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Transcription profiling of mouse D4 and C2 ES cell lines assessed for chimerism and germline transmission

ABSTRACT: Two independent ES cell lines (D4 and C2) were assessed for chimerism and germline transmission. Although these lines were able to produce chimerism at early passage, no germ line transmission was seen. After passaging in a proprietary medium and subcloning by detaching loosely connected cells and culturing in the recommended medium, both lines experienced an increase in potential as evidenced by an enhanced ability to go germ line. Analysis of early passage, and late passage detached and attached cells will allow the determination of genes that may be implicated in the increase of potential seen in these cells. Note: additional replicates may be added at a later date. Experiment Overall Design: this experiment include 6 samples and 34 replicates

ORGANISM(S): Mus musculus

SUBMITTER: OGIC Info Ontario Genomics Innovation Centre (OGIC)

PROVIDER: E-GEOD-4087 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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D4 and C2 assessed for chimerism and germline transmission

Project description:Two independent ES cell lines (D4 and C2) were assessed for chimerism and germline transmission. Although these lines were able to produce chimerism at early passage, no germ line transmission was seen. After passaging in a proprietary medium and subcloning by detaching loosely connected cells and culturing in the recommended medium, both lines experienced an increase in potential as evidenced by an enhanced ability to go germ line. Analysis of early passage, and late passage detached and attached cells will allow the determination of genes that may be implicated in the increase of potential seen in these cells. Note: additional replicates may be added at a later date. Keywords: embryonic stem cells, chimerism, germline transmission

2006-01-24 | GSE4087 | GEO

Expression data from embryonic stem cells (ESCs) and re-derived cell lines

Project description:Our recovered cell lines, derived from bone marrow (BM), expressed all markers known for embryonic stem cells and were able to differentiate into three germ layers although germ line transmission is yet to be further defined. No germline transmission of the re-derived cell lines indicated their pluripotency decreased. We used gene array to compare the gene-expression of ESCs and re-derived cell lines.

2010-02-10 | GSE20220 | GEO

Epigenetic profiling in Utx germline conditional knockouts and F1 offspring

Project description:Susceptibility to cancer is highly heritable, but much of this heritability remains unexplained. Some "missing" cancer heritability may be mediated by epigenetic changes in the parental germ line that do not involve transmission of genetic variants from parent to offspring. These data describe the finding that deletion of the chromatin regulator Utx (Kdm6a) in the mouse male germ line results in an elevated tumor incidence in genetically wild type offspring. This effect increases following passage through two successive generations of Utx male germline deletion, but is lost following passage through a wild type germ line. We find widespread redistribution of the H3K27me3 mark in Utx mutant germ cells, and further define approximately 200 regions marked by H3K27me3 that exhibit increased DNA methylation, both in sperm of Utx mutants and in somatic tissue of their progeny. These hypermethylated regions are located in functional enhancers and may alter regulation of genes involved in cancer initiation or progression. The results indicate that epigenetic changes in the male germ line can profoundly impact cancer susceptibility in adult offspring.

2019-04-01 | GSE102313 | GEO

Tbx3 improves the germ-line competency of induced pluripotent stem cells

Project description:Induced pluripotent stem (iPS) cells can be obtained through the introduction of defined factors into somatic cells. The combination of Oct4, Sox2 and Klf4 (OSK) constitutes the minimal requirement for generating iPS cells from mouse embryonic fibroblasts (MEFs). These cells are thought to resemble embryonic stem cells (ESCs) based on global gene expression analyses; but, few studies have tested their ability and efficiency in contributing to chimerism, colonization of germ tissues, and most importantly, germ-line transmission and life-birth from iPS cells produced with tetraploid complementation. Through the genomic analyses of ESC genes that have roles in pluripotency and fusion-mediated somatic cell reprogramming, we identified Tbx3 as a transcription factor that significantly improves the quality of iPS cells. Induced-PS cells generated with OSK + Tbx3 (OSKT) are superior in both germ cell contribution to the gonads and germ-line transmission frequency. However, global gene expression profiling could not distinguish between OSK and OSKT iPS cells. Genome-wide ChIP-sequencing analysis of Tbx3 binding sites in ESCs suggests that Tbx3 regulates pluripotency-associated and reprogramming factors, in addition to sharing many common downstream regulatory targets with Oct4, Sox2, Nanog and Smad1. This study underscores the intrinsic qualitative differences between iPS cells generated by different methods and highlights the need to rigorously characterize iPS cells beyond in vitro studies.

2009-11-25 | GSE19164 | GEO

Mus musculus

Project description:D4 and C2 assessed for chimerism and germline transmission

| PRJNA95241 | ENA

Human Embryonic Stem Cell Sublines

Project description:Human embryonic stem (ES) cell lines acquire recurrent karyotypic abnormalities that may promote growth and survival in long-term culture. Cells with these abnormalities are often present at low levels in human ES cell cultures, requiring subcloning for isolation and analyses. We have developed a rapid method to isolate either abnormal or normal clones from karyotypically mosaic human ES cell cultures that we call Genetic Diagnosis at Passage (G-DAP). We have used this technique to isolate three distinct abnormal sublines from H9 human ES cells in continuous culture. These sublines were characterized by G-banding, fluorescence in situ hybridization (FISH), spectral karyotyping (SKY), and array comparative genomic hybridization (aCGH). One subline (H9.DT) has, as it’s only abnormality, a duplication of 12p capped by a 5q subtelomere. A related subline (H9.TSF) has an additional copy of the derivative chromosome 12, partial trisomy of 17q, and trisomy 14. The third subline (H9.DE) has an interstitial deletion of 18q as the sole anomaly. Despite these karyotypic abnormalities, all three sublines retain markers of the undifferentiated state. The subline H9.TSF demonstrated the ability to form embryoid bodies consisting of all three germ layers. Significantly, H9.DT and H9.TSF sublines show a classic karyotype progression that mirrors that seen in both hematopoietic and solid tumors. This progression was accompanied by an impressive increase in growth potential. The isolation of human ES cell sublines with clonal cytogenetic abnormalities provides a valuable tool for study of factors that promote in vitro genetic changes and for analysis of mechanisms of aneuploidy related to genetic progression found in human cancers.

2008-07-18 | GSE12119 | GEO

H3K27me3 maintains the transcription program during epigenetic reprogramming in the mouse germ line [RNA-seq D4]

Project description:To investigate the role of EZH2 in transcription regulation in mouse primordial germ cell like cells (PGCLCs), we isolated Ctrl and Ezh2 KO PGCLCs. Our data demonstrates that EZH2-mediated H3K27me3 is dispensible for transcription regulation in PGCLCs.

2021-09-27 | GSE163375 | GEO

Description of the D4/D4 genotype in Miniature horses with dwarfism.

Project description:Four causative mutations (D1, D2, D3*, and D4) of chondrodysplastic dwarfism have been described in the equine aggrecan (ACAN) gene. Homozygotes for one of these mutations and heterozygotes for any combination of these mutations exhibit the disproportionate dwarfism phenotype. However, no case description of homozygotes for D4 (D4/D4) has been reported in the literature, to our knowledge. We report 2 Miniature horses with the genotype D4/D4 in the ACAN gene. Clinically, the 2 dwarfs had a domed head that was large compared to the rest of the body, mandibular prognathism, and short and bowed limbs, mainly in the proximal region of the metatarsal bones. Radiographic examination revealed contour irregularities of the subchondral bone in the long bones and confirmed mandibular prognathism; histopathology revealed irregular chondrocyte organization. To determine the genotypes of the horses, we performed DNA extraction from white blood cells, PCR, and Sanger sequencing. Genotyping demonstrated that these 2 animals had the D4/D4 genotype in the ACAN gene. The D4/D4 dwarfs were clinically similar to animals with the other ACAN genotypes reported for this disease. Identification of heterozygous animals makes mating selection possible and is the most important control measure to minimize economic losses and casualties.

| S-EPMC7003212 | biostudies-literature

CNV ML-DmBG3-c2 Cells

Project description:modENCODE_submission_2553 This submission comes from a modENCODE project of David MacAlpine. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: Analysis of copy number variation across modENCODE Drosophila cell line by high throughput sequencing. We observe numerous copy number variations for the different cell lines, with each cell line having a distinct ploidy signature. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Keywords: deep sequencing analysis

2010-01-21 | GSE19958 | GEO

Campylobacter jejuni murine adaptation: unadapted v. adapted during growth in C57 BL/6 IL-10-/- germ-free mice.

Project description:Expression arrays comparing Campylobacter jejuni 11168 before and after serial passage in C57 BL/6 IL-10 deficient mice. Transcript abundance was compared between C. jejuni variants during growth in the ceca of C57 BL/6 IL-10 deficient germ-free mice.

2010-08-28 | GSE23811 | GEO

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