cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.22002/4c93a-0py96
title: T9_ABK triple mutant

description: This is a sample that was prepared when Paul vsited
description: <strong>Tilt Series Date:</strong> 2017-01-25</p>
<strong>Data Taken By:</strong> Poorna Subramanian</p>
<strong>Species / Specimen:</strong> Porphyromonas gingivalis</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: 160.0 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> Paul Veith and Eric Reynolds</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/psa2017-01-25-23/rawdata/</p>sq40023.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/psa2017-01-25-23/rawdata/sq40023.mrc"
        > <i class="download icon"></i> Download </a></p>

        sq40023_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/psa2017-01-25-23/3dimage_81522/sq40023_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/ce0d1-r9287
title: P. aeruginosa T6SS minicell

description: Pseudomonas JT1599Grid box YWC247
description: <strong>Tilt Series Date:</strong> 2017-04-14</p>
<strong>Data Taken By:</strong> Yi-Wei Chang</p>
<strong>Species / Specimen:</strong> Pseudomonas aeruginosa</p>
<strong>Strain:</strong> </p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1.5°, constant angular increment, dosage: 120.0 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 Jonida Toska at John Mekalanos lab</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ycw2017-04-14-30/rawdata/</p>20170414_YWC247_10039.mrc,  Tilt Series (Pixel Size 0.39 nm), 2.3 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ycw2017-04-14-30/rawdata/20170414_YWC247_10039.mrc"
        > <i class="download icon"></i> Download </a></p>

        20170414_YWC247_10039_part81_3.rec,  Reconstruction (Pixel Size 1.56 nm), 534.5 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/ycw2017-04-14-30/3dimage_83702/20170414_YWC247_10039_part81_3.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.5281/zenodo.16973358
title: A Revised Landform Map for Areas Prone to Dust Emission in the Southwestern United States: Shapefile Data for the Mojave and Sonoran Desert Regions

description: Purpose: This repository contains a landform dataset in shapefile format for the Mojave and Sonoran Desert regions.

Technical Documentation: LeGrand, Sandra L., Taylor S. Hodgdon, Matthew F. Bigl, and Brendan A. West. 2025. A Revised Landform Map for Areas Prone to Dust Emission in the Southwestern United States. ERDC TR-25-18. US Army Engineer Research and Development Center. https://dx.doi.org/10.21079/11681/49861.

Data are provided in shapefile format and use the following codes:




Landform Name
Landform Code


Aeolian dunes
Qed


Aeolian sands
Qe


Alluvial fans
Qa


Alluvial plains
Qap


Alluvial wash 
Qal


Badlands
Qbl


Bedrock/plateau/pediment
BPP


Broad river valley
Qrv


Fine-grained lake deposits
Ql


Open mine/tailings 
Mi


Pluvial lake features
Qb


Recent volcanic deposits 
Qv


River margins / active agriculture
Qrm


Urban/developed area
Ud


Water
W




 

Note: The previous release on Zenodo contained an error where polygons for only 1 of the 15 classes were included due to a selection or definition query being active when the file was exported. The current version (Zenodo release v2) reflects the dataset described by the technical report by LeGrand et al. (2025).
DOI: 10.22002/x77q6-dtd38
title: 411V mass spec

description: CF4Q 30µM CF4Q3µM CheA6µMCheW725 µM Vesicle in Kinase buffer .  [added 2015-09-21 10:47:53] CF4Q 411V30µM CF4Q3µM CheA6µMCheW725 µM Vesicle in Kinase buffer
description: <strong>Tilt Series Date:</strong> 2015-03-30</p>
<strong>Data Taken By:</strong> Ariane Briegel</p>
<strong>Species / Specimen:</strong> Escherichia coli in vitro</p>
<strong>Strain:</strong> </p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 2°, constant angular increment, dosage: 80.0 eV/Å²,  defocus: 8.0 μm,  magnification: 34000x. </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> Lynmarie Thompson</p>
description: Files available via S3 at ttps://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/aba2015-03-30-7/rawdata/</p>MassSpec411V2015March0007.mrc,  Tilt Series (Pixel Size 0.32 nm), 1.7 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/aba2015-03-30-7/rawdata/MassSpec411V2015March0007.mrc"
        > <i class="download icon"></i> Download </a></p>

        MassSpec411V2015March0007_full.rec,  Reconstruction (Pixel Size 1.28 nm), 445.4 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/aba2015-03-30-7/3dimage_53519/MassSpec411V2015March0007_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.15468/dl.85uamp
title: Occurrence Download

description: A dataset containing 1542181 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Bufonidae"
 ]
}

 The dataset includes 1542181 records from 4481 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001972-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.jza9gy
title: Occurrence Download

description: A dataset containing 81634 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "TaxonKey is Helictochloa pratensis"
 ]
}

 The dataset includes 81634 records from 496 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005840-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.22002/ca73a-92n65
title: T5_504Cys_Aumalemaide_5nm

description: This is a sample in which N terminus residue 504 has been mutated to Cys residue. Mini cells have been isolated by high speed centrifugation and cells are Au malemaide labelled. No fiducials added.
description: <strong>Tilt Series Date:</strong> 2017-02-17</p>
<strong>Data Taken By:</strong> Poorna Subramanian</p>
<strong>Species / Specimen:</strong> Escherichia coli</p>
<strong>Strain:</strong> EC93 stick, UPEC536</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-65.0°, 65.0°), step: 1.0°, constant angular increment, dosage: 125.0 eV/Å²,  defocus: -10.0 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> autoPatch</p>
<strong>Collaborators and Roles:</strong> Zach Ruhe and Chris Hayes</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Freezing in vitrobot. Humidifier was not working. I wouldn't really trust the conditions.See pages 104-105</p>
<strong>Sample Preparation:</strong> Sample prepared by Taylor Steven</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/psa2017-02-17-21/rawdata/</p>sq90013.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/psa2017-02-17-21/rawdata/sq90013.mrc"
        > <i class="download icon"></i> Download </a></p>

        sq90013.rec,  Reconstruction (Pixel Size 1.56 nm), 1.1 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/psa2017-02-17-21/3dimage_82478/sq90013.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/64eq8-ex382
title: Xac WT pBRaφ pBRR MCS5 GFP

description: Xanthomonas citri   pv citri 306
description: <strong>Tilt Series Date:</strong> 2017-12-15</p>
<strong>Data Taken By:</strong> Debnath Ghosal</p>
<strong>Species / Specimen:</strong> Unspecified</p>
<strong>Strain:</strong> None</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: -7.0 μm,  magnification: 27500x. </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> Chuck Farah lab made the strain, data collected by Debnath Ghosal.</p>
<strong>Sample Preparation:</strong> Vitrobot (MK iv) settings: 100% humidity, 4µl sample, Blot force 6, blot time 6 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/dga2017-12-15-35/rawdata/</p>XanGFP15122017a0031.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/dga2017-12-15-35/rawdata/XanGFP15122017a0031.mrc"
        > <i class="download icon"></i> Download </a></p>

        XanGFP15122017a0031_part61_1.rec,  Reconstruction (Pixel Size 1.56 nm), 445.4 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/dga2017-12-15-35/3dimage_91344/XanGFP15122017a0031_part61_1.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/90gm5-4dt76
title: V.cholerae

description: This was imaged to study Yi-wei Msh in V.cholerae. This strain expresses Msh pilus but not any other pili.
description: <strong>Tilt Series Date:</strong> 2017-01-06</p>
<strong>Data Taken By:</strong> Poorna Subramanian</p>
<strong>Species / Specimen:</strong> Vibrio cholerae</p>
<strong>Strain:</strong> O1 biovar El Tor</p>
<strong>Tilt Series Settings:</strong>  Single Axis, tilt range: (-60.0°, 60.0°), step: 1.0°, constant angular increment, dosage: 160.0 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> Yi-wei</p>
<strong>Purification / Growth Conditions / Treatment:</strong> growth and freezing conditions: pg 95-97 in notebook. next time for vitrobot use: 6, 2.5, 1. 3.5 and 4 ul sample volume</p>
<strong>Sample Preparation:</strong> single tilt. constant angular increment, step: 1.0. tilt range: -60, 60.         dosage: 160e/A2. defocus: -6um. magnification: 27500.</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/psa2017-01-06-116/rawdata/</p>sq80001.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/psa2017-01-06-116/rawdata/sq80001.mrc"
        > <i class="download icon"></i> Download </a></p>

        sq80001_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/psa2017-01-06-116/3dimage_80517/sq80001_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.15468/dl.edhk85
title: Occurrence Download

description: A dataset containing 383 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Continent is South America",
 "Country is one of (Ecuador, Colombia, Peru)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Lupinus pubescens",
 "Year 1994-2025"
 ]
}

 The dataset includes 383 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005891-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.22002/59jba-xta67
title: Saccharomyces cerevisiae - JAWY1

description: Raw data files of Saccharomyces cerevisiae - JAWY1
description: <strong>Tilt Series Date:</strong> 2016-12-12</p>
<strong>Data Taken By:</strong> Shrawan kumar Mageswaran</p>
<strong>Species / Specimen:</strong> Unspecified</p>
<strong>Strain:</strong> None</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: 27500x. </p>
<strong>Microscope:</strong> Caltech Polara</p>
<strong>Acquisition Software:</strong> SerialEM</p>
<strong>Upload Method:</strong> reupload_downloaded</p>
<strong>Processing Software Used:</strong> IMOD</p>
<strong>Collaborators and Roles:</strong> Obtained from Dr. Greg Odorizzi @ Univ of Colorado at Boulder.</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Cells were grown overnight, diluted to 0.2 OD in the morning and allowed to grow till OD ~0.6. Heat shocked @38 deg C for 1hr50min and recovered @28deg C for 20 min (except sm2016-12-12-3 alias TS16 which was heat shocked for 1.5 hr and recovered for 40 min)</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/smk2016-12-12-6/rawdata/</p>TS10.mrc,  Tilt Series (Pixel Size 1.5 nm), 1.7 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/smk2016-12-12-6/rawdata/TS10.mrc"
        > <i class="download icon"></i> Download </a></p>

        TS10_4bin_NS_DB.rec,  Reconstruction (Pixel Size 0.0 nm), 284.5 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/smk2016-12-12-6/3dimage_81147/TS10_4bin_NS_DB.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.22002/99wyf-cje11
title: Azospirillum delta Operon1 and 4

description: Raw data files of Azospirillum delta Operon1 and 4
description: <strong>Tilt Series Date:</strong> 2015-04-15</p>
<strong>Data Taken By:</strong> Ariane Briegel</p>
<strong>Species / Specimen:</strong> Azospirillum brasilense</p>
<strong>Strain:</strong> </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: 8.0 μm,  magnification: 34000x. </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> Gladys Alexandre, University of Tennessee</p>
<strong>Purification / Growth Conditions / Treatment:</strong> Grow overnight in 5 mL MMAB+N + 200 μg/mL Ampicillin at RT (on bench) without shaking- Spin down 10' at 3,500 x g- Resuspend pellet in 5 mL MMAB-N- Spin down 10' at 3,500 x g- Resuspend pellet in 5 mL MMAB-N + 200 μg/mL Ampicillin- Leave at RT (on bench) without shaking overnight</p>
description: Files available via S3 at https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/aba2015-04-15-20/rawdata/</p>AzoDEltoOp1Op4April0010.mrc,  Tilt Series (Pixel Size 0.32 nm), 3.4 GB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/aba2015-04-15-20/rawdata/AzoDEltoOp1Op4April0010.mrc"
        > <i class="download icon"></i> Download </a></p>

        AzoDEltoOp1Op4April0010_full.rec,  Reconstruction (Pixel Size 1.28 nm), 712.7 MB  
        
<a role="button" class="ui compact mini button" href="https://sdsc.osn.xsede.org/ini210004tommorrell/tomography_archive/aba2015-04-15-20/3dimage_54100/AzoDEltoOp1Op4April0010_full.rec"
        > <i class="download icon"></i> Download </a></p>
DOI: 10.15468/dl.t9g6cs
title: Occurrence Download

description: A dataset containing 797 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Cipuropsis capituligera (Griseb.) Christenh. & Byng"
 ]
}

 The dataset includes 797 records from 66 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0022853-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6gc4zs
title: Occurrence Download

description: A dataset containing 2554 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-4.47328 36.66305,-4.44582 36.66305,-4.44582 36.68189,-4.47328 36.68189,-4.47328 36.66305))",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Plantae"
 ]
}

 The dataset includes 2554 records from 20 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0022854-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9kgxhd
title: Occurrence Download

description: A dataset containing 317 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Evaluación de los patrones fenológicos y reproductivos de la población de Ceroxylon quindiuense (Arecaceae) en la microcuenca del Río Tochecito, Tolima"
 ]
}

 The dataset includes 317 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000103-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.r45u4f
title: Occurrence Download

description: A dataset containing 18915 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "TaxonKey is Fumana ericoides"
 ]
}

 The dataset includes 18915 records from 176 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000102-250827131500795/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.17882/105467
title: IPOCOM project: CTD data along the French Mediterranean coast, NW Mediterranean, spring 2024.

description: This dataset contains the CTD data collected during the IPOCOM project (Fish inventory using environmental DNA), between 21/05/2024 and 10/06/2024, along the French Mediterranean coast (PACA and Occitanie regions), jointly by the Andromède océanologie (France) and MARBEC MARine Biodiversity, Exploitation and Conservation (France) teams.
The CTD data were obtained using RBR concerto3 autonomous logger from Victoria IV trimaran belonging to Scopra, France and chartered by the University of Montpellier.
133 transects (1 was 2.5-km long and 132 were 5-km long) were performed along the deepest local limit of the Posidonia oceanica seagrass meadow from Menton to Cerbère, latitude 42.3-43.9°N and longitude 2.7-7.6°E.
In PACA, the sampling depth was -26 m in mean (±10 m) and in Occitanie the mean depth was -7 m (±5 m), 5 m above the seabed in mean for both regions.
The sensors measured and recorded conductivity (mS/cm), temperature (°C), pressure (dBar), dissolved O2 concentration (µmol/L) and turbidity (NTU). Other parameters were derived from the previous measurements: sea pressure (dbar) removing atmospheric pressure, depth (m) simplifying and using density parameter, salinity (PSU) or Practical Salinity Scale (PSS-78), speed of sound (m/s) based on UNESCO algorithm, specific conductivity (µS/cm) and dissolved O2 saturation (%).
All parameters were measured or calculated at depths ranging from – 0.5 m to -56 m (Table 1). Recordings were made every 0.5 seconds (2 Hz frequency). The accuracy, specified by the manufacturer, was ±0.003mS/cm for conductivity, ±0.002°C for temperature, ±0,1 dbar for pressure (Depth), a maximum of ±2μmol/L or ±1.5% for dissolved O2 concentration and saturation. RBR Concerto3 was factory calibrated before.
The downloadable files are a csv of CTD probe data, a geopackage of all transects spatialized with mean, min, max, sd and median for all parameters of CTD probe, a pdf showing the evolution of all the variables, accompanied by a text explaining the problems encountered.
DOI: 10.17882/105470
title: clam sequences from eDNA and tissue samples

description: Clams are coastal resources widely exploited by both fishing and aquaculture. Most inhabit shallow waters, especially lagoons, that are transitional zones between the sea and land. In the Mediterranean French lagoons, two clam species are usually exploited, the native European clam, Ruditapes decussatus, and the introduced Manila clam, Ruditapes philippinarum. However, several other clam species can be found such as the pink clam or the golden carpet shell. Those animals are relatively small, spend most of their lives buried and are difficult to identify based on shell morphology. Consequently, they are very difficult to detect in the field. Therefore, we tested a metabarcoding approach to detect clam species from environmental DNA (eDNA) samples. After an in silico comparison between an universal and a group-specific metabarcode, we conducted an in vivo experiment to characterise this metabarcode on the targeted group of species and tested it in situ in two French lagoons.
The dataset is encompassing two files describing:
the 130 Amplicon Sequence Variants (ASVs) obtained after the bioinformatic analysis of the raw sequence data (see related dataset). They correspond to a small fragment of the 16S ribosomal gene, mainly from three clam species. They were obtained from water samples in an experimental design, and in situ locations in the Thau and Berre lagoons. The file (SEANOE_130ASVs. xls) is giving the sequence, the taxonomy associated, as well as the number of sequences by ASV in each of the aquariums containing or not clams, in the different sites in the Thau and Berre lagoons, and in the tissue positive controls. A link is made by column “Haplotype_ID (clams)” with the 9 clam haplotypes of the second file. the 9 clam haplotypes present in the tissue samples from the experimental design (tab “Haplotypes in tissue samples”) and the comparison of the percentage of each haplotype in each aquarium between eDNA and tissue samples (tab"EDNA tissue comparison"). This file is named SEANOE_haplotypes.xls.