MDA-LM2 TARBP2 knockdown and control cells were treated with 10μg/mL α-amanitin (final concentration in the medium). After 9 hours, nuclear RNA was harvested from the cells using the Norgen Cytoplasmic and Nuclear RNA Purification Kit per the manufacturer’s protocol. This RNA was prepared for microarray using TargetAmp-Nano Labeling Kit for Illumina (Epicentre). Labeled RNA was purified using RNeasy Minelute Kit (Qiagen) and submitted for analysis to the Rockefeller University genomics core facility using Illumina HT-12 v4 Expression BeadChip microarrays. The Lumi package in R was used to transform and normalize signal intensities.
Ht 12 v4 expression beadchip microarrays
Manufactured by Illumina
The HT-12 v4 Expression BeadChip microarrays are a high-throughput gene expression profiling platform developed by Illumina. The BeadChip contains probes designed to measure the expression levels of over 47,000 transcripts and known splice variants across the human genome. This product is designed to provide comprehensive coverage of well-characterized genes, gene candidates, and splice variants.
Automatically generated - may contain errors
Lab products found in correlation
Nanodrop 2000, by Thermo Fisher Scientific (2 mentions)
Rneasy minelute kit, by Qiagen (1 mentions)
Targetamp nano labeling kit, by Illumina (1 mentions)
Cytoplasmic and nuclear rna purification kit, by Norgen Biotek (1 mentions)
Infinium methylationepic beadchip microarray, by Illumina (1 mentions)
Ingenuity pathway analysis (ipa), by Qiagen (1 mentions)
3 protocols using ht 12 v4 expression beadchip microarrays
1
Transcriptional Profiling of RNA-Binding Protein Knockdown
2
Umbilical Vein Endothelial Cell Profiling
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Forty deidentified primary human umbilical vein endothelial cell (HUVEC) lines were obtained from Promocell and were cultured until passage four. Each cell line was split in half, and one half was treated with 20ng/mL TNFa for 24 hours while the other half was left untreated. Cells were then pelleted, and DNA and RNA were isolated. Gene expression was measured with Illumina HT-12 V4 expression BeadChip microarrays by Eurofins Genomics, and DNA methylation was measured with Illumina Infinium MethylationEPIC BeadChip microarrays.
3
Comprehensive RNA Profiling from Frozen Tissue
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RNA was isolated from frozen tissue sections (10–30 mg) using AllPrep® DNA/RNA/miRNA kits (Qiagen, Valencia, CA) according to a modified manufacturer protocol using 1% β‐mercaptoethanol. After extraction, the total RNA concentration was determined via NanoDrop 2000 (Thermo Scientific, Waltham, MA). RNA quality was assessed using RNA integrity numbers obtained through using a RNA 6000 Nanokit for the 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA). A cutoff RNA integrity number of ≥7.0 was considered to be sufficient for evaluation of global gene expression using HT‐12 v4 Expression BeadChip microarrays (Illumina, San Diego, CA). Genes identified within enriched gene groups were analyzed for correlations with significant echocardiographic and histologic outcomes. Causal network analysis in Ingenuity Pathway Analysis (Qiagen, Valencia, CA)30 was used to identify potential upstream regulators for differentially expressed genes.
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