ReadMe
<p dir="ltr">*This README.md file was generated on 20240926 by Corien Bakermans*</p><p><br></p><p dir="ltr">General Information</p><p>------------------</p><p><br></p><p dir="ltr">### Title:&l...
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| _version_ | 1849927625313615872 |
|---|---|
| author | Corien Bakermans (19747213) |
| author_facet | Corien Bakermans (19747213) |
| author_role | author |
| dc.creator.none.fl_str_mv | Corien Bakermans (19747213) |
| dc.date.none.fl_str_mv | 2025-11-25T21:33:32Z |
| dc.identifier.none.fl_str_mv | 10.6084/m9.figshare.27115375.v1 |
| dc.relation.none.fl_str_mv | https://figshare.com/articles/dataset/ReadMe/27115375 |
| dc.rights.none.fl_str_mv | CC BY 4.0 info:eu-repo/semantics/openAccess |
| dc.subject.none.fl_str_mv | Invertebrate biology Mars extremophiles simulant analogs tardigrades |
| dc.title.none.fl_str_mv | ReadMe |
| dc.type.none.fl_str_mv | Dataset info:eu-repo/semantics/publishedVersion dataset |
| description | <p dir="ltr">*This README.md file was generated on 20240926 by Corien Bakermans*</p><p><br></p><p dir="ltr">General Information</p><p>------------------</p><p><br></p><p dir="ltr">### Title:</p><p><br></p><p dir="ltr">*Data and Code for "Short-term survival of tardigrades (Hypsibius exemplaris and Ramazzottius cf. varieornatus) in Martian regolith simulants (MGS-1 and OUCM-1)"*</p><p><br></p><p dir="ltr">### Author Information:</p><p><br></p><p dir="ltr">- Principal Investigator: Corien Bakermans (ORCID 0000-0002-3471-2570)</p><p dir="ltr">- Co-investigators: Matteo Vecchi and Gillian Pearce</p><p><br></p><p><br></p><p dir="ltr">### Date of data collection/creation:</p><p dir="ltr">20240301 to 20240930</p><p><br></p><p dir="ltr">### Geographic location of data collection:</p><p dir="ltr">Samples collected from:</p><p dir="ltr">Sample 132 (44.387468 - 10.021142)</p><p dir="ltr">Sample 284 (44.387520 - 10.021026)</p><p dir="ltr">Sample 778 (44.396427 - 10.004250)</p><p dir="ltr">Lab experiments performed in Bakermans lab at Penn State Altoona, Altoona, PA, USA</p><p><br></p><p><br></p><p dir="ltr">### Funders and sponsors of data collection:</p><p dir="ltr">MV funded by the Polonez Bis grant No. 2022/45/P/NZ8/01512 and the National Science Centre and the European Union framework Programme for Research and Innovation Horizon 2020 under the Marie Skłodowska-Curie grant.</p><p dir="ltr">CB funded by a grant from Penn State Altoona’s Office of Research and Engagement.</p><p><br></p><p><br></p><p dir="ltr">Sharing/Access Information</p><p>--------------------------</p><p><br></p><p dir="ltr">### License & restrictions on data reuse:</p><p dir="ltr">Creative Commons Attribution 4.0 International (CC BY 4.0)</p><p><br></p><p dir="ltr">### Recommended citation for the data:</p><p dir="ltr">C Bakermans, M Vecchi, G Pearce (submitted 2024) Short-term survival of tardigrades (Hypsibius exemplaris and Ramazzottius cf. varieornatus) in Martian regolith simulants (MGS-1 and OUCM-1). Journal TBD.</p><p><br></p><p dir="ltr">### Related publications:</p><p dir="ltr">n/a</p><p><br></p><p dir="ltr">### Links to other publicly accessible locations of the data:</p><p dir="ltr">n/a</p><p><br></p><p dir="ltr">### Related data sets:</p><p dir="ltr">n/a</p><p><br></p><p><br></p><p dir="ltr">Data & File Overview</p><p>--------------------</p><p><br></p><p dir="ltr">### File list:</p><p dir="ltr">Bakermans_supplement_Rscript.R</p><p dir="ltr">A text file containing code in R for data analyses.</p><p><br></p><p dir="ltr">RawCount.txt</p><p dir="ltr">A tab-delimited text file containing experimental data.</p><p><br></p><p dir="ltr">ImageCatalog.xlsx</p><p dir="ltr">An excel file containing filenames and descriptions of images and videos of tardigrades during treatments.</p><p><br></p><p dir="ltr">Images and Videos</p><p dir="ltr">A folder containing image and video files.</p><p><br></p><p dir="ltr">### Additional notes:</p><p dir="ltr">R script run with R version 4.4.1 (2024-06-14 ucrt) and RStudio 2024.047.2+764</p><p><br></p><p dir="ltr">File/Format-Specific Information</p><p>--------------------------------</p><p><br></p><p dir="ltr">### 'Bakermans_supplement_Rscript.R'</p><p dir="ltr">-R code for data analyses (confidence interval of binomial distribution, generalized linear model, creating plots of data and model)</p><p><br></p><p dir="ltr">### 'RawCount.txt'</p><p dir="ltr">- Number of variables: 7</p><p dir="ltr">- Number of cases/rows: 86</p><p dir="ltr">- Variable list:</p><p dir="ltr">time (days)</p><p dir="ltr">Simulant (martian regolith simulant MGS-1 or OUCM-1 or washed MGS-1 or none [control])</p><p dir="ltr">Tardigrade (population used: Hyp = Hypsibius exemplaris, S132 = Ramazzottius sp. S132, S284 = Ramazzottius sp. S284, S778 = Ramazzottius sp. S778)</p><p dir="ltr">replicate (replicate number)</p><p dir="ltr">active (number of moving/active tardigrades)</p><p dir="ltr">inactive (number of inactive tardigrades)</p><p dir="ltr">total (= active + inactive)</p><p><br></p><p dir="ltr">### 'ImageCatalog.xlsx'</p><p dir="ltr">- Number of sheets: 2 ('Catalog of Images' and 'Descriptors explained')</p><p dir="ltr">- Number of cases/rows: 89</p><p dir="ltr">- Variable list: FOLDER, FILE NAME, LIVE/DEAD, Inoculum, Tardigrade Color or other note, Time (days), Treatment, Image Quality, format, Number, Notes, Figure</p><p dir="ltr">- Variables defined in sheet 'Descriptors explained'</p><p dir="ltr">- Missing data: cell left blank</p><p><br></p><p dir="ltr">### 'Images and Videos'</p><p dir="ltr">- Folder containing images (.png) and videos (.mov) of tardigrades during treatment.</p><p dir="ltr">- Images and videos taken with an iPhone 12 mini mounted (Novagrade phone adapter) onto the ocular lens of a compound light microscope.</p><p dir="ltr">- All images taken with 100x microscope magnification. Images may include additional digital magnification (maximum 5x). Videos may include additional digital magnification (maximum 3x).</p><p dir="ltr">- Images captured in HEIC format (JPeg/h.264) and later converted to .png.</p><p dir="ltr">- Videos recorded at 1080p HD at 30 fps.</p><p><br></p><p dir="ltr">Methodological Information</p><p>--------------------------</p><p dir="ltr">Tardigrades were exposed to martian regolith simulants in 1.5 mL microcentrifuge tubes as follows. To each tube, 0.25 g dry simulant (control, MGS-1, OUCM-1, or washed MGS-1) and 0.25 mL inoculum (with A. pyrenoidosa) was added and mixed by inverting gently several times. Duplicate or triplicate tubes were prepared for each time point*treatment*population. Tubes were incubated on their sides at 15°C (Ramazzottius sp.) or 20°C (H. exemplaris) for 12 hours light, 12 hours dark under full-spectrum LED lights. Tubes were opened for 10-15 minutes every two days for an air exchange. At time points (0, 2, 4 days), tardigrades were collected by adding 1.0 mL of a 1.15 g mL-1 density solution of LUDOX® TM-50 colloidal silica; mixing well; centrifuging for 1 min 1000x g; and transferring the supernatant to a Sedgewick Rafter slide. Slides were viewed at 100× magnification and tardigrades counted. Tardigrades that showed movement were counted as alive; immobile tardigrades were counted as inactive and presumed dead. Exuviae were not counted. Images and videos taken with an iPhone 12 mini mounted (Novagrade phone adapter) onto the ocular lens. Due to the low number of available Ramazzottius sp., and limited availability of simulants, it was not possible to test all treatments for all tardigrade populations.</p><p><br></p><p dir="ltr">Statistical analyses. Data were fitted to a generalized linear model with binomial distribution in R with active tardigrades as the response variable. Time, species, time*simulant, and time*species were used as predictors. For the tardigrade population the intercept was H. exemplaris and for the treatment the intercept was the controls. Residuals were examined for normality and heteroscedasticity by visual inspection of plots produced by the R function check_model from the package “performance”.</p><p><br></p> |
| eu_rights_str_mv | openAccess |
| id | Manara_206f1a126f918e237d8c9e8b49dc14d6 |
| identifier_str_mv | 10.6084/m9.figshare.27115375.v1 |
| network_acronym_str | Manara |
| network_name_str | ManaraRepo |
| oai_identifier_str | oai:figshare.com:article/27115375 |
| publishDate | 2025 |
| repository.mail.fl_str_mv | |
| repository.name.fl_str_mv | |
| repository_id_str | |
| rights_invalid_str_mv | CC BY 4.0 |
| spelling | ReadMeCorien Bakermans (19747213)Invertebrate biologyMarsextremophilessimulantanalogstardigrades<p dir="ltr">*This README.md file was generated on 20240926 by Corien Bakermans*</p><p><br></p><p dir="ltr">General Information</p><p>------------------</p><p><br></p><p dir="ltr">### Title:</p><p><br></p><p dir="ltr">*Data and Code for "Short-term survival of tardigrades (Hypsibius exemplaris and Ramazzottius cf. varieornatus) in Martian regolith simulants (MGS-1 and OUCM-1)"*</p><p><br></p><p dir="ltr">### Author Information:</p><p><br></p><p dir="ltr">- Principal Investigator: Corien Bakermans (ORCID 0000-0002-3471-2570)</p><p dir="ltr">- Co-investigators: Matteo Vecchi and Gillian Pearce</p><p><br></p><p><br></p><p dir="ltr">### Date of data collection/creation:</p><p dir="ltr">20240301 to 20240930</p><p><br></p><p dir="ltr">### Geographic location of data collection:</p><p dir="ltr">Samples collected from:</p><p dir="ltr">Sample 132 (44.387468 - 10.021142)</p><p dir="ltr">Sample 284 (44.387520 - 10.021026)</p><p dir="ltr">Sample 778 (44.396427 - 10.004250)</p><p dir="ltr">Lab experiments performed in Bakermans lab at Penn State Altoona, Altoona, PA, USA</p><p><br></p><p><br></p><p dir="ltr">### Funders and sponsors of data collection:</p><p dir="ltr">MV funded by the Polonez Bis grant No. 2022/45/P/NZ8/01512 and the National Science Centre and the European Union framework Programme for Research and Innovation Horizon 2020 under the Marie Skłodowska-Curie grant.</p><p dir="ltr">CB funded by a grant from Penn State Altoona’s Office of Research and Engagement.</p><p><br></p><p><br></p><p dir="ltr">Sharing/Access Information</p><p>--------------------------</p><p><br></p><p dir="ltr">### License & restrictions on data reuse:</p><p dir="ltr">Creative Commons Attribution 4.0 International (CC BY 4.0)</p><p><br></p><p dir="ltr">### Recommended citation for the data:</p><p dir="ltr">C Bakermans, M Vecchi, G Pearce (submitted 2024) Short-term survival of tardigrades (Hypsibius exemplaris and Ramazzottius cf. varieornatus) in Martian regolith simulants (MGS-1 and OUCM-1). Journal TBD.</p><p><br></p><p dir="ltr">### Related publications:</p><p dir="ltr">n/a</p><p><br></p><p dir="ltr">### Links to other publicly accessible locations of the data:</p><p dir="ltr">n/a</p><p><br></p><p dir="ltr">### Related data sets:</p><p dir="ltr">n/a</p><p><br></p><p><br></p><p dir="ltr">Data & File Overview</p><p>--------------------</p><p><br></p><p dir="ltr">### File list:</p><p dir="ltr">Bakermans_supplement_Rscript.R</p><p dir="ltr">A text file containing code in R for data analyses.</p><p><br></p><p dir="ltr">RawCount.txt</p><p dir="ltr">A tab-delimited text file containing experimental data.</p><p><br></p><p dir="ltr">ImageCatalog.xlsx</p><p dir="ltr">An excel file containing filenames and descriptions of images and videos of tardigrades during treatments.</p><p><br></p><p dir="ltr">Images and Videos</p><p dir="ltr">A folder containing image and video files.</p><p><br></p><p dir="ltr">### Additional notes:</p><p dir="ltr">R script run with R version 4.4.1 (2024-06-14 ucrt) and RStudio 2024.047.2+764</p><p><br></p><p dir="ltr">File/Format-Specific Information</p><p>--------------------------------</p><p><br></p><p dir="ltr">### 'Bakermans_supplement_Rscript.R'</p><p dir="ltr">-R code for data analyses (confidence interval of binomial distribution, generalized linear model, creating plots of data and model)</p><p><br></p><p dir="ltr">### 'RawCount.txt'</p><p dir="ltr">- Number of variables: 7</p><p dir="ltr">- Number of cases/rows: 86</p><p dir="ltr">- Variable list:</p><p dir="ltr">time (days)</p><p dir="ltr">Simulant (martian regolith simulant MGS-1 or OUCM-1 or washed MGS-1 or none [control])</p><p dir="ltr">Tardigrade (population used: Hyp = Hypsibius exemplaris, S132 = Ramazzottius sp. S132, S284 = Ramazzottius sp. S284, S778 = Ramazzottius sp. S778)</p><p dir="ltr">replicate (replicate number)</p><p dir="ltr">active (number of moving/active tardigrades)</p><p dir="ltr">inactive (number of inactive tardigrades)</p><p dir="ltr">total (= active + inactive)</p><p><br></p><p dir="ltr">### 'ImageCatalog.xlsx'</p><p dir="ltr">- Number of sheets: 2 ('Catalog of Images' and 'Descriptors explained')</p><p dir="ltr">- Number of cases/rows: 89</p><p dir="ltr">- Variable list: FOLDER, FILE NAME, LIVE/DEAD, Inoculum, Tardigrade Color or other note, Time (days), Treatment, Image Quality, format, Number, Notes, Figure</p><p dir="ltr">- Variables defined in sheet 'Descriptors explained'</p><p dir="ltr">- Missing data: cell left blank</p><p><br></p><p dir="ltr">### 'Images and Videos'</p><p dir="ltr">- Folder containing images (.png) and videos (.mov) of tardigrades during treatment.</p><p dir="ltr">- Images and videos taken with an iPhone 12 mini mounted (Novagrade phone adapter) onto the ocular lens of a compound light microscope.</p><p dir="ltr">- All images taken with 100x microscope magnification. Images may include additional digital magnification (maximum 5x). Videos may include additional digital magnification (maximum 3x).</p><p dir="ltr">- Images captured in HEIC format (JPeg/h.264) and later converted to .png.</p><p dir="ltr">- Videos recorded at 1080p HD at 30 fps.</p><p><br></p><p dir="ltr">Methodological Information</p><p>--------------------------</p><p dir="ltr">Tardigrades were exposed to martian regolith simulants in 1.5 mL microcentrifuge tubes as follows. To each tube, 0.25 g dry simulant (control, MGS-1, OUCM-1, or washed MGS-1) and 0.25 mL inoculum (with A. pyrenoidosa) was added and mixed by inverting gently several times. Duplicate or triplicate tubes were prepared for each time point*treatment*population. Tubes were incubated on their sides at 15°C (Ramazzottius sp.) or 20°C (H. exemplaris) for 12 hours light, 12 hours dark under full-spectrum LED lights. Tubes were opened for 10-15 minutes every two days for an air exchange. At time points (0, 2, 4 days), tardigrades were collected by adding 1.0 mL of a 1.15 g mL-1 density solution of LUDOX® TM-50 colloidal silica; mixing well; centrifuging for 1 min 1000x g; and transferring the supernatant to a Sedgewick Rafter slide. Slides were viewed at 100× magnification and tardigrades counted. Tardigrades that showed movement were counted as alive; immobile tardigrades were counted as inactive and presumed dead. Exuviae were not counted. Images and videos taken with an iPhone 12 mini mounted (Novagrade phone adapter) onto the ocular lens. Due to the low number of available Ramazzottius sp., and limited availability of simulants, it was not possible to test all treatments for all tardigrade populations.</p><p><br></p><p dir="ltr">Statistical analyses. Data were fitted to a generalized linear model with binomial distribution in R with active tardigrades as the response variable. Time, species, time*simulant, and time*species were used as predictors. For the tardigrade population the intercept was H. exemplaris and for the treatment the intercept was the controls. Residuals were examined for normality and heteroscedasticity by visual inspection of plots produced by the R function check_model from the package “performance”.</p><p><br></p>2025-11-25T21:33:32ZDatasetinfo:eu-repo/semantics/publishedVersiondataset10.6084/m9.figshare.27115375.v1https://figshare.com/articles/dataset/ReadMe/27115375CC BY 4.0info:eu-repo/semantics/openAccessoai:figshare.com:article/271153752025-11-25T21:33:32Z |
| spellingShingle | ReadMe Corien Bakermans (19747213) Invertebrate biology Mars extremophiles simulant analogs tardigrades |
| status_str | publishedVersion |
| title | ReadMe |
| title_full | ReadMe |
| title_fullStr | ReadMe |
| title_full_unstemmed | ReadMe |
| title_short | ReadMe |
| title_sort | ReadMe |
| topic | Invertebrate biology Mars extremophiles simulant analogs tardigrades |