GEO DataSets

(Submitter supplied) Female human induced pluripotent stem cell (hiPSC) lines exhibit considerable variability in X-inactivation status. Some lines maintain one transcriptionally active X chromosome (Xa) and one inactive X (Xi) from donor cells. However, hiPSC lines that have two Xas are infrequently produced. We show here Xinactivation status in female hiPSC lines depends on derivation conditions. hiPSC lines generated using the Kyoto method, which employs leukemia inhibitory factor (LIF)-expressing SNL feeders, frequently had two Xas. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL4133

15 Samples

Download data: TXT

(Submitter supplied) Female human ESC-lines can carry active X-chromosomes (Xa) or an XIST-RNA- coated inactive X-chromosome (Xi XIST+ ). Additionally, many ESC-lines have abnormal X-chromosome-inactivation (XCI)-states where the Xi no longer expresses XIST-RNA and has transcriptionally active regions (eroded Xi=Xe). The fate of each XCI-state upon differentiation is unclear because individual lines often contain a mixture of XCI-states. more...

Organism:

Homo sapiens

Type:

Genome variation profiling by SNP array

Platform:

GPL6801

15 Samples

Download data: CEL, CSV

(Submitter supplied) Female human ESC-lines can carry active X-chromosomes (Xa) or an XIST-RNA-coated inactive X-chromosome (XiXIST+). Additionally, many ESC lines have abnormal X-chromosomeinactivation (XCI)-states where the Xi no longer expresses XIST-RNA and has transcriptionally active regions (eroded Xi=Xe). The fate of each XCI-state upon differentiation is unclear because individual lines often contain a mixture of XCI-states. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

41 Samples

Download data: TSV

(Submitter supplied) We compared human female hiPSC lines (all derived from IMR-90 fibroblasts) that were XIST RNA-positive and XIST RNA-negative. We also examined the gene expression patterns for 2 female hIPSCs (derived from different disease model fibroblasts) that were also negative for XIST RNA. hiPS 12D-1 is derived from Huntington's Disease patient and 6C-1 is derived from a Type I Diabetes Mellitus patient (Park et al Nature 2008).

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

13 Samples

Download data: CEL

(Submitter supplied) Erasure of epigenetic memory is required to convert somatic cells towards pluripotency. Reactivation of the inactive X chromosome (Xi) has been used to model epigenetic reprogramming in mouse, but human studies are hampered by Xi epigenetic instability and difficulties in tracking partially reprogrammed iPSCs. Here we used cell fusion to examine the earliest events in the reprogramming-induced Xi reactivation of human female fibroblasts. more...

Organism:

Homo sapiens; Homo sapiens x Mus musculus hybrid cell line

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL16791 GPL19068

4 Samples

Download data: TXT

(Submitter supplied) Two independent induced pluripotent stem cell lines: ES4CL1 (derived from foreskin) and MR90C2 (derived from lung Fibroblast) were maintained on inactivated mouse embryonic fibroblast (MEF) feeder cells in the presence of ESC media containing DMEM, 20% knock-out serum replacement with 100ng/mL of bFGF. 7 days after seeding, cells were harvested in TrypLE Express and FACs sorted using antibodies detecting the presence of cell surface antigens GCTM-2 and CD9. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6884

24 Samples

Download data: TXT

(Submitter supplied) Induction and reversal of chromatin silencing is critical for successful development, tissue homeostasis and the derivation of induced pluripotent stem cells (iPSCs). X-chromosome inactivation (XCI) and reactivation (XCR) in female cells represent chromosome-wide transitions between active and inactive chromatin states. While XCI has long been studied and provided important insights into gene regulation, the dynamics and mechanisms underlying the reversal of stable chromatin silencing of X-linked genes are much less understood. more...

Organism:

Mus musculus musculus x Mus musculus castaneus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26166

7 Samples

Download data: XLS

(Submitter supplied) Comparison of human iPSC lines, ESC and fibroblasts to determine their expression patterns. All early passage female lines profiled expressed XIST RNA which is an indicator of an inactive X chromosome. Genes on the X-chromosome were also analyzed for overall levels of gene expression compared to human fibroblasts.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

13 Samples

Download data: CEL

(Submitter supplied) We have been able to derive EpiSC-like pESC lines from in vivo produced porcine blastocysts. Our cell lines showed AP activity, expressions of the genes Oct4, Sox2, Nanog, Rex1, TDGF1, bFGF, FGFR1, FGFR2, Nodal and Activin-A involved in pluripotency and signaling pathways and in vitro differentiation potential, displaying similarities to epiblast stem cells or hES cells.

Organism:

Sus scrofa

Type:

Expression profiling by array

Platform:

GPL3533

3 Samples

Download data: CEL

(Submitter supplied) Human induced pluripotent stem cells (hiPSCs) show variable differentiation potential due to their epigenomic heterogeneity, whose extent/attributes remain unclear, except for well-studied elements/chromosomes such as imprints and the X chromosomes. Here, we show that seven hiPSC lines with variable germline potential exhibit substantial epigenomic heterogeneity, despite their uniform transcriptomes. more...

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL11154

6 Samples

Download data: BIGWIG, TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing

Platforms:

GPL11154 GPL16791

102 Samples

Download data: BIGWIG, TXT

(Submitter supplied) Human induced pluripotent stem cells (hiPSCs) show variable differentiation potential due to their epigenomic heterogeneity, whose extent/attributes remain unclear, except for well-studied elements/chromosomes such as imprints and the X chromosomes. Here, we show that seven hiPSC lines with variable germline potential exhibit substantial epigenomic heterogeneity, despite their uniform transcriptomes. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

13 Samples

Download data: TXT

(Submitter supplied) Human induced pluripotent stem cells (hiPSCs) show variable differentiation potential due to their epigenomic heterogeneity, whose extent/attributes remain unclear, except for well-studied elements/chromosomes such as imprints and the X chromosomes. Here, we show that seven hiPSC lines with variable germline potential exhibit substantial epigenomic heterogeneity, despite their uniform transcriptomes. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL16791

83 Samples

Download data: BIGWIG

(Submitter supplied) In order to recover nuclei with two active X chromosomes (class I), we developed a reprogramming strategy by supplementing hESC media with the small molecules sodium butyrate, and 3-deazaneplanocin A (DZNep). In order to determine how B+D affects global gene expression, we performed microarray analysis in triplicate in the HSF-6 (8) C and HSF-6 (8) B+D treated cultures. We also evaluated HSF-6 (S9) B+D in triplicate and identified no statistically significant changes in gene expression in HSF-6 (S9) B+D compared to HSF-6 (8) B+D treated cultures. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

9 Samples

Download data: CEL, CHP

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL14550

36 Samples

Download data: TXT

(Submitter supplied) Hepatocytes generated from human induced pluripotent stem cells (hiPSCs) are unprecedented resources for pharmaceuticals and cell therapy. However, little attention has so far been paid to variations among hiPSC lines in terms of their hepatic differentiation. We developed an improved hepatic differentiation protocol and compared multiple hiPSC lines. This comparison indicated that the hepatic differentiation propensity varies among sibling hiPSC clones derived from the same adult human dermal fibroblasts (aHDFs). more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL14550

12 Samples

Download data: TXT

(Submitter supplied) Hepatocytes generated from human induced pluripotent stem cells (hiPSCs) are unprecedented resources for pharmaceuticals and cell therapy. However, little attention has so far been paid to variations among hiPSC lines in terms of their hepatic differentiation. We developed an improved hepatic differentiation protocol and compared multiple hiPSC lines. This comparison indicated that the hepatic differentiation propensity varies among sibling hiPSC clones derived from the same adult human dermal fibroblasts (aHDFs). more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL14550

24 Samples

Download data: TXT

(Submitter supplied) Induced pluripotent stem cells (iPSCs) have been generated from various somatic cells under feeder-layer conditions. These feeder-derived iPSCs generated in different labs exhibit greater variability than between different traditional embryo derived hESC lines. For that reason, it is important to develop a standard and defined system for deriving autologous patient stem cells. We have generated iPSCs under feeder-free conditions using Matrigel coated vessels in chemically defined medium, mTeSR1. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6244

21 Samples

Download data: CEL

(Submitter supplied) Transcriptional profiling of Human ESCs vs Human iPSCs, Human NSCs-ES vs Human NSCs-iPS iPSCs generated by using different method, and are not very good at Neural differentiation comapred with Human ESCs

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL17077

24 Samples

Download data: TXT

(Submitter supplied) X chromosome inactivation (XCI) is a dosage compensation mechanism in female cells to regulate X-linked gene expression. We report here that subcultures from established lines of female hESCs displayed variations (0-100%) in the expression of XCI markers such as XIST RNA coating and enrichment of histone H3 lysine 27 trimethylation (H3K27me3) on inactive X chromosome. Surprisingly, regardless of the presence or absence of XCI markers in different cultures, all female hESCs we examined (H7, H9, and HSF6 cells) exhibit a mono-allelic expression pattern for a majority of X-linked genes. more...

Organism:

Homo sapiens

Type:

Expression profiling by genome tiling array; Methylation profiling by genome tiling array; SNP genotyping by SNP array

4 related Platforms

9 Samples

Download data: CEL, CHP, TXT