cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.22002/mnc4p-6pe39
title: JV6781_ΔdotLOB

description: ΔdotLOB (Deletion of Dot/Icm ATPases dotL, dotO, dotB)
description: <strong>Tilt Series Date:</strong> 2017-07-17</p>
<strong>Data Taken By:</strong> Debnath Ghosal</p>
<strong>Species / Specimen:</strong> Legionella pneumophila</p>
<strong>Strain:</strong> Philadelphia-1_Lp02</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 2°, constant angular increment, dosage: 100.0 eV/Å²,  defocus: -7.0 μm,  magnification: 27500x. </p>
<strong>Microscope:</strong> Caltech Polara</p>
<strong>Acquisition Software:</strong> UCSFTomo</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> Raptor</p>
<strong>Collaborators and Roles:</strong> Strain sent to us by Joseph P. Vogel, Washington University School of Medicine. Data collected and processed by Debnath Ghosal at F30, Caltech.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Cells were grown in AYE liquid culture with following supplements: ferric nitrate, cysteine hydrochloride and thymidine. Scrape cells off a plate, dissolve in the media, adjust the cell density to 0.6 and make a dilution series. Start O/N culture with all of them and freeze cells next day from the one in early stationary phase that is OD ~ 3.0. This time cell density was ~2.6</p>
<strong>Sample Preparation:</strong> 6 grids were frozen for this strain at OD~ 2.6, cell density was increased to 2x by centrifugation. Vitrobot (MK iv) settings: 100% humidity, 4µl sample, Blot force 6, blot time 4 sec. Wait time 0 sec. Drain time 1 sec. Ethane/propane mix. Grid: Quantifoil Cu 2/2 200. Add gold to cells prior to freezing: 1ul of gold to 4 ul of cells, freeze.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2017-07-17-84/rawdata/</p>20170718e_JV67810011.mrc,  Tilt Series (Pixel Size 0.39 nm), 1.7 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2017-07-17-84/rawdata/20170718e_JV67810011.mrc"
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        20170718e_JV67810011.rec,  Reconstruction (Pixel Size 1.56 nm), 889.0 MB  
        
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DOI: 10.22002/wasp0-cxm42
title: Vibrio cholerae SAD2095

description: SAD2095 (T2SS and T4 competence pili)
description: <strong>Tilt Series Date:</strong> 2019-09-05</p>
<strong>Data Taken By:</strong> Sara Weaver</p>
<strong>Species / Specimen:</strong> Vibrio cholerae</p>
<strong>Strain:</strong> SAD2095</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (60.0°, -60.0°), step: 1.0°, constant angular increment, dosage: 134.0 eV/Å²,  defocus: -4.0 μm,  magnification: 26000x. </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> Strain from Ankur B Dalia ankdalia@indiana.edu, PhD, Assistant Professor, Indiana University. Cells grown, samples prepared by Andrew Schacht, data collected by Sara Weaver, Strain from Ankur B Dalia ankdalia@indiana.edu, PhD, Assistant Professor, Indiana University. Cells grown, data collected by Sara Weaver, and Matthew Sazinsky.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> 2019/06/05: 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 ~8 hours. This induced expression of the transcription factor TfoX to turn on the T2SS Type IV competence pilus.</p>
<strong>Sample Preparation:</strong> 2019/06/05 spun gold (100 uL 10 nm gold + 25 uL 5% BSA) at 15,000rpm for 20 minutes, removed supernatant. Resuspended gold beads in 300 uL liquid culture that was washed in 7 g/L instant ocean, resuspended in 50 uL instant ocean.  40 uL was then aliquoted into the gold pellet Vitrobot 4 deg C and 100% humidity, 3uL of gold/sample slurry on carbon/copper, extra thick carbon, Quantifoil Finder grids R2/2 (EmiTech glow discharge 15 mA 60 s) Blot force +2, blot time 3 s, no waiting time, no drain time. Plunged into ethane/propane mix.</p>
description: Files available via S3 at ttps://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/swj2019-09-05-14/rawdata/</p>20190905_ASBox2Grid2_TS13-half1.mrc,  Tilt Series (Pixel Size 0.336 nm), 2.9 GB  
        
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        20190905_ASBox2Grid2_TS13-half1_full.rec,  Reconstruction (Pixel Size 1.344 nm), 737.3 MB  
        
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DOI: 10.15468/dl.sv43cv
title: Occurrence Download

description: A dataset containing 34 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Gobio insuyanus)",
 "BasisOfRecord is one of (Specimen, Literature Occurrence, Human Observation, Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1991",
 "Year is less than or equal to 2025"
 ]
}

 The dataset includes 34 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013710-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.22002/881th-tzr41
title: Vibrio cholerae SAD2095

description: SAD2095 (T2SS and T4 competence pili)
description: <strong>Tilt Series Date:</strong> 2019-09-05</p>
<strong>Data Taken By:</strong> Sara Weaver</p>
<strong>Species / Specimen:</strong> Vibrio cholerae</p>
<strong>Strain:</strong> SAD2095</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (60.0°, -60.0°), step: 1.0°, constant angular increment, dosage: 134.0 eV/Å²,  defocus: -4.0 μm,  magnification: 26000x. </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> None</p>
<strong>Collaborators and Roles:</strong> Strain from Ankur B Dalia ankdalia@indiana.edu, PhD, Assistant Professor, Indiana University. Cells grown, samples prepared by Andrew Schacht, data collected by Sara Weaver, Strain from Ankur B Dalia ankdalia@indiana.edu, PhD, Assistant Professor, Indiana University. Cells grown, data collected by Sara Weaver, and Matthew Sazinsky.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> 2019/06/05: 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 ~8 hours. This induced expression of the transcription factor TfoX to turn on the T2SS Type IV competence pilus.</p>
<strong>Sample Preparation:</strong> 2019/06/05 spun gold (100 uL 10 nm gold + 25 uL 5% BSA) at 15,000rpm for 20 minutes, removed supernatant. Resuspended gold beads in 300 uL liquid culture that was washed in 7 g/L instant ocean, resuspended in 50 uL instant ocean.  40 uL was then aliquoted into the gold pellet Vitrobot 4 deg C and 100% humidity, 3uL of gold/sample slurry on carbon/copper, extra thick carbon, Quantifoil Finder grids R2/2 (EmiTech glow discharge 15 mA 60 s) Blot force +2, 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/swj2019-09-05-5/rawdata/</p>20190905_ASBox2Grid2_TS5.mrc,  Tilt Series (Pixel Size 0.336 nm), 5.7 GB  
        
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        20190905_ASBox2Grid2_TS5.mrc.mdoc,  63.9 kB  
        
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DOI: 10.22002/6j33f-17f58
title: Rhodobacter 1558 lyse ficoll

description: Rhodobacter sphaeroides JPA 1558 lysed with crowding agents
description: <strong>Tilt Series Date:</strong> 2013-09-26</p>
<strong>Data Taken By:</strong> Ariane Briegel</p>
<strong>Species / Specimen:</strong> Rhodobacter sphaeroides</p>
<strong>Strain:</strong> ATCC 17023</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1°, constant angular increment, dosage: 160.0 eV/Å²,  defocus: -12.0 μm,  magnification: 22500x. </p>
<strong>Microscope:</strong> Caltech Polara</p>
<strong>Acquisition Software:</strong> UCSFTomo</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> Raptor</p>
<strong>Collaborators and Roles:</strong> Judy Armitage</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Spun down for 10' at 5100 rpm. Resuspended pellets in 5 mL PEG-Trehalose-Ficoll-Sucrose-Tris-HCl buffer (7.5% PEG 8000, 4% Trehalose, 20% Sucrose, 25 mM Tris-HCl pH 7.0,10% Ficoll)    * 2.14 mL PEG 8000   * 1 mL Trehalose   * 2 g Sucrose   * 1 g Ficoll   * Q.S. 10 mL 25 mM Tris-HCl, pH 7.0Note:  Ficoll didn't go into solution after 4 hours, so spun down and used aqueous phase.  In future, try less Ficoll?Add 500 µL of 50 mg/mL lysozyme stock (make fresh, in 10 mM Tris-HCl, pH 8.0) for a final concentration of 5 mg/mL Incubate 15' at room temperature Add 28 µL of magnesium chloride, 3.3 µL of calcium chloride, and 5.5 µL of DNase IIncubate 30' at 37 degrees Celsius Spin down for 10' at 5100 rpm.Resuspend with gentle pipetting in 200 µL K-phosphate-PEG-Trehalose-Sucrose buffer (7.5% PEG-8000, 4% Trehalose, 20% Sucrose, 5 mM K-phosphate buffer)    * 2.14 mL PEG 8000   * 1 mL Trehalose   * 2 g Sucrose   * Q.S. 10 mL 5 mM K-phosphate buffer, pH 7.0 9/17/13:  Seems to work well.  Good spheroplast formation, and intact clusters.Freeze grids in grid box "Waldo Ficoll"</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/aba2013-09-26-2/rawdata/</p>Waldo22mag160dose0002.mrc,  Tilt Series (Pixel Size 0.48 nm), 3.4 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/aba2013-09-26-2/rawdata/Waldo22mag160dose0002.mrc"
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        Waldo22mag160dose0002_part121_3.rec,  Reconstruction (Pixel Size 0.96 nm), 2.9 GB  
        
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DOI: 10.22002/edy25-g5c71
title: H.pylori 26695 delta-cagA / AGS

description: grid box: YWC082
description: <strong>Tilt Series Date:</strong> 2014-02-15</p>
<strong>Data Taken By:</strong> Yi-Wei Chang</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: 1.0°, constant angular increment, dosage: 210.0 eV/Å²,  defocus: -10.0 μm,  magnification: 22500x. </p>
<strong>Microscope:</strong> Caltech Polara</p>
<strong>Acquisition Software:</strong> UCSFTomo</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> Raptor</p>
<strong>Collaborators and Roles:</strong> H.pylori & AGS cells from Carrie Shaffer</p>
<strong>Purification / Growth Conditions / Treatment:</strong> H.pylori cells grown in BLBB + 5% heat inactivated fetal bovine serum at 37 degrees in 5% CO2 chamber for O/N, OD600=~0.5. AGS cells cultivated on QF Au finder grid for 1 day in RPMI + 10% FBS. Infect by pylori for 4 hr.</p>
<strong>Sample Preparation:</strong> Vitrobot settings: 100% humidity, 37 C, 3µl BSA treated 20 nm gold (100 ul gold+ 25 ul BSA, pellets from 6 tubes merged into ~30 ul final solution). Manual blot by Whatman 40 filter paper for 3 sec. Ethane/propane mix.</p>
  ycw2014-02-15-5_slicer3701.jpg: Helicobacter pylori 26695 delta-cagA co-cultured with AGS cells. .   .  Patches of filament bundles.  Cell is unhealthy and lysing. ycw2014-02-15-5_slicer3702.jpg: Helicobacter pylori 26695 delta-cagA co-cultured with AGS cells. .   .  Three tubes projecting from Hp cell.  Possibly T4SS related. ycw2014-02-15-5_slicer3703.jpg: Helicobacter pylori 26695 delta-cagA co-cultured with AGS cells. .   .  Two tubes visilbe.  Top tube has small tubes projecting from it.  Possibly T4SS related. ycw2014-02-15-5_slicer3704.jpg: Helicobacter pylori 26695 delta-cagA co-cultured with AGS cells. .   .  Two tubes visible projecting from cells.  Possibly T4SS related. ycw2014-02-15-5_slicer3705.jpg: Helicobacter pylori 26695 delta-cagA co-cultured with AGS cells. .   .  View down tube.  Possibly T4SS related.
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ycw2014-02-15-5/rawdata/</p>20140215_YWC082_10001.mrc,  Tilt Series (Pixel Size 0.48 nm), 3.4 GB  
        
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        20140215_YWC082_10001_part121_7.rec,  Reconstruction (Pixel Size 1.92 nm), 712.7 MB  
        
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DOI: 10.22002/8hg43-ypa11
title: MEF cells - Septin2 knock down

description: Septin2 was knockdown using retroviral delivery of shRNA. Purpose - mitochondrial division in the absence of Septin2.
description: <strong>Tilt Series Date:</strong> 2019-01-05</p>
<strong>Data Taken By:</strong> Shrawan kumar Mageswaran</p>
<strong>Species / Specimen:</strong> MEF cells</p>
<strong>Strain:</strong> </p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 2°, constant angular increment, dosage: 100.0 eV/Å²,  defocus: -8.0 μm,  magnification: 33000x. </p>
<strong>Microscope:</strong> Caltech Titan Krios</p>
<strong>Acquisition Software:</strong> SerialEM</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> IMOD, tomo3D</p>
<strong>Collaborators and Roles:</strong> Chun-Shik from Chan lab helped design the shRNA against Septin2 and provided transduction protocol. Shrawan and Danielle Grotjahn created cell line. Danielle FIB-milled the cells and Shrawan performed ECT.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Cells were grown on R2/2 quantifoil gold grids coated with 0.1 mg/mL fibronectin.</p>
<strong>Sample Preparation:</strong> Cells were treated with 10µM FCCP, plunge frozen and FIB-milled.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/smk2019-01-05-11/rawdata/</p>TS5.mrc,  Tilt Series (Pixel Size 0.432 nm), 1.7 GB  
        
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DOI: 10.22002/0e6m0-91r60
title: mini cells

description: Mini cells (FtsA FtsZ over-expression)
description: <strong>Tilt Series Date:</strong> 2019-11-15</p>
<strong>Data Taken By:</strong> Yuxi Liu</p>
<strong>Species / Specimen:</strong> Legionella pneumophila</p>
<strong>Strain:</strong> Philadelphia-1_Lp02</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-54.0°, 54.0°), step: 3°, constant angular increment, dosage: 100.0 eV/Å²,  defocus: -5.0 μm,  magnification: 33000x. </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> None</p>
<strong>Collaborators and Roles:</strong> Strain from Craig Roy lab</p>
<strong>Purification / Growth Conditions / Treatment:</strong> FtsA FtsZ over-expression induced by 0.1mM IPTG in liquid culture. O.D. reached 1.8 after ~40 hours. </p>
<strong>Sample Preparation:</strong> Concentrate 600uL of O.D. 1.8 cells, collect supernatant from 500Xg 2min spin, then concentrate again w/ 1000xg 5min spin. Resuspend pellet to 50uL as stock. Vitrobot set to 22 C, 100% humidity. Apply 4uL of 20X diluted stock, blot manually. Quantifoil R2/2 copper.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ylx2019-11-15-38/rawdata/</p>20191115_Lpmini_56.mrc,  Tilt Series (Pixel Size 0.1339 nm), 7.2 GB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/3hq4h-3p004
title: P_aeruginosa_PA14_DfliF_Krios

description: Raw data files of P_aeruginosa_PA14_DfliF_Krios
description: <strong>Tilt Series Date:</strong> 2018-09-29</p>
<strong>Data Taken By:</strong> Mohammed Kaplan</p>
<strong>Species / Specimen:</strong> Pseudomonas aeruginosa</p>
<strong>Strain:</strong> </p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (50.0°, -50.0°), step: 2°, constant angular increment, dosage: 160.0 eV/Å²,  defocus: -9.0 μm,  magnification: 26000x. </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> I (mohammed) obtained the cells from Shannon Park (Dianne Newman lab). The cells are available in their library of Pseudomonas aeruginosa PA14.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> I inoculated one colony from an LB agar plate and grew the cells overnight in LB with 100 ug/ml of Gentamycin. Then I concentrated the cells three times and mixed them with gold nanoparticles and added 3 ul on to thick carbon R2 grids and blotted them and plunge froze them (force either 6 or 3, time either 3 or 2 seconds respectively, drain time 1 second).</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2018-09-29-77/rawdata/</p>test.mrc,  Tilt Series (Pixel Size 0.53 nm), 56.9 MB  
        
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DOI: 10.22002/71tc9-q0y41
title: MEF cells with FCCP

description: Raw data files of MEF cells with FCCP
description: <strong>Tilt Series Date:</strong> 2018-10-10</p>
<strong>Data Taken By:</strong> Shrawan kumar Mageswaran</p>
<strong>Species / Specimen:</strong> MEF cells</p>
<strong>Strain:</strong> </p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 2°, constant angular increment, dosage: 100.0 eV/Å²,  defocus: -8.0 μm,  magnification: 33000x. </p>
<strong>Microscope:</strong> Caltech Titan Krios</p>
<strong>Acquisition Software:</strong> SerialEM</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> IMOD, tomo3D</p>
<strong>Collaborators and Roles:</strong> Wei Yang froze grids. Danielle Grotjahn FIB-milled cells and Danielle/Songye performed ECT. Cells courtesy of Chan lab.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Cells were grown on R2/2 quantifoil gold grids treated with 0.1 mg/mL fibronectin.</p>
<strong>Sample Preparation:</strong> Cells were treated for 3 min with 10 µM FCCP before plunge freezing and FIB-milling.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/smk2018-10-10-3/rawdata/</p>TS2_Lam2.mrc,  Tilt Series (Pixel Size 0.432 nm), 2.2 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/smk2018-10-10-3/rawdata/TS2_Lam2.mrc"
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DOI: 10.22002/qa9b0-maf37
title: BacillusSubtilis_328_4hr

description: Bacillus subtitles strain 328 overexpressing ymdB.
description: <strong>Tilt Series Date:</strong> 2020-02-26</p>
<strong>Data Taken By:</strong> Mohammed Kaplan</p>
<strong>Species / Specimen:</strong> Bacillus subtilis</p>
<strong>Strain:</strong> AB328, ΔponA ΔymdB amyE::ymdB Δhag</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> None</p>
<strong>Collaborators and Roles:</strong> Samples were prepared with Ritesh and Amit from Ilan Rosenshine and Sigal ben Yehuda labs at . the Hebrew university. See tomograms mka2020-02-08-x.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Samples were prepared as mentioned in Bacillus subtitles tomograms taken on 8th of February . 2020.</p>
<strong>Sample Preparation:</strong> Samples were prepared as mentioned in Bacillus subtitles tomograms taken on 8th of February . 2020. See tomograms mka2020-02-08-x.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2020-02-26-6/rawdata/</p>Bsubtilis_328_024.mrc,  Tilt Series (Pixel Size 0.449 nm), 1.9 GB  
        
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