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Links from GEO DataSets

Items: 20

1.

DNA Methylation Dynamics in Human Induced Pluripotent Stem Cells over Time (Agilent)

(Submitter supplied) We examined genome-wide gene expression with human iPSC lines derived from different cell types, and human ESC lines using Agilent Whole Human Genome Microarray chips G4112F.
Organism:
Homo sapiens
Type:
Expression profiling by array
Platform:
GPL6480
16 Samples
Download data: TXT
Series
Accession:
GSE24677
ID:
200024677
2.

DNA Methylation Dynamics in Human Induced Pluripotent Stem Cells over Time

(Submitter supplied) We examined genome-wide DNA methylation with 22 human iPSC lines derived from different cell types and human ESC lines using Illumina’s Infinium HumanMethylation27 and focused on aberrant methylation sites in iPSCs for up to 42-week continuous cultivation. The iPSCs exhibited distinct epigenetic distances from ESCs at early passage. Continuous passaging of the iPSCs diminishes these differences between iPSCs and ESCs.
Organism:
Homo sapiens
Type:
Methylation profiling by array
Platform:
GPL8490
47 Samples
Download data: TXT
Series
Accession:
GSE24676
ID:
200024676
3.

Gene expression signatures for human iPS cell lines

(Submitter supplied) The reprogramming of human fibroblasts to generate induced pluripotent stem cells (hiPSCs) has been achieved through the expression of only a few exotic factors1-8, which is morphologically and molecularly verified in outer cellular states by characteristic markers, due to the remodeling of the somatic cell transcription programs in inner cellular states to the ES-like condition. Transcription factor-induced reprogramming to self-renewal and pluripotency raises the question as to how the exotic factors act to bring about these changes in the two cellular states9-11. more...
Organism:
Homo sapiens
Type:
Expression profiling by array
Dataset:
GDS3842
Platform:
GPL4133
51 Samples
Download data: TXT
Series
Accession:
GSE20750
ID:
200020750
4.
Full record GDS3842

Transcription factor-induced pluripotent stem cells

Analysis of induced pluripotent stem cells (iPSC) and their parental somatic cells (SC) from amniotic mesodermal (AM), placental artery endothelial (PAE), uterine endometrium (UtE), and MRC sources. Results identify potential candidates for linkage between inner and outer cellular states in iPSCs.
Organism:
Homo sapiens
Type:
Expression profiling by array, count, 13 cell line, 2 cell type, 14 other sets
Platform:
GPL4133
Series:
GSE20750
51 Samples
Download data: TXT
5.

Defining Differentiated Methylation Regions Especial for Pluripotency Acquisition and Maintenance in Human Stem Cell

(Submitter supplied) Here, we determined the DNA methylation profiles of 12 human cell lines, including 2 ESC lines, 2 pESC lines,4 virally-delivered iPSC lines, 2 episomal-delivered iPSC lines, and 2 parent cell lines that iPSCs derived from using Illumina’s Infinium HumanMethylation450. The iPSCs exhibited a hypermethylation status similarly to ESCs but distinct differences from the parent cells. Genes of common methylation pattern between iPSCs and ESCs were regarded as critical factors for stemness, while differences existing between iPSCs and ESCs implied that iPSCs partly retained the parental characteristics and gained de novo methylation aberrances during cell reprogramming. more...
Organism:
Homo sapiens
Type:
Non-coding RNA profiling by genome tiling array
Platform:
GPL13534
12 Samples
Download data: IDAT, TXT
Series
Accession:
GSE57992
ID:
200057992
6.

UCSD Human Reference Epigenome Mapping Project

(Submitter supplied) The human embryonic stem cells (hESCs) are a unique model system for investigating the mechanisms of human development due to their ability to replicate indefinitely while retaining the capacity to differentiate into a host of functionally distinct cell types. In addition, these cells could be potentially used as therapeutic agents in regenerative medicine. Differentiation of hESCs involves selective activation or silencing of genes, a process controlled in part by the epigenetic state of the cell. more...
Organism:
Homo sapiens
Type:
Genome binding/occupancy profiling by high throughput sequencing; Methylation profiling by high throughput sequencing; Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing
6 related Platforms
878 Samples
Download data: BAM, BED, WIG
7.

Molecular and Functional Resemblance of Terminally Differentiated Cells Derived from Isogenic Human iPSCs and Somatic Cell Nuclear Transfer Derived ESCs

(Submitter supplied) Here we performed genome-wide RNA-seq and Reduced Representation Bisulfite Sequencing (RRBS-seq) in isogenic human induced pluripotent stem cells (iPSCs) and somatic cell nuclear transfer-derived embryonic stem cells (nt-ESCs), genetically matched in vitro fertilization-derived ESCs (IVF-ESCs), and their respective differentiated cells (cardiomyocytes and endothelial cells). We generated the transcriptome and DNA methylome map in human pluripotent stem cells and their differentiated cells with single-nucleotide resolution. more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing
Platforms:
GPL16791 GPL17301
54 Samples
Download data: TXT
8.

Regulation of DNA methylation landscape in human somatic cell reprogramming by miR-29 family

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing; Methylation profiling by array; Methylation profiling by high throughput sequencing
Platforms:
GPL13534 GPL11154
50 Samples
Download data: IDAT, WIG
Series
Accession:
GSE81794
ID:
200081794
9.

Regulation of DNA methylation landscape in human somatic cell reprogramming by miR-29 family (MeDIP-seq)

(Submitter supplied) Reprogramming to pluripotency after overexpression of OCT4, SOX2, KLF4 and MYC is accompanied by global genomic and epigenomic changes. Histone modification and DNA methylation states in iPSCs have been shown to be highly similar with embryonic stem cells (ESCs). However, epigenetic differences still exist between iPSCs and ESCs. In particular, aberrant DNA methylation states found in iPSCs are a major concern for using iPSCs in a clinical setting. more...
Organism:
Homo sapiens
Type:
Methylation profiling by high throughput sequencing
Platform:
GPL11154
16 Samples
Download data: WIG
Series
Accession:
GSE81793
ID:
200081793
10.

Regulation of DNA methylation landscape in human somatic cell reprogramming by miR-29 family (RNA-seq)

(Submitter supplied) Reprogramming to pluripotency after overexpression of OCT4, SOX2, KLF4 and MYC is accompanied by global genomic and epigenomic changes. Histone modification and DNA methylation states in iPSCs have been shown to be highly similar with embryonic stem cells (ESCs). However, epigenetic differences still exist between iPSCs and ESCs. In particular, aberrant DNA methylation states found in iPSCs are a major concern for using iPSCs in a clinical setting. more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL11154
20 Samples
Download data: XLSX
11.

Regulation of DNA methylation landscape in human somatic cell reprogramming by miR-29 family (illumina 450K)

(Submitter supplied) Reprogramming to pluripotency after overexpression of OCT4, SOX2, KLF4 and MYC is accompanied by global genomic and epigenomic changes. Histone modification and DNA methylation states in iPSCs have been shown to be highly similar with embryonic stem cells (ESCs). However, epigenetic differences still exist between iPSCs and ESCs. In particular, aberrant DNA methylation states found in iPSCs are a major concern for using iPSCs in a clinical setting. more...
Organism:
Homo sapiens
Type:
Methylation profiling by array
Platform:
GPL13534
14 Samples
Download data: IDAT, TXT
Series
Accession:
GSE81790
ID:
200081790
12.

DNA methylation data from human keratinocyte-derived iPS cells (N9) and ES cells

(Submitter supplied) Genome-wide DNA methylation of early and late passaged keratinocyte-derived iPS cells were compared to ES cells. We used custom Nimblegen microarrays to determine the genome-wide DNA methylation in human keratinocyte-derived iPS cells and ES cells
Organism:
Homo sapiens
Type:
Methylation profiling by genome tiling array
Platform:
GPL13611
17 Samples
Download data: XYS
Series
Accession:
GSE31742
ID:
200031742
13.

Donor cell type influences the epigenome and differentiation potential of human induced pluripotent stem cells

(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:
GPL13134 GPL13611 GPL570
49 Samples
Download data: CEL, XYS
Series
Accession:
GSE27224
ID:
200027224
14.

Expression data of human somatic cell types and induced pluripotent stem cells

(Submitter supplied) Transcription factor-mediated reprogramming yields induced pluripotent stem cells (iPSC) by erasing tissue specific methylation and re-setting DNA methylation status to an embryonic stage. We compared bona fide human iPSC derived from umbilical cord blood (CB) and neonatal keratinocytes (K). Through both incomplete erasure of tissue specific methylation and de novo tissue specific methylation, CB-iPSC and K-iPSC are distinct in genome-wide DNA methylation profiles. more...
Organism:
Homo sapiens
Type:
Expression profiling by array
Platform:
GPL570
8 Samples
Download data: CEL
Series
Accession:
GSE27186
ID:
200027186
15.

DNA methylation data from human iPS cells, ES cells, cord blood, and keratinocytes

(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 human iPS cells, ES cells, and somatic cells
Organism:
Homo sapiens
Type:
Methylation profiling by genome tiling array
Platform:
GPL13134
24 Samples
Download data: XYS
Series
Accession:
GSE27134
ID:
200027134
16.

5-hydroxymethylcytosine-mediated epigenetic modifications between iPSCs and hESCs

(Submitter supplied) Mammalian somatic cells can be directly reprogrammed into induced pluripotent stem cells (iPSCs) by introducing defined sets of transcription factors. Somatic cell reprogramming involves epigenomic reconfiguration, conferring iPSCs with characteristics similar to embryonic stem (ES) cells. Human ES cells contain 5-hydroxymethylcytosine (5hmC), which is generated though the oxidation of 5-methylcytosine (5mC) by the TET family of enzymes. more...
Organism:
Homo sapiens
Type:
Methylation profiling by high throughput sequencing
Platform:
GPL11154
19 Samples
Download data: BED
Series
Accession:
GSE37050
ID:
200037050
17.

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
18.

X Chromosome Dosage Influences DNA Methylation Dynamics During Reprogramming to Mouse iPSCs

(Submitter supplied) A dramatic difference in global DNA methylation between male and female cells characterizes mouse embryonic stem cells (ESCs), unlike somatic cells. We analyzed DNA methylation changes during reprogramming of male and female somatic cells and in resulting induced pluripotent stem cells (iPSCs). At an intermediate reprogramming stage, somatic and pluripotency enhancers are targeted for partial methylation and demethylation. more...
Organism:
Mus musculus
Type:
Methylation profiling by high throughput sequencing
Platform:
GPL13112
13 Samples
Download data: TXT
Series
Accession:
GSE111042
ID:
200111042
19.

Aberrant DNA methylation reprogramming during iPS cell generation is dependent on the choice of reprogramming factors

(Submitter supplied) we generate iPSCs from a common fibroblast cell source using either the Yamanaka factors (OCT4, SOX2, KLF4 and MYC) or the Thomson factors (OCT4, SOX2, NANOG and LIN28) and determined their genome-wide DNA methylation profiles. In addition to shared DNA methylation aberrations present in all our iPSCs, we identify Yamanaka-iPSC (Y-iPSCs)-specific and Thomson-iPSCs (T-iPSC)-specific recurrent aberrations.
Organism:
Homo sapiens
Type:
Methylation profiling by genome tiling array
Platform:
GPL13534
18 Samples
Download data: TXT
Series
Accession:
GSE54115
ID:
200054115
20.

Epigenetic signature of human induced pluripotent stem cells identified with the linear machine learning model

(Submitter supplied) Human induced pluripotent stem cells (iPSCs) were established as an artificial embryonic stem cells (ESCs) to avoid immune rejection, for ethical issues in regenerative medicine, and for biological research. Comparison analyses in previous studies revealed that there is no hot spot that distinguishes iPSCs from ESCs. We herewith established a learning model using Jubatus, as a machine learning platform, with linear model for classification to distinguish human iPSCs from ESCs based on DNA methylation profiles. more...
Organism:
Homo sapiens
Type:
Methylation profiling by array
Platforms:
GPL13534 GPL21145
18 Samples
Download data: IDAT, TXT
Series
Accession:
GSE141521
ID:
200141521
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