Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcription profiling of mouse E10.5 limb bud ZPA and the rest of the E10.5 limb bud from Shhgfpcre heterozygotes separated by FACS

ABSTRACT: Comparing gene expression of cells from the E10.5 limb bud ZPA and the rest of the E10.5 limb bud from Shhgfpcre heterozygotes separated by FACS. Experiment Overall Design: 8 samples, 4 ZPA and 4 rest of the limb

ORGANISM(S): Mus musculus

SUBMITTER: Brian Harfe

PROVIDER: E-GEOD-7598 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Identification of genes expressed in the mouse limb using a novel ZPA microarray approach.

Rock Jason R JR Lopez M Cecilia MC Baker Henry V HV Harfe Brian D BD

Gene expression patterns : GEP 20070902 1

One well-studied signaling center in the developing vertebrate limb, the zone of polarizing activity (ZPA), produces the morphogen sonic hedgehog that is necessary for normal growth and pattern formation. To identify additional factors expressed in the ZPA of the mouse limb bud, the Shhgfpcre allele was used to purify ZPA cells using fluorescence-activated cell sorting. Microarray technology was then used to identify genes whose expression was elevated in the ZPA compared to the rest of the limb ...[more]

PMID: 17911046

Similar Datasets

Bhlha9 deficiency effect in limb bud

Project description:Analysis of mouse limb bud (E10.5) lacking the Bhlha9 gene. Bhlha9 knockout mouse shows syndactyly and poliosis in the limb. This microarray results provides insight into the molecular mechanisms underlying Bhlha9 function in the limb development DNA microarray analysis was performed using Affymetrix mouse genome 430 2.0 array. RNA samples were obtained from the whole limb bud of the E10.5 wild-type and Bhlha9 knockout embryos described above. Total RNA (200 ng) was reverse-transcribed and biotinylated using the GeneChip 3â² IVT Express Kit (Affymetrix). The microarray data were summarized using the MAS 5.0 method.

2016-05-31 | E-GEOD-81223 | biostudies-arrayexpress

Bhlha9 deficiency effect in limb bud

2016-05-31 | GSE81223 | GEO

Chip-chip from Mouse E10.5 anterior and posterior immortalised limb cell lines and limb tissue for H3K27me3 antibody and from Mouse E10.5 anterior and posterior limb tissue for Ring1B antibody.

2012-09-18 | GSE38526 | GEO

Chip-chip from Mouse E10.5 anterior and posterior immortalised limb cell lines and limb tissue for H3K27me3 antibody and from Mouse E10.5 anterior and posterior limb tissue for Ring1B antibody.

Project description:Anterior-posterior differences in H3K27me3 and Ring1B enrichment over the 5 prime Hoxd genes in E10.5 murine distal forelimbs. Chromatin immunoprecipitation (ChIP) of H3K27me3 together with Ring1B and by ChIP-on-chip analysis demonstrated that over the 5 prime HoxD locus H3K27me3 enrichment is decreased and Ring1B enrichment is sparse in limb cells derived from the distal posterior forelimb bud of E10.5 mouse embryos. Array design includes 2 biological replicates for H3K27me3 in the cell lines and Ring1B in the limb tissue, and 2 biological replicates and 2 dye swap replicates for H3K27me3 in the limb tissue.

2012-09-18 | E-GEOD-38526 | biostudies-arrayexpress

Identification and characterization of genes expressed in the mouse ZPA using a novel microarray approach

Project description:Comparing gene expression of cells from the E10.5 limb bud ZPA and the rest of the E10.5 limb bud from Shhgfpcre heterozygotes separated by FACS. Keywords: comparison, cell-type comparison, experiemental versus control

2008-01-01 | GSE7598 | GEO

Gene expression profiles of E10.5 ureteric bud cells. (GUDMAP Series_id: 39)

Project description:The long term objective is to create an encyclopedia of the expression levels of all genes in multiple components of the developing kidney. The central thesis is straightforward. The combination of fluorescent activated cell sorting (FACS) plus microarray analysis offers a powerful, efficient and effective method for the creation of a global gene expression atlas of the developing kidney. Microarrays with essentially complete genome coverage can be used to quantitate expression levels of every gene in FACS isolated components of the developing kidney. The ensuing rapid read-out provides an expression atlas that is more sensitive, more economical and more complete than would be possible by in situ hybridizations alone. HoxB7-GFP transgenic mice were utilized to isolate the ureteric bud cells from E10.5 embryonic kidneys. The ureteric bud cells were isolated from embryos using microdissection, trypsin treatment and FACS. The RNA was isolated from purified ureteric bud cells and the gene expression profiles were determined by microarrays.

2010-05-27 | E-GEOD-21558 | biostudies-arrayexpress

Early limb bud transcriptome analysis between anterior and posterior domain

Project description:Shh signal mediated by Gli family of transcription factors regulates digit growth and patterning in early limb development. Shh expression in the posterior margin of the limb bud defines the zone of polarizing activity. However, much less is know about downstream targets that mediate Shh signal functions. In this dataset, we include the expression data obtained from dissected anterior and posterior halves of mouse limb bud respectively. These data are used to obtain 889 transcripts that were upregulated 1.3 fold or more in the posterior limb bud, and 1189 transcripts that were enriched in the anterior limb bud at 1.3 fold or more.

2013-01-06 | GSE41691 | GEO

Early limb bud transcriptome analysis between anterior and posterior domain

2013-01-06 | E-GEOD-41691 | biostudies-arrayexpress

Hnrnpk is essential for embryonic limb bud development as a transcription activator and insulator collaborator

Project description:Proper development of limb bud relies on the concordance of various signals, otherwise limb deformities occur. We report that heterogeneous nuclear ribonucleoprotein K (hnRNPK) is essential for limb bud development. here, we knock out Hnrnpk in limb bud and exert the RNA-seq, ATAC-seq, CUT&RUN-seq, and Hi-C assay using primary limb bud cells to explore the function of Hnrnpk in limb bud development.

2024-04-15 | GSE186411 | GEO

Transcriptional trajectories highlight the transition from anterior-posterior to proximal-distal patterning in the early limb bud [scRNA-seq]

Project description:Limb patterning relies in a large part on the function of the Hox family of developmental genes. While the differential expression of Hox genes shifts from the anterior-posterior (A-P) to the proximal-distal (P-D) axis around embryonic day 11 (E11), whether this shift coincides with a more global change of P-D versus A-P patterning program remains unclear. By performing and analyzing the transcriptome of the developing limb bud from E10.5 to E12.5, at single cell resolution, we have uncovered transcriptional trajectories which revealed a general switch from A-P to P-D genetic program between E10.5 and E11.5. Interestingly, the transcriptional trajectories at E10.5 all end with cells expressing either proximal or distal markers suggesting a progressive acquisition of P-D identity. Moreover, we observed that distally expressed Hox genes, namely Hoxa13 and Hoxd13, act as a key determinant for P-D patterning as their transcriptional control results in their distal restricted expression, which in turn restricts Hoxa11 in the proximal limb bud domain, in progenitor cells of the zeugopod. Finally, we identified three categories of genes expressed in the distal limb mesenchyme characterized by distinct temporal expression dynamics. As anticipated from previous results, HOX13 binding was observed within or in the neighborhood of several of these genes consistent with previous evidence suggesting that the transition from the early/proximal to the late/distal transcriptome of the limb mesenchyme largely relies on HOX13 function.

2020-12-15 | GSE158820 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

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