cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.22002/hmg7m-e5z89
title: MT310_xyl(+)_AuCl50uM(+)

description: Raw data files of MT310_xyl(+)_AuCl50uM(+)
description: <strong>Tilt Series Date:</strong> 2009-06-09</p>
<strong>Data Taken By:</strong> Zhuo Li</p>
<strong>Species / Specimen:</strong> Caulobacter crescentus</p>
<strong>Strain:</strong> NA1000</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: -12.0 μm,  magnification: 0x. </p>
<strong>Acquisition Software:</strong> Leginon</p>
<strong>Upload Method:</strong> webload</p>
<strong>Processing Software Used:</strong> RAPTOR, Peach</p>
<strong>Collaborators and Roles:</strong> The MT310 strain was constructed by Martin Thanbichler; cells were cultured and treated by Zhuo Li; data were collected and processed by Zhuo Li.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> The cells were induced by xylose and treated with 50 uM AuCl for 20 hours.</p>
<strong>Sample Preparation:</strong> 10 nm gold. </p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/zla2009-06-09-4/rawdata/</p>09jun09a_Au50uma_023.mrc,  Tilt Series (Pixel Size 0.95 nm), 1.0 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/zla2009-06-09-4/rawdata/09jun09a_Au50uma_023.mrc"
        > <i class="download icon"></i> Download </a></p>

        09jun09a_Au50uma_023_part.rec,  Reconstruction (Pixel Size 1.9 nm), 471.9 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/zla2009-06-09-4/3dimage_5111/09jun09a_Au50uma_023_part.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.15468/dl.eba2kc
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Triplophysa lacustris)",
 "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 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002666-250827131500795/datasets/export for details.
DOI: 10.22002/rh2r2-q8e82
title: O. tauri @ G2/M, no drugs

description: O. tauri cell synchronization .
description: <strong>Tilt Series Date:</strong> 2007-09-27</p>
<strong>Data Taken By:</strong> Lu Gan</p>
<strong>Species / Specimen:</strong> Ostreococcus tauri</p>
<strong>Strain:</strong> RCC745</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-56.0°, 56.0°), step: 1.0°, constant angular increment, dosage: 100.0 eV/Å²,  defocus: -10.0 μm,  magnification: 0x. </p>
<strong>Acquisition Software:</strong> UCSF Tomo</p>
<strong>Upload Method:</strong> rundir</p>
<strong>Processing Software Used:</strong> imod</p>
<strong>Collaborators and Roles:</strong> prepared by Lu Gan at Caltech; data collected by Lu Gan; processed by Lu Gan</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Treated with HU for 12 hours, then incubated in fresh MK for</p>
<strong>Sample Preparation:</strong> Q-foil R3.5/1, BSA treated 10nm gold, 100% humidity, -2mm offset,</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/lga2007-09-27-12/rawdata/</p>RCC745_+HU_8PM_04.mrc,  Tilt Series (Pixel Size 1.26 nm), 163.7 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/lga2007-09-27-12/rawdata/RCC745_+HU_8PM_04.mrc"
        > <i class="download icon"></i> Download </a></p>

        RCC745_+HU_8PM_04.rec,  Reconstruction (Pixel Size 2.52 nm), 302.8 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/lga2007-09-27-12/3dimage_3242/RCC745_+HU_8PM_04.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/m2yy2-h3m19
title: O. tauri MG132 arrest

description: Ostreococcus tauri cryosections
description: <strong>Tilt Series Date:</strong> 2009-07-23</p>
<strong>Data Taken By:</strong> Lu Gan</p>
<strong>Species / Specimen:</strong> Ostreococcus tauri</p>
<strong>Strain:</strong> RCC745</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1.5°, constant angular increment, dosage: 100.0 eV/Å²,  defocus: -10.0 μm,  magnification: 18000x. </p>
<strong>Acquisition Software:</strong> UCSF tomo</p>
<strong>Upload Method:</strong> rundir</p>
<strong>Processing Software Used:</strong> imod</p>
<strong>Collaborators and Roles:</strong> prepared by Lu Gan at Caltech; high-pressure frozen and cryosectioned by Mark Ladinsky; data collected by Lu Gan; processed by Lu Gan</p>
<strong>Purification / Growth Conditions / Treatment:</strong> 9h in 1mM Hydroxyurea, 12h in 50uM Propyzamide, 70m in 50uM MG132</p>
<strong>Sample Preparation:</strong> Cryoprotectant: 10mg/ml BSA, 2X 10nm gold, 20% Dextran; Cells mixed w/ cryoprotectant shortly before HPF </p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/lga2009-07-23-18/3dimage_11463/</p>RCC745_MGtovis_118.rec,  Reconstruction (Pixel Size 1.26 nm), 367.0 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/lga2009-07-23-18/3dimage_11463/RCC745_MGtovis_118.rec"
        > <i class="download icon"></i> Download </a></p>

        RCC745_MGtovis_118.mrc,  Tilt Series (Pixel Size 1.26 nm), 536.9 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/lga2009-07-23-18/rawdata/RCC745_MGtovis_118.mrc"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/ntay6-ffa78
title: O. tauri Propyzamide release

description: Ostreococcus tauri cryosections
description: <strong>Tilt Series Date:</strong> 2010-02-12</p>
<strong>Data Taken By:</strong> Lu Gan</p>
<strong>Species / Specimen:</strong> Ostreococcus tauri</p>
<strong>Strain:</strong> RCC745</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-66.0°, 66.0°), step: 2.0°, constant angular increment, dosage: 100.0 eV/Å²,  defocus: -10.0 μm,  magnification: 18000x. </p>
<strong>Acquisition Software:</strong> UCSF tomo</p>
<strong>Upload Method:</strong> rundir</p>
<strong>Processing Software Used:</strong> imod</p>
<strong>Collaborators and Roles:</strong> prepared by Lu Gan at Caltech; high-pressure frozen and cryosectioned by Mark Ladinsky; data collected by Lu Gan; processed by Lu Gan</p>
<strong>Purification / Growth Conditions / Treatment:</strong> 9h in 1mM Hydroxyurea, 15h in 30uM Propyzamide, Washout Propyzamide</p>
<strong>Sample Preparation:</strong> Cryoprotectant: 10mg/ml BSA, 2X 10nm gold, 20% Dextran; Cells mixed w/ cryoprotectant shortly before HPF </p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/lga2010-02-12-20/rawdata/</p>RCC745_RELtovis_023.mrc,  Tilt Series (Pixel Size 1.26 nm), 771.8 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/lga2010-02-12-20/rawdata/RCC745_RELtovis_023.mrc"
        > <i class="download icon"></i> Download </a></p>

        RCC745_RELtovis_023.rec,  Reconstruction (Pixel Size 1.26 nm), 308.1 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/lga2010-02-12-20/3dimage_12381/RCC745_RELtovis_023.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/8hg23-m9v51
title: Myxococcus xanthus delta-tsaP

description: Grid box YWC121
description: <strong>Tilt Series Date:</strong> 2014-10-22</p>
<strong>Data Taken By:</strong> Yi-Wei Chang</p>
<strong>Species / Specimen:</strong> Myxococcus xanthus</p>
<strong>Strain:</strong> </p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1.0°, 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> UCSFTomo</p>
<strong>Upload Method:</strong> pipeline</p>
<strong>Processing Software Used:</strong> Raptor</p>
<strong>Collaborators and Roles:</strong> Strain form Lotte Sogaard-Andersen</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Cells grown 2 days in 200 rpm shaking CTT medium at 30 degrees without antibiotics. OD600=0.8</p>
<strong>Sample Preparation:</strong> Vitrobot (MK vi) settings: 100% humidity, 3µl sample, 10 mg/ml BSA treated gold. Blot force 6, blot time 2.5 sec. Wait time 0 sec. Drain time 1 sec. Ethane/propane mix. Grid: Quantifoil Cu 2/2 200.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ycw2014-10-22-34/rawdata/</p>20141022_YWC121_40002.mrc,  Tilt Series (Pixel Size 0.39 nm), 3.4 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ycw2014-10-22-34/rawdata/20141022_YWC121_40002.mrc"
        > <i class="download icon"></i> Download </a></p>

        20141022_YWC121_40002_full.rec,  Reconstruction (Pixel Size 1.56 nm), 712.7 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ycw2014-10-22-34/3dimage_47432/20141022_YWC121_40002_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/rtg67-and51
title: Myxococcus xanthus pilM-YFP

description: strain SA4088grid box YWC101
description: <strong>Tilt Series Date:</strong> 2014-05-16</p>
<strong>Data Taken By:</strong> Yi-Wei Chang</p>
<strong>Species / Specimen:</strong> Myxococcus xanthus</p>
<strong>Strain:</strong> </p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-65.0°, 65.0°), step: 1.0°, constant angular increment, dosage: 200.0 eV/Å²,  defocus: -8.0 μm,  magnification: 26000x. </p>
<strong>Microscope:</strong> Janelia Titan</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 form Lotte Sogaard-Andersen</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Cells grown 48 hr in shaking CTT medium at 30 degrees without antibiotics. OD600=0.9</p>
<strong>Sample Preparation:</strong> Vitrobot settings: 100% humidity, 3µl sample, 10 mg/ml BSA treated 10 nm gold. -4 offset, 4 sec blot time, no drain. Ethane/propane mix. Grid: Quantifoil Cu 2/2 200.</p>
  ycw2014-05-16-5_slicer6729.jpg: unknown filaments
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ycw2014-05-16-5/3dimage_42727/</p>20140516_Janelia_YWC096_10034_part131_6.rec,  Reconstruction (Pixel Size 1.32 nm), 688.9 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ycw2014-05-16-5/3dimage_42727/20140516_Janelia_YWC096_10034_part131_6.rec"
        > <i class="download icon"></i> Download </a></p>

        20140516_Janelia_YWC096_10034.mrc,  Tilt Series (Pixel Size 0.33 nm), 3.6 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ycw2014-05-16-5/rawdata/20140516_Janelia_YWC096_10034.mrc"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/w6mbt-d3q67
title: Myxococcus xanthus TM530

description: Wza0 knockoutGrid box YWC029
description: <strong>Tilt Series Date:</strong> 2013-10-26</p>
<strong>Data Taken By:</strong> Yi-Wei Chang</p>
<strong>Species / Specimen:</strong> Myxococcus xanthus</p>
<strong>Strain:</strong> </p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1.0°, constant angular increment, dosage: 220.0 eV/Å²,  defocus: -6.0 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 from Tam Mignot</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Cells grown 48 hr in CTT medium at 30 degrees without antibiotics. OD600=0.7</p>
<strong>Sample Preparation:</strong> Vitrobot settings: 100% humidity, 3µl sample, 10 mg/ml BSA treated gold. -3 offset, 4 sec blot time, no drain. Ethane/propane mix. Grid: Quantifoil Cu 2/2 200</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ycw2013-10-26-9/rawdata/</p>20131025_YWC029_30009.mrc,  Tilt Series (Pixel Size 0.39 nm), 3.4 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ycw2013-10-26-9/rawdata/20131025_YWC029_30009.mrc"
        > <i class="download icon"></i> Download </a></p>

        20131025_YWC029_30009_part121_4.rec,  Reconstruction (Pixel Size 1.56 nm), 712.7 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ycw2013-10-26-9/3dimage_33432/20131025_YWC029_30009_part121_4.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/y3xbs-dgr52
title: Myxococcus xanthus DK1622 wt

description: For T4P averaging
description: <strong>Tilt Series Date:</strong> 2013-08-26</p>
<strong>Data Taken By:</strong> Yi-Wei Chang</p>
<strong>Species / Specimen:</strong> Myxococcus xanthus</p>
<strong>Strain:</strong> </p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-65.0°, 65.0°), step: 1.0°, constant angular increment, dosage: 200.0 eV/Å²,  defocus: -6.0 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 from Martin Thanbichler</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Cells grown 48 hr in CTT medium at 30 degrees without antibiotics. OD600=0.7</p>
<strong>Sample Preparation:</strong> Vitrobot settings: 100% humidity, 3µl sample, 10 mg/ml BSA treated gold. -3 offset, 4 sec blot time, no drain. Ethane/propane mix. Grid: Quantifoil Cu 2/2 200</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ycw2013-08-26-72/rawdata/</p>20130826_DK1622_WT_30013.mrc,  Tilt Series (Pixel Size 0.39 nm), 3.7 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ycw2013-08-26-72/rawdata/20130826_DK1622_WT_30013.mrc"
        > <i class="download icon"></i> Download </a></p>

        20130826_DK1622_WT_30013_part131_2.rec,  Reconstruction (Pixel Size 1.56 nm), 712.7 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ycw2013-08-26-72/3dimage_30258/20130826_DK1622_WT_30013_part131_2.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.15468/dl.8gf5jw
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Spiraea douglasii",
 "Country is Ukraine",
 "HasCoordinate is true"
 ]
}

 The dataset includes 2 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002667-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.22002/zpz2v-kxd82
title: Myxococcus xanthus delta-pilQ

description: grid box YWC061
description: <strong>Tilt Series Date:</strong> 2013-12-30</p>
<strong>Data Taken By:</strong> Yi-Wei Chang</p>
<strong>Species / Specimen:</strong> Myxococcus xanthus</p>
<strong>Strain:</strong> </p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-65.0°, 65.0°), step: 1.0°, constant angular increment, dosage: 180.0 eV/Å²,  defocus: -8.0 μm,  magnification: 26000x. </p>
<strong>Microscope:</strong> Janelia Titan</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 form Lotte Sogaard-Andersen</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Cells grown 48 hr in shaking CTT medium at 30 degrees without antibiotics. OD600=0.7</p>
<strong>Sample Preparation:</strong> Vitrobot settings: 100% humidity, 3µl sample, 10 mg/ml BSA treated gold. -4 offset, 4 sec blot time, 1s drain. Ethane/propane mix. Grid: Quantifoil Cu 2/2 Finder. 20 nm gold beads.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ycw2013-12-30-79/rawdata/</p>20131230_Janelia_YWC061_10058.mrc,  Tilt Series (Pixel Size 0.42 nm), 3.6 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ycw2013-12-30-79/rawdata/20131230_Janelia_YWC061_10058.mrc"
        > <i class="download icon"></i> Download </a></p>

        20131230_Janelia_YWC061_10058_full.rec,  Reconstruction (Pixel Size 1.68 nm), 688.9 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ycw2013-12-30-79/3dimage_37357/20131230_Janelia_YWC061_10058_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/fpr59-pjb32
title: CCcenK_glu

description: C. crescentus CenK, glucose depletion .
description: <strong>Tilt Series Date:</strong> 2006-07-06</p>
<strong>Data Taken By:</strong> Lu Gan</p>
<strong>Species / Specimen:</strong> Caulobacter crescentus</p>
<strong>Strain:</strong> NA1000</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1°, constant angular increment, dosage: 120.0 eV/Å²,  defocus: -10.0 μm,  magnification: 0x. </p>
<strong>Acquisition Software:</strong> Leginon</p>
<strong>Upload Method:</strong> rundir</p>
<strong>Processing Software Used:</strong> imod</p>
<strong>Collaborators and Roles:</strong> prepared by Lu Gan at Caltech; data collected by Lu Gan; processed by Lu Gan; collaboration with Jeff Skerker and Michael Laub at MIT</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Depleted 40 hours in PYE + 0.1% glucose</p>
<strong>Sample Preparation:</strong> Quantifoil R2/1, BSA treated 10nm gold, 100% humidity, -2mm offset,</p>
  lga2006-07-06-3_slicer9402.jpg: Caulobacter crescentus .  OMV .  extracellular vesicles
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/lga2006-07-06-3/rawdata/</p>CCcenK_glu03.mrc,  Tilt Series (Pixel Size 1.2 nm), 1.0 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/lga2006-07-06-3/rawdata/CCcenK_glu03.mrc"
        > <i class="download icon"></i> Download </a></p>

        CCcenK_glu03.rec,  Reconstruction (Pixel Size 2.4 nm), 259.3 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/lga2006-07-06-3/3dimage_2948/CCcenK_glu03.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/qp7vb-9pm49
title: CCcenR_glu

description: C. crescentus CenR, glucose depletion .
description: <strong>Tilt Series Date:</strong> 2006-09-21</p>
<strong>Data Taken By:</strong> Lu Gan</p>
<strong>Species / Specimen:</strong> Caulobacter crescentus</p>
<strong>Strain:</strong> NA1000</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 0.7°, constant angular increment, dosage: 160.0 eV/Å²,  defocus: -10.0 μm,  magnification: 0x. </p>
<strong>Acquisition Software:</strong> Leginon</p>
<strong>Upload Method:</strong> rundir</p>
<strong>Processing Software Used:</strong> imod</p>
<strong>Collaborators and Roles:</strong> prepared by Lu Gan at Caltech; data collected by Lu Gan; processed by Lu Gan; collaboration with Jeff Skerker and Michael Laub at MIT</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Depleted 36 hours in PYE + 0.1% glucose</p>
<strong>Sample Preparation:</strong> Quantifoil R2/1, BSA treated 10nm gold, 100% humidity, -2mm offset,</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/lga2006-09-21-4/rawdata/</p>CCcenR_glu10.mrc,  Tilt Series (Pixel Size 0.67 nm), 1.4 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/lga2006-09-21-4/rawdata/CCcenR_glu10.mrc"
        > <i class="download icon"></i> Download </a></p>

        CCcenR_glu10.rec,  Reconstruction (Pixel Size 1.34 nm), 344.0 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/lga2006-09-21-4/3dimage_2984/CCcenR_glu10.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.6084/m9.figshare.29999641
title: Structural Variations and Phylogenetic Implications of Mitochondrial Genomes in Oaks

description: Despite their pivotal role in eukaryotic evolution, plant mitochondrial genomes remain enigmatic owing to their structural plasticity and limited exploration in nonmodel woody species—a critical knowledge gap that hinders a comprehensive understanding of plant diversification mechanisms. As a keystone genus in Northern Hemisphere ecosystems, Quercus species exhibit exceptional ecological adaptability and phylogenetic diversity, serving as a model clade for studying plant diversification and adaptation. Here, we assembled and annotated complete mitochondrial genomes from 15 phylogenetically representative Quercus species via a hybrid sequencing approach combining next-generation and long-read sequencing technologies. Our analyses revealed six distinct mitochondrial genome architectures with sizes ranging from 339 kb to 622 kb. These genomes encode 34-41 genes, 20-28 tRNAs, and 2-5 rRNAs, demonstrating remarkable intragenus variation in organellar gene inventories. Notably, we identified extensive horizontal gene transfer events between the mitochondrial and chloroplast genomes, involving 11-24 migrated gene fragments with transferred sequences spanning 5,265 bp to 12,723 bp. Comparative repeat analysis demonstrated that dispersed repeats predominantly drive mitochondrial genome expansion, with total repeat length showing a significant positive correlation with genome size (R2=0.64, P&lt;0.001). Phylogenomic reconstruction based on 39 concatenated mitochondrial genes resolved deep evolutionary relationships within Quercus, revealing substantial topological discordance with nuclear genome-derived phylogenies and suggesting distinct cytoplasmic vs. nuclear inheritance histories. This study provides crucial genomic resources and evolutionary insights that refine our understanding of organellar genome dynamics in oaks while establishing a framework for resolving cytonuclear discordance in plant phylogenomics.