cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.22002/gn7yc-qhy39
title: AimB depletion w/ Glucose

description: Raw data files of AimB depletion w/ Glucose
description: <strong>Tilt Series Date:</strong> 2009-07-30</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: 190.0 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 AimB depletion strain was constructed by John Werner in Zemer Gitai's lab. Depletion was done by Zhuo Li. Data were collected and processed by Zhuo Li.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> The AimB depletion strain was depleted serially with 0.2% glucose. </p>
<strong>Sample Preparation:</strong> 10 nm</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/zla2009-07-30-5/rawdata/</p>09jul30a_AimBglu_005.mrc,  Tilt Series (Pixel Size 1.2 nm), 1.0 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        09jul30a_AimBglu_005_full.rec,  Reconstruction (Pixel Size 2.4 nm), 367.0 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/30yd3-mh865
title: HeLa CHMP4A+VPS4DN

description: HeLa cells transfected with CHMP4A & VPS4DN constructs
description: <strong>Tilt Series Date:</strong> 2011-02-07</p>
<strong>Data Taken By:</strong> Cora Woodward</p>
<strong>Species / Specimen:</strong> HeLa cells</p>
<strong>Strain:</strong> ATCC</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1°, constant angular increment, dosage: 150.0 eV/Å²,  defocus: -6.0 μm,  magnification: 22500x. </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> Constructs provided by Wes Sundquist. Cells transfected, frozen and imaged at Caltech by Cora Woodward</p>
<strong>Purification / Growth Conditions / Treatment:</strong> whole cells grown on grids and transfected with polyfect</p>
<strong>Sample Preparation:</strong> manual blotting</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/cwl2011-02-07-1/rawdata/</p>11feb07_C50_1d_005.st,  Tilt Series (Pixel Size 0.5 nm), 1.0 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/cwl2011-02-07-1/rawdata/11feb07_C50_1d_005.st"
        > <i class="download icon"></i> Download </a></p>

        11feb07_C50_1d_005_full.rec,  Reconstruction (Pixel Size 2.0 nm), 4.5 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/cwl2011-02-07-1/3dimage_68003/11feb07_C50_1d_005_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/fy8hx-dat55
title: Hyphomonas EB session15 27.5KX

description: high-order DNA, H-NS, nucleoid, asymmetric cell division
description: <strong>Tilt Series Date:</strong> 2009-06-05</p>
<strong>Data Taken By:</strong> Jian Shi</p>
<strong>Species / Specimen:</strong> Hyphomonas neptunium</p>
<strong>Strain:</strong> ATCC 15444</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-64.0°, 64.0°), step: 2°, constant angular increment, dosage: 150.0 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> raptor</p>
<strong>Collaborators and Roles:</strong> Cultured by Jian; data collected by Jian; processed by Jian</p>
<strong>Purification / Growth Conditions / Treatment:</strong> exponential phase in PYE media, EM 0.1mg/ml...</p>
<strong>Sample Preparation:</strong> QF grid, 10nm gold, 100% humidity...</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/jsa2009-06-05-64/rawdata/</p>09jun05a_bx467d_018.mrc,  Tilt Series (Pixel Size 0.774 nm), 553.7 MB  
        
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        09jun05a_bx467d_018_full.rec,  Reconstruction (Pixel Size 1.548 nm), 377.5 MB  
        
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DOI: 10.34894/fwtbjg
title: Rotterdam 35 TV Commercials (TVC35) fMRI Dataset

description: &lt;div&gt;An fMRI dataset (Study 1a and 1b) reported in the following paper:&lt;br&gt;&lt;/div&gt;&lt;div&gt;&lt;br&gt;&lt;/div&gt;&lt;div&gt;Chan, H. Y., Smidts, A., Schoots, V. C., Dietvorst, R. C., & Boksem, M. A. (2019). Neural similarity at temporal lobe and cerebellum predicts out-of-sample preference and recall for video stimuli. &lt;i&gt;NeuroImage, 197&lt;/i&gt;, 391-401.&lt;/div&gt;&lt;div&gt;&lt;br&gt;&lt;/div&gt;

&lt;p&gt;&lt;div&gt;Participant:&lt;/div&gt;&lt;div&gt;&lt;br&gt;&lt;/div&gt;&lt;div&gt;Participants from two separate sites (Study 1a: N = 40; Study 1b: N = 20) were recruited from the general public by a marketing research company in the Netherlands. &lt;/div&gt;&lt;div&gt;&lt;br&gt;&lt;/div&gt;&lt;/p&gt;

&lt;p&gt;&lt;div&gt;Task:&lt;/div&gt;&lt;div&gt;&lt;br&gt;&lt;/div&gt;&lt;div&gt;Inside scanner, participants watched 35 commercials, presented in randomized order. Immediately after each commercial, participants indicated their liking via button presses without time limit, then waited for 6–10s with a blank screen before another commercial began. The scanning lasted about 35 min. Within three days after scanning, they completed an online survey in which they further rated each of the commercials.&lt;/div&gt;&lt;div&gt;&lt;br&gt;&lt;/div&gt;&lt;/p&gt;

&lt;p&gt;&lt;div&gt;Stimuli:&lt;/div&gt;&lt;div&gt;&lt;br&gt;&lt;/div&gt;&lt;div&gt;Thirty-five commercials from seven well-known brands, aired on national TV networks during 2009–2015, were used as stimuli. Their lengths varied from 25s to 60s (M = 40.5s; SD = 9.4s). On average, the commercials appeared on air for 7.4 weeks (SD = 2.2 weeks).&lt;/div&gt;&lt;/p&gt;
description: If you use this dataset, please cite: Chan, Hang-Yee; Boksem, Maarten; Smidts, Ale (2019). Rotterdam 35 TV Commercials (TVC35) fMRI Dataset. Erasmus University Rotterdam (EUR). Dataset. https://doi.org/10.25397/eur.10062311
DOI: 10.22002/kxr9e-erw47
title: CB15N w/ methanol control

description: Raw data files of CB15N w/ methanol control
description: <strong>Tilt Series Date:</strong> 2009-10-10</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: (-63.0°, 63.0°), step: 1°, constant angular increment, dosage: 190.0 eV/Å²,  defocus: -12.0 μm,  magnification: 18000x. </p>
<strong>Acquisition Software:</strong> Leginon</p>
<strong>Upload Method:</strong> webload</p>
<strong>Processing Software Used:</strong> RAPTOR, Peach, IMOD</p>
<strong>Collaborators and Roles:</strong> Experiments done by ZL.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Exponential phase in PYE</p>
<strong>Sample Preparation:</strong> Quantifoil R2/1 or R2/2, 10nm gold, 100% humidity</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/zla2009-10-10-50/rawdata/</p>09oct10b_WTCCmet_050.mrc,  Tilt Series (Pixel Size 1.192 nm), 1.1 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/zla2009-10-10-50/rawdata/09oct10b_WTCCmet_050.mrc"
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        09oct10b_WTCCmet_050_part.rec,  Reconstruction (Pixel Size 2.384 nm), 471.9 MB  
        
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DOI: 10.15468/dl.h7dw86
title: Occurrence Download

description: A dataset containing 87 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Odonata",
 "Geometry POLYGON ((47.5465 -25.2196, 47.6434 -24.9401, 46.1382 -24.9401, 46.1382 -25.8059, 46.3822 -25.6931, 46.8647 -25.6616, 47.5465 -25.2196))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Living Specimen, Observation, Human Observation, Machine Observation, Material sample, Literature Occurrence, Material citation, Occurrence evidence)"
 ]
}

 The dataset includes 87 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0045437-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.22002/tzfbe-km327
title: Rhodobacter 1558 cryosections

description: Cryosections by MArk Ladinsky
description: <strong>Tilt Series Date:</strong> 2010-09-27</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: (-61.0°, 64.0°), step: °, constant angular increment, dosage: 120.0 eV/Å²,  defocus: -8.0 μm,  magnification: 34000x. </p>
<strong>Acquisition Software:</strong> Leginon</p>
<strong>Upload Method:</strong> webload</p>
<strong>Processing Software Used:</strong> IMOD</p>
<strong>Collaborators and Roles:</strong> Judy Armitage</p>
<strong>Purification / Growth Conditions / Treatment:</strong> grown in SUX media</p>
<strong>Sample Preparation:</strong> prepared for cryosectioning (gold prep see JWIKI)</p>
description: Files available via S3 at ://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/aba2010-09-27-31/rawdata/</p>10sep27a_Rhsections_037.st,  Tilt Series (Pixel Size 0.0 nm), 528.5 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/aba2010-09-27-31/rawdata/10sep27a_Rhsections_037.st"
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        10sep27a_Rhsections_037.rec,  Reconstruction (Pixel Size 0.0 nm), 38.8 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/aba2010-09-27-31/3dimage_14905/10sep27a_Rhsections_037.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/8ws72-e9c83
title: B. subtilis AD3268

description: Raw data files of B. subtilis AD3268
description: <strong>Tilt Series Date:</strong> 2011-12-09</p>
<strong>Data Taken By:</strong> Elitza Tocheva</p>
<strong>Species / Specimen:</strong> Bacillus subtilis </p>
<strong>Strain:</strong> AD3268, ponA null, Alp7A</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1°, constant angular increment, dosage: 200.0 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> Joe Pogliano</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Cells were grown in LB</p>
<strong>Sample Preparation:</strong> Vitrobot</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2011-12-09-9/rawdata/</p>32680009.mrc,  Tilt Series (Pixel Size 1.9 nm), 1.0 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2011-12-09-9/rawdata/32680009.mrc"
        > <i class="download icon"></i> Download </a></p>

        32680009_full.rec,  Reconstruction (Pixel Size 3.8 nm), 929.0 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2011-12-09-9/3dimage_16074/32680009_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/dnjz9-6d726
title: Acetonema longum

description: Acetonema longum tests of periplasmic layers
description: <strong>Tilt Series Date:</strong> 2010-12-05</p>
<strong>Data Taken By:</strong> Elitza Tocheva</p>
<strong>Species / Specimen:</strong> Acetonema longum</p>
<strong>Strain:</strong> None</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1°, constant angular increment, dosage: 200.0 eV/Å²,  defocus: -10.0 μm,  magnification: 22500x. </p>
<strong>Acquisition Software:</strong> Leginon</p>
<strong>Upload Method:</strong> uploadraptor</p>
<strong>Processing Software Used:</strong> Raptor</p>
<strong>Collaborators and Roles:</strong> cells grown by Eric Matson</p>
<strong>Purification / Growth Conditions / Treatment:</strong> glucose, anaerobic</p>
<strong>Sample Preparation:</strong> quantifoil grid R2/2, 20nm gold, 100% humidity</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2010-12-05-4/rawdata/</p>10dec05b_NT1_002.mrc,  Tilt Series (Pixel Size 0.95 nm), 1.7 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2010-12-05-4/rawdata/10dec05b_NT1_002.mrc"
        > <i class="download icon"></i> Download </a></p>

        cell2_full.rec,  Reconstruction (Pixel Size 1.9 nm), 1.3 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2010-12-05-4/3dimage_24656/cell2_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/00337-cp846
title: E.coli "strain8" Tsr-A413G

description: CheA-on state
description: <strong>Tilt Series Date:</strong> 2011-11-28</p>
<strong>Data Taken By:</strong> Ariane Briegel</p>
<strong>Species / Specimen:</strong> Escherichia coli</p>
<strong>Strain:</strong> </p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-63.0°, 63.0°), step: 1°, constant angular increment, dosage: 160.0 eV/Å²,  defocus: -10.0 μm,  magnification: 34000x. </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 Sandy Parkinson</p>
<strong>Purification / Growth Conditions / Treatment:</strong> grown in TB medium</p>
<strong>Sample Preparation:</strong> Lysed with Penicillin for one hour</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/aba2011-11-28-33/rawdata/</p>strain8nov2011_0030.mrc,  Tilt Series (Pixel Size 0.644 nm), 1.1 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/aba2011-11-28-33/rawdata/strain8nov2011_0030.mrc"
        > <i class="download icon"></i> Download </a></p>

        strain8nov2011_0030_part.rec,  Reconstruction (Pixel Size 1.288 nm), 516.1 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/kar03-kg762
title: Pfl 052709 627

description: Prosthecobacter fluviatilis, 09may28a_627_052709_001,
description: <strong>Tilt Series Date:</strong> 2009-05-28</p>
<strong>Data Taken By:</strong> Martin Pilhofer</p>
<strong>Species / Specimen:</strong> Prosthecobacter fluviatilis</p>
<strong>Strain:</strong> None</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: -10.0 μm,  magnification: 22500x. </p>
<strong>Acquisition Software:</strong> Leginon</p>
<strong>Upload Method:</strong> rundir</p>
<strong>Processing Software Used:</strong> raptor</p>
<strong>Collaborators and Roles:</strong> cultured by Martin Pilhofer; data collected by Martin Pilhofer; processed by Martin Pilhofer</p>
<strong>Sample Preparation:</strong> quantifoil grid, 10nm gold, 100% humidity, blotting 1/-2/2/0/1/4/200</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mpa2009-05-28-1/rawdata/</p>09may28a_627_052709_001.mrc,  Tilt Series (Pixel Size 0.95 nm), 1.0 GB  
        
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        09may28a_627_052709_001_full.rec,  Reconstruction (Pixel Size 1.9 nm), 838.9 MB  
        
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DOI: 10.5281/zenodo.14435420
title: Global phylogeny, biogeography, and evolution of the agarophyte family Gracilariaceae with key insights into broadly distributed and cultivated species

description: File: Gracilariaceae_COX1_RefSeq_Curated_v1.fasta

This file contains a curated set of reference sequences for the mitochondrial cytochrome c oxidase subunit 1 (COX1) gene from species within the red algal family Gracilariaceae. These sequences have been carefully selected and verified to represent taxonomically accepted species names, providing a reliable resource for species identification and phylogenetic analyses. The dataset has been curated to ensure accuracy and consistency, making it suitable for use in BLAST searches, phylogenetic reconstructions, and other molecular systematic studies. This is version 1 of the dataset. Future updates may include additional sequences or corrections. The file is in FASTA format.

File: Gracilariaceae_rbcL_RefSeq_Curated_v1.fasta

This file contains a curated set of reference sequences for the plastid ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit (rbcL) gene from species within the red algal family Gracilariaceae. These sequences have been carefully selected and verified to represent taxonomically accepted species names, providing a reliable resource for species identification and phylogenetic analyses. The dataset has been curated to ensure accuracy and consistency, making it suitable for use in BLAST searches, phylogenetic reconstructions, and other molecular systematic studies. This is version 1 of the dataset. Future updates may include additional sequences or corrections. The file is in FASTA format.
DOI: 10.5281/zenodo.14435421
title: Global phylogeny, biogeography, and evolution of the agarophyte family Gracilariaceae with key insights into broadly distributed and cultivated species

description: File: Gracilariaceae_COX1_RefSeq_Curated_v1.fasta

This file contains a curated set of reference sequences for the mitochondrial cytochrome c oxidase subunit 1 (COX1) gene from species within the red algal family Gracilariaceae. These sequences have been carefully selected and verified to represent taxonomically accepted species names, providing a reliable resource for species identification and phylogenetic analyses. The dataset has been curated to ensure accuracy and consistency, making it suitable for use in BLAST searches, phylogenetic reconstructions, and other molecular systematic studies. This is version 1 of the dataset. Future updates may include additional sequences or corrections. The file is in FASTA format.

File: Gracilariaceae_rbcL_RefSeq_Curated_v1.fasta

This file contains a curated set of reference sequences for the plastid ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit (rbcL) gene from species within the red algal family Gracilariaceae. These sequences have been carefully selected and verified to represent taxonomically accepted species names, providing a reliable resource for species identification and phylogenetic analyses. The dataset has been curated to ensure accuracy and consistency, making it suitable for use in BLAST searches, phylogenetic reconstructions, and other molecular systematic studies. This is version 1 of the dataset. Future updates may include additional sequences or corrections. The file is in FASTA format.
DOI: 10.22002/39s81-xyd91
title: Delftia acidovorans in NB

description: Delftia acidovorans Cs1-4 grown in NB
description: <strong>Tilt Series Date:</strong> 2009-03-30</p>
<strong>Data Taken By:</strong> Elitza Tocheva</p>
<strong>Species / Specimen:</strong> Delftia acidovorans</p>
<strong>Strain:</strong> Cs1-4</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 2°, constant angular increment, dosage: 200.0 eV/Å²,  defocus: 0.0 μm,  magnification: 22500x. </p>
<strong>Acquisition Software:</strong> Leginon</p>
<strong>Upload Method:</strong> rundir</p>
<strong>Processing Software Used:</strong> </p>
<strong>Collaborators and Roles:</strong> grown by Bill Hickey at UW-Madison; data collected and processed by Elitza Tocheva</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Grown in NB.</p>
<strong>Sample Preparation:</strong> 20nm gold, 2s blot, -2 offset</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/etl2009-03-30-15/rawdata/</p>09mar30c_WTonNB_024_orig.st,  Tilt Series (Pixel Size 0.962 nm), 1.0 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        09mar30c_WTonNB_024.rec,  Reconstruction (Pixel Size 0.0 nm), 392.2 MB  
        
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