The peptide chip was removed from the microfluidic device and scanned using Anon GenePix 4400A (Molecular devices) scanner using GenePix Pro 7 software. TIFF image files were further processed through Array-Pro Analyzer software and pixel density values were obtained as a text file (output data).
Genepix 4400a
Manufactured by Molecular Devices
Sourced in United States
The GenePix 4400A is a high-performance microarray scanner designed for rapid and accurate data acquisition. It features a dual-laser system for simultaneous scanning of Cy3 and Cy5 fluorescence channels, enabling efficient analysis of gene expression and other microarray-based applications.
Automatically generated - may contain errors
Lab products found in correlation
Genepix pro 7, by Molecular Devices (2 mentions)
Glutathione bead, by Cytiva (2 mentions)
Alexa488 conjugated anti gst antibody, by Thermo Fisher Scientific (1 mentions)
1 step human coupled ivt kit, by Thermo Fisher Scientific (1 mentions)
Matlab, by MathWorks (1 mentions)
Mirvana mirna isolation kit, by Thermo Fisher Scientific (1 mentions)
Cy3 and cy5 dyes, by GE Healthcare (1 mentions)
Amino allyl messageamp 2 arna amplification kit, by Thermo Fisher Scientific (1 mentions)
Nimblescan 2, by Roche (1 mentions)
3d gene human oligo chip 25k, by Toray (1 mentions)
Quantibody human cytokine array q1000, by RayBiotech (1 mentions)
14 protocols using genepix 4400a
1
Peptide Chip Scanning and Analysis
2
Characterizing hSAMD1 Transcription Factor Binding
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Sequences of two distinct hSAMD1-WH regions [amino acids 1 to 110 (WH1) and 28 to 110 (WH2)] were cloned into the pT7CFE1-NHis-GST-CHA plasmid (Thermo Fisher Scientific, 88871). GST-fusion proteins were expressed using the 1-Step Human Coupled IVT Kit (Thermo Fisher Scientific). Expressed protein concentrations were estimated from anti-GST Western blots. Subsequently, custom-designed “all-10mer” universal oligonucleotide arrays in 8 × 60 K GSE array format (Agilent Technologies, AMADID 030236) were double-stranded, and PBM experiments were performed essentially as described previously (16 (link)) with Alexa 488–conjugated anti-GST antibody (Invitrogen, A-11131). Each of the two WH domain constructs (hSAMD1-WH1 and hSAMD1-WH2) was assayed in duplicate at a final concentration of 600 nM in PBS-based binding and wash buffers on fresh slides. Scans were acquired using a GenePix 4400A (Molecular Devices) microarray scanner. Microarray data quantification, normalization, and motif derivation were performed essentially as described previously using the Universal PBM Analysis Suite and the Seed-and-Wobble motif-derivation algorithm (16 (link)).
3
Microarray Data Analysis Protocol
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Hybridization was carried out according the instructions supplies with the CodeLink Controls and Buffer Kit (Applied Microarrays, Inc.). For each experimental sample, 10 μg of biotin-labeled material was the nominal amount of material used on the CodeLink Bioarrays. The arrays and labeled material were incubated together at a constant temperature of 37°C overnight. GenePix 4400A (Molecular Devices, Inc.) was used to scan each labeled array. CodeLink Expression Analysis v5.0 (Applied Microarrays, Inc.) software was used for the data analysis. Net intensity was calculated by withdrawing surrounding background of the spot from row intensity. Normalization is performed by adjusting the median of all the read microarray data with a fixed value. Microarray Data Analysis Tool version 3.2 (Filgen, Inc.) was used as described in the manufacturer's instruction for all subsequent data analysis. This software uses pathway information and data from either GenMAPP (http://www.genmapp.org/ ) or WikiPathways. We used data from the WikiPathways database because it is an open, collaborative platform dedicated to curating biological pathways (http://www.wikipathways.org/index.php/WikiPathways ).
4
Serological Analysis of DENV Antibody Responses
5
Endothelial Cell Transcriptome Analysis of GO-Y078 Treatment
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Human umbilical vein endothelial cells were treated with 0.5 μmol/L GO‐Y078 for 72 hours or 0.04% of DMSO as a control. Samples were prepared in triplicate for each condition. Total RNA was extracted using the mirVana miRNA Isolation Kit (Life Technologies, Carlsbad, CA, USA). After qualification, equal amounts from each set were mixed and labeled as GO‐Y078‐treated and control groups. The analysis was conducted by Filgen Inc. (Nagoya, Japan). Transcripts from both groups were analyzed using CodeLink Human Whole Genome Bioarray (Applied Microarrays, Inc., Tempe, AZ, USA) composed of 57 000 transcripts, including 45 000 known genes. The data were scanned using GenePix 4400A (Molecular Devices Inc., Sunnyvale, CA, USA) and analyzed using CodeLink Expression Analysis v 5.0 (Applied Microarrays, Inc.) after quantile normalization. The microarray data analysis tool (version 3.2; Filgen Inc.) was used for data analysis.
6
Whole-Genome CGH of Germline DNA
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Whole-genome array comparative genomic hybridization (CGH) was performed as per the manufacturer’s instructions on 24 germline DNA samples from the CMN cohort, using Roche Nimblegen 135K oligonucleotide arrays and sex-matched commercial pooled controls. 1–3 μg of patient DNA and control DNA (Megapool reference DNA, male: EA-100M, female: EA-100F, Kreatech, The Netherlands) was labeled using NimbleGen Dual-Color DNA Labeling Kit and hybridized to the oligonucleotide array using the NimbleGen Hybridization System. Two-color array scanning was performed using a Molecular Devices GenePix 4400A (Molecular Devices, Sunnyvale, CA, USA) at a resolution of 2.5 microns. Data were extracted using Deva software (NimbleGen), and analyzed using InfoQuant CGHFusion (version 5.7.0–6.1.0) or later Chromosome Analysis Suite 4.0 (ChAS 4.0, Thermo Fisher Scientific). Abnormal copy number was called as per diagnostic facility criteria: at least 3 consecutive probe points above or below the zero line, with an average ratio of difference in fluorescence at least +/−0.4 in those points, and excluding areas where copy-number variants had already been reported.
7
Microarray Analysis of Transcriptome
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The total RNA samples (2μg) were reverse transcribed to cDNA, which was further transcribed into amino allyl-modified aRNA using the Amino Allyl MessageAmp II aRNA Amplification Kit (Life Technologies). The resulting aRNA was labeled with Cy3 and Cy5 dyes (GE Healthcare), then the labeled samples were loaded onto a 3D-Gene Mouse Oligo chip 24k ver.1.1 (TORAY, Tokyo, Japan), and then incubated for 16 h at 37 °C. The signal intensity data were quantified from hybridization images using a GenePix 4400a (Molecular Devices, Sunnyvale, CA, USA) and analyzed using GenePix Pro7 software (Molecular Devices). Any genes displaying signal intensities less than or equal to 10 both Cy5 and Cy3 were omitted from the data list. The resulting values were normalized using the global median normalization. Furthermore, the genes showing signal intensities less than or equal to 100 were omitted in order to define the credibility of the dataset. Finally, the Cy5/Cy3 ratio was calculated for all available genes. Whole analyses were carried out using the Excel (Microsoft, Redmond, WA, USA) and Avadis software programs (Strand Life Sciences, Bangalore, India).
8
Peptide Chip Scanning and Analysis
9
Protein binding microarray for PHF1 and MTF2
10
Protein binding microarray for PHF1 and MTF2
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GST-fusion proteins for human PHF1 (165-360) and MTF2 (180-369) were expressed in BL21 (DE3) cells and affinity purified using Glutathione beads (Amersham). Subsequently, custom-designed “all-10mer” universal oligonucleotide arrays in 8 x 60K GSE array format (Agilent Technologies; AMADID #030236) were double-stranded and duplicate protein binding microarray experiments were performed essentially as described23 (link),28 (link). MTF2 was assayed at a final concentration of either 500 nM or 900 nM, while PHF1 was assayed at a final concentration of 900 nM, in binding reactions containing 50 μM zinc acetate, on either a fresh slide or a slide that had been stripped exactly once. Scans were acquired using a GenePix 4400A (Molecular Devices) microarray scanner. Microarray data quantification, normalization, and motif derivation were performed essentially as described previously using the Universal PBM Analysis Suite and the Seed-and-Wobble motif-derivation algorithm23 (link),28 (link).
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