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Pluripotent stem cells: Normal diploid line vs lines with deletions of Chr7

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Homo sapiens

PROVIDER: GSE65410 | GEO | 2015/02/16

SECONDARY ACCESSION(S): PRJNA273921

REPOSITORIES: GEO

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Pluripotent stem cells: Normal diploid line vs lines with deletions of Chr7

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2015-02-16 | E-GEOD-65410 | biostudies-arrayexpress

Human Pluripotent stem cells: Normal diploid line vs lines with deletions of Chr7

Project description:Mapping deletions of Chr7 in human iPSC and ESCs derived from patients cells through reprogramming or chromosome engineering

2015-02-16 | GSE65386 | GEO

Human induced Pluripotent stem cells: Normal diploid line vs lines with deletions of Chr7

Project description:Mapping deletions of Chr7 in human iPSC derived from patients cells through reprogramming

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Human Pluripotent stem cells: Normal diploid line vs lines with deletions of Chr7

Project description:Mapping deletions of Chr7 in human iPSC and ESCs derived from patients cells through reprogramming or chromosome engineering Two-condition experiment, normal diploid hPSCs vs del7q-hPSCs

2015-02-16 | E-GEOD-65386 | biostudies-arrayexpress

Human induced Pluripotent stem cells: Normal diploid line vs lines with deletions of Chr7

Project description:Mapping deletions of Chr7 in human iPSC derived from patients cells through reprogramming Two-condition experiment, normal diploid iPSCs vs del7q-iPSCs

2015-02-16 | E-GEOD-65387 | biostudies-arrayexpress

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

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Normal human pluripotent stem cell lines exhibit pervasive mosaic aneuploidy.

Project description:Human pluripotent stem cell (hPSC) lines have been considered to be homogeneously euploid. Here we report that normal hPSC--including induced pluripotent--lines are karyotypic mosaics of euploid cells intermixed with many cells showing non-clonal aneuploidies as identified by chromosome counting, spectral karyotyping (SKY) and fluorescent in situ hybridization (FISH) of interphase/non-mitotic cells. This mosaic aneuploidy resembles that observed in progenitor cells of the developing brain and preimplantation embryos, suggesting that it is a normal, rather than pathological, feature of stem cell lines. The karyotypic heterogeneity generated by mosaic aneuploidy may contribute to the reported functional and phenotypic heterogeneity of hPSCs lines, as well as their therapeutic efficacy and safety following transplantation.

| S-EPMC3156708 | biostudies-literature

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

Glioblastoma Cell lines vs. Normal Glial Cells

Project description:Examination of alternative splicing in 4 glioblastoma cell lines (U118, t98g, a172, U87) vs. FGG cells grown in culture. 4 Cancer Cell lines vs. Normal Cells in a dye-swap design with 2 replicates in each dye orientation (4 tumor lines x 2 reps x 2 dye-orientations = 16 arrays)

| S-ECPF-GEOD-20723 | biostudies-other

Engineering of targeted megabase-scale deletions in human induced pluripotent stem cells.

Project description:Recurrent chromosomal deletions spanning several megabases are often found in hematological malignancies. The ability to engineer deletions in model systems to functionally study their effects on the phenotype would enable, first, determination of whether a given deletion is pathogenic or neutral and, second, identification of the critical genes. Incomplete synteny makes modeling of deletions of megabase scale challenging or impossible in the mouse or other model organisms. Furthermore, despite the breakthroughs in targeted nuclease technologies in recent years, engineering of megabase-scale deletions remains challenging and has not been achieved in normal diploid human cells. Large deletions of the long arm of chromosome 7 (chr7q) occur frequently in myelodysplastic syndrome (MDS) and are associated with poor prognosis. We previously found that we can model chr7q deletions in human induced pluripotent stem cells (iPSCs) using a modified Cre-loxP strategy. However, this strategy did not afford control over the length and boundaries of the engineered deletions, which were initiated through random chromosome breaks. Here we developed strategies enabling the generation of defined and precise chromosomal deletions of up to 22 Mb, using two different strategies: "classic" Cre-loxP recombination and CRISPR/Cas9-mediated DNA cleavage. As proof of principle, we illustrate that phenotypic characterization of the hematopoiesis derived from these iPSCs upon in vitro differentiation allows further definition of the critical region of chr7q whose hemizygosity impairs hematopoietic differentiation potential. The strategies we present here can be broadly applicable to engineering of diverse chromosomal deletions in human cells.

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