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Cancer cell line CNV samples

This tab separated file includes all cancer cell line samples used for cell line heterogeneity analysis. Columns: sample ID, original NCIT code, cellosaurus ID, bins. All bins, duplications (1) and deletions (2), are merged while keeping their original order. Bin size: 5 Mb. This dataset belongs to the publication: https://doi.org/10.1101/2024.05.15.594310

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.

Profiling phage-host interactions between Skunavirus receptor binding proteins and lactococcal cell wall polysaccharide structures

Open the record for dataset details and reuse information.

Baseline embeddings from the BBBC022 dataset used in "Semisupervised contrastive learning for bioactivity prediction using Cell Painting image data"

3 Baseline embeddings aclculated from the BBBC022 dataset. A self-supervised contrastive learning-based model, DINO and CellProfiler were used  to calculate the embeddings.

opencc-by-4.0Mar 2024View details →

Confocal dataset of Purkinjie cells from clarified cerebellum slices from L7GFP mouse

<div> <div> <h3>TITLE: Confocal dataset of Purkinjie cells from larified cerebellum slices from L7GFP mouse  </h3> </div> <div>  SUMMARY:   </div> <div> We have processed cerebellar material from transgenic mice expressing the green fluorescent protein (GFP). Specifically, in L7GFP mice, the expression of GFP in Purkinje is specifically driven by the Pcp-2 promoter (Zhang, X., Baader, S. L., Biang, F., Müller, W., and Oberdick, J. (2001). High level Purkinje cell specific expression of green fluorescent protein in transgenic mice. Histochem. Cell Biol. 115, 455–464).  The sample were firstly clarified using the optimization of the CLARITY protocol developed by our group, and then acquired using a confocal microscope.    </div> <div>  EXPERIMENTAL METHODS AND MATERIALS:   </div> <div> Data contained in this folder belong to an adult male L7GFP mouse, processed as in Magliaro et al., 2016 (<a href="https://www.frontiersin.org/journals/neuroscience/articles/10.3389/fnins.2016.00179/full#h3" target="_blank" rel="noreferrer noopener">https://www.frontiersin.org/journals/neuroscience/articles/10.3389/fnins.2016.00179/full#h3</a>).  </div> <div>  Briefly, the L7GFP mouse was anesthetized with a lethal dose of 7% chloral hydrate and then perfused with 20 mL of Phosphate Buffered Saline and then 20 mL of a solution, containing 4% acrylamide, 0.05% bis-acrylamide and 0.25% VA-044 thermally triggered initiator at 4°C, as described in Chung et al. (2013) (Chung, K., Wallace, J., Kim, S.-Y., Kalyanasundaram, S., Andalman, A. S., Davidson, T. J., et al. (2013). Structural and molecular interrogation of intact biological systems. Nature 497, 332–337. doi: 10.1038/nature12107). The brain was extracted and submerged in 20 mL hydrogel solution for 3 days at 4°C in a 50 mL Falcon tube to allow gel diffusion into the tissue. Then a vacuum was applied to the tube for 10 min to enable hydrogel formation. Hydrogel polymerization was thermally initiated by incubating the infused tissue overnight at 37°C. At this point, the mouse cerebellum was isolated and then cut into 1 mm-thick coronal slices using a Leica VT1200S vibratome. The cut settings were reported in Mattei et al., 2015 (Mattei, G., Cristiani, I., Magliaro, C., and Ahluwalia, A. (2015). Profile analysis of hepatic porcine and murine brain tissue slices obtained with a vibratome. PeerJ 3:e932. doi: 10.7717/peerj.932). Each slice was finally placed in a 50 mL Falcon tube at 37°C with 20 mL of CLARITY clearing solution (200 mM Boric Acid and 4% Sodium Dodecyl Sulphate, pH adjusted to 8.5 by adding 1 M NaOH dropwise) for 5 days, as this is demonstrated to be the optimal clearing time in Magliaro et al., 2016 (<a href="https://www.frontiersin.org/journals/neuroscience/articles/10.3389/fnins.2016.00179/full#h3" target="_blank" rel="noreferrer noopener">https://www.frontiersin.org/journals/neuroscience/articles/10.3389/fnins.2016.00179/full#h3</a>).  </div> <div> </div> <div> Confocal microscopy data   </div> <div> Image stacks of samples were mounted on a glass slide with FocusClear™ (Celexplorer Labs Co., Hsinchu, Taiwan) and then acquired with a confocal microscope (Nikon A1).  The confocal settings were the following: 4.84 W laser power, emission and excitation wavelengths of 488 nm and 502 nm respectively.  Refer to metadata.xlsx file for detailed info. </div> <div>   </div> <div> Ethical approval  </div> <div> The mouse was obtained from the Department of Translational Research, New Technologies in Medicine and Surgery of the University of Pisa (Italy). Mice were used to perform the experiments, which were conducted in conformity with the European Communities Council Directive of 24 November 1986 (86/609/EEC and 2010/63/UE) and in agreement with the Italian DM26/14. Experiments were approved by the Italian Ministry of Health and Ethical Committee of the University of Pisa.   </div> <div>    </div> </div>

opencc-by-4.0Apr 2024View details →

Correlative microscopy of rat cultured hippocampal pyramidal cell from 40x confocal imaging to super-resolution 93x 3D STED of dendritic spines

This dataset contain multi-scale image of rat hippocampal pyramidal cell related to our paper "From tissues to segmentation: a modular framework for multi-scale neuron isolation" by Cauzzo et al. Nature Comm (2024).

Figures 27–30 in Cell structure and microtubule organisation during gametogenesis of Ulva mutabilis Føyn (Chlorophyta)

Figures 27–30: Tubulin immunofluorescence in released gametes of Ulva mUtabilis. (27) Released gamete bearing two equal flagella. Note that cortical microtubule bundles (tubulin fluorescence) extend from basal body towards the posterior. Scale bar: 20 µm. (28) Differential interference contrast microscopy-image of gamete in Figure 27. Scale bar: 20 µm. (29 and 30) Two gametes in which (apart from the two flagella) an intensely fluorescent microtubule bundle starting from flagellar basal body is directed to cytoplasm (arrows). Scale bar: 20 µm.

Figures 5–8 in Cell structure and microtubule organisation during gametogenesis of Ulva mutabilis Føyn (Chlorophyta)

Figures 5–8: Transmission electron micrographs of cells of Ulva mUtabilis 48 h after the induction of gametogenesis. (5) The cell is polarised with most of the cytoplasm and organelles gathered at the tip area. The external cell wall has formed a projection towards the apical region. The cell wall appears differentiated at this area (N: nucleus). Scale bar: 2 µm. (6) Detail of the apical wall of the previous image, showing the loose structure of the wall and the formation of amorphous dark-stained material. Scale bar: 0.35 µm. (7) More advanced stage of a wall projection. The dark-stained material covers the projection, while its central part appears as a plug, consisting of amorphous material. The internal wall layer under the tip is considerably thickened and pushes the plug out (asterisk). Scale bar: 4 µm. (8) Cross-section of a cell with a plug-like cap. The dark-stained material is extended covering the cap. Scale bar: 0.33 µm.

Figures 9–14 in Cell structure and microtubule organisation during gametogenesis of Ulva mutabilis Føyn (Chlorophyta)

Figures 9–14: Immunolocalization of tubulin in developing gametangia of Ulva mUtabilis. (9) Interphase cell before induction of gametogenesis. The microtubules are mainly peripherally arranged in more or less parallel bundles. Scale bar: 20 µm. (10) Early stage, 36–48 h after induction of gametogenesis. Intensely fluorescent microtubule bundles traverse the cortical cytoplasm converging on a particular area (arrow localises the conical cell projection). Scale bar: 20 µm. (11) More advanced stage, 48–60 h after induction of gametogenesis, showing microtubules starting from a pointed site at basal part of gametangium. Scale bar: 20 µm. (12) Αdvanced stage, 48–60 h after induction of gametogenesis, showing microtubules organised in a basketlike configuration, leaving a circular opening at the top (arrow). Scale bar: 20 µm. (13) Gametangium, 60–72 h after induction of gametogenesis. The microtubule-free area at the top appears broader than before (arrow). Scale bar: 20 µm. (14) Hoechst 33258 staining of the nucleus of the cell in Figure 12. Scale bar: 20 µm.

Figures 2–4 in Cell structure and microtubule organisation during gametogenesis of Ulva mutabilis Føyn (Chlorophyta)

Figures 2–4: Vegetative cells of Ulva mUtabilis before induction of gametogenesis. (2) Light micrograph of a semithin section showing a unilayered thallus. Note the difference in staining between external and internal cell wall layer. Scale bar: 20 µm. (3) Transmission electron micrograph of a thallus cell before induction of gametogenesis. The nucleus (N) has a relatively central position and the chloroplast (CHL) occupies a large part of the cytoplasm (CYT). Note the thick external wall. Scale bar: 3.6 µm. (4) Detail of external wall of a cell before induction of gametogenesis. Wall shows strict stratification, i.e. a thick internal amorphous layer, a median region with multiple fibrillar layers and an external dark-stained region (see brackets). Scale bar: 1 µm.

Figure 1 in Cell structure and microtubule organisation during gametogenesis of Ulva mutabilis Føyn (Chlorophyta)

Figure 1: Time course of induced gametogenesis and discharge of gametangia from Ulva mUtabilis in relation to the swarming inhibitor (SWI) synthesis and action (summary of new and previous results). Gametogenesis was induced in Ulva mUtabilis [mutant slender sl-G(mt +)]. The "determination phase" and "differentiation phase" are defined as described by Stratmann et al. (1996). The "swarming phase" is the time period when gamete release can be induced by light or a medium change, or may occur later spontaneously. (A) Regular vegetative G1 cell cycle phase in which gametogenesis can be induced by the removal of sporulation inhibitors SI-1 and SI-2 from the medium. (B) Regular vegetative S phase in which the genome is replicated normally or, after induction of gametogenesis, the period of SWI synthesis and excretion. (C) Next G1 phase after induction of gametogenesis. (D) Next S phase after induction of gametogenesis and accumulation of starch granules. (E) Time of irreversible commitment to gametangium differentiation. (F) Period of progamete formation, chloroplast reorientation and papilla initiation. (G) Period of progamete multiplication to 16 cells, and papilla maturation. (H) Period of gamete and pore cap maturation. (I) Period when the exit pores are open and when gamete release can be induced by light and/or depletion of SWI in the medium. (J) Period when the gametangia become insensitive to SWI and gamete release may occur spontaneously and asynchronously. Figure is from Wichard and Oertel (2010) with permission of © Wiley 2010. Images show the transformation of blade cells into gametangia. Microscopic images for stages a, f, h and i are shown (scale bars: 25 µm).

Dataset of molecular structures of PNAS article " Ca2+ permeation through C-terminal cleaved, but not full-length human Pannexin1 hemichannels, mediates cell death"

The PMFWT_91_80.tar.gz file contains the WT molecular system described in the cited article. Briefly, the package contains the structure and topology files for AMBER software, along with configuration files to run Umbrella Sampling method and calculation of PMF of a Ca+2 ion traslocating the human pannexin channel (WT).  The TRUCWT_91_80.tar.gz file contains the truncated molecular system described in the cited article. Briefly, the package contains the structure and topology files for AMBER software, along with configuration files to run Umbrella Sampling method and calculation of PMF of a Ca+2 ion traslocating the truncated human pannexin channel as described in the article. Two NetCDF trajectories (*.nc) of a single PMF window are provided for each system.

opencc-by-4.0Sep 2024View details →

Figure 2 in Oxidative and osmotolerant effects in Salvator merianae (Squamata: Teiidae) red blood cells during hibernation

Figure 2. Logarithmic in base 10 values of oxidative biomolecules level for each period collected (n = 6). Wilcox Test: P = 0.31. Sum symbol (+) is the mean and SD are the horizontal lines; median is the vertical line within the boxes and range is distance from the median to the end of the boxes.

opencc-by-4.0Sep 2024View details →

Figure 1 in Oxidative and osmotolerant effects in Salvator merianae (Squamata: Teiidae) red blood cells during hibernation

Figure 1. (a) Osmotic fragility in percentage by saline concentration from both periods studied (GLM: F = 2.56, P = 0.03). No statistical differences were observed between individualized pairs of saline concentrations; (b) Overall osmotic fragility difference between periods considering only periods effect (GLM: F = 9.72, P = 0.01) (n = 6). Sum symbol (+) is the mean and SD are the horizontal lines; median is the vertical line within the boxes and range is distance from the median to the end of the boxes.

opencc-by-4.0Sep 2024View details →

Figure 3 in Oxidative and osmotolerant effects in Salvator merianae (Squamata: Teiidae) red blood cells during hibernation

Figure 3. Logarithmic in base 10 values of (a) Enzymatic activity level of glutathione peroxidase – GPx and (b) activity of glutathione reductase - GR of red blood cells in hibernation and active periods (n = 6). T-test, P = 0.68 and P = 0.10, respectively. Sum symbol (+) is the mean and SD are the horizontal lines; median is the vertical line within the boxes and range is distance from the median to the end of the boxes.

Figure 6 in Gastroesophageal tube of the Iguana iguana (Iguanidae): histological description, histochemical and immunohistochemical analysis of 5-HT and SS cells

Figure 6. Immunoreactivity for Serotonin (5-HT) a-g and Somatostatin (SS) i-h in histological sections of the oesophagus (a,b), cranial stomach (c), middle stomach (d,e) and caudal stomach (f-i) of I. iguana. a-g Serotonin-positive cells (arrow). h,i Somatostatin-positive cells (arrowhead) in the caudal region of the stomach.

Figure 5 in Gastroesophageal tube of the Iguana iguana (Iguanidae): histological description, histochemical and immunohistochemical analysis of 5-HT and SS cells

Figure 5. Histological sections of caudal region in stomach. The epithelium lining (EP) is simple columnar with gastric glands (G) in the lamina propria (LP). M: mucosa. Note the thickening of the muscular layer (ML) and the presence of serosa (S). Detail of mucous layer with epithelium (EP), lamina propria (LP), gastric glans (G), muscularis mucosa (MM) and submucosa (SM). HE staining. Bars = 300 µm.

Figure 4 in Gastroesophageal tube of the Iguana iguana (Iguanidae): histological description, histochemical and immunohistochemical analysis of 5-HT and SS cells

Figure 4. Histological sections of cranial and middle region in stomach. Note the gastric glands are more developed in the middle region, occupying a large part of the lamina propria (star). M: mucosa, SM: submucosa, ML: muscular layer and S: serosa. HE staining.

Figure 1 in Gastroesophageal tube of the Iguana iguana (Iguanidae): histological description, histochemical and immunohistochemical analysis of 5-HT and SS cells

Figure 1. Histological sections of the mucosa layer of I. iguana in different regions of the oesophagus and stomach. HE. Bars = 100 µm. Caudal eosophagus 20 µm.

Figure 3 in Gastroesophageal tube of the Iguana iguana (Iguanidae): histological description, histochemical and immunohistochemical analysis of 5-HT and SS cells

Figure 3. Histological sections of cervical oesophagus of I. iguana. Observe longitudinal folds. Absence of glands in the lamina propria (LP) and submucosa (SM), and evident muscular layer (ML) and adventitia (A). Bars = 3 mm. Detail of mucous layer with epithelium (EP), lamina propria (LP) and muscularis mucosa (MM). Gomori`s tricrome staining.