Gene expression profiles of individual blastomeres of early Ciona embryos
Ontology highlight
ABSTRACT:
ORGANISM(S): Ciona intestinalis
PROVIDER: GSE45548 | GEO | 2013/10/29
SECONDARY ACCESSION(S): PRJNA194613
REPOSITORIES: GEO
Similar Datasets
Project description:We examined gene expression profiles of individual blastomeres of early Ciona embryos using microarrays. We examined gene expression profiles of individual blastomeres of the 8-cell, 16-cell and 32-cell embryos by dissecting with a fine glass needle. We also examined gene expression profiles of unfertilized eggs and embryos from the 1- to 32-cell stages.
2013-10-29 | E-GEOD-45548 | biostudies-arrayexpress
Project description:Gene expression profiles of individual blastomeres of early Ciona embryos
| PRJNA194613 | ENA
Project description:We have examined whether twin blastomeres from 2-cell stage mouse embryos differ in mRNA content. Amplified mRNA from 12 blastomeres derived from six embryos approximately mid-way through their second cell cycle was analyzed. Probes displaying normalized values greater than 0.25 were selected and examined for consistent bias in expression within blastomere pairs. Although transcript content varied both between individual embryos and twin blastomeres, no consistent asymmetries were observed for the majority of genes. On the other hand, 769 genes displayed a greater than 1.4-fold difference in expression across 5 of 6 pairs of blastomeres and 178 genes differed across all 6 pairs. These genes separated into two groups by class discovery clustering. Of the 769 differentially expressed genes, 163 were significantly up- or down-regulated in one sister blastomere compared to the other. Transcripts encoding proteins implicated in RNA processing and cytoskeletal organization were highly represented among the most abundant, differentially distributed mRNA. We conclude that there are many differences that distinguish twin blastomeres derived from a single 2-cell stage embryo but that only a few of these differences are consistent across multiple pairs of embryos. We hypothesize that a stochastically-based lack of synchrony in cell cycle progression between the two cells might explain some or all of the asymmetries in transcript composition.
2010-05-15 | GSE21688 | GEO
Project description:Nuclear pore complex (NPC) structure and maturity changed during early development before MBT in zebrafish embryos. Aiming to further confirm the difference of NPCs among different stages during MZT, we first isolated nuclei from 32-cell and 512-cell stage embryos as most zygotic genes have not been transcribed at these two stages yet. The lysates from identical number (about 12,500 nuclei per stage) isolated nuclei were then trypsin-digested and fractionated, followed by high-resolution LC-MS/MS analysis on the Q-Exactive HF-X mass spectrometers using a label-free assay. Whole blastomeres from 32-cell and 512-cell were also prepared with yolk removal to serve as total protein profile control, and the same amount lysates were analyzed by high-resolution LC-MS/MS with TMT labelled. Each sample for MS analysis had two repeats. Correlation analysis revealed that the abundance ratio from isolated Nuclei and whole deyolking balstomeres did not correlate well, but samples in Nuclei or Whole blastomeres were well correlated. This result indicates the convincible sample preparation as well as the variability in nuclei composition in early developmental period before MBT.
2023-08-25 | PXD017896 | Pride
Project description:We have examined whether twin blastomeres from 2-cell stage mouse embryos differ in mRNA content. Amplified mRNA from 12 blastomeres derived from six embryos approximately mid-way through their second cell cycle was analyzed. Probes displaying normalized values greater than 0.25 were selected and examined for consistent bias in expression within blastomere pairs. Although transcript content varied both between individual embryos and twin blastomeres, no consistent asymmetries were observed for the majority of genes. On the other hand, 769 genes displayed a greater than 1.4-fold difference in expression across 5 of 6 pairs of blastomeres and 178 genes differed across all 6 pairs. These genes separated into two groups by class discovery clustering. Of the 769 differentially expressed genes, 163 were significantly up- or down-regulated in one sister blastomere compared to the other. Transcripts encoding proteins implicated in RNA processing and cytoskeletal organization were highly represented among the most abundant, differentially distributed mRNA. We conclude that there are many differences that distinguish twin blastomeres derived from a single 2-cell stage embryo but that only a few of these differences are consistent across multiple pairs of embryos. We hypothesize that a stochastically-based lack of synchrony in cell cycle progression between the two cells might explain some or all of the asymmetries in transcript composition. 6 pairs of blastomeres were analyzed for a total of 12 samples.
2010-05-28 | E-GEOD-21688 | biostudies-arrayexpress
Project description:In multicellular organisms, heterogametes of oocytes and sperms are fertilized and resulting zygotes give rise to new individuals. The ability of zygotes that produce a fully formed individual from single cell when placed in a supportive environment is defined as totipotency. Given that totipotent cells are the source of all multicellular organisms, better understanding of totipotency has a profound effect on not only biology but also our society. However, the exact distribution of totipotent cells in mammals remains elusive, although zygotes and single blastomeres at 2-cell stage embryos has been thought to be only mouse cells to be totipotent. We now show that a single blastomere isolated from 2- and 4-cell stage embryos gives rise to a fertile adult individual when it placed in a uterus, although isolation of blastomeres at these stage results in the disturbance of transcriptome in single blastomere derived embryos. Single blastomeres from 8-cell and morula stage embryos that were separately cultured in vitro exhibited severe defects in the formation of epiblast and primitive endoderm in the inner cell mass and the development to blastocysts, respectively. Our results thus indicate that totipotency of mouse zygotes extends to single blastomeres of 4-cell stage embryos.
2021-05-27 | GSE163427 | GEO
Project description:Ciona develops according to a stereotyped or invariant lineage. This allowed us to collect precisely defined replicates of all eight blastomeres of the right half of the embryo at the 16-cell stage of Ciona. We manually dissected each embryo, collecting and identifying each cell before library preparation and single-cell RNA-seq to give us a data set of 8 blastomeres x 4 embryos (32 cells). We sequenced these on MiSeq and HiSeq 2500. A fifth embryo was only sequenced on MiSeq and excluded from subsequent analysis.
2020-03-06 | E-MTAB-6117 | biostudies-arrayexpress
Project description:Cleavage and morphogenesis of Ciona embryos was blocked by treatment with cytochalasin B prior to gastrulation. Drug treated embryos and DMSO treated controls were harvested at stage 19.5 (after control embryos had undergone neurulation and were completing notochord intercalation). Only 55 genes showed a significant difference in expression between the two treatments.
2017-09-19 | GSE102141 | GEO
Project description:This dataset provides gene expression levels of single cell and pooled embryos as part of a study on zygotic genome activation in Ciona embryogenesis. The single cell RNA-seq data suggested that Cyclin B3 was a key mediator of this process. This was confirmed by performing RNA-seq on pooled RNA isolated from embryos where Cyclin B3 was knocked down (using morpholinos) or overexpressed (using mRNA injections).
2018-07-06 | GSE110588 | GEO
Project description:The establishment of body axes and specification of early embryonic cells depend on maternally supplied transcripts and/or proteins, several of which are localized at specific regions of fertilized eggs and early embryos. The ascidian is known to exhibit a mosaic mode of development, and this mode is largely dependent on localized maternal factors. Using blastomere isolation, microarray and whole-mount in situ hybridization, the present study of Ciona intestinalis demonstrates that maternal transcripts of a total of 17 genes are localized at the posterior-most region of fertilized eggs and early embryos. Ten of them are newly identified in the present study, while the remaining seven genes have already been characterized in the previous studies. In addition, maternal transcripts of two genes, in addition to 14 genes encoded by the mitochondrial genome, showed a mitochondria-like distribution. Despite the present comprehensive approach, we could not identify maternal transcripts that are clearly localized to the animal-pole side, the vegetal-pole side, the anterior-side or other specific regions of the early embryo. Therefore, we concluded that the posterior-most localization and mitochondria-like distribution appear to be major specialized patterns of maternal transcripts in the early Ciona embryos. Four kinds of sample. Two series comparison (A4.1+a4.2+b4.2 blastomeres vs B4.1 blastomeres and Animal blastomeres vs Vegetal blastomeres) were examined including dye swap analyses.
2010-06-19 | E-GEOD-15637 | biostudies-arrayexpress