Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Comparison of gene expression in embryos in wich the nodal-related genes have been inhibited and in control embryos

ABSTRACT: Embryos were injected with either water or Cerberus Short mRNA and harvested at Stage 10.5 for RNA analysis. Keywords: Knock-down analysis

ORGANISM(S): Xenopus tropicalis Xenopus laevis

PROVIDER: GSE4777 | GEO | 2007/05/05

SECONDARY ACCESSION(S): PRJNA95549

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Comparison of gene expression in embryos in wich Smicl has been knocked-down and in control embryos

Project description:Embryos were injected with either control or Smicl antisense morpholino oligonucleotides and harvested at Stage 10.5 for RNA analysis. Keywords: Knock-down analysis

2009-05-30 | GSE4952 | GEO

Comparison of gene expression in embryos in wich Activin B has been knocked-down and in control embryos

Project description:Embryos were injected with either control or Activin antisense morpholino oligonucleotides and harvested at Stage 10.5 for RNA analysis. Keywords: Knock-down analysis

2007-05-04 | GSE4771 | GEO

Comparison of gene expression in embryos in wich Smicl has been knocked-down and in control embryos

Project description:Embryos were injected with either control or Smicl antisense morpholino oligonucleotides and harvested at Stage 10.5 for RNA analysis. Keywords: Knock-down analysis Embryos from three different spawnings where injected at one cell stage with either control or Smicl antisense morpholino oligonucleotides and cultured to early gastrula stage 10.5 for RNA isolation. Some embryos were cultured to further development to check their phenotypes. Each slide was hybridised with a mixture 1:1 of sample and control cDNAs, each labelled with a different dye. Hybridisations were carried out as dye-swapped technical replicates, therefore six microarray slides were hybridized

2010-05-18 | E-GEOD-4952 | biostudies-arrayexpress

Differential expression analysis of triple knockdown of TBP and TBP-related factors (TKD) in Xenopus laevis embryos at early developmental stage 10.5

Project description:We sequenced cDNA prepared from ribosomal RNA depleted total RNA of 10-10 embryos co-injected with TBP-,TBP2- and TLF-AS antisense oligonucleotides and with water to create expression profiles of triple knockdown of TBP/TBP-related factors (TKD) and control, respectively, in Xenopus laevis at early developmental stage 10.5. (according to Nieuwkoop and Faber). We executed differential expression analysis of sequence count data (DEseq).

2016-03-07 | GSE76994 | GEO

Differential expression analysis of Gcn5 knockdown embryos at early developmental stage 10.5 in Xenopus laevis

Project description:We sequenced cDNA prepared from ribosomal RNA depleted total RNA of 10-10 embryos injected with Gcn5-antisense oligonucleotides and with water to create expression profiles of Gcn5 knockdown and control, respectively, in Xenopus laevis at early embryonic developmental stage 10.5. (according to Nieuwkoop and Faber), and we executed differential expression analysis of sequence count data (DEseq).

2016-03-07 | GSE76991 | GEO

Transcription profiling of Xenopus laevis early gastrulation embryos injected with antisense oligonucleotides against TBP, TLF or TBP2

Project description:Xenopus laevis embryos were injected with antisense oligonucleotides against TBP, TLF or TBP2. Embryos were allowed to develop up to stage 7 (non-injected control embryos) or stage 10.5 (early gastrula, control and antisense injected embryos) and subsequently collected for RNA and protein isolation. The transcriptome profile of antisense injected and control embryos was compared.

2007-08-29 | E-MEXP-1009 | biostudies-arrayexpress

Transcription profiling of Xenopus laevis early gastrulation embryos injected with alpha-amanitin against RNA polymerase II activity

Project description:Xenopus laevis embryos were injected with alpha-amanitin to inhibit RNA polymerase II activity. Embryos were allowed to develop up to stage 10.5 (early gastrula, control and alpha-amanitin injected embryos) and subsequently collected for RNA isolation. The transcriptome profiles of alpha-amanitin injected and control embryos were compared.

2016-03-07 | E-MTAB-3614 | biostudies-arrayexpress

Differential Nodal level promotes mesendoderm cell fate segregation mediated by chromatin organization

Project description:Purpose: To investigate the mechanism of prechordal plate and anterior endoderm separation . Methods: Nodal injected explants (injected with 10pg ndr2 mRNA) constructed from lft1 mutants and ndr1 morphants were harvested at 6hpf. Libraries were prepared using Chromium Controller and Chromium Single Cell 3’Library & Gel Bead Kit v3 (10x Genomics, PN-1000075) according to the manufacturer’s protocol for 10000 cells recovery. For single-cell multiomics, zebrafish embryos at 6 hpf were harvested. Libraries were prepared using Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Bundle (10x Genomics, 4 rxns PN-1000285) according to the manufacturer’s protocol for 10000 cells recovery. Results: A total of 10,614 single-cell transcriptomes and 4,335 multiomics were collected after stringent quality control measures. Conclusions: A slight bias in Nodal signaling promotes a differential chromatin structure between prechordal plate and endoderm, which drives a differential expression of those key regulators, such as gsc and ripply1 in these two cell lineages, and further regulates mesendoderm cell fate separation.

2023-01-28 | GSE223636 | GEO

Spemann organizer transcriptome induction by early β-Catenin, Wnt, Nodal and Siamois signals in Xenopus laevis

Project description:During Xenopus gastrulation, dorsal stabilization of β-Catenin at the earliest stage and subsequent target genes expression are critical for dorsal-ventral axis determination. However, many β-Catenin targets that mediate this process are still unkown. Here through RNA-seq analysis of β-Catenin knockdown embryos and self-regulating dorsal and ventral half embryos at early gastrula, we define an early β-Catenin gene signature that is downregulated by β-Catenin MO and enriched in dorsal gastrula tissues. This gene signature includes classic Spemann organizer genes, as well as other novel genes. Further analyses revealed that the early β-Catenin gene signature is positively correlated with LiCl treated, Wnt8 and Siamois mRNA-induced genes, consistent with their early role in dorsal-ventral axis formation. Our results also show that St 10.5 is the appropriate stage to uncover β-Catenin target genes that regulate dorsal-ventral patterning than St 9. Meanwhile, the multi-growth factor antagonist Cerberus inhibits part of the early β-Catenin gene signature and also controls the expression of a unique set of genes. Our findings provide new insight into the pivotal role of β-catenin in dorsal-ventral axis determination and can serve a fruitful resource for this field.

2017-03-15 | GSE93195 | GEO

Pair wise comparison between STD-MO and klf4-MO embryos

Project description:Direct pairwise comparison of the differential expression patterns between embryos injected with Standard olignucleotide morpholinoes and those injected with an anti-klf4 morpholino. Keywords: Direct pairwise comparison

2008-08-01 | GSE8656 | GEO

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