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Gene expression data from human erythroleukemic cells in a time dependent manner after PMA treatment

ABSTRACT: The molecular regulation of megakaryocytic differentiation is poorly understood. Using a myelogenous leukemia cell line, K562, which can partly recapitulate the process in response to phorbol 12-myristate 13-acetate (PMA), we performed a microarray-based gene expression profiling using Illumina HumanRef-8 Expression Beadchip to identify genes that play significant roles in megakaryopoiesis. Time course microarray data were obtained at 8 time points. Illumina HumanRef-8 Expression Beadchip has ~over 24,000 transcripts a piece. Duplicate experiments were performed for each time point. Here, we reported raw data of two independent experiments. After microarray data analysis, selecting genes with significant detection p-value produced ~14,000 probes out of total 23,920 probes. Quantile normalization was carried out for each dataset at 8 time points using the average expression value. The K-means clustering method (k=12) was used to classify those probes according to characteristic temporal pattern. We selected transcription factors shown fold changes in a time dependent manner to examine genes related for megakaryopoiesis. Finally, we can suggest that FosB which belongs to the Fos family of AP1 transcription factors is related in megakaryopoiesis.

ORGANISM(S): Homo sapiens

PROVIDER: GSE12736 | GEO | 2009/06/01

SECONDARY ACCESSION(S): PRJNA111039

REPOSITORIES: GEO

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Homo sapiens

Project description:Spermatozoal RNA Profiles (HumanRef-8 BeadChip)

| PRJNA104125 | ENA

Comparisons of Affymetrix Whole-Transcript Human Gene 1.0 ST array with standard 3' expression arrays

Project description:The recently released Affymetrix Human Gene 1.0 ST array has two major differences compared with standard 3'™ based arrays: (1) it interrogates the entire mRNA transcript, and (2) it uses cDNA targets. To assess the impact of these differences on array performance, we performed series of comparative hybridizations between the Human Gene 1.0 ST and the Affymetrix HG-U133 Plus 2.0 and the Illumina HumanRef-8 BeadChip arrays. Additionally, both cRNA and cDNA targets were probed on the HG-U133 Plus 2.0 array. The results show that the overall reproducibility is best using the Gene 1.0 ST array. When looking only at the high intensity probes, the reproducibility of the Gene 1.0 ST array and the Illumina BeadChip array is equally good. Concordance of array results was assessed using different inter-platform mappings. The Gene 1.0 ST is most concordant with the HG-U133 array hybridized with cDNA targets, thus showing the impact of the target type. Agreements are better between platforms with designs which choose probes from the 3' end of the gene. Overall, the high degree of correspondence provides strong evidence for the reliability of the Gene 1.0 ST array. Keywords: Cross-platform comparison

2008-02-01 | GSE9819 | GEO

Genome wide analysis of overexpression of miR-203 in primary mouse cortical neurons

Project description:Effect of lentiviral mediated overexpression of miR-203 in mouse cortical neurons at different days in vivo Total RNA isolated from E15 cortical cultures using QIAGEN miRNeasy mini kit (QIAGEN; 217004) were processed on an Illumina mouse Ref8 v2 beadchip microarrays following the manufacture’s protocol. Microarray data analysis was performed using R and Bioconductor packages. Raw expression data were log2 transformed and normalized by quantile normalization. Probes were considered robustly expressed if the detection P value was 0.05 for at least half of the samples in the data set. Probes were re-mapped to mouse Ensembl gene IDs (v67; May 2012 data freeze) for comparison with RNA-sequencing data.

2018-08-28 | GSE89580 | GEO

Hela cells treated with or without IFNgamma at different time points

Project description:The purpose of this study is to define which genes are IFNgamma sensitive, resistant, or irrelevant in our desired 16MB Human genome. Different ISGs(Interferon sensitive genes) were categorized based on this expression array data and can be visulized in our 16MB IFNgamma genes DB. Keywords: treated/untreated different time point comparison HeLa cells left untreated or 6, 24 and 48 hours after IFNgamma treatment were collected for RNA isolation as previously described (Pattenden et al., EMBO (2002) 21: 1978). Briefly, cells were washed with cold PBS, scraped and spun down at 1200 rpm for 5 min. Cell pellet was suspended in Trizol (invitrogen), left for 5 minutes at room temperature and was chloroform extracted. RNA was precipitated with isoprpanol and s8spendeed in RNAse-free water. RNA was Dnase treated (Ambion). Microarray whole genome analysis was performed on Illumina HumanRef-6 Expression Beadchip. Raw intensities from three independent biological replicates was processed by Illumina BeadStudio software (Illumina, Toronto, ON). Compared to data normalized by various procedures, the data submitted (average raw value) provides the best validation by real-time PCR.

2009-01-14 | E-GEOD-11299 | biostudies-arrayexpress

Profiling ethylene-responsive genes expressed in the latex of Hevea brasiliensis using cDNA microarray

Project description:Ethylene is commonly used as a latex stimulant of Hevea brasiliensis by application of ethephon (chloro-2-ethylphosphonic acid); however, the molecular mechanism by which ethylene increases latex production is not clear. To better understand the effects of ethylene stimulation on the laticiferous cells of rubber trees, a latex expressed sequence tag (EST)-based complementary DNA microarray containing 2973 unique genes (probes) was first developed and used to analyze the latex gene expression changes at three different time-points after ethephon treatment: 8, 24 and 48 h. Transcript levels of 163 genes were significantly altered with fold-change values ≥ 2 or ≤ –2 (q-value < 0.05) in ethephon-treated compared with control rubber trees. Of the 163 genes, 92 were up-regulated and 71 down-regulated. The microarray results were further confirmed using real-time quantitative reverse transcript-PCR for 20 selected genes.

2016-06-01 | GSE74060 | GEO

Gene expression in the hippocampus of Mef2c-HET mice

Project description:Gene expression of Mef2c-het mice vs. WT littermates in hippocampus Total RNA isolated from hippocampus of P1 and P30 aged Mef2c-HET and WT mice using QIAGEN miRNeasy mini kit (QIAGEN; Cat #217004) were processed on an Illumina mouse Ref8 v2 beadchip microarrays following the manufacture’s protocol. Microarray data analysis was performed using R and Bioconductor packages. Raw expression data were log2 transformed and normalized by quantile normalization. Probes were considered robustly expressed if the detection P value was 0.01 for at least half of the samples in the data set.

2017-08-30 | GSE103298 | GEO

Transcriptional profiles of adult Schistosoma japonicum in response to insulin

Project description:To define the differential gene regulation of adult Schistosoma japonicum in response to host insulin, we utilised a parasite microarray with 38,444 probes representing 19,222 genes. We cultured male and female adult worms were exposed to insulin and glucose; and then parasites were collected at three time-points. There were 1,437 probes (1101 genes) up or down regulated (±1.5 fold change) by insulin after 0.5, 3, 24 hours, with the majority, 712 probes (577 genes) and 623 probes (486 genes) were up-regulated at 24 hour of adding insulin in males and females respectively compared with the control (without insulin).

2008-12-12 | GSE13891 | GEO

Expression profiling of formalin-fixed, paraffin-embedded (FFPE) breast cancer metastases of the lymph node and autopsy tissues [DASL HumanRef-v3 samples]

Project description:We performed an expression profiling study of 168 primary breast tumors, lymph node metastases, and autopsy samples of primary breast tumours and metastases to liver, chest wall, lymph node, lung, and spleen, as well as positive and negative RNA controls, with technical replicates, to assess quality control methodology and probe-level reproducibility of the Illumina DASL microarray assay. The experiment included both Illumina DASL HumanRef-v3 and DASL HT-12; this series includes only the 120 HumanRef-v3 samples .

2012-10-02 | GSE32489 | GEO

Expression data for human epithelium from subjects with atopic dermatitis, psoriasis and nonatopic controls

Project description:The expression and function of tight junction genes, in particular claudin-1, was studied in order to further understanding of the biology underlying atopic dermatitis. Gene expression profiling was performed on total RNA from nonlesional epidermal samples from 5 subjects with atopic dermatitis, 4 subjects with psoriasis, and 5 nonatopic controls using the Illumina Sentrix HumanRef-8 Expression BeadChip. There were duplicate (technical replicate) arrays run for 2 of the nonatopic control samples (the normalized transformed expression values of replicate pairs were averaged before performing data analysis, also, for each probe, the combined value for replicate pairs of Detection Pvalues was taken to be their minimum - so a Present call for one of the replicate pair of expression values results in a Present call for the combined (average) expression value). Details of the design and the results found are given in the paper associated with this GEO Series.

2011-01-29 | E-GEOD-26952 | biostudies-arrayexpress

PTSD Raw Data

Project description:PTSD - Posttraumatic stress disorder. 33 samples taken from PMBCs of survivors of psychological trauma, in two time points: in ER, few hours after the truma, and four months later. Some of the patients devepled chronic PTSD (17 samples) and others recovered and set to be the Control group (16 samples). This is the raw data consists of 12,600 probes from U95A chip. Samples are labeled with 3 tags: P/C for PTSD or Control, ER/M4 - for time point of sample, D/ND for Decrement or Non-decrement symptoms over time. (e.g. sample 23C-M4-D was taken 4 months after trauma from patient 23 which belongs to the control group and showed decrease in symptoms) . Samples include the expression value, the GeneBank accession number and Affymetrix indication of valid calls. Keywords: other

2004-11-20 | GSE845 | GEO

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