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Links from GEO DataSets

Items: 20

1.

Generation of induced pluripotent stem cells by efficient reprogramming of adult bone marrow cells

(Submitter supplied) Reprogramming of somatic cells provides potential for the generation of specific cell types, which could be a key step in the study and treatment of human diseases. In vitro reprogramming of somatic cells into a pluripotent embryonic stem (ES) cell–like state has been reported by retroviral transduction of murine fibroblasts using four embryonic transcription factors or through cell fusion of somatic and pluripotent stem cells. more...
Organism:
Mus musculus
Type:
Expression profiling by array
Platform:
GPL4134
4 Samples
Download data: TXT
Series
Accession:
GSE15775
ID:
200015775
2.

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
3.

Transcriptional profiles by deep sequencing (RNA-seq) of in vivo-generated mouse iPSCs, in vitro-generated mouse iPSCs, and mouse ESCs

(Submitter supplied) We have generated “reprogrammable” transgenic mice that ubiquitously express the four Yamanaka factors in an inducible manner. Transitory induction of the transgene results in multiple teratomas emerging from a variety of organs, thus indicating that full reprogramming into iPSCs can occur in vivo. By performing bone marrow transplant experiments, we demonstrate that both hematopoietic cells, as well as non-hematopoietic cells can be reprogrammed in vivo. more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL11002
14 Samples
Download data: FPKM_TRACKING
Series
Accession:
GSE48364
ID:
200048364
4.

Direct Reprogramming of Fibroblasts into Epiblast Stem Cells

(Submitter supplied) Embryonic stem cells (ESCs), which are derived from the primitive ectoderm of pre-implantation blastocysts, are pluripotent cells and can thus contribute to the formation of all somatic cell lineages in chimeric animals. Similarly, epiblast stem cells (EpiSCs), which are derived from epiblast tissue of post-implantation embryos, are also pluripotent and can give rise to derivatives of all three germ layers in teratoma assays. more...
Organism:
Mus musculus
Type:
Expression profiling by array
Platform:
GPL6885
24 Samples
Download data: TXT
Series
Accession:
GSE21516
ID:
200021516
5.

Expression analysis of stepwise induction of iPS cells

(Submitter supplied) We were able to achieve an initial stable intermediate phase by the transduction of Oct4, Klf4, and c-Myc. Furthermore, over-expression of Sox2 in these intermediate stage cells leads to final iPS cell phase. After examining the gene expression profiles from the initial to final iPS cell phases, we have identified Sox2 downstream genes important for iPS cell induction.
Organism:
Mus musculus
Type:
Expression profiling by array
Platform:
GPL6885
16 Samples
Download data: TXT
Series
Accession:
GSE28197
ID:
200028197
6.

Pluripotent stem cells induced from adult neural stem cells by reprogramming with two factors

(Submitter supplied) Reprogramming of somatic cells is a valuable tool to understand the mechanisms of regaining pluripotency and further opens up the possibility of generating patient-specific pluripotent stem cells. Reprogramming of mouse and human somatic cells into pluripotent stem cells, designated as induced pluripotent stem (iPS) cells, has been possible with the expression of the transcription factor quartet Oct4 (also known as Pou5f1), Sox2, c-Myc, and Klf4. more...
Organism:
Mus musculus
Type:
Expression profiling by array
Platform:
GPL1261
11 Samples
Download data: CEL
Series
Accession:
GSE10806
ID:
200010806
7.

Genome-wide maps of Tbx3 binding sites in mouse ESCs

(Submitter supplied) 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). 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. more...
Organism:
Mus musculus
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL9250
2 Samples
Download data: BED
Series
Accession:
GSE19219
ID:
200019219
8.

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

(Submitter supplied) 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. more...
Organism:
Mus musculus
Type:
Expression profiling by array
Platform:
GPL6103
36 Samples
Download data: TXT
Series
Accession:
GSE19164
ID:
200019164
9.

Direct generation of induced pluripotent stem cells from human non-mobilized blood

(Submitter supplied) The use of induced pluripotent stem cells (iPSCs) is an exciting frontier in the study and treatment of human diseases through the generation of specific cell types. Here we show the derivation of iPSCs from human non-mobilized peripheral blood (PB) and bone marrow (BM) mononuclear cells (MNCs) by retroviral transduction of OCT3/4, SOX2, KLF4 and c-MYC. The PB- and BM-derived iPSCs were indistinguishable from human embryonic stem cells (hESCs) with respect to morphology, expression of surface antigens and pluripotency-associated transcription factors, global gene expression profiles and differentiation potential in vitro and in vivo. more...
Organism:
Homo sapiens
Type:
Expression profiling by array
Platform:
GPL4133
7 Samples
Download data: TXT
Series
Accession:
GSE20127
ID:
200020127
10.

Gene expression profiles of induced pluripotent stem cells (iPSCs) and skin fibroblasts from orangutans

(Submitter supplied) Orangutans are an endangered species whose natural habitats are restricted to the Southeast Asian islands of Borneo and Sumatra. For potential species conservation and functional genomics studies, we derived induced pluripotent stem cells (iPSCs) from cryopreserved skin fibroblasts obtained from captive orangutans. We report the gene expression profiles of iPSCs and skin fibroblasts derived from orangtuans.
Organism:
Homo sapiens; Pongo abelii
Type:
Expression profiling by array
Platform:
GPL571
8 Samples
Download data: CEL
Series
Accession:
GSE69603
ID:
200069603
11.

Global gene expression analyses of paused iPSCs

(Submitter supplied) Low Klf4 expression reproducibly gives rise to a homogeneous population of partially reprogrammed iPSCs. Upregulation of Klf4 allows these cells to resume reprogramming, indicating that they are paused iPSCs that remain on the path towards pluripotency. Paused iPSCs with different Klf4 expression levels remain at distinct intermediate stages of reprogramming.
Organism:
Mus musculus
Type:
Expression profiling by array
Platform:
GPL6885
24 Samples
Download data: TXT
Series
Accession:
GSE56406
ID:
200056406
12.

Generation of human induced pluripotent stem cells from mesenchymal cells of gut mesentery by Oct4/Sox2/Nanog

(Submitter supplied) Background and aim: Human Induced pluripotent stem (iPS) cells have been derived from dermal fibroblasts, keratinocytes and blood cells by ectopic expression of defined transcription factors.1–5 Application of this approach in human cells would have enormous potential and generate patient-specific pluripotent stem cells to accelerate the implementation of stem cells for clinical treatment of degenerative diseases. more...
Organism:
Homo sapiens
Type:
Expression profiling by array
Platform:
GPL570
3 Samples
Download data: CEL, CHP, TXT
Series
Accession:
GSE18180
ID:
200018180
13.

Generation of germ-line competent induced pluripotent stem cells

(Submitter supplied) We have previously shown that pluripotent stem cells are induced from mouse fibroblasts by retroviral introduction of Oct3/4, Sox2, c-Myc and Klf4, and subsequent selection for Fbx15 expression. These iPS (induced pluripotent stem) cells are similar to embryonic stem (ES) cells in morphology, proliferation and teratoma formation. Fbx15-iPS cells, however, are different in gene expression and DNA methylation patterns and fail to produce adult chimeras. more...
Organism:
Mus musculus
Type:
Expression profiling by array
Platform:
GPL2881
10 Samples
Download data: TXT
Series
Accession:
GSE7841
ID:
200007841
14.

Induction of pluripotent-like cells derived from MEF by defined factors

(Submitter supplied) Differentiated cells can be reprogrammed to an embryonic-like state by transfer of their nuclear contents into oocytes or by fusion with embryonic stem (ES) cells. Little is known about the factors that induce this reprogramming. Here we show that the combination of four factors, Oct3/4, Sox2, c-Myc, and Klf4, can generate pluripotent-like stem cells directly from mouse embryonic or adult fibroblast cultures. more...
Organism:
Mus musculus
Type:
Expression profiling by array
Platform:
GPL2881
9 Samples
Download data: TXT
Series
Accession:
GSE5259
ID:
200005259
15.

human induced pluripotent stem cell

(Submitter supplied) Successful reprogramming of differentiated human somatic cells into a pluripotent state would allow creation of patient- and disease-specific stem cells. We previously reported generation of induced pluripotent stem (iPS) cells, capable of germline transmission, from mouse somatic cells by transduction of four defined transcription factors. Here, we demonstrate the generation of iPS cells from adult human dermal fibroblasts with the same four factors: Oct3/4, Sox2, Klf4, and c-Myc. more...
Organism:
Homo sapiens
Type:
Expression profiling by array
Platform:
GPL4133
2 Samples
Download data: TXT
Series
Accession:
GSE9561
ID:
200009561
16.

Global gene-expression analyses of the Esrrb knockdown cells

(Submitter supplied) In the murine system, Oct4, Sox2, c-Myc and Klf4 are sufficient to convert fibroblasts to induced pluripotent stem (iPS) cells that exhibit many characteristics of embryonic stem (ES) cells. Herein, we show that the orphan nuclear receptor Esrrb works in conjunction with Oct4 and Sox2 to mediate reprogramming of mouse embryonic fibroblasts (MEFs) to iPS cells. Esrrb reprogrammed cells share similar expression and epigenetic signatures as ES cells. more...
Organism:
Mus musculus
Type:
Expression profiling by array
Platform:
GPL6105
18 Samples
Download data: TXT
Series
Accession:
GSE13212
ID:
200013212
17.

Global gene-expression analyses of the Esrrb reprogrammed cells

(Submitter supplied) In the murine system, Oct4, Sox2, c-Myc and Klf4 are sufficient to convert fibroblasts to induced pluripotent stem (iPS) cells that exhibit many characteristics of embryonic stem (ES) cells. Herein, we show that the orphan nuclear receptor Esrrb works in conjunction with Oct4 and Sox2 to mediate reprogramming of mouse embryonic fibroblasts (MEFs) to iPS cells. Esrrb reprogrammed cells share similar expression and epigenetic signatures as ES cells. more...
Organism:
Mus musculus
Type:
Expression profiling by array
Platform:
GPL6105
16 Samples
Download data: TXT
Series
Accession:
GSE13211
ID:
200013211
18.

Global gene-expression analyses of the Esrrb reprogrammed cells and Esrrb knockdown cells

(Submitter supplied) In the murine system, Oct4, Sox2, c-Myc and Klf4 are sufficient to convert fibroblasts to induced pluripotent stem (iPS) cells that exhibit many characteristics of embryonic stem (ES) cells. Herein, we show that the orphan nuclear receptor Esrrb works in conjunction with Oct4 and Sox2 to mediate reprogramming of mouse embryonic fibroblasts (MEFs) to iPS cells. Esrrb reprogrammed cells share similar expression and epigenetic signatures as ES cells. more...
Organism:
Mus musculus
Type:
Expression profiling by array
Platform:
GPL6105
34 Samples
Download data
Series
Accession:
GSE13190
ID:
200013190
19.

Reprogramming of fibroblasts into induced pluripotent stem cells with Bmi1

(Submitter supplied) Somatic cells can be reprogrammed into induced pluripotent stem (iPS) cells by Oct4, Sox2, Klf4, plus c-Myc. Recently, Sox2 plus Oct4 were shown to reprogram fibroblasts and Oct4 alone to reprogram mouse and human neural stem cells (NSCs) into iPS cells. Here we report that Bmi1 leads to dedifferentiation of mouse fibroblasts into NSC-like cells and, in combination with Oct4, replaces Sox2, Klf4 and c-Myc during reprogramming fibroblasts to iPS cells. more...
Organism:
Mus musculus
Type:
Expression profiling by array
Platform:
GPL4134
12 Samples
Download data: TXT, XLS
Series
Accession:
GSE24208
ID:
200024208
20.

Expression data from human primary cumulus cells culture (hCC)

(Submitter supplied) The cumulus cells niche that surrounds the oocyte is essential for its maturation and presumably for the oocyte to acquire its competence to confer pluripotency. The cells cultured from the human oocyte cumulus niche (hCC) could be used as feeders for the propagation of human pluripotent stem cells in vitro. We used microarrays to establish the molecular portrait of the hCC at different passages
Organism:
Homo sapiens
Type:
Expression profiling by array
Platform:
GPL570
3 Samples
Download data: CEL, CHP
Series
Accession:
GSE65115
ID:
200065115
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