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Links from GEO DataSets

Items: 17

1.

C9/ALS Human Embryonic Stem Cells and C9/ALS Induced Pluripotent Stem Cells

(Submitter supplied) We established two HESC lines with a C9 mutation (SZ-ALS1, SZ-ALS3) from embryos, which were obtained through preimplantation genetic diagnosis (PGD) and donated for cell line derivation by a family in which the mother was an expansion carrier (originally diagnosed as a carrier of an expansion with >40 repeats in blood by a repeat primed PCR). In addition, we generated halo-identical and unrelated C9/ALS iPSCs from a skin biopsies of the C9 carrier mother (patient H, 30 years-old), and from an unrelated C9/ALS patient, 2 years following disease-onset (patient M, 65 years-old).
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL18573
9 Samples
Download data: TXT
2.

A panel of CpG methylation patterns distinguishes human embryonic stem cells and induced pluripotent stem cells

(Submitter supplied) Genome wide DNA methylation profiling of normal human embryonic stem cells, induced pluripotent stem cells, and somatic cells. The Illumina Infinium 27k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 27,000 CpGs in 5 normal hESCs, 15 hiPSCs (vector-containing and vector-free), and 5 somatic cells.
Organism:
Homo sapiens
Type:
Methylation profiling by array
Platform:
GPL8490
46 Samples
Download data: TXT
Series
Accession:
GSE42043
ID:
200042043
3.

DNA methylation and gene expression changes during human embryonic stem cell differentiation

(Submitter supplied) Investigate the genome-wide DNA methylation and gene expression changes during human embryonic stem cell differentiation.
Organism:
Homo sapiens
Type:
Expression profiling by array; Methylation profiling by genome tiling array
Platforms:
GPL14617 GPL4133
16 Samples
Download data: TXT
Series
Accession:
GSE32371
ID:
200032371
4.

DNA methylation data from a separate set of human iPS cells and fibroblasts, and ES cells

(Submitter supplied) We used custom Nimblegen microarrays to determine the DNA methylation profiles of iPS cells, ES cells, and fibroblasts.
Organism:
Homo sapiens
Type:
Methylation profiling by genome tiling array
Platform:
GPL9275
8 Samples
Download data: PAIR
Series
Accession:
GSE24820
ID:
200024820
5.

DNA methylation data from human iPS cells and fibroblasts

(Submitter supplied) DNA methylation is often inversely correlated with gene expression. We used custom Nimblegen microarrays to determine the relationship between DNA methylation and gene expression in 6 iPS cell lines and the fibroblasts from which they were derived.
Organism:
Homo sapiens
Type:
Methylation profiling by genome tiling array
Platform:
GPL9275
12 Samples
Download data: PAIR
Series
Accession:
GSE18227
ID:
200018227
6.

Expression data from human iPS cells and fibroblasts

(Submitter supplied) DNA methylation is often inversely correlated with gene expression. We used expression microarrays to determine the relationship between DNA methylation and gene expression in 6 iPS cell lines and the fibroblasts from which they were derived.
Organism:
Homo sapiens
Type:
Expression profiling by array
Platform:
GPL570
12 Samples
Download data: CEL
Series
Accession:
GSE18226
ID:
200018226
7.

Human iPS cells and fibroblasts

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Homo sapiens
Type:
Expression profiling by array; Methylation profiling by genome tiling array
Platforms:
GPL9275 GPL570
32 Samples
Download data: CEL, PAIR
Series
Accession:
GSE18111
ID:
200018111
8.

Comparative analysis of hESCs and iPSCs-derived hepatocyte-like cells reveals current drawbacks and possible strategies for improved differentiation

(Submitter supplied) Two independent protocols for deriving HLCs from hESCs and iPSCs were adopted and further characterization included immunocytochemistry, real-time RT-PCR, and in vitro functional assays. Comparative microarray-based gene expression profiling was conducted on these cells and compared to the transcriptomes of human fetal liver and adult liver progenitors. HLCs derived from hESCs and hiPSCs showed significant functional similarities, similar expression of genes important for liver physiology and common pathways. more...
Organism:
Homo sapiens
Type:
Expression profiling by array
Platform:
GPL6883
32 Samples
Download data: TXT
Series
Accession:
GSE25744
ID:
200025744
9.

Efficient hematopoietic redifferentiation of induced pluripotent stem cells derived from primitive murine bone marrow cells

(Submitter supplied) Heterogeneity among iPSC lines with regard to their gene expression profile and differentiation potential has been described and has been at least partly linked to the tissue of origin. We generated iPSCs from primitive (linneg) and non-adherent differentiated (linpos) bone marrow cells (BM-iPSC), and compared their differentiation potential to that of fibroblast-derived iPSCs (Fib-iPSC) and ESCs. In the undifferentiated state, individual iPSC clones but also ESCs proved remarkably similar when analyzed for alkaline phosphatase and SSEA-1 staining, endogenous expression of the pluripotency genes Nanog, Oct4, and Sox2, or global gene expression profiles. However, substantial differences between iPSC clones were observed after induction of differentiation, which became most obvious upon cytokine-mediated instruction towards the hematopoietic lineage. All three BM-iPSC lines derived from undifferentiated cells yielded high proportions of cells expressing the hematopoietic differentiation marker CD41, and in two of these lines, high proportions of CD41+/CD45+ cells were detected. In contrast, little hematopoiesis-specific surface marker expression was detected in linpos BM-iPSC and FIB-iPSC lines. These results were corroborated by functional studies demonstrating robust colony outgrowth from hematopoietic progenitors in two of the linneg BM-iPSCs only. Thus, in summary our data demonstrate efficient generation of iPSCs from primitive hematopoietic tissue as well as efficient hematopoietic redifferentiation for linneg BM-iPSC lines, thereby further supporting the notion of an epigenetic memory in iPSCs. Murine embryonic fibroblasts (MEFs) from C3H mice were cultured in low-glucose DMEM supplemented with 10% heat-inactivated fetal calf serum gold (PAA, Pasching, Austria), penicillin-streptomycin, 1 mM L-glutamine and 0.05 mM beta-mercaptoethanol on gelatine-coated dishes. C3H MEFs were grown to confluence, inactivated with 10 ug/ml Mitomycin C (Sigma) and used as feeder layers. Virus production was performed in a four plasmid-manner. Briefly, 3.5x10^6 293T cells were seeded 24h prior to transfection in 10 cm dishes. 293T cells were cultivated in high-glucose DMEM (Gibco) supplemented with 10% heat-inactivated FCS, penicillin-streptomycin and 1 mM L-glutamine. Cells were transfected with 5 ug lentiviral vector, 8 ug pcDNA3.GP.4xCTE (expressing HIV-1 gag/pol), 5 ug pRSV-Rev and 2 ug pMD.G (encoding the VSV glycoprotein) using the calcium phosphate method in the presence of HEPES and chloroquine. Supernatants were harvested 48h and 72h after transfection, filtered and subsequently 50x concentrated by ultracentrifugation. Titers determined based on real-time PCR, were in the range of 1-5x10^7/ml. For iPSC generation, bone marrow cells were isolated from femurs and tibias of Oct4-GFP transgenic mice (OG2) and immunomagnetically separated into lineage negative (Lin-) and lineage positive (Lin+) populations using the mouse lineage depletion kit (Miltenyi Biotec). Lin- cells were cultivated in serum-free StemSpan medium (Stem Cell Technology) supplemented with 2 mM L-glutamine, penicillin-streptomycin, 10 ng/ml mSCF, 20 ng/ml mTPO, 20 ng/ml, 20 ng/ml IGF-2 and 10 ng/ml FGF-1 (all Peprotech). Lin+ cells were cultivated in Iscove's modified eagle medium (IMDM), supplemented with 15% heat-inactivated FCS, 1 mM L-glutamine, penicillin-streptomycin, 100 ng/ml mSCF, 100 ng/ml mFLT3-L, 10 ng/ml hIL-3 and 100 ng/ml hIL-11. Both Lin- and Lin+ cells were pre-stimulated in the aforementioned media for 48 h. Thereafter, 2x10^5 Lin- and and Lin+ bone marrow cells were transduced on Retronection-coated plates (Takara) with lentiviral vectors encoding for human Oct4, Sox2, Klf4 and c-Myc using a multiplicity of infection (MOI) of 50 per virus. Twenty-four hours after transduction, media were supplemented with 2 mM valproic acid. Transduced bone marrow cells were kept in hematopoietic medium until 5 or 7 days post transduction (p.t.) and then transferred onto Mitomycin C-treated MEF feeders on gelatine-coated dishes. Henceforward, cells were cultivated in ES cell medium (knockout DMEM (Gibco), 15% ES-tested FCS, 1 mM L-glutamine, 0.1 mM non-essential amino acids (Gibco), 100 uM beta-mercaptoethanol (Sigma), penicillin-streptomycin and 103 units/ml leukemia inhibitory factor (LIF, provided by the Max-Planck-Institute, Munster, Germany). Upon appearance of GFP-positive ESC-like colonies, single colonies were picked based on morphology and GFP expression. Murine ESCs and iPSCs were cultured on Mitomycin C-treated MEF feeders in the aforementioned ES medium. Murine ESCs and iPSCs were passaged every 2-3 days. The murine embryonic fibroblast-derived iPSC lines (MEF-iPS, 3FLV2, 4FLV1) were generated by transduction of OG2-MEFs with the same lentiviral vector constructs using standard technology. For iPSC lines 3FLV2 and 4FLV1, complete reprogramming was demonstrated by alkaline phosphatase and SSEA1-staining, pluripotency factor expression and teratoma formation.
Organism:
Mus musculus
Type:
Expression profiling by array
Platform:
GPL6885
7 Samples
Download data: TXT
Series
Accession:
GSE29635
ID:
200029635
10.

Maintenance of hESCs in mesenchymal stem cell-conditioned media augments hematopoietic specification

(Submitter supplied) The realization of human embryonic stem cells (hESC) as a model for human developmental hematopoiesis and potential cell replacement strategies relies on an improved understanding of the extrinsic and intrinsic factors regulating hematopoietic-specific hESC differentiation. Mesenchymal stem cells (hMSCs) are multipotent cells of mesodermal origin that form part of hematopoietic stem cell niches and have an important role in the regulation of hematopoiesis through production of secreted factors and/or cell-to-cell interactions. more...
Organism:
Homo sapiens
Type:
Methylation profiling by array
Platform:
GPL8490
6 Samples
Download data: TXT
Series
Accession:
GSE30456
ID:
200030456
11.

Gene expression profiles of induced pluripotent mesenchymal stromal cells [Affymetrix]

(Submitter supplied) Reprogramming of somatic cells into induced pluripotent stem cells (iPSC) is an epigenetic phenomenon. We have reprogrammed mesenchymal stromal cells (MSC) from human bone marrow by retrovirus-mediated overexpression of OCT-3/4, SOX2, c-MYC, and KLF4. This series summarizes gene expression profiles of eight iP-MSC clones derived from three different donors. These datasets were subsequently used for PluriTest analysis (Muller FJ, Schuldt B et al., Nat. more...
Organism:
Homo sapiens
Type:
Expression profiling by array
Platform:
GPL6244
8 Samples
Download data: CEL
Series
Accession:
GSE38806
ID:
200038806
12.

Pluripotent Stem Cells Escape From Senescence-Associated DNA Methylation Changes

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Homo sapiens
Type:
Expression profiling by array; Methylation profiling by genome tiling array
Platforms:
GPL13534 GPL6244
38 Samples
Download data: CEL
Series
Accession:
GSE37067
ID:
200037067
13.

Pluripotent Stem Cells Escape From Senescence-Associated DNA Methylation Changes [Illumina]

(Submitter supplied) Pluripotent stem cells evade replicative senescence, whereas other primary cells lose their proliferation and differentiation potential after a limited number of cell divisions – and this is accompanied by specific senescence-associated DNA methylation (SA-DNAm) changes. Here, we investigate SA-DNAm changes in mesenchymal stromal cells (MSC) upon long-term culture, irradiation-induced senescence, immortalization and reprogramming into induced pluripotent stem cells (iPSC) using high density HumanMethylation450 BeadChips. more...
Organism:
Homo sapiens
Type:
Methylation profiling by genome tiling array
Platform:
GPL13534
24 Samples
Download data: TXT
Series
Accession:
GSE37066
ID:
200037066
14.

Long-term culture associated gene expression changes in MSC [Affymetrix]

(Submitter supplied) Mesenchymal stromal cells (MSC) were isolated from human bone marrow. Here, we have compared gene expression profiles of MSC at early and late passages. Long-term culture associated gene expression changes were then correlated with DNA-methylation profiles. The goal of this study was to determine if senescence-associated DNA-methylation (SA-DNAm) changes are reflected by differential gene expression. more...
Organism:
Homo sapiens
Type:
Expression profiling by array
Platform:
GPL6244
6 Samples
Download data: CEL
Series
Accession:
GSE37065
ID:
200037065
15.

Induced Pluripotent Mesenchymal Stromal Cell Clones Retain Donor-Derived Differences in DNA Methylation Profiles

(Submitter supplied) Reprogramming of somatic cells into induced pluripotent stem cells (iPSC) is an epigenetic phenomenon. It has been suggested that iPSC retain some tissue-specific memory whereas little is known about inter-individual epigenetic variation of iPSC clones. In this study we have reprogrammed mesenchymal stromal cells (MSC) from human bone marrow by retrovirus-mediated overexpression of OCT-3/4, SOX2, c-MYC, and KLF4. more...
Organism:
Homo sapiens
Type:
Methylation profiling by genome tiling array
Platform:
GPL13534
16 Samples
Download data: TXT
Series
Accession:
GSE34688
ID:
200034688
16.

Screening ethnically diverse human embryonic stem cells identifies a chromosome 20 minimal amplicon conferring growth advantage

(Submitter supplied) The International Stem Cell Initiative analyzed 127 human embryonic stem cell lines and 11 induced pluripotent cell lines, from 39 laboratories worldwide for genetic changes occurring during culture. Most cell lines were analyzed at an early and late passage. Population structure analysis from SNP detection revealed that the cell lines included representatives of all major ethnic groups. Most lines remained karyotypically normal, but there was a progressive tendency to acquire changes on prolonged culture, commonly affecting chromosomes 1, 12, 17 and 20. more...
Organism:
Homo sapiens
Type:
Genome variation profiling by SNP array; SNP genotyping by SNP array
Platform:
GPL8882
263 Samples
Download data: TXT
Series
Accession:
GSE33522
ID:
200033522
17.

Expression data from hESCs, hiPSCs and human fibroblasts.

(Submitter supplied) Detailed analysis comparing hiPSC lines that were newly generated and compared them to already established hiPSC lines We used microarrays to detail various hiPSC lines to confirm faithful reprogramming.
Organism:
Homo sapiens
Type:
Expression profiling by array
Platform:
GPL570
10 Samples
Download data: CEL
Series
Accession:
GSE22392
ID:
200022392
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