Gene expression levels with various artificial mutations and inter-species array
Ontology highlight
ABSTRACT: This SuperSeries is composed of the following subset Series: GSE30978: Gene expression levels with various artificial mutations -- exact match GSE30981: Gene expression levels with various artificial mutations -- with mismatch GSE31201: Inter-species array between human, rat and mouse Refer to individual Series
Project description:Intracranial pediatric germ cell tumors (GCTs) have different histological differentiations, prognosis and clinical behaviors. Prognosis of patients with germinoma and mature teratoma is good, while patients with other types of GCTs, termed as nongerminomatous malignant germ cell tumors (NGMGCTs), require more extensive drug and irradiation treatment regimen. The mechanisms underlying different prognosis of various GCT subgroups remain elusive. We presented the first miRNA profile of pediatric primary intracranial GCTs. 12 central nervous system GCT cases with different histological subtypes are subjected to miRNA expression analysis. The histological subtypes are germinoma, mixed GCT of germinoma and mature teratoma , immature teratoma , mixed GCTs of NGMGCTs category, yolk sac tumor, immature teratoma, and embryonal carcinoma.
Project description:We propose a new microarray method, called an inter-species array, that can measure gene expression levels of multiple species at once. As the array operates simply by changing the probes on an Agilent commercial customized array, and conventional facilities and protocols can be used, the method is cost-efficient. We generated an array for humans, rats and mice that covers 6683 genes. The number of genes is larger than that of previous arrays. We measured the expression of genes in astrocyte cells for humans and rats, and in cortex cells for rats and mice. Single array with multiple species samples.
Project description:We checked the effects of mutations on expression levels by using systematically mutated probes. We used Agilent custom microarray whose probe length is 60bp. To check artificial mutation effect, we designed 56 patterns of mutations, 24 patterns of insertions and deletions. On the microarray, we used 7,987 probes from Agilent human gene probes. In these experiments, we checked the difference of expression levels about at least 73 probes for each mutation type. We performed microarray experiments with an Agilent 4x44k custom microarray. We measured gene expressions using a qPCR Human reference total RNA sample provided by CloneTech. Gene expression profiles were normalized with quintile normalization according to the Agilent protocol except that only non-mutated 219 probes were used. 6 replicate samples
Project description:We performed microarray analysis with two different chip platforms, Affymetrix and Agilent, on bone metastasis samples from breast cancer patients with only bone metastases and metastases in bone and visceral organs. We collected bone metastases biopsies from breast cancer patients with only bone metastases and metastases in bone and visceral organs. RNA was extracted from these samples and subjected to microarray analysis with the Agilent platform. Data were compared with a signsture obtained with the Affymetrix platform, to obtain a signature of differentially regulated genes between the two groups of patients This Series represents the Agilent data only. The Affymetrix data are provided in GEO Series GSE11078.
Project description:In order to characterize iHep cells more precisely, we conducted global gene expression analyses using microarrays to compare among the gene expression profiles of MEFs, iHep cells and adult mouse hepatocytes. Three MEF samples that were individually prepared from 13.5 days post coitum (dpc) embryos, three types of iHep cells and hepatocytes obtained from the adult mouse liver were used.
Project description:A comparative study to determine the pepper leaf curl virus resistance machanism between resistant and susceptible genotypes at three leaf stage. To study the molecular mechanism of pepper leaf curl virus (PepLCV) resistance, pepper plants were exposed to PepLCV through artificial inoculation and hybridization on Agilent tomato microarrays. The expression analysis of PepLCV resistant and susceptible genotypes after artificial inoculation at three leaf stage showed that the resistance against PepLCV is due to sum of expression of hundreds of genes at a particular stage. Tomato microarrays consisting of 43,803 probes were used for whole genome expression analysis of chilli peppers for resistance against PepLCV. Transcripts from the leaves of resistant (BS-35) and susceptible plants (IVPBC-535) were compared in response to PepLCV inoculation at three leaf stage.
Project description:Hepatocellular carcinoma (HCC) is the third leading cause of cancer-related death worldwide. We sequenced and analyzed the whole genomes of primary HCCs. To examine the influence of transcription-coupled repair (TCR) on somatic substitution patterns in HCC, we performed expression microarrays analysis and compared gene expression levels and the number of substitutions in 7 HCCs. Seven primary HCC were analyzed and compared with somatic substituion numbers.
Project description:The 2.2 Mb long dystrophin (DMD) gene, the largest gene in the human genome, corresponds to roughly 0.1% of the entire human DNA sequence. Mutations in this gene cause Duchenne muscular dystrophy and other milder X-linked, recessive dystrophinopathies. Using a custom-made tiling array, specifically designed for the DMD locus, we identified a variety of novel long non-coding RNAs (ncRNAs), both sense and antisense oriented, whose expression profiles mirror that of DMD gene. Importantly, these transcripts are intronic in origin and specifically localized to the nucleus and are transcribed contextually with dystrophin isoforms or primed by MyoD-induced myogenic differentiation. Furthermore, their forced ectopic expression in both human muscle and neuronal cells causes a specific and negative regulation of endogenous dystrophin full length isoforms and significantly down-regulate the activity of a luciferase reporter construct carrying the minimal promoter regions of the muscle dystrophin isoform. Consistent with this apparently repressive role, we found that, in muscle samples of DMD symptomatic female carriers, lncRNAs expression levels inversely correlate with those of muscle full length DMD isoforms. Overall these findings unveil an unprecedented complexity of the transcriptional pattern of the DMD locus and reveal that DMD-specific lncRNAs may contribute to the orchestration and homeostasis of the muscle dystrophin expression pattern by selective targeting and down-modulation of dystrophin promoter transcriptional activity. We tiled the entire DMD gene, in both sense and antisense directions, using the web-based Agilent eArray database, Version 4.5 (Agilent Technologies), with 60-mer oligos every 66 bp of repeat-masked genome sequence. We defined probe sets for both orientations, encompassing the DMD exons, promoters, introns, predicted MiRNA (identified by PromiRII) and conserved non-coding sequences (CNSs) identified within dystrophin introns using the VISTA programme (http://genome.lbl.gov/vista/index.shtml). Two specific sets of probes were designed to cover, in both directions, the cDNA sequences of a group of control genes identified in the Gene Expression Omnibus (GEO) database http://www.ncbi.nlm.nih.gov/geo/) and expressed equally in both normal and dystrophic muscles. Each probe set was opportunely distributed and replicated several times in order to obtain two 4x44k microarrays, referred to as DMD GEx Sense and DMD GEx Antisense, respectively, able to detect transcripts in the same and opposite directions as that of DMD gene transcription. Three commercial poly A+ RNAs from normal human brain, heart and skeletal muscle tissues were utilised (Ambion). Skin poly A+ RNA was isolated from total Skin RNA (Stratagene) using the Qiagen Oligotex kit. All RNA samples were checked for purity using a ND-1000 spectrophotometer (NanoDrop Technologies), and for integrity by electrophoresis on a 2100 BioAnalyzer (Agilent Technologies). Sample labelling and hybridisation were performed according to the protocols provided by Agilent (One-Color Microarray-Based Gene Expression Analysis version 5.0.1). The array was analysed using the Agilent scanner and Feature Extraction software (v9.1).
Project description:We checked the effects of mutations on expression levels by using systematically mutated probes. We used Agilent custom microarray whose probe length is 60bp. To check artificial mutation effect, we designed 56 patterns of mutations, 24 patterns of insertions and deletions. On the microarray, we used 7,987 probes from Agilent human gene probes. In these experiments, we checked the difference of expression levels about at least 73 probes for each mutation type. We performed microarray experiments with an Agilent custom microarray. We measured gene expressions using a qPCR Human reference total RNA sample provided by CloneTech. Gene expression profiles were normalized with quintile normalization according to the Agilent protocol except that only non-mutated 219 probes were used. 6 replicate samples
Project description:To know the difference of transcriptome between Wild type and Akt1+/- mice, 8weeks and 35weeks female mice were subjected to microarray analysis. Wild type and Akt1+/- mice in age 8weeks and 35weeks were subjected to microarray analysis. Liver, muscle and visceral fat were used. Only female mice were used.