Humanht 12 v4

Manufactured by Illumina

Sourced in United States

The HumanHT-12 V4.0 is a gene expression microarray platform designed by Illumina. It is used to analyze the expression levels of over 47,000 human transcripts and known genes. The array provides a comprehensive coverage of genes and transcripts with probes derived from the National Center for Biotechnology Information Reference Sequence (NCBI RefSeq) database and other sources.

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Lab products found in correlation

Humanht 12 v3, by Illumina (3 mentions) Human genome u133 plus 2.0 array, by Thermo Fisher Scientific (3 mentions) Affymetrix human genome u133 plus 2.0 array, by Thermo Fisher Scientific (2 mentions) Wg 6 v3, by Illumina (2 mentions) Wg 6 v3 arrays, by Illumina (2 mentions) Ht 12 v4 arrays, by Illumina (2 mentions) Hiseq 2500, by Illumina (2 mentions) Genomestudio, by Illumina (2 mentions) Humanmethylation450 beadchip, by Illumina (2 mentions) Trizol reagent, by Thermo Fisher Scientific (2 mentions) Rnease kit, by Qiagen (2 mentions) Nanodrop 1000a spectrophotometer, by Thermo Fisher Scientific (2 mentions) Bioanalyzer rna nano chip, by Agilent Technologies (2 mentions) Humanwg 6 v3, by Illumina (2 mentions) Mouse genome 430 2.0 array, by Thermo Fisher Scientific (2 mentions) Mousewg 6 v2, by Illumina (2 mentions) Genome analyzer, by Illumina (1 mentions) Ingenuity pathway analysis (ipa), by Qiagen (1 mentions) Infinium 27k human methylation beadchip, by Illumina (1 mentions) Agilent 014850 whole human genome microarray 4x44k g4112f, by Agilent Technologies (1 mentions)

Spelling variants of this product

HumanHT-12 v4 BeadChip arrays (19 citations) HumanHT-12 v4 Sentrix Expression BeadChip (4 citations) HumanHT-12 WG-DASL V4.0 R2 (3 citations) HumanHT-12_V4_0_R2 microarray chips (3 citations) HumanHT-12 v4 platform (3 citations) HumanHT-12 V4.0 platform (3 citations) HumanHT-12 v4 Illumina beadarray technology (2 citations) HumanHT-12 V4.0 expression (2 citations) HumanHT-12 v4.0 Expression BeadChip kit (2 citations) HumanHT-12 V4.0 expression beadchip technology (2 citations)

56 protocols using humanht 12 v4

Identifying miR-1246 and miR-1290 Targets

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Potential miR-1246 and miR-1290 targets were identified by using two sets of wide-transcriptome microarray profiles: NuLi-1 relative to NuLi-1 cells overexpressing miR-1246 or miR-1290 (Illumina humanHT12_V4), and A549 relative to A549 cells knocking down miR-1246 or miR-1290 (Illumina humanHT12_V4). The following criteria were used to identify the possible miR-1246 or miR-1290 target genes: (1) genes downregulated >1.5-fold on miR-1246 or miR-1290 overexpression in NuLi-1 cells, and (2) genes upregulated >1.5-fold on miR-1246 or miR-1290 downregulation in A549 cells. All potential targets were subsequently verified by qRT–PCR.

Zhang W.C., Chin T.M., Yang H., Nga M.E., Lunny D.P., Lim E.K., Sun L.L., Pang Y.H., Leow Y.N., Malusay S.R., Lim P.X., Lee J.Z., Tan B.J., Shyh-Chang N., Lim E.H., Lim W.T., Tan D.S., Tan E.H., Tai B.C., Soo R.A., Tam W.L, & Lim B. (2016). Tumour-initiating cell-specific miR-1246 and miR-1290 expression converge to promote non-small cell lung cancer progression. Nature Communications, 7, 11702.

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Bladder Cancer Microarray Analysis

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Microarray analyses were preformed on tumor samples from 17 BC patients treated at the P.A. Herzen Moscow Oncological Research Institute. Of these samples, nine were examined at the Institute of Bioorganic Chemistry (IBC; Moscow, Russia) and eight at the University of Lethbridge (UL; Alberta, Canada). All tumor samples were examined using Illumina microarrays (series Illumina Human HT-12 v4). On each Illumina microchip (both at IBC and at UL), we investigated tumor samples and the control samples from the intact bladder: three at IBC and four at UL.

Lezhnina K., Kovalchuk O., Zhavoronkov A.A., Korzinkin M.B., Zabolotneva A.A., Shegay P.V., Sokov D.G., Gaifullin N.M., Rusakov I.G., Aliper A.M., Roumiantsev S.A., Alekseev B.Y., Borisov N.M, & Buzdin A.A. (2014). Novel robust biomarkers for human bladder cancer based on activation of intracellular signaling pathways. Oncotarget, 5(19), 9022-9032.

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Gene Expression Analysis of Tumor Samples

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For gene expression analysis, tumor blocks from both studies were sampled horizontally through the vertical growth phase using a TMA needle as previously described (Conway et al., 2009 (link)). RNA was extracted and gene expression data were generated for 502 cancer-related genes using the Illumina Human Cancer panel DASL assay as previously described (Conway et al., 2009 (link)) and the data from the two groups were then merged to make the test dataset (Jewell et al., 2010 (link)).
In the first validation dataset (Leeds replication), we generated whole genome gene expression profiles using Illumina human HT12 v4 (~30,000 probes) from an independent set of tumors from within the Cohort Study using the sampling technique previously described (Conway et al., 2009 (link)).
Independent validation (Lund replication) was provided in a separate sample set of primary melanoma tumors using the whole-genome DASL assay at Lund University (Harbst et al., 2012 (link)).

Jewell R., Elliott F., Laye J., Nsengimana J., Davies J., Walker C., Conway C., Mitra A., Harland M., Cook M.G., Boon A., Storr S., Safuan S., Martin S.G., Jirström K., Olsson H., Ingvar C., Lauss M., Bishop T., Jönsson G, & Newton-Bishop J. (2014). The clinico-pathological and gene expression patterns associated with ulceration of primary melanoma. Pigment cell & melanoma research, 28(1), 94-104.

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Detailed Telomere Characterization Protocols

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Detailed experimental procedures are available in the Supplemental Information. Cell culture techniques, telomere length analysis, telomeric overhang assay, analysis of metaphase spreads, TIF analysis, ChIP, telomeric FISH, IF, and immunoblotting analysis were performed as described previously (Sfeir et al., 2010 (link); Takai et al., 2010 (link)). TALENs knockout of TERF2IP was performed using standard protocols (Chen et al., 2011 (link)). The assay for telomeric position was published previously (Crabbe et al., 2012 (link)). Microarray analysis was performed using Whole Human Genome DNA microarrays (Illumina HumanHT-12 v4) with GeneSpring v12.6 for data analysis. Microarray data is deposited in the Gene Expression Omnibus under the accession number GSE61900.

Kabir S., Hockemeyer D, & de Lange T. (2014). TALEN gene knockouts reveal no requirement for the conserved human shelterin protein Rap1 in telomere protection and length regulation. Cell reports, 9(4), 1273-1280.

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Multi-Cohort Gene Expression and Clinical Data Analysis

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Gene expression levels and clinical data from four independent cohorts were downloaded from public databases. Gene expression and clinical data from the TCGA cohort (n = 566) were downloaded from the UCSC Cancer Genomics Browser (https://xena.ucsc.edu/public). Data from the Institute for Medical Informatics, Statistics and Epidemiology (Leipzig cohort, GSE65858, n = 270), Fred Hutchinson Cancer Research Center (FHCRC cohort, GSE41613, n = 97), and MD Anderson Cancer Center (MDACC cohort, GSE42743, n = 74) were downloaded from the National Center for Biotechnology Information Gene Expression Omnibus database (http://www.ncbi.nlm.nih.gov/geo). The gene expression profile of the TCGA cohort was measured using Illumina HiSeq 2000 (Illumina Inc., San Diego, CA, USA), that of the Leipzig cohort using Illumina HumanHT‐12 v4.0 Expression Beadchip, and those of the FHCRC and MDACC cohorts using Affymetrix Human Genome U133 Plus 2.0 Array (Affymetrix Inc., Santa Clara, CA, USA).

Kim S.I., Woo S.R., Noh J.K., Lee M.K., Lee Y.C., Lee J.W., Ko S, & Eun Y. (2022). Clinical significance of FAT1 gene mutation and mRNA expression in patients with head and neck squamous cell carcinoma. Molecular Oncology, 16(8), 1661-1679.

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Whole Genome Expression Profiling of Juvenile Idiopathic Arthritis

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Complementary RNA was produced from reverse-transcribed complementary DNA using an Illumina TotalPrep RNA amplification kit (Ambion), hybridized to Illumina WG-6 v3 or Illumina HT-12 v4 human whole genome microarrays, and stained according to the manufacturer’s directions. Microarray hybridizations were undertaken in 2 separate batches. The first batch consisted of samples from the 19 healthy controls as well as samples from the JIA patients: 26 obtained at month 0, 2 at month 4, and 1 at month 12. These samples were hybridized on Illumina WG-6 v3 arrays. The second batch consisted of the remaining 18 JIA patient samples from month 0 and 47 JIA patient samples from month 4. These samples were hybridized on Illumina HT-12 v4 arrays. Complementary RNA preparation and hybridizations of the second batch were carried out 12 months after the first batch.

Jiang K., Sawle A.D., Frank M.B., Chen Y., Wallace C.A, & Jarvis J.N. (2014). Whole Blood Gene Expression Profiling Predicts Therapeutic Response at Six Months in Patients With Polyarticular Juvenile Idiopathic Arthritis. Arthritis & Rheumatology (Hoboken, N.j.), 66(5), 1363-1371.

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Gene Expression Profiling of Juvenile Idiopathic Arthritis

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Complementary RNA was produced from reverse-transcribed complementary DNA using an Illumina TotalPrep RNA amplification kit (Ambion), hybridized to Illumina WG-6 v3 or Illumina HT-12 v4 human whole genome microarrays, and stained according to the manufacturer's directions. Microarray hybridizations were undertaken in 2 separate batches. The first batch consisted of samples from the 19 healthy controls as well as samples from the JIA patients: 26 obtained at month 0, 2 at month 4, and 1 at month 12. These samples were hybridized on Illumina WG-6 v3 arrays. The second batch consisted of the remaining 18 JIA patient samples from month 0 and 47 JIA patient samples from month 4. These samples were hybridized on Illumina HT-12 v4 arrays. Complementary RNA preparation and hybridizations of the second batch were carried out 12 months after the first batch.

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Analyzing IFN-α-2b Induced Fibroblast Transcriptome

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The gene expression dataset GSE38652 was obtained from the GEO database (https://www.ncbi.nlm.nih.gov/geo/). The screening basis included (a) IFN-α-2b as the processing factor, (b) fibroblasts as the intervention object, and (c) the organism as Homo sapiens. GSE38652 is based on the GPL10558 (Illumina HumanHT-12 V4.0 expression beadchip) platform, and all data can be obtained online for free. Use GEO2R (https://www.ncbi.nlm.nih.gov/geo/geo2r/) online software to analyze raw data and identify differentially expressed genes (DEGs). P < 0.05 and |logFC| ≥ 1 were used as cut-off criteria to obtain DEGs.

Liu Z., Fan Z., Wang R., Li X., Chen H, & Wang J. (2023). IFN-α-2b Reduces Postoperative Arthrofibrosis in Rats by Inhibiting Fibroblast Proliferation and Migration through STAT1/p21 Signaling Pathway. Mediators of Inflammation, 2023, 1699946.

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Ferroptosis-related Gene Expression Profiling in Melanoma

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A list of total 104 ferroptosis-related genes was obtained from FerrDb (http://www.zhounan.org/ferrdb/) and shown in Supplementary Table S1. The RNA expression datasets of SKCM (472 samples) and other 32 cancer types in TCGA were downloaded from the Xena browser (http://xena.ucsc.edu/) and listed in Supplementary Table S2. Three melanoma datasets were obtained from the GEO database (https://www.ncbi.nlm.nih.gov/geo) for further research, including GSE98394 (Illumina HiSeq 2500, 27 normal samples and 51 tumor samples), GSE65904 (Illumina HumanHT-12 V4.0, 210 samples with clinical data), and GSE91061 (Illumina Genome Analyzer, paired expression data before and after nivolumab treatment from 24 responsers and 18 non-responsers). All the GEO expression data were sorted into the form of log2(FPKM+1) and presented in Supplementary Table S3.

Qian B., Wu K., Lou X., Li K., Wu L, & Zhang D. (2022). Ferroptosis Associates With Diagnosis and Prognosis by Promoting Antitumor Immune Response in Melanoma. Frontiers in Cell and Developmental Biology, 10, 915198.

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RNA Extraction and Differential Gene Expression in MSCs

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The RNA extraction, cRNA generation, and hybridization onto HumanHT-12 v4.0 (Illumina, CA, USA), followed by scanning, were performed as described previously (Sathiyanathan et al., 2017 (link)). The background-subtracted data generated by GenomeStudio (Illumina) was read on R with the Bioconductor packages “limma” and “illuminaio.” Comparative analysis of the normalized (function “neqc()”) donor-corrected data found differentially expressed genes which were filtered by applying a statistical significance of p_adj ≤ 0.05. Gene ontology of the resultant entity list was performed by Ingenuity Pathway Analysis (QIAGEN, Germany). A heatmap of the differentially expressed genes involved in the four most significant biological processes relevant to MSC function that are predicted to increase/decrease in the analyzed data were constructed on Morpheus (https://software.broadinstitute.org/morpheus/). The acccession number for the data reported in this paper is GEO: GSE131164.

Ling L., Ren X., Cao X., Hassan A.B., Mah S., Sathiyanathan P., Smith R.A., Tan C.L., Eio M., Samsonraj R.M., van Wijnen A.J., Raghunath M., Nurcombe V., Hui J.H, & Cool S.M. (2020). Enhancing the Efficacy of Stem Cell Therapy with Glycosaminoglycans. Stem Cell Reports, 14(1), 105-121.

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