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45 results for “Electrophoresis”
Segmented Gel Electrophoresis Images used for Training GelGenie Models
<p>This repository contains gel images and corresponding hand-labelled segmentation maps (575 total) from various sources. The images have various sizes, shapes, gel contents and imaging conditions. In more detail:</p> <ul> <li>The matthew_gels (301 total), matthew_gels_2 (85 total) and nathan_gels (37 total) folders contain images originating from previous experiments in the Dunn Lab. </li> <li>The quantitation_ladder_gels (35 total) were generated specifically for the GelGenie project and contain gel ladders in each well. These were used to generate the data for Figure 1 in the main paper.</li> <li>The stella_gels_for_finetuning (26 total) folder contains gel images provided to us from Siyuan Stella Wang (Wyss Institute/Dana-Farber Cancer Institute) which we used to finetune our U-Net model and produce the results in Figure 4C of the main paper.</li> <li>The external_gels (25 total) images were gifted to us from 5 different researchers: Yichen Zhao (images generated at the University of Waterloo), Huangchen Cui (images generated at Tsinghua University), Thomas Mayer (images generated at the Technical University of Munich), Joana Reis (images generated at the Dana-Farber Cancer Institute) and Ricarda Törner (images generated at the Dana-Farber Cancer Institute). These were used as an external unseen test set for our fine-tuned model.</li> <li>The lsdb_gels (66 total) folder contains segmentation maps of images downloaded from the RGB Caps dataset, which is available from https://dbarchive.biosciencedbc.jp/en/rgp-caps/desc.html. The original images have been shared with a Creative Commons Attribution-Share Alike 2.1 Japan license. Permission was obtained from the data depositors for the training of our models on these images, as well as for the sharing of derived segmentation masks using the CC-BY license. To use this portion of the dataset, you will need to download the original images from the website, and place them alongside our segmentation masks, mirroring the same setup used for all the other datasets in this repository.</li> </ul> <p>The folders are organised as follows:</p> <ul> <li>The images, val_images and test_images contain the original images, split into training/validation/testing partitions respectively (except for the lsdb_gels dataset).</li> <li>The masks, val_masks and test_masks contain the corresponding segmentation maps for each image in the main folders (they have identical naming i.e. an image named test_image.tif will have a segmentation map labelled test_image.tif).</li> <li>The external_gels folder does not have validation or test partitions.</li> </ul> <p>The segmentation maps are 8-bit images, for which a white pixel (0) corresponds to a background pixel and a brown pixel (1) corresponds to a foreground pixel.</p> <p>This is the main dataset used to train the GelGenie models, for which the corresponding source code and GUI can be downloaded at https://github.com/mattaq31/GelGenie.</p>
Chemical probing of U2 snRNA - Capillary electrophoresis chromatograms
<p>1m7 chemical probing of the synthetic RNA consisting of the first 100 nucleotides of U2 snRNA along with a series of mutations in the Stem I region and data analysis was carried out essentially as described previously in "Kladwang W, VanLang CC, Cordero P, Das R (2011) A two-dimensional mutate-and-map strategy for non-coding RNA structure. Nat Chem 3: 954-962". </p> <p>Briefly synthetic U2 snRNA templates flanked by two stable stem-loops to use as probing standards and a 3′ tail for primer extensions were generated by PCR from overlapping oligonucleotides and used in T7 run-off transcription reactions. The transcribed RNA was separated on a 5% (v/v) denaturing polyacrylamide gel. Correlating bands identified by UV shadowing were excised, and the RNA was isolated from excised bands by soaking gel slices in 0.3 M sodium acetate pH 4.8, 1 mM EDTA, 10% phenol overnight followed by ethanol precipitation.</p> <p>For chemical probing, 0.6 pmol of RNA in 50mM Na-HEPES was heated to 95 ˚C for 3 minutes and allowed to fold at room temperature for 20 minutes followed by the addition of 10 mM magnesium chloride. The RNA was aliquoted into a 96-well plate with 5 mM 1m7 or water and incubated for 10 minutes at room temperature followed by the addition of oligo dT magnetic beads (Ambion) in 0.25 M Na-MES pH 6.0, 1.5 M NaCl, and 6.4 nM FAM-labeled primer. RNA/primers were isolated by magnetic bead immobilization, washed twice with 70% ethanol, and resuspended in 2.5 μL water.</p> <p>For reverse transcription, 20 units SuperScript III reverse transcriptase (Thermo Fisher Scientific), 5 mM dithiothreitol, 0.8 mM dNTPs, 50 mM Tris-HCl pH 8.3, 75 mM potassium chloride, and 3 mM magnesium chloride was added, and reactions were incubated for 30 minutes at 48˚C. Ladders were generated by the addition of ddNTPs to additional control reactions. Following reverse transcription, 0.2 M sodium hydroxide was added, and samples were incubated for 3 minutes at 90˚C to degrade the remaining RNA. Samples were neutralized by the addition of 1.4 M sodium chloride and 0.6 M hydrogen chloride, followed by 1.3 M sodium acetate pH 5.2. DNA was purified by magnetic bead immobilization, washed twice with 70% ethanol, and resuspended in Hi-Di formamide supplemented with R0X350 dye standards (1:8 ROXF) (Thermo Fisher Scientific). 1:3 and 1:15 dilutions of the samples in ROXF were analyzed by capillary electrophoresis (ELIM Biopharmaceuticals).</p>
Data from: Microrobots powered by concentration polarization electrophoresis
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Coupling gel electrophoresis with photoluminescence imaging reveals biochrome complexes in modern and fossil shells
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FIG. 3 in Taxonomic separation by isozyme electrophoresis of two closely related species of Cicada L. (Hemiptera: Cicadoidea) in Portugal
FIG. 3. CK banding patterns in Cicada orni and C. barbara. The enzyme phenotypes are identified across the bottom of the illustrations with the phenotypes of the Greek specimens of C. orni on the left, the Portuguese C. orni in the middle and the Portuguese C. barbara on the right.
FIG. 2 in Taxonomic separation by isozyme electrophoresis of two closely related species of Cicada L. (Hemiptera: Cicadoidea) in Portugal
FIG. 2. AAT banding patterns in Cicada orni and C. barbara. The enzyme phenotypes are identified across the bottom of the illustrations with the phenotypes of the Greek specimens of C. orni on the left, the Portuguese C. orni in the middle and the Portuguese C. barbara on the right.
FIG. 1 in Taxonomic separation by isozyme electrophoresis of two closely related species of Cicada L. (Hemiptera: Cicadoidea) in Portugal
FIG. 1. MDH banding patterns in Cicada orni and C. barbara. The enzyme phenotypes are identified across the bottom of the illustrations with the phenotypes of the Greek specimens of C. orni on the left, the Portuguese C. orni in the middle and the Portuguese C. barbara on the right.
Figure 2 in Species status of two colour morphs of Eupelmus vesicularis (Hymenoptera: Eupelmidae) as revealed by allozyme electrophoresis, morphometric and host preference data
Figure 2. Scaterplots of pairs of variables for Eupelmus vesicularis light colour and dark colour forms. Note: All measurements in mm.
Figure 4 in Species status of two colour morphs of Eupelmus vesicularis (Hymenoptera: Eupelmidae) as revealed by allozyme electrophoresis, morphometric and host preference data
Figure 4. Enzyme electromorphs of Eupelmus vesicularis light colour form (left) and dark colour form (right). Notes: The direction of current flow is indicated by +; the specimen loading point is shown by an arrow.
Figure 3 in Species status of two colour morphs of Eupelmus vesicularis (Hymenoptera: Eupelmidae) as revealed by allozyme electrophoresis, morphometric and host preference data
Figure 3. Plot of the first two factors from the principal component analysis of the log-transformed raw measurements.
Figure 1 in Species status of two colour morphs of Eupelmus vesicularis (Hymenoptera: Eupelmidae) as revealed by allozyme electrophoresis, morphometric and host preference data
Figure 1. Measurements of forewing rudiment and hind tibia for morphometric analysis of Eupelmus vesicularis (female). Notes: ti3L, hind tibia length; waL, forewing apical part length; wbL, forewing base length.
FIG. 4 in Allozyme electrophoresis demonstrates the presence of a species boundary in freshwater crabs (Decapoda: Potamonautidae)
FIG. 4. Allele frequencies at the LDH locus in the 25 populations of Potamonautes studied. Refer to Žgure 1 for collection localities.
FIG. 1 in Allozyme electrophoresis demonstrates the presence of a species boundary in freshwater crabs (Decapoda: Potamonautidae)
FIG. 1. Sampling localities of the 25 populations of Potamonautes studied. Potamonautes granularis (), P. perlatus () and P. sidneyi () were collected from the Western Cape (WC), Eastern Cape (EC), KwaZulu-Natal (KZN), Mpumalanga (MP) and the Northern Province (NP). Localities include: (1) Klawer, (2) Doring River, (3) Clanwilliam, (4) Paarl, (5) Tokai, (6) Liesbeek, (7) Bonnievale, (8) Tradouw Pass, (9) Tsitsikamma, (10) Smitskraal, (11) Hankey, (12) Belmont, (13) Umtata, (14) Pinetown, (15) University of Zululand, (16) Dakaneni, (17) Blood River, (18) Oliviershoek, (19) Mahai, (20) Cathedral Peak, (21) Wakkerstroom, (22) Vaal River, (23) Sterkspruit, (24) Mukhasa and (25) Tchiombedi.
FIG. 2 in Allozyme electrophoresis demonstrates the presence of a species boundary in freshwater crabs (Decapoda: Potamonautidae)
FIG. 2. UPGMA-dendrogram, reecting genetic similarity amongst the 25 Potamonautes populations studied, as calculated from Nei's (1978) unbiased genetic identities (I) obtained in pair-wise comparisons of populations.
FIG. 5 in Allozyme electrophoresis demonstrates the presence of a species boundary in freshwater crabs (Decapoda: Potamonautidae)
FIG. 5. Scatterplots of geographic distance (km) over Nei's (1978) unbiased genetic identity (I) for each pair-wise comparison of (a) the eight P. perlatus populations, and (b) the 13 P. sidneyi populations studied. Solid lines represent least-squares regressions and dotted lines represent 95% conŽdence limits.
Gel Electrophoresis
<p>This figure represent the SDS Gel Electrophoresis</p>
Protein Electrophoresis as a Tool for Complications Prediction in COVID-19 Hospitalised Patients
ClinicalTrials.gov study NCT04414059. IPD Sharing: Not stated. Countries: 1. Publications: 21.
Fig. 1. Gel electrophoresis stained with ethidium bromide showing 2 in First record of a spotted fever group Rickettsia sp. and Theileria annulata in Hyalomma dromedarii (Acari: Ixodidae) ticks in the United Arab Emirates
Fig. 1. Gel electrophoresis stained with ethidium bromide showing 2 DNA positive samples of Theileria annulata and spotted fever group (SFG) Rickettsia sp. amplified by PCR. Lane M: represents 100-bp DNA ladder (Promega, USA).
Fig. 4 in Analysis of Water-Soluble Proteins by Two-Dimensional Electrophoresis in the Encystment Process of Colpoda cucullus Nag-1 and Cytoskeletal Dynamics
Fig. 4. NIH image analyses of CBB-stained α-tubulin spots of gels (closed circles) separated by 2-D PAGE of water-insoluble fraction (So- game et al. 2014b), CBB-stained β-tubulin fragment spots of gels (p19 in Fig. 2, open circles) contained in water-soluble fraction, and total α-tubulin immunoblotting bands (open squares) (Fig. 3) of C. cucullus Nag-1. Ordinate indicates integrated optical density (IOD) reflecting relative protein amounts. Abscissa indicates the time lapse after onset of encystment induction.
Data from: Determination of sulfonamides in milk by capillary electrophoresis with PEG@MoS2 as a dispersive solid-phase extraction sorbent
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Allen Brain Atlas
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International Brain Laboratory public data
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OpenNeuro
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