) imaged these cells on the Polara to see if the have the iron cores in order to send them to Israel (Sharon Wolf) to perform EDX and confirm the components of the iron cores.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Chemostat 2 days growth and chemically fixed. The samples were prepared by Sahand (USC).</p>
<strong>Sample Preparation:</strong> I prepared these samples by blot force 6, blot time 3s and drain time 1. I also used the Bdellovibrio conditions (force -5, time 4 s). 10 nm Gold nanoparticles were added.</p>
description: Files available via S3 at ps://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2018-08-09-38/rawdata/</p>SheweTilt18.mrc,  Tilt Series (Pixel Size 0.39 nm), 1.4 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2018-08-09-38/rawdata/SheweTilt18.mrc"
        > <i class="download icon"></i> Download </a></p>

        SheweTilt18_full.rec,  Reconstruction (Pixel Size 1.56 nm), 444.5 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2018-08-09-38/3dimage_94093/SheweTilt18_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/mvwxx-jfw95
title: EPEC_8770_U2OS

description: EPEC cells strain 8770 incubated with U2OS. The aim is to see bacterial nanotubes connected  .  to the eukaryotic cell.
description: <strong>Tilt Series Date:</strong> 2020-02-15</p>
<strong>Data Taken By:</strong> Mohammed Kaplan</p>
<strong>Species / Specimen:</strong> Escherichia coli</p>
<strong>Strain:</strong> 8770, EPEC 8612 + Δbfp ΔtraD-ygeB ΔfinO-traI</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 3°, constant angular increment, dosage: 100.0 eV/Å²,  defocus: -6.0 μm,  magnification: 19500x. </p>
<strong>Microscope:</strong> Caltech Titan Krios</p>
<strong>Acquisition Software:</strong> Serial EM</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> Raptor</p>
<strong>Collaborators and Roles:</strong> The strain EPEC 8770 is obtained from Ritesh (Ilan Rosenshine lab, the Hebrew university) and . Amit (Sigal ben Yehuda lab). U2OS was obtained from Wei Zhao in the Jensen lab.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> U2OS were grown on gold finders grids overnight in DMEM medium at 37 C. next day the grids were washed with PBS and incubated with DMEM+FCS and bacteria were added . (1:100)  and the grids were cultured for 3.5 hours at 37C. Then the grids were washed twice with PBS and incubated with starvation buffer for 1 hour. The samples were plunge . frozen.</p>
<strong>Sample Preparation:</strong> Samples were blotted manually.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2020-02-15-9/rawdata/</p>EPEC_8770_U2OS_010_af.mrc,  Tilt Series (Pixel Size 0.449 nm), 1.9 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2020-02-15-9/rawdata/EPEC_8770_U2OS_010_af.mrc"
        > <i class="download icon"></i> Download </a></p>

        EPEC_8770_U2OS_010_af_part41_4.rec,  Reconstruction (Pixel Size 1.796 nm), 737.3 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2020-02-15-9/3dimage_111331/EPEC_8770_U2OS_010_af_part41_4.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/45rhe-srk29
title: Hpylori_dFliF_FISE

description: These are H_pylori cells that are lacking FliP protein. In these cells, FliF protein was knocked out  .  to examine its relation to the hat-like complex.
description: <strong>Tilt Series Date:</strong> 2020-10-08</p>
<strong>Data Taken By:</strong> Mohammed Kaplan</p>
<strong>Species / Specimen:</strong> Helicobacter pylori</p>
<strong>Strain:</strong> 26695</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 3°, constant angular increment, dosage: 120.0 eV/Å²,  defocus: -8.0 μm,  magnification: 19500x. </p>
<strong>Microscope:</strong> Caltech Titan Krios</p>
<strong>Acquisition Software:</strong> Serial EM</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> Raptor</p>
<strong>Collaborators and Roles:</strong> The cells were prepared and sent by Carrie Schaffer from the university of Kentucky.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> The cells were grown at 37C with 5% CO2 on sheep blood agar plates for 2 days from a -80C . stock. No growth was seen on the plates after 24 hr therefore the plates were kept in the . incubator for another 24Hr.</p>
<strong>Sample Preparation:</strong> The samples were prepared with Vitrobot IV. Blotting conditions were either: blot force 6, blot . time 3, drain time 1 OR blot force -3, blot time 4, drain time 1, 100%  humidity. Cu grids. 20 nm . gold.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2020-10-08-65/rawdata/</p>Hpylori_DFliF_FISE_079.mrc,  Tilt Series (Pixel Size 0.452 nm), 1.9 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2020-10-08-65/rawdata/Hpylori_DFliF_FISE_079.mrc"
        > <i class="download icon"></i> Download </a></p>

        Hpylori_DFliF_FISE_079_part41_10.rec,  Reconstruction (Pixel Size 1.808 nm), 737.3 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2020-10-08-65/3dimage_113610/Hpylori_DFliF_FISE_079_part41_10.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/jfx8b-3z443
title: BacillusSubtilis_293

description: Bacterial nanotubes (like what is described in Sigal ben Yehuda and Ilan Rosenshine work).
description: <strong>Tilt Series Date:</strong> 2020-02-16</p>
<strong>Data Taken By:</strong> Mohammed Kaplan</p>
<strong>Species / Specimen:</strong> Bacillus subtilis</p>
<strong>Strain:</strong> AB293, ΔponA amyE::fliP-2XHA sacA::ymdB Δmbl</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 3°, constant angular increment, dosage: 150.0 eV/Å²,  defocus: -6.0 μm,  magnification: 19500x. </p>
<strong>Microscope:</strong> Caltech Titan Krios</p>
<strong>Acquisition Software:</strong> Serial EM</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> Raptor</p>
<strong>Collaborators and Roles:</strong> The samples were prepared with Amit and Ritesh (from Sigal Ben Yehuda and Ilan Rosenshine . labs at the Hebrew University). These Samples were incubated for four hours on grids on plates</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Cells were streaked on an agar plate from a -80C stock and incubated at 37C. Next day, the . cells were inoculated in 3 ml of LB and grown at 37C to OD 0.8-1. Cells were then added to . grids on agar plates and incubated for 4 hours at 37 C. The grids were washed with PBS and . then blotted and plunge frozen.</p>
<strong>Sample Preparation:</strong> The sample was manually blotted to increase the chance of finding an intercellular nanotube.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2020-02-16-39/rawdata/</p>Bsubtilis_293_067_af.mrc,  Tilt Series (Pixel Size 0.449 nm), 1.9 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2020-02-16-39/rawdata/Bsubtilis_293_067_af.mrc"
        > <i class="download icon"></i> Download </a></p>

        Bsubtilis_293_067_af_full.rec,  Reconstruction (Pixel Size 1.796 nm), 737.3 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2020-02-16-39/3dimage_111453/Bsubtilis_293_067_af_full.rec"
        > <i class="download icon"></i> Download </a></p>