Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR12705450_1.fastq.gz | Fastqsanger.gz | |||
| SRR12705450_2.fastq.gz | Fastqsanger.gz | |||
| SRR12705451_1.fastq.gz | Fastqsanger.gz | |||
| SRR12705451_2.fastq.gz | Fastqsanger.gz | |||
| SRR12705452_1.fastq.gz | Fastqsanger.gz |
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Project description:amplicon and shotgun metagenomic sequencing of nitrate-dependent Sb(III) oxidizers
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Project description:In the fire ant Solenopsis invicta, a colony queen number is determined by the founding queen's genotypes at the 13 Mb supergene with the non-recombining variants SB and Sb. Single-queen colonies are always headed by SB/SB queens while multiple-queens colonies are always headed by SB/Sb queens. The two variants of the supergene, SB and Sb are completely linked to the two alleles (B and b) of the gene Gp-9. SB/SB and SB/Sb queens differ in many physiological traits including their maturation rate and odor. To explain why SB/SB and SB/Sb queens have different odors, and why SB/SB virgins mature faster and accumulate more fat, we measured expression of ~6000 genes in virgin queens 1 and 11 days after eclosion and in reproductive queens. Keywords: fire ants, Solenopsis invicta, Supergene, queen, Gp-9, social form, maturation, fat storage, queen odor, cuticular hydrocarbon, worker discrimination, monogyne, polygyne, transposon, chemical signaling
2012-11-07 | GSE42062 | GEO
Project description:Queen discrimination behavior in the red imported fire ant Solenopsis invicta maintains its two types of societies: colonies with one (monogyne) or many (polygyne) queens, yet the underlying genetic mechanism is poorly understood. This behavior is controlled by two supergene alleles, SB and Sb, with ~600 genes. Polygyne workers, having either the SB/SB or SB/Sb genotype, accept additional SB/Sb queens into their colonies but kill SB/SB queens. While monogyne workers, all SB/SB, reject all additional queens regardless of genotype. Because the SB and Sb alleles do not recombine, it is difficult to determine which genes within the supergene mediate this differential worker behavior. We hypothesized that the alternate worker genotypes sense queens differently because of different patterns of gene expression in their main sensory organ, the antennae. To identify such differentially expressed genes, we sequenced RNA from four biological replicates of pooled antennae from three groups of workers: monogyne SB/SB, polygyne SB/SB, and polygyne SB/Sb. We identified 81 differentially expressed protein coding genes with 14 encoding potential odor metabolism and perception proteins. We focused on the two differentially expressed odorant perception genes: an odorant binding protein SiOBP12 and an odorant receptor SiOR463. We found that the SiOR463 was lost in the Sb-genome. In contrast, the SiOBP12 has an Sb-specific duplication SiOBP12b’, which was expressed in the SB/Sb worker antennae, while both paralogs SiOBP12 and SiOBP12b’ were expressed in the body. This result indicates that SiOBP12b’ has gained an antennal promoter or enhancer and suggests neofunctionalization, perhaps for queen discrimination behavior.
2020-04-10 | GSE126674 | GEO
Project description:Queen discrimination behavior in the red imported fire ant Solenopsis invicta maintains its two types of societies: colonies with one (monogyne) or many (polygyne) queens, yet the underlying genetic mechanism is poorly understood. This behavior is controlled by two supergene alleles, SB and Sb, with ~600 genes. Polygyne workers, having either the SB/SB or SB/Sb genotype, accept additional SB/Sb queens into their colonies but kill SB/SB queens. While monogyne workers, all SB/SB, reject all additional queens regardless of genotype. Because the SB and Sb alleles do not recombine, it is difficult to determine which genes within the supergene mediate this differential worker behavior. We hypothesized that the alternate worker genotypes sense queens differently because of different patterns of gene expression in their main sensory organ, the antennae. To identify such differentially expressed genes, we sequenced RNA from four biological replicates of pooled antennae from three groups of workers: monogyne SB/SB, polygyne SB/SB, and polygyne SB/Sb. We identified 81 differentially expressed protein coding genes with 14 encoding potential odor metabolism and perception proteins. We focused on the two differentially expressed odorant perception genes: an odorant binding protein SiOBP12 and an odorant receptor SiOR463. We found that the SiOR463 was lost in the Sb-genome. In contrast, the SiOBP12 has an Sb-specific duplication SiOBP12b’, which was expressed in the SB/Sb worker antennae, while both paralogs SiOBP12 and SiOBP12b’ were expressed in the body. This result indicates that SiOBP12b’ has gained an antennal promoter or enhancer and suggests neofunctionalization, perhaps for queen discrimination behavior.
2020-04-10 | GSE126673 | GEO
Project description:Queen discrimination behavior in the red imported fire ant Solenopsis invicta maintains its two types of societies: colonies with one (monogyne) or many (polygyne) queens, yet the underlying genetic mechanism is poorly understood. This behavior is controlled by two supergene alleles, SB and Sb, with ~600 genes. Polygyne workers, having either the SB/SB or SB/Sb genotype, accept additional SB/Sb queens into their colonies but kill SB/SB queens. While monogyne workers, all SB/SB, reject all additional queens regardless of genotype. Because the SB and Sb alleles do not recombine, it is difficult to determine which genes within the supergene mediate this differential worker behavior. We hypothesized that the alternate worker genotypes sense queens differently because of different patterns of gene expression in their main sensory organ, the antennae. To identify such differentially expressed genes, we sequenced RNA from four biological replicates of pooled antennae from three groups of workers: monogyne SB/SB, polygyne SB/SB, and polygyne SB/Sb. We identified 81 differentially expressed protein coding genes with 14 encoding potential odor metabolism and perception proteins. We focused on the two differentially expressed odorant perception genes: an odorant binding protein SiOBP12 and an odorant receptor SiOR463. We found that the SiOR463 was lost in the Sb-genome. In contrast, the SiOBP12 has an Sb-specific duplication SiOBP12b’, which was expressed in the SB/Sb worker antennae, while both paralogs SiOBP12 and SiOBP12b’ were expressed in the body. This result indicates that SiOBP12b’ has gained an antennal promoter or enhancer and suggests neofunctionalization, perhaps for queen discrimination behavior.
2020-04-10 | GSE126368 | GEO
Project description:Sleep bruxism (SB) is a disorder in which patients repeatedly make involuntary jaw movements during sleep. In this study, we performed bulk RNA sequencing (CTRL:SB = 3:3) using iPS cell-derived neurons established from SB patients to investigate gene expression patterns specific to SB patients.
2024-11-13 | GSE277985 | GEO
Project description:Sleep bruxism (SB) is a disorder in which patients repeatedly make involuntary jaw movements during sleep. In this study, we performed single nucleus RNA sequencing (CTRL:SB = 1:1) using iPS cell-derived neurons established from SB patients to investigate gene expression of each neural subtype specific to SB patients.
2024-11-13 | GSE278284 | GEO
Project description:In the fire ant Solenopsis invicta, a colony queen number is determined by the founding queen's genotypes at the 13 Mb supergene with the non-recombining variants SB and Sb. Single-queen colonies are always headed by SB/SB queens while multiple-queens colonies are always headed by SB/Sb queens. The two variants of the supergene, SB and Sb are completely linked to the two alleles (B and b) of the gene Gp-9. SB/SB and SB/Sb queens differ in many physiological traits including their maturation rate and odor. To explain why SB/SB and SB/Sb queens have different odors, and why SB/SB virgins mature faster and accumulate more fat, we measured expression of ~6000 genes in virgin queens 1 and 11 days after eclosion and in reproductive queens. Keywords: fire ants, Solenopsis invicta, Supergene, queen, Gp-9, social form, maturation, fat storage, queen odor, cuticular hydrocarbon, worker discrimination, monogyne, polygyne, transposon, chemical signaling Six-condition experiment: 1-day-old SB/SB virgins, 1-day-old SB/Sb virgins, 11-day-old SB/SB virgins, 11-day-old SB/Sb virgins, SB/SB reproductive queens, SB/Sb reproductive queens. Biological replicates: 8 for 1-day-old SB/SB virgins and 1-day-old SB/Sb virgins that were collected in 2008; 8 for 1-day-old SB/SB virgins, 1-day-old SB/Sb virgins that were collected in 2009; 7 for 11-day-old SB/SB virgins and 11-day-old SB/Sb virgins that were collected in 2008; 8 for 11-day-old SB/SB virgins and 11-day-old SB/Sb virgins that were collected in 2009; 8 for SB/SB and SB/Sb reproductive queens (only collected in 2009). Samples were labeled with Cy3 and were compared to the same common reference RNA labeled with Cy5. Samples from 2008 were hybridized on the microarrays batch I and samples from 2009 were hybridized on the microarrays batch J.
2012-11-07 | E-GEOD-42062 | biostudies-arrayexpress
Project description:Distinct miRNA expression patterns may reflect anomalies related to fetal malformations such as spinal bifida (SB) or congenital diaphragmatic hernia (CDH), which could shed light on novel pathomechanism determination and subsequent diagnostic significance evaluation. The aim of this study was to determine the miRNA maternal expression profile in plasma and amniotic fluid samples of women carrying fetuses with SB and CDH.
2024-03-20 | GSE242364 | GEO
Project description:Promoting rumen development is closely related to the health and efficient growth of ruminants. We investigated the effect of sodium butyrate (SB) on rumen epithelium (RE), and whether the YAP1/TAZ-dependent alteration was involved in the RE developmental process induced by sodium butyrate. In the SB-treated cells, theYAP1/TAZ-dependent changes were not observed. SB increased the expression of genes involved in short-chain fatty acid (SCFA) metabolism, while YAP1/TAZ did not. Thus, SB mediated RE development was not associated with YAP1/TAZ.
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