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Links from GEO DataSets

Items: 20

1.

Construction of A Human Cell Landscape by Single-cell mRNA-seq

(Submitter supplied) We used single-cell RNA sequencing to determine the cell type composition of all major human organs and construct a basic scheme for the human cell landscape (HCL). We reveal a single-cell hierarchy for many tissues that have not been well characterized previously. We present a “single-cell HCL analysis’’ pipeline that accurately defines human cell types and exemplify its utility in stem cell biology. more...
Organism:
Homo sapiens; Mus musculus
Type:
Expression profiling by high throughput sequencing
Platforms:
GPL20795 GPL21273
141 Samples
Download data: TXT
Series
Accession:
GSE134355
ID:
200134355
2.

Human embryoid bodies as a novel system for genomic studies of functionally diverse cell types

(Submitter supplied) Embryoid bodies, 3D aggregates of spontaneously differentiating iPSCs, have the potential to be a useful model system for genomic studies of diverse cell types. We first collected single-cell RNA-sequencing data from embryoid bodies (EBs) generated from 3 Yoruba individuals (18858, 18511, and 19160) in 3 replicates. We classify functional heterogeneity in EB cells using unsupervised clustering, differential expression analysis, reference annotation, and topic modelling. more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platforms:
GPL24676 GPL20301
24 Samples
Download data: MTX, TSV, TXT
Series
Accession:
GSE178274
ID:
200178274
3.

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
4.

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
5.

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
6.
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
7.
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
8.
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
9.

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
10.

Human induced pluripotent stem cell-derived macrophages share ontogeny with MYB-independent tissue-resident macrophages

(Submitter supplied) Tissue-resident macrophages such as microglia, Kupffer and Langerhans cells derive from Myb-independent yolk sac (YS) progenitors generated before the emergence of hematopoietic stem cells (HSCs). Myb-independent YS-derived resident macrophages self-renew locally, independently of circulating monocytes and HSCs. In contrast, adult blood monocytes as well as infiltrating, gut and dermal macrophages derive from Myb-dependent HSCs. more...
Organism:
Homo sapiens
Type:
SNP genotyping by SNP array
Platform:
GPL22678
7 Samples
Download data: TXT
Series
Accession:
GSE93285
ID:
200093285
11.

Augmented murine hematopoietic stem and progenitor cell reconstruction through conventional co-housing

(Submitter supplied) Background and methods: The effects of microbiota toward hematopoietic stem and progenitor cells (HSPCs) were very much complicated based on previous reports. In the current study, normal inbred C57BL6 (B6) mice from the Jackson Laboratory were maintained in the SPF environment for three weeks. Baseline complete blood counts were normal, and animals were then separated into two groups: 1) SPF mice stayed in the SPF facility, and 2) SPF mice being transferred to a conventional facility for co-housing (CVT). more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL21493
8 Samples
Download data: CSV
Series
Accession:
GSE142235
ID:
200142235
12.

Single-cell RNA-seq reveals a distinct transcriptome signature of hematopoiesis in GATA2 deficiency

(Submitter supplied) Background and Purpose: Constitutional GATA2 deficiency caused by heterozygous germline GATA2 mutation has a broad spectrum of clinical phenotypes including systemic infections, lymphedema, cytopenias, MDS and AML. A comprehensive profiling of transcriptome of hematopoiesis in GATA2 deficiency is currently lacking. Methods: We performed single-cell RNA sequencing of sorted bone marrow CD34+ hematopoietic stem and progenitor cells (HSPCs) from eight GATA2 deficiency patients, who had various well characterized GATA2 mutations and clinically manifest myelodysplasia. more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL21290
13 Samples
Download data: CSV
Series
Accession:
GSE135194
ID:
200135194
13.

The transcriptional landscape of mouse blood stem/progenitor cell transitions at single cell resolution

(Submitter supplied) Current gene-expression databases for the haematopoietic system provide information on gene expression profiles present in bulk populations. Although informative, these studies lack the resolution that can be gained at a single-cell level. In particular, population-average data assumes homogeneity within the population and may as such obscure the ability to detect the heterogeneity of decision-making processes in individual cells. more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL17021
3840 Samples
Download data: TXT
Series
Accession:
GSE81682
ID:
200081682
14.

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
15.

Identification of RUNX1 targets in iLSCs

(Submitter supplied) We identified 2 phenotypically and functionally distinct populations in our AML-iPSC line upon hematopoietic differentiation. One population is phenotypically and functionally a leukemia stem cell population (iLSCs = Samples A) and the second is more differentiated (iBlasts = Samples S). We found RUNX1 to be critical for iLSC maintenance and used gene expression and chromatin accessibility analyses after RUNX1 KD in iLSCs and iBlasts to identify the molecular mechanism of RUNX1 in iLSCs.
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL18573
24 Samples
Download data: CSV, TXT
16.

Acute Myeloid Leukemia iPSCs reveal a role for RUNX1 in the maintenance of human Leukemia Stem Cells

(Submitter supplied) Leukemia stem cells (LSCs) in acute myeloid leukemia (AML) are believed to possess distinct biological properties than the bulk AML cells, but their rarity and the unavailability of universal immunophenotypic markers for their prospective isolation hampers their study. We report that hematopoietic cells from genetically clonal AML patient-derived induced pluripotent stem cells (iPSCs) contain two morphologically and immunophenotypically distinct subpopulations: a cell fraction with a hematopoietic stem cell (HSC) immunophenotype exhibiting adherent growth which we termed induced leukemai stem cells (iLSCs) and a non-adherent fraction of more differentiated cells, which we termed induced blasts (iBlasts). more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL11154
6 Samples
Download data: CSV
Series
Accession:
GSE124992
ID:
200124992
17.

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
18.

Transcriptomal changes during differentiation of human iPS cells to PGC-like cells

(Submitter supplied) Pluripotent stem cell-derived human primordial germ cell (PGC)-like cells (hPGCLCs) may provide important opportunities to study human PGCs. We produced CD38+ hPGCLCs with a high efficiency [~43% of FACS-sorted embryoid body (EB) cells] from primed-pluripotency induced pluripotent stem cells (iPSCs) via 72-hour reprogramming towards ERK-independent naïve pluripotency. RNA-seq confirmed transcriptomal consistency of our hPGCLCs with hPGCLCs previously produced using various other methods. more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL18573
56 Samples
Download data: XLSX
Series
Accession:
GSE102943
ID:
200102943
19.

Expression data from ESC and in vitro derived somatic cells and germ cells

(Submitter supplied) We performed gene expression profiling on in vitro derived PGCs, undifferentiated ESCs, and somatic cells from the EB to examine germ cell expression in ESC-derived cells
Organism:
Mus musculus
Type:
Expression profiling by array
Platform:
GPL1261
10 Samples
Download data: CEL, CHP
Series
Accession:
GSE33121
ID:
200033121
20.

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
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