Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

12 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Cardiac transcriptome of Tcf21-depleted Xenopus embryos

ABSTRACT: The aim of the approach was to use RNAseq analysis to identify genes expressed in Xenopus epicardium that were affected by embryonic depletion of the epicardial transcription factor Tcf21 compared to control-MO injected siblings. Both upregulated and downregulated genes were validated by RT-PCR and whole embryo in situ hybridization to validate gene expression and assess spatio-temporal distribution of genes of interest within the heart and epicardium. Approximately 70-100 stage 44-46 Xenopus laevis hearts were dissected to isolate total mRNA from which poly-adenylated RNA was extracted using the Illumina standard protocol. This experiment represents one replicate from pooled hearts. mRNA profiles of stage 44-45 Xenopus laevis sibling hearts from control or Tcf21-depleted embryos, were generated by deep sequencing using Illumina GAII.

ORGANISM(S): Xenopus laevis

SUBMITTER: Panna Tandon

PROVIDER: E-GEOD-45786 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Tcf21 regulates the specification and maturation of proepicardial cells.

Tandon Panna P Miteva Yana V YV Kuchenbrod Lauren M LM Cristea Ileana M IM Conlon Frank L FL

Development (Cambridge, England) 20130501 11

The epicardium is a mesothelial cell layer essential for vertebrate heart development and pertinent for cardiac repair post-injury in the adult. The epicardium initially forms from a dynamic precursor structure, the proepicardial organ, from which cells migrate onto the heart surface. During the initial stage of epicardial development crucial epicardial-derived cell lineages are thought to be determined. Here, we define an essential requirement for transcription factor Tcf21 during early stages ...[more]

PMID: 23637334

Similar Datasets

Cardiac transcriptome of Tcf21-depleted Xenopus embryos

Project description:The aim of the approach was to use RNAseq analysis to identify genes expressed in Xenopus epicardium that were affected by embryonic depletion of the epicardial transcription factor Tcf21 compared to control-MO injected siblings. Both upregulated and downregulated genes were validated by RT-PCR and whole embryo in situ hybridization to validate gene expression and assess spatio-temporal distribution of genes of interest within the heart and epicardium. Approximately 70-100 stage 44-46 Xenopus laevis hearts were dissected to isolate total mRNA from which poly-adenylated RNA was extracted using the Illumina standard protocol. This experiment represents one replicate from pooled hearts.

2013-07-05 | GSE45786 | GEO

Expression data from juvenile Xenopus laevis inner ear tissue

Project description:We implemented a functional genomics approach as a means to undertake a large-scale analysis of the Xenopus laevis inner ear transcriptome through microarray analysis. Microarray analysis uncovered genes within the X. laevis inner ear transcriptome associated with inner ear function and impairment in other organisms, thereby supporting the inclusion of Xenopus in cross-species genetic studies of the inner ear. Gene expression analysis of Xenopus laevis juvenile inner ear tissue. Inner ear RNA isolated from three groups of 5-10 juvenile X. laevis. Each biological replicate represents pooled inner ear RNA from 10-19 inner ears.

2012-05-04 | E-GEOD-37767 | biostudies-arrayexpress

Transcription profiling of mouse heart from E12.5 wildtype- and Sp3 animals

Project description:Mice lacking the zinc finger transcription factor Specificity protein 3 (Sp3) die prenatally in the C57Bl/6 background. To elucidate the cause of mortality we analyzed the potential role of Sp3 in embryonic heart development. Sp3 null hearts display defective looping at E10.5, and at E14.5 the Sp3 null mutants have developed a range of severe cardiac malformations. In an attempt to position Sp3 in the cardiac developmental hierarchy, we analysed the expression patterns of >15 marker genes in Sp3 null hearts. Expression of Cardiac ankyrin repeat protein (Carp) was downregulated prematurely after E12.5, while expression of the other marker genes was not affected. ChIP analysis revealed that Sp3 is bound to the Carp promoter region in vivo. Microarray analysis indicates that small molecule metabolism and cell-cell interactions are the most significantly affected biological processes in E12.5 Sp3 null myocardium. Since the epicardium showed distension from the myocardium, we studied expression of Wt1, a marker for epicardial cells. Wt1 expression was diminished in epicardium-derived cells in the myocardium of Sp3 null hearts. We conclude that Sp3 is required for normal cardiac development, and suggest that it has a crucial role in myocardial differentiation. ( Experiment Overall Design: Hearts were dissected from E12.5 wildtype (n=3) and Sp3 knockout (n=3) fetuses. Total RNA was isolated from individual hearts; 5Î¼g was used for labelling and hybridization to 430 2.0 Gene Chips (a total of 6).

2008-06-17 | E-GEOD-9124 | biostudies-arrayexpress

Identification of Tcf21 downstream genes in the epicardial cells and cardiomyocytes by transcriptomic analysis

Project description:Purpose: Studying the epicardium-myocardium crosstalk in the zebrafish larval heart. To do so, we aimed to identify, with RNA-seq, the genes dysregulated following the loss of the epicardial marker gene tcf21 in sorted epicardial cells and cardiomyocytes. Results: We first analyzed the transcriptome of epicardial and myocardial WT cells and identified cell-type specific/enriched genes. Then, we identified several differential expressed genes in tcf21 mutants, including several ligand-receptor couples known to mediate the epicardium-myocardium crosstalk.

2022-10-12 | GSE174505 | GEO

Comparison of the gene expression expression profile of activated and resting epicardium

Project description:Zebrafish can regenerate their hearts. As a first response to injury, the epicardium reacts by upregulalion of developmental marker genes. Here we compared in an unbiased manner the expression of the epicardium from uninjured zebrafish hearts and hearts at 3 days postcryoinjury. To label epicardial cells of uninjured hearts we usd pard3:GFP (POon et al 2010) and to label epicardium of the injured heart wt1b:eGFP (Perner et al 2007)

2019-07-30 | GSE118457 | GEO

Transcription profiling of Xenopus eye primordia vs. posterior neural plate vs. lateral endoderm normalized the whole embryos

Project description:Tissues from the eye primordia, lateral endoderm, and posterior; neural plate of stage 15 Xenopus laevis embryos were isolated and normalized to stage 15 whole embryos. Three biological replicates were prepared for each tissue and the expression patterns were profiled using Affymetrix Xenopus Laevis GeneChip microarrays. Experiment Overall Design: Tissues from the eye primordia, lateral endoderm, and posterior Experiment Overall Design: neural plate of stage 15 Xenopus laevis embryos were isolated and normalized to stage 15 whole embryos. Three biological replicates were prepared for each tissue and the expression patterns were profiled using Affymetrix Xenopus Laevis GeneChip microarrays.

2009-09-15 | E-GEOD-9175 | biostudies-arrayexpress

Next generation sequencing identifies differentially localized transcripts in Xenopus laevis and Xenopus tropicalis oocytes

Project description:RNA-seq technology was used to identify differentially localized transcripts from Xenopus laevis and Xenopus tropicalis stage VI oocytes. Besides the discovery of a group of novel animally enriched RNAs, this study revealed a surprisingly low conservation of vegetal RNA localization between the two frog species. mRNA profiles of Xenopus laevis and Xenopus tropicalis animal and vegetal oocyte halves were generated by RNA-seq technology. For Xenopus laevis, animal and vegetal oocyte RNA preparations from two different females were generated in duplicates. For Xenopus tropicalis, animal and vegetal oocyte RNA preparations from two different females were analyzed.

2015-12-09 | E-GEOD-58420 | biostudies-arrayexpress

Xenopus laevis

Project description:Xenopus laevis

| PRJNA269132 | ENA

Transcription profiling of Xenopus embryos

Project description:Xenopus laevis embryos were injected with mRNA for EFTFs at 2-cell stage. Animal caps collected at stage 9, cultured to the equivalent of stage 15 and RNA extracted. Four biological replicates of the EFTF-injected and GFP-injected (control) caps were used to profile transcript expression patterns using Affymetrix Xenopus Laevis GeneChip microarrays. Experiment Overall Design: Xenopus laevis embryos were injected with mRNA for EFTFs at 2-cell stage. Animal caps collected at stage 9, cultured to the equivalent of stage 15 and RNA extracted. Four biological replicates of the EFTF-injected and GFP-injected (control) caps were used to profile transcript expression patterns using Affymetrix Xenopus Laevis GeneChip microarrays.

2009-09-15 | E-GEOD-9173 | biostudies-arrayexpress

Parkin-mediated mitophagy evokes perinatal cardiac mitochondria maturation

Project description:Exclusion of Parkin from mitochondria of perinatal cardiomyocytes interrupts structural and molecular transformations essential to normal perinatal-adult mitochondrial replacement. mRNA-sequencing from cardiac total RNA was performed at P1, P21 and 5-week stages of nontransgenic (ntg) and human-Mfn2-overexpressing (Mfn2wt) hearts, and also of tet-off control (tetoff) and human-Mfn2 T111A/S442A-overexpressing (Mfn2AA) hearts. Libraries from all P1 samples were prepared and analyzed together, and similarly all P21 libraries, and all 5-week libraries together. To facilitate comparison across time points by accounting for batch effect, new libraries were prepared starting from total RNA from selected P21 ntg and 5-week ntg hearts subjected to prior analysis, during the same batch preparation as all P1 samples, and analyzed together. Correction for differences observed between libraries prepared from the same total RNA, but at different times, allows comparison across timepoints.

2015-12-04 | E-GEOD-68921 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data