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Peripheral blood lymphocytes: ALS patients vs. healthy controls

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.

ORGANISM(S): Homo sapiens

PROVIDER: GSE28253 | GEO | 2011/12/11

SECONDARY ACCESSION(S): PRJNA139801

REPOSITORIES: GEO

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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

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Peripheral blood lymphocytes: ALS patients vs. healthy controls

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