Find research datasets worth reusing

opencc-by-4.0Jul 2022View details →

Scanning electron microscope images of Dunaliela tertiolecta and Phaeodactylum tricornutum cultures and scanning electron microscope images and cryogenic electron microscope images of isolated small cellular particles from respective conditioned media

Scanning electron microscope images of cultures of microalgae Dunaliela tertiolecta and Phaeodactylum tricornutum and scanning electron microscope images and cryogenic electron microscope images of isolated small cellular particles from respective conditioned media are presented. Each image is supplemented by description of the preparation of the sample and the data on the imaging technique and equipment. The data are curated by Veronika Kralj-Iglic and Anna Romolo, University of Ljubljana, Faculty of Health Sciences, Laboratory of Clinical Biophysics.

opencc-by-4.0Oct 2021View details →

Figure 2 in Enhancing survival of Demodex folliculorum (Acari: Demodecidae) under in vitro condition: Effect of temperature and culture media

Figure 2. Microphotograph (40×) of Demodex folliculorum mites in the hair follicle of six individuals with a clinical diagnosis of blepharitis. Note the different life stages of the mites (a = adult; l = larva; n = nymph; o = ovum).

opencc-by-4.0Oct 2021View details →

Figure 1 in Enhancing survival of Demodex folliculorum (Acari: Demodecidae) under in vitro condition: Effect of temperature and culture media

Figure 1. Photograph of the eyelids of a patient with cylindrical dandruff attached to the eyelid margin and around the eyelash base.

opencc-by-4.0Dec 2022View details →

Effect of culture conditions on the early stages of development of Codium tomentosum

This dataset was generated by the experimental work performed to evaluate of the effect of culture conditions on the early stages of development of Codium tomentosum in the laboratory. The data is relevant for research on the reproduction and the development of propagation protocols for C. tomentosum.

opencc-by-4.0Aug 2022View details →

Raw data on dynamic light scattering assessment of small cellular particles isolated from conditioned culture media of Dunaliella tertiolecta and Phaeodactylum tricornutum. Effect of Triton X-100 and temperature

Raw data on dynamic light scattering assessment of small cellular particles isolated from conditioned culture media of microalgae Dunaliella tertiolecta (D. tertiolecta) and Phaeodactylum tricurnutum (P. tricornutum) by dynamic light scattering are presented. The project contains spreadsheet files with the measured dependencies of g2 function on time. We collected several g2 functions for each setting (3 for D. tertiolecta samples, 5 for D. tertiolecta with added TX100, 3 for P. tricornutum samples, 3 for P. tricornutum with added TX100). Curves were analyzed independently and compared with the respective averaged curve fitted by the inverse Laplace transform program CONTIN (freely available at: <a href="http://s-provencher.com/index.shtml">http://s-provencher.com/index.shtml</a>, the code was accessed 25. 1. 2011). The correlation curves were fitted with up to 50 exponents. For analysis of stability of small cellular particles with respect to temperature change, we have overall reports for each microalgae type and reports on the size distribution function, data for the g2 function and dependence of scattered light intensity on time for each temperature measured. There were 14 temperatures chosen for each type of microalgae. The files are marked with respective temperatures. The samples were prepared as described below: Cultivation of the algae: Cultures of D. tertiolecta CCAP 19/22 and P. tricornutum CCAP 1052/1A from the Culture Collection of Algae and Protozoa (CCAP) of SAMS (Oban, Scotland) were grown in artificial seawater (Reef Crystals, Aquarium Systems, France). 22 g of salt was dissolved in one litre of distilled water, sterile filtered (0.2-micron cellulose filters, ref. 11107-47-CAN, Sartorius Stedim Biotech GmbH, Germany), autoclaved, and supplemented with Guillard’s (F/2) Marine Water Enrichment Solution (ref. G0154, Sigma Aldrich, USA). Cultures were grown in a respirometer (Echo, Slovenia) in 0.5-L borosilicate bottles, at 20 °C and 20 % illumination (approximately 250 μmol/m2s) with a 14-hour light / 10-hour dark cycle, with aeration of 0.2 L/min. Isolation of small cellular nanoparticles: Small cellular particles were isolated by differential centrifugation, using a protocol widely used for the isolation of extracellular vesicles (Théry C, Amigorena S, Raposo G, Clayton A. Isolation and Characterization of Exosomes from Cell Culture Supernatants and Biological Fluids. Current Protocols in Cell Biology. 2006;30(1). doi:10.1002/0471143030.cb0322s30). Microalgal cells were removed by low-speed centrifugation (300 g, 10 min, 4°C, centrifuge Centric 260R with rotor RA 6/50 (Domel, Slovenia)), using 50 mL conical centrifuge tubes (ref. S.078.02.008.050, Isolab Laborgeräte GmbH, Germany); and 2000 g, 10 min, 4°C (Centric 400R centrifuge with rotor RS4/100 (Domel, Slovenia)), using 15 mL conical centrifuge tubes (ref. S.078.02.001.050, Isolab Laborgeräte GmbH, Germany). Each step was repeated twice. Then, the cell-depleted medium was centrifuged twice at 10 000g and 4°C for 30 min (Beckman L8-70M ultracentrifuge, rotor SW55Ti (Beckman Coulter, USA)), using thin-wall polypropylene centrifuge tubes (ref. 326819, Beckman Coulter, USA) to remove larger cell debris. Finally, small cellular particles were pelleted by centrifugation at 118 000 g and 4°C, for 70 min in the same type of ultracentrifuge and ultracentrifuge tubes. The isolate obtained from about 30 mL of conditioned media was not visible to the eye. For treatment with Triton X-100, the sample was incubated with Triton X-100 at concentration of 0.1%. Dynamic light scattering (DLS): The average hydrodynamic radius (Rh) of NPs and the average intensity of scattered light (I) were assessed for characterization of small cellular particles by DLS. The value of I was interpreted as a measure of small cellular particles concentration (in the case of preserved particle size distribution) or as a topological change (in the case of altered particle size distribution)(Paterna A, Rao E, Adamo G, et al. Isolation of Extracellular Vesicles From Microalgae: A Renewable and Scalable Bioprocess. Front Bioeng Biotechnol. 2022;10:836747. doi:10.3389/fbioe.2022.836747; Brown W, ed. Dynamic Light Scattering: The Method and Some Applications. Clarendon Press ; Oxford University Press; 1993). For analysis of the samples we used Instrument 3D-DLS-SLS cross-correlation spectrometer from LS Instruments GmbH (Fribourg, Switzerla nd) with a 100 mW DPSS laser (Cobolt Flamenco, Cobolt AB, Sweden) having a wavelength λ0 = 660 nm. Before measurements, samples were equilibrated in a decalin bath at 25 °C for 15 min. The scattered light was measured at an angle θ = 90° for 120 s. The correlation functions and integral time-averaged intensities I(θ)&equiv; I(q) (where q is the scattering vector, defined as q =(4πn0/λ0)sin(θ/2), with n0  the refractive index of the medium, in our case estimated by the corresponding value for water, i.e. n0 = 1.33 at 25°C), were recorded simultaneously. The Rh values of small cellular particles were obtained from the diffusion coefficients (D) that were assessed from the correlation function of the scattered electric field (g1(t)). The g1(t) function was calculated from the measured correlation function of the scattered light intensity g2(t) by applying Siegert’s relation (Schärtl W. Light Scattering from Polymer Solutions and Nanoparticle Dispersions. Springer; 2007; Shurer CR, Kuo JCH, Roberts LM, et al. Physical Principles of Membrane Shape Regulation by the Glycocalyx. Cell. 2019;177(7):1757-1770.e21. doi:10.1016/j.cell.2019.04.017). To convert D to Rh, the Stokes-Einstein equation was used (Rh = kT6πηD, where k is the Boltzmann constant, T is the absolute temperature, and η is the viscosity of the medium in which the particles diffuse). It was assumed that particles have a spherical shape. The viscosity of the medium was not known. We approximated the viscosity value to that of of water at 25°C.To test the effect of Triton X-100 on the samples, 0.1% (V/V) of Triton X-100 was added to the sample before the measurement. The change in Rh distribution and the change of scattered light intensity (ΔI = Isample - Isample+0.1%.TX100) was determined. The analysis was made with an in-house created software based on the inverse Laplace transform program CONTIN (freely available at: <a href="http://s-provencher.com/index.shtml">http://s-provencher.com/index.shtml</a>, the code was accessed 25. 1. 2011). We collected several intensity correlation functions for each setting. Curves were analyzed independently and compared with the averaged curve. The correlation curves were fitted with up to 50 exponents. To test the effect of Triton X-100 on NPs, 0.1% (V/V) of Triton X-100 was added to the sample before the measurement. The change in Rh distribution and the change of scattered light intensity (ΔI = Isample - Isample+0.1%.TritonX-100) was determined. Thermal stability analysis was performed using the LitesizerTM 500 instrument (Anton Paar GmbH). Samples were heated from 15 °C to 80 °C in 5 °C steps. When the target temperature was reached, the samples were equilibrated for another 5 minutes before 10 measurements of 20 s duration were performed. The size distributions were determined from the mean correlation function using the Anton Paar Kalliope Professional; Version 2.16.0. (Anton Paar GmbH), <a href="https://www.anton-paar.com/corp-en/products/details/software-for-particle-analysis-kalliopetm/">https://www.anton-paar.com/corp-en/products/details/software-for-particle-analysis-kalliopetm/</a>,  applying the CONTIN approach. A new version of KalliopeTM 4.12.0 <a href="https://www.kalliope.com/2021/05/03/versione-firmware-4-12-0/?lang=en">https://www.kalliope.com/2021/05/03/versione-firmware-4-12-0/?lang=en</a> is freely available online.

Supplementary material 3 from: Siddique AB, Khokon AM, Unterseher M (2017) What do we learn from cultures in the omics age? High-throughput sequencing and cultivation of leaf-inhabiting endophytes from beech (Fagus sylvatica L.) revealed complementary community composition but similar correlations with local habitat conditions. MycoKeys 20: 1-16. https://doi.org/10.3897/mycokeys.20.11265

Common OTU lists and Statistical analysis : Explanation note: This file contains detected OTUs in both methods and biodiversity analysis (GLM and t-test)

Supplementary material 2 from: Siddique AB, Khokon AM, Unterseher M (2017) What do we learn from cultures in the omics age? High-throughput sequencing and cultivation of leaf-inhabiting endophytes from beech (Fagus sylvatica L.) revealed complementary community composition but similar correlations with local habitat conditions. MycoKeys 20: 1-16. https://doi.org/10.3897/mycokeys.20.11265

Biodiversity workflow in R : Explanation note: Bundle of files for biodiversity analysis in R. All necessary input files and a commented script of R-commands are provided.

Supplementary material 4 from: Siddique AB, Khokon AM, Unterseher M (2017) What do we learn from cultures in the omics age? High-throughput sequencing and cultivation of leaf-inhabiting endophytes from beech (Fagus sylvatica L.) revealed complementary community composition but similar correlations with local habitat conditions. MycoKeys 20: 1-16. https://doi.org/10.3897/mycokeys.20.11265

Master data sheet : Explanation note: Spreadsheet file containing information about read abundances of operational taxonomic units (OTUs) and sample metadata. Here, data were prepared for subsequent biodiversity analysis in R.

Supplementary material 1 from: Siddique AB, Khokon AM, Unterseher M (2017) What do we learn from cultures in the omics age? High-throughput sequencing and cultivation of leaf-inhabiting endophytes from beech (Fagus sylvatica L.) revealed complementary community composition but similar correlations with local habitat conditions. MycoKeys 20: 1-16. https://doi.org/10.3897/mycokeys.20.11265

Bioinformatics pipeline : Explanation note: This file provides all steps and commands necessary for quality filtering and demultiplexing of raw paired fastq sequences.

opencc-by-4.0Jun 2024View details →

Isotopic and physiologic data for coccolithophores cultured in various CO2 and pH conditions

Open the record for dataset details and reuse information.

ClinicalTrials.gov32/100

Impact of Dry vs Humidified Culture Conditions on Blastocyst Development and Aneuploidy: A Time-lapse Sibling Oocyte Study

ClinicalTrials.gov study NCT07270250. IPD Sharing: NO. Countries: 1. Publications: 6.

closedIPD-NOFeb 2026View details →

Figure 5 from: Siddique AB, Khokon AM, Unterseher M (2017) What do we learn from cultures in the omics age? High-throughput sequencing and cultivation of leaf-inhabiting endophytes from beech (Fagus sylvatica L.) revealed complementary community composition but similar correlations with local habitat conditions. MycoKeys 20: 1-16. https://doi.org/10.3897/mycokeys.20.11265

Figure 5 - Relative abundance distribution of fungal leaf-inhabiting endophytes of beech among the five main trophic guilds as revealed by analysis with FUNGuild (Nguyen et al. 2016). A compares the two localities for each trophic guild on the basis of Illumina data B compares the two localities for each trophic guild on the basis of cultivation data.

Figure 4 from: Siddique AB, Khokon AM, Unterseher M (2017) What do we learn from cultures in the omics age? High-throughput sequencing and cultivation of leaf-inhabiting endophytes from beech (Fagus sylvatica L.) revealed complementary community composition but similar correlations with local habitat conditions. MycoKeys 20: 1-16. https://doi.org/10.3897/mycokeys.20.11265

Figure 4 - Relative abundance of fungal leaf-inhabiting endophytes of beech among the five main trophic guilds as revealed by analysis with FUNGuild (Nguyen et al. 2016). A compares the two methods for each trophic guild and unassigned data. B displays the trophic guilds and unassigned taxa for Illumina data, C for cultivation data. Abbreviations in [B and C]: U = Unassigned, P = Pathotrophs, PSa = Patho-Saprotrophs, PSy = Patho-Symbiotrophs, Sa = Saprotrophs, Sy = Symbiotrophs

Figure 2 from: Siddique AB, Khokon AM, Unterseher M (2017) What do we learn from cultures in the omics age? High-throughput sequencing and cultivation of leaf-inhabiting endophytes from beech (Fagus sylvatica L.) revealed complementary community composition but similar correlations with local habitat conditions. MycoKeys 20: 1-16. https://doi.org/10.3897/mycokeys.20.11265

Figure 2 - . Principal coordinate analysis (PCoA) of fungal leaf-inhabiting endophytes of beech display strongly differing assemblages obtained with Illumina sequencing and cultivation. Both methods revealed differing mycobiomes from valley and from mountain leaves, although these differences were less pronounced for cultivation data. Abbreviations: IM = Illumina data from mountain samples, IV = Illumina data from valley samples, CM = cultivation data from mountain samples, CV = cultivation data from valley samples

Figure 3 from: Siddique AB, Khokon AM, Unterseher M (2017) What do we learn from cultures in the omics age? High-throughput sequencing and cultivation of leaf-inhabiting endophytes from beech (Fagus sylvatica L.) revealed complementary community composition but similar correlations with local habitat conditions. MycoKeys 20: 1-16. https://doi.org/10.3897/mycokeys.20.11265

Figure 3 - Abundance distribution of the 20 most abundant orders of fungal leaf-inhabiting endophytes of beech on a logarithmic scale. Three of the five most abundant orders from high-throughput sequencing were also most abundant in cultivation data.

Figure 1 from: Siddique AB, Khokon AM, Unterseher M (2017) What do we learn from cultures in the omics age? High-throughput sequencing and cultivation of leaf-inhabiting endophytes from beech (Fagus sylvatica L.) revealed complementary community composition but similar correlations with local habitat conditions. MycoKeys 20: 1-16. https://doi.org/10.3897/mycokeys.20.11265

Figure 1 - Diversity indexes and accumulation curves for a Illumina and b cultivation data of fungal leaf-inhabiting endophytes of beech. Except of the accumulation curves of cultivation data, both methods revealed a clear and partly significant trend of higher fungal diversity at the valley site.