Journal: The FEBS journal

Article Title: A novel 2D-based approach to the discovery of candidate substrates for the metalloendopeptidase meprin.

doi: 10.1111/j.1742-4658.2008.06592.x

Figure Lengend Snippet: Fig. 1. Simple 2D IEF ⁄ SDS ⁄ PAGE-based image analysis procedure. The procedure is based on qualitative differences among reference gels (level 1 match-sets) of each group of five gel replicates (three pooled biological gel replicates and two more technical gel repli- cates). Gel replicates of each group (activated meprin versus non-activated meprin) were cut virtually into four equally spaced quadrants for four independent image analyses. Reference gels of each group were then clustered into a new set for higher-level image analysis. The spot matching features of PDQUEST (version 7.3.1) allowed for detection of unique protein spots. The combined higher- level match-set is the final fusion of all annotated unique spots into one big 2D reference map.

Article Snippet: 2D IEF ⁄ SDS ⁄PAGE-based image analysis was performed using the program pdquest, version 7.3.1 (Bio-Rad Laboratories).

Techniques:

Journal: The FEBS journal

Article Title: A novel 2D-based approach to the discovery of candidate substrates for the metalloendopeptidase meprin.

doi: 10.1111/j.1742-4658.2008.06592.x

Figure Lengend Snippet: Fig. 2. Application of a simple 2D IEF ⁄ SDS ⁄ PAGE-based protease proteomic approach in substrate finding. A representative image analysis of the first quadrant is shown. Two hundred and fifty micrograms of conditioned medium protein from trypsin activated and non-activated MDCKa ⁄ b cells was separated by IEF in a 24 cm long IPG pH 3–10 NL strip. Vertical separation was according to mass in a 12.5% SDS gel. Optimized Ruthenium staining: for each condition (activated meprin versus non-activated meprin), three pooled biological gel replicates (from 18 dishes per pooled sample) and two more technical gel replicates (of one pooled sample) were produced for subsequent image analysis. Unique protein spots are labelled in level 1 and higher-level match-sets with SSP assigned by the image analysis software.

Article Snippet: 2D IEF ⁄ SDS ⁄PAGE-based image analysis was performed using the program pdquest, version 7.3.1 (Bio-Rad Laboratories).

Techniques: Stripping Membranes, SDS-Gel, Staining, Produced, Software

Journal: bioRxiv

Article Title: Rapid multiplex small DNA sequencing on the MinION nanopore sequencing platform

doi: 10.1101/257196

Figure Lengend Snippet: Comparison of MinION library preparation workflows. 2D library is a previously reported workflow ( W ei and W illiams 2016 ); 1D multiplex library is manufacturer’s workflow using a native barcoding kit and a 1D genomic sequencing kit on the current MinION platform; Rapid 1D multiplex library is a new rapid barcoding MinION library preparation workflow reported in this study developed to sequence short reads (<1000 bp) on the current platform. The length of each bar indicates the time needed. The steps are color-coded (Yellow: fragmentation; Red: end preparation including end-repair and dA-tail; blue: size selection and purification; dark blue: MyOne C1 bead purification; purple: sequencing)

Article Snippet: Using Dynabeads TM MyOne TM Streptavidin C1 bead-based 2D library purification (Invitrogen, Cat. 65001), the library was eluted from the beads in ELB buffer at 37 °C for 10 min ( ) ( W ei and W illiams 2016 ).

Techniques: Comparison, Multiplex Assay, Genomic Sequencing, Sequencing, Size Selection, Purification