Transcriptome profiles of sturgeon lateral line electroreceptor and mechanoreceptor during regeneration
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ABSTRACT:
PROVIDER: PRJNA634667 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR11835780_1.fastq.gz | Fastqsanger.gz | |||
| SRR11835780_2.fastq.gz | Fastqsanger.gz | |||
| SRR11835781_1.fastq.gz | Fastqsanger.gz | |||
| SRR11835781_2.fastq.gz | Fastqsanger.gz | |||
| SRR11835782_1.fastq.gz | Fastqsanger.gz |
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Project description:BackgroundThe electrosensory ampullary organs (AOs) and mechanosensory neuromasts (NMs) found in sturgeon and some other non-neopterygian fish or amphibians are both originated from lateral line placodes. However, these two sensory organs have characteristic morphological and physiological differences. The molecular mechanisms for the specification of AOs and NMs are not clearly understood.ResultsWe sequenced the transcriptome for neomycin treated sturgeon AOs and NMs in the early regeneration stages, and de novo assembled a sturgeon transcriptome. By comparing the gene expression differences among untreated AOs, NMs and general epithelia (EPs), we located some specific genes for these two sensory organs. In sturgeon lateral line, the voltage-gated calcium channels and voltage-gated potassium channels were predominant calcium and potassium channel subtypes, respectively. And by correlating gene expression with the regeneration process, we predicated several candidate key transcriptional regulation related genes might be involved in AOs and NMs regeneration.ConclusionsGenes with specific expression in the two lateral line sensory organs suggests their important roles in mechanoreceptor and electroreceptor formation. The candidate transcriptional regulation related genes may be important for mechano- and electro- receptor specification, in a "dosage-related" manner. These results suggested the molecular basis for specification of these two sensory organs in sturgeon.
| S-EPMC7720607 | biostudies-literature
Project description:Deafness due to the terminal loss of inner ear hair cells is one of the most common sensory diseases. However, non-mammalian animals (e.g. birds, amphibian and fish) regenerate damaged hair cells. In order to better understand the reasons underpinning such regeneration disparities in vertebrates, we set out to define the changes in gene expression associated with the regeneration of hair cells in the zebrafish lateral line at high resolution. We performed RNA-Seq analyses on regenerating support cells purified by fluorescence activated cell sorting (FACS). The zebrafish lateral line provides an experimentally accessible system to define the complex signaling events triggered by injury and regeneration, because these cells can be acutely killed by exposure to neomycin, after which they regenerate rapidly. Lateral line hair cells are located in the center of a mechanosensory organ known as the neuromast and are surrounded by inner support cells and an outer ring of mantle cells. Tg(sqET20) larvae express GFP strongly in mantle cells and to a lesser degree in inner support cells. We isolated GFP positive and GFP negative cells from 5 days post fertilization (dpf) Tg(sqET20) larvae at 1, 3 and 5 hours post neomycin treatment, as well as from a non-treated control. Transgenic zebrafish Tg(sqET20) larvae at 5 days post fertilization were exposed to neomycin, dissociated, and FACS sorted into GFP positive and GFP negative populations at 1, 3, and 5 hours following treatment, along with a mock treated 1 hr control. The experiment was performed in triplicate, for a total of 24 samples.
2014-03-26 | E-GEOD-56176 | biostudies-arrayexpress
Project description:Deafness due to the terminal loss of inner ear hair cells is one of the most common sensory diseases. However, non-mammalian animals (e.g. birds, amphibian and fish) regenerate damaged hair cells. In order to better understand the reasons underpinning such regeneration disparities in vertebrates, we set out to define the changes in gene expression associated with the regeneration of hair cells in the zebrafish lateral line at high resolution. We performed RNA-Seq analyses on regenerating support cells purified by fluorescence activated cell sorting (FACS). The zebrafish lateral line provides an experimentally accessible system to define the complex signaling events triggered by injury and regeneration, because these cells can be acutely killed by exposure to neomycin, after which they regenerate rapidly. Lateral line hair cells are located in the center of a mechanosensory organ known as the neuromast and are surrounded by inner support cells and an outer ring of mantle cells. Tg(sqET20) larvae express GFP strongly in mantle cells and to a lesser degree in inner support cells. We isolated GFP positive and GFP negative cells from 5 days post fertilization (dpf) Tg(sqET20) larvae at 1, 3 and 5 hours post neomycin treatment, as well as from a non-treated control.
2014-03-26 | GSE56176 | GEO
Project description:The larvae were treated with 200 μM neomycin to deplete the hair cells in neuromast and ampullary organ. Two kinds of sensory epithelia at the ventral side of head were separated at 12 hour-post treatment (hpt) and 24 hpt, respectively. Mechano- and electro- sensory epithelia before neomycin treating were collected respectively as control (untreated).The epithelia near but without two kinds of sensors (EPs) were also collected. Total RNAs were extracted by TRIzol (Invitrogen) using standard protocols. RNA libraries were prepared by TruSeq RNA Sample Prep Kit (Illumina), following the manufacturer's instructions.
2020-12-15 | GSE151096 | GEO
Project description:Hearing loss is most commonly caused by the destruction of mechanosensory hair cells in the ear. This condition is usually permanent: Despite the presence of putative hair-cell progenitors in the cochlea, hair cells are not naturally replenished in adult mammals. Unlike those of the mammalian ear, the progenitor cells of nonmammalian vertebrates can regenerate hair cells through- out life. The basis of this difference remains largely unexplored but may lie in molecular dissimilarities that affect how progenitors respond to hair-cell death. We analyzed gene expression in hair-cell progenitors of the lateral-line system. We developed a transgenic line of zebrafish called alpl:mCherry that expresses a red fluorescent protein in the presumptive hair-cell progenitors known as mantle cells. Fluorescence-activated cell sorting from the skins of transgenic larvae, followed by microarray-based expression analysis, revealed a constellation of transcripts that are specifically enriched in these cells versus hair cells and non-fluorescent skin cells. Gene expression analysis after hair-cell ablation uncovered a cohort of genes that are differentially regulated early in regeneration, suggesting possible roles in the response of progen- itors to hair-cell death. These results provide a resource for studying hair-cell regeneration and the biology of sensory progenitor cells.
2014-04-01 | GSE55853 | GEO
Project description:In this study, we utilized the microfluidics chip technology on the gonads of Amur sturgeon to identifiy gender-specific miRNAs. The probes of all miRNAs about 663 published in fish and our novel miRNAs from sturgeon were chosed in the microarray experiment. Above 4µg to 8µg total RNA from one female and one male separativley were performed the miRNA microarray assays.Each probe was repeated five times on the chip to ensure reproducibility of microarray.
2016-06-30 | E-GEOD-62787 | biostudies-arrayexpress
Project description:In this study, we utilized the microfluidics chip technology on the gonads of Amur sturgeon to identifiy gender-specific miRNAs. The probes of all miRNAs about 663 published in fish and our novel miRNAs from sturgeon were chosed in the microarray experiment.
2016-06-30 | GSE62787 | GEO
Project description:In this study, we utilized the microfluidics chip technology on the gonads of Amur sturgeon to identifiy gender-specific sRNAs. The probes of all miRNAs about 2751 published in fish and our novel miRNAs from sturgeon were chosed in the microarray experiment.
2019-05-29 | GSE83840 | GEO
Project description:Hearing loss is most commonly caused by the destruction of mechanosensory hair cells in the ear. This condition is usually permanent: Despite the presence of putative hair-cell progenitors in the cochlea, hair cells are not naturally replenished in adult mammals. Unlike those of the mammalian ear, the progenitor cells of nonmammalian vertebrates can regenerate hair cells through- out life. The basis of this difference remains largely unexplored but may lie in molecular dissimilarities that affect how progenitors respond to hair-cell death. We analyzed gene expression in hair-cell progenitors of the lateral-line system. We developed a transgenic line of zebrafish called alpl:mCherry that expresses a red fluorescent protein in the presumptive hair-cell progenitors known as mantle cells. Fluorescence-activated cell sorting from the skins of transgenic larvae, followed by microarray-based expression analysis, revealed a constellation of transcripts that are specifically enriched in these cells versus hair cells and non-fluorescent skin cells. Gene expression analysis after hair-cell ablation uncovered a cohort of genes that are differentially regulated early in regeneration, suggesting possible roles in the response of progen- itors to hair-cell death. These results provide a resource for studying hair-cell regeneration and the biology of sensory progenitor cells. Two sets of analyses were performed. The first compared baseline expression levels in four sorted cell types from two different transgenic lines of zebrafish, alpl:mCherry;pou4f3:GFP and alpl:mCherry:ET20. alpl:mCherry;pou4f3:GFP larvae express GFP in hair cells and mCherry in mantle cells. alpl:mCherry:ET20 larvae express GFP in most mantle cells and mChery in all mantle cells. The four cell types compared were GFP+ hair cells, mCherry+ mantle cells, mCherry+/GFP+ mantle cells from alpl:mCherry:ET20 larvae, and non-fluorescent (NF) cells. Two hair-cell, five mCherry+ mantle cell, four mCherry+/GFP+ mantle cell, and six NF cell samples were analyzed. This excludes a few samples that were discardced based on failure to cluster by principal component analysis. A second analysis, separately imported, compared gene expression in mCherry+ mantle cells and NF cells at four time points following chemical ablation of hair cells with copper sulfate. These were one, three, five, and eleven hours after treatment (hpCu). Untreated samples served as controls. For mCherry+ cells, five untreated and four each of 1 hpCu, 3 hpCu, 5 hpCu and 11 hpCu were analyzed. For NF cells, six untreated, seven 1 hpCu, and four each of 3 hpCu, 5 hpCu and 11 hpCu samples were analyzed. Untreated mCherry+ and NF cells were shared between both analyses.
2014-04-01 | E-GEOD-55853 | biostudies-arrayexpress
Project description:Microarray expriments were performed in 5 tissues of Amur sturgeon, included liver, spleen, brain ,muscle and heart.
2015-12-30 | GSE57102 | GEO