Microarray expression analyses of control versus ROR single LKO (liver-specific knockout) and LDKO livers at ZT22 were performed on livers from n = 4 mice per genotype. Total RNA was extracted from liver tissue using Trizol reagent (Life Techologies) followed by RNeasy minikit (Qiagen). RNA from each liver was individually processed with the Ambio WT expression kit and GeneChIP WT terminal labeling and control kit (Affymetrix) and hybridized to the Mouse Gene 2.0 ST arrays (Affymetrix). Array images were captured on a GCS3000 laser scanner (Affymetrix) and analyzed by the Penn Microarray Core using the Partek genomics suite. Subsequent data analysis was performed using the oligo package in R-BioConductor (Huber et al. 2015 (link)). Differentially regulated genes in the knockout were selected using a threshold of expression fold change >1.3 and false discovery rate of 15%. Microarray data are available in Gene Expression Omnibus (GSE101116).
Genechip wt terminal labeling and control kit
Manufactured by Thermo Fisher Scientific
Sourced in United States
The GeneChip WT Terminal Labeling and Control Kit is a lab equipment product designed for the labeling and control of gene expression analysis samples. The kit provides the necessary reagents and components to perform terminal labeling of fragmented, single-stranded cDNA derived from total RNA.
Automatically generated - may contain errors
Lab products found in correlation
Rneasy mini kit, by Qiagen (2 mentions)
Human genechip primeview array, by Thermo Fisher Scientific (2 mentions)
3 ivt expression kit, by Thermo Fisher Scientific (2 mentions)
Genechip fluidics station 450, by Thermo Fisher Scientific (2 mentions)
Agilent 2100 bioanalyzer, by Agilent Technologies (2 mentions)
Mouse gene 2.0 st array, by Thermo Fisher Scientific (1 mentions)
Gcs3000 laser scanner, by Thermo Fisher Scientific (1 mentions)
Ambion wt expression kit, by Thermo Fisher Scientific (1 mentions)
Genespringgx 7, by Agilent Technologies (1 mentions)
Genechip human gene 1.0 st array, by Thermo Fisher Scientific (1 mentions)
Genechip scanner 7g, by Thermo Fisher Scientific (1 mentions)
Nanodrop 2000, by Agilent Technologies (1 mentions)
Expression console, by Thermo Fisher Scientific (1 mentions)
Human genome u133 plus 2.0 array, by Thermo Fisher Scientific (1 mentions)
5 protocols using genechip wt terminal labeling and control kit
1
Transcriptional Profiling of Liver ROR and LDKO
2
Microarray Analysis of UV-Induced Gene Expression
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The condition used in microarray experiment and the analysis methods have been already described by Ujfaludi et al.23 (link).
Briefly, the total RNA samples from control and UV treated Hker E6SFM cells were prepared with RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions. Each category included three independent experimental triplicates. The global expression pattern was analysed on GeneChip® Human Gene 1.0 ST arrays (Affymetrix). Ambion WT Expression Kit (Life Technologies) and GeneChip WT Terminal Labeling and Control Kit (Affymetrix) were used for amplifying and labelling 250 ng of total RNA samples according to the manufacturer’s protocol. Analyses were performed by using GeneSpring® GX7.3.1 (Agilent) software. Raw data (CEL files) were analysed by using the RMA algorithm. Data were normalized by using per-chip normalization (global scaling). Genes (probe sets) showed low expression rate (raw expression <100) were filtered first.
Briefly, the total RNA samples from control and UV treated Hker E6SFM cells were prepared with RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions. Each category included three independent experimental triplicates. The global expression pattern was analysed on GeneChip® Human Gene 1.0 ST arrays (Affymetrix). Ambion WT Expression Kit (Life Technologies) and GeneChip WT Terminal Labeling and Control Kit (Affymetrix) were used for amplifying and labelling 250 ng of total RNA samples according to the manufacturer’s protocol. Analyses were performed by using GeneSpring® GX7.3.1 (Agilent) software. Raw data (CEL files) were analysed by using the RMA algorithm. Data were normalized by using per-chip normalization (global scaling). Genes (probe sets) showed low expression rate (raw expression <100) were filtered first.
3
Transcriptome Analysis of Human Samples
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Affymetrix GeneChip Human Primeview array (Affymetrix, Santa Clara, CA, USA) was used to analyze global expression pattern of 28,869 well-annotated genes. 3'IVT Expression Kit (Affymetrix) and GeneChip WT Terminal Labeling and Control Kit (Affymetrix) were used for amplifying and labeling 250 ng of RNA samples. Samples were hybridized at 45°C for 16 h and then standard washing protocol was performed using GeneChip Fluidics Station 450 (Affymetrix) and the arrays were scanned on GeneChip Scanner 7G (Affymetrix) procedure. Data of this study have been deposited in NCBI's Gene Expression Omnibus and are accessible through GEO Series accession number GSE134480 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE134480 ).
4
Microarray Analysis of GIST Samples
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All samples were frozen in liquid nitrogen at −80°C. The total RNA of samples was extracted by TRIZOL method, and the total RNA was examined by NanoDrop 2000 and Agilent Bioanalyzer 2100. The qualified sample goes into the chip experiment. The standards of quality control are: Thermo NanoDrop 2000:1.7 < A260/A280 < 2.2; Agilent 2100 Bioanalyzer: RIN ≥ 7.0 and 28S/18S > 0.7. Affymetrix GeneChip Human Primeview array (Affymetrix, Santa Clara, CA, United States) was used to analyze global expression pattern of 28,869 well-annotated genes. RNA samples were amplified and labeled using the 3′IVT Expression Kit and GeneChip WT Terminal Labeling and Control Kit from Affymetrix. Affymetrix’s GeneChip Fluidics Station 450 was used to carry out the normal washing treatment after the samples were hybridized at 45°C for 16 h. The arrays were then scanned using the GeneChip Scanner 7G procedure. Quantile normalization of gene expression was performed using the normalizeBetweenArrays function in limma.
We also downloaded the following gene expression profiles from the GEO: GSE13861 (including six GIST and 19 surrounding normal fresh frozen tissues) (Cho et al., 2011 (link)) for further analysis.
We also downloaded the following gene expression profiles from the GEO: GSE13861 (including six GIST and 19 surrounding normal fresh frozen tissues) (Cho et al., 2011 (link)) for further analysis.
5
Microarray-based Transcriptome Analysis
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The cRNA was amplified, labeled using GeneChip ® WT Terminal Labeling and Control Kit (Affymetrix, Santa Clara, CA, USA), and hybridized to an Affinity Human Genome U133 Plus 2.0 array (for 47,000 transcriptional products) according to the manufacturer's instructions. All hybridized microarrays were scanned by an Affymetrix scanner. Relative hybridization intensities and background hybridization values were calculated using the Affymetrix Expression Console T M .
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