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Links from GEO DataSets

Items: 15

1.
Full record GDS4124

Genetic reprogramming of prostate cancer-associated stromal cells

Analysis of induced pluripotent stem cells (iPSCs) obtained from sorted CD90+ prostate cancer (CP)-associated stromal cells cultured and transfected with stem cell transcription factor POU5F1/LIN28/NANOG/SOX2 expression vectors. Results provide insight into the stemness of CP stromal-derived iPSCs.
Organism:
Homo sapiens
Type:
Expression profiling by array, transformed count, 5 cell type, 2 protocol sets
Platform:
GPL570
Series:
GSE35373
6 Samples
Download data: CEL
DataSet
Accession:
GDS4124
ID:
4124
2.

Reprogramming of prostate cancer-associated stromal cells

(Submitter supplied) CD90+ prostate cancer-associated (CP) stromal cells represent a disease cell type found only in tumor tissue. Genetic reprogramming by induced pluripotent stem (iPS) cell technology might be used to “normal gene expression of diseased cells thereby providing a cure. The resultant iPS cells would no longer express the disease program, and, like stem cells, might respond to normal differentiative signaling. more...
Organism:
Homo sapiens
Type:
Expression profiling by array
Dataset:
GDS4124
Platform:
GPL570
6 Samples
Download data: CEL
Series
Accession:
GSE35373
ID:
200035373
3.

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
4.

Expresion profile of MEF reprogrammed with Yamanaka´s factor together with FoxA2 and Gata4

(Submitter supplied) In a pilot experiment to reprogramme MEF into endoderm, we infected MEF with the Yamanaka´s factors (O: Oct4, K: Klf4, S: Sox2, M:Myc), FoxA2 (F) and Gata4 (G). Global gene expression of isolated clones was performed.
Organism:
Mus musculus
Type:
Expression profiling by array
Platform:
GPL6246
13 Samples
Download data: CEL
Series
Accession:
GSE37548
ID:
200037548
5.

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
6.

Development of gene expression signature for defining the cell potency of muscle derived stem cells (MDSC) from mice of diffferent genotypes

(Submitter supplied) In order to determine the cell potency, by identification of genes responsible for pluri/multi potency, we performed a global gene expression profiling of MDSC isolated from five week old male wild type(WT), C57Bl6J and another hypertrophied musculature mouse genotype called myostatin null (Mstn-/-) mice using microarray analysis and compared this gene expression to that of a standard mouse ES cell line W4. more...
Organism:
Mus musculus
Type:
Expression profiling by array
Platform:
GPL10787
6 Samples
Download data: TXT, XLS
Series
Accession:
GSE39765
ID:
200039765
7.

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
8.

Transcriptome Signature and Regulation in Human Somatic Cell Reprogramming

(Submitter supplied) Reprogramming of somatic cells produces induced pluripotent stem cells (iPSCs) that are invaluable resources for biomedical research. Transcriptional and epigenetic changes have been investigated to facilitate our understanding of the reprogramming process. Here, we extended the previous transcriptome studies by performing RNA-seq on cells defined by a combination of multiple cellular surface markers. more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL11154
30 Samples
Download data: TXT
9.

CpG Methylation profile of Invasive Prostate Cancer Cells compared to Non-invasive

(Submitter supplied) Two established cell lines, LNCaP and DU145 and two primary prostate cancer cell lines, PCSC1-2 were invaded toward a stem cell media through Matrigel. DNA was isolated from Non-invasive cells and invasive cells.
Organism:
Homo sapiens
Type:
Methylation profiling by genome tiling array
4 related Platforms
16 Samples
Download data: TXT
Series
Accession:
GSE25824
ID:
200025824
10.

Global gene expression analysis of (1) chemically reprogrammed iPS cells, and (2) chemical-treated cells

(Submitter supplied) Analysis of iPS cells generated with a small molecule, RepSox (RS), as well as a time-course of gene expression changes in cells treated with RS. The former was done to verify the similarity of the iPS cells with mES cells; the latter was aimed at elucidating the mechanism of drug action in the context of reprogramming.
Organism:
Mus musculus
Type:
Expression profiling by array
Platforms:
GPL6103 GPL6885
33 Samples
Download data: TXT
Series
Accession:
GSE18286
ID:
200018286
11.

SOX2 Mediates Metabolic Reprogramming of Prostate Cancer Cells

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL20301
10 Samples
Download data: TXT
Series
Accession:
GSE166185
ID:
200166185
12.

SOX2 Mediates Metabolic Reprogramming of Prostate Cancer Cells (RNA-Seq)

(Submitter supplied) To determine the genes regulated by SOX2, we performed RNA-Seq on CWR-R1 control cells and SOX2KO cells with intact AR signaling and identified differentially expressed genes (DEGs)
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL20301
6 Samples
Download data: TXT
13.

SOX2 Mediates Metabolic Reprogramming of Prostate Cancer Cells (ChIP-Seq)

(Submitter supplied) To mechanistically define the function of SOX2 in prostate cancer cells and how it contributes to therapeutic resistance, we performed paired SOX2 chromatin immunoprecipitation-sequencing (ChIP-Seq) and RNA-sequencing (RNA-Seq) on a SOX2-positive CRPC cell line, CWR-R1, to determine which genes SOX2 binds and potentially regulates. To identify novel prostate cancer-specific SOX2 gene targets in CRPC cells distinct from known SOX2 stem cell genes, we conducted parallel SOX2 ChIP-Seq and RNA-Seq in the WA01 embryonic stem cell line and compared results to identified SOX2 targets from CWR-R1 cells
Organism:
Homo sapiens
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL20301
4 Samples
Download data: TXT
Series
Accession:
GSE166183
ID:
200166183
14.

Gene expression down-regulation in prostate tumor-associated stromal cells involves organ-specific genes

(Submitter supplied) The prostate stroma is a key mediator of epithelial differentiation and development, and potentially plays a role in the initiation and progression of prostate cancer. Isolation and characterization of viable populations of the constituent cell types of prostate tumors could provide valuable insight into the biology of cancer. The CD90+ stromal fibromuscular cells from tumor specimens were isolated by cell-sorting and analyzed by DNA microarray. more...
Organism:
Homo sapiens
Type:
Expression profiling by array
Platform:
GPL570
25 Samples
Download data: CEL
Series
Accession:
GSE17906
ID:
200017906
15.

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
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