Journal: bioRxiv

Article Title: Deep learning enables fast and dense single-molecule localization with high accuracy

doi: 10.1101/2020.10.26.355164

Figure Lengend Snippet: a) DECODE can reduce acquisition times by one order of magnitude. The same sample of microtubules, labeled with anti- α tubulin primary and AF647 secondary antibodies, imaged with different UV activation intensities to result in different emitter densities between 0.08 and 0.86 emitters per frame per μm 2 and acquisition times between 93 and 1120 s, while keeping the total number of localizations the same. For high-density activation, we show a comparison with CSpline. b) Fourier Ring Correlation curves for DECODE and CSpline for different emitter densities. c) Resolution estimates obtained using the Fourier Ring Correlation and 0.143 criterion across densities for both methods. d) Fast live-cell SMLM on the nuclear pore complex protein Nup96-mMaple acquired in 3 seconds. e) DECODE enables ultra-high labeling densities. Microtubules labeled with a high concentration of anti- α and anti- β tubulin primary and AF647 secondary antibodies. e1, e2) Magnified regions as indicated in a. Data acquired with high-density labeling shows continuous structures. As a comparison, the same sample was acquired after pre-bleaching of the fluorophores to reach the single-molecule blinking regime. Here, single labels are resolved in the superresolution reconstruction and lead to a sparse decoration of the microtubules. e3, e4) Side view reconstructions of regions as indicated in e1, e2 resolving the hollow, cylinder-like structure of immunolabeled microtubules. f) Representative raw camera frames for the high-density and single-emitter acquisitions, respectively. Scale bars: 10 μm (d inset, f), 1 μm (a, d, e, e1, e2), 100 nm (e3,e4).

Article Snippet: For imaging of live cells, coverslips containing Nup96-mMaple cells (catalog no. 300461, CLS Cell Line Service, Eppelheim, Germany) were rinsed twice with warm PBS before they were mounted onto a custom manufactured sample holder in 1 mL growth medium containing 20 mM HEPES buffer and imaged directly.

Techniques: Labeling, Activation Assay, Concentration Assay, Immunolabeling

Journal: British Journal of Cancer

Article Title: Combined proteome and transcriptome analyses for the discovery of urinary biomarkers for urothelial carcinoma

doi: 10.1038/bjc.2013.157

Figure Lengend Snippet: Classification of the proteins identified in the conditioned medium of UCB cell lines. The proteins identified in the conditioned media and in the corresponding cells were divided into categories using the GO Cellular Components function in STRING 9.0 ( www.string-db.org ). The number of proteins in each analysis was: 5637=622/546, EJ28=649/717, HB-CLS-2=822/462 (cell pellet/secretome).

Article Snippet: 5637 and HB-CLS-2 cells were purchased from CLS Cell Lines Service GmbH (Eppelheim, Germany) and EJ28 cells were a kind gift from Elizabeth Hodgkins, University of Birmingham.

Techniques: