Single cell RNA seq for Ciona late tailbud embryos
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ABSTRACT:
PROVIDER: PRJNA474542 | ENA |
REPOSITORIES: ENA
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Project description:We applied single cell RNA seq with 10x genomics platform to study the cell identity change in Ciona late tailbud embryos. By comparing single cell data from Pax3/7>Foxc amd control embryos, we found ectopic expression of FoxC in BTN cells transformed into PSC cells, which suggest common shared origin of BTNs and PSCs.
2018-07-31 | GSE115331 | GEO
Project description:Purpose: Understand how the misexpression of key sensory cell determinant POU IV affects cell type specification of various sensory neurons in the peripheral nervous system in Ciona. Methods: CesA>POU IV (2.5ng/l) + CesA>GFP (5.0ng/l) injected eggs and control eggs were fertilized side by side, and allowed to develop to the late tailbud stage (13.5h after fertilization at 18°C). For each sample, 120 morphologically normal embryos were used for single cell RNA-seq assays. Dissociation of the embryos and single cell RNA-seq assays by 10x Genomics chromium system were done as described in 9. Horie R. et al., Shared evolutionary origin of vertebrate neural crest and cranial placodes. Nature 560, 228-232 (2018). Results: Misexpression of POU IV leads to the formation of Synthetic Cell Types that exhibit properties of other sensory neurons, especially those of bipolar tail neurons (BTNs) and a synthetic gene battery that is not found in any wildtype sensory neuron.
2021-12-29 | GSE192645 | GEO
Project description:Single-cell RNA-seq data for control and POU IV-misexpressed Ciona intestinalis embryos at late tailbud (LTB) stage
| PRJNA792554 | ENA
Project description:XBP transcription factors are well-known regulators of the the unfolded protein response and are required for plasma cell differentiation. However, recent studies have shown that the XBP1 gene is also expressed in the developing notochord of Ciona and various vertebrates, and to date its role in the formation of this organ is largely uncharacterized. We identified putative targets of Ci-XBP1 through a microarray screen, using RNAs extracted from embryos expressing mutant forms of this transcriptional regulator in the notochord. We expressed in the Ciona notochord a dominant-negative version of Ci-XBP1 (XBP DBD::GFP) by cloning its DNA-binding domain (DBD) downstream of the Ci-Brachyury (Ci-Bra) promoter. We created a constitutive activator form of Ci-XBP by fusing its DBD to the VP16 transactivation domain (Bra>XBP DBD::VP16::GFP). These constructs were introduced into 1-cell stage embryos and grown to the initial tailbud (iTb) stage to identify Ci-XBP notochord target genes.
2022-01-20 | GSE46751 | GEO
Project description:Despite being found in the notochord of several chordates, the roles of the Tbx2 subfamily of T-box transcription factors in the development of this tissue remain largely unknown. We explored the targets of the only Tbx2 subfamily member in Ciona intestinalis, Ci-Tbx2/3, by expressing mutant forms of the transcriptional regulator using the Ci-Bra promoter region. We produced a dominant interfering version of Ci-Tbx2/3 (Tbx2/3DBD) through expression of a truncated version consisting only of its DNA-binding domain (DBD) and a constitutive activator form by attaching the T-box of Ci-Tbx2/3 to the VP16 transactivation domain (Tbx2/3VP16). These constructs were introduced into 1-cell stage embryos and grown to the neurula (N) or mid-tailbud (mTb) stage to capture targets regulated throughout notochord morphogenesis.
2013-04-27 | GSE42267 | 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:Despite being found in the notochord of several chordates, the roles of the Tbx2 subfamily of T-box transcription factors in the development of this tissue remain largely unknown. We explored the targets of the only Tbx2 subfamily member in Ciona intestinalis, Ci-Tbx2/3, by expressing mutant forms of the transcriptional regulator using the Ci-Bra promoter region. We produced a dominant interfering version of Ci-Tbx2/3 (Tbx2/3DBD) through expression of a truncated version consisting only of its DNA-binding domain (DBD) and a constitutive activator form by attaching the T-box of Ci-Tbx2/3 to the VP16 transactivation domain (Tbx2/3VP16). These constructs were introduced into 1-cell stage embryos and grown to the neurula (N) or mid-tailbud (mTb) stage to capture targets regulated throughout notochord morphogenesis. Ci-Tbx2/3 targets were ascertained using whole-genome custom Affymetrix microarrays to compare the transcription levels of Tbx2/3DBD and Tbx2/3VP16 expressing embryos to wild-type controls (Bra>GFP) at the neurula or mTb stages.
2013-04-27 | E-GEOD-42267 | biostudies-arrayexpress
Project description:Eight different types of sample (three samples each) were used in this study of cardiac cell migration in the tunicate Ciona intestinalis. The B7.5 lineage cells were isolated by Fluorescent Activated Cell Sorting (FACS) at the tailbud stage, when the cardiac precursors (anterior B7.5 lineage cells) are migrating into the trunk, while their sister cells (posterior 7.5 lineage cells) remain in the tail, where they form muscle cells. Cells were sorted at the late gastrula stage, prior to migration induction and after manipulation of the FGF-MAPK-Ets signaling pathway (targeted expression of dominant negative FGF receptor and Ets:VP16 fusion protein, targeted expression was achieved using the Mesp cis-regulatory DNA), FoxF function (a direct target of FGF-MAPK-Ets signaling, required primarily for cell migration) by targeted expression of FoxF:VP16 (constitutive activator) or FoxF:WRPW (constitutive repressor, dominant negative), Mesp function (over-expression of Mesp:VP16 inhibits primarily cell migration). Finally, the "whole embryo" samples were collected from dissociated whole tailbud embryos, without FACS. in summary the eight conditions are: "wt (files LC-wt-1,-2,-3)": wild_type B7.5 lineage cells, expressing GFP, sorted at the tailbud stage "Ets:VP16 (files LC-EV-1,-2,-3)": B7.5 lineage cells, expressing GFP and Ets:VP16, sorted at the tailbud stage "DnFGFR (files LC-dnFGFR-1,-2,-3)": B7.5 lineage cells, expressing GFP and dominant-negative FGF receptor, sorted at the tailbud stage. "FoxF:VP16 (files LC-FV-1,-2,-3)": B7.5 lineage cells, expressing GFP and FoxF:VP16, sorted at the tailbud stage. "FoxF:WRPW (files LC-FW-1,-2,-3)": B7.5 lineage cells, expressing GFP and FoxF:WRPW, sorted at the tailbud stage". "Mesp:VP16 (files LC-MV-1,-2,-3)": B7.5 lineage cells, expressing GFP and Mesp:VP16, sorted at the tailbud stage. "Late Gastrula (files LC-LG-1,-2,-3)": wild_type B7.5 lineage cells, expressing GFP, sorted at the late gastrula stage "whole embryo (files LC-whole-1,-2,-3": whole embryos, dissociated at the tailbud stage, not sorted.
2008-06-01 | E-MEXP-1478 | 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:We examined gene expression profiles of individual blastomeres of early Ciona embryos using microarrays.
2013-10-29 | GSE45548 | GEO