Microarray analyses were carried out as described previously20 (link)21 (link). To identify DAZL-associating mRNAs, input and immunoprecipitated RNAs were isolated as described above. RNA quality was checked using a 2100 Bioanalyzer (Agilent). RNAs were reverse-transcribed and labelled with Cy3 using Low RNA Input Linear Amplification Kits (Agilent). The Cy3-labelled complementary RNAs were hybridized to a Whole Mouse Genome Oligo Microarray (G4122F, Agilent) using Gene Expression Hybridization Kits (Agilent) according to the manufacturer's procedure. A Microarray Scanner System (G2565BA, Agilent) was used for scanning arrays, and the generated images were processed using Feature Extraction software (version 9.1, Agilent). The data obtained from two replicates for each sample were processed using the Subio Platform (version 1.16, Subio, Kagoshima, Japan) as follows: all values <1 were replaced with 1, the data were normalized to the 75th percentiles, and fold-changes were calculated from log2-transformed signal intensities.
Gene expression hybridization kit
Manufactured by Agilent Technologies
Sourced in United States, Japan, China
The Gene Expression Hybridization Kit is a laboratory equipment product designed for gene expression analysis. It provides the necessary components and reagents to perform hybridization experiments, a crucial step in the gene expression profiling process. The kit includes all the necessary materials to hybridize labeled samples to microarray slides or other gene expression platforms.
Automatically generated - may contain errors
Lab products found in correlation
Rneasy mini kit, by Qiagen (70 mentions)
Gene expression wash buffer kit, by Agilent Technologies (57 mentions)
Agilent microarray scanner, by Agilent Technologies (47 mentions)
Low input quick amp labeling kit, by Agilent Technologies (41 mentions)
Hybridization oven, by Agilent Technologies (29 mentions)
Agilent 2100 bioanalyzer, by Agilent Technologies (28 mentions)
Feature extraction software 10, by Agilent Technologies (23 mentions)
Trizol reagent, by Thermo Fisher Scientific (18 mentions)
Feature extraction software, by Agilent Technologies (16 mentions)
Gene spring software 11, by Agilent Technologies (16 mentions)
Surescan microarray scanner, by Agilent Technologies (15 mentions)
Quick amp labeling kit, by Agilent Technologies (13 mentions)
Gene expression wash buffer, by Agilent Technologies (13 mentions)
Microarray scanner, by Agilent Technologies (11 mentions)
Dna microarray scanner, by Agilent Technologies (10 mentions)
2100 bioanalyzer, by Agilent Technologies (9 mentions)
Scanner g2505c, by Agilent Technologies (9 mentions)
Nanodrop nd 1000 spectrophotometer, by Thermo Fisher Scientific (9 mentions)
Agilent low input quick amp labeling kit, by Agilent Technologies (8 mentions)
Agilent feature extraction software, by Agilent Technologies (8 mentions)
219 protocols using gene expression hybridization kit
1
Microarray Analysis of DAZL-Bound mRNAs
2
Whole Blood RNA Extraction and Microarray Analysis
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Whole blood was collected from each participant when in a non-stimulated state; PAXgene Blood RNA Kits (QIAGEN, Hilden, Germany) were then used to collect samples of total RNA. For each participant, we used the Low Input Quick Amp Labeling Kit (Agilent Technologies, Inc., Santa Clara CA, USA) according to the manufacturer’s protocol and 100 ng of total RNA to synthesize each labeled cRNA sample. We used Gene Expression Hybridization kits (Agilent Technologies, Inc.) to hybridize labeled cRNA to arrays from SurePrint G3 Human Gene Expression 8×60 K Microarray Kits (Agilent Technologies, Inc., design ID: 028004); Gene Expression Wash Packs (Agilent Technologies, Inc.) were then used according to the manufacturer’s protocols to wash each microarray. Each microarray was scanned with a DNA Microarray Scanner (Agilent Technologies, Inc.), and Feature Extraction Ver.9.5.3 (Agilent Technologies, Inc.) was used to measure signal intensity.
3
Microarray-based Transcriptomics of C. elegans
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
After the 24-h exposure, all 400 worms per well were collected into a cryogenic vial and spun at 1150×g for 2.5 min. Supernatant was removed and the vial were flash frozen in liquid nitrogen and stored at − 80 °C. Total RNA was extracted from each vial using RNeasy mini kits (Qiagen, Valencia, CA) and treated as one biological replicate. Four of the five replicates (total RNA samples) per treatment were chosen for further microarray hybridization. One hundred ng of total RNA was first reverse-transcribed into cDNA, followed by cDNA labeling using Low Input Quick Amp Labeling Kits (Agilent, Palo Alto, CA) in the presence of cyanine 3-CTP dye. The labeled cDNA was hybridized to the C. elegans-specific 44 K-olig array (one sample/array) at 65 °C for 17 h using Agilent’s Gene Expression Hybridization Kits [39 (link)]. A total of 48 samples (3 chemicals × 4 treatments per chemical × 4 replicates per treatment) were randomly assigned and hybridized to six 8 × 60 K-array slides containing 44 K oligonucleotide probes per array.
4
Liver RNA Extraction and Microarray Analysis
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Total RNA was extracted from frozen liver tissue of rats from naïve, sepsis + simvastatin pre-treatment, sepsis + simvastatin post-treatment and simvastatin + vehicle (20 mg each) with RNeasy isolation kit (Qiagen, Hilden, Germany) according to the manufacturer's instructions. RNA integrity was determined using an Agilent 2100 Bioanalyzer (Agilent Technologies, Mississauga, ON, Canada) and a Nanodrop 2000 spectrophotometer (Thermo Scientific); only high quality RNAs were used for microarray analysis.
Complementary RNA was generated using Low Input Quick Amp Labelling kits (Agilent Technologies) following the manufacturer's instructions. Either oligo-dT primer or a random primer/oligo-dT primer mixture (WT primer) was used for first strand synthesis. An in vitro transcription for synthesis of cRNA labelled with cyanine 3-CTP was performed after second strand synthesis. Gene Expression Hybridization Kits (Agilent Technologies) were used according to the manufacturer's instructions. 600 ng cRNA was hybridized on an 8x60K microarray at 65°C for 17 h. Fluorescence signals on microarrays were detected by a SureScan Microarray Scanner (Agilent Technologies) at a resolution of 3 microns for SurePrint G3 Gene Expression Microarrays, generating a 20 bit TIFF file.
Complementary RNA was generated using Low Input Quick Amp Labelling kits (Agilent Technologies) following the manufacturer's instructions. Either oligo-dT primer or a random primer/oligo-dT primer mixture (WT primer) was used for first strand synthesis. An in vitro transcription for synthesis of cRNA labelled with cyanine 3-CTP was performed after second strand synthesis. Gene Expression Hybridization Kits (Agilent Technologies) were used according to the manufacturer's instructions. 600 ng cRNA was hybridized on an 8x60K microarray at 65°C for 17 h. Fluorescence signals on microarrays were detected by a SureScan Microarray Scanner (Agilent Technologies) at a resolution of 3 microns for SurePrint G3 Gene Expression Microarrays, generating a 20 bit TIFF file.
5
Exosomal RNA Extraction and Microarray Analysis
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Total exosomal RNA was extracted using Serum/Plasma Kit (QIAGEN, Germany) according to the manufacturer’s instructions and checked for RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, U.S.A.). Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit (Agilent technologies, U.S.A.), following the manufacturer’s instructions. Labeled cRNA was purified by RNeasy mini kit (QIAGEN, Germany). Each slide was hybridized with 1.65 μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Agilent technologies, U.S.A.) in Hybridization Oven (Agilent technologies, U.S.A.), according to the manufacturer’s instructions. After 17 h hybridization, slides were washed in staining dishes (Thermo Shandon, U.S.A.) with Gene Expression Wash Buffer Kit (Agilent technologies, U.S.A.), followed the manufacturer’s instructions. Slides were scanned by Agilent Microarray Scanner (Agilent technologies, U.S.A.) with default settings. Data were extracted with Feature Extraction software 12.0 (Agilent technologies, U.S.A.). Raw data were normalized by Quantile algorithm, limma packages in R.
6
Exosomal RNA Extraction and Microarray Analysis
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Total exosomal RNA was extracted using exoRNeasy Serum/Plasma Maxi Kit (QIAGEN, Germany) according to the manufacturer’s instructions and checked for RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, USA). Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit (Agilent technologies, USA), following the manufacturer’s instructions. Labeled cRNA was purified by RNeasy mini kit (QIAGEN, Germany). Each slide was hybridized with 1.65 μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Agilent technologies, USA) in Hybridization Oven (Agilent technologies, USA), according to the manufacturer’s instructions. After 17 h hybridization, slides were washed in staining dishes (Thermo Shandon, USA) with Gene Expression Wash Buffer Kit (Agilent technologies, USA), followed the manufacturer’s instructions. Slides were scanned by Agilent Microarray Scanner (Agilent technologies, USA) with default settings. Data were extracted with Feature Extraction software 12.0 (Agilent technologies, USA). Raw data were normalized by Quantile algorithm, limma packages in R.
7
MSCs-TCs Interaction Gene Expression
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
To define alterations of gene expression profiles during MSCs‐TCs interaction, gene expression profiles were evaluated in co‐culture of MSCs and TCs at the concentration of 105, as compared with MSCs or TCs alone. We also investigated potential effects of activated TCs or MSCs stimulated with LPS on MSCs or TCs, as compared with MSCs or TCs alone, or co‐culture of TCs and MSCs without activation. Gene expression profiles were measured as previously described.7 Briefly, total RNAs were isolated, amplified, labeled by One‐Color Low Input Quick Amp Labeling Kit (Agilent technologies, Santa Clara, CA, US), and purified using RNeasy mini kit (QIAGEN, GmBH, Germany). Each slide was hybridized using Gene Expression Hybridization Kit (Agilent) in Hybridization Oven (Agilent), washed in dishes with Gene Expression Wash Buffer Kit (Agilent) for 16 h, and then scanned using Agilent Microarray Scanner equipped with default settings. Data were measured with Feature Extraction software 10.7 and raw data were normalized with Quantile algorithm, Gene Spring Software 11.0 (Agilent).
8
Microarray-based Gene Expression Analysis
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Expression of predicted target genes was determined using microarray data of another cohort examined in our laboratory. Microarray analysis was performed using Whole Human Genome Oligo Microarray (4×44K) (Agilent Technologies, Santa Clara, CA, USA). Total RNA was extracted and was purified using mirVana™ miRNA Isolation kit (catalog no. AM1561; Ambion, Austin, TX, USA), according to the manufacturer's instructions. RIN was determined using Bioanalyzer 2100 (Agilent Technologies) to inspect RNA integration. None of the samples showed RNA degradation (RIN ≥7.0 and 28S/18S ≥0.7). Total RNA was amplified and was labeled using Low Input Quick Amp labeling kit, One-Color (catalog no. 5190-2305; Agilent Technologies). Labeled cRNA was purified using RNeasy mini kit (catalog no. 74106; Qiagen, GmBH, Hilden, Germany). Next, each slide was hybridized with Cy3-labeled cRNA by using Gene Expression Hybridization kit (catalog no. 5188-5242; Agilent Technologies), according to the manufacturer's instructions. After hybridization, the slides were scanned using a microarray scanner (catalog no. G2565CA; Agilent Technologies). Data were extracted using Feature Extraction software 10.7 (Agilent Technologies), and raw data were normalized using Quantile algorithm, limma packages in R.
9
RNA Extraction and Microarray Analysis
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
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).
10
Microarray Analysis of CO2 Stress Response
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Cells (1 × 109 cells) were harvested at two time points - 5 g/L and 50 g/L of CO2 released - by centrifugation at 1000 g for 5 min at 4 °C and the cell pellets were washed with DEPC-treated water and then frozen in methanol at −80 °C. Total RNA was extracted with Trizol reagent (Gibco BRL, Life Technologies) and was purified with the RNeasy kit (Qiagen). The quantity and the quality of the extracted RNA were checked by spectrometry (NanoDrop 1000, Thermo Scientific). We used the Agilent 8x15k gene expression microarrays (Design ID 016322, Agilent Technologies, Santa Clara, CA, USA) according to the manufacturer’s instructions. Fluorescent cRNAs were synthesized from 100 ng of total RNA using the One color RNA Spike-In kit (Agilent Technologies). Labeled cRNA was purified with the RNeasy kit (Qiagen). Microarrays were hybridized for 17 h at 65 °C in a rotating hybridization oven (Corning), with the Gene Expression Hybridization kit (Agilent). The hybridization signal was detected with a GenePix 4000B laser scanner (Axon Instruments).
About PubCompare
Our mission is to provide scientists with the largest repository of trustworthy protocols and intelligent analytical tools, thereby offering them extensive information to design robust protocols aimed at minimizing the risk of failures.
We believe that the most crucial aspect is to grant scientists access to a wide range of reliable sources and new useful tools that surpass human capabilities.
However, we trust in allowing scientists to determine how to construct their own protocols based on this information, as they are the experts in their field.
Ready to get started?
Sign up for free.
Registration takes 20 seconds.
Available from any computer
No download required
Revolutionizing how scientists
search and build protocols!