Journal: bioRxiv

Article Title: Matrix tropism influences endometriotic cell attachment patterns

doi: 10.1101/2025.02.22.639314

Figure Lengend Snippet: Methodology for preparing, seeding, and analyzing microarrays. a) 1 kPa and 6kPa PA solutions are prepared as described in 2.2. b) Slides are washed, etched, and silanized before prepolymer solution is deposited in the printing region of interest and cured and dehydrated. c) ECM combinations are diluted in printing buffer to a final concentration of 250 μg/mL and arrayed onto the slide(s) with a liquid handler. d) 200,000 cells per microarray were seeded in monoculture or coculture and incubated for 30 minutes. e) Microarrays were washed with PBS and then incubated for 24 hours at which point f) microarrays were fixed in 4% PFA and stained with phalloidin and DAPI with fluoromount. g) Fixed and mounted slides were imaged on the Zeiss AxioScan.Z1. h) Images were exported and cropped into identified islands using MATLAB. CellProfiler was used to identify fluorescent regions of the cell (nuclei, actin) and partition information including cell count, cell area, etc. i) The outputs of cell profiler are then analyzed in R Studio.

Article Snippet: After the washes, the PBS was removed from the slides, 100 μL of DAPI Fluoromount-G (SouthernBiotech, 0100-20) solution was added on top of the microarrays and sandwiched with a coverslip (Electron Microscopy Sciences, 63765-01), sealed with clear nail polish, and stored protected from light at 4°C until imaging.

Techniques: Concentration Assay, Microarray, Incubation, Staining, Cell Counting

Journal: Oncogene

Article Title: Reduced Arginyltransferase 1 is a driver and a potential prognostic indicator of prostate cancer metastasis

doi: 10.1038/s41388-018-0462-2

Figure Lengend Snippet: (A) Box and whisker graph showing mRNA level in Fragments per Kilobase of transcript per million mapped reads (FPKM) of Ate1 in primary tumors from patients with metastatic or non-metastatic status in comparison to normal prostate tissue. The data for mRNA were retrieved from the TCGA-PRAD dataset as well as the Beltran dataset . The mRNA levels were assessed by RNA sequencing in these databases. See for additional information on the normalization protocol. (B) Analysis of dataset of RNA level examined by microarray in excised primary prostate cancer tissue mRNA that had up to 5 years of patient follow-up after time of radical prostatectomy . Samples were separated into groups by patient outcome (metastatic or not) to determine the relationship between future metastatic outcome and the Ate1 mRNA levels in the primary tumors. (C) Quantification of Ate1 protein levels on human primary prostate tumor sites by immunohistochemistry, with DAPI staining for loading normalization with DNA. The analysis was performed on human prostate cancer arrays containing primary prostate tumors with either metastatic or non-metastatic outcome, as well as normal (non-diseased) prostate tissues. The samples were separately grouped by the patient outcome (metastatic or non-metastatic) for analysis. (D) Protein level of Ate1 in tissue samples from C were further stratified by Gleason Score and metastatic outcomes. See also for representative images. (E) A representative Western blot showing protein levels of Ate1 in multiple human prostate cancer cell lines, including androgen-dependent and indolent cell line LNCaP, its castration-resistant derivative LNCaP c4–2b cells, castration-resistant and intermediate aggressive cell lines DU145 and PC3, and the castration-resistant and highly aggressive PC3-ML, a derivative of PC3. Actin was used as a loading control. The graph shows the quantification from 3 independent repeats, showing a trend of reduced Ate1 correlating with cell line progression and aggressive phenotypes. Statistical significance was assessed with two-tailed Mann-Whitney U test for the human samples, and with the Student’s t-test for cell-based data. * = p<0.05, ** = p<0.01, *** = p<0.001. The monoclonal Ate1 antibody (clone 6F11, Millipore) used in this study has been shown to be highly specific for Western blot and IHC( , ). See also for additional data demonstrating the specificity of this antibody.

Article Snippet: Slides containing human prostate tissue sections (Biomax, Derwood, US) was stained with monoclonal rat anti-Ate1 (Clone 6F11; Millipore #MABS436) and DAPI.

Techniques: Whisker Assay, Comparison, RNA Sequencing, Microarray, Immunohistochemistry, Staining, Western Blot, Control, Two Tailed Test, MANN-WHITNEY

Journal: BMC Genomics

Article Title: The Zea mays mutants opaque-2 and opaque-7 disclose extensive changes in endosperm metabolism as revealed by protein, amino acid, and transcriptome-wide analyses

doi: 10.1186/1471-2164-12-41

Figure Lengend Snippet: Selected list of ESTs with significantly (P > 0.05) different mRNA levels.

Article Snippet: Microarray slides containing the entire Zeastar unigene set were hybridized with probes derived from endosperm tissue of normal, o2 , o7 , and o2o7 A69Y inbreds, harvested at 14 DAP, a developmental stage in which the synthesis of starch and storage protein is known to begin [ ].

Techniques: Starch, Binding Assay, Transduction

Journal: Cell

Article Title: FBXO44 promotes DNA replication-coupled repetitive element silencing in cancer cells

doi: 10.1016/j.cell.2020.11.042

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: After 3 × 10 min washes with KCMT buffer, cells were stained with DAPI (Thermo Fisher Scientific no. D1306), coverslips mounted with anti-fade mounting medium (Vector Laboratories no. H-1000), and slides examined by fluorescence microscopy (Nikon Inverted TE300) or confocal microscopy (Zeiss LSM 710 NLO).

Techniques: Marker, Microarray, Recombinant, Plasmid Preparation, Imaging, Staining, Immunoprecipitation, Cell Isolation, Software