Transcription profiling of chick extra-embryonic vascular system to correlate global gene regulation to morphogenesis and maturation
Ontology highlight
ABSTRACT:
ORGANISM(S): Gallus gallus
SUBMITTER: John De Vos
PROVIDER: E-GEOD-11636 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:We performed gene expression profiling on chicken livers at five important embryonic developmental stages (E7, E12, E14, E17 and E21), which were selected from chicken lines with significant differences in abdominal fat content. Each developmental stage had its unique gene expression pattern and stage-specific differentially expressed genes (DEGs). Furthermore, the three rapid growth periods (E12, E14 and E17) had similar expression patterns. Between the two broiler lines, E17 had the largest number of significantly differentially expressed genes (979), specifically enriched in fatty acid metabolism and biosynthesis, PPAR signaling and glycolysis pathways. Therefore, genome-wide gene expression recapitulated the developmental pattern of chicken embryos, and found the important molecular pathways for hepatic lipid metabolism.
2018-06-04 | GSE101182 | GEO
Project description:Tibetan chickens, a unique plateau breed, have good performances to adapt to high-altitude hypoxic environments. A number of positively selected genes have been reported in Tibetan chickens; however, the mechanisms of gene expression for hypoxia adaptation are not fully understood. In the present study, eggs from Tibetan (TC) and Chahua (CH) chickens were incubated under hypoxic and normoxic conditions, and vascularization in the chorioallantoic membrane (CAM) of embryos was observed. We found that the vessel density index (VDI) in CAM of TCs was lower than in CHs under hypoxia incubation.Proteomic analyses of CAM tissues were performed in TC and CH embryos under hypoxic incubation using iTRAQ. We obtained 387 differentially expressed proteins (DEPs) that were mainly enriched in angiogenesis, vasculature development, blood vessel morphogenesis, blood circulation, renin-angiotensin system, and HIF-1 and VEGF signaling pathways. Twenty-six genes involved in angiogenesis and blood circulation, two genes involved in ion transport, and six genes that regulated energy metabolism were identified as candidate functional genes in regulating hypoxic adaption of chicken embryos. Therefore, this research provided insights into the molecular mechanism of hypoxia adaptation in Tibetan chickens.
2021-09-08 | PXD012607 | Pride
Project description:Background/Aims: Tibetan chickens, a unique plateau breed, have good performances to adapt to high-altitude hypoxic environments. A number of positively selected genes have been reported in Tibetan chickens; however, the mechanisms of gene expression for hypoxia adaptation are not fully understood. Methods: Eggs from Tibetan (TC) and Chahua (CH) chickens were incubated under hypoxic and normoxic conditions, and vessel density index (VDI) in the chorioallantoic membrane (CAM) of embryos was measured. Meanwhile, Transcriptomic and proteomic analyses of CAM tissues were performed in TC and CH embryos under hypoxic incubation using RNA-seq and iTRAQ. Results: We found that the vessel density index (VDI) in CAM of TCs was lower than in CHs under hypoxia incubation. In the transcriptomic and proteomic analyses, 160 differentially expressed genes (DEGs) and 387 differentially expressed proteins (DEPs) that were mainly enriched in angiogenesis, vasculature development, blood vessel morphogenesis, blood circulation, renin-angiotensin system, and HIF-1 and VEGF signaling pathways. Twenty-six genes involved in angiogenesis and blood circulation, two genes involved in ion transport, and six genes that regulated energy metabolism were identified as candidate functional genes in regulating hypoxic adaption of chicken embryos. Conclusion: Combination of transcriptomic and proteomic data revealed several key candidate regulators and pathways that might play high-priority roles in the hypoxic adaptation of Tibetan chickens by regulating angiogenesis and promoting blood circulation, thus explaining the blunt responses to hypoxic conditions on CAM angiogenesis in Tibetan chicken embryos. This research provided insights into the molecular mechanism of hypoxia adaptation in Tibetan chickens.
2020-07-13 | GSE126082 | GEO
Project description:Human papillomavirus (HPV) is the etiological agent of cervical cancer. Three viral proteins, E5, E6 and E7 have been implicated in cell transformation. Increased expression of sialic acid and sialylated antigens have been reported during cervix transformation, these results agree with the increased mRNA levels of the sialyltransferases genes ST6GAL1 and ST3GAL3 reported in premalignant and malignant tissue of the cervix. E6 and E7 HPV oncoproteins modify the expression of some glycogenes. The role of E5 HPV oncoprotein in the glycogene expression changes in premalignant and malignant cervical tissue has not been reported. The objective of this work was to identify glycogenes that modify their expression by E5 HPV oncoprotein in HaCaT cell line. A gene expression microarray was performed on HaCaT cells that stably expressed the HPV16 E5 oncogene. Analysis revealed alteration in some glycogenes including upregulation of ST6GAL1 and ST3GAL3. The increased mRNA levels of both genes were confirmed by qRT-PCR. In addition, an in-silico analysis was performed to identify glycosylation networks altered in presence of E5 oncoprotein. The analysis showed that E5 could modify the sialic acid expression, keratan sulfate synthesis, N-glycosylation and biosynthesis of glycosaminoglycans. This is the first report of the role of HPV16 E5 oncoprotein on glycogenes expression changes. Moreover, our results suggest that the increase of the sialyltransferases genes reported in premalignant and malignant cervical tissue, could be the result of the expression of E5 oncoprotein. These results provide information of the possible role of HPV infection on the sialylation changes in the cervical epithelium identified in premalignant lesions and cancer.
2018-08-21 | GSE118776 | GEO
Project description:Bovine, as one of the most significant domestic animals providing humans with milk and meat, while also serving as bioreactors for producing valuable proteins, pose challenges in establishing embryo-derived stable pluripotent stem cells (PSCs) due to the unclear relationship between embryonic epiblast development and maintenance of stem cell pluripotency and self-renewal. Here, we selected six key stages of bovine embryo development (E5, E6, E7, E10, E12, E14) to track pluripotency changes and their signal pathway dependence using modified single-cell transcription sequencing technology. Based on the remarkable similarity of the dependence of WNT/β-catenin, LIF/STAT3, TGFβ/Smads, and FGF/ERK signaling pathways between bovine and porcine during early embryonic lineages development, we have successfully established bovine embryonic epiblast stem cells (bEpiSCs) using porcine pre-gastrulation epiblast stem cell culture system 3i/LAF. The generated bEpiSCs exhibited consistent pluripotency gene expression levels and maintained clonal morphology, normal karyotype, and proliferative capacity for over 110 passages. Moreover, their high-efficiency teratoma formation potential as well as their ability to differentiate into various cell lineages were demonstrated. At the transcriptome level, bEpiSCs displayed similarities with bovine Formative epiblast cells. We also assessed the application potential of bEpiSCs in targeted differentiation towards muscle cells and as donor cells for somatic cell nuclear transfer (SCNT). In summary, this study establish stable Formative bEpiSCs which hold promise for advancements in cell-cultured meat production, gene-edited cloned cattle generation, and animal breeding.
2024-10-20 | GSE256201 | GEO
Project description:Purpose: The morphology of the RPE shows minimal change as the neural retina and choriocapillaris differentiate. Nonetheless, initial studies of barrier-related proteins suggest extensive remodeling of the RPE in response to this changing environment. A genomic approach was used to investigate the extent of this remodeling. Methods: RPE was isolated from E7, E10, E14 and E18 chick embryos and total RNA extracted for probing the entire genome on Affymetrix microarray chips. Statistical parameters using ANOVA were adjusted to yield a theoretical false discovery rate of 5%. STEM software was used to cluster genes into statistically related patterns of expression. Gene ontology clustering, using Affymetrix software was used for functional clustering. The proteinlounge.com database was used as a source of known biological pathways. Results: Of the 37,694 probe sets on the microarray, 17,199 were not absent. Of the 20,495 expressed probes, the expression of 8,889 was developmentally regulated. 4814 of these could be clustered into 12 patterns of expression that were statistically significant. The developmental patterns of expression for 22 tight and adherens junction proteins have been reported. Only two showed small variations from the patterns revealed by the microarray. Further, as would be predicted, expression of genes that promote progression through the cell cycle decreased and genes that inhibit progression increased with age. The data indicate extensive remodeling of the extracellular matrix, cell surface receptors, cell-cell junctions, transcellular ion transport and signal transduction pathways throughout development. Notably, the appearance of claudin 20, ZO-3 and cadherins 13 and 20 very late in development suggest barrier properties continue to change after functional junctions are formed. Conclusions: The data reveal a far more dynamic view of the RPE and its interactions with its environment than would be expected from morphological examination. The remodeling of junctional complexes, extracellular matrix interactions and transcellular transport capabilities indicates a continuous remodeling of the blood-retinal barrier. These data provide a standard whereby culture models of RPE function and regulation may be judged. SUBMITTER_CITATION: Rizzolo LJ, Chen X, Weitzman M, Sun R and Zhang H (2007) Analysis of the RPE transcriptome reveals dynamic changes during the development of the outer blood-retinal barrier. Mol. Vis. 13: in press. Experiment Overall Design: Sheets of RPE were isolated from chicken embryos on Embryonic day 7 (E7), E10, E14 and E18 and stored in RNAlatter (Qiagen, Valencia, CA), as described <Rahner C, Fukuhara M, Peng S, Kojima S, Rizzolo LJ. The apical and basal environments of the retinal pigment epithelium regulate the maturation of tight junctions during development. J Cell Sci. 2004;117:3307-18>. To isolate total RNA, the RNeasy Protect kit (Qiagen) was used according to the manufacturer's protocols. For each age, 3-4 independent preparations were used for analysis on Affymetrix microarrays of the chicken genome (Santa Clara, CA). For each preparation, sheets of RPE were pooled from 20-30 eyes. The quality of the total RNA was assessed by the Keck Center, Yale University using formamide gels and a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA)
2008-11-08 | E-GEOD-7176 | biostudies-arrayexpress
Project description:This study investigates the processes of angiogenesis and lymphangiogenesis in an in vitro mouse Embryoid Body (EB) model while maintaining as closely as possible an in vivo environment that is observed in human and murine placental development. Several studies have documented that human placental development is profoundly influenced by oxygen tension. Further the developing murine embryo also experiences hypoxic conditions prior to parturition, which regulates early organogenesis and embryonic blood vessel formation in vivo. Embryonic stem (ES) cells derived from 129/SvJ mice were differentiated into embryoid bodies (EBs) and were subjected to two oxygen treatments: normoxia (21% O2) and hypoxia (2.6%). Hypoxia was achieved in a humidified chamber flushed with 95% N2/5% CO2 until the oxygen level was stably maintained at 2.6%. EBs were transferred on days E8, E12, E15 and E18 to hypoxia or maintained in normoxia. After 2 days of differential oxygen treatments, these EBs were analyzed at E10, E14, E17 and E20 respectively. A 4 x 2, reference-based, experimental design was utilized consisting of 4 timepoints (E10, E14, E17 and E20) subjected to 2 oxygen treatments (normoxia, hypoxia) with n=4 biological replicates present in each group. All EB samples were handled in parallel through all experimental steps. Each EB RNA sample was amplified, labeled with Cy5, and compared to the same Mouse Universal Reference RNA sample (Stratagene, La Jolla, CA) that was amplified and labeled with Cy3 dye. No dye swaps were utilized.
2012-08-11 | E-GEOD-17613 | biostudies-arrayexpress
Project description:40-PE Smart-Seq of RNA isolated from single 2-cell embryos, single morulae, single blastocysts, single E7 embryos epiblast halves and single E7 trophectoderm halves. For all preimplantation stages, embryos were grown ex-vivo from three experimental groups of zygotes: zygotes injected with the mRNA of a recombinant OGA (named BtGH84) (Btgh_injected), zygotes injected with a catalytically dead version of BtGH84 (dBtgh_injected) (control nr.1) and non-injected zygotes (non_injected) (control nr.2). Postimplantation E7 embryos were grown from two experimental group of zygotes: Btgh-injected and dBtgh-injected (control) and transferred at the 2-cell stage to foster mothers. All samples from the same embryonic stage were processed for single embryo (or single-embryo single-tissue) Smart-Seq library preparation at the same time and then sequenced in the same NextSeq500 run. The different embryonic stages were processed on different days and sequenced in different NextSeq500 runs.
2024-03-30 | E-MTAB-12981 | biostudies-arrayexpress
Project description:Paracrine Hedgehog (Hh) signaling regulates growth and patterning in many Drosophila organs. We mapped chromatin binding sites for Cubitus interruptus (Ci), the transcription factor that mediates outputs of Hh signal transduction, and we analyzed transcription profiles of control and mutant embryos to identify genes that are regulated by Hh. Putative targets we identified include several Hh pathway components, most previously identified targets, and many targets that are novel. Analysis of expression patterns of pathway components and target genes gave evidence of autocrine Hh signaling in the optic primordium of the embryo. And, every Hh target we analyzed that is not a pathway component appeared to be regulated by Hh in a tissue-specific manner. We present evidence that Hh-dependent tissue specificity is dependent upon transcription factors that are Hh-independent, suggesting that “pre-patterns” of transcription factors partner with Ci to make Hh-dependent gene expression position-specific. We utilized the DamID method to identify regions of CiRep methylated genomic DNA in stage 10-11 Drosophila embryos.
2010-11-03 | GSE24024 | GEO
Project description:Paracrine Hedgehog (Hh) signaling regulates growth and patterning in many Drosophila organs. We mapped chromatin binding sites for Cubitus interruptus (Ci), the transcription factor that mediates outputs of Hh signal transduction, and we analyzed transcription profiles of control and mutant embryos to identify genes that are regulated by Hh. Putative targets we identified include several Hh pathway components, most previously identified targets, and many targets that are novel. Analysis of expression patterns of pathway components and target genes gave evidence of autocrine Hh signaling in the optic primordium of the embryo. And, every Hh target we analyzed that is not a pathway component appeared to be regulated by Hh in a tissue-specific manner. We present evidence that Hh-dependent tissue specificity is dependent upon transcription factors that are Hh-independent, suggesting that “pre-patterns” of transcription factors partner with Ci to make Hh-dependent gene expression position-specific. We utilized the DamID method to identify regions of CiAct methylated genomic DNA in stage 10-11 Drosophila embryos.
2010-11-03 | GSE23999 | GEO