Ht 12 v4 expression beadchip

Manufactured by Illumina

Sourced in United States

The HT-12 v4 Expression BeadChips are high-throughput gene expression microarray products manufactured by Illumina. They are designed to analyze the expression levels of over 47,000 transcripts and known splice variants across the human genome. The BeadChips utilize Illumina's proprietary BeadArray technology to enable genome-wide expression profiling in a single experiment.

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Lab products found in correlation

Tempus blood rna tube, by Thermo Fisher Scientific (6 mentions) Genomestudio, by Illumina (4 mentions) Hiscan, by Illumina (3 mentions) Nanodrop nd 1000 spectrophotometer, by Thermo Fisher Scientific (3 mentions) Trizol reagent, by Thermo Fisher Scientific (2 mentions) Agilent 2100 bioanalyzer, by Agilent Technologies (2 mentions) Beadarray reader, by Illumina (2 mentions) Fragment analyzer, by Agilent Technologies (1 mentions) Direct zol rna kit, by Zymo Research (1 mentions) Paxgene blood rna kit, by Qiagen (1 mentions) Tapestation 4200, by Agilent Technologies (1 mentions) Paxgene tube, by Qiagen (1 mentions) Reliaprep rna cell miniprep system, by Promega (1 mentions) Qubit fluorimeter, by Thermo Fisher Scientific (1 mentions) Iscan platform, by Illumina (1 mentions) Turbo dnase, by Thermo Fisher Scientific (1 mentions) Superscript 3 reverse transcriptase, by Thermo Fisher Scientific (1 mentions) Mirneasy mini kit, by Qiagen (1 mentions) Qiazol reagent, by Qiagen (1 mentions) Agilent 2100 bioanalyser, by Agilent Technologies (1 mentions)

Spelling variants of this product

BeadChips (68 citations) Human HT-12 v4.0 Expression BeadChips (22 citations) Expression BeadChips (6 citations) Human HT-12 v4.0 Gene Expression BeadChips (4 citations)

27 protocols using ht 12 v4 expression beadchip

Transcriptional Profiling of Interferon-Treated Fibroblasts

Cited 1 time

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Patient dermal fibroblasts in triplicate wells and control fibroblasts
from three independent donors in 24-well plates were treated with 1000 IU/mL
IFN-α, IFN-β, IFN-γ or medium alone for 10 h. RNA was
isolated by using the ReliaPrep RNA Cell Miniprep System (Promega) according to
manufacturers’ instructions. Microarrays were performed by ServiceXS Ltd.
(Leiden, Netherlands). 200 ng of total RNA were used to synthesize biotinylated
cRNA target, which was subject to QC checks, then hybridized (750 ng cRNA per
sample) to Illumina HT-12 v4 Expression Bead Chips (Illumina Inc. San Diego,
USA). Data from two Illumina HT-12 v4 Expression Bead Chips per sample were
background corrected in Illumina Beadstudio with further analysis carried out
using the Lumi and Limma Bioconductor packages in R (33 (link), 34 (link)).
Normalization of background corrected data was applied through variance
stabilizing transformation (VST) and robust spline normalization (RSN) in Lumi
(35 (link)). Testing for differential
expression between IFN-treated patient and control cells was done with linear
models and empirical Bayesian statistics, utilizing a multi-level experiment
approach through Limma. Gene lists for each comparison were generated. Data
plots were created using the ggplot2 library in R.

Duncan C.J., Mohamad S.M., Young D.F., Skelton A.J., Leahy T.R., Munday D.C., Butler K.M., Morfopoulou S., Brown J.R., Hubank M., Connell J., Gavin P.J., McMahon C., Dempsey E., Lynch N.E., Jacques T.S., Valappil M., Cant A.J., Breuer J., Engelhardt K.R., Randall R.E, & Hambleton S. (2015). Human IFNAR2 deficiency: lessons for antiviral immunity. Science translational medicine, 7(307), 307ra154.

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Transcriptome Analysis of Treatment-Naïve Patients

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For a subset of 242, mostly treatment-naïve patients from data set DE1 (73 male and 169 female) whole-blood RNA was collected using Tempus Blood RNA Tubes (Applied Biosystems). RNA was hybridized to Illumina HT-12 v4 Expression BeadChips (Illumina) and further processed as described in the Supplementary Materials. In summary, QC was conducted in R 3.2.1 using the packages beadarray and lumi (64 (link), 65 (link)). Probes were transformed and normalized through variance stabilization and normalization (66 (link)). Probes, which showed a detection P < 0.05 in more than 10% of the samples, which could not be mapped to a known transcript, or which were identified as cross-hybridizing by the Re-Annotator pipeline (67 (link)), were removed. This left 20,302 transcripts from 242 samples. Technical batch effects were identified by inspecting the association of the first two principal components of expression levels with amplification round, amplification plate, and amplification plate column and row, as well as expression chip. The data were then adjusted using ComBat (68 (link)). Gene expression and methylation data of the two control cohorts MPIP and GTP were published and described previously and are summarized in the Supplementary Materials (25 (link)–28 (link)).

Andlauer T.F., Buck D., Antony G., Bayas A., Bechmann L., Berthele A., Chan A., Gasperi C., Gold R., Graetz C., Haas J., Hecker M., Infante-Duarte C., Knop M., Kümpfel T., Limmroth V., Linker R.A., Loleit V., Luessi F., Meuth S.G., Mühlau M., Nischwitz S., Paul F., Pütz M., Ruck T., Salmen A., Stangel M., Stellmann J.P., Stürner K.H., Tackenberg B., Then Bergh F., Tumani H., Warnke C., Weber F., Wiendl H., Wildemann B., Zettl U.K., Ziemann U., Zipp F., Arloth J., Weber P., Radivojkov-Blagojevic M., Scheinhardt M.O., Dankowski T., Bettecken T., Lichtner P., Czamara D., Carrillo-Roa T., Binder E.B., Berger K., Bertram L., Franke A., Gieger C., Herms S., Homuth G., Ising M., Jöckel K.H., Kacprowski T., Kloiber S., Laudes M., Lieb W., Lill C.M., Lucae S., Meitinger T., Moebus S., Müller-Nurasyid M., Nöthen M.M., Petersmann A., Rawal R., Schminke U., Strauch K., Völzke H., Waldenberger M., Wellmann J., Porcu E., Mulas A., Pitzalis M., Sidore C., Zara I., Cucca F., Zoledziewska M., Ziegler A., Hemmer B, & Müller-Myhsok B. (2016). Novel multiple sclerosis susceptibility loci implicated in epigenetic regulation. Science Advances, 2(6), e1501678.

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Transcriptomic Landscape Analysis of iPSC

Cited 2 times

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After extraction by Trizol reagent (Thermo Fisher Scientific) RNA was purified by the Direct-zol RNA kit (Zymo Research, Irvine, CA, USA) according to manufacturer’s instructions. Quality analysis of RNA samples was performed on a fragment analyzer (Advanced Analytical Technologies (Agilent), Ankeny, IA, USA). RNA of samples with a RIN (RNA integrity number as a means of quality assessment) equal to 7 or greater was further processed and hybridized to Illumina HT-12 v4 Expression BeadChips (Illumina, San Diego, CA, USA) and measured on the Illumina HiScan. Expression data was processed through SOM machine learning as described in our previous publication on rubella virus-infected iPSC lines [24 (link)]. Briefly, we applied the R-program “oposSOM” [64 (link)] which generates images of the transcriptomic landscape of each sample revealing clusters of over- and under-expressed genes as red and blue spot-like areas. Their functional context was evaluated by means of gene set analysis as implemented in [65 (link)].

Böhnke J., Pinkert S., Schmidt M., Binder H., Bilz N.C., Jung M., Reibetanz U., Beling A., Rujescu D, & Claus C. (2021). Coxsackievirus B3 Infection of Human iPSC Lines and Derived Primary Germ-Layer Cells Regarding Receptor Expression. International Journal of Molecular Sciences, 22(3), 1220.

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Whole Blood RNA Profiling Protocol

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Whole blood (5 mL) collected by venepuncture was immediately placed into Paxgene tubes (QIAGEN GmbH, Germany) and stored at -80°C for later processing for RNA. RNA was extracted using PAXgene Blood RNA kits (QIAGEN GmbH, Germany) according to manufacturer’s instructions. RNA integrity and purity were checked using Tape Station 4200 (Agilent Technologies, USA). Samples used for beadchip analysis had RNA integrity (RIN) mean±SD values 6.75±0.67 (range 5.5–7.7). Globin mRNA was depleted using GLOBINclear-Human kits (ThermoFischer Scientific, USA). RNA was reverse transcribed and biotin-labelled using the Illumina TotalPrep RNA Amplification kit (ThermoFischer Scientific, USA). The resulting biotinylated cRNA was hybridised to Illumina HT12v4 Expression BeadChips, specifically HumanHT-12_V4_0_R2_15002873_B, containing 47,323 genome wide gene probes, and 887 control probes. Samples from different control or clinical groups were distributed evenly across 3 (experiment 1) or 4 (experiment 2) beadchips. All RNA preparation and processing of samples over beadchips was carried out at Sandor Lifesciences Pvt. Ltd. (Hyderabad, India).

Fakiola M., Singh O.P., Syn G., Singh T., Singh B., Chakravarty J., Sundar S, & Blackwell J.M. (2019). Transcriptional blood signatures for active and amphotericin B treated visceral leishmaniasis in India. PLoS Neglected Tropical Diseases, 13(8), e0007673.

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Functional Analysis of SNP-Sex Interaction

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To functionally classify the observed SNP-sex interaction at 5q31.1, we analyzed blood gene expression profiles of candidate genes for association with CPBs. For 3,527 LIFE-Adult participants, whole blood was collected in Tempus Blood RNA Tubes (Life Technologies) and relocated to -80°C before further processing. Isolated RNA was processed and hybridized to Illumina HT-12 v4 Expression BeadChips (Illumina, San Diego, CA, USA) and measured on the Illumina HiScan. Raw data of 48,107 gene-expression probes were extracted by Illumina GenomeStudio without additional background correction. Data were further processed within R/Bioconductor. Expression values were log2-transformed and quantile-normalized. Batch effects of expression BeadChips were corrected using an empirical Bayes method [38 (link)]. Restricting on subjects with CPBs, a sample size of 935 (537 men, 398 women) was available. Of the 40 candidate genes obtained from eQTL data and nearby gene annotation of the lead SNP, 32 were available with high quality probes in our data. All gene-expressions were adjusted for age, lymphocytes and monocytes.

Pott J., Beutner F., Horn K., Kirsten H., Olischer K., Wirkner K., Loeffler M, & Scholz M. (2020). Genome-wide analysis of carotid plaque burden suggests a role of IL5 in men. PLoS ONE, 15(5), e0233728.

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Differential Gene Expression in Asthmatic HBECs

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Total RNA was extracted from HBECs cultured for 24 hours stimulated with 50 μg/ml NIST and unstimulated, in the presence and absence of 100nM 1,25(OH)₂D3, from four different donors (two healthy and two asthmatic). Cell culture monolayers were lysed with Qiazol reagent (QIAGEN, USA) then homogenised with QIAshredder columns before storage at -80°C pending extraction of total RNA using a miRNeasy Mini Kit (QIAGEN, USA) according to an adapted manufacturer’s protocol with an off-column DNA digest with TurboDNase (Ambion, USA). mRNA was quantified using a Qubit Fluorimeter (Invitrogen, USA) and quality controlled using an Agilent 2100 Bioanalyser (Agilent Technologies, USA). Samples were prepared for array analysis using SuperScript III Reverse Transcriptase (Invitrogen, USA) and TargetAmp Nano-g Biotin-aRNA Labelling Kit (Epicentre, Illumina, USA). The microarray was conducted on Illumina HT-12v4 Expression BeadChips (Illumina, USA) on an iScan platform (Illumina, USA). Raw array signal intensities were processed in GenomeStudio (Illumina, USA) with a quantile normalisation before export for analysis in GenomicsSuite (Partek, USA). ANOVA analysis was conducted of the normalised data in GenomicsSuite (Partek, USA).

Pfeffer P.E., Lu H., Mann E.H., Chen Y.H., Ho T.R., Cousins D.J., Corrigan C., Kelly F.J., Mudway I.S, & Hawrylowicz C.M. (2018). Effects of vitamin D on inflammatory and oxidative stress responses of human bronchial epithelial cells exposed to particulate matter. PLoS ONE, 13(8), e0200040.

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Adipose Tissue Sampling and RNA Analysis

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Paired samples of s.c. and omental visceral adipose tissue were obtained from 55 individuals (38 women, 17 men). The age ranged from 18 to 85 years and the BMI from 16.1 to 75.5 kg/m². All adipose tissue samples were collected during laparoscopic abdominal surgery as described previously (53 ). Adipose tissue was immediately frozen in liquid nitrogen and stored at -80°C. RNA from adipose tissue was extracted by using RNeasy Lipid tissue Mini Kit (Qiagen). Quantity and integrity of RNA was monitored with NanoVue plus Spectrophotometer (GE Healthcare, Freiburg, Germany). One microgram of total RNA from SC and Vis adipose tissue (305 ng RNA from adipocytes and SVF) was reverse-transcribed with standard reagents (Life technologies, Darmstadt, Germany). Expression of PLA2G4A, CEP350 and SOAT1 was measured with HT12v4 expression bead chips (Illumina, Inc., San Diego, CA, USA). The study was approved by the Ethics Committee of the University of Leipzig (approval no: 159-12-21052012), and performed in accordance to the declaration of Helsinki. All subjects gave written informed consent before taking part in this study.

Vogel H., Kamitz A., Hallahan N., Lebek S., Schallschmidt T., Jonas W., Jähnert M., Gottmann P., Zellner L., Kanzleiter T., Damen M., Altenhofen D., Burkhardt R., Renner S., Dahlhoff M., Wolf E., Müller T.D., Blüher M., Joost H.G., Chadt A., Al-Hasani H, & Schürmann A. (2018). A collective diabetes cross in combination with a computational framework to dissect the genetics of human obesity and Type 2 diabetes. Human Molecular Genetics, 27(17), 3099-3112.

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Globin-depleted Blood RNA Analysis

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Total RNA was extracted from whole blood collected in Tempus™
Blood RNA tubes according to the manufacturer’s directions (Applied
Biosystems/ThermoFisher Scientific, Waltham, MA). Alpha and beta globin mRNA was
removed from total RNA using Globinclear (Ambion/ThermoFisher Scientific) before
being analyzed on Illumina HT-12 v4 Expression BeadChips at the Genomics
Research Core of the University of Pittsburgh. All microarray data have been
deposited in the Gene Expression Omnibus database (https://www.ncbi.nlm.nih.gov/geo/) GEO accession number:
GSE110106.

Zheng X., O’Connell C.M., Zhong W., Nagarajan U.M., Tripathy M., Lee D., Russell A.N., Wiesenfeld H., Hillier S, & Darville T. (2018). Discovery of Blood Transcriptional Endotypes in Women with Pelvic Inflammatory Disease. Journal of immunology (Baltimore, Md. : 1950), 200(8), 2941-2956.

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Microarray Gene Expression Analysis of EMT

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Total RNA was isolated using TRIZOL (Invitrogen) and assessed using the NanoDrop ND‐1000 spectrophotometer (Thermo Fisher Scientific) and Agilent 2100 bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). Microarray gene expression analysis was performed using Illumina HT‐12 v4 Expression BeadChips (Illumina, San Diego, CA, USA). The RNA was first biotinylated and amplified using the Illumina TotalPrep‐96 RNA Amplification Kit, followed by cDNA synthesis, cDNA purification, cRNA synthesis and cRNA purification. The samples were then hybridized onto the arrays for 16 hour at 56°C. The arrays were washed and scanned using the Illumina BeadArray Reader. Data were then exported and analyzed using GenomeStudio v2011.11 software (Illumina).
An EMT score was calculated as the average expression level of mesenchymal genes minus the average expression level of epithelial genes from a 76 gene EMT signature.22, 29 The mRNA expression z‐scores of the 76 genes analyzed on the Affymetrix HG‐U133 Plus 2.0 platform were obtained from the Cancer Cell Line Encyclopedia database through cBioPortal (http://www.cbioportal.org/).30, 31

Mimura K., Teh J.L., Okayama H., Shiraishi K., Kua L., Koh V., Smoot D.T., Ashktorab H., Oike T., Suzuki Y., Fazreen Z., Asuncion B.R., Shabbir A., Yong W., So J., Soong R, & Kono K. (2017). PD‐L1 expression is mainly regulated by interferon gamma associated with JAK‐STAT pathway in gastric cancer. Cancer Science, 109(1), 43-53.

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RNA Extraction and Measurement from Blood Samples

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In LIFE-Heart, RNA of 4143 patients was extracted from peripheral blood mononuclear cells (PBMCs). Details of RNA extraction can be found elsewhere [37 (link), 38 ]. In the Sorb study, 988 samples of PBMCs were isolated from blood samples. The full sample preparation procedure is described elsewhere [39 ]. For LIFE-Adult participants, 3173 whole blood samples were collected and stored at − 80 °C in Tempus Blood RNA Tubes (Life Technologies). See the Supplemental Methods for a detailed description of the sampling and measurement process in each study.
RNA measurement was performed using Illumina HT-12 v4 Expression BeadChips (Illumina, San Diego, CA, USA) and scanned on the Illumina iScan according to the manufacturer’s specifications [37 (link)].

Beuchel C., Dittrich J., Becker S., Kirsten H., Tönjes A., Kovacs P., Stumvoll M., Loeffler M., Teren A., Thiery J., Isermann B., Ceglarek U, & Scholz M. (2023). An atlas of genome-wide gene expression and metabolite associations and possible mediation effects towards body mass index. Journal of Molecular Medicine (Berlin, Germany), 101(10), 1305-1321.

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