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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Expression data sets for untreated and reprogrammed fibroblasts

ABSTRACT: To understand global transcriptome during reprogramming fibroblasts to blood cells, we have analysed transcriptomes of untreated fibroblasts, CDH5 positives cells sorted at day 8 and C-Kit positive cells sorted at day 12. 6 samples, 2 biological replcated of untreated fibrobalsts, Day 8 CDH5 positive cells, Day 12 C-Kit Positive cells

ORGANISM(S): Mus musculus

SUBMITTER: Kiran Batta

PROVIDER: E-GEOD-59428 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Direct reprogramming of murine fibroblasts to hematopoietic progenitor cells.

Batta Kiran K Florkowska Magdalena M Kouskoff Valerie V Lacaud Georges G

Cell reports 20141126 5

Recent reports have shown that somatic cells, under appropriate culture conditions, could be directly reprogrammed to cardiac, hepatic, or neuronal phenotype by lineage-specific transcription factors. In this study, we demonstrate that both embryonic and adult somatic fibroblasts can be efficiently reprogrammed to clonal multilineage hematopoietic progenitors by the ectopic expression of the transcription factors ERG, GATA2, LMO2, RUNX1c, and SCL. These reprogrammed cells were stably expanded on ...[more]

PMID: 25466247

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Expression data sets for untreated and reprogrammed fibroblasts

Project description:To understand global transcriptome during reprogramming fibroblasts to blood cells, we have analysed transcriptomes of untreated fibroblasts, CDH5 positives cells sorted at day 8 and C-Kit positive cells sorted at day 12.

2014-12-21 | GSE59428 | GEO

ER71/ETV2-mediated direct reprogramming of human dermal fibroblasts (HDFs) into endothelial-like cells

Project description:Samples 1-6: HDFs transduced with ER71/ETV2 were sorted on KDR expression at day 7. The isolated KDR+ cells together with human umbilical venous endothelial cells (HUVECs) and untransduced HDFs were subjected to genomic gene expression profiling. A significant number of genes related with vessel development and angiogenesis was significantly upregulated in KDR+ cells, compared to control HDFs. These findings strongly argue that ER71/ETV2 directly reprograms human fibroblasts to functional endothelial-like cells, which could be useful for disease investigation as well as autologous cell therapy. Samples 7-12: HDFs transduced with ER71/ETV2 were sorted on KDR expression at day 7. The isolated KDR+ cells were further cultured up to day 93. The further cultured cells together with human umbilical venous endothelial cells (HUVECs) and untransduced HDFs were subjected to genomic gene expression profiling. A significant number of genes related with vessel development and angiogenesis was significantly upregulated in the further cultured cells, compared to control HDFs. These findings strongly argue that ER71/ETV2 directly reprograms human fibroblasts to functional endothelial-like cells, which could be useful for disease investigation as well as autologous cell therapy. Samples 1-6: HDFs transduced with ER71/ETV2 were sorted on KDR expression at day 7. The isolated KDR+ cells together with human umbilical venous endothelial cells (HUVECs) and untransduced HDFs were subjected to genomic gene expression profiling. Samples 7-12: HDFs transduced with ER71/ETV2 were sorted on KDR expression at day 7. The isolated KDR+ cells were further cultured up to day 93. The further cultured cells together with human umbilical venous endothelial cells (HUVECs) and untransduced HDFs were subjected to genomic gene expression profiling.

2013-09-12 | E-GEOD-50801 | biostudies-arrayexpress

Expression data of MACS sorted cells (SSEA-1+ and SSEA-1-) from porcine fetal fibroblast cell line

Project description:A subset of cells in cellular populations may be preferentially reprogrammed into pluripotent stem cells due to their innate gene expression characteristics. SSEA-1+ sorted cells were shown to be more amenable to reprogramming than other cells in porcine fetal fibroblast cell lines. This microarray data reveals which genes are unique to the SSEA1+ sorted cells and helps to give them an identity. Porcine fetal fibroblasts were subjected to Magnetic Activated Cell Sorting using anti-SSEA-1. Five biological replicates were performed resulting in 5 SSEA-1 positive fractions and 5 SSEA-1 negative fractions which were analyzed.

2015-08-13 | E-GEOD-72025 | biostudies-arrayexpress

microRNA profile analysis of sorted cells during different reprogramming stages

Project description:Mouse embryonic fibroblasts were reprogrammed using Oct4, Sox2, Klf4 and cMyc genes. At day 5, cells were sorted as Thy1 positive and Thy1 negative populations. microRNA expression profile from Thy1+ and Thy1- cells was compared with original MEFs (D0) to identify significantly changed microRNAs during initial stage of reprogramming

2015-09-12 | E-MTAB-2932 | biostudies-arrayexpress

Transcriptome analysis of cells in mouse hairy melanocytic nevi

Project description:RNA-seq data was obtained from different skin cell types at two time points: postnatal day P30, when WT dorsal hair follicles are in actively growing state (aka anagen) and P56, when WT hair follicles are in resting state (aka telogen). Cell types include: Bulge stem cells (B), dermal papilla fibroblasts (DP), secondary hair germ cells (HG), melanocytes (Melan), myeloid cells (Myel) and CD45-positive immune cells (I). All cell were FACS sorted and only live single cells were collected for RNA extraction.

2023-03-14 | GSE111999 | GEO

Co-expression network analysis from genes involved with neural-differentiation shows specific pattern in patients with schizophrenia

Project description:Schizophrenia is a severe and debilitating neuropsychiatric disorder with the involvement of genetic and environmental factors contributing to its pathogenesis. The specific role of the brain cell types in the disease remains uncovered due to the difficulties in accessing diseased tissue. This study analysed molecular alterations in human induced pluripotent stem cells derived from fibroblasts from control subject and individual with schizophrenia and further differentiated to neuron to identify genes relevant for the development of schizophrenia. We identified 228 genes that are involved with metabolic processes, signal transduction, nervous system development, regulation of neurogenesis and neuronal differentiation. These genes were analysed in expression microarrays of post-mortem brain tissue (frontal cortex) of additional patients with schizophrenia and normal individuals revealing only six common genes: CACNA1E, CEBPB, DUX4, EDNRA, SPHK1 and SPRY4. Furthermore, a co-expression network analysis of the 228 genes revealed a non-conserved module enriched for genes associated with oxidative stress and negative regulation of cell differentiation as involved with schizophrenia. This study supports the relevance of using cellular approaches to dissect molecular aspects of neurogenesis with impact in the schizophrenic brain. Biopsies of primary human fibroblasts from a 48-year-old woman with DSM-IVTR schizophrenia defined as treatment-resistant under clozapine treatment (SZCP) were collected in parallel with a control subject (CON) negative for any major lifetime DSM-IVTR diagnosis. Fibroblasts underwent primary culture procedures to generate hiPSCs and were subsequently differentiated into neurons (NPC). Samples generation and culture conditions are described in Paulsen et al. (2011). Five replicates of expression microarray experiments using a reference design, where test sample (NPC) is derived from reference sample (hiPSC).

2014-10-09 | E-GEOD-62105 | biostudies-arrayexpress

The effect of very-high-molecular-mass hyaluronan (vHMM-HA) on CD44-overexpressing IMR90 cells

Project description:Naked mole-rat skin fibroblasts (NSF) produces vHMM-HA. Although NSF-HA has been shown to suppress NSF transformation, it is still unclear if exceptional polymer length of vHMM-HA is important for its functions. Here, we compared the effect of intact control NSF-HA (cNSF-HA) ) on the transcriptome of CD44-overexpressing IMR90 cells.

2020-04-25 | E-MTAB-8943 | biostudies-arrayexpress

Therapeutic potential of induced neural stem cells for spinal cord injury

Project description:The spinal cord does not spontaneously regenerate after injury and a treatment that ensures functional recovery after spinal cord injury (SCI) is still not available. Recently, fibroblasts have been directly converted into induced neural stem cells (iNSCs) following the forced expression of different combinations of transcription factors. Although directly converted iNSCs have been considered as a potentialcell source for clinical applications, their therapeutic potential has not been investigated yet. Here we show that iNSCs directly converted from mouse fibroblasts enhance the functional recovery after SCI in rats. Mouse embryonic fibroblasts (MEFs) were directly converted into iNSCs using four transcription factors (Brn4, Sox2, Klf4 and c-Myc). iNSCs showed gene expression profiles similar to cNSCs as determined by microarray analysis. MEFs were derived from C3H mouse strain embryos at embryonic day (E)13.5 after removing the head and all internal organs including the gonads and the spinal cord. 5x10^4 fibroblasts were transduced with replication-defective retroviral particles coding for Sox2, Klf4, c-Myc, and Brn4. After 48 h, the transduced fibroblasts were cultured in standard NSC medium. iNSC clusters were observed 4-5 weeks after transduction and expanded. Both MEFs and cNSCs were used as negative and positive control, respectively.

2013-10-01 | E-GEOD-51331 | biostudies-arrayexpress

DNA Methylation profiling of human iNBSCs, iPSC-derived NBSCs and adult dermal fibroblasts

Project description:We describe a so far uncharacterized, embryonic and self-renewing Neural Plate Border Stem Cell (NBSC) population with the capacity to differentiate into central nervous and neural crest lineages. NBSCs can be obtained by neural transcription factor-mediated reprogramming (BRN2, SOX2, KLF4, and ZIC3) of human adult dermal fibroblasts and peripheral blood cells (induced Neural Plate Border Stem Cells, iNBSCs) or by directed differentiation from human induced pluripotent stem cells (NBSCs). Moreover, human (i)NBSCs share molecular and functional features with an endogenous NBSC population isolated from neural folds of E8.5 mouse embryos. Upon differentiation, iNBSCs give rise to either (1) radial glia-type stem cells, dopaminergic and serotonergic neurons, motoneurons, astrocytes, and oligodendrocytes or (2) cells from the neural crest lineage. Here we provide array-based methylation data of iNBSCs reprogrammed from adult dermal fibroblasts (ADF), iPSC-derived NBSCs and adult dermal fibroblasts. The data provided demonstrate robust changes in the methylation landscape after reprogramming of human adult dermal fibroblasts into iNBSCs.

2018-12-20 | E-MTAB-5808 | biostudies-arrayexpress

Generation of Inner Ear Hair Cells by Direct Lineage Conversion of Primary Somatic Cells [ChIP-seq]

Project description:We purified seven different cell populations and performed RNA sequencing to profile transcriptional similarities and differences between them. The seven cell types were 1) Atoh1-GFP positive cochlear hair cells from the organ of Corti of postnatal day one mice, 2) Atoh1-GFP negative cells from the organ of Corti of postnatal day one mice, 3) Atoh1-GFP positive induced hair cells generated by overexpression of Six1, Atoh1, Pou4f3, and Gfi1, 4) dsRed transduced control mouse embryonic fibroblasts, 5) Atoh1-GFP positive Merkel cells from postnatal day 1 mice, 6) Atoh1-GFP positive Cerebellar granule precursor cells from postnatal day 1 mice, and 7) Atoh1-GFP positive Gut secretory cells from postnatal day one mice.

2020-05-28 | GSE149259 | GEO

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