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Microarray platform comparison study of hippocampal gene expression in DCLK1 transgenic and wild-type mice

ABSTRACT: The aim of the present study was to compare, on a statistical basis, the performance of different microarray platforms to detect differences in gene expression in a realistic and challenging biological setting. Gene expression profiles in the hippocampus of five wild-type and five transgenic δC-doublecortin-like kinase mice were evaluated with five microarray platforms: Applied Biosystems, Affymetrix, Agilent, Illumina and home-spotted oligonucleotide arrays. We observed considerable overlap between the different platforms, the overlap being better detectable with significance level-based ranking than with a p-value based cut-off. Confirming the qualitative agreement between platforms, Pathway analysis consistently demonstrated aberrances in GABA-ergic signalling in the transgenic mice, even though pathways were represented by only partially overlapping genes on the different platforms. Keywords: microarray platform comparison

ORGANISM(S): Mus musculus

PROVIDER: GSE8349 | GEO | 2008/03/25

SECONDARY ACCESSION(S): PRJNA101361

REPOSITORIES: GEO

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Microarray platform comparison study of hippocampal gene expression in DCLK1 transgenic and wild-type mice

Project description:The aim of the present study was to compare, on a statistical basis, the performance of different microarray platforms to detect differences in gene expression in a realistic and challenging biological setting. Gene expression profiles in the hippocampus of five wild-type and five transgenic Î´C-doublecortin-like kinase mice were evaluated with five microarray platforms: Applied Biosystems, Affymetrix, Agilent, Illumina and home-spotted oligonucleotide arrays. We observed considerable overlap between the different platforms, the overlap being better detectable with significance level-based ranking than with a p-value based cut-off. Confirming the qualitative agreement between platforms, Pathway analysis consistently demonstrated aberrances in GABA-ergic signalling in the transgenic mice, even though pathways were represented by only partially overlapping genes on the different platforms. Keywords: microarray platform comparison 5 biological replicates for each experimental group were analyzed on each of the five platforms. For two-color arrays a dye swap was performed. ABI_raw_data.csv contains the raw data for GSM206638 to GSM206647. Illumina_raw_data.csv contains the raw data for GSM206887 to GSM206896. In these files, the sample identifiers are included in the column headers.

2010-06-25 | E-GEOD-8349 | biostudies-arrayexpress

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Solexa / Illumina deep sequencing of the hippocampal transcriptome of wild-type and DLCK transgenic mice

Project description:The hippocampal expression profiles of wild-type mice and mice transgenic for deltaC-doublecortin-like kinase were compared with Solexa/Illumina deep sequencing technology and five different microarray platforms. With Illumina's digital gene expression assay, we obtained approximately 2.4 million sequence tags per sample, their abundance spanning four orders of magnitude. Results were highly reproducible, even across laboratories. With a dedicated Bayesian model, we found differential expression of 3179 transcripts with an estimated false-discovery rate of 8.5%. This is a much higher figure than found for microarrays. The overlap in differentially expressed transcripts found with deep sequencing and microarrays was most significant for Affymetrix. The changes in expression observed by deep sequencing were larger than observed by microarrays or quantitative PCR. Relevant processes such as calmodulin-dependent protein kinase activity and vesicle transport along microtubules were found affected by deep sequencing but not by microarrays. While undetectable by microarrays, antisense transcription was found for 51% of all genes and alternative polyadenylation for 47%. We conclude that deep sequencing provides a major advance in robustness, comparability and richness of expression profiling data and is expected to boost collaborative, comparative and integrative genomics studies. Keywords: SAGE, 17mer, NlaIII, mRNA expression, transgenic mice

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Repeatability and comparability of microRNA microarray

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Gene expression profile of Dclk1+ murine normal intestinal and tumor cells

Project description:Accumulating evidence has shown the existence of tumor stem cells, and many researchers and clinicians are focusing on the therapeutic potential of targeting tumor stem cells. Previously, we reported that doublecortin like kinase 1 (Dclk1) marks tumor stem cells but not normal stem cells in ApcMin/+ mouse intestine, and that selective ablation of Dclk1+ cells results in collapse of the intestinal tumors without any apparent damages in the normal mucosa. Here, we sought to clarify gene expresion profile of Dclk1+ cells by microarray analyses in mouse normal intestinal epithelium and ApcMin/+ mouse intestinal tumors. Microarray analyses demonstrated that genes related to microtubules and actin cytoskeleton (e.g., Rac2) were highly expressed in Dclk1+ normal intestinal and tumor cells. We found the expression of Src family kinases (i.e., Hck, Lyn, Csk, and Ptpn6) in Dclk1+ normal intestinal and tumor cells.

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DCLK1 small extracellular vesicle proteome

Project description:Doublecortin-like kinase 1 (DCLK1) is a putative cancer stem cell marker, a promising diagnostic and prognostic maker for malignant tumors and a proposed driver gene for gastric cancer. Here we show that DCLK1 expression in the gastric cancer cell line MKN1 impacts EV biogenesis both quantitatively and qualitatively in a kinase dependent manner, revealing a hitherto unknown role for this putative oncogenic kinase. Importantly, the proteome of EVs isolated from DCLK1 expressing gastric cancer cells is enriched for proteins involved in tumor-promoting biological processes, raising the prospect of establishing DCLK1 as a novel anti-cancer target.

2021-03-23 | PXD021371 | Pride

Repeatability and comparability of microRNA microarray

Project description:We compared repeatability and comparability of microRNA microarray using 5 different platforms. and compared microarray data generated from five different microRNA microarray platforms with quantitative RT-PCR. Our data suggested that the most accurate and repeatable methods for microRNA expression profiling are Agilent and Toray, and the numbers of detected microRNA at Toray are more than at Agilent. Keywords: repeatability, comparability, microRNA, microarray We compared repeatability and comparability of microRNA microarray using 5 different platforms (Agilent, Ambion, Exiqon, Invitrogen, and Toray). In addition, we compared microarray data generated from five different microRNA microarray platforms with quantitative RT-PCR.

2010-05-19 | E-GEOD-13860 | biostudies-arrayexpress

Transcription profiling of whole adult mouse and adult mouse colon in different dilutions analysed in multiple centers

Project description:This data is part of a large-scale platform comparison experiment. Whole mouse and adult mouse colon RNA was mixed at different concentrations (100:0, 75:25, 50:50, 25:75, and 0:100) and distributed across multiple centers for analysis. Eight microarray platforms and RT-PCR were tested for different labeling protocols, amplification protocols, and data preprocessing approaches in order to maximize data intercomparability. The role of universal reference RNA was also examined. Probes of different platforms were matched using gene symbols and/or RefSeq/GenBank accession numbers. Several different normalization procedures were applied. Evaluation criteria included linearity, sensitivity/specificity, and reproducibility within and between platforms, labeling methods, and laboratories. Experiment Overall Design: Whole mouse (sacrificed on day 1, strain: C57BL/6) and adult mouse (8 weeks, strain: C57BL/6 ) colon RNA from multiple animals was pooled respectively. RNA was purified following the manufacturerâs recommendations and integrity was analyzed using an Agilent BioAnalyzer 2100 according to manufacturer instructions. Five RNA samples were created by mixing the two original samples at different concentrations (100:0, 75:25, 50:50, 25:75, and 0:100). The five master mix samples were then divided into duplicate sets of the five sample RNAs, distributed to individual laboratories, and hybridized to eight different microarray platforms at several different genome centers. The five samples included here were prepared from 10ng of total RNA using a T7 double amplification protocol as described in Schwab et al., 2003 and hybridized to Affymetrix MOE430 arrays as recommended by the manufacturer using the standard protocol. No replicates were produced.

2008-06-12 | E-GEOD-2850 | biostudies-arrayexpress

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Project description:Atherosclerosis is a chronic inflammatory disease with high morbidity and mortality rates worldwide. Doublecortin-like kinase 1 (DCLK1), a microtubule-associated protein kinase, is involved in neurogenesis and human cancers. However, the role of DCLK1 in atherosclerosis remains undefined. In this study, we identified up-regulated DCLK1 in macrophages in atherosclerotic lesions of ApoE-/- mice fed an HFD and determined that macrophage-specific DCLK1 deletion attenuates atherosclerosis by reducing inflammation in mice. Mechanistically, RNA sequencing analysis indicated that DCLK1 mediates oxLDL-induced inflammation via NF-κB signaling pathway in primary macrophages. Co-immunoprecipitation followed by LC-MS/MS analysis identified IKKβ as a binding protein of DCLK1. We confirmed that DCLK1 directly interacts with IKKβ and phosphorylates IKKβ at S177/181, thereby facilitating subsequent NF-κB activation and inflammatory gene expression in macrophages. Finally, a pharmacological inhibitor of DCLK1 prevents atherosclerotic progression and inflammation both in vitro and in vivo. Our findings demonstrated that macrophage DCLK1 promotes inflammatory atherosclerosis by binding to IKKβ and activating IKKβ/NF-κB. This study reports DCLK1 as a new IKKβ regulator in inflammation and a potential therapeutic target for inflammatory atherosclerosis.

2022-12-24 | GSE221647 | GEO

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