cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.22002/f1jxs-31b39
title: Eco 020509 27b

description: Escherichia coli, 09feb08c_12_2_1_020509_27_050, btub filaments,
description: <strong>Tilt Series Date:</strong> 2009-02-08</p>
<strong>Data Taken By:</strong> Martin Pilhofer</p>
<strong>Species / Specimen:</strong> Escherichia coli</p>
<strong>Strain:</strong> 12.2.1 Martin</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/mpa2009-02-08-10/rawdata/</p>09feb08c_12_2_1_020509_27_050.mrc,  Tilt Series (Pixel Size 0.95 nm), 1.0 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        09feb08c_12_2_1_020509_27_050_full.rec,  Reconstruction (Pixel Size 1.9 nm), 838.9 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.15468/dl.aghuxt
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Polyplectron malacense",
 "Country is China",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0047563-250811113504898/datasets/export for details.
DOI: 10.22002/c9nz9-efk63
title: Pva 052709 359bl

description: Prosthecobacter vanneervenii, 09jun01a_Pvaold359bl_006,
description: <strong>Tilt Series Date:</strong> 2009-06-01</p>
<strong>Data Taken By:</strong> Martin Pilhofer</p>
<strong>Species / Specimen:</strong> Prosthecobacter vanneervenii</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/mpa2009-06-01-2/rawdata/</p>09jun01a_Pvaold359bl_006.mrc,  Tilt Series (Pixel Size 0.95 nm), 1.0 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        09jun01a_Pvaold359bl_006_full.rec,  Reconstruction (Pixel Size 1.9 nm), 838.9 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.4121/ad21c652-ad75-4a99-a09a-46c7d8f383d6
title: Data underlying chapter 4 of PhD thesis: Building the genome of a minimal synthetic cell

description: This dataset belongs to the PhD thesis of Céline Cleij titled "Building the genome of a minimal synthetic cell".Specifically, the dataset belongs to Chapter 4 titled "<em>De novo</em> design and assembly of minimal genomes for the synthetic cell".<br>Authors: Céline Cleij, Pascale Daran-Lapujade, Christophe DanelonCorresponding authors: Pascale Daran-Lapujade and Christophe DanelonContact information: p.a.s.daran-lapujade@tudelft.nl and danelon@insa-toulouse.fr<br>This dataset contains data collected during experiments as part of Céline Cleij's PhD project. The data was collected from 2023-2025.<br>All data processing and analysis steps are described in detail in the Methods section of thesis chapter 4.Designed SynMG sequences (GenBank) were prepared with the SnapGene software, using the plasmid maps of the sequenced template plasmids and the designed primer sequences.Raw Nanopore sequencing reads (fastq) were obtained by Plasmidsaurus (Eugene, OR, USA) using Nanopore sequencing technology.Consensus SynMG sequences (GenBank) were obtained by Plasmidsaurus after processing of the raw reads, and were manually annotated in SnapGene.The overview of relevant mutations ("Relevant mutations in SynMG variants") was prepared in Excel, based on mutations in consensus sequences and raw reads obtained from sequencing.LC-MS data was obtained after processing in the Mascot software.The tables S4.1-S4.15 were prepared in Excel. <br><br>The data is grouped into eight files: <br>i) Zip file "Designed SynMG sequences"Files are named after the SynMG version (SynMG1 or SynMG2).<br>ii) Zip file "S. cerevisiae - Raw Nanopore sequencing reads"Files are named after the yeast strain from which total DNA was extracted, and after the SynMG variant which was assembled in this strain.<br>iii) Zip file "S. cerevisiae - Consensus SynMG sequences"Files are named after the yeast strain from which total DNA was extracted, and after the SynMG variant which was assembled in this strain.<br>iv) Zip file "E. coli - Raw Nanopore sequencing reads"Files are named after the E. coli strain from which SynChr DNA was extracted, and after the SynMG variant which was amplified in this strain.<br>v) Zip file "E. coli - Consensus SynMG sequences"Files are named after the E. coli strain from which SynChr DNA was extracted, and after the SynMG variant which was amplified in this strain.<br>vi) Excel file "Relevant mutations in SynMG variants"This Excel file contains an overview of all relevant mutations SynMG1.1, SynMG1.2, SynMG1.3, SynMG2.1 and SynMG2.2 compared to the designed maps. <br>vii) Excel file "LC-MS data"This Excel file contains LC-MS data used for making Figure 4A, B & D.<br>viii) Excel file "Tables S4.1-S4.15"This Excel file contains the supplementary tables S4.1 to S4.15, which contain information about all used strains, synthetic chromosomes, plasmids, primers and SHRs used in this study.<br>
DOI: 10.4121/ad21c652-ad75-4a99-a09a-46c7d8f383d6.v2
title: Data underlying chapter 4 of PhD thesis: Building the genome of a minimal synthetic cell

description: This dataset belongs to the PhD thesis of Céline Cleij titled "Building the genome of a minimal synthetic cell".Specifically, the dataset belongs to Chapter 4 titled "<em>De novo</em> design and assembly of minimal genomes for the synthetic cell".<br>Authors: Céline Cleij, Pascale Daran-Lapujade, Christophe DanelonCorresponding authors: Pascale Daran-Lapujade and Christophe DanelonContact information: p.a.s.daran-lapujade@tudelft.nl and danelon@insa-toulouse.fr<br>This dataset contains data collected during experiments as part of Céline Cleij's PhD project. The data was collected from 2023-2025.<br>All data processing and analysis steps are described in detail in the Methods section of thesis chapter 4.Designed SynMG sequences (GenBank) were prepared with the SnapGene software, using the plasmid maps of the sequenced template plasmids and the designed primer sequences.Raw Nanopore sequencing reads (fastq) were obtained by Plasmidsaurus (Eugene, OR, USA) using Nanopore sequencing technology.Consensus SynMG sequences (GenBank) were obtained by Plasmidsaurus after processing of the raw reads, and were manually annotated in SnapGene.The overview of relevant mutations ("Relevant mutations in SynMG variants") was prepared in Excel, based on mutations in consensus sequences and raw reads obtained from sequencing.LC-MS data was obtained after processing in the Mascot software.The tables S4.1-S4.15 were prepared in Excel. <br><br>The data is grouped into eight files: <br>i) Zip file "Designed SynMG sequences"Files are named after the SynMG version (SynMG1 or SynMG2).<br>ii) Zip file "S. cerevisiae - Raw Nanopore sequencing reads"Files are named after the yeast strain from which total DNA was extracted, and after the SynMG variant which was assembled in this strain.<br>iii) Zip file "S. cerevisiae - Consensus SynMG sequences"Files are named after the yeast strain from which total DNA was extracted, and after the SynMG variant which was assembled in this strain.<br>iv) Zip file "E. coli - Raw Nanopore sequencing reads"Files are named after the E. coli strain from which SynChr DNA was extracted, and after the SynMG variant which was amplified in this strain.<br>v) Zip file "E. coli - Consensus SynMG sequences"Files are named after the E. coli strain from which SynChr DNA was extracted, and after the SynMG variant which was amplified in this strain.<br>vi) Excel file "Relevant mutations in SynMG variants"This Excel file contains an overview of all relevant mutations SynMG1.1, SynMG1.2, SynMG1.3, SynMG2.1 and SynMG2.2 compared to the designed maps. <br>vii) Excel file "LC-MS data"This Excel file contains LC-MS data used for making Figure 4A, B & D.<br>viii) Excel file "Tables S4.1-S4.15"This Excel file contains the supplementary tables S4.1 to S4.15, which contain information about all used strains, synthetic chromosomes, plasmids, primers and SHRs used in this study.<br>
DOI: 10.22002/wp4pp-49864
title: Pfl 121509 MP30

description: Prosthecobacter fluviatilis, EtBr, 09dec18a_MP30_PflEtBr_025, helical structure,
description: <strong>Tilt Series Date:</strong> 2009-12-18</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>
  mpa2009-12-18-23_slicer9395.jpg: Prosthecobacter fluviatilis  .  REZ ribosome exclusion zone
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mpa2009-12-18-23/rawdata/</p>09dec18a_MP30_PflEtBr_025.mrc,  Tilt Series (Pixel Size 0.95 nm), 1.0 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        09dec18a_MP30_PflEtBr_025_part.rec,  Reconstruction (Pixel Size 1.9 nm), 838.9 MB  
        
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DOI: 10.22002/8nq5m-x1v65
title: A22-treated wild type

description: Raw data files of A22-treated wild type
description: <strong>Tilt Series Date:</strong> 2009-07-26</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> Cell culture and treatment by Zhuo Li. Data collected by Zhuo Li. Processed by Zhuo Li. </p>
<strong>Purification / Growth Conditions / Treatment:</strong> Exponentially growing NA1000 cells were treated with 10 ug/ml A22 for 2 hours before freezing. </p>
<strong>Sample Preparation:</strong> 10 nm gold. </p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/zla2009-07-26-36/rawdata/</p>09jul26c_A22wt_036.mrc,  Tilt Series (Pixel Size 1.2 nm), 1.0 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        09jul26c_A22wt_036_part.rec,  Reconstruction (Pixel Size 2.4 nm), 367.0 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/8zrnh-2yq39
title: Hyphomonas EB session14 27.5KX

description: high-order DNA, H-NS, nucleoid, asymmetric cell division
description: <strong>Tilt Series Date:</strong> 2009-05-22</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: (-62.0°, 62.0°), step: 2°, constant angular increment, dosage: 130.0 eV/Å²,  defocus: -7.0 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> Cultured by Jian; data collected by Jian; processed by Jian</p>
<strong>Purification / Growth Conditions / Treatment:</strong> exponential phase in PYE media, treated with EB...</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/jsa2009-05-22-18/rawdata/</p>09may22a_bx200d_021.mrc,  Tilt Series (Pixel Size 0.774 nm), 520.1 MB  
        
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        > <i class="download icon"></i> Download </a></p>

        09may22a_bx200d_021_1k.rec,  Reconstruction (Pixel Size 1.548 nm), 74.6 MB  
        
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DOI: 10.22002/5p1va-1yr75
title: MT310_xyl(+)_AuCl2uM(+)

description: Raw data files of MT310_xyl(+)_AuCl2uM(+)
description: <strong>Tilt Series Date:</strong> 2009-06-14</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: 180.0 eV/Å²,  defocus: -12.0 μm,  magnification: 0x. </p>
<strong>Acquisition Software:</strong> UCSF Tomo</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 cultured and treated by Zhuo Li; Data collected and processed by Zhuo Li.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> MT310 cells were induced with xylose and treated with 2 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/zla2009-06-14-11/rawdata/</p>09jun14a_Au2_011.mrc,  Tilt Series (Pixel Size 0.95 nm), 1.0 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        09jun14a_Au2_011_part.rec,  Reconstruction (Pixel Size 1.9 nm), 471.9 MB  
        
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DOI: 10.22002/jr0gm-zkp53
title: Hyphomonas EB session21 34KX

description: high-order DNA, H-NS, nucleoid, asymmetric cell division
description: <strong>Tilt Series Date:</strong> 2009-07-14</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: (-60.0°, 60.0°), step: 2°, constant angular increment, dosage: 130.0 eV/Å²,  defocus: -7.0 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, EB 0.02mg/ml overnight 4degree...</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/jsa2009-07-14-9/rawdata/</p>09jul14a_b200c_009.mrc,  Tilt Series (Pixel Size 0.632 nm), 553.7 MB  
        
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        > <i class="download icon"></i> Download </a></p>

        09jul14a_b200c_009_part.rec,  Reconstruction (Pixel Size 1.264 nm), 367.0 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/ak5d8-pre43
title: Pdb 121509 MP35

description: Prosthecobacter debontii, 09dec18a_MP35_II_Pdb_087, putative btub structure,
description: <strong>Tilt Series Date:</strong> 2009-12-18</p>
<strong>Data Taken By:</strong> Martin Pilhofer</p>
<strong>Species / Specimen:</strong> Prosthecobacter debontii</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>
  mpa2009-12-18-62_slicer7927.jpg: Unknown filament .  Prosthecobacter debontii
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mpa2009-12-18-62/rawdata/</p>09dec18a_MP35_II_Pdb_087.mrc,  Tilt Series (Pixel Size 0.95 nm), 1.0 GB  
        
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        > <i class="download icon"></i> Download </a></p>

        09dec18a_MP35_II_Pdb_087_part.rec,  Reconstruction (Pixel Size 1.9 nm), 838.9 MB  
        
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        > <i class="download icon"></i> Download </a></p>
DOI: 10.15468/dl.7nnadj
title: Occurrence Download

description: A dataset containing 23 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Rhodeus amarus",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Geometry POLYGON ((-6.6 29.26705, -6.6 50.94, 40.81373 50.94, 40.81373 29.26705, -6.6 29.26705))",
 "BasisOfRecord is one of (Human Observation, Machine Observation, Observation, Material sample)"
 ]
}

 The dataset includes 23 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0047490-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.22002/8phxw-41666
title: HeLa CHMP4A+VPS4DN

description: HeLa cells transfected with CHMP4A & VPS4DN constructs
description: <strong>Tilt Series Date:</strong> 2011-02-09</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/cwl2011-02-09-5/3dimage_68041/</p>11feb09b_C50-4d_007_full.rec,  Reconstruction (Pixel Size 2.0 nm), 453.0 MB  
        
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        11feb09b_C50-4d_007.st,  Tilt Series (Pixel Size 0.5 nm), 1.0 GB  
        
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