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opencc-by-4.0Dec 2019View details →

Tumor growth kinetics of human LM2-4LUC+ triple negative breast carcinoma cells

Cell culture and data set Tumor growth data used in this study were obtained from experiments involving the use of a LM2-4LUC+ cells (or LM2-4), a metastatic variant of the  human triple-negative breast carcinoma MDA-MB-231 cells. Animal studies were performed as described previously under Roswell Park Comprehensive Cancer Center (RPCCC) Institutional Animal Care and Use Committee (IACUC) protocol number 1227M [1-7]. Tumor growth data were pooled from eight separate experiments conducted with a total of 581 observations, and represent control (vehicle-treated) animals from published studies [1-7]. Vehicle formulation was carboxymethylcellulose sodium (USP, 0.5% w/v), NaCl (USP, 1.8% w/v), Tween-80 (NF, 0.4% w/v), benzyl alcohol (NF, 0.9% w/v), and reverse osmosis deionized water (added to final volume) and adjusted to pH 6 (see [3]) and was given at 10ml/kg/day for 7-14 days prior after tumor implantation and before tumor resection [1-7]. <ul> </ul> Tumor injections LM2-4LUC+ cells were orthotopically implanted (106 cells per injection) into the right inguinal mammary fat pads of 6- to 8-week-old female severe combined immunodeficient (SCID) mice. Tumor measurements Tumor size was measured regularly with calipers to a maximum volume of  2 cm3, calculated by the formula  \(V = \frac{\pi}{6} w^2 L\) (ellipsoid) where L is the largest and w is the smallest tumor diameter. Please cite: Vaghi C, Rodallec A, Fanciullino R, Ciccolini J, Mochel JP, et al. (2020) Population modeling of tumor growth curves and the reduced Gompertz model improve prediction of the age of experimental tumors, PLoS Comput Biol, 16, p. e1007178. <a href="https://doi.org/10.1371/journal.pcbi.1007178">https://doi.org/10.1371/journal.pcbi.1007178</a>   In the file, the columns correspond to: <ul> <li>ID: identifier of the animal</li> <li>Time: day of the tumor measurement after implantation</li> <li>Observation: tumor measurement (in mm3)</li> </ul>   References [1] Benzekry, S., Lamont, C., Beheshti, A., Tracz, A., Ebos, J. M. L., Hlatky, L., & Hahnfeldt, P. (2014). Classical mathematical models for description and prediction of experimental tumor growth. PLoS Comput Biol, 10(8), e1003800. http://doi.org/10.1371/journal.pcbi.1003800 [2] Benzekry S, Tracz A, Mastri M, Corbelli R, Barbolosi D, Ebos JML. (2016) Modeling Spontaneous Metastasis Following Surgery: An In Vivo-In Silico Approach. Cancer Res.;76(3):535–547. doi:10.1158/0008-5472.CAN-15-1389. [3] Ebos JML, Lee CR, Bogdanovic E, Alami J, Van Slyke P, Francia G, et al. (2008) Vascular Endothelial Growth Factor-Mediated Decrease in Plasma Soluble Vascular Endothelial Growth Factor Receptor-2 Levels as a Surrogate Biomarker for Tumor Growth. Cancer Res.;68(2):521–529. doi:10.1158/0008-5472.CAN-07-3217. [4] Ebos JML, Mastri M, Lee CR, Tracz A, Hudson JM, Attwood K, et al. (2014) Neoadjuvant antiangiogenic therapy reveals contrasts in primary and metastatic tumor efficacy. EMBO Mol Med;6:1561–76. https://doi.org/10.15252/emmm.201403989 [5] Ebos JML, Lee CR, Cruz-Munoz W, Bjarnason GA, Christensen JG, Kerbel RS. (2009) Accelerated metastasis after short-term treatment with a potent inhibitor of tumor angiogenesis. Cancer Cell;15:232–9. https://doi.org/10.1016/j.ccr.2009.01.021 [6] Mastri M, Tracz A, Lee CR, Dolan M, Attwood K, Christensen JG, et al. (2018) A Transient Pseudosenescent Secretome Promotes Tumor Growth after Antiangiogenic Therapy Withdrawal. Cell Rep.; 25 (13):3706–20 e8. Epub 2018/12/28. https://doi.org/10.1016/j.celrep.2018.12.017 [7] Vaghi C, Rodallec A, Fanciullino R, Ciccolini J, Mochel JP, et al. (2020) Population modeling of tumor growth curves and the reduced Gompertz model improve prediction of the age of experimental tumors, PLoS Comput Biol, 16, p. e1007178. <a href="https://doi.org/10.1371/journal.pcbi.1007178">https://doi.org/10.1371/journal.pcbi.1007178</a>

opencc-by-4.0Oct 2023View details →

In vivo treatment with insulin-like growth factor 1 reduces CCR5 expression on vaccine-induced activated CD4+ T-cells

Dataset of the publication "In vivo treatment with insulin-like growth factor 1 reduces CCR5 expression on vaccine-induced activated CD4+ T-cells" by Bissa et al. on the journal Vaccines. Each folder contains the original files reporting the data used to generate the manuscript.For flowcytometry based assays the Flow panel is included in the folders. For ELISA based assays the schemes of the plates are included in the folders. The excel table "Bissa et al._Vaccines_2023_Animal IDs and viral acquisition" reports the IDs and grouping of the animals together with their viral acquisitionThe excel table "Bissa et al._Vaccines_2023_Master table" reports each data used to generate the figures and supplemental materials included in the publication

opencc-by-4.0Oct 2017View details →

Data: multimodal cell tracking from systemic administration to tumour growth by combining gold nanorods and reporter genes

This data set includes multispectral optoacoustic tomography images supporting an article on cell tracking (preprint: bioRxiv 199836; https://doi.org/10.1101/199836). The corresponding bioluminescence results are included too, as well as the spectra used for the multispectral processing.

opencc-by-4.0Feb 2023View details →

Altered nanoparticle uptake by lung carcinoma cells when stimulated with epidermal growth factor

This dataset provides the raw data supporting the paper "Altered nanoparticle uptake by lung carcinoma cells when stimulated with epidermal growth factor". The focus of the study was to investigate the uptake of two different sizes of silica NPs and gold NPs in lung epithelial cells A549 in the presence of epidermal growth factor (EGF).  The data set includes: <ul> <li>Screening for EGF receptor using western blot and confocal microscopy (Figure 1 and Figure S1)</li> <li>Investigating expression of RAC1/CDC42 proteins upon EGF stimulation using Western blot (Figure 2)</li> <li>Investigating expression of RAC1 gene upon EGF stimulation using RT-qPCR (Figure S2)</li> <li>Evaluating uptake of endocytic markers upon EGF stimulation using confocal laser scanning microscopy (Figure 3, Figure S4) and flow cytometry (Figure 3)</li> <li>Nanoparticle characterization using TEM (Figure 4, Figure S6) and UV-Vis (Figure S5, Figure S6)</li> <li>Evaluating silica nanoparticle uptake upon EGF stimulation using confocal laser scanning microscopy (Figure 5, Figure S8) and flow cytometry (Figure 5)</li> <li>Evaluating gold nanoparticle uptake upon EGF stimulation using dark-field microscopy and ICP-AES (Figure 6)</li> <li>Investigating expression of c-MYC gene upon EGF stimulation using RT-qPCR (Figure 6)</li> <li>Cell viability results, analysed via lactate dehydrogenase assay (Figure S3) and MTS assay (Figure S9)</li> <li>Raw integrated density data from dark-field images (Figure S9)</li> </ul>

opencc-by-4.0Nov 2020View details →

Dataset - A lung-on-chip model reveals an essential role for alveolar epithelial cells in controlling bacterial growth during early M. tuberculosis infection

Description of the sub-folders Name, type of data, corresponding Figure in the manuscript 3D view of the LoC model - .tiff image stack, Figure 1. Bacterial Growth Rate Data  - .tiff image stacks, .csv files and MATLAB code to extract the fluorescence intensity over time, Figure 2, Figure 2 - figure supplement 2, Figure 2 - figure supplement 4, Figure 3, Figure 3 - figure supplement 2, Figure 4. AT Characterization - .tiff image stacks and MATLAB code to extract the number and volume of lamellar bodies from the stack of confocal images, Figure 1, Figure 1 - figure supplement 1, Figue 1 - figure supplement 2. AT Infection in LoC model - .tiff image stacks, Figure 2 - figure supplement 1. AT Infection in vivo - .tiff image stacks, Figure 1 - figure supplement 3. Simulations of in vivo infections - .dat files of growth rates in macrophages for the WT and ESX-1 deficient populations and MATLAB code to simulate an infection from this data, Figure 4.

opencc-by-4.0Feb 2017View details →

Research data supporting "Online quantitative monitoring of live cell engineered cartilage growth using diffuse fiber-optic Raman spectroscopy"

Research data supporting the publication: M. Bergholt, 2017, Online quantitative monitoring of live cell engineered cartilage growth using diffuse fiber-optic Raman spectroscopy, Biomaterials, Volume 140, September 2017, Pages 128–137, DOI: 10.1016/j.biomaterials.2017.06.015

opencc-zeroJul 2024View details →

Cell growth dataset for "Suppression of bacterial cell death underlies the antagonistic interaction between ciprofloxacin and tetracycline in Escherichia coli"

<div>This dataset contains growth data of E. coli cells measured by optical density at a wavelenght of 600 nm (OD600) to determine the conditions where the combination of ciprofloxacin (CIP) and tetracycline (TET) is antagonistic (or suppressive), using a medium that supports fast, intermediate and slow growth (M9 based medium supplemented with: glucose and amino acid, glucose, and glycerol, respectively).</div> <div>Two types of assays were performed: a checkerboard assay with a 2-dimension gradient of antibiotic concentrations shown in "Fig-S1-Growth_rates-Checkerboard_assay.zip", and bulk growth rates assay  shown in "Fig-S2-Bulk_doubling_rates-Bioreactor.zip". </div> <div>These experiments are presented in the supplementary figures of the following manuscript published as preprint in bioRxiv:  https://doi.org/10.1101/2024.04.18.590101.</div> <div> </div> Fig-S1-Growth_rates-Checkerboard_assay.zip: <div>- growth-OD600-Blank_correct.xlsx: contains the blank corrected (subtracted by initial OD of sterile medium) OD600 data for each well measured in the checkerboard assay. The negative control is named as "Blank B" in the spreasheet and the antibiotic concentrations for each well is defined in column C (Content).</div> <div>- growth_data.xlsx: contains the processed data from "Growth-OD600-Blank_correct.xlsx":growth curves were smoothed with a 5-window moving median and outliers corrected using the filloutliers function in MATLAB. Outliers that were missed were manually corrected.</div> <div>- time_h.xlsx: contains the time in hours used by the matlab function to build the dose response figure S1B.</div> <div>- analysis_code_checkerboard_assay.m: matlab function used to build the dose response figure S1B.</div>   Fig-S2-Bulk_doubling_rates-Bioreactor.zip: - "bulk_doubling rates_gly/glu/gluaa.csv": contains the calculated doubling rates for each of three experimental replicates (rows) and for each antibiotic treatment (columns: Ctrl, CIP, TET, CIP-TET) as shown in Figure S2. These values were used to calculated the Bliss independence (for further details see https://gitlab.com/MEKlab/single-cell-suppression-2024/figure plotting.ipynb    - Folders containing OD600 measurements and calculated growth rates for each growth medium, which are further separated into folders for each experimental replicate. Each replicate folder is labelled as the date the experiment was performed (denoted as "*" hereon). Each contains the following: raw optical density data (*.txt files), summary of experiment and results (*.docx file), the function compute_growth_rates.m, and the script Growth_curves_*.m. <div>For more information on methods, strains used and table header descriptions, please refer to the README.txt. </div>

Text-fig. 10. Platanoxylon cf. haydenii, a, e, h: UF 279-34470; b, c, d, f g: UF 279-34469. a, b: Diffuse porous wood with vessels solitary and in small multiples, which are mostly tangential or oblique, diffuse and diffuse-in-aggregates axial parenchyma., TS. c–e: Scalariform perforation plates. f, g: Opposite intervessel pits, TLS. h: Two size classes of rays, TLS. Platanus sp., UF 279- 24552. i: Predominantly solitary vessels, diffuse and diffuse-in-aggregates parenchyma, growth ring boundary distinct, noded rays, TS. j: Simple perforation plates (PP), RLS. k: Body of ray with procumbent ray cells, RLS. l: Scalariform perforation plate, RLS. m: Rays of two sizes, wide rays>10-seriate, TLS. Scale bars: 200 µm in a, b, h, i, m; 100 µm in j, k: 50 µm in c, d, e, f, l. in A Diverse Assemblage Of Late Eocene Woods From Oregon, Western Usa

Text-fig. 10. Platanoxylon cf. haydenii, a, e, h: UF 279-34470; b, c, d, f g: UF 279-34469. a, b: Diffuse porous wood with vessels solitary and in small multiples, which are mostly tangential or oblique, diffuse and diffuse-in-aggregates axial parenchyma., TS. c–e: Scalariform perforation plates. f, g: Opposite intervessel pits, TLS. h: Two size classes of rays, TLS. Platanus sp., UF 279- 24552. i: Predominantly solitary vessels, diffuse and diffuse-in-aggregates parenchyma, growth ring boundary distinct, noded rays, TS. j: Simple perforation plates (PP), RLS. k: Body of ray with procumbent ray cells, RLS. l: Scalariform perforation plate, RLS. m: Rays of two sizes, wide rays>10-seriate, TLS. Scale bars: 200 µm in a, b, h, i, m; 100 µm in j, k: 50 µm in c, d, e, f, l.

Text-fig. 7. Hamamelidoxylon crystalliferum sp. nov., UF 279-34464. a: Diffuse porous wood with exclusively solitary vessels, tending to be angular in outline, TS. b: Growth ring boundary, marked by radially narrowed fibers, latewood vessels narrower than earlywood vessels of the next ring, fibers thick-walled, no axial parenchyma visible, TS. c: Scalariform intervessel pits in narrow vessel (left), fibers with distinctly bordered pits, TLS. d: Scalariform perforation plate, tyloses (T) formation from marginal ray cell, TLS. e: Scalariform perforation plates with fewer than 15 bars (PP), RLS. f: Vessel-ray parenchyma pits with in A Diverse Assemblage Of Late Eocene Woods From Oregon, Western Usa

Text-fig. 7. Hamamelidoxylon crystalliferum sp. nov., UF 279-34464. a: Diffuse porous wood with exclusively solitary vessels, tending to be angular in outline, TS. b: Growth ring boundary, marked by radially narrowed fibers, latewood vessels narrower than earlywood vessels of the next ring, fibers thick-walled, no axial parenchyma visible, TS. c: Scalariform intervessel pits in narrow vessel (left), fibers with distinctly bordered pits, TLS. d: Scalariform perforation plate, tyloses (T) formation from marginal ray cell, TLS. e: Scalariform perforation plates with fewer than 15 bars (PP), RLS. f: Vessel-ray parenchyma pits with

Text-fig. 1. Pistacia terrazasae sp. nov., a: UF 279-85025; b–i: UF 279-24545. a: Ring-porous wood with widely spaced solitary earlywood vessels; latewood vessels in radial multiples of 4 or more and in clusters, TS. b: Growth ring boundary, fiber walls thin to thick, TS. c: Simple perforation plates, alternate intervessel pits, helical thickenings in vessels, TLS. d: Multiseriate rays to 4-seriate, tyloses in vessels, helical thickenings throughout body of vessel element, and alternate intervessel pitting, TLS. e: Vessel-ray parenchyma pitting with reduced borders, oval in outline, RLS. f: Marginal row of upright cells, one inflated and crystalliferous, procumbent body cells, RLS. g: Multiseriate rays mostly 3-seriate, occasionally 4-seriate, uniseriate rays usually <10 cells tall, TLS. h: Ray with enlarged crystalliferous marginal cell, to left of C, TLS. i: Ray with canal, TLS. Scale bars: 200 µm in a, g; 100 µm in b, d, h; 50 µm in c, i; 20 µm in e, f. in A Diverse Assemblage Of Late Eocene Woods From Oregon, Western Usa

Text-fig. 1. Pistacia terrazasae sp. nov., a: UF 279-85025; b–i: UF 279-24545. a: Ring-porous wood with widely spaced solitary earlywood vessels; latewood vessels in radial multiples of 4 or more and in clusters, TS. b: Growth ring boundary, fiber walls thin to thick, TS. c: Simple perforation plates, alternate intervessel pits, helical thickenings in vessels, TLS. d: Multiseriate rays to 4-seriate, tyloses in vessels, helical thickenings throughout body of vessel element, and alternate intervessel pitting, TLS. e: Vessel-ray parenchyma pitting with reduced borders, oval in outline, RLS. f: Marginal row of upright cells, one inflated and crystalliferous, procumbent body cells, RLS. g: Multiseriate rays mostly 3-seriate, occasionally 4-seriate, uniseriate rays usually <10 cells tall, TLS. h: Ray with enlarged crystalliferous marginal cell, to left of C, TLS. i: Ray with canal, TLS. Scale bars: 200 µm in a, g; 100 µm in b, d, h; 50 µm in c, i; 20 µm in e, f.

Text-fig. 2. Celtis popsii sp. nov., UF 279-34460. a: Growth ring with earlywood of multiple rows of vessels solitary and in radial multiples; latewood vessels in wavy tangential bands, TS. b: Growth ring boundary, latewood vessels in multiples with axial parenchyma confluent, TS. c: Simple perforation plates, alternate intervessel pits, polygonal in outline, TLS. d: Vessel-ray parenchyma pits to right of VRP, oval in outline, with slightly reduced borders, RLS. e: Rays tending to two sizes, some multiseriate rays with distinct sheath cells, multiseriate rays usually with 1 marginal row of square to upright cells, occasionally with 4 or more; uniseriate rays less than 10 cells high, TLS. f: Detail of multiseriate ray with distinct sheath cells, vessel element end walls, TLS. Scale bars: 200 µm in a, e; 100 µm in b; 50 µm in c, f; 20 µm in d. in A Diverse Assemblage Of Late Eocene Woods From Oregon, Western Usa

Text-fig. 2. Celtis popsii sp. nov., UF 279-34460. a: Growth ring with earlywood of multiple rows of vessels solitary and in radial multiples; latewood vessels in wavy tangential bands, TS. b: Growth ring boundary, latewood vessels in multiples with axial parenchyma confluent, TS. c: Simple perforation plates, alternate intervessel pits, polygonal in outline, TLS. d: Vessel-ray parenchyma pits to right of VRP, oval in outline, with slightly reduced borders, RLS. e: Rays tending to two sizes, some multiseriate rays with distinct sheath cells, multiseriate rays usually with 1 marginal row of square to upright cells, occasionally with 4 or more; uniseriate rays less than 10 cells high, TLS. f: Detail of multiseriate ray with distinct sheath cells, vessel element end walls, TLS. Scale bars: 200 µm in a, e; 100 µm in b; 50 µm in c, f; 20 µm in d.

opencc-by-4.0May 2024View details →

How mRNA influences cell growth

This dataset contains the data from different published articles used in the article of Calabrese et al. (PNAS DOI: 10.1073/pnas.2400679121 BioRxiv DOI: https://doi.org/10.1101/2023.03.17.533181). The collection of data files is divided in three folders, each referring to a figure in the main text of Calabrese et al. Each folder contains their own README describe their content.

dryad40/100

Data from: Live-cell analysis of IMPDH protein levels during yeast colony growth provides insights into the regulation of GTP synthesis

Here we present real-time, live-cell analysis of accumulation of the Imd2 isoform of IMPDH in Saccharomyces cervisiae yeast cells forming a monolayer colony in a microfluidic device over a 50-hour time course. We observe two distinct phases of increased Imd2 accumulation: a guanine-insensitive phase early in outgrowth and a guanine-sensitive phase later, when cells become crowded. We show that the IMPDH inhibitor mycophenolic acid enhances both phases of increase. Deletion of a transcription attenuator upstream of the mRNA start site that decreases Imd2 mRNA synthesis in the presence of high GTP increases the baseline level of Imd2 protein ten-fold and abolishes guanine-sensitive but not guanine-insensitive induction. Our results suggest that at least two mechanisms of yeast Imd2 regulation exist, the known GTP-dependent attenuation of RNA polymerase II elongation and a GTP concentration-independent pathway that may be controlled by cell growth state.

opencc-zeroJun 2024View details →

opencc-by-4.0Nov 2011View details →

Text-fig. 2: Microscopic photo of the wood from Kučlín (specimen No. G 4723, NM, transverse section) shoving growth ring boundary with markedly rounded tracheids and abundant axial parenchyma (dark cells) present both in late- and earlywood (scale bar = 100 µm). in Silicified Stem From The Late Eocene Fossil Locality Of Kučlín (Czech Republic): Overview And New Remarks

Text-fig. 2: Microscopic photo of the wood from Kučlín (specimen No. G 4723, NM, transverse section) shoving growth ring boundary with markedly rounded tracheids and abundant axial parenchyma (dark cells) present both in late- and earlywood (scale bar = 100 µm).