Ontology highlight
ABSTRACT:
PROVIDER: PRJNA957439 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR24216652_1.fastq.gz | Fastqsanger.gz | |||
| SRR24216652_2.fastq.gz | Fastqsanger.gz | |||
| SRR24216653_1.fastq.gz | Fastqsanger.gz | |||
| SRR24216653_2.fastq.gz | Fastqsanger.gz | |||
| SRR24216654_1.fastq.gz | Fastqsanger.gz |
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Project description:We adopted a combinatorial hybridization based single-cell RNA-seq method to generate tissue based transcriptome atlas of adult axolotl and whole organism transcriptome atlas of larva axolotl. Gene expression profiling of over 1million single cells across 19 organs constructed the first adult axolotl cell atlas. Comparison between neoteny and metamorphosis organs revealed transcriptome heterogeneity of structural cells in different tissues and a sophisticated regulatory network. Furthermore, we described dynamic gene expression pattern during neotenic larva axolotl limb development. These data serve as a rich resource to explore molecular identity of axolotl as well as its metamorphosis.
2022-06-17 | GSE182746 | GEO
Project description:Here, we developed a single-cell sequencing method based on combinatorial hybridization to generate a tissue-based transcriptomic landscape of the neotenic and metamorphosed axolotl. We performed gene expression profiling of over 1 million single cells across 19 tissues to construct the first adult axolotl cell landscape. Comparison of single-cell transcriptomes between the tissues of neotenic and metamorphosed axolotls revealed the heterogeneity of non-immune parenchymal cells in different tissues and established their regulatory network. Furthermore, we described dynamic gene expression patterns during limb development in neotenic axolotls. This system-level single-cell analysis of molecular characteristics in neotenic and metamorphosed axolotls, serves as a resource to explore the molecular identity of the axolotl and facilitates better understanding of metamorphosis.
2022-06-17 | GSE201446 | GEO
Project description:We used a RNA-seq approach to determine the effect of 3,5-di-iodothyronine (T2) and 3,5,3'-tri-iodothyronine (T3) exogenous treatment on the transcriptome of tilapia (Oreochromis niloticus) liver, cerebellum, and thalamus-pituitary. We identified a total of 169, 154 and 2863 genes that were Thyroid hormone-regulated (FDR < 0.05) in tilapia cerebellum, thalamus-pituitary and liver, respectively. Among those, 130, 96 and 349 genes were uniquely regulated by T3, whereas 22, 40 and 929 were only regulated by T2 in the cerebellum, thalamus-pituitary and liver.
2017-04-10 | GSE96046 | GEO
Project description:Study abstract: Axolotl salamanders (Ambystoma mexicanum) remain aquatic in their natural state, during which biomechanical forces on their diarthrodial limb joints are likely reduced relative to salamanders living on land. However, even as sexually mature adults, these amphibians can be induced to metamorphose into a weight-bearing terrestrial stage by environmental stress or the exogenous administration of thyroxine hormone. In some respects, this aquatic to terrestrial transition of axolotl salamanders through metamorphosis may model developmental and changing biomechanical skeletal forces in mammals during the prenatal to postnatal transition at birth and in the early postnatal period. To assess differences in the appendicular skeleton as a function of metamorphosis, anatomical and gene expression parameters were compared in skeletal tissues between aquatic and terrestrial axolotls that were the same age and genetically full siblings. The length of long bones and area of cuboidal bones in the appendicular skeleton, as well as the cellularity of cartilaginous and interzone tissues of femorotibial joints were generally higher in aquatic axolotls compared to their metamorphosed terrestrial siblings. A comparison of steady state mRNA transcripts encoding aggrecan core protein (ACAN), type II collagen (COL2A1), and growth and differentiation factor 5 (GDF5) in femorotibial cartilaginous and interzone tissues did not reveal any significant differences between aquatic and terrestrial axolotls. RNAseq samples: Total RNA was isolated from whole body tissue samples of Mexican axolotl salamanders (Ambystoma mexicanum) at the following developmental stages: Embryo at the tail bud stage, newly hatched larva, larva at the limb bud stage, juvenile at 8.5 centimeters, and adult using variations of guanidinium-based protocols. RNA quantity, purity, and integrity of both the individual samples and the resulting pool were determined with an Agilent 2100 Bioanalyzer using the Eukaryotic Total RNA nano series II analysis kit. The pooled RNA sample was poly-A selected and used for Illumina random priming directional library prep. Four lanes were sequenced only on one end providing single end reads and 4 lanes were sequenced at both ends giving paired-end reads. The library was sequenced on an Illumina HiSeq 2000 for 75bp reads producing 147,248,512 single end reads and 2 x 153,254,667 paired-end reads.
2018-07-29 | E-MTAB-6092 | biostudies-arrayexpress
Project description:Uncovering novel roles for thyroid hormones in teleost fishes: Differential transcriptome regulation in brain and liver by 3,5-T2 and 3’,3,5-T3
| PRJNA378665 | ENA
Project description:The evolutionary origins of the gene network underlying cellular pluripotency, a central theme in developmental biology, have yet to be elucidated. In mammals, Oct4 is a factor crucial in the reprogramming of differentiated cells into induced pluripotent stem cells. The Oct4 and Pou2 genes evolved from a POU class V gene ancestor, but it is unknown whether pluripotency induced by Oct4 gene activity is a feature specific to mammals or was already present in ancestral vertebrates. Here we report that different vertebrate Pou2 and Oct4 homologues can induce pluripotency in mouse and human fibroblasts and that the inability of zebrafish Pou2 to establish pluripotency is not representative of all Pou2 genes, as medaka Pou2 and axolotl Pou2 are able to reprogram somatic cells into pluripotent cells. Therefore, our results indicate that induction of pluripotency is not a feature specific to mammals, but existed in the Oct4/Pou2 common ancestral vertebrate. 16 samples were analyzed Notation: O: stands for OCT4 reprogramming factor from human; o: stands for Oct4 reprogramming factor from Axolotl S: stands for SOX2 reprogramming factor from human; s: stands for SOX2 reprogramming factor from Axolotl K: stands for KLF4 reprogramming factor from human
2014-03-23 | E-GEOD-21302 | biostudies-arrayexpress
Project description:Many known miRNAs in fish come from zebrafish and fugu whose genome sequence data are available. The Japanese flounder undergoes typical metamorphosis which is characterized by major morphological, functional, and behavioral changes during growth due to this metamorphosis from larva to juvenile. Metamorphosis is a biological process by which an animal physically develops after birth or hatching, involving a conspicuous and relatively abrupt change in the animal's body structure through cell growth and differentiation. Here, the high-throughput sequencing was adopted to identify the miRNAs during metamorphosis in the Japanese flounder. We found abundant microRNAs during metamorphosis in the Japanese flounder.
2010-12-23 | GSE25995 | GEO
Project description:Humans and other tetrapods are considered to require apical-ectodermal-ridge, AER, cells for limb development, and AER-like cells are suggested to be re-formed to initiate limb regeneration. Paradoxically, the presence of AER in the axolotl, the primary regeneration model organism, remains controversial. Here, by leveraging a single-cell transcriptomics-based multi-species atlas, composed of axolotl, human, mouse, chicken, and frog cells, we first established that axolotls contain cells with AER characteristics. Surprisingly, further analyses and spatial transcriptomics revealed that axolotl limbs do not fully re-form AER cells during regeneration. Moreover, the axolotl mesoderm displays part of the AER machinery, revealing a novel program for limb (re)growth. These results clarify the debate about the axolotl AER and the extent to which the limb developmental program is recapitulated during regeneration.
2023-09-20 | GSE243225 | GEO
Project description:In order to understand the genomic and transcriptomic variability of the axolotl pallium, as well as reconstruct their intrinsic gene regulatory networks, we performed single-nucleus multiome sequencing (RNA and open chromatin) of whole axolotl pallium.
2022-07-20 | E-MTAB-11666 | biostudies-arrayexpress
Project description:The piRNA pathway protects animal germlines form active transposons. Mammals employ a cytoplasmic pathway to post-transcriptionally destroy transposon transcripts and a nuclear pathway that mediates DNA methylation to epigenetically silence transposon expression. When the modern version of these pathways evolved remains unknown. We found that the mammalian version of the cytoplasmic pathway evolved in lobe-finned fish, as defined by the use of the 3ʹ exonuclease Pnldc1 for precursor piRNA trimming. The nuclear pathway evolved during early in tetrapod evolution and is already found in its current configuration in the salamander, Ambystoma mexicanum. Interestingly, the nuclear pathway was lost during bird evolution. We found evidence that both the cytoplasmic and nuclear piRNA pathways are active in both the male and female axolotl germlines. Analysis of axolotl testes and oocytes revealed diverse repertoires of piRNAs and persuasive post-transcriptional targeting of young transposons. We found high levels of genome methylation in axolotl spermatozoa with full-length transposons being highly methylated. Furthermore, CpG island methylation in axolotl is associated with transposon silencing. In summary, we find that the mammalian version of the piRNA pathway has ancient vertebrate origins, and it has been safeguarding the germline across most of tetrapod evolution.
2025-10-06 | GSE290049 | GEO