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Hybridization oven

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The Hybridization Oven is a laboratory instrument designed to provide a controlled environment for the hybridization process. It maintains a consistent temperature and rotation speed to ensure uniform mixing and incubation of samples during hybridization experiments.

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Lab products found in correlation

Beadarray reader, by Illumina (5 mentions) Genomestudio software, by Illumina (4 mentions) Freedom evo robot, by Tecan (3 mentions) Iscan reader, by Illumina (2 mentions) Infinium humanmethylation450 beadchip, by Illumina (2 mentions) Iscan microarray scanner, by Illumina (2 mentions) M elution buffer, by Zymo Research (2 mentions) Ez 96 dna methylation magprep kit, by Zymo Research (2 mentions) Totalprep rna amplification kit, by Thermo Fisher Scientific (2 mentions) Iscan system, by Illumina (2 mentions) Rneasy minelute cleanup kit, by Qiagen (2 mentions) Genomestudio, by Illumina (2 mentions) Beadchips, by Illumina (2 mentions) Quant it picogreen dsdna products, by Thermo Fisher Scientific (1 mentions) Methylation 450k kit, by Illumina (1 mentions) Ez 96 dna methylation gold kit, by Zymo Research (1 mentions) Humanht 12 v4 expression beadchip array, by Illumina (1 mentions) Mirvana mirna isolation kit, by Thermo Fisher Scientific (1 mentions) Microrna expression profiling assay guide, by Illumina (1 mentions) Rnaeasy column, by Qiagen (1 mentions)

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Illumina Hybridization Oven Cat# SE-901-1001 (2 citations)

17 protocols using hybridization oven

1

Methylation Analysis of LM-7 Cells with SAM Treatment

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LM-7 cells were treated with vehicle or 150 μmol/L of SAM for 6 days. Genomic DNA was quantified using Picogreen protocol (Quant-iT™ PicoGreen® dsDNA Products, Invitrogen, P-7589) and read on a SpctraMAX GeminiXS Spectrophotometer. Bisulfite conversion of 500 ng of genomic DNA was performed using the EZ-96 DNA Methylation-GOLD Kit (Zymo Research, Irvine, CA). The Illumina Methylation 450K kit (San Diego, California, USA) was used for the microarray experiment as described by the manufacturer's protocol, except that 8 μL of bisulfite converted template was utilized to initiate the amplification step. The Illumina hybridization oven was used for incubating amplified DNA (37°C) and for BeadChips hybridization (48°C). A Hybex incubator was used for fragmentation (37°C) and denaturation (95°C) steps. The X-stain step was carried out in a Tecan Freedom evo robot with a Te-Flow module. Arrays were scanned in Illumina iScan Reader. Data analysis was performed with the Methylation module (version 1.9.0) of the GenomeStudio software (Illumina; version 2011.1) using HumanMethylation450_15017482_v1.2. bpm manifest. Statistical threshold was set at a false discovery rate of >0.05, differential score (statistical power) of >0.13, and delta beta (differential methylation) between the groups was set at >0.15.
Parashar S., Cheishvili D., Arakelian A., Hussain Z., Tanvir I., Khan H.A., Szyf M, & Rabbani S.A. (2015). S-adenosylmethionine blocks osteosarcoma cells proliferation and invasion in vitro and tumor metastasis in vivo: therapeutic and diagnostic clinical applications. Cancer Medicine, 4(5), 732-744.
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2

Genome-wide DNA methylation profiling

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Genomic DNA was bisulfite-converted using an EZ-96 DNA Methylation MagPrep Kit (Zymo Research) according to the manufacturer's instructions. We applied 500 ng of genomic DNA to bisulfite treatment, and eluted purified, bisulfite-converted DNA in 20 μl of M-Elution Buffer (Zymo Research). DNA methylation levels were measured on Infinium HumanMethylation450 BeadChips (Illumina) following the manufacturer's protocol. In brief, 4 μl of bisulfite-converted DNA was isothermally amplified, enzymatically fragmented and precipitated. Next, precipitated DNA was resuspended in hybridization buffer and dispensed onto the BeadChips. To limit batch effects, samples were randomly distributed across slides and arrays. The hybridization was performed at 48 °C for 20 h using a Hybridization Oven (Illumina). After hybridization, BeadChips were washed and processed through a single-nucleotide extension followed by immunohistochemistry staining using a Freedom EVO robot (Tecan). Finally, the BeadChips were imaged using an iScan Microarray Scanner (Illumina).
Paul D.S., Teschendorff A.E., Dang M.A., Lowe R., Hawa M.I., Ecker S., Beyan H., Cunningham S., Fouts A.R., Ramelius A., Burden F., Farrow S., Rowlston S., Rehnstrom K., Frontini M., Downes K., Busche S., Cheung W.A., Ge B., Simon M.M., Bujold D., Kwan T., Bourque G., Datta A., Lowy E., Clarke L., Flicek P., Libertini E., Heath S., Gut M., Gut I.G., Ouwehand W.H., Pastinen T., Soranzo N., Hofer S.E., Karges B., Meissner T., Boehm B.O., Cilio C., Elding Larsson H., Lernmark Å., Steck A.K., Rakyan V.K., Beck S, & Leslie R.D. (2016). Increased DNA methylation variability in type 1 diabetes across three immune effector cell types. Nature Communications, 7, 13555.
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3

Microarray Analysis of miR-130b Targets

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Briefly, RNA samples were isolated from TC71 cells transiently expressing miR-130b mimic or a scrambled control for target preparation. High quality total RNA was amplified and purified using the Illumina TotalPrep RNA Amplification Kit (Ambion, Cat. no. IL1791) following the manufacturer’s instructions. An aliquot of 750 ng of amplified products was loaded on Illumina HumanHT-12 v4 Expression BeadChip arrays and hybridized at 58 °C in an Illumina Hybridization Oven (Illumina, San Diego, CA, USA; Cat. no. BD-103-0204) for 17 h, washed and incubated with straptavidin-Cy3 to detect biotin-labeled cRNA on the arrays. Arrays were dried and scanned with the BeadArray Reader (Illumina). Data were analyzed using the Genome Studio software (Illumina).
The microarray data were generated by the University of Texas Medical School Genomics Core Facility. Pathway Analysis was performed using MetaCore™ Pathway Analysis v 6.15 (Thomson Reuters). The data discussed in this publication have been deposited in NCBI’s Gene Expression Omnibus27 (link) and are accessible through GEO Series accession number GSE83548 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE83548). Venn diagrams were generated using the program BioVenn28 (link) (http://www.cmbi.ru.nl/cdd/biovenn).
Satterfield L., Shuck R., Kurenbekova L., Allen-Rhoades W., Edwards D., Huang S., Rajapakshe K., Coarfa C., Donehower L.A, & Yustein J.T. (2017). miR-130b directly targets Arhgap1 to drive activation of a metastatic CDC42-PAK1-AP1 positive feedback loop in Ewing sarcoma. International journal of cancer, 141(10), 2062-2075.
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4

miRNA Expression Profiling in Cerebral Ischemia

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Rats which had been operated successfully were randomly divided into the following groups: Sham, MCAO, MCAO + EA group (n = 6 for each group). After reperfusion, the rats received EA treatment. At 28 d post-MCAO, RNA was isolated from each cerebral ischemic penumbra using the mirVana miRNA Isolation Kit (Ambion, USA). The miRNA microarray was implemented according to MicroRNA Expression Profiling Assay Guide (Illumina Inc., USA). After adding a stretch of poly A tail to the 3′-end of each sequence in the 1000 ng intact total RNA sample. Then the biotinylated cDNAs were linked with miRNA specific oligos in an assay specific extension plate. The oligos were hybridized to the cDNA, mis-hybridized and excess oligos were washed away. In this process, the BeadChips were hybridized using the hybridization chamber. The BeadChips were hybridized overnight in the Illumina hybridization oven, with a temperature ramp from 60 °C to 45 °C. The Illumina BeadArray Reader (Illumina Inc.) used a laser to excite the fluor of the single-base extension product on the beads of the BeadChip sections.
Deng B., Bai F., Zhou H., Zhou D., Ma Z., Xiong L, & Wang Q. (2016). Electroacupuncture enhances rehabilitation through miR-181b targeting PirB after ischemic stroke. Scientific Reports, 6, 38997.
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5

Transcriptome Analysis of Knee Joints

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Total RNA (300 ng) from knee joints was purified using TRIzol (Life Technologies Corp.) and Qiagen RNAeasy columns (Qiagen, Valencia, CA, USA) as described.(14 (link)) Briefly, RNA was amplified using the Illumina Total Prep RNA Amplification Kit (Illumina, San Diego, CA, USA), and assessed by RNA integrity number (RIN) number. For each group, 3 independent RNA sample animals were examined to control for variation in expression. An aliquot of 1.5 μg of amplified products were loaded onto Illumina Sentrix Beadchip Array Mouse WG-6.v2 arrays, hybridized at 58°C in an Illumina Hybridization Oven for 17 hours, washed, and incubated with Streptavidin-Cy3 to detect biotin-labeled cRNA on the arrays. Arrays were dried and scanned with BeadArray Reader (Illumina). Data were analyzed using GenomeStudio software (Illumina). Clustering and pathway analysis were performed with GenomeStudio software and Ingenuity Pathway Analysis software (Ingenuity Systems, Inc., Redwood City, CA, USA), respectively. A p value of < 0.05 was considered significant. The mRNAs were classified into functional categories.
Posey K.L., Coustry F., Veerisetty A.C., Liu P., Alcorn J.L, & Hecht J.T. (2014). Chondrocyte-Specific Pathology During Skeletal Growth and Therapeutics in a Murine Model of Pseudoachondroplasia. Journal of bone and mineral research : the official journal of the American Society for Bone and Mineral Research, 29(5), 1258-1268.
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6

DNA Methylation Profiling using Illumina HumanMethylation450K

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Fragmented DNA was dispensed onto the multichannel HumanMethylation450K BeadChips and hybridization performed in an Illumina Hybridization oven for 20 h. BeadChips were washed, primer extended, and stained per manufacturer protocols. BeadChips were coated and then imaged on an Illumina iScan Reader and images were processed with GenomeStudio software methylation module (v. 1.8 or later; Illumina).
Nylander-French L.A., Wu M.C., French J.E., Boyer J.C., Smeester L., Sanders A.P, & Fry R.C. (2014). DNA methylation modifies urine biomarker levels in 1,6-hexamethylene diisocyanate exposed workers: A pilot study. Toxicology letters, 231(2), 217-226.
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7

Illumina Mouse Gene Expression Profiling

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Biotinylated cRNA (1500 ng) was hybridized to Illumina MouseWG-6 v2.0 arrays (Illumina, San Diego, CA, USA) and the arrays were washed, stained, and scanned as described in the Illumina WGGEX Direct Hybridization Assay Guide (Part# 11322355 A, Illumina, www.illumina.com). Briefly, biotinylated cRNA was mixed with hybridization buffer, denatured at 65°C, and introduced to the array. Hybridization was carried out at 58°C for 16–20 hours in a hybridization oven (Illumina). Next, the arrays were then removed, washed, and stained using streptavidin-Cy3. Finally, the stained arrays were dried and scanned using the Illumina iScan system (Illumina).
Motomura K., Romero R., Tarca A.L., Galaz J., Bhatti G., Done B., Arenas-Hernandez M., Levenson D., Slutsky R., Hsu C.D, & Gomez-Lopez N. (2020). Pregnancy-specific transcriptional changes upon endotoxin exposure in mice. Journal of perinatal medicine, 48(7), 700-722.
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8

Xiaoyaosan Herbal Compound Prescription

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The Chinese herbal compound prescription used in the experiment was Xiaoyaosan which was recorded in the “Prescriptions of the Bureau of Taiping People's Welfare Pharmacy.” Xiaoyaosan consists of the following eight herbs: Chinese thorowax root (30 g), Angelica sinensis (30 g), Radix Paeoniae Alba (30 g), Rhizoma Atractylodis (30 g), Wolfiporia extensa (30 g), Radix Glycyrrhizae (15 g), Ginger (15 g), and Mint (10 g). The preparation of herbal drugs was purchased from Beijing Tongrentang Group Co., Ltd., and dissolved in solution at a concentration of 1.67 g/ml. SYBR ExscriptTM RT-PCR kits and TRIzol, PrimeScriptTM RT Reagent kits were purchased from TaKaRa Company (Japan). The hybridization kit and chip tester including a hybridization oven, rat expression profile chip, a chip scanner, a chip washing system, and all other reagents were provided by Illumina Company (USA). In situ hybridization kits for GABRA1 and CRHR2 were provided by Boster (Wuhan). Mouse anti-GABRA1 and rabbit anti-CRHR2 antibodies were provided by Abcam.
Li X.H., Zhou X.M., Li X.J., Liu Y.Y., Liu Q., Guo X.L., Yang L.Q, & Chen J.X. (2019). Effects of Xiaoyaosan on the Hippocampal Gene Expression Profile in Rats Subjected to Chronic Immobilization Stress. Frontiers in Psychiatry, 10, 178.
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9

Illumina BeadChip RNA Expression Analysis

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RNA sample preparation for microarrays and the subsequent hybridization to the Illumina beadchips were performed at the University of Iowa DNA Facility. Three Human HT-12 v4 BeadChips (Illumina) were processed individually in this experiment with 1 sample from an untreated control and 11 samples from polarized macrophages loaded onto each array. Briefly, 100 ng total RNA from each of the 36 samples was amplified and converted to biotin-cRNA using the Epicenter TargetAmp-Nano Labeling Kit for Illumina Expression BeadChip (Illumina). The biotin-aRNA product was purified using the RNeasy MinElute Cleanup Kit (Qiagen) according to modifications from Epicenter. Seven hundred fifty nanograms of this product were mixed with Illumina hybridization buffer, placed onto each beadchip array, and incubated with rocking at 58°C for 17 h in an Illumina Hybridization Oven. Following hybridization, the arrays were washed, blocked, and stained with streptavidin-Cy3 using the Whole-Genome Gene Expression Direct Hybridization Assay (Illumina). Beadchip arrays were scanned with the iScan System (Illumina) and data were collected using the GenomeStudio software v2011.1 (Illumina). The expression data has been deposited in NCBI Geo repository (GSE68854).
Sudan B., Wacker M.A., Wilson M.E, & Graff J.W. (2015). A Systematic Approach to Identify Markers of Distinctly Activated Human Macrophages. Frontiers in Immunology, 6, 253.
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10

Transcriptional Profiling of Metastatic Tumors

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Briefly, RNA samples were isolated from localized tumors, primary tumors from metastatic mice and metastatic lung lesions for target preparation. Total RNA was amplified and purified using the Illumina TotalPrep RNA Amplification Kit (Ambion, Cat. no. IL1791) following the manufacturer’s instructions. An aliquot of 750 ng of amplified products was loaded onto Illumina Sentrix Beadchip Array Mouse Ref8.v2 arrays and hybridized at 58 °C in an Illumina Hybridization Oven (Illumina, San Diego, CA, USA; Cat. no. 198361) for 17 h, washed and incubated with straptavidin-Cy3 to detect biotin-labeled cRNA on the arrays. Arrays were dried and scanned with the BeadArray Reader (Illumina). Data were analyzed using the Genome Studio software (Illumina).
The microarray data were generated by the University of Texas Medical School Genomics Core Facility. Array data are available at the Gene Expression Omnibus (GEO, accession GSE43281).
Zhao S., Kurenbekova L., Gao Y., Roos A., Creighton C., Rao P., Hicks J., Man T.K., Lau C., Brown A., Jones S., Lazar A., Ingram D., Lev D., Donehower L, & Yustein J. (2015). NKD2, a negative regulator of Wnt signaling, suppresses tumor growth and metastasis in osteosarcoma. Oncogene, 34(39), 5069-5079.
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