Peripheral blood lymphocytes: ALS patients vs. healthy controls
Ontology highlight
ABSTRACT: Transcripional profiling of lymphocytes from patients with amyotrophic lateral sclerosis (ALS) (n=11) and healthy control subjects (n=11). The goal was to determine disease response expression signatures relevant of ALS pathogenesis that affect brain and spinal cord. The reference design was used: each Cy5-labeled cRNA sample from ALS patient or healthy control subject was cohybridized on Agilent-014850 Whole Human Genome Microarray 4x44K G4112F with the reference pool formed with equal amounts of Cy3-labeled cRNAs from each sample from the healthy control group.
Project description:Transcripional profiling of lymphocytes from patients with amyotrophic lateral sclerosis (ALS) (n=11) and healthy control subjects (n=11). The goal was to determine disease response expression signatures relevant of ALS pathogenesis that affect brain and spinal cord. The reference design was used: each Cy5-labeled cRNA sample from ALS patient or healthy control subject was cohybridized on Agilent-014850 Whole Human Genome Microarray 4x44K G4112F with the reference pool formed with equal amounts of Cy3-labeled cRNAs from each sample from the healthy control group. Eleven lymphocyte samples from definite sporadic ALS patients and eleven samples from healthy control subjects were used.
Project description:RNA from 11 individual mouse cell lines were reverse-transcribed to cDNA, labeled with Cy5 and cohybridized with Cy3-labeled UMRR onto 7,500-spot mouse oligo microarrays (UNC). The data was analyzed using GeneTraffic software. 300-1000 spots out of 8,000 were flagged on each microarray and excluded from further analysis. Spots with hybridization signals in Cy5 channel higher than 1000 and with Cy5/Cy3 ratio greater than 2 were collected and the number of spots with these characteristics on only one microarray was determined. A reference experiment design type is where all samples are compared to a common reference. Keywords: reference_design
Project description:Array CGH of H. pylori strain BCS100 after challenge to a new host (patients and experiment described in Graham et al., 2004, Gut, 53:1235-1243). Genomic DNA (500 ng) from the ouput from singel colony isolates obtained 15 or 90 days post innoculation were labeled with Cy5 (red) and cohybridized with 500 ng of genomic DNA from the innoculating strain BCS100 labeled with Cy3 (green). A reference experiement design type is where all samples are compared to a common reference. Keywords: reference_design
Project description:Lycopersicon esculentum cv. Moneymaker tomato plants were grown for 4 weeks in greenhouse conditions (16h/8h light/darkness, 27 °C). L. esculentum was randomly sorted into two groups of 16 plants each and a third reference group of 6 plants. All plants were contained individually in mesh bags. One group of 16 plants was infested with 25 female adult tomato psyllids that were 2-3 days old per plant. The other two groups of 16 and 6 plants were not infested (healthy control, and reference pool). After 3 days, the adults were removed from the infested plants to allow for egg eclosion and eventually nymphal development. In this study, leaves infested and healthy plants were harvested for RNA extraction at 0, 3, 11, and 17 days after infestation with tomato psyllids. The reference pool was harvested on day 0. Tissue (all-leaflets) from at least three plants per group was collected, flash frozen in liquid nitrogen and pooled for each time point (0, 3, 11 and 17 days after infestation) to represent treatments for before feeding (0 d), adult feeding and egg deposition (3 d), 1st and 2nd instar feeding (11 d) and 3rd to 5th instar feeding (17 d ), respectively. The whole experiment was repeated three times (three biological replicates). Plant tissues were ground using a cold mortar and pestle. Total tomato leaf RNA was extracted using the hot-phenol protocol. The RNA was precipitated, pooled, cleaned with a kit and stored at –80C. Two populations of single-stranded cDNAs will be generated from the aliquots and labeled with the cyanine Cy3 and Cy5 fluorophores. RNA isolated from the reference pool (0 d) will be pooled from each replicate and will be labeled with Cy5; this is the reference sample for each hybridization. RNA isolated from leaves infested with tomato psyllids and healthy uninfested plants from each time point will be query samples labeled with Cy3. The two samples of labeled cDNA will be simultaneously hybridized to the same microarray. Keywords: Reference design
Project description:Gene Expression Profiling of Oral Squamous Cell Carcinoma (OSCC) was performed to delineate candidate genes clusters with potential to distinguish normal and tumor tissue from oral cavity. All tissue samples were collected after obtaining written informed consent. The RNA profile of 27 OSCC patients was compared with 4 independent controls and 1 pooled control oral cavity tissue from healthy donors. Agilent one-color experiment, Organism: Human, Agilent-014850 Whole Human Genome Microarray 4x44K G4112F
Project description:In this study, we compared global gene expressions between pre- and post- intravenous immunoglobulin (IVIG) administration in nineteen Kawasaki disease (KD) patients. Peripheral blood mononuclear cells (PBMCs) obtained from nineteen patients before and after IVIG treatment was extracted using a PAXgene blood RNA isolation kit. Amplified cRNAs of each patient were analyzed using with Agilent Whole Human Genome Microarray 4x44K G4112F array.
Project description:RNA from 11 individual mouse cell lines were reverse-transcribed to cDNA, labeled with Cy5 and cohybridized with Cy3-labeled UMRR onto 7,500-spot mouse oligo microarrays (UNC). The data was analyzed using GeneTraffic software. 300-1000 spots out of 8,000 were flagged on each microarray and excluded from further analysis. Spots with hybridization signals in Cy5 channel higher than 1000 and with Cy5/Cy3 ratio greater than 2 were collected and the number of spots with these characteristics on only one microarray was determined. A reference experiment design type is where all samples are compared to a common reference. Computed
Project description:Total RNA from each sample was quantified using the NanoDrop ND-1000. The sample preparation and microarray hybridization were performed based on the Arraystar’s standard protocols. Briefly, total RNA from each sample was amplified and transcribed into fluorescent cRNA utilizing random primer according to Arraystar’s Super RNA Labeling protocol (Arraystar Inc.). The labeled cRNAs were hybridized onto the Arraystar Human circRNA Array (8x15K, Arraystar). After having washed the slides, the arrays were scanned by the Agilent Scanner G2505C.
Project description:Human expression microarray analysis of the 11 samples that you submitted. Total RNA from each sample was quantified using the NanoDrop ND-1000 and the RNA integrity was assessed using standard denaturing agarose gel electrophoresis. For microarray analysis, Agilent Array platform was employed. The sample preparation and microarray hybridization were performed according to the manufacturer’s standard protocols. Briefly, total RNA from each sample was amplified and transcribed into fluorescent cRNA with using the manufacturer’s Agilent’s Quick Amp Labeling protocol (version 5.7, Agilent Technologies). The labeled cRNAs were hybridized onto the Whole Human Genome Oligo Microarray (4x44K, Agilent Technologies). After having washed the slides, the arrays were scanned by the Agilent Scanner G2505C. Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using the GeneSpring GX v11.5 software package (Agilent Technologies). After quantile normalization of the raw data, genes that at least 7 out of 11 samples have flags in Detected (“All Targets Value”) were chosen for further data analysis.
Project description:Total RNA was quantified by the NanoDrop ND-2000 (Thermo Scientific)and the RNA integrity was assessed using Agilent Bioanalyzer 2100 (Agilent Technologies). The sample labeling, microarray hybridization and washing were performed based on the manufacturer's standard protocols. Briefly, total RNA were transcribed to double strand cDNA, then synthesized into cRNA and labeled with Cyanine-3-CTP. The labeled cRNAs were hybridized onto the microarray. After washing, the arrays were scanned by the Agilent Scanner G2505C (Agilent Technologies).