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On the relevance of technical variation due to building pools in microarray experiments [Honey bee]

ABSTRACT: The objective of the study was to assess the technical error due to blending of individual samples into pools in different experimental data sets. The blending error variance component corresponds to random effects for inaccuracies, which were modeled on the logarithmic scale of normalized gene expression. It's estimation based on a linear mixed model, fitted for each transcript.

ORGANISM(S): Apis mellifera

PROVIDER: GSE72943 | GEO | 2015/09/11

SECONDARY ACCESSION(S): PRJNA295389

REPOSITORIES: GEO

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On the relevance of technical variation due to building pools in microarray experiments [Honey bee]

Project description:The objective of the study was to assess the technical error due to blending of individual samples into pools in different experimental data sets. The blending error variance component corresponds to random effects for inaccuracies, which were modeled on the logarithmic scale of normalized gene expression. It's estimation based on a linear mixed model, fitted for each transcript. Honey bees showing hygienic behavior towards Varroa-parasitized brood were compared with controls and among each other. Tissues from mushroom body, antennal lobe and Antennae of honey bees were processed for microarray analysis. They were measured as single samples as well as pooled samples from 2 or 4 individuals.

2015-09-11 | E-GEOD-72943 | biostudies-arrayexpress

On the relevance of technical variation due to building pools in microarray experiments [Mouse]

2015-09-10 | GSE72861 | GEO

On the relevance of technical variation due to building pools in microarray experiments

Project description:The objective of the study was to assess the technical error due to blending of individual samples into pools in experimental data. The blending error variance component corresponds to random effects for inaccuracies, which were modeled on the logarithmic scale of normalized gene expression. It's estimation based on a linear mixed model, fitted for each transcript. Ovaries from 30 animals of line FL1 and of the control line DUKsi were collected at the metestrous stage. They were combined to 6 pools of 5 individuals each and processed for microarray analysis. Additionally, the 10 individuals used for the first two pools of each line were processed.

2015-09-10 | E-GEOD-72861 | biostudies-arrayexpress

On the relevance of technical variation due to building pools in microarray experiments

Project description:This SuperSeries is composed of the SubSeries listed below.

2015-09-11 | GSE72944 | GEO

On the relevance of technical variation due to building pools in microarray experiments

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2015-09-11 | E-GEOD-72944 | biostudies-arrayexpress

On the relevance of technical variation due to building pools in microarray experiments.

Project description:Pooled samples are frequently used in experiments measuring gene expression. In this method, RNA from different individuals sharing the same experimental conditions and explanatory variables is blended and their concentrations are jointly measured. As a matter of principle, individuals are represented in equal shares in each pool. However, some degree of disproportionality may arise from the limits of technical precision. As a consequence a special kind of technical error occurs, which can be modelled by a respective variance component. Previously published theory - allowing for variable pool sizes - has been applied to four microarray gene expression data sets from different species in order to assess the practical relevance of this type of technical error in terms of significance and size of this variance component.The number of transcripts with a significant variance component due to imperfect blending was found to be 4329 (23 %) in mouse data and 7093 (49 %) in honey bees, but only 6 in rats and none whatsoever in human data. These results correspond to a false discovery rate of 5 % in each data set. The number of transcripts found to be differentially expressed between treatments was always higher when the blending error variance was neglected. Simulations clearly indicated overly-optimistic (anti-conservative) test results in terms of false discovery rates whenever this source of variability was not represented in the model.Imperfect equality of shares when blending RNA from different individuals into joint pools of variable size is a source of technical variation with relevance for experimental design, practice at the laboratory bench and data analysis. Its potentially adverse effects, incorrect identification of differentially expressed transcripts and overly-optimistic significance tests, can be fully avoided, however, by the sound application of recently established theory and models for data analysis.

| S-EPMC4667463 | biostudies-literature

Honey Bee

Project description:Apis cerana, Apis florea, Apis dorsata, Apis mellifera, Trigona Genome sequencing and assembly

| PRJNA1127320 | ENA

Honey bee "Apis mellifera intermissa"

Project description:Apis mellifera intermissa (Buttel-Reepen, 1906) is the native honeybee subspecies of Algeria. A.m.intermissa occurs in Tunisia, Algeria and Morocco, between the Atlas and the Mediterranean and Atlantic coasts (Ruttner, 1988), in an area of more than 2500 km long. Intermissa indicates the position through this bee races between tropical Africa and European breeds (Peyvel, 1994). The settlement area of the Tellian extends from Tunisia to Morocco. Ruttner et al (1978) describes the pure Tellian. It is a black hair of his coat poverty brings out the black color. It is a small size, there are some times light illumination on the tergites. This bee is very aggressive, nervous, sick to take part, as swarms huge fall and even produced many brood and can build up to one hundred queen cells (Le Conte, 2002). A.m.intermissa is prone to swarming, shows an aggressive behaviour and an abundant use of propolis (Ruttner 1988). This study is part of the project funded by the USAID Grant No. TA-MOU-08-M29-075.

2016-02-01 | GSE45464 | GEO

Honey bee: Apis mellifera syriaca

Project description:Apis mellifera syriaca is the native honeybee subspecies of Jordan and much of the Middle East. It expresses behavioral adaptations to a regional climate with very high temperatures, nectar dearth in summer, attacks of the Oriental wasp Vespa orientalis and in most cases it is resistant to varroa mites. The Thorax control sample of A. m. syriaca in this experiment was originally collected and stored since 2001 from Wadi Ben Hammad a remote valley in the southern region of Jordan. Using morphometric and Mitochondrial DNA markers it was proved that bees from this area had show higher similarity than other samples collected from the Middle East as represented by reference samples collected in 1952 by Brother Adam. The samples L1-L5 are collected from the National Center for Agricultural Research and Extension breading apiary which was originally established for the conservation of Apis mellifera syriaca. Goal was to use the genetic information in the breeding for varroa resistant bees and to determine the successfulness of this conservation program. Project funded by USAID-MERC grant number: TA-MOU-09-M29-075.

2016-02-01 | GSE43554 | GEO

Transcriptome of honey bee larvae

Project description:Honey bee drones, queens and workers have vastly different phenotypes. Here we profile the the expression level of mRNAs and microRNAs of honeybee, drones, queens and workers at the L5 larval stage (91 hours +/- 1).

2015-09-06 | GSE61253 | GEO

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