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Transcription profile of primordium gut organs

ABSTRACT: The mechanisms of gastrointestinal morphogenesis in mammals are not well understood. This is partly due to the lack of organ specific gene expression pattern in the gastrointestinal tract during development. The initiation of organ bud formation occurs at E9.5-E11.5 in mice. These primordia for the digestive organs, including esophagus, stomach, and intestine, protrude from a tube-like structured endoderm, and have their own distinct morphogenesis. Thus, using mouse embryos, we surveyed transcription of prospective these three regions at E11.5 during gastrointestinal morphogenesis. This early digestive organ specific transcription profile will be useful for understanding of the mechanisms of gastrointestinal development.

ORGANISM(S): Mus musculus

PROVIDER: GSE30742 | GEO | 2012/06/01

SECONDARY ACCESSION(S): PRJNA144113

REPOSITORIES: GEO

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Transcription profile of primordium gut organs

Project description:The mechanisms of gastrointestinal morphogenesis in mammals are not well understood. This is partly due to the lack of organ specific gene expression pattern in the gastrointestinal tract during development. The initiation of organ bud formation occurs at E9.5-E11.5 in mice. These primordia for the digestive organs, including esophagus, stomach, and intestine, protrude from a tube-like structured endoderm, and have their own distinct morphogenesis. Thus, using mouse embryos, we surveyed transcription of prospective these three regions at E11.5 during gastrointestinal morphogenesis. This early digestive organ specific transcription profile will be useful for understanding of the mechanisms of gastrointestinal development. Mouse gut organs morphogenesis begin at E9.5-E11.5. The primordium esophagus, stomach, and intestine at E11.5 were dissected and analysed transcription profile.

2012-05-31 | E-GEOD-30742 | biostudies-arrayexpress

Transcription profile of primordium gut organs

Project description:Induced pluripotent stem (iPS) cells are a novel stem cell population induced from mouse and human adult somatic cells through reprogramming by transduction of defined transcription factors. Recently, researchers success in generation various cells from iPSCs. Lung progenitor cells are able to differentiate to all of the cells exist in adult lung, attract attention for regenerative medicine. It is known to present between embryonic day 9.5 from 13.5 in mice. We can realized at regenerative medicine in lung using lung progenitor cell surface markers defined by compering each endoderm primordia of organ formation. We investigated the differences in gene expression of each endoderm organ. Mouse gut organs morphogenesis begin at E9.5-E11.5. The primordium lung, esophagus, stomach, and intestine at E11.5 were dissected and analysed transcription profile.

2014-03-25 | E-GEOD-55312 | biostudies-arrayexpress

Transcription profile of primordium gut organs

2014-03-25 | GSE55312 | GEO

The BAF complex does not mediate GLI repression (WT Cut&RUN)

Project description:Purpose: This study seeks to identify SMARCC1-bound regions in the mouse limb. Methods: To identify SMARCC1 bound regions in the limb, we performed Cut&Run on pooled anterior and posterior wild-type forelimbs at E11.5 (43-44s; 3 replicates each) and on whole forelimb pairs at E9.5 (21-24s; 2 replicates). We identified 28,082 SMARCC1-bound regions in the anterior forelimb at E11.5, 42,530 regions in the E11.5 posterior limb, and 10,792 SMARCC1-bound regions at E9.5 (FDR<0.05). Results: We find that SMARCC1 is bound to most limb enhancer regions at late stages (E11.5). Additionally, We find that SMARCC1 is bound to the majority of HH-responsive GLI enhancers at E11.5 but only a small portion of GLI enhancers at E9.5.

2024-02-03 | GSE224507 | GEO

RNA-seq Analysis of intestinal tubes from the Unfed and Fed Xenopus laevis tadpoles

Project description:In this study, we assessed nutrient-dependent organ morphogenesis in Xenopus laevis. We performed the RNA-seq analysis of the gastrointestinal (GI) tract for both fed and unfed tadpoles to identify feeding-dependent inter-organ transmitters secreted from GI tract post-prandially during development. We found that one of the GI hormones, glucose-dependent insulinotropic polypeptide (GIP), is required for thyroid morphogenesis.

2022-01-24 | GSE194146 | GEO

The expression data from mandibular arch and tongue primordia in mouse embryos.

Project description:The mouse hypoglossal nerve originates from the occipital motor nuclei and projects a long distance, reaching the vicinity of the tongue primordia, the lateral lingual swelling, at E11.5. However, the details of how the hypoglossal nerve correctly projects to the primordia are not well understood. To investigate the molecular basis of hypoglossal nerve elongation, we employed cDNA microarray technology and screened for candidate genes involved in the axon guidance event.

2023-12-06 | GSE249490 | GEO

Transcriptome profiling of wild type primordial germ cells (PGC) by RNAseq

Project description:Purpose: To identify molecular pathways underlying epigenetic reprogramming in early germ cell precursors, we examined global gene expression of wild type primordial germ cells using mRNA sequencing. Methods: Given the limited number of PGCs collected from E9.5 to E13.5 (ranging from 300 to 5000), we used a low-input RNA sequencing method, Smart-Seq. RNA libraries were pooled and sequenced by Illumina Hiseq. Results: We generated >22 million uniquely mapped reads per sample and identified >10 thousand transcripts per genotype (RPKM>0.1). Hierarchical clustering and correlation analysis on gene expression indicates samples were clearly separated according to their genotypes with Spearman correlation coefficient of 0.98/0.99 within biological replicates. Compared with E9.5 PGCs, 479 genes were significantly up-regulated and 248 genes were down-regulated in E11.5 PGCs. When compared with E11.5 PGCs, male E13.5 PGCs had 362 up-regulated, and 239 down-regulated genes, whereas female E13.5 PGCs had 1163 up-regulated and 333 down-regulated genes. Overall, the number of up-regulated genes was greater than that of the down-regulated genes in every comparison, suggesting that gene expression is generally activated during PGC reprogramming. mRNA profiles of primordial germ cells derived from developmental embryos stages (E9.5, E11.5 and E13.5) were generated by deep sequencing, in duplicates (E9.5 and E11.5) or triplicates (E13.5f and E13.5m), using Illumina Hiseq.

2012-10-31 | E-GEOD-41908 | biostudies-arrayexpress

Analysis of age-associated transcriptome changes in uterus and decidua

Project description:We use RNA-sequencing to measure global transcription in uteri of young and aged (~1yr old) C57BL/6 females at day 3.5 (E3.5) of pregnancy, and of the decidual part of E11.5 placentas developed in young and aged (~1yr old) females. We report dys-regulation of gene expression in the E3.5 uteri and E11.5 deciduae of aged mice. We compare the transcriptome of young and aged E11.5 deciduae with that of young deciduae from E9.5-E12.5 of pregnancy, and report that aged E11.5 deciduae are developmentally retarded in comparison to young deciduae.

2017-09-14 | GSE98901 | GEO

Understanding the development of oral epithelial organs through single cell transcriptomic analysis

Project description:During vertebrate craniofacial development, the oral epithelium begins as a simple and morphologically homogeneous tissue. It then gives rise to locally complex structures, including the developing teeth, salivary glands, and taste buds. While there is significant knowledge about the molecular mechanisms regulating the morphogenesis of these organs at later stages, how the epithelium is initially patterned and specified to generate diverse cell types and organs remains largely unknown. To elucidate the genetic programs that direct the formation of distinct oral epithelial populations, we conducted single cell RNA-sequencing using mandibular epithelia from embryonic day (E) 12.0 mouse embryos and whole mandibles from E9.5 mouse embryos. The goal of this study is therefore to generate a detailed transcriptional atlas of the developing mandibular epithelium.

2022-05-27 | GSE202921 | GEO

RNA sequence of embryonic dorsal skin and AGM (Aorta-gonad-mesonephros) tissues

Project description:Purpose: The goals of this study are to identify the different gene expresion level in dorsal skin cells or AGM region at different embryonic stages Methods: Dorsal skin cells were collected from different-staged embryo: E9.5, E10.5 E12.5 and E14.5. AGM were collected from different-staged embryo: E9.5, E10.5 and E11.5. In duplicate. RNA were extrated and analyzed using RNA sequencing. For dorsal skine tissues, we screened the genes were highly expressed at early embryonic stage E9.5, but not later stages (E10.5, E12.5, and E14.5). For embryonic AGM tissues, we selected the genes were highly expressed at early embryonic stage E9.5, but not later stages (E10.5 and E11.5). The gene list were filtered based on secreted potein candidates. These gene candidates might function as novel embryonic anti-tumor factors Results: Using an optimized data analysis workflow, we mapped the gene list for potential secretory anti-tumor factors. Conclusions: One of the top gene from the gene lists is NEPN which we hypotherze it has unique anti-tumor function in the early embryonic microenvirnemt and might be used as a novel cancer therapeutic drug

2021-06-01 | GSE125271 | GEO

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