DNA was isolated from the CTCL cell lines using the QiaAmp DNA Blood Mini kit (Qiagen). Normal human reference DNA from multiple anonymous male donors was used as the reference DNA (Promega). Labeling and hybridization procedures were performed using the SureTag DNA Labelling kit, according to instructions (Agilent Technologies, USA). Equal quantities of fluorescently labeled DNA were mixed and co‐hybridized to a 44 K DNA microarray (G4426B‐014950, Agilent Technologies). After hybridization and washing, according to the manufacturer's protocol, scanning was performed on a G2505B Micro Array Scanner (Agilent Technologies). Feature extraction and data analysis were carried out using Feature Extraction (version 10.7.3.1) and Agilent Genomic Workbench version 7, respectively (Agilent Technologies). The ADM‐1 algorithm and a threshold of 6 were applied, and borders for aberrations were set to ±0.25 (log2 ratio) with a minimum number of three probes per region (default settings recommended by Agilent Technologies).
Suretag dna labelling kit
Manufactured by Agilent Technologies
Sourced in United States
The SureTag DNA Labelling Kit is a product offered by Agilent Technologies. It is designed for the labelling of DNA samples. The kit provides the necessary reagents and protocols to enable the efficient labelling of DNA for various downstream applications.
Automatically generated - may contain errors
Lab products found in correlation
Feature extraction version 10, by Agilent Technologies (1 mentions)
Agilent genomic workbench version 7, by Agilent Technologies (1 mentions)
Qiaamp dna blood mini kit, by Qiagen (1 mentions)
G2505b micro array scanner, by Agilent Technologies (1 mentions)
Reference dna, by Promega (1 mentions)
Mirneasy ffpe kit, by Qiagen (1 mentions)
Rneasy ffpe, by Qiagen (1 mentions)
Qiaamp dna mini kit, by Qiagen (1 mentions)
Turbo dnase, by Thermo Fisher Scientific (1 mentions)
Repli g cell wga wta kit, by Qiagen (1 mentions)
4 protocols using suretag dna labelling kit
1
DNA Microarray Analysis of CTCL Cell Lines
2
RNA Extraction and Labeling for Microarray
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2-4 whole fixed spheroids for each treatment were lifted from the 96 well LiMT plates. RNA from these samples was extracted using the Qiagen miRNeasy FFPE Kit according to the Qiagen RNeasy FFPE Handbook 09/2011. The RNA yield was quantified using a Nanodrop spectrophotometer and extracted RNA was treated with DNase to remove any trace of genomic DNA. 50 ng of RNA was used to generate amplified cDNA with the Sigma TransPlex Whole Transcriptome Amplification system.The cDNA was purified then quantified via Nanodrop spectroscopy. 1800 ng of cDNA generated in the transplex reaction was labelled using the Agilent SureTag DNA labelling Kit and the specific activity (pmol Cy3/ug cDNA) and concentration (ug/ml) of labelled cDNA were quantified by NanoDrop spectroscopy. A specific activity of 15–50 pmol Cy3/ug DNA was considered sufficient for hybridisation on Agilent arrays.
3
RNA Extraction and Labeling from Liver 3D Microtissues
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RNA was extracted from 2 to 4 fixed rat or human liver 3D microtissues from each treatment (2 replicates per treatment) using the Qiagen miRNeasy FFPE Kit and labelled using the Agilent SureTag DNA labelling Kit according to previously published methods [15 (link)].
4
Panvirus Microarray Screening of Tick RNA Viromes
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Twenty-five μl of extracted NA from 20 randomly selected tick pools were treated with 4 U TURBO™ DNase (ThermoFisher, Waltham, MA, USA) and enriched for RNA virus using an unpublished I. ricinus tickmodified version of the published protocol (Matranga et al., 2016) (link). Five μl of enriched RNA were used for random whole transcriptome amplification (WTA) using the Repli-g Cell WGA & WTA kit (Qiagen, Hilden, Germany) according to the manufactures instructions. Amplified cDNA was purified using the QiaAmp DNA mini kit (Qiagen, Hilden, Germany) and 1.5 μg of purified cDNA was labelled with Cy5 using the SureTag DNA labelling kit (Agilent, Santa Clara, CA, USA). The labelled DNA was pooled according to the sampling date and tick life-cycle stage and hybridized to a PanVirus microarray (SurePrint G3 Custom Gene Expression Microarray (4 x 180 K) (Agilent, Santa Clara, CA, USA)) containing 60-160 probes for each sequenced virus described in Gen-Bank (2016) . Microarray data was analysed using a simple Excel-based data analysis method as described previously (Erlandsson et al., 2011; (link)Rosenstierne et al., 2014) (link).
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