GEO DataSets

Analysis of embryonic (e11.5) proximal hindlimb bud tissues deficient for transcription factor Lmx1b. In the developing limb, dorsal-ventral patterning is controlled by LMX1B, expressed in the dorsal mesenchyme. Results provide insight into the Lmx1b-dependent genes in the developing limb bud.

Organism:

Mus musculus

Type:

Expression profiling by array, transformed count, 2 genotype/variation sets

Platform:

GPL1261

Series:

GSE10516

6 Samples

Download data: CEL

(Submitter supplied) A control vs. genetic knockout experiment aimed at determining what RNAs are upregulated or downregulated in e11.5 mouse proximal limb tissue lacking the Lmx1b gene. Because Lmx1b is required for dorsal-ventral patterning of the limb, this screen gives insight into what putative downstream targets of Lmx1b contribute to dorsal-ventral patterning. Keywords: Genetic allele comparison

Organism:

Mus musculus

Type:

Expression profiling by array

Dataset:

GDS3320

Platform:

GPL1261

6 Samples

Download data: CEL

(Submitter supplied) A control vs. genetic knockout experiment aimed at determining what RNAs are upregulated or downregulated in E13.5 mouse limb tissue lacking the Lmx1b gene. Because LMX1B is required for dorsal-ventral patterning of the limb, this screen gives insight into what putative downstream targets of Lmx1b contribute to dorsal-ventral patterning.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6246

20 Samples

Download data: CEL

(Submitter supplied) LMX1B is a LIM-homeodomain transcription factor essential for development. Putative LMX1B target genes have been identified through mouse gene targeting studies; however, in the absence of in vivo molecular characterization of their regulation, their identity as direct LMX1B targets remains hypothetical. We describe here the first molecular characterization of LMX1B target gene regulation. A tetracycline-inducible expression system and microarray analysis showed that a subset of NF-kappa B target genes, including IL-6 and IL-8 are upregulated in LMX1B-expressing HeLa cells. more...

Organism:

Homo sapiens; Mus musculus

Type:

Expression profiling by array

Platforms:

GPL6244 GPL4134

10 Samples

Download data: CEL, CHP, TXT

(Submitter supplied) Lmx1b regulates dorsalization of limb fates, but the mechanism of this regulation has not been characterized. To identify candidate genes regulated by Lmx1b we compared the limbs from Lmx1b KO mice to wild type mice during limb dorsalization (e11.5-13.5). Differentially expressed genes that we common to all three stages examined were considered to be likely candidates for Lmx1b regulation and further evaluated.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL1261

12 Samples

Download data: CEL

(Submitter supplied) 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

Organism:

Mus musculus

Type:

Expression profiling by array

Dataset:

GDS3403

Platform:

GPL1261

8 Samples

Download data: CEL, EXP

Analysis of zone of polarizing activity (ZPA) from limb buds of E10.5 embryos. The ZPA is a signaling center that is necessary for the normal anteroposterior patterning of the vertebrate limb. Results identify genes, beyond Sonic hedgehog (shh), expressed in the ZPA compared to the rest of the limb.

Organism:

Mus musculus

Type:

Expression profiling by array, count, 2 cell type sets

Platform:

GPL1261

Series:

GSE7598

8 Samples

Download data: CEL, EXP

(Submitter supplied) Lmx1b is a homeodomain transcription factor responsible for limb dorsalization. Despite striking double-ventral (loss-of-function) and double-dorsal (gain-of-function) limb phenotypes, no direct downstream gene targets in the limb have been confirmed. To determine direct targets of Lmx1b during limb dorsalization (E12.5), we performed chromatin immunoprecipitation followed by next generation sequencing (ChIP-seq). more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19057

3 Samples

Download data: BED, BW

(Submitter supplied) Samples used for hybridization consisted of non-pooled (NP) RNA extracts from 8 groups in each of two time periods after drug administration: oil vehicle treated control embryonic limb bud mesoderm and ectoderm, phosphate buffered saline vehicle control embryonic limb bud mesoderm and ectoderm, acetazolamide treated embryonic limb bud mesoderm and ectoderm, and cadmium sulfate treated embryonic limb bud mesoderm and ectoderm. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL81

48 Samples

Download data: CEL

(Submitter supplied) To study gene expression during endodermal organogenesis, we sought to identify genes expressed in restricted domains during organogenesis. For gene expression analysis, six morphologically distinct endodermal domains were dissected at E11.5: the esophageal region; the lung and distal tracheal region; the stomach region; the hepatic region; the dorsal and ventral pancreatic region; and the intestinal region. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6885

28 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13112

17 Samples

Download data: BED, TXT

(Submitter supplied) The combinatorial expression of the Hox genes along the body axes, referred to as the HOX code, is a major determinant of cell fate and plays a prevailing role in generating the animal body plan. In developing limb buds, the paralogous group 13 genes of the HoxA and HoxD clusters are essential for patterning the distal-most limb structures, the digits. Inactivation of HOXA13 and HOXD13 transcription factors (HOX13) leads to complete digit agenesis in mice, but how HOX13 regulate transcriptional outcomes and confer identity to the distal-most limb cells has remained elusive. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

5 Samples

Download data: TXT

(Submitter supplied) The combinatorial expression of the Hox genes along the body axes, referred to as the HOX code, is a major determinant of cell fate and plays a prevailing role in generating the animal body plan. In developing limb buds, the paralogous group 13 genes of the HoxA and HoxD clusters are essential for patterning the distal-most limb structures, the digits. Inactivation of HOXA13 and HOXD13 transcription factors (HOX13) leads to complete digit agenesis in mice, but how HOX13 regulate transcriptional outcomes and confer identity to the distal-most limb cells has remained elusive. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13112

12 Samples

Download data: BED

(Submitter supplied) Mammalian digit tip regeneration is linked to the presence of nail tissue, but a nail-explicit model is missing. Here, we report that nail-less double-ventral digits of ΔLARM1/2 mutants that lack limb-specific Lmx1b enhancers, fail to regenerate. To separate the nail’s effect from the lack of DV polarity, we also interrogate double-dorsal double-nail digits and show that they regenerate. Thus, DV polarity is not a prerequisite for regeneration and the nail requirement is supported. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

10 Samples

Download data: BW, TXT

(Submitter supplied) Single cell Chromatin Accessibility profiling of forelimb bud at stage E11.5 in WT and Hox13 mutant (10x Chromium)

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL21103

2 Samples

Download data: BW, RDATA, SNAP, ZIP

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17021

13 Samples

Download data: BIGWIG

(Submitter supplied) Pioneer factors are transcription factors able to recognize their target site even concealed in “closed” chromatin, eventually eliciting the switch to accessible targets for other transcription factors and the transcriptional machinery. As such, pioneer factors play a key role in switching cell fate. Here, we provide evidence that HOXA13 and HOXD13 (HOX13 hereafter), two transcription factors of the Hox family of developmental genes, act as pioneer factors in the developing limb. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17021

6 Samples

Download data: BIGWIG, TXT

(Submitter supplied) Pioneer factors are transcription factors able to recognize their target site even concealed in “closed” chromatin, eventually eliciting the switch to accessible targets for other transcription factors and the transcriptional machinery. As such, pioneer factors play a key role in switching cell fate. Here, we provide evidence that HOXA13 and HOXD13 (HOX13 hereafter), two transcription factors of the Hox family of developmental genes, act as pioneer factors in the developing limb. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17021

7 Samples

Download data: BIGWIG

(Submitter supplied) Ablation of the mouse gene for Onecut-2 was reported previously, but characterization of the resulting knockout mice was focused on in utero development, principally embryonic development of liver and pancreas. Here, we examine postnatal development of these Onecut-2 knockout mice, especially the critical period prior to weaning. Microarray technology was used to determine the effect of Onecut-2 ablation on gene expression in duodenum, whose epithelium has among the highest levels of Onecut-2. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6246

12 Samples

Download data: CEL

(Submitter supplied) 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. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

3 Samples

Download data: R