A total of 6 Toray 3D-Gene Mouse Oligo chip 24 K (Toray Industries, Inc., Tokyo, Japan) microarrays were analyzed per treatment. Each chip utilized a 0.5 μg portion of combined total RNA from a matched pair of male and female samples. RNA was amplified and labeled using an Amino Allyl MessageAmp II aRNA Amplification kit (Life Technologies Japan Ltd.) according to the manufacturer's instructions. Each sample of aRNA was labeled with fluorescence Cy3 or Cy5 and cohybridized at 37°C for 16 hours. These were subsequently washed and dried. Hybridization signals were scanned using Scan Array Express (Perkin Elmer, MA, USA) and global background analysis was performed using GenePx Pro (MDS Analytical Technologies, CA, USA). All 36 arrays were then normalized together as one experiment to reduce nonbiological variability.
3d gene mouse oligo chip 24k
Manufactured by Toray
Sourced in Japan
The 3D-Gene Mouse Oligo chip 24k is a microarray platform designed for gene expression analysis in mice. It contains 24,000 probes that target mouse genes, allowing for comprehensive assessment of the mouse transcriptome.
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Lab products found in correlation
Amino allyl messageamp 2 arna amplification kit, by Thermo Fisher Scientific (7 mentions)
3d gene scanner, by Toray (7 mentions)
3d gene extraction software, by Toray (3 mentions)
Scanarray express, by PerkinElmer (2 mentions)
Rneasy mini kit, by Qiagen (2 mentions)
3d gene extraction, by Toray (2 mentions)
Image lab, by Bio-Rad (1 mentions)
Cell recovery solution, by Corning (1 mentions)
Tissuelyser 2, by Qiagen (1 mentions)
Qiazol lysis reagent, by Qiagen (1 mentions)
Mirneasy mini kit, by Qiagen (1 mentions)
Genespring gx 10, by Agilent Technologies (1 mentions)
Rneasy micro kit, by Qiagen (1 mentions)
Silica based spin column, by Toray (1 mentions)
Cyanine5, by GE Healthcare (1 mentions)
Agilent 2100 bioanalyzer, by Agilent Technologies (1 mentions)
Scan array lite scanner, by PerkinElmer (1 mentions)
Sepasol rna 1 super g, by Nacalai Tesque (1 mentions)
16 protocols using 3d gene mouse oligo chip 24k
1
Mouse Oligo Chip Microarray Analysis
2
Transcriptional Analysis of Key Regulatory Genes in Fetal Brain
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Total mRNA extracted from 12 fetal brains from each treatment group were utilized. A total of 6 Toray 3D-Gene Mouse Oligo chip 24 K (Toray Industries, Inc., Tokyo, Japan) microarrays were analyzed per treatment. Each chip utilized a 0.5 µg portion of combined total RNA from a matched pair of male and female samples. RNA was amplified and labeled using an Amino Allyl MessageAmp II RNA Amplification kit (Life Technologies Japan Ltd.) according to the manufacturer’s instructions. Each sample of RNA was labeled with fluorescence Cy3 or Cy5 and cohybridized at 37°C for 16 hours. These were subsequently washed and dried. Hybridization signals were scanned using Scan Array Express (Perkin Elmer, MA, USA) and global background analysis was performed using GenePx Pro (MDS Analytical Technologies, CA, USA). All 36 arrays were then normalized together as one experiment to reduce nonbiological variability. Mapk, Atf2, P53 and Hif-1α gene expression were analyzed. Housekeeping gene Hprt was used as a standard control.
3
Liver Transcriptome Profiling using Oligo-DNA Microarray
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For the Oligo-DNA microarray analysis between livers from LE2KO and controls fed HFHSD, the “3D-Gene” Mouse Oligo chip 24k (Toray Industries Inc., Tokyo, Japan), which contains 23,522 distinct genes, was used. Total RNA was labeled with Cy3 or Cy5 using the Amino Allyl Message AMP II aRNA Amplification Kit (Applied Biosystems). The Cy3- or Cy5-labeled aRNA samples were pooled in a hybridization buffer, and hybridized for 16 h. The hybridization was performed using the supplied protocols (www.3d-gene.com (accessed on 28 July 2022)). Pathway analysis was performed by Toray (Japan).
4
Microarray Analysis of Tamoxifen's Effects
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One month after treatment with Tam or the vehicle (corn oil), soleus muscles from each group of PC-deletion mice were dissected, frozen in liquid nitrogen, and stored at − 80 °C. The mRNA of these samples was subjected to microarray analysis using the 3D Gene Mouse Oligo Chip 24 K (Toray Industries Inc., Tokyo, Japan), as described previously [15 (link)]. The signal corresponding to each gene was normalized using the global normalization method (Cy3/Cy5 ratio median = 1). Intensity values greater than two standard deviations above the background signal were considered valid. GO enrichment analysis was conducted using the metascape.org website.
5
Microarray Analysis of Colon Organoids
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Total RNA extraction was carried out using the RNeasy Mini Kit (Qiagen). For microarray analysis, RNA samples from distal colon organoids before (n = 1) and after (n = 1) treatment with LY411575 (1 μM) were outsourced to Kamakura Techno-Science Inc. Synthesis, amplification and Cy5-labeling of probes and their hybridization on 3D-Gene Mouse Oligo chip 24k (Toray Industries) were performed according to the supplier’s protocol (www.3d-gene.com). Data were acquired on 3D-gene Scanner (Toray Industries Inc.) and normalized by using global normalization method (the median of the detected signal intensity was adjusted to 25). Genes that showed >2.5-fold differences in expression values between two samples are presented (Supplementary Tables S1 , S2 ). For semi-quantitative RT-PCR, RNA samples from organoids before (n = 3) and after 48-hr treatment with either 1 μM LY411575 (n = 3) or vehicle (DMSO) alone (n = 3) were isolated. Aliquots of 300 ng of total RNA were used for cDNA synthesis in 21 μl of reaction volume. One microliter of cDNA was used for the following RT-PCR. Primer sequences and the detail of reactions are listed in Supplementary Table S3 . PCR products were separated on agarose gels and visualized using ImageLab (Bio-Rad).
6
Differential Gene Expression Analysis of ID8 and ID8-KRAS Cell Lines
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Total RNA from ID8 and ID8-KRAS cells was extracted using an RNeasy mini kit (QIAGEN, Hilden, Germany). For oligo DNA microarray analysis, RNA samples were collected, and the 3D-Gene mouse oligo chip 24 k (Toray Industries Inc., Tokyo, Japan) was used. For efficient hybridization, this 3D microarray was constructed with a well as the space between the probes and cylinder-stems and 70-mer oligonucleotide probes on the top. Total RNA was labeled with Cy5 using the Amino Allyl MessageAMP II aRNA amplification kit (Applied Biosystems, CA, USA). The Cy5-labeled amino allyl RNA pools and hybridization buffer were hybridized for 16 h. Hybridization was performed using the supplier’s protocols. The hybridization signals were obtained using 3D gene scanner (Toray Industries Inc., Tokyo, Japan), and processed with 3D gene extraction (Toray Industries Inc.). Detected signals for each gene were normalized using the global normalization method (the median of the detected signal intensity was adjusted to 25). Transcripts with a fold change > 2 and p values < 0.05 were considered differentially expressed.
7
Gene Expression Analysis of Matrigel-Cultured Cells
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Cells incubated in Matrigel for indicated times were isolated from Matrigel using Cell recovery solution (CORNING, Corning, New York), and used to further gene expression analyses. Gene expression profile was determined by reverse transcription‐polymerase chain reaction (RT‐PCR), quantitative PCR and flow cytometry analysis as described previously.16 For gene expression microarrays, total RNA isolated from sorted CapSCs and ctPCs (three independent isolated cell samples) was applied to microarray analysis on a 3D‐Gene Mouse Oligo Chip 24K (Toray Industries Inc., Tokyo, Japan) as described previously.16
8
Murine Lung Tissue RNA Analysis
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Murine lung tissue at 8 weeks (25 mg/tube), a 5-mm stainless ball, and 700 μL QIAzol Lysis Reagent (Qiagen, Hilden, Germany) were added to 2-mL tubes. The sample was homogenized twice using TissueLyser II (Qiagen) at 20 Hz for 5 min. The homogenized sample was used as the tissue lysate. Total RNA was extracted from the tissue lysate using the miRNeasy Mini Kit (Qiagen). Total RNA (10 μg per mouse) from six B6 or ME mice was mixed and used for the microarray analysis. Total RNA was labeled with Cy3 for B6 or Cy5 for ME by using the Amino Allyl MessageAMP II aRNA Amplification Kit (Thermo Fisher Scientific). Hybridization and microarray analysis for the expression of 23,474 genes was performed using 3D-Gene Mouse Oligo chip 24 k (Toray Industries Inc., Tokyo, Japan) and 3D-Gene Scanner (Toray Industries Inc.). Detected signals for each gene were normalized using global normalization method (Cy5/Cy3 ratio median = 1). Genes with a fold change of > 2 and < 0.5 were considered to be upregulated and downregulated genes, respectively.
9
Genome-wide expression profiling of cell lines
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Genome-wide expression arrays (Illumina, San Diego, CA, USA) were used for the analysis of SAS (human WG6, version 3, 48 803 genes) and HepG2 (human WG6, version 1, 47 296 genes). Data were analyzed by TransGenic (Kumamoto, Japan). For MM102, a 3D-Gene mouse Oligo chip 24k (23 522 genes; Toray Industries, Tokyo, Japan) was used and the data were analyzed by Toray Industries using GeneSpring GX10 (Agilent Technologies, Santa Clara, CA, USA). HepG2 versus HepG2 cancer stem cell (CSC) analysis was carried out by MOGERA-Array self (Tohoku Chemical, Iwate, Japan).
10
Profiling gene expression in Apc mutant mice
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Normal ileal crypts were isolated from the ApcΔ716 and Apc Id2 mice as previously described (Sato et al., 2009 (link)). Total RNA was purified using the RNeasy Micro Kit (Qiagen). Gene expression profiles were analyzed using the 3D-Gene Mouse Oligo Chip 24k (Toray Industries, Kanagawa, Japan).
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