RNA-seq transcriptome profiling of equine inner cell mass and trophectoderm
Ontology highlight
ABSTRACT:
ORGANISM(S): Equus caballus
PROVIDER: GSE51431 | GEO | 2014/05/02
SECONDARY ACCESSION(S): PRJNA223157
REPOSITORIES: GEO
Similar Datasets
Project description:Transcriptomic analysis of ICM and TE from in vivo-derived equine blastocysts using Illumina sequencing technology RNA was extracted from individual equine blastocyst ICM and TE (Arcturus Picopure), cDNA was synthesized and amplified (Nugen Ovation V2) and indexed libraries were created for sequencing (TruSeq DNA V1)
2014-05-02 | E-GEOD-51431 | biostudies-arrayexpress
Project description:Aneuploidy has been well documented in blastocyst embryos, but prior studies have been limited in scale and/or lack mechanistic data. We previously reported preclinical validation of microarray 24-chromosome preimplantation genetic screening (PGS) in a 24-hour protocol. The method diagnoses chromosome copy number, structural chromosome aberrations, parental source of aneuploidy, and distinguishes certain meiotic from mitotic errors. In this study our objective was to examine aneuploidy in human blastocysts and determine correspondence of karyotypes between trophectoderm (TE) and inner cell mass (ICM). We disaggregated 51 blastocysts from seventeen couples into ICM and one or two TE fractions. The average maternal age was 31. Next, we ran 24-chromosome microarray molecular karyotyping on all of the samples, and then performed a retrospective analysis of the data. The average per-chromosome confidence was 99.95%. Approximately 80% of blastocysts were euploid. The majority of aneuploid embryos were simple aneuploid, i.e., one or two whole-chromosome imbalances. Structural chromosome aberrations, which are common in cleavage stage embryos, occurred in only three blastocysts (5.8%). All TE biopsies derived from the same embryos were concordant. Forty-nine of fifty-one (96.1%) inner cell mass (ICM) samples were concordant with TE biopsies derived from the same embryos. Discordance between TE and ICM occurred only in the two embryos with structural chromosome aberration. We conclude that trophectoderm karyotype is an excellent predictor of inner cell mass karyotype. Discordance between TE and ICM occurred only in embryos with structural chromosome aberrations. We thawed all fractions at 22°C, and then added Arcturus PicoPure Lysis Buffer (Molecular Devices, Sunnyvale, CA) to each of the biopsies. The tubes were incubated at 56°C for one hour, and then heat inactivated at 95°C for 10 minutes. DNA from the lysed biospsies was amplified using a commercial kit (GE Healthcare, Waukesha, WI) for multiple displacement amplification (MDA). MDA reactions were incubated at 30°C for 2.5 hours and then heat-inactivated at 65°C for five minutes. The amplified samples were genotyped using Illumina (San Diego, CA, USA) Infinium II genotyping microarrays (CytoSNP-12 chips) using a modified 24-hour protocol, as described previously*. Previously, we developed a genotyping microarray molecular karyotyping technology that uses parental genetic data to increase accuracy and determine mechanism and source of aneuploidy*. The algorithm uses parental genotypes and the observed distribution of unprocessed single cell microarray channel intensities to diagnose whole-chromosome imbalances and structural chromosome aberrations*. Because parental genotypes are available, the algorithm readily identifies parental source of whole-chromosome imbalances and structural chromosome aberrations. Additionally, the algorithm uses parental information, high confidence disomic single cell measurements on children, and recombination probabilities (genome.ucsc.edu) to determine the phase of the parental chromosomes. The phased data is then used to determine whether certain trisomies and uniparental disomies were mitotic or meiotic in origin*. *Johnson DS, Gemelos G, Baner J, Ryan A, Cinnioglu C, Banjevic M, Ross R, Alper M, Barrett B, Frederick J, Potter D, Behr B, Rabinowitz M. (2010). Preclinical validation of a microarray method for full molecular karyotyping of blastomeres in a 24-hour protocol. Human Reproduction January 24 [Epub ahead of print].
2010-09-28 | E-GEOD-22864 | biostudies-arrayexpress
Project description:Aneuploidy has been well documented in blastocyst embryos, but prior studies have been limited in scale and/or lack mechanistic data. We previously reported preclinical validation of microarray 24-chromosome preimplantation genetic screening (PGS) in a 24-hour protocol. The method diagnoses chromosome copy number, structural chromosome aberrations, parental source of aneuploidy, and distinguishes certain meiotic from mitotic errors. In this study our objective was to examine aneuploidy in human blastocysts and determine correspondence of karyotypes between trophectoderm (TE) and inner cell mass (ICM). We disaggregated 51 blastocysts from seventeen couples into ICM and one or two TE fractions. The average maternal age was 31. Next, we ran 24-chromosome microarray molecular karyotyping on all of the samples, and then performed a retrospective analysis of the data. The average per-chromosome confidence was 99.95%. Approximately 80% of blastocysts were euploid. The majority of aneuploid embryos were simple aneuploid, i.e., one or two whole-chromosome imbalances. Structural chromosome aberrations, which are common in cleavage stage embryos, occurred in only three blastocysts (5.8%). All TE biopsies derived from the same embryos were concordant. Forty-nine of fifty-one (96.1%) inner cell mass (ICM) samples were concordant with TE biopsies derived from the same embryos. Discordance between TE and ICM occurred only in the two embryos with structural chromosome aberration. We conclude that trophectoderm karyotype is an excellent predictor of inner cell mass karyotype. Discordance between TE and ICM occurred only in embryos with structural chromosome aberrations.
2010-09-28 | GSE22864 | GEO
Project description:Selection of high-quality embryos is important to achieve successful pregnancy in assisted reproductive technology (ART). Recently, it has been debated whether RNA-sequencing (RNA-seq) should be applied to ART to predict embryo quality. However, the information on which genes can serve as markers for pregnant expectancy is limited. Furthermore, there is no information on which transcriptome of trophectoderm (TE) or inner cell mass (ICM) is more highly correlated with pregnant expectancy. Here we performed RNA-seq analysis for TE and ICM, respectively, in human blastocysts of which the expectation of pregnancy was retrospectively determined by the clinical outcomes of 1,890 cases of frozen-thawed blastocyst transfer. We identified dozens of genes that were correlated with the expected pregnancy rate in ICM and TE, respectively, with a larger number of genes identified in TE. Importantly, downregulated genes in TE of blastocysts classified as having lower expectation of pregnancy included tight junction-related genes, such as CXADR, CLDN10, and ATP1B1, which were implicated in peri-implantation development. Additionally, we showed that aneuploidy estimation by RNA-seq datasets does not correlate with pregnancy expectation. Our study thus provide an expanded list of candidate genes for prediction of pregnancy in human blastocyst embryos.
2022-09-30 | GSE205171 | GEO
Project description:This study describes the generation and analysis of the transcriptional profile of bovine inner cell mass (ICM) and trophectoderm (TE), obtained from in vivo developed embryos by using a bovine-embryo specific array (EmbryoGENE) containing 37,238 probes.
2015-12-02 | GSE75555 | GEO
Project description:Networks of interacting co-regulated genes distinguish the inner cell mass (ICM) from the differentiated trophectoderm (TE) in the preimplantation blastocyst, in a species specific manner. In mouse the ground state pluripotency of the ICM appears to be maintained in murine embryonic stem cells (ESCs) derived from the ICM. This is not the case for human ESCs. In order to gain insight into this phenomenon, we have used network analysis to quantify how similar human (h)ESCs are to the human ICM. Using the hESC lines MAN1, HUES3 and HUES7 we have shown that all have only a limited overlap with ICM specific gene expression, but that this overlap is enriched for network properties that correspond to key aspects of function including transcription factor activity and the hierarchy of network modules. These analyses provide an important framework which highlights the developmental origins of hESCs.
2019-03-31 | GSE121982 | GEO
Project description:IL-6 has been shown to be required for somatic cell reprogramming into induced pluripotent stem cells (iPSCs). However, how the cytokine is regulated and if it plays a role during embryo development remains unknown. Here we describe that IL-6 is strictly necessary for C/EBPa-enhanced reprogramming of B cells into iPSCs but not for B cell to macrophage transdifferentiation. C/EBPa induces the expression of both Il6 and Il6ra genes in B cells and in PSCs. During preimplantation embryo development C/EBPa is expressed in blastocysts where it is required for the maintenance of Il6. The expression of Cebpa is enriched in trophectoderm together with Il6 whereas the receptor gene Il6ra is predominantly expressed in the inner cell mass (ICM), in both mouse and humans. Blastocysts secrete IL-6 and neutralization of the cytokine delays the morula to blastocyst transition. Our study indicates that the trophectoderm acts as a niche for the ICM through the secretion of C/EBPa-regulated IL-6, facilitating efficient blastocyst development.
2022-08-11 | GSE202613 | GEO
Project description:IL-6 has been shown to be required for somatic cell reprogramming into induced pluripotent stem cells (iPSCs). However, how the cytokine is regulated and if it plays a role during embryo development remains unknown. Here we describe that IL-6 is strictly necessary for C/EBPa-enhanced reprogramming of B cells into iPSCs but not for B cell to macrophage transdifferentiation. C/EBPa induces the expression of both Il6 and Il6ra genes in B cells and in PSCs. During preimplantation embryo development C/EBPa is expressed in blastocysts where it is required for the maintenance of Il6. The expression of Cebpa is enriched in trophectoderm together with Il6 whereas the receptor gene Il6ra is predominantly expressed in the inner cell mass (ICM), in both mouse and humans. Blastocysts secrete IL-6 and neutralization of the cytokine delays the morula to blastocyst transition. Our study indicates that the trophectoderm acts as a niche for the ICM through the secretion of C/EBPa-regulated IL-6, facilitating efficient blastocyst development.
2022-08-11 | GSE202611 | GEO
Project description:Mammalian preimplantation development involves highly conserved genetic programs across species. However, temporal differences in gene network activation and membership differences in gene modules are also observed. In this study, we focus on understanding the activation of crucial gene networks in trophoectoderm (TE) and inner cell mass across species using human, monkey, and mouse models. By single cell RNA sequencing analysis in cynomolgus monkey early embryos, we find relatively late major embryonic genome activation occurring at early morula stages. Gene network preservation analysis reveals that genetic programs in monkey embryos more closely resemble human embryos compared to mouse, supporting the notion that preimplantation development in primate species are divergent from rodent species. For example, primate blastocysts show differential expression of ICM and TE genes such as X and Y, whereas mouse show differences in A and B expression. Interestingly, the overall conservation of TE gene networks is higher than ICM across three species, suggesting a more conserved developmental program in TE lineage differentiation. Additionally, TE-specific gene networks are exclusively activated at the blastocyst stage with low or no expression in morula or earlier embryos. In contrast, a majority of ICM-specific genes are strongly activated during the first major wave of EGA, which are further fine-tuned during late morula and blastocyst stages. Taken together, our study provides new insight into mammalian preimplantation development and sequential activation of lineage-specific genetic programs of TE versus ICM.
2022-06-30 | GSE75764 | GEO
Project description:Inner cell mass (ICM) cells of two independent E3.5 blastocysts were profiled by transcriptome sequencing to assess the expression of extracellular matrix components.
2014-05-15 | E-MTAB-2555 | biostudies-arrayexpress