Cyanine3 (cy3)

A. baumannii ATCC17978 cells in the exponential phase of growth were treated for 30 min at 37°C with 64 μg/ml OA dissolved in ethanol. Microarray analysis was performed as previously described [30 (link)]. RNA was isolated using the RNeasy Mini kit (Qiagen), and RNA concentrations were estimated by measuring absorbance at 260 nm. The cDNA probes for microarray analysis were prepared by reverse transcription of total RNA (50 μg). The cDNA probes were cleaned up using a Microcon YM-30 column (Millipore) and then coupled to Cy3 or Cy5 (GE Healthcare). The dried Cy3- or Cy5-labeled cDNA probes were then resuspended in 55μl of 2x HI-RPM hybridization buffer (Agilent) containing 30% formamide (v/v), 5× saline-sodium citrate, 0.1% SDS (w/v), and 0.1 mg/ml salmon sperm DNA. The Cy3- or Cy5-labeled cDNA probes were mixed together and hybridized onto a microarray chip (MYcroarray.com). The hybridization images on the slides were scanned using an Axon 4000B (Axon Instruments), and data quantification was performed using GenePix Pro 6.0 (Axon Instrument). Genes that were upregulated more than 1.5-fold in at least two replicates were selected. The microarray data were deposited in the National Center for Biotechnology Information GEO site (under accession number GSE 60239). Microarray data were confirmed by quantitative reverse transcription PCR (RT-PCR).

Human Genome CGH Microarray 244A slides (Agilent Technologies, CA, USA) were used for FFPE extracted DNA samples. We followed the protocol described in [30 (link), 31 (link)]. A total of 2.5 μg sex matched control DNA (Promega, WI, USA) was fragmented by sonication. The FFPE DNA was fragmented only if there was any large molecular weight DNA. About 500 ng of the fragmented samples were then run on 1.5% agarose gel for 1 hour to check the extent of fragmentation of the DNA. Once fragmentation was deemed appropriate, 2 μg of the control DNA was labeled with Cy3 (Agilent technologies, CA, USA) and 2μg of FFPE DNA with Cy5 (Agilent technologies, CA, USA) for 30 minutes at 85°C. After labeling the DNA was purified using KREA pure columns (Agilent technologies, CA, USA). The samples were then measured on a Nanodrop and Degree of Labeling (DOL) was calculated according to the following formula;
$\mathrm{D}\mathrm{e}\mathrm{g}\mathrm{r}\mathrm{e}\mathrm{e}\mathrm{o}\mathrm{f}\mathrm{L}\mathrm{a}\mathrm{b}\mathrm{e}\mathrm{l}\mathrm{i}\mathrm{n}\mathrm{g}=\left(340\mathrm{x}\mathrm{p}\mathrm{m}\mathrm{o}\mathrm{l}/\mathrm{\mu }\mathrm{l}\mathrm{o}\mathrm{f}\mathrm{d}\mathrm{y}\mathrm{e}\right)/\left(\mathrm{n}\mathrm{g}/\mathrm{l}\mathrm{\mu }\mathrm{o}\mathrm{f}\mathrm{G}\mathrm{e}\mathrm{n}\mathrm{o}\mathrm{m}\mathrm{i}\mathrm{c}\mathrm{D}\mathrm{N}\mathrm{A}\mathrm{x}1000\right)$
The samples were hybridized onto microarray slides only if the DOL was between 1.5–2.5%.

RNA was extracted from parental HL60 and R- HL60 cells using TRIzol reagent (Thermo Fisher Scientific, Waltham, MA, USA) and submitted to Welgene Biotech (http://www.welgene.com.tw/, accessed on 1 November 2021) for array. Subsequently, 0.2 μg of total RNA was amplified using a Low Input Quick Amp Labeling Kit (Agilent Technologies, Santa Clara, CA, USA) and labeled with fluorescent Cy3 (Agilent Technologies) during the in vitro transcription process. Through incubation with fragmentation buffer at 60°C for 30 min, 0.6 μg of Cy3-labled cRNA was fragmented to an approximate average size of 50–100 nucleotides. Then, correspondingly fragmented and labeled cRNA was pooled and hybridized for use with a SurePrint Microarray (Agilent Technologies) at 65 °C for 17 h. The Cy3 microarray was scanned at 535 nm with a microarray scanner (Agilent Technologies) after purging with a nitrogen gun and drying. The scans were analyzed using Feature Extraction 10.7.3.1 (Agilent Technologies). The raw signal data were subjected to quantile normalization to identify differential gene expression. The DEGs were subjected to an enrichment test for functional assay, and cluster Profiler 3.14 was used for KEGG pathway analyses.

All pancreas samples were fixed in zinc (BD) for 4 h followed by an additional 2 h of fixation in 4% formaldehyde and then were cryoprotected in 30% sucrose overnight before freezing. Whole-mount staining was done as described^{28 (link)}. Tomato and CFDA-SE were detected by direct fluorescence. DAB (3,3′-diaminobenzidine) staining was performed with the ABC method. The primary antibody for immunostaining was guinea pig polyclonal insulin (Dako, Carpinteria, CA, USA). The secondary antibodies for indirect fluorescent staining were Cy2-, Cy3-, or Cy5-conjugated donkey streptavidin- and guinea pig-specific (Dako). Nuclear staining was performed with DAPI (4′,6-diamidino-2-phenylindole; Dako).