Journal: Nature Communications

Article Title: Cyclic microchip assay for measurement of hundreds of functional proteins in single neurons

doi: 10.1038/s41467-022-31336-x

Figure Lengend Snippet: a Schematic illustration of the CycMIST process to analyze multiple proteins through the MIST microbeads array. b Distribution of the number of oligo DNA-coated microbeads on each 75 μm × 75 μm area of a MIST array that is corresponding to a PDMS microwell, n = 3 independent MIST array. c Distribution of the number of same kind oligo DNA-coated microbeads on the same MIST array, n = 5 independent MIST array. d Characterization of the CycMIST sensitivity by varying the concentrations of 50 biotinylated complementary oligo DNAs on the MIST array, n = 10 independent experiments. This is the same procedure in single-cell protein detection experiments except cell loading and conjugate binding. e Consistency of fluorescence intensities for 4 decoding cycles and for 3 fluorescent color dyes (Alexa Fluor 488, Cy3 and Cy5), n = 5 independent experiments. f Sample images of multiplexed assay of 50 proteins from a single cell by CycMIST and the 4 decoding cycles images. The greyscale images are protein detection result, and the color images are the decoding cycles from cycle 1 to cycle 4. The bottom panel is the zoom-in images from the squares in the up panel. Scale bar: 20 μm (up panel); 5 μm (bottom panel). Data are presented as mean values ± SD of more than three independent experiments, and error bars are within symbol size if not shown. The term (arb. units) is abbreviated for arbitrary units.

Article Snippet: Custom designed oligo DNAs were purchased from Integrated DNA Technologies and used as received.

Techniques: Binding Assay, Fluorescence

Journal: PLoS ONE

Article Title: Design, Validation and Annotation of Transcriptome-Wide Oligonucleotide Probes for the Oligochaete Annelid Eisenia fetida

doi: 10.1371/journal.pone.0014266

Figure Lengend Snippet: Design of four 244K-oligo probe test arrays using Agilent's eArray.

Article Snippet: One pooled E. fetida RNA sample representing multiple developmental stages (cocoon, juvenile and adult) along with ten spike-in RNAs of known concentrations was hybridized to each of eight custom-designed 244K oligo arrays (two arrays per design) fabricated by Agilent.

Techniques: Expressing

Journal: BMC Genomics

Article Title: Global transcriptional response of Caulobacter crescentus to iron availability

doi: 10.1186/1471-2164-14-549

Figure Lengend Snippet: Overview of iron-responsive and Fur-regulated genes in C. crescentus identified by microarray analyses. The Venn diagrams were constructed using the number of up- and down-regulated genes from experiments comparing wild type cells exposed to iron-limiting versus iron-replete conditions or comparing fur mutant strain versus wild type strain both in iron-replete condition. The complete set of the genes belonging to each group is listed in Tables , , , and Additional file : Table S1. The upstream region of these genes (−200 to +50 bp relative to the start codon) were searched for sequence motifs using the MEME tool. A 19-pb palindromic motif, corresponding to the Fur binding site, was exclusively found in the group of genes regulated by both iron and Fur.

Article Snippet: Labeled cDNA samples were hybridized to a custom-designed DNA oligo microarray (Agilent) (each gene is covered by 9–11 probes located −300 to +200 relative to the translational start site) using a protocol previously described [ , ].

Techniques: Microarray, Construct, Mutagenesis, Sequencing, Binding Assay

Journal: PLoS ONE

Article Title: Expression Profiling of Major Histocompatibility and Natural Killer Complex Genes Reveals Candidates for Controlling Risk of Graft versus Host Disease

doi: 10.1371/journal.pone.0016582

Figure Lengend Snippet: The 20 most strongly regulated non-MHC/non-NKC genes in allogeneic skin explants compared to syngeneic controls as revealed by the microarray experiment.

Article Snippet: For the expression profiling, a custom-designed oligo DNA microarray (Agilent) was used.

Techniques: Microarray, Sequencing, Derivative Assay

Journal: PLoS ONE

Article Title: Expression Profiling of Major Histocompatibility and Natural Killer Complex Genes Reveals Candidates for Controlling Risk of Graft versus Host Disease

doi: 10.1371/journal.pone.0016582

Figure Lengend Snippet: A subgroup of 8 samples used for the microarray experiment (see Fig. 1 ) was analyzed by qRT-PCR for the expression of 10 MHC and 3 NKC genes. The ΔΔct value was calculated, i.e. the Δct ( Gapdh – gene of interest) of the allogeneic skin explant samples minus Δct ( Gapdh – gene of interest) of the corresponding control sample. The control sample was either a parallel skin explant exposed to syngeneic lymphocytes as in the microarray experiment (syngeneic control, black bars) or a parallel skin explant sample cultured in medium only (medium control, white bars). The means of the ΔΔct values plus standard errors of the mean (SEM) are shown. A positive value indicates an up-regulation of gene expression in the allogeneic samples.

Article Snippet: For the expression profiling, a custom-designed oligo DNA microarray (Agilent) was used.

Techniques: Microarray, Quantitative RT-PCR, Expressing, Cell Culture