TRIzol® reagent was purchased from Invitrogen Life Technologies, and the RNeasy Mini Kit was obtained from Qiagen (Valencia, CA, USA). The Quick Amp Labeling Kit (One-Color), gene expression hybridization kit, gene expression wash buffer, and microarray scanner were obtained from Agilent (California, USA). The magnetic stir plate was obtained from Corning Incorporated (New York, USA).
Gene expression wash buffer
Manufactured by Agilent Technologies
Sourced in United States
Gene Expression Wash Buffer is a laboratory reagent used to clean and prepare samples for gene expression analysis. It is designed to remove unwanted substances from the samples, ensuring accurate and reliable results during the gene expression measurement process.
Automatically generated - may contain errors
Lab products found in correlation
Gene expression hybridization kit, by Agilent Technologies (13 mentions)
Agilent microarray scanner, by Agilent Technologies (9 mentions)
Microarray scanner, by Agilent Technologies (7 mentions)
Trizol reagent, by Thermo Fisher Scientific (6 mentions)
Mirna complete labeling and hyb kit, by Agilent Technologies (6 mentions)
Quick amp labeling kit, by Agilent Technologies (5 mentions)
Low input quick amp labeling kit, by Agilent Technologies (5 mentions)
Agilent gene expression hybridization kit, by Agilent Technologies (4 mentions)
Agilent 2100 bioanalyzer, by Agilent Technologies (4 mentions)
Feature extraction software, by Agilent Technologies (3 mentions)
Genespring software, by Agilent Technologies (3 mentions)
Micro bio spin column, by Bio-Rad (3 mentions)
Feature extraction 10, by Agilent Technologies (3 mentions)
Scan control a 8, by Agilent Technologies (3 mentions)
Microrna spike in kit, by Agilent Technologies (3 mentions)
High resolution c scanner, by Agilent Technologies (3 mentions)
Spike in control, by Agilent Technologies (3 mentions)
Rneasy mini kit, by Qiagen (2 mentions)
Rneasy mini spin column, by Qiagen (2 mentions)
Isogen, by Nippon Gene (2 mentions)
35 protocols using gene expression wash buffer
1
RNA Extraction and Microarray Analysis
2
Profiling of HCV-E2-Stimulated Exosomal miRNAs
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Microarray assay of non-stimulated or HCV-E2-stimulated MC-derived exosomes was performed using miR marker reagents and hybridization kits, and human miR microarray kit (all from Agilent Technologies, Palo Alto, CA, USA). Total RNA (100 ng) from each sample was first phosphorylated and then labeled with Cyanine 3-pCp. The labeled RNA was purified using a Micro-Bio-spin column (Bio-Rad Laboratories, Inc., Hercules, CA, USA) followed by hybridization with human miRNA microarray slides at 55°C for 20 h. After hybridization, the slides were washed with gene expression wash buffer (Agilent) and scanned on an Agilent microarray scanner using Agilent's Scan Control A.7.0.1 software. The original hybridization intensity was obtained using Agilent's feature extraction software and 2,006 miRNAs were detected.
3
RNA Integrity Assessment and Microarray Analysis
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We evaluated the RNA integrity number (RIN) of cells from AP-positive fractions using an Agilent 2100 Bioanalyzer system. We selected three RNAs with a relatively high RIN value from each group and performed complementary RNA (cRNA) labeling and amplification using a Low Input Quick Amp Labeling Kit (Agilent Technologies, Santa Clara, CA, USA). We refined the cRNA labeling using RNeasy Mini spin columns (QIAGEN) and hybridized the cRNAs using a Gene Expression Hybridization Kit (Agilent Technologies). The glass slide was cleaned with Gene Expression Wash Buffer (Agilent Technologies). Hybridized cRNAs were scanned on a Microarray Scanner (Agilent Technologies), and the spots were quantified.
4
RNA Extraction and Microarray Analysis of PYC-Treated Cells
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Total RNA was extracted from PYC-treated (10 μg/mL, 72 h) and untreated B10 cells using ISOGEN (Nippon Gene Co. Tokyo, Japan) from cells growing in the linear phase of PYC treatment. RNA quality was measured using an Agilent 2100 bioanalyzer and showed an RNA integrity number (RIN) of 9.8 (7.0 < RIN ≤ 10 is suitable for analysis). Microarray analysis was performed by Hokkaido System Science Co., Ltd. (Sapporo, Japan) using the SurePrint G3 Human 8 × 60 K ver 3.0 slides (Agilent Technologies Co., Santa Clara, CA, USA). RNA samples were labeled with Cy3 or Cy5, hybridized on slides using a gene expression hybridization kit (Agilent Technologies Co.), washed with gene expression wash buffer (Agilent Technologies Co.), and scanned using a microarray scanner (G2505C, Agilent Technologies Co.). Raw images were processed using the Agilent Feature Extraction software (12.0.3.1).
5
Rat lncRNA Microarray Analysis
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Microarray experiments (n=3) were performed by OE Biotech Co., Ltd. Total RNA was extracted using TRIzol® (Invitrogen; Thermo Fisher Scientific, Inc.) and quantified using NanoDrop ND-2000 (Thermo Fisher Scientific, Inc.). RNA integrity was assessed using the Agilent Bioanalyzer 2100 (Agilent Technologies, Inc.). Sample labeling (Quick Amp Labeling kit; cat. no. 5190-2305), microarray hybridization (Agilent Gene Expression Hybridization kit; cat. no. 5188-5242) and washing (Gene Expression Wash Buffer; cat. no. 5188-5325 and 5188-5326; all Agilent Technologies, Inc.) were performed based on the manufacturer's standard protocols. Total RNA was transcribed to double-stranded cDNA, then synthesized into cRNA and labeled with Cyanine-3-CTP. Labeled cRNAs were subsequently hybridized onto the 8x60 K Agilent Rat long non-coding RNA (lncRNA) Array. Following washing, the arrays were scanned using the Agilent Scanner G2505C (Agilent Technologies, Inc.). Feature Extraction software (v.10.7.1.1; Agilent Technologies, Inc.) was used to analyze array images to obtain raw data. Genespring software (v.13.1; Agilent Technologies, Inc.) was utilized to conclude basic analysis using raw data.
6
Microarray Analysis of Cochlea Gene Expression
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To analyze gene expression of each cochlea turn, 12 SurePrint G3 Mouse Exon Microarrays (Agilent Technologies), which were spotted with 165,984 exon probes (24,547 genes), were hybridized to labeled cRNA (4 microarrays were used for each turn sample). Prior to the hybridization step, Cyanine 3-labeled cRNAs were fragmented using 25X fragmentation buffer at 60°C in a water bath for 30 min and then hybridized to a microarray slide for 17 hours at 65°C in a hybridization oven and washed using Gene Expression Wash Buffer (Agilent Technologies).
7
Labeling and Hybridization of miRNA Microarray
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Total RNA (0.1 μg) was dephosphorylated and labeled with pCp-Cy3 by using the Agilent miRNA Complete Labeling and Hyb Kit (Agilent Technologies). Hybridization buffer (Agilent Technologies) was added to the labeled mixture to a final volume of 45 μl. The mixture was heated at 100 °C for 5 min and immediately cooled to 0 °C. Each 45-μl sample was hybridized onto an Agilent human miRNA Microarray R21 (Agilent Technologies) at 55 °C for 20 h. After hybridization, slides were washed in Gene Expression Wash Buffer at room temperature for 5 min and then in Gene Expression Wash Buffer 2 at 37 °C for 5 min (Agilent Technologies). Microarrays were scanned with an Agilent microarray scanner (model G2505C; Agilent Technologies) at 535 nm for Cy3. Feature Extraction software version 10.7.3.1 (Agilent Technologies) was used for image analysis. Microarray data were uploaded in the Gene Expression Omnibus (GEO) database of the National Center for Biotechnology Information [GEO:GSE118806].
8
Mouse miRNA Expression Profiling
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Total RNA was isolated using a miRNeasy kit (Qiagen). After dephosphorylation and denaturation, the total RNA was labeled with cyanine 3-pCp and subsequently hybridized to an Agilent mouse microRNA microarray (release version 15) using the microRNA Complete Labeling and Hyb Kit (Agilent Technologies, Inc.). After hybridization for 20 h, the slides were washed using the Gene Expression Wash Buffer (Agilent Technologies, Inc.), scanned using an Agilent Scanner G2565BA, and processed and analyzed using Agilent Feature Extraction Software version 9.5.1. The raw data were analyzed using GeneSpring GX software version 12.5 (Agilent Technologies, Inc.).
9
Differential Gene Expression in CD166 Cells
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CD166(−) and CD166 (+) cells were sorted from bulk Li-7 cells and total RNAs were extracted using an RNeasy kit (Qiagen, Valencia, CA). Samples of RNA were quantified with a spectrophotometer and then used to generate Cy-3-labelled cRNA according to the manufacturer’s instructions. The dye content and concentration of cRNA were measured by spectrophotometry (NanoDrop Technologies, Wilmington, DE). A 1650 ng aliquot of Cy3-labelled cRNA was hybridized to oligonucleotides immobilized on the surface of microarray slides (Agilent Technologies, Palo Alto, CA) at 65°C for 17 hr; the slides were washed and treated with Gene Expression Wash Buffer (Agilent Technologies) and then scanned using an Agilent Microarray Scanner. All steps were performed according to the manufacturer’s instructions (Agilent Technologies). The data was analyzed with GeneSpring software (Version 12.5, Agilent Technologies).
10
Screening circRNA Expression in TNBC
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In this retrospective study, for circRNAs expression
screening, we obtained four pairs of tumorous and
paracancerous tissues from four triple negative
BC patients and extracted total RNA for circRNA
microarray assay. In detail, four pairs of BC tissues
and paracancerous tissues were sectioned from clinical
patients. TRIzol reagent was used for RNA extraction
fromtissues, and NanoDrop-1000 and agarose gel
electrophoresis were used for RNA concentration and
integrity detecting, respectively. According to standard
microarray hybridization instructions, the RNA was
first purified, and then reverse transcribed to cDNA,
cDNA was further transcribed into cy3-fluorescent
cRNA, and finally cRNA was hybridized with
Human circRNA Arrays (Arraystar). The hybridized
microarray was washed with Gene Expression Wash
Buffer (Agilent p/n 5188-5325) and the images were
scanned by Agilent Scanner G2505C software.
screening, we obtained four pairs of tumorous and
paracancerous tissues from four triple negative
BC patients and extracted total RNA for circRNA
microarray assay. In detail, four pairs of BC tissues
and paracancerous tissues were sectioned from clinical
patients. TRIzol reagent was used for RNA extraction
fromtissues, and NanoDrop-1000 and agarose gel
electrophoresis were used for RNA concentration and
integrity detecting, respectively. According to standard
microarray hybridization instructions, the RNA was
first purified, and then reverse transcribed to cDNA,
cDNA was further transcribed into cy3-fluorescent
cRNA, and finally cRNA was hybridized with
Human circRNA Arrays (Arraystar). The hybridized
microarray was washed with Gene Expression Wash
Buffer (Agilent p/n 5188-5325) and the images were
scanned by Agilent Scanner G2505C software.
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