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RNA-sequencing technology identifies specific genes expressed in the ICM of mouse embryos

ABSTRACT: RNA-seq data from whole mouse embryos at E3.75 (stage where the three cell types: TE, PrE and EPI are well resolved) and from dissected ICMs in order to identify genes expressed specifically in the ICM

ORGANISM(S): Mus musculus

PROVIDER: GSE44553 | GEO | 2013/04/23

SECONDARY ACCESSION(S): PRJNA190711

REPOSITORIES: GEO

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RNA-sequencing technology identifies specific genes expressed in the ICM of mouse embryos

Project description:RNA-seq data from whole mouse embryos at E3.75 (stage where the three cell types: TE, PrE and EPI are well resolved) and from dissected ICMs in order to identify genes expressed specifically in the ICM We used E3.75 whole mouse embryos at the blastocyst stage and immunosurgically dissected ICMs for RNA extraction and sequencing

2013-04-23 | E-GEOD-44553 | biostudies-arrayexpress

Peri-infarct region transcriptome of SCID mice trated with saline control, iPSC-derived cardiomyocytes (iCM), or iCM-derived exosomes (iCM-Ex)

Project description:iPSC-derived iCMs represent a potential therapy for ischemic cardiomyopathy. Previous studies demonstrated enhanced cardiac function following injection of iCMs into the peri-infarct region in mice models. Cardioprotection despite poor engraftment suggests that iCMs may modulate their therapeutic activity by secreted molecules. Exosomes are discrete packages of secreted molecules that are readily taken up by target cells. iCM and iCM-Ex treatment of acute myocardial infarctions (Mis) significantly improved cardiac function in SCID mice. We used microarrays to identify differentially-regulated genes in iCM- or iCM-Ex treated mice and control mice.

2020-01-24 | GSE144171 | GEO

Single cell expression data from ICM cells of mouse blastocysts

Project description:Transcriptional reactivation of the paternal X chromosome occurs in specific cells of the mouse blastocyst between E(mbryonic day)3.5 and E4.5 during pre- to peri-implantation development. While the trophectoderm (TE) and the primitive endoderm (PE) maintain Xist RNA expression and thereby imprinted silencing of genes on the Xp, the epiblast (EPI) cells within the inner cell mass (ICM) gradually downregulate Xist and undergo XCR. To identify differentially expressed genes with potential roles in the XCR process, we performed single-cell expression profiling of ICM cells of blastocysts prior (E3.5, EPI Xist+), during (E4.25, EPI Xist+/Xist-) and after (E4.5, EPI Xist-) XCR. Single cell cDNAs were then assigned to cell-type of origin using qPCR for lineage-specific marker genes (epiblast: Nanog+, PE: Gata6+, TE: Cdx2+). Cells were considered of male sex if they expressed the male marker Eif2s3y or female sex in absence of Eif2s3y and presence of Xist expression in PE cells of the same embryo. Furthermore, female E4.5 epiblast cDNAs were classified according to Xist expression as before (Xist+) or after (Xist-) downregulation during XCR.

2022-11-13 | GSE208430 | GEO

High-throughput screen for genes predominantly expressed in the ICM of mouse blastocysts by whole mount in situ hybridiz

Project description:We attempted to identify candidate genes that are expressed more highly in the ICM than in TE cells. Mouse ES cells are cultured from the ICM, whereas mouse TS cells are cultured from the TE. Although these cells have been cultured in vitro, they represent the in vitro equivalents of the ICM and TE. Therefore, genes which are expressed more highly in ES than TS in microarray studies were good candidates for genes predominantly expressed in the ICM in blastocysts. We attempted to identify candidate genes that are expressed more highly in the ICM than in TE cells. Mouse ES cells are cultured from the ICM, whereas mouse TS cells are cultured from the TE. Although these cells have been cultured in vitro, they represent the in vitro equivalents of the ICM and TE. Therefore, genes which are expressed more highly in ES than TS in microarray studies were good candidates for genes predominantly expressed in the ICM in blastocysts.

2010-06-09 | E-GEOD-3214 | biostudies-arrayexpress

High-throughput screen for genes predominantly expressed in the ICM of mouse blastocysts by whole mount in situ hybridiz

2005-08-30 | GSE3214 | GEO

Lineage regulators TFAP2C and NR5A2 function as bipotency activators in totipotent embryos

Project description:During the first lineage segregation, a mammalian totipotent embryo differentiates into inner cell mass (ICM) and trophectoderm (TE). However, how transcription factors (TFs) regulate this earliest cell fate decision in vivo remains elusive, with their regulomes primarily inferred from cultured cells. Here, we investigated the TF regulomes during the first mouse lineage specification across 6 stages, spanning the pre-initiation, initiation, commitment, and maintenance phases. Unexpectedly, we found TFAP2C, a trophoblast regulator, bound and activated both early TE and ICM genes at the totipotent (2-8-cell) stages (“bipotency activation”). Tfap2c deficiency caused downregulation of early ICM genes, including Nanog, Nr5a2, Tdgf1, and early TE genes, including Tfeb and Itgb5 in 8-cell embryos. Transcription defects in both ICM and TE lineages were also found in blastocysts, accompanied by increased apoptosis and reduced cell numbers in ICMs. Upon trophoblast commitment, TFAP2C left early-ICM genes but acquired binding to late-TE genes in blastocysts where it co-bound with CDX2, and later to extra-embryonic ectoderm (ExE) genes where it cooperatively co-occupied with the former ICM regulator SOX2. Finally, “bipotency activation” in totipotent embryos also applied to a pluripotency regulator NR5A2 which similarly bound and activated both ICM and TE lineage genes at the 8-cell stage. These data reveal a unique transcription circuity of totipotency underpinned by highly adaptable lineage regulators.

2023-11-23 | GSE216256 | GEO

Preimplantation mouse embryo proteome during 8C to 16C division

Project description:Preimplantation stages of mouse embryo development involve temporal and spatial specification and segregation of three late blastocyst cell lineages; trophectoderm (TE), primitive endoderm (PrE) and epiblast (EPI). Spatial separation of the outer TE lineage from the two inner-cell-mass (ICM) lineages (PrE and EPI) starts with the 8- to 16-cell transition and concludes following transit through the 16- to 32-cell stages. This results in a nascent early blastocyst ICM derived from descendants of primary founding inner cells and a secondarily contributed population; of which subsequent relative EPI versus PrE potencies are subject to debate. We showed that generation of primary but not the secondary ICM populations is highly dependent on temporally discreet activation of the mammalian target of rapamycin (mTOR – specifically mTORC1) around 8-cell stage M-phase entry. Moreover, that this role is mediated via the regulated function of the 7-methylguanosine- (7mG) cap binding initiation complex (EIF4F) and potentiating the translation of a subset of key but otherwise intransigent mRNAs containing 5’ UTR terminal oligopyrimidine (TOP-) sequence motifs. To find out translation of which mRNAs is regulated by mTOR during 8- to 16-cell transition, we analysed proteomes of control and mTOR-inhibited embryos during this time window.

2023-08-18 | PXD039423 | Pride

Genome-wide Promoter Mapping of Histone H3 Lysine 4 and Lysine 27 Methylation in Preimplantation Embryos

Project description:First lineage specification in the mammalian blastocyst embryo leads to formation of the inner cell mass (ICM) and trophectoderm (TE), which respectively give rise to the embryo proper and extraembryonic tissues. We show histone methylation asymmetry on promoters in the first two developmental lineages, and highlight epigenetic skewing associated with derivation of embryonic stem (ES) cells. Comparison of histone methylation patterns on promoters in the ICM, TE and in ES cells derived from ICM. ChIP-chip experiments using anti-H3K4me3 or anti-H3K27me3 antibodies. Two or three replicates per sample.

2010-05-14 | E-GEOD-17387 | biostudies-arrayexpress

Peri-infarct region transcriptome of SCID mice trated with saline control, iPSC-derived cardiomyocytes (iCM), or iCM-derived exosomes (iCM-Ex)

Project description:Peri-infarct region transcriptome of SCID mice trated with saline control, iPSC-derived cardiomyocytes (iCM), or iCM-derived exosomes (iCM-Ex)

| PRJNA602924 | ENA

Effects of thyroid hormone on human preimplantation embryos

Project description:We found that the exposure of human preimplantation embryos to triiodothyronine (T3) has a profound impact on gene transcription only in the cells of inner cell mass (ICM) and no effect on cells of trophectoderm (TE).

2022-05-20 | GSE131488 | GEO

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