Gene expression of C2C12 cells was profiled using MouseRef-8-v2-BeadChip (Illumina). The array was scanned using a BeadStation 500 System (Illumina).
Beadstation 500 system
Manufactured by Illumina
Sourced in United States
The BeadStation 500 System is a laboratory instrument designed for high-throughput genetic analysis. It is a versatile platform that supports a range of Illumina's microarray-based products, including genotyping and gene expression arrays. The system automates the process of hybridizing samples to BeadChips, washing, staining, and imaging, providing consistent and reliable results.
Automatically generated - may contain errors
Lab products found in correlation
Mouseref 8v2 beadchip, by Illumina (2 mentions)
Rneasy mini kit, by Qiagen (2 mentions)
Humanht 12 v4 beadchip, by Illumina (1 mentions)
Genomestudio data analysis software s gene expression module gsgx version 1, by Illumina (1 mentions)
Streptavidin cy3, by Cytiva (1 mentions)
2100 bioanalyzer, by Agilent Technologies (1 mentions)
Mousewg 6 v2.0 expression beadchip, by Illumina (1 mentions)
Rneasy micro kit, by Qiagen (1 mentions)
Dnase, by Qiagen (1 mentions)
Totalprep rna amplification kit, by Thermo Fisher Scientific (1 mentions)
Agilent 2100 bioanalyzer, by Agilent Technologies (1 mentions)
Rneasy kit, by Qiagen (1 mentions)
6 protocols using beadstation 500 system
1
Profiling C2C12 Cell Gene Expression
2
Illumina-Based Gene Expression Profiling in MDA-MB-231 Cells
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For gene expression profiling in MDA-MB-231 cell lines, we used the Illumina HumanHT-12-v4-BeadChip (Illumina). Total RNA isolated from the cell lines with control siRNA or PIN1 siRNA or treated with DMSO or KPT-6566 for 48 h were reverse transcribed and amplified, according to standard protocols and in vitro transcription was then carried out to generate cRNA. cRNA was hybridized onto each array (three biological replicates for the KPT-6566 condition and two for PIN1 siRNA condition) and then labelled with Cy3-streptavidin (Amersham Biosciences). The array was then scanned using a BeadStation 500 system (Illumina). The probe intensities were calculated and normalized using GenomeStudio Data Analysis Software's Gene Expression Module (GSGX) Version 1.9 (Illumina). Further data processing was performed in the R computing environment version 3.2 (http://www.r-project.org/ ), with BioConductor packages (http://www.bioconductor.org/ ).
3
Transcriptomic Profiling of Spermatogonial Stem Cells
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Total RNA was isolated from SSCs, iSSCs and mSSCs using an RNeasy mini kit (Qiagen, Valencia, CA, USA), and RNA integrity was assessed using a Bioanalyzer 2100 instrument (Agilent, Santa Clara, CA, USA). The RNA integrity numbers (RINs) were higher than 8 for all samples. Biological replicates were obtained from independently cultured SSCs (n=3), mSSCs (n=3) and iSSCs (n=2). For all replicates, the total RNA was reversed-transcribed into cDNA, amplified and then hybridized onto an Illumina MouseRef-8-v2-BeadChip gene expression array, according to the standard protocols of the manufacturer. The array was then scanned using the BeadStation 500 System (Illumina, San Diego, CA, USA) to quantify the signal of the probes. We normalized the log2 intensities of all probes using the quantile normalization method.14 (link) The raw data were deposited into the gene expression omnibus (GEO) database (Accession ID: GSE86072).
4
Retinal RNA Extraction and Microarray
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Retinal total RNA (naïve control n = 4; Zymosan, PBS, MSC injected n = 5) was extracted using the RNeasy micro kit (Qiagen, Manchester, U.K., https://www.qiagen.com ) according to manufacturer's instructions. Genomic DNA was removed by DNase (Qiagen, Manchester, U.K., https://www.qiagen.com ) treatment. RNA samples were amplified using the TotalPrep Amplification Kit (Applied Biosystems, Leicestershire, U.K., https://www.lifetechnologies.com ). Biotin‐labeled cRNA (1.5 µg) was hybridized on the Illumina mouse WG‐6 v2.0 Expression Beadchip at 55°C for 18 hours. Hybridized BeadChips were then labeled with streptavidin‐Cy3 and scanned with the Illumina BeadStation 500 system. Microarray data were quantile normalized and log 2 transformed prior to analysis.
5
Illumina-Based Transcriptome Profiling Protocol
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Total RNAs were amplified and purified using the Ambion Illumina RNA amplification kit (Ambion, USA) to yield biotinylated cRNA according to the manufacturer’s instruction. Briefly, 550 ng of total RNAs was reverse-transcribed using an oligo (dT) primer and second-strand cRNA were synthesized and labeled with biotin-dNTP. After purification, cRNA were quantified using the ND-1000 Spectrophotometer (NanoDrop, USA). The 750 ng of labeled cRNA samples was hybridized to the Illumina MouseRef-8-v2-BeadChip overnight at 58°C according to the manufacturer’s instruction (Illumina, Inc., USA). The array was scanned using the BeadStation 500 System (Illumina, USA) to acquire the signal of the probes. The data were normalized as log2 intensity values for each dataset using a quantile normalization method (Bolstad et al., 2003 (link)).
6
RNA Extraction and Illumina Microarray Analysis
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Total RNA was prepared from 99 clinical tumor tissues using the RNeasy Mini kit (Qiagen, UK) according to the manufacturer’s protocol. Briefly, clinical samples were lysed with a reagent in a microcentrifuge tube, and 70% ethanol was added to the lysate. After vortexing for 10 s, the lysate was transferred to a RNeasy spin column and centrifuged at 8,000 x g for 15 s. The spin columns were then washed with RW1 and RPE buffer. Total RNA was eluted in 50 μL RNase-free water and stored at -80°C until use. The concentrations of total RNA were determined using a NanoDrop spectrophotometer (ND-1000; Thermo Scientific, USA) and RNA integrity number (RIN) values were assessed using Agilent 2100 bioanalyzer (Agilent Technologies, Inc. USA).
For Illumina microarray analysis, 1.5 μg of total RNA was amplified and labeled with biotinylated nucleotides using Illumina Total Prep RNA amplification kit (Ambion, USA) according to previous studies (Kwon et al., 2017 (link)). Samples were purified using the RNeasy kit (Qiagen, UK). Hybridization, washing and scanning with Sentrix HumanHT-12 v4 Expression Bead Chip (Illumina, USA) were performed according to the Illumina BeadStation 500× System Manual.
For Illumina microarray analysis, 1.5 μg of total RNA was amplified and labeled with biotinylated nucleotides using Illumina Total Prep RNA amplification kit (Ambion, USA) according to previous studies (Kwon et al., 2017 (link)). Samples were purified using the RNeasy kit (Qiagen, UK). Hybridization, washing and scanning with Sentrix HumanHT-12 v4 Expression Bead Chip (Illumina, USA) were performed according to the Illumina BeadStation 500× System Manual.
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