Pitx2 positions the embryonic axis and regulates twinning
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ABSTRACT: Two experiments performed as follows: One-color microarray experiment comparing the Posterior Marginal Zone (PMZ) and an equivalent anterior explant (AMZ). RNA from the pooled explants (36 of each type) was analysed in triplicate using the A-AFFY-103 array design. One-color microarray experiment comparing the cVg1-expressing site of the anterior cut halves (cVg1-like) and an equivalent cVg1-non-expressing site of the anterior cut halves (cVg1-unlike). RNA from the pooled explants (63 of each type) was analysed in triplicate using the A-AFFY-103 array design.
Project description:To identify the genes responsible for rhizome extension, we transcriptome analysis performed in leaves and rhizome of cut and uncut explants (leaves cut and leaves uncut explants)
Project description:This experiment was performed in order to identify transcriptional differences between the anterior- and posterior-halves of mouse sclerotome. Cells-derived from the anterior- and posterior-sclerotome-halves from maturing mouse somites were compared to identify transcripts that are differentially expressed between these two halves of the somite. c57b6-/- female mice were time-mated, and at 9.5-dpc embryos were harvested. Theiler stage 17 embryos were selected for dissection. A stripe of segmented paraxial mesoderm corresponding to somites SX-SXVIII (standard somite nomenclature) was dissected from one-side of an embryo. The most anterior-third of up to 7 sclerotomes within each sample were dissected and pooled in RNALater. RNA was isolated using RNeasy Micro RNA extraction spin columns (Qiagen). Reverse transcription and initial cDNA amplification was performed using 18 PCR cycles with the SMART cDNA system (Clontech). Amplified cDNA was then re-amplified and labeled using the GeneChip® IVT Labeling Kit (Affymetrix).
Project description:Pools of 3 E14 eda null half skin pairs were cultured for 90 minutes or 4 hours in hanging drops of medium containing 2ug/mL of Fc-Eda-A1 (treated halves) or the equivalent amount of solvent (control halves). Biological triplicates for each condition were performed.
Project description:Purpose: To identify cell types and cellular transcriptional profiles in airway explants and precision cut lung slices obtained from non-disease human lung tissue.
Project description:Purpose: To investingate cell types in wild-type zebrafish explants. Methods: Wild-type explants (injected with phenol red) were harvested at 10hpf. 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. Results: A total of 9,968 single-cell transcriptomes were collected after stringent quality control measures. Conclusions: 6 Cell types were identified, wild-type explants mainly contains the anterior neural ectoderm and epidermis at 10 hpf.
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. Two samples were analyzed. We generate pairwise comparisons between anterior and posterior limb tissues. Genes with a fold-change ≥1.3 were selected.
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.
Project description:VIGS (virus-induced gene silencing) was used to silence a putative LRR-RLK, Affy ID Rbaal9i05_at, in barley. Expression patterns in leaves were compared between untreated control leaves, virus treated leaves, VIGS-Rbaal knockdown leaves and VIGS-Rbaal/PDS (phytoene desaturase) co-silenced leaves. ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, David L Parrott. The equivalent experiment is BB108 at PLEXdb.]
Project description:The experiment were perfomed as a part of our Vertebrate Evo-Devo project. The aim of the project is to compare transcription profiles of normal (unmanipulated, wild-type, whole embryo) vertebrate embryos. Total RNA was collected from wild type G.gallus whole embryos at 15 different stages (Stages:HH1,2,4,6,8,9,11,14,16,19,24,27,32,34,38), and hybridized to A-AFFY-103 Chicken Genome Array. All the stages contains data from two biological replications. Each staged-samples consists of pooled total RNA from several whole embryos.
Project description:We analyzed anterior halves of NF stage 15 embryos that were treated with 10uM DMSO (control), or 1uM RA and 10uM 4-oxo-RA (experimental) for changes in gene expression induced by the two mophogens. RNA-sequencing revealed significant overlap in genes upregulated by both RA and 4-oxo-RA, and to a lesser extent, those downregulated by them. We report all Zic-1 targets described in accompanying manuscript to be regulated by both RA and 4-oxo-RA.