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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Expression data from +7 hNPCs and diploid hNPCs

ABSTRACT: Human Neural progenitor cells have been found to have karyotypic abnormalities. In this study we explored the gene changes between hNPCs that are karyotypically normal and hNPCs with a trisomy of chromosome 7. We used Affymetrix GeneChips to study gene expression changes between karyotypically normal hNPCs and trisomy 7 hNPCs. Cells grown in culture for ~20 passages from diploid and + 7 hNPCs were selected for RNA extraction and hybridization on Affymetrix microarrays.

ORGANISM(S): Homo sapiens

SUBMITTER: Dhruv Sareen

PROVIDER: E-GEOD-18349 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Expression data from +7 hNPCs and diploid hNPCs

Project description:Human Neural progenitor cells have been found to have karyotypic abnormalities. In this study we explored the gene changes between hNPCs that are karyotypically normal and hNPCs with a trisomy of chromosome 7. We used Affymetrix GeneChips to study gene expression changes between karyotypically normal hNPCs and trisomy 7 hNPCs.

2009-10-01 | GSE18349 | GEO

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

Human induced pluripotent stem cells: diploid, chr7q deletion, spontaneous chr7 correction

2015-02-16 | GSE65215 | GEO

RNAi knock down of CDC7 in human IMR90 primary diploid fibroblasts derived from embryonic lung tissue

Project description:Transcriptional profiling of siRNA-mediated inhibition of CDC7 in IMR90 primary diploid fibroblasts derived from embryonic lung tissue.

2010-09-03 | E-MEXP-2115 | biostudies-arrayexpress

Differential gene expression profilings between diploid and triploid Fujian Oyster

Project description:The systematic deep sequencing analysis provided a comprehensive understanding of the transcriptome complexity of 2n and 3n Fujian oyster. This information broadens our understanding of the mechanisms of C.angulata polyploidization and contributes to molecular and genetic research by enriching the oyster database. This is the first report on genome-wide transcriptional analysis of adductor muscle of diploid and triploid Fujian oyster and has demonstrated triploid oysters are morphologically almost identical to their diploid counterparts, but have faster growth, due to the reorientation of energetic allocation from gametogenesis to somatic investment. This study provides a foundation for further analysis of the gene expression patterns and signaling pathways which regulate the molecular mechanisms of diploid and triploid oyster. Examination of 3 different samples, including diploid (DF and DM) and triplod(T) oyster.

2014-03-06 | E-GEOD-55610 | biostudies-arrayexpress

Watermelon Proteome - To determine the differential expression of proteins in leaf and fruit of diploid and tetraploid watermelon

Project description:To determine the differential expression of proteins in leaf and fruit of diploid and tetraploid watermelon

2019-11-11 | PXD005179 | Pride

Expression data from diploid and aneuoploid human pluripotent stem cells, teratomas derived from them, and pluripotent-like cells recovered from these teratomas

Project description:Human pluripotent stem cells (hPSCs) tend to acquire genomic aberrations in culture, the most common of which is the trisomy of chromosome 12. Interestingly, trisomy 12 is also prevalent in germ cell tumors (GCTs). Here, we aimed to dissect the cellular and molecular implications of trisomy 12 in hPSCs. A genome-wide gene expression analysis revealed that trisomy 12 profoundly affects the global gene expression profile of hPSCs, inducing a transcriptional program very similar to that of CGTs. Direct comparison of the proliferation, replication, differentiation and apoptosis between diploid and aneuploid hPSCs revealed that trisomy 12 significantly increases the proliferation rate of hPSCs. Increased replication largely accounts for the increased proliferation observed, and may explain the selection advantage that trisomy 12 confers to hPSCs. A comparison of the tumors induced by diploid and aneuploid hPSCs further demonstrated that trisomy 12 increases the tumorigenicity of hPSCs, inducing transcriptionally-distinct teratomas, from which pluripotent cells can be recovered. Lastly, a chemical screen of 89 anticancer drugs against diploid and aneuploid hPSCs discovered that trisomy 12 raises the sensitivity of hPSCs to several replication inhibitors, suggesting that the increased proliferation and tumorigenicity of these aberrant cells also makes them more vulnerable, and might potentially be used for their selective elimination from culture. Together, our findings demonstrate the extensive effect of trisomy 12 on the gene expression signature and on the cellular behavior of hPSCs, and highlight the danger posed by this trisomy for the successful use of hPSCs in basic research and in regenerative medicine.

2014-09-01 | GSE51455 | GEO

The addition of chromosome 8 leads to characteristic dysregulation of gene expression on all chromosome and transformed-associated phenotypes

Project description:To examain effects of trisomy 8 on gene expression in normal human cells, we have employed whole genome microarray expression profiling. To study the effects of aneuploidy in normal human cells, we generated cells which are artificially trisomic chromosome 8 (trisomy 8) using human primary fibroblast cells by microcell-mediated chromosome transfer (HE35tri8 clones). Gene expression in trisomy 8 clones (HE35tri8-1, 2 and3) and euploid clones (HE35-1, 2 and 4). Three independent experiments were performed at each clone.

2011-10-07 | E-GEOD-28076 | biostudies-arrayexpress

Human induced pluripotent stem cells: diploid, chr7q deletion, spontaneous chr7 correction

Project description:Gene expression analysis, a) comparing isogenic karyotypically normal iPSCs to del7q-iPSCs, b) comparing del7q-iPSCs to spontaneously corrected iPSCs. The chr7q deletion results in reduced expression levels of a large number of genes in the chr7q deleted region Two-condition experiment, del7q-iPSCs vs. isogenic normal iPSCs and del7q-iPSCs vs spontaneously corrected-iPSCs. Biological replicates: 3 control replicates, 3 del7q-iPSC replicates and 3 spontaneously corrected-iPSC replicates

2015-02-16 | E-GEOD-65215 | biostudies-arrayexpress

Identification of dysregulated genes in lymphocytes from children with Down syndrome

Project description:The aim of this study was to analyze global changes of gene expression in lymphocytes from children with trisomy 21 by means of the serial analysis of gene expression (SAGE) methodology. Comparison between DS and normal profiles revealed that most of the transcripts were expressed at similar levels. Among the 242 significantly differentially expressed SAGE tags, many of them corresponded to genes involved in transcription, RNA processing, signaling, immune response and lipid metabolism. Our results indicate that trisomy 21 induces a modest dysregulation of disomic genes that may be related to the immunological perturbations seen in DS. Keywords: SAGE analysis in normal and Down syndrome lymphocytes Lymphocytes were isolated from peripheral blood of normal and karyotypically confirmed full trisomy 21 children. Children included in the study, ranging in age from 1-4 years, were self reported as free of chronic or acute infections. Total RNA was isolated with TRIzol reagent (Invitrogen). The SAGE libraries were constructed using pooled RNA from six DS children (DS library) and six normal children (control group) to eliminate any individual variation. SAGE was performed by means of the I-SAGE kit (Invitrogen) following the manufacturer’s instructions.

2007-04-25 | E-GEOD-7464 | biostudies-arrayexpress

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