Total RNA was extracted using the RNeasy Mini kit (Qiagen, Milan, Italy); RNA concentration and purity was determined by using a NanoPhotometer spectrophotometer (IMPLEN) and the RNA integrity (RIN) checked with a 2100 Bioanalyzer and a RNA 6000 Nano LabChip kit (Agilent Technologies). The labeling and hybridization steps were carried out according to the Agilent protocol (Two‐Color Microarray‐Based Gene Expression Analysis version 5.7), using a two‐color design in which HCT‐8/R cells were contrasted within parental HCT‐8.. The labeled samples were hybridized to Agilent Human GE 4 × 44K microarray in Agilent microarray chambers (G2534A) at 65° for 18 h. GE arrays were scanned using a Genepix 4000B microarray scanner at 5‐μm resolution (Axon Instruments, Foster City, CA, USA). Image analysis and initial quality control were performed using the Agilent Feature Extraction Software v9.5. Differentially genes were identified by t‐test, comparing normalized red (HCT‐8/R) versus green (parental HCT‐8) signals. Pathways analysis was performed using GO‐elite version 1.2 beta (http://www.genmapp . org/go_elite).
Genepix 4000b microarray scanner
Manufactured by Molecular Devices
Sourced in United States
The GenePix 4000B Microarray Scanner is a high-performance instrument designed for the acquisition of microarray data. It features a dual-laser excitation system and high-resolution scanning capabilities to capture detailed and accurate images of microarray slides.
Automatically generated - may contain errors
Lab products found in correlation
Genepix pro 6, by Molecular Devices (12 mentions)
Rneasy mini kit, by Qiagen (6 mentions)
Genepix pro 6.0 analysis software, by Molecular Devices (6 mentions)
Trizol, by Thermo Fisher Scientific (4 mentions)
Mirneasy mini kit, by Qiagen (3 mentions)
Alexa fluor 555, by Thermo Fisher Scientific (3 mentions)
Alexa fluor 647, by Thermo Fisher Scientific (3 mentions)
Blocking solution, by Thermo Fisher Scientific (3 mentions)
Protoarray human protein microarrays, by Thermo Fisher Scientific (3 mentions)
Protoarray prospector software, by Thermo Fisher Scientific (3 mentions)
Af647 conjugated goat anti human igg antibodies, by Thermo Fisher Scientific (3 mentions)
Trizol reagent, by Thermo Fisher Scientific (2 mentions)
Mircury lna array, by Qiagen (2 mentions)
Mircury array power labeling kit, by Qiagen (2 mentions)
Rabbit anti krt23, by Merck Group (2 mentions)
Mouse anti krt18, by Thermo Fisher Scientific (2 mentions)
Mouse anti krt14, by Thermo Fisher Scientific (2 mentions)
Rabbit anti krt19, by GeneTex (2 mentions)
Genepix pro 7.0 analysis software, by Molecular Devices (2 mentions)
Prism software, by GraphPad (2 mentions)
96 protocols using genepix 4000b microarray scanner
1
Microarray Analysis of Colorectal Cancer Cells
2
Cy3-labeled aRNA Microarray Protocol
3
Identifying LNC942 Binding Proteins
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The HuProtTM human proteome microarray (Wayen Biotechnologies, Shanghai) was used to identify potent LNC942 binding proteins.20 Briefly, proteome microarrays were blocked with a pre‐cold SuperBlock T20 Blocking Buffer (Thermo Scientific, USA) for 2 h with gentle agitation. The microarrays were washed with TBST (Tis buffered saline + Tween) and incubated with biotin‐labelled anti‐sense (control) or sense LNC942 probes for 1 h at RT. After being washed in TBST, the dried microarrays were scanned with a GenePix 4000B microarray scanner (Axon Instruments, USA) to evaluate the results. Both probes corresponding to a protein were required to have a z‐score of ⩾3 in two repeated array experiments was considered a positive interaction, resulting in 209 positive hits.
4
Profiling miRNA Expression in Obese Rats
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Total RNA of the CC from obese rats with or without ED was harvested and extracted using Trizol reagent (Invitrogen, San Diego, CA, USA) according to the manufacturer’s instructions. The concentration and purity of RNA were determined by measuring absorbance in a spectrophotometer at 260 and 280 nm. Quantified RNA samples were labeled using the miRCURYTM array labeling kit (Exiqon, Vedbaek, Denmark) and hybridized on the miRCURYTM array microarray kit (Exiqon). After washing, the microarrays were scanned with a GenePix4000B microarray scanner (Axon Instruments, Sunnyvale, CA, USA) and analyzed with Pro 6.0 software (Axon Instruments). Expression data were normalized using median normalization. After normalization, average values of the replicate spots of each miRNA were used for statistical analysis. Differentially expressed miRNAs were identified as a fold change greater than 1.5.
5
Microarray Analysis of Orm1 Knockdown in Mouse Liver
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Total RNA was isolated from mouse liver tissues at 48 h after PH treated with siControl or siOrm as described above. After fragmentation of complementary RNA, microarray studies were performed by the RIKEN Research Resource Center using Affymetrix GeneChip Mouse Genome 430A 2.0 Array. The arrays were scanned using a GenePix4000B Microarray Scanner (Axon Instruments, Foster City, CA, USA). Data analysis was performed with GeneSpring GX13.0 (Agilent Technologies). Signal intensities for each probe were normalized to the 75th percentile without baseline transformation. Genes that were differentially expressed following Orm1 knockdown were identified by a fold change of > 2 and selected for pathway analysis. All data are MIAME compliant, and the raw data have been deposited in the Gene Expression Omnibus (RRID: SCR_007303, www.ncbi.nlm.nih.gov/geo , accession no. GSE83733 ).
6
Hypoxic Transcriptome Analysis by miRNA Microarray
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Total cellular RNA was purified from cells cultured under hypoxic conditions using TRIzol® reagent and the RNeasy mini kit (Qiagen GmbH) according to the manufacturer's instructions. The RNA samples were quantified using a NanoDrop spectrophotometer (NanoDrop Technologies; Thermo Fisher Scientific, Inc.), and then labeled using the miRCURY™ Hy3™/Hy5™ Power labelling kit (Qiagen GmbH). The labelled samples were hybridized to a microarray (NimbleGen Systems, Inc.) for 16-20 h, and the array sections were scanned using the GenePix 4000B micro-array scanner (Axon Instruments). The results were read and analyzed using GenePix Pro V6.0 (Molecular Devices, LLC). A heat map diagram was used to display the data for two-way hierarchical clustering of genes and samples.
7
miRNA Profiling via Microarray
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The microarray analysis for the miRNA profiling was performed at Kangcheng Technology (Shanghai, China) using the miRCURY LNA™ microRNA Array (v.19.0; Exiqon, Vedbaek, Denmark). Total RNA for the miRNA microarray was isolated using TRIzol (Invitrogen, Carlsbad, USA) and purified with an RNeasy mini kit (QIAGEN, Duesseldorf, Germany) according to the manufacturers’ instructions. RNA quality and quantity were measured using a NanodropND-1000 nanodrop spectrophotometer (Thermo Fisher Scientific, Waltham, USA) and the RNA integrity was determined by gel electrophoresis. After miRNA labeling, the samples were hybridized on the miRCURY LNA™ array. The slides were scanned using a GenePix 4000B microarray scanner (Axon Instruments, Foster City, USA).
8
Adipokine Profiling of Mature Adipocytes
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After the differentiation of hMSCs, mature adipocytes were treated with 100 μmol/L of EA. Twenty-four hours later, the supernatant was discarded, and then, the adipocytes were washed with ice-cold PBS 3 times and collected and stored at -80°C. To gain insight into the variably and characteristically expressed adipokines in adipocytes, chips of RayBio Human Labelbased Antibody Array I (AAH-ADI-M) were applied to measure the expression levels of 62 adipokines simultaneously, and the presence of adipokines was identified by the Genepix 4000B Microarray Scanner (Axon Instruments, Inc., USA).
9
Amniotic Fluid RNA Extraction
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On days 13, 15, and 17 of gestation, 6 animals randomly selected from each group were deeply anesthetized with pentobarbital sodium (45mg/kg, cas 57-33-0, Merck, Darmstadt, Germany) and then AF was carefully collected in a 1-ml sterilized syringe after abdominal exposure with minimal trauma. Total RNA was harvested using TRIzol (Invitrogen, Carlsbad, CA) and an RNeasy mini kit (Qiagen, Hilden, Germany) according to the manufacturers’ instructions. Before labelling with the miRCURY Hy3/Hy5 Power labelling kit, the yield and integrity of total RNA were assessed using a spectrometer (ND-2000, NanoDrop Technologies Inc., Rockland, DE) and gel electrophoresis. Then the samples were hybridized on miRCURY LNA arrays (ver.16.0; Exiqon, Vedbaek, Denmark) and after washing steps, the slides were imaged on a GenePix 4000B microarray scanner and raw data were acquired from the scanned images using GenePix Pro 6.0 software (Axon Instruments, Foster City, CA, USA). We have submitted the microarray data to the Gene Expression Omnibus (Accession No. GSE70324)
10
Non-Invasive Blood Pressure Measurement
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The instruments used included rat tail-artery non-invasive blood pressure tail-cuff apparatus (BP-98A; Softron, Tokyo, Japan), inverted fluorescence microscope BX51, polarization microscope BH2 (both from Olympus, Tokyo, Japan) and GenePix 4000B Microarray Scanner (Axon Instruments, Union City, CA, USA).
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