cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.22002/cjm05-qcb11
title: Ecoli_Cojugation

description: These are donor E coli cells (ANB35) and recipient Ecoli cells (ANB24). These are the same  .  cells described in the Science paper (Direct visualization of horizontal gene transfer). The .  cells were mixed on the grid and then plunge frozen and imaged with cryo-ET without CLEM. .  Targets were imaged with cryo-ET randomly.
description: <strong>Tilt Series Date:</strong> 2019-02-28</p>
<strong>Data Taken By:</strong> Mohammed Kaplan</p>
<strong>Species / Specimen:</strong> Escherichia coli</p>
<strong>Strain:</strong> </p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-50.0°, 50.0°), step: 1°, constant angular increment, dosage: 130.0 eV/Å²,  defocus: -10.0 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> The cells were sent to the Jensen lab from the lab of Ariel Lindner in Paris. These are the same . cells used in their Science paper (direct visualization of horizontal gene transfer).</p>
<strong>Purification / Growth Conditions / Treatment:</strong> ANB 35 were grown in LB while ANB24 (Recipient) in M9. I followed the same protocol . described in the Science paper described above.</p>
<strong>Sample Preparation:</strong> The donor and recipient cells were mixed on the EM grid, incubated in the vitrobot chamber with . 100% humidity and then blotted and plunge frozen.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2019-02-28-51/rawdata/</p>Ecoli_CONjugation12.mrc,  Tilt Series (Pixel Size 0.541 nm), 2.9 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2019-02-28-51/rawdata/Ecoli_CONjugation12.mrc"
        > <i class="download icon"></i> Download </a></p>

        Ecoli_CONjugation12_full.rec,  Reconstruction (Pixel Size 2.164 nm), 445.4 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2019-02-28-51/3dimage_107103/Ecoli_CONjugation12_full.rec"
        > <i class="download icon"></i> Download </a></p>

        Ecoli_CONjugation12.mrc.mdoc,  51.0 kB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2019-02-28-51/rawdata/Ecoli_CONjugation12.mrc.mdoc"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/8m68d-fzj15
title: Ecoli_EPEC_8612

description: These are E coli cells (EPEC 8612) obtained from Ritesh (Ilan Rosenshine lab at the Hebrew  .  university). The idea is to image bacterial nanotubes in these cells.
description: <strong>Tilt Series Date:</strong> 2020-02-09</p>
<strong>Data Taken By:</strong> Mohammed Kaplan</p>
<strong>Species / Specimen:</strong> Escherichia coli</p>
<strong>Strain:</strong> 8612, EPEC Δrof1-escLΔrof3-mpcΔescN-espFΔflhBAΔfliOPQRΔminCD</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 2°, 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> These cells were prepared with Ritesh in Ilan Rosenshine lab at the Hebrew University.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> The cells were incubated on grids on agar plates (DMEM agar plates for three hours) and then . on starvation medium agar plate for 1 hour Then washed with PBS and blotted and then plunge . frozen. Yuxi helped in sample preparation and data collection</p>
<strong>Sample Preparation:</strong> The cells were incubated on grids on agar plates (DMEM agar plates for three hours) and then . on starvation medium agar plate for 1 hour</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2020-02-09-22/rawdata/</p>EPEC_8612_tilt37.mrc,  Tilt Series (Pixel Size 0.449 nm), 2.0 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2020-02-09-22/rawdata/EPEC_8612_tilt37.mrc"
        > <i class="download icon"></i> Download </a></p>

        EPEC_8612_tilt37_full.rec,  Reconstruction (Pixel Size 1.796 nm), 501.1 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2020-02-09-22/3dimage_110740/EPEC_8612_tilt37_full.rec"
        > <i class="download icon"></i> Download </a></p>

        EPEC_8612_tilt37.mrc.mdoc,  34.2 kB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2020-02-09-22/rawdata/EPEC_8612_tilt37.mrc.mdoc"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.5281/zenodo.16925922
title: Balanced contractility and adhesion drive polarization in a minimal elastic actomyosin network

description: The data contained in this repository supports the associated research article entitled

Balanced contractility and adhesion drive polarization in a minimal elastic actomyosin network

Zeno Messi, Franck Raynaud, Nathan W. Goehring and Alexander B. Verkhovsky

Contents:

paper_archive.tar.bz2.part**

 An split archive containing:



the code that implements the model described in the article

all the raw data used in the article

the python scripts used to analyse the data

data generated from the raw data (2) with the analysis scripts (3)

the python notebook used to create figures and videos of the article from the raw (2) and analysed (4) data

A python script to generate videos of the article


To decrompress the archive, you can use your favourite compressing software.

simuls_spreadsheet.xlsx

A spreadsheet containing the reference of all the simulations used in figures and videos together with their parameter sets.

balanced-contractility-and-adhesion-drive-polarization-in-a-minimal-elastic-actomyosin-network-1.0.0.tar.bz2

Release state of the gitlab repository at the time of submission.

This data is associated with a gitlab that describes how to re-generate the analysis data, videos and figures of the article, as well as how to run simulations.

https://gitlab.unige.ch/Zeno.Messi/balanced-contractility-and-adhesion-drive-polarization-in-a-minimal-elastic-actomyosin-network
DOI: 10.5281/zenodo.16925923
title: Balanced contractility and adhesion drive polarization in a minimal elastic actomyosin network

description: The data contained in this repository supports the associated research article entitled

Balanced contractility and adhesion drive polarization in a minimal elastic actomyosin network

Zeno Messi, Franck Raynaud, Nathan W. Goehring and Alexander B. Verkhovsky

Contents:

paper_archive.tar.bz2.part**

 An split archive containing:



the code that implements the model described in the article

all the raw data used in the article

the python scripts used to analyse the data

data generated from the raw data (2) with the analysis scripts (3)

the python notebook used to create figures and videos of the article from the raw (2) and analysed (4) data

A python script to generate videos of the article


To decrompress the archive, you can use your favourite compressing software.

simuls_spreadsheet.xlsx

A spreadsheet containing the reference of all the simulations used in figures and videos together with their parameter sets.

balanced-contractility-and-adhesion-drive-polarization-in-a-minimal-elastic-actomyosin-network-1.0.0.tar.bz2

Release state of the gitlab repository at the time of submission.

This data is associated with a gitlab that describes how to re-generate the analysis data, videos and figures of the article, as well as how to run simulations.

https://gitlab.unige.ch/Zeno.Messi/balanced-contractility-and-adhesion-drive-polarization-in-a-minimal-elastic-actomyosin-network
DOI: 10.22002/f3pab-8w156
title: Ecoli_Cojugation

description: These are donor E coli cells (ANB35) and recipient Ecoli cells (ANB24). These are the same  .  cells described in the Science paper (Direct visualization of horizontal gene transfer). The .  cells were mixed on the grid and then plunge frozen and imaged with cryo-ET without CLEM. .  Targets were imaged with cryo-ET randomly.
description: <strong>Tilt Series Date:</strong> 2019-02-28</p>
<strong>Data Taken By:</strong> Mohammed Kaplan</p>
<strong>Species / Specimen:</strong> Escherichia coli</p>
<strong>Strain:</strong> </p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-50.0°, 50.0°), step: 1°, constant angular increment, dosage: 130.0 eV/Å²,  defocus: -10.0 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> The cells were sent to the Jensen lab from the lab of Ariel Lindner in Paris. These are the same . cells used in their Science paper (direct visualization of horizontal gene transfer).</p>
<strong>Purification / Growth Conditions / Treatment:</strong> ANB 35 were grown in LB while ANB24 (Recipient) in M9. I followed the same protocol . described in the Science paper described above.</p>
<strong>Sample Preparation:</strong> The donor and recipient cells were mixed on the EM grid, incubated in the vitrobot chamber with . 100% humidity and then blotted and plunge frozen.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2019-02-28-92/rawdata/</p>Ecoli_CONjugation52.mrc,  Tilt Series (Pixel Size 0.541 nm), 2.9 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2019-02-28-92/rawdata/Ecoli_CONjugation52.mrc"
        > <i class="download icon"></i> Download </a></p>

        Ecoli_CONjugation52_part101_1.rec,  Reconstruction (Pixel Size 2.164 nm), 445.4 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2019-02-28-92/3dimage_107186/Ecoli_CONjugation52_part101_1.rec"
        > <i class="download icon"></i> Download </a></p>

        Ecoli_CONjugation52.mrc.mdoc,  51.0 kB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2019-02-28-92/rawdata/Ecoli_CONjugation52.mrc.mdoc"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/28pkp-kpy17
title: Ecoli_Cojugation

description: These are donor E coli cells (ANB35) and recipient Ecoli cells (ANB24). These are the same  .  cells described in the Science paper (Direct visualization of horizontal gene transfer). The .  cells were mixed on the grid and then plunge frozen and imaged with cryo-ET without CLEM. .  Targets were imaged with cryo-ET randomly.
description: <strong>Tilt Series Date:</strong> 2019-02-28</p>
<strong>Data Taken By:</strong> Mohammed Kaplan</p>
<strong>Species / Specimen:</strong> Escherichia coli</p>
<strong>Strain:</strong> </p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-50.0°, 50.0°), step: 1°, constant angular increment, dosage: 130.0 eV/Å²,  defocus: -10.0 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> The cells were sent to the Jensen lab from the lab of Ariel Lindner in Paris. These are the same . cells used in their Science paper (direct visualization of horizontal gene transfer).</p>
<strong>Purification / Growth Conditions / Treatment:</strong> ANB 35 were grown in LB while ANB24 (Recipient) in M9. I followed the same protocol . described in the Science paper described above.</p>
<strong>Sample Preparation:</strong> The donor and recipient cells were mixed on the EM grid, incubated in the vitrobot chamber with . 100% humidity and then blotted and plunge frozen.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2019-02-28-55/rawdata/</p>Ecoli_CONjugation14.mrc,  Tilt Series (Pixel Size 0.541 nm), 2.9 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2019-02-28-55/rawdata/Ecoli_CONjugation14.mrc"
        > <i class="download icon"></i> Download </a></p>

        Ecoli_CONjugation14_full.rec,  Reconstruction (Pixel Size 2.164 nm), 445.4 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2019-02-28-55/3dimage_107112/Ecoli_CONjugation14_full.rec"
        > <i class="download icon"></i> Download </a></p>

        Ecoli_CONjugation14.mrc.mdoc,  51.0 kB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2019-02-28-55/rawdata/Ecoli_CONjugation14.mrc.mdoc"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.15468/dl.zr2mtf
title: Occurrence Download

description: A dataset containing 1316 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Chrysolophus pictus",
 "Country is China",
 "HasCoordinate is true"
 ]
}

 The dataset includes 1316 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0047324-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.22002/hs1pm-4qe50
title: D. flos-aquae Gas Vesicles

description: Gas vesicles purified from D. flos-aquae, WT
description: <strong>Tilt Series Date:</strong> 2020-11-04</p>
<strong>Data Taken By:</strong> Przemek Dutka</p>
<strong>Species / Specimen:</strong> Dolichospermum flos-aquae</p>
<strong>Strain:</strong> CCAP 1403/13F</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 3°, constant angular increment, dosage: 50.0 eV/Å²,  defocus: 2.5 μm,  magnification: 64000x. </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> Batchruntomo</p>
<strong>Collaborators and Roles:</strong> purified by Dina Malounda the Shapiro lab; data collected by Przemek . Dutka and Songye Chen</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Lakshmanan, A., Lu, G., Farhadi, A. et al. Preparation of biogenic gas . vesicle nanostructures for use as contrast agents for ultrasound and . MRI. Nat Protoc 12, 2050–2080 (2017). . https://doi.org/10.1038/nprot.2017.081. Sample in 10mM Hepes, pH7.4; OD 5.0</p>
<strong>Sample Preparation:</strong> Quantifoil C2/2 200mesh extra thick carbon, 10nm BSA-gold, 100% . humidity, Blot time 4, Blot force 3, temp 4C</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/pda2020-11-04-11/rawdata/</p>AnaGVOD5_1_movies.mrc,  Tilt Series (Pixel Size 0.14 nm), 1.9 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/pda2020-11-04-11/rawdata/AnaGVOD5_1_movies.mrc"
        > <i class="download icon"></i> Download </a></p>

        AnaGVOD5_1_movies.rec,  Reconstruction (Pixel Size 0.56 nm), 367.9 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/pda2020-11-04-11/3dimage_115864/AnaGVOD5_1_movies.rec"
        > <i class="download icon"></i> Download </a></p>

        AnaGVOD5_1.mrc.mdoc,  26.9 kB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/pda2020-11-04-11/rawdata/AnaGVOD5_1.mrc.mdoc"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/xh3dh-83k82
title: Ecoli_Cojugation

description: These are donor E coli cells (ANB35) and recipient Ecoli cells (ANB24). These are the same  .  cells described in the Science paper (Direct visualization of horizontal gene transfer). The .  cells were mixed on the grid and then plunge frozen and imaged with cryo-ET without CLEM. .  Targets were imaged with cryo-ET randomly.
description: <strong>Tilt Series Date:</strong> 2019-02-28</p>
<strong>Data Taken By:</strong> Mohammed Kaplan</p>
<strong>Species / Specimen:</strong> Escherichia coli</p>
<strong>Strain:</strong> </p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-50.0°, 50.0°), step: 1°, constant angular increment, dosage: 130.0 eV/Å²,  defocus: -10.0 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> The cells were sent to the Jensen lab from the lab of Ariel Lindner in Paris. These are the same . cells used in their Science paper (direct visualization of horizontal gene transfer).</p>
<strong>Purification / Growth Conditions / Treatment:</strong> ANB 35 were grown in LB while ANB24 (Recipient) in M9. I followed the same protocol . described in the Science paper described above.</p>
<strong>Sample Preparation:</strong> The donor and recipient cells were mixed on the EM grid, incubated in the vitrobot chamber with . 100% humidity and then blotted and plunge frozen.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2019-02-28-40/rawdata/</p>Ecoli_Conjugation9.mrc,  Tilt Series (Pixel Size 0.541 nm), 2.6 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2019-02-28-40/rawdata/Ecoli_Conjugation9.mrc"
        > <i class="download icon"></i> Download </a></p>

        Ecoli_Conjugation9_full.rec,  Reconstruction (Pixel Size 2.164 nm), 445.4 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2019-02-28-40/3dimage_107064/Ecoli_Conjugation9_full.rec"
        > <i class="download icon"></i> Download </a></p>

        Ecoli_Conjugation9.mrc.mdoc,  45.7 kB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2019-02-28-40/rawdata/Ecoli_Conjugation9.mrc.mdoc"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/xvbr8-m3j07
title: Ecoli_Cojugation

description: These are donor E coli cells (ANB35) and recipient Ecoli cells (ANB24). These are the same  .  cells described in the Science paper (Direct visualization of horizontal gene transfer). The .  cells were mixed on the grid and then plunge frozen and imaged with cryo-ET without CLEM. .  Targets were imaged with cryo-ET randomly.
description: <strong>Tilt Series Date:</strong> 2019-02-28</p>
<strong>Data Taken By:</strong> Mohammed Kaplan</p>
<strong>Species / Specimen:</strong> Escherichia coli</p>
<strong>Strain:</strong> </p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-50.0°, 50.0°), step: 1°, constant angular increment, dosage: 130.0 eV/Å²,  defocus: -10.0 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> The cells were sent to the Jensen lab from the lab of Ariel Lindner in Paris. These are the same . cells used in their Science paper (direct visualization of horizontal gene transfer).</p>
<strong>Purification / Growth Conditions / Treatment:</strong> ANB 35 were grown in LB while ANB24 (Recipient) in M9. I followed the same protocol . described in the Science paper described above.</p>
<strong>Sample Preparation:</strong> The donor and recipient cells were mixed on the EM grid, incubated in the vitrobot chamber with . 100% humidity and then blotted and plunge frozen.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2019-02-28-99/rawdata/</p>Ecoli_CONjugation59.mrc,  Tilt Series (Pixel Size 0.541 nm), 2.9 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2019-02-28-99/rawdata/Ecoli_CONjugation59.mrc"
        > <i class="download icon"></i> Download </a></p>

        Ecoli_CONjugation59_full.rec,  Reconstruction (Pixel Size 2.164 nm), 445.4 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2019-02-28-99/3dimage_107201/Ecoli_CONjugation59_full.rec"
        > <i class="download icon"></i> Download </a></p>

        Ecoli_CONjugation59.mrc.mdoc,  51.1 kB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/mka2019-02-28-99/rawdata/Ecoli_CONjugation59.mrc.mdoc"
        > <i class="download icon"></i> Download </a></p>