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Expression analysis of circadian light response in Drosophila recombinant inbred lines (RIL)

ABSTRACT: The aim of this study was to identify quantitative trait loci (QTL) associated with variation in circadian photosensitivity in Drosophila, by measuring the locomotor response to early night light pulse (Zt15). We used QTL mapping of recombinant inbred lines (RIL), which was followed by microarrays expression comparison of two RI lines which differed significantly in their light response (RIL 104 shows a strong long phase delay response while RIL 58 shows a weak light response).

ORGANISM(S): Drosophila melanogaster

PROVIDER: GSE77116 | GEO | 2016/02/09

SECONDARY ACCESSION(S): PRJNA309484

REPOSITORIES: GEO

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Expression analysis of circadian light response in Drosophila recombinant inbred lines (RIL)

Project description:The aim of this study was to identify quantitative trait loci (QTL) associated with variation in circadian photosensitivity in Drosophila, by measuring the locomotor response to early night light pulse (Zt15). We used QTL mapping of recombinant inbred lines (RIL), which was followed by microarrays expression comparison of two RI lines which differed significantly in their light response (RIL 104 shows a strong long phase delay response while RIL 58 shows a weak light response). Each of the two strains was sampled after light pulse, and without a light pulse (control), totalling 8 samples: 2x lines (L) x treatments (T) x 2 replicates

2016-02-09 | E-GEOD-77116 | biostudies-arrayexpress

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Project description:affy_zeawall_ril_maize - Four major QTL explaining lignin content and cell wall degradability variation have been identified in the F288 x F271 RIL progeny (Roussel et al., 2002, Maydica 47: 9-20). Gene expression has been considered as a way in identification of candidate gene underlying QTL. Five lines chosen for their allelic pattern at four main QTL were considered for expression studies, two lines with all four favorable alleles (RIL99, RIL54), two lines with the unfavorable allele at bin 6.06 QTL position (RIL39 , RIL71), and one line with the unfavorable allele at bin 9.02 QTL position (RIL118). Expression study will be investigated in ear internode at two stages emerging tassel and early silking stages with two replicates. Plants were cropped at INRA Lusignan (Vienne, France) in 2009 in a bloc design with two four-row replicates. Below-ear internodes of five representative RIL plants of one row in each replicate were harvested at the two stages and pooled. Keywords: genotype comparison, time course

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affy_zeawall_ril_maize - Expression studies in 5 early maize RIL with contracted allelic patterns at major QTL posititions

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Hfq RIL-seq analysis

Project description:In this study we used RIL-seq (RNA interaction by ligation and sequencing) to identify Hfq-mediated RNA-RNA interactions in V. cholerae.

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rilkit-eqtl analysis (random pair design). Tools to optimize the use of RIL populations for natural diversity studies and QTL cloning

Project description:gnp07_rilkit - rilkit-eqtl analysis (random pair design). To provide quantitative geneticists studying natural variation in our RIL populations with information and resources necessary to speed up QTL cloning and candidate genes identification. This articulates around the creation of two major resources and their integration into databases to make the information accessible to users: A. Whole transcriptome survey, B. Production of complementary material. Comparison of 164 Cvi/Col(8RV) Recombinant Inbred Lines (RILs) and 164 Bur/Col (20RV) RILs.

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rilkit-eqtl analysis (random pair design). Tools to optimize the use of RIL populations for natural diversity studies and QTL cloning

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Molecular insights on the peripheral and intra-tumoral effects of systemic high dose rIL-2 (Aldesleukin) administration for the treatment of metastatic melanoma

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2012-10-01 | GSE32611 | GEO

Quantitative trait loci mapping and transcriptome analysis reveal candidate genes regulating the response to ozone in Arabidopsis thaliana

Project description:The formation of Reactive oxygen species (ROS) has been detected in all cellular departments and even in apoplastic space of plants. As multifaceted molecule, ROS are known to accumulate in response to various stresses, and ROS burst accompanied with transcriptomic reprogramming leading to defense response or programmed cell death. Acute ozone exposure has been used as a noninvasive tool to study ROS burst induced defense response and cell death for a long time. Moreover the variation of ozone sensitivity in different Arabidopsis accessions highlights the flexibility of complex genetic architecture to adapt to specific stresses. In this study, we combine classic Quantitative Trait Loci (QTL) mapping and RNA-seq to identify the cause QTLs and potential gene candidates in response to ozone. RNA sequencing was performed on both control and ozone treated 3 weeks old accessions C24 (ozone tolerant), Te (ozone sensitive) and on a RIL line CT101 (a hypersensitive line of RIL population from reciprocal cross between C24 and Te), in triplicate. We identified 69 potential genes candidates inside the QTL regions and about 200 potential genes outside QTL region in response to ozone by comparing control to treatment within same genotype or comparing control between genotypes.

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