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111,247 results for “cells”
Kriegerdenkmal Celle Neustadt
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Data set of CA1 pyramidal cell models using an intact whole hippocampus preparation
<p>The frequency-current (f-I) profiles of pyramidal cells are presented. Each .abf file contains the f-I curve data for the respective cell (as labelled PYR1, PYR2, PYR3 and PYR4 for Pyramidal cell 1, Pyramidal cell 2, Pyramidal cell 3 and Pyramidal cell 4). That is, they contain the cell's response to the application of a series of depolarizing current steps of 1 s duration while the cells are held in current clamp, as well as the current clamp data itself. Each recording is 2 s total. Amplitudes of the input were increased incrementally with step sizes of 10 pA for PYR1, PYR3, and PYR4, and a step size of 25 pA for PYR 2. PYR1 first spikes on the 5th of 30 steps with 38.7 pA of depolarizing input. PYR2 first spikes on the 3rd of 13 steps with 1.2 pA of input. PYR3 first spikes on the 7th of 34 steps with 62.0 pA of input, and PYR4 first spikes on the 7th of 30 steps with 12.1 pA of input.</p>
Data of quantitative, ratiometric dual fluorescence reporter assay at the single-cell level
<p>The data set shows the evaluation of a new dual fluorescence reporter assay using three test genes, vimentin, lamin A/C and Arp3. This fluorescence protein-based reported assay successfully predicts siRNA efficacy with high fidelity. Data include images of Hela cells transfected with Vim-T4 ad Vim-T5 knockdown contructs; images of dual fluorescence assay; data analysis for knockdown experiments, Western blotting analysis of vimentin-knockdown in Hela cells, knockdown of endogenous lamin A/C in Hela cells; quantification of lamin A/C knockdown in Hela cells; dual fluorescence assay of human vimentin genes using three plasmids; Western blotting of Arp3 knockdown in SCC9 cells.</p> <p>All files can be opened using LibreOffice or OpenOffice. Some of the ODS files have a minor problem when opening them in Excel in the Windows computers. Excel will give warning about some unreadable contents. By choosing the repair option, the file contents will be shown without changes compared to the original data. Detailed explanation is given in the “Explanation file”.</p>
Data set of CA1 pyramidal cell recordings using an intact whole hippocampus preparation, including recordings of rebound firing (V2)
<p>The frequency-current (f-I) profiles and an example of rebound firing of pyramidal cells are presented. Four .abf files contain the f-I curve data for the respective cell (as labelled PYR1, PYR2, PYR3 and PYR4 for Pyramidal cell 1, Pyramidal cell 2, Pyramidal cell 3 and Pyramidal cell 4). That is, they contain the cell's response to the application of a series of depolarizing current steps of 1 s duration while the cells are held in current clamp, as well as the current clamp data itself. Each recording is 2 s total. Amplitudes of the input were increased incrementally with step sizes of 10 pA for PYR1, PYR3, and PYR4, and a step size of 25 pA for PYR 2. PYR1 first spikes on the 5th of 30 steps with 38.7 pA of depolarizing input. PYR2 first spikes on the 3rd of 13 steps with 1.2 pA of input. PYR3 first spikes on the 7th of 34 steps with 62.0 pA of input, and PYR4 first spikes on the 7th of 30 steps with 12.1 pA of input. In the .abf file labelled PYR5_rebound, an example of rebound firing of a pyramidal cell following hyperpolarizing input is given. While the cell was held at -52 mV in current clamp, as series of 1 s hyperpolarizing steps (10 steps, 25 pA increments) were used to record the post- hyperpolarization rebound spiking. For the figure showing this rebound spiking (Figure 1), the first two hyperpolarizing steps and the respective firing are shown. For visualization purposes, the spike artifact in the current clamp input trace was removed and replaced with the mean current in the Figure. </p>
Data set of CA1 pyramidal cell models using an intact whole hippocampus preparationV2
<p>The frequency-current (f-I) profiles and an example of rebound firing of pyramidal cells are presented. Four .abf files contain the f-I curve data for the respective cell (as labelled PYR1, PYR2, PYR3 and PYR4 for Pyramidal cell 1, Pyramidal cell 2, Pyramidal cell 3 and Pyramidal cell 4). That is, they contain the cell's response to the application of a series of depolarizing current steps of 1 s duration while the cells are held in current clamp, as well as the current clamp data itself. Each recording is 2 s total. Amplitudes of the input were increased incrementally with step sizes of 10 pA for PYR1, PYR3, and PYR4, and a step size of 25 pA for PYR 2. PYR1 first spikes on the 5th of 30 steps with 38.7 pA of depolarizing input. PYR2 first spikes on the 3rd of 13 steps with 1.2 pA of input. PYR3 first spikes on the 7th of 34 steps with 62.0 pA of input, and PYR4 first spikes on the 7th of 30 steps with 12.1 pA of input. In the .abf file labelled PYR5_rebound, an example of rebound firing of a pyramidal cell following hyperpolarizing input is given. While the cell was held at -52 mV in current clamp, as series of 1 s hyperpolarizing steps (10 steps, 25 pA increments) were used to record the post- hyperpolarization rebound spiking. For the figure showing this rebound spiking (Figure 1), the first two hyperpolarizing steps and the respective firing are shown. For visualization purposes, the spike artifact in the current clamp input trace was removed and replaced with the mean current in the Figure.</p>
Supplementary Material: HIV-1-Induced Small T Cell Syncytia Can Transfer Virus Particles to Target Cells through Transient Contacts
<p>Videos supplementary to <em>Viruses</em> <strong>2015</strong>, <em>7</em>(12), 6590-6603; doi:10.3390/v7122959</p> <p><strong>Captions:</strong></p> <p><strong>Movie S1.</strong> <strong>HIV-1-infected cells in the lymph node of humanized mice.</strong></p> <p>Humanized BLT mice were injected in the footpad with HIV-nGFP, where GFP is highly enriched in cellular nuclei, and the draining popliteal lymph node prepared for MP-IVM at day 2. Representative infected cells (GFP+; green) that display one, two or three discernible nuclei are shown (<strong>top</strong>). In the bottom panels, green fluorescence signals above 80% of the intensity maximum were used to define cell nuclei, which are shown in white. The syncytium with two discernible nuclei remains elongated throughout the recording, while the syncytium with three discernible nuclei switches between coordinated and uncoordinated motility. Each individual frame is a maximum intensity projection of 11 <em>z</em>-stacks spaced 4 μm apart (for a total volume of 40 μm). Time is shown in minutes and seconds. Scale bar = 20 μm. See also Figure 1A.</p> <p><strong>Movie S2.</strong> <strong>Syncytia in the lymph node contact uninfected T cells without undergoing cell-cell fusion</strong>.</p> <p><em>In vitro</em>-generated central memory CD4+ T cells, either infected with HIV-GFP (GFP+; green) or uninfected (labeled with CellTracker Orange; red), were adoptively transferred by footpad injection into BLT mice pretreated with antiretroviral drugs (100 mg/kg FTC, 150 mg/kg TDF). After 12 h, the draining popliteal lymph node was prepared for MP-IVM. Two representative movies of T cell migration prior to (yellow circle) and during<br /> (blue circle) transient interactions with syncytia are shown, demonstrating cellular interactions without fusion. Each individual frame is a maximum intensity projection of 11 <em>z</em>-stacks spaced 4 μm apart (for a total volume of 40 μm). Time is shown in minutes and seconds. Scale bar = 40 μm. See also Figure 1F,G.</p> <p><strong>Movie S3.</strong> <strong>CD4</strong><strong>+ T cells in 3D culture form small syncytia with elongated morphology</strong>.</p> <p>Primary human CD4+ T cells isolated from a healthy donor were infected with VSV-G-pseudotyped NL4-3<sup>Gag-iGFP</sup> virus. The next day, cells were embedded in a 3D collagen gel as described in the Experimental Section, and 12 h later imaged live at 37 °C using a 20× objective on a DeltaVision widefield microscope. Six 3 µm-spaced Z-slices were taken every 20 s, and were subsequently projected into one image. The syncytium seen here in green has two nuclei located at opposite ends, and a central bulged region with high amounts of viral Gag. The diffuse fluorescence is a result of this syncytium being located at a higher part of the gel, where the limitations of widefield imaging become more prominent. See also Figure 2A.</p> <p><strong>Movie S4.</strong> <strong>Small CEM-SS syncytia in 3D culture can dynamically change their morphology</strong>.</p> <p>CEM-SS cells were infected with VSV-G-pseudotyped NL4-3<sup>Gag-iGFP</sup> virus. The next day, cells were embedded in a 3D Matrigel gel as described in the Experimental Section, and 24 h later imaged live at 37 °C using a<br /> 40× objective on a DeltaVision widefield microscope. Seven 2 μm-spaced Z-slices were taken every 5 min, and were subsequently projected into one image. A syncytium with two nuclei (dark areas within the cell in the GFP channel) begins with two lobes, which merge into a coordinated round morphology as the cell begins to migrate through the gel and leaves the plane of focus. See also Figure 2B.</p> <p><strong>Movie S5.</strong> <strong>CD4</strong><strong>+ T cells in 3D culture exhibit </strong><strong><em>in vivo</em>-like migratory behavior</strong>.</p> <p>Primary human CD4<sup>+</sup> T cells were infected, embedded in collagen, and imaged as in Movie S3 (though with a<br /> 10 s time lapse). The uninucleated infected cell migrating across the field moves by 108 μm over 560 s, for a mean velocity of 11.58 μm/min. Such fast directed amoeboid motility is not typically observed in classical 2D culture and requires the presence of a 3D ECM. See also Figure 2C.</p> <p><strong>Movie S6.</strong> <strong>Uninucleated infected cells and syncytia can transfer virus to target cells without fusion.</strong></p> <p>CEM-SS cells were infected, embedded in Matrigel, and imaged as in Movie S4. Virus transfer from a uninucleated infected cell (top) and a syncytium (bottom left) to a number of target cells (denoted by T) can be seen here.<br /> The uninucleated infected cell transfers virus to target cells T1–T5, and the syncytium transfers virus to target cells T6–T7. Images shown represent brightfield in gray (bottom right), or Gag-iGFP in green, shown either with normal scaling (bottom left, and merged with brightfield at top right), or with a 0.6 gamma correction applied and enhanced scaling to better show appearance of Gag-iGFP puncta on target cells (top left). Scale bar = 30 μm. A yellow arrow indicates the moment where the uninucleated infected cell begins transferring virus to target cells T1–T3, and all of the other transfer events in this field are happening at roughly the same time. At this time, Gag-iGFP puncta appear to distribute between cells T1–T3 in a progressive fashion, beginning from the point of contact with the infected cell (see also Figure 3A, middle panel). Cells T4 and T5 also receive virus particles from this infected cell, and T4 can be seen migrating away at the end. Also note a trail of released virus left behind by the uninucleated infected cell as it migrates from left to right from 08:00:00 to 09:10:00 (see also Movies S7 and S9, Figure 4 for similar events in syncytia). The syncytium’s targets, T6 and T7, are already in intimate contact with it at the start of the movie, and are obscured by lobes of the syncytium. At the 10:45:00 mark, cell T6 breaks free from the syncytium, now harboring a large amount of virus particles on its surface, as the syncytium slowly migrates away, and cell T7 also appears to harbor virus particles on its surface by the final time point.</p> <p><strong>Movie S7.</strong> <strong>A virus transfer event between a syncytium and two uninfected target cells.</strong></p> <p>CEM-SS cells were infected, embedded in Matrigel, and imaged as in Movies S4 and S6. The syncytium shown here initially has two nuclei, but soon fuses with an uninfected cell and now has three clearly visible nuclei. It remains stationary for several hours, before beginning to migrate towards a pair of uninfected target cells (top). Very soon after contact, virus particles can be seen covering the surface of both cells, one of which eventually migrates away. See also Figure 3A (left panel). Note also another instance of a dense accumulation of cell-free virus particles in what appears to be a pocket within the hydrogel that the syncytium moves one of its lobes out of, revealing the deposited free virus, before it moves back into the pocket. See also Figure 4A.</p> <p><strong>Movie S8.</strong> <strong>Cell-to-cell transfer of virus can take place while cells are migrating.</strong></p> <p>CEM-SS cells were infected, later mixed with CMAC-labeled uninfected CEM-SS cells (shown in blue), embedded in collagen, and imaged as above. A syncytium with two nuclei (one of which bears CMAC signal, indicating that it formed recently and not before the infected culture was mixed with the labeled uninfected cells) migrates across the field. Its trailing edge contacts an uninfected CMAC-labeled cell, which is then dragged along with it, and finally dropped in the corner of the field. The target cell now bears virus particles on its surface, and is no longer in contact with the syncytium, which has moved into a different focal plane and stopped migrating (not shown). The image was refocused at the 10:30:00 mark to better show the target cell and the virus particles on its surface. Note that this movie also shows an instance of newly synthesized Gag-iGFP appearing in a previously uninfected cell (not the target cell contacted by the syncytium). This non-CMAC labeled uninfected cell appears in the bottom left of the field at 07:20:00 and exhibits steadily increasing diffuse intracellular signal, as documented in Figure 3A (right) and Figure 3B,C (green traces).</p> <p><strong>Movie S9.</strong> <strong>Migrating infected cells can deposit a trail of released virus particles</strong>.</p> <p>CEM-SS cells were infected, embedded in Matrigel, and imaged as in Movies S4, S6, and S7. A syncytium with 3 nuclei switches into a coordinated morphology and begins migrating across the field. Released virus particles can be seen in its wake (also shown enlarged and with increased brightness as an inset). Shortly after the end of the movie, the cell-free virus accumulation appeared to dissipate (not shown), but it could not be determined whether this was because of photobleaching or if they had in fact diffused away. See also Figure 4B.</p>
MiL-FISH: Multi-labelled oligonucleotides for fluorescence in situ hybridisation improve visualization of bacterial cells
<p>Comparison of mono-, MiL- and CARD-FISH on LR-White embedded <em>Olavius algarvensis</em> cross sections A: Ethanol preserved specimen, cu = cuticle, sym = symbionts, sep = septum, epi = epidermis, mu = muscle, vbv = ventral blood vessel & nerve chord, chl = chloragogen tissue, grid square = example of region shown in images B, C, D and E.</p> <p>Probes for Gammaproteobacteria (Gam42a; green) and a subgroup of sulfate-reducing Deltaproteobacteria (DSS658; red) on B) mono-FISH on ethanol preserved specimen, 19 hour hybridisation. C) mono-FISH on ethanol preserved specimen, 3 hour hybridisation and D) CARD-FISH on Carnoy’s / PFA fixed specimen, 3-hour hybridisation. E) MiL-FISH on Carnoy’s / PFA fixed specimen, 3 hour hybridisation. Scale bar = 5 µm.</p>
MiL-FISH: Multi-labelled oligonucleotides for fluorescence in situ hybridisation improve visualization of bacterial cells
<p>Sections of LR-White embedded <em>Olavius algarvensis </em>eggs. A) DAPI stained overview of egg after first cleavage, grid square = region in B, cle = cleavage. B) Gamma- (ii) and Delta- (i) proteobacteria hybridised with 4x labelled Gam42a & 4x labelled DSS658 probe respectively. Autofluorescence of egg yolk is overcome and bacteria are seen to closely associated with the developing embryo. y = egg yolk C) DAPI stained overview of juvenile worm in egg, grid square = region in D. D) Gamma 1 symbiont phylotype (iii) hybridised with 16S rRNA specific probe labelled with 2x FITC and 2x Cy3 to produce yellow in the overlay. Symbiont cells are incorporated between cuticle and epidermis and in close proximity to egg yolk. y = egg yolk, c = cuticle. Scale: A & C = 50 µm, B & D = 5 µm.</p>
MiL-FISH: Multi-labelled oligonucleotides for fluorescence in situ hybridisation improve visualization of bacterial cells
<p>Epifluorescence images of MiL-FISH labelled microorganisms: A) <em>Beggiatoa sp. </em>hybridised with Gam42a, B) <em>Desulfococcus biacutus </em>with DSS658, C) <em>Roseobacter sp. </em>with Ros537, D) <em>Sulfurimonas denitrificans </em>with EPSY914, E) <em>Rhodopirellula sp. </em>SH1 T with PLA46, F) <em>Gramella forsetii </em>with CF319a, G) <em>Metallosphaera sedula </em>with Arch915, H) Composite image of all seven microbial partners in an artificial mix. Letters correlate to images of individual organisms A-G. Scale bar: A & H = 10 µm, B-G = 5 µm.</p> <p>From:</p> <p>Schimak MP, Kleiner M, Wetzel S, Liebeke M, Dubilier N, Fuchs BM. 2015. MiL-FISH: Multi-labelled oligonucleotides for fluorescence in situ hybridisation improve visualization of bacterial cells. Applied and Environmental Microbiology. Accepted manuscript posted online. doi:10.1128/AEM.02776-15</p>
Simulated data for testing cell type adjustment methods
<p>***NOTE: An updated version of this dataset is available at https://zenodo.org/record/46746#.VtW7MmSAOko</p> <p>Different simulation scenarios on which to test cell type adjustment methods for epigenome-wide association studies. Each .RData file contains a matrix of methylation beta-values from a simulated blood cell mixture "sim_beta", a list of simulated differentially methylated positions "dmr", and a phenotype "disease_status".</p>
Updated simulated data for testing cell type adjustment methods
<p>Different simulation scenarios on which to test cell type adjustment methods for epigenome-wide association studies. Each .RData file contains a matrix of methylation beta-values from a simulated blood cell mixture "sim_beta", a list of simulated differentially methylated positions "dmr", and a phenotype "disease_status". Updated version with new simulation scenarios. Each of "simulated_data_many_assoc.tar.gz" and "simulated_data_few_assoc.tar.gz" contain 10 replications of those simulation scenarios. The other .RData files represent only one replication of each scenario.</p>
Dendritic cell subsets in oral mucosa of allergic and healthy subjects
<p><strong>Abstract</strong></p> <p>Immunohistochemistry was used to identify, enumerate, and describe the tissue distribution of Langerhans type (CD1a and CD207), myeloid (CD1c and CD141), and plasmacytoid (CD303 and CD304) dendritic cell subsets in oral mucosa of allergic and non-allergic individuals. Allergic individuals have more CD141+ myeloid cells in epithelium and more CD1a+ Langerhans cells in the lamina propria compared to healthy controls, but similar numbers for the other DC subtypes. Our data are the first to describe the presence of CD303+ plasmacytoid DCs in human oral mucosa and a dense intraepithelial network of CD141+ DCs. The number of Langerhans type DCs (CD1a and CD207) and myeloid DCs (CD1c), was higher in the oral mucosa than in the nasal mucosa of the same individual independent of the atopic status.</p>
Parallel reverse genetic screening in mutant human cells using transcriptomics - Data and analyses
<p>This dataset contains data files and analysis code associated with manuscript entitled "Parallel reverse genetic screening in mutant human cells using transcriptomics".</p> <p>Data files include expression profiles for over 1800 RNA-seq samples and annotations.</p> <p>Analysis files include R scripts to generate summary figures.</p>
Action potential dependent sIPSCs from 3-4 months old C57BL/6J X SJL female mice hippocampus CA1 pyramidal cell
<p>species : Mus musculus</p> <p>sex : female</p> <p>strain : C57BL/6J X SJL</p> <p>age : 3 - 4 months</p> <p>Voltage-clamp recordings of GABAA spontaneous inhibitory post-synaptic currents (sIPSCs) were obtained from 3-4 months old C57BL/6J X SJL female mice . The dataset contains 701 individual events recorded from 7 different neurons (expB1-B7).</p>
Panasonic NCR18650B formation, RPT and half cell data set
<p>This dataset is a complement to a publication in "Batteries":</p> <p>Durability and Reliability of EV Batteries Under Electric Utility Grid Operations.</p> <p>Part1: Cell-to-cell variations and preliminary testing </p> <p>The data consists on matlab files for each tested cell.</p>
Reproducible in-silico omics analyses - GSE37703: Differential analysis of HOXA1 in adult cells dataset
<p>GSE37703: Differential analysis of HOXA1 in adult cells at isoform resolution by RNA-Seq’ for quantification by Kallisto and differential abundance with Sleuth dataset used for the "Reproducible in-silico omics analyses across clouds and clusters" paper.</p>
Filtered and annotated SNV and indel variants in the PC3 and LNCaP human prostate cancer cell lines
<p>150bp paired-end reads (insert size 350bp) were obtained using the Illumina HiSeqX sequencer. Samtools v1.3.1 mpileup and bcftools were used to interrogate indexed BAM files, from whole-genome reads aligned to human reference genome GRCh38 build 82, and generate a VCF (Variant Call Format) file of single nucleotide variants (SNVs) and short indel variants. Variants private, or unique to a particular cell line, or shared by both were next identified. Variants (likely to be common germline variants) present in HapMap, 1000 genomes phase 3 (2,504 human genomes), and the National Heart Lung and Blood Institute’s Exome Sequencing Project (ESP) (bundled variant data file available at https://goo.gl/mEogvD) were excluded. Variant files (VCF) were filtered using SnpSift with the following parameters: 'QUAL \textgreater= 200 \&\& DP \textgreater= 30', where QUAL denotes minimum variance confidence and DP total depth threshold. Filtered variants were annotated using SnpEff v4.3g. Please see https://github.com/sciseim/PCaWGS for associated scripts.</p> <p> </p>
de novo genome assembly of the LNCaP human prostate cancer cell line
<p>Whole-genome sequencing reads from the LNCaP human prostate cancer cell line were used to generate a <em>de novo </em>assembly with SGA v0.10.15. Please see https://github.com/sciseim/PCaWGS for associated scripts. Library preparation was performed using a TruSeq Nano DNA kit (Illumina) with a target insert size of 350bp. Paired-end libraries (150bp) were sequenced using a HiSeqX sequencer (Illumina).</p>
de novo genome assembly of the PC3 human prostate cancer cell line
<p>Whole-genome sequencing reads from the PC3 human prostate cancer cell line were used to generate a <em>de novo </em>assembly with SGA v0.10.15. Please see https://github.com/sciseim/PCaWGS for associated scripts. Library preparation was performed using a TruSeq Nano DNA kit (Illumina) with a target insert size of 350bp. Paired-end libraries (150bp) were sequenced using a HiSeqX sequencer (Illumina).</p> <p> </p> <p> </p> <p> </p>
Sequence data for the article "Whole transcriptome analysis of thousands of FACS-sorted single cells with the single cell nanoCAGE protocol" - single cells dataset
<p>Sequence data (Illumina MiSeq runs) for the article "Whole transcriptome analysis of thousands of FACS-sorted single cells with the single cell nanoCAGE protocol". dataset of 2300 single cells. File names indicate unique sequencing runs. In the manuscripts, the informations about cell lines are found in the Supplemental Table 1. </p>
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