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Expression data from FIRE deficient mice

ABSTRACT: We used microarrays to examine changes in gene expression in the absence of the FIRE enhancer of Csf1r in mice.

ORGANISM(S): Mus musculus

PROVIDER: GSE108207 | GEO | 2019/03/18

REPOSITORIES: GEO

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Expression data from FIRE deficient mice

Project description:Expression data from FIRE deficient mice

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Project description:We used microarray to examine changes in gene expression in the absence of Csf1r in the brain and spleen. Spleen gene expression was compared to BMDM to identify splenic-specific genes.

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Transcriptional profiling by array of Solenopsis invicta (fire ant) workers to identify genes and gene pathways responsible for division of labor

Project description:We used whole-genome fire ant microarrays to examine the molecular basis for division of labor in fire ant workers by comparing foraging and non-foraging workers from monogyne colonies. Fire ant colonies were collected in the field and transported into the lab were they were reared in standard conditions. We created a nesting chamber containing the queen, the brood and workers performing nursing tasks and a foraging area, separated from the nesting chamber and provided with food and water sources. Foraging workers were collected in the foraging area while non-foraging workers were collected in the nesting chamber. Total RNA was isolated from pools of whole workers and processed for microarrays.

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Fire ant worker brain transcriptomes

Project description:Transcriptomes of dissected brains from workers from polygyne fire ants were analyzed. Four replicates were obtained.

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Transcriptional profiling by array of Solenopsis invicta (fire ant) workers to identify genes and gene pathways responding to the queen presence

Project description:We used whole-genome fire ant microarrays to examine the molecular basis for social organization in Solenopsis invicta. Monogyne (single queen) fire ant colonies were collected in the field and transported into the lab were they were reared in standard conditions for two weeks. At this point, each colony was split into two sub-colonies: one sub-colony contained the functional mother queen (queenright) while the other was left queenless. Each sub-colony included a nesting chamber, containing the brood and workers performing nursing tasks, and a foraging area, separated from the nesting chamber and provided with food and water sources. For both queenright and queenless sub-colonies, foraging workers were collected in the foraging area while non-foraging workers were collected in the nesting chamber. Total RNA was isolated from pools of 10 whole workers and processed for microarrays.

2014-01-08 | E-MTAB-2108 | biostudies-arrayexpress

Fire ant adult vs brood comparison for microarray quality control

Project description:Ants display a range of fascinating behaviors, a remarkable level of intra-species phenotypic plasticity and many other interesting characteristics. Here we present a new tool to study the molecular mechanisms underlying these traits: a tentatively annotated expressed sequence tag (EST) resource for the fire ant Solenopsis invicta. From a normalized cDNA library we obtained 21,715 ESTs, which represent 11,864 putatively different transcripts with very diverse molecular functions. All ESTs were used to construct a cDNA microarray. We compared mixed adults to mixed brood to test the quality of the microarrays. Keywords: microarray quality control

2006-10-14 | GSE5995 | GEO

DNA methylomes of the fire ant Solenopsis invicta.

Project description:We used whole bodies of four different adult fire ant morphs (alate queens, workers, haploid males, and diploid males) from a single polygyne colony to generate single-base resolution DNA methylation maps.

2013-03-27 | GSE39959 | GEO

Fire chronosequences (ITS)

Project description:Fire effects on fungal communities

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Calibration of a custom designed microarray for European Fire Salamander

Project description:A custom 8x60 k expression microarray for larvae of European fire salamander (Salamandra salamandra) was designed based on transcriptome sequencing. It is known the fact, that oligonucleotide probes differ in the binding behavior towards their target sequences. Therefore, we performed a calibration of our microarray where we assessed the binding behavior of the individual probes empirically. This information was used to normalize gene expression data measurements with the same microarray in another experiment. Please refer to the accompanying publication (Czypionka et al. 2015." Ecological transcriptomics – a non-lethal sampling approach for endangered fire salamanders" Methods in Ecology and Evolution) for more information.

2015-06-20 | GSE70055 | GEO

Identification of apple miRNAs and their potentialrole in Fire Blight resistance

Project description:miRNAs are key players in multiple biological processes, therefore analysis and characterization of these small regulatory RNAs is a critical step towards better understanding of animal and plant biology. In apple (Malus domestica) two hundred microRNAs are known, which most probably represents only a fraction of miRNAome diversity. As a result, more effort is required to better annotate miRNAs and their functions in this economically important species. We performed deep sequencing of twelve small RNA libraries obtained for fire blight resistant and fire blight sensitive trees. In the sequencing results we identified 116 novel microRNAs and confirmed a majority of previously reported apple miRNAs. We then experimentally verified selected candidates with RT-PCR and stem-loop qPCR and performed differential expression analysis. Finally, we identified and characterized putative targets of all known apple miRNAs. In this study we considerably expand the apple miRNAome by identifying and characterizing dozens of novel microRNAs. Moreover, our data suggests that apple microRNAs might be considered as regulators and markers of fire blight resistance.

2015-01-09 | GSE59482 | GEO

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