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Links from GEO DataSets

Items: 20

1.
Full record GDS3770

Early-passage induced pluripotent stem (iPS) cells derived from various somatic cell populations

Analysis of iPSCs (at p4) derived from different cell types (fibroblasts, hematopoietic, myogenic cells) through ectopic expression of transcription factors Oct4, Sox2, Klf4, cMyc. Results provide insight into the influence of cellular origin on transcriptional patterns of derivative iPSCs.
Organism:
Mus musculus
Type:
Expression profiling by array, transformed count, 4 cell type sets
Platform:
GPL6246
Series:
GSE22908
12 Samples
Download data: CEL, CHP
2.

Early passage mouse induced pluripotent stem (iPS) cells derivated from various somatic cell origins

(Submitter supplied) Induced pluripotent stem (iPS) cells have been derived from various somatic cell populations through ectopic expression of defined factors. It remains unclear whether iPS cells generated from different cell types are molecularly and functionally similar. Here, we show that iPS cells obtained from fibroblasts, hematopoietic and myogenic cells exhibit distinct transcriptional and epigenetic patterns. Moreover, we demonstrate that cellular origin influences the in vitro differentiation potentials of iPS cells into embryoid bodies and different hematopoietic cells. Our results suggest that low-passage iPS cells retain a transient epigenetic memory of their somatic cells of origin, which manifests as differential gene expression and altered differentiation capacity. These observations might affect ongoing attempts to use iPS cells for disease modeling and also could be exploited for potential therapeutic applications to enhance differentiation into desired cell lineages. This series consists of triplicated mRNA expression microarray data (Affymetrix mouse gene ST 1.0) for an early passage (passage 4) of mouse iPS cells derived from bone marrow granulocytes, splenic B cells, tail tip fibroblasts, and skeletel muscle precursor cells.
Organism:
Mus musculus
Type:
Expression profiling by array
Dataset:
GDS3770
Platform:
GPL6246
12 Samples
Download data: CEL, CHP
Series
Accession:
GSE22908
ID:
200022908
3.

Cell of origin influences molecular and functional properties of murine induced pluripotent stem cells

(Submitter supplied) Induced pluripotent stem cells (iPSCs) have been derived from various somatic cell populations through ectopic expression of defined factors. It remains unclear whether iPSCs generated from different cell types are molecularly and functionally similar. Here, we show that iPSCs obtained from fibroblasts, hematopoietic and myogenic cells exhibit distinct transcriptional and epigenetic patterns. Moreover, we demonstrate that cellular origin influences the in vitro differentiation potentials of iPSCs into embryoid bodies (EBs) and different hematopoietic cells. more...
Organism:
Mus musculus
Type:
Methylation profiling by genome tiling array
Platform:
GPL10283
18 Samples
Download data: PAIR
Series
Accession:
GSE22827
ID:
200022827
4.

Expressoin data from iPSC with different cell of origin

(Submitter supplied) Induced pluripotent stem cells (iPSCs) have been derived from various somatic cell populations through ectopic expression of defined factors. It remains unclear whether iPSCs generated from different cell types are molecularly and functionally similar. We use expresson profiling to determine differnces in iPSCs with different cell of origin.
Organism:
Mus musculus
Type:
Expression profiling by array
Datasets:
GDS3771 GDS3772
Platforms:
GPL8321 GPL8759
45 Samples
Download data: CEL
Series
Accession:
GSE22043
ID:
200022043
5.
Full record GDS3772

Continuous passaging effect on induced pluripotent stem (iPS) cells derived from various somatic cell populations (II)

Analysis of iPSCs (from p4 to p16) derived from different cell types (fibroblasts, hematopoietic, myogenic cells) through ectopic expression of transcription factors Oct4, Sox2, Klf4, cMyc. Results provide insight into the effect of passaging on iPSC functionality.
Organism:
Mus musculus
Type:
Expression profiling by array, transformed count, 4 cell type sets
Platform:
GPL8321
Series:
GSE22043
12 Samples
Download data: CEL
6.
Full record GDS3771

Continuous passaging effect on induced pluripotent stem (iPS) cells derived from various somatic cell populations (I)

Analysis of iPSCs (at p10) derived from different cell types (fibroblasts, hematopoietic cells) through ectopic expression of transcription factors Oct4, Sox2, Klf4, cMyc. Results provide insight into the effect of passaging on iPSC functionality.
Organism:
Mus musculus
Type:
Expression profiling by array, transformed count, 5 cell type, 3 growth protocol sets
Platform:
GPL8759
Series:
GSE22043
33 Samples
Download data: CEL
7.

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
8.

MicroRNAs Contribute to iPSC-Somatic Donor Memory

(Submitter supplied) miRNA expression analysis in iPSC derived from CD133+cells from Cord Blood
Organism:
Homo sapiens; synthetic construct
Type:
Non-coding RNA profiling by array
Platform:
GPL16384
6 Samples
Download data: CEL
Series
Accession:
GSE45219
ID:
200045219
9.

High-throughput sequencing of sequentially reprogrammed iPS cells reveals key epigenetic modifications correlated with reduced pluripotency of iPS cells

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Methylation profiling by high throughput sequencing
Platform:
GPL13112
105 Samples
Download data: BED, TXT
Series
Accession:
GSE36294
ID:
200036294
10.

High-throughput sequencing of sequentially reprogrammed iPS cells reveals key epigenetic modifications correlated with reduced pluripotency of iPS cells [MeDIP-seq]

(Submitter supplied) Full pluripotency of induced pluripotent stem (iPS) cells has been determined as viable all-iPS mice can be generated through tetraploid complementation. Subsequently, activation of imprinted Dlk-Dio3 gene cluster has been suggested to correlate with the pluripotency of iPS cells1. However, evidence from recent studies has demonstrated that loss of imprinting at the Dlk-Dio3 locus did not correlate strictly with the reduced pluripotency of iPS cells. more...
Organism:
Mus musculus
Type:
Methylation profiling by high throughput sequencing
Platform:
GPL13112
13 Samples
Download data: BED
Series
Accession:
GSE36293
ID:
200036293
11.

High-throughput sequencing of sequentially reprogrammed iPS cells reveals key epigenetic modifications correlated with reduced pluripotency of iPS cells [ChIP-seq]

(Submitter supplied) Full pluripotency of induced pluripotent stem (iPS) cells has been determined as viable all-iPS mice can be generated through tetraploid complementation. Subsequently, activation of imprinted Dlk-Dio3 gene cluster has been suggested to correlate with the pluripotency of iPS cells1. However, evidence from recent studies has demonstrated that loss of imprinting at the Dlk-Dio3 locus did not correlate strictly with the reduced pluripotency of iPS cells. more...
Organism:
Mus musculus
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL13112
53 Samples
Download data: BED
Series
Accession:
GSE36292
ID:
200036292
12.

High-throughput sequencing of sequentially reprogrammed iPS cells reveals key epigenetic modifications correlated with reduced pluripotency of iPS cells [sRNA-seq]

(Submitter supplied) Full pluripotency of induced pluripotent stem (iPS) cells has been determined as viable all-iPS mice can be generated through tetraploid complementation. Subsequently, activation of imprinted Dlk-Dio3 gene cluster has been suggested to correlate with the pluripotency of iPS cells1. However, evidence from recent studies has demonstrated that loss of imprinting at the Dlk-Dio3 locus did not correlate strictly with the reduced pluripotency of iPS cells. more...
Organism:
Mus musculus
Type:
Non-coding RNA profiling by high throughput sequencing
Platform:
GPL13112
13 Samples
Download data: TXT
Series
Accession:
GSE36291
ID:
200036291
13.

High-throughput sequencing of sequentially reprogrammed iPS cells reveals key epigenetic modifications correlated with reduced pluripotency of iPS cells [RNA-seq]

(Submitter supplied) Full pluripotency of induced pluripotent stem (iPS) cells has been determined as viable all-iPS mice can be generated through tetraploid complementation. Subsequently, activation of imprinted Dlk-Dio3 gene cluster has been suggested to correlate with the pluripotency of iPS cells1. However, evidence from recent studies has demonstrated that loss of imprinting at the Dlk-Dio3 locus did not correlate strictly with the reduced pluripotency of iPS cells. more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL13112
26 Samples
Download data: TXT
Series
Accession:
GSE36290
ID:
200036290
14.

Highly efficient derivation of ventricular cardiomyocytes from induced pluripotent stem cells with a distinct epigenetic signature

(Submitter supplied) The generation of sufficient numbers of mature ventricular myocytes for effective cell-based therapy is a central barrier for cardiac regenerative medicine. Here we demonstrate that induced pluripotent stem cells (iPSCs) can be derived from murine ventricular myocytes, and consistent with other reports of iPSCs derived from various somatic cell types, ventricular myocyte derived iPSCs (ViPSCs) exhibit a markedly higher propensity to differentiate into beating cardiomyocytes as compared to genetically-matched embryonic stem cells (ESCs) or iPSCs derived from tail-tip fibroblasts. more...
Organism:
Mus musculus
Type:
Expression profiling by array
Platform:
GPL1261
11 Samples
Download data: CEL
Series
Accession:
GSE32598
ID:
200032598
15.

Erythroid differentiation of human induced pluripotent stem cells is independent of donor cell type of origin

(Submitter supplied) Epigenetic memory in induced pluripotent stem cells (iPSCs), with regards to their somatic cell type of origin, might lead to variations in their differentiation capacities. In this context, iPSCs from human CD34+ hematopoietic stem cells (HSCs) might be more suitable for hematopoietic differentiation than commonly used fibroblast-derived iPSCs. To investigate the influence of an epigenetic memory on the ex vivo expansion of iPSCs into erythroid cells, we compared iPSCs from human neural stem cells (NSCs) and human cord blood-derived CD34+ HSCs and evaluated their potential for differentiation into hematopoietic progenitor and mature red blood cells (RBCs). more...
Organism:
Homo sapiens
Type:
Expression profiling by array
Platform:
GPL10558
8 Samples
Download data: TXT
Series
Accession:
GSE55109
ID:
200055109
16.

DNA methylation data from mouse iPS cells, ES cells, and ntES cells

(Submitter supplied) Genome-wide DNA methylation was studied to determine whether iPS cells retain epigenetic memory at loci associated with its tissue of origin. We used custom Nimblegen microarrays to determine the genome-wide DNA methylation in mouse iPS cells.
Organism:
Mus musculus
Type:
Methylation profiling by genome tiling array
Platforms:
GPL10680 GPL10683
85 Samples
Download data: XYS
Series
Accession:
GSE22851
ID:
200022851
17.

Differentiation stage-specific donor memory in induced pluripotent stem cells (iPSC) generated from hepatic lineage cells

(Submitter supplied) Recent studies suggested that embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs) may represent different pluripotent states as defined by gene expression profiles and differentiation potential. Here we addressed a contribution of a lineage stage-specific donor cell memory in modulating the functional properties of iPSCs. iPSCs were generated from hepatic lineage cells at an early (hepatoblast-derived, HB-iPSCs) and end stage (adult hepatocyte, AH-iPSCs) of hepatocyte differentiation as well as from mouse fetal fibroblasts (MEF-iPSCs) using a lentiviral vector encoding four pluripotency-inducing factors Oct4, Sox2, Klf4, and c-Myc. more...
Organism:
Mus musculus
Type:
Expression profiling by array
Platform:
GPL6885
28 Samples
Download data: TXT
Series
Accession:
GSE33110
ID:
200033110
18.

Efficient differentiation of steroidogenic and germ-like cells from epigenetically-related iPSCs derived from ovarian granulosa cells

(Submitter supplied) To explore restoration of ovarian function using epigenetically-related, induced pluripotent stem cells (iPSCs), we functionally evaluated the epigenetic memory of novel iPSC lines, derived from mouse and human ovarian granulosa cells (GCs) using c-Myc, Klf4, Sox2 and Oct4 retroviral vectors. The stem cell identity of the mouse and human GC-derived iPSCs (mGriPSCs, hGriPSCs) was verified by demonstrating embryonic stem cell (ESC) antigen expression using immunocytochemistry and RT-PCR analysis, as well as formation of embryoid bodies (EBs) and teratomas that are capable of differentiating into cells from all three germ layers. more...
Organism:
Mus musculus
Type:
Expression profiling by array
Platform:
GPL6887
18 Samples
Download data: TXT
Series
Accession:
GSE62565
ID:
200062565
19.

Enhancing Mammary Differentiation by Overcoming Lineage Specific Epigenetic Modification and Signature Gene Expression of Fibroblast Derived iPSCs

(Submitter supplied) Recent studies showed that Induced pluripotent stem cells (iPSCs) could hold memory of their origin and exhibit skewed differentiation potential. This finding reveals a severe limit for the application of iPSCs in cell-based therapy in case certain cell types are not available for reprograming from patients. Here we show that under a typical condition for mammary differentiation, iPSCs derived from mouse mammary epithelium cells (ME-iPSCs) exhibit mammary signature gene expression and chromatin epigenetic modification, leading to smooth progress for mammary gland formation. more...
Organism:
Mus musculus
Type:
Expression profiling by array
Platform:
GPL10740
9 Samples
Download data: CEL
Series
Accession:
GSE38471
ID:
200038471
20.

Origin-dependent neural cell identities in differentiated human iPS cells in vitro and after transplantation into the rodent brain

(Submitter supplied) The differentiation capability of induced pluripotent stem cells (iPSCs) towards certain cell types for disease modelling and drug screening assays might be influenced by their somatic cell of origin. Here, we have compared the neural induction of human iPSCs generated from either fetal neural stem cells (fNSCs), dermal fibroblasts or CD34+ hematopoietic stem cells. Neural progenitor cells (NSCs) and neurons could be generated at similar efficiencies from all iPSCs. more...
Organism:
Homo sapiens
Type:
Expression profiling by array
Platform:
GPL10558
43 Samples
Download data: TXT
Series
Accession:
GSE55107
ID:
200055107
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