Mus musculus
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ABSTRACT:
PROVIDER: PRJNA152585 | ENA |
REPOSITORIES: ENA
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Project description:Samples of adherent and suspension cells undergoing reprogramming were collected at day 0, day2, day6, day15 (with doxycycline) and day25 (without doxycycline). Reprogramming under adherent and suspension conditions was compared by PCC analysis, non-hierarchical clustering and by functional criteria for differentially expressed genes.
2012-03-25 | E-GEOD-35422 | biostudies-arrayexpress
Project description:Samples of adherent and suspension cells undergoing reprogramming were collected at day 0, day2, day6, day15 (with doxycycline) and day25 (without doxycycline).
2012-03-25 | GSE35422 | GEO
Project description:Direct reprogramming of human fibroblasts to a pluripotent state has been achieved through ectopic expression of the transcription factors OCT4, SOX2, and either cMYC and KLF4 or NANOG and LIN28. Little is known, however, about the mechanisms by which reprogramming occurs, which is in part limited by the low efficiency of conversion. To this end, we sought to create a doxycycline-inducible lentiviral system to convert primary human fibroblasts and keratinocytes into human induced pluripotent stem (hiPS) cells. hiPS cells generated with this system were molecularly and functionally similar to human embryonic stem (hES) cells, demonstrated by gene expression profiles, DNA methylation status, and differentiation potential. While expression of the viral transgenes was required for several weeks in fibroblasts, we found that 10 days was sufficient for the reprogramming of keratinocytes, suggesting that the kinetics of reprogramming are cell-type dependent. Using our inducible system, we developed a strategy to induce hiPS cell formation at high frequency by generating differentiated cells that contain the viral transgenes in a pattern that enables successful induction of pluripotency. Upon addition of doxycycline to differentiated hiPS-derived cells, we obtained “secondary” hiPS cells at a frequency at least 100-fold greater than the initial conversion. The ability to reprogram cells with high efficiency provides a unique platform to dissect the underlying molecular and biochemical processes that accompany nuclear reprogramming.
2008-09-12 | GSE12390 | GEO
Project description:AIM: To detect differences in transcriptional profiles after knocking down Brca1, Bard1 or Wdr5, compared to a negative control in early reprogramming to pluripotency. DESCRIPTION: RNA-seq profiles of early reprogramming mouse embryonic fibroblasts (MEFs) transduced with lentivirus containing doxycycline-inducible OSKM factors to induce pluripotency . Before starting reprogramming, OSKM-MEFs were transfected with different siRNAs and then they were reprogrammed for 3 or 6 days.
2019-03-14 | GSE118677 | GEO
Project description:AIM: To detect differences in transcriptional profiles after knocking down Ncor1 or Oct4, compared to a negative control in early reprogramming to pluripotency. DESCRIPTION: RNA-seq profiles of early reprogramming mouse embryonic fibroblasts (MEFs) transduced with lentivirus containing doxycycline-inducible OSKM factors to induce pluripotency . Before starting reprogramming, OSKM-MEFs were transfected with different siRNAs and then they were reprogrammed for 3 or 6 days.
2020-03-27 | GSE139376 | GEO
Project description:In vertebrates, all cells except circulating blood cells must adhere to support their normal growth and functions. The adherence to extracellular matrix and/or other cells is critical and adherent cells placed in non-adherent conditions either die or form multicellular spheroids. Placing cells in non-adherent conditions has been used to induce differentiation in teratocarcinoma cells and more recently to form organoids . Because of such important consequences induced by cell adhesion on cell growth and function, the transition between adherent and non-adherent states is rather rare. There are however physiological situations, such as blood cells diapedesis, during which cells that circulate into the blood stream must adhere to the endothelial cells and cross the endothelial barrier to reach target tissues. Another example of transition, from an adherent to a non-adherent state, is observed in the metastasic process, where cells detach from the tumor mass and circulate in the blood and lymphatic vasculature prior to reattaching and extravasating to colonize distant organs. The comparative analysis of the only effects of adherence on cellular functions is complicated by the fact that in many study models the acquisition or loss of adherence induces major alterations in cell physiology that would obscure the effects of the adherence itself. For example, P19 teratocarcinoma cells differentiate in suspension spheroids while they do not in adhering conditions. In this context, the comparison between spheroids and adherent cells would not be a comparison between adherent and non-adherent cells, but between differentiated cells adhering between them and undifferentiated cells adhering on plastic. Mouse macrophage cell lines represent one of the rare experimental models that may be suitable to compare the adherent and non-adherent states. Indeed, they grow equally well under adherent and non-adherent conditions and keep their differentiated functions under both conditions. We therefore decided to use this model to analyze the changes between the adherent and the non-adherent state using a broad approach, based on proteomics.
2021-09-09 | PXD021593 | Pride
Project description:We generated three kinds of genetically identical mouse reprogrammed cells: induced pluripotent stem cells (iPSCs), nuclear transfer embryonic stem cells (ntESCs) and iPSC-nt-ESCs that are established after successively reprogramming of iPSCs by nuclear transfer (NT). NtESCs show better developmental potential than iPSCs, whereas iPSC-nt-ESCs display worse developmental potential than iPSCs. We used microarrays to distinguish the gene expression differences among three pluriptoent stem cells and identified that imprinted genes had a similar expression pattern in iPSCs and iPSC-nt-ESCs. We sought to obtain genetic identical pluripotent stem cell lines in order to minimize genetic variations among different reprogrammed cells. To that end, we established a genetically homogenous secondary reprogramming system, in which mouse embryonic fibroblasts (MEFs) carrying doxycycline (dox)-inducible lentiviruses expressing Oct4, Sox2, Klf4 and c-Myc were isolated and used as donors for different reprogramming experiments. We generated iPSCs after plating MEFs in the presence of dox in ES culture conditions, and then derived ntESCs after transplantation of the nucleus from the same MEFs into enucleated oocyte. Furthermore, we successively reprogrammed iPSCs by means of NT and established a set of nt-iPSC lines. Pluripotent stem cells generated from different reprogramming strategies were for RNA extraction and hybridization on Affymetrix microarrays.
2011-05-31 | E-GEOD-24705 | biostudies-arrayexpress
Project description:Here we performed a ChIP-seq experiment on a sample of adherent cultures of mouse neural stem cells (NS5 cell line) expressing an inducible HA-tagged version of the proneural factor MyT1 (MyT1-HA, under TetON control) after activation by doxycycline hyclate (DOX). This resulted in the generation of a genome-wide map of MyT1-HA binding to chromatin.
2016-09-09 | E-MTAB-4330 | biostudies-arrayexpress
Project description:Direct reprogramming of human fibroblasts to a pluripotent state has been achieved through ectopic expression of the transcription factors OCT4, SOX2, and either cMYC and KLF4 or NANOG and LIN28. Little is known, however, about the mechanisms by which reprogramming occurs, which is in part limited by the low efficiency of conversion. To this end, we sought to create a doxycycline-inducible lentiviral system to convert primary human fibroblasts and keratinocytes into human induced pluripotent stem (hiPS) cells. hiPS cells generated with this system were molecularly and functionally similar to human embryonic stem (hES) cells, demonstrated by gene expression profiles, DNA methylation status, and differentiation potential. While expression of the viral transgenes was required for several weeks in fibroblasts, we found that 10 days was sufficient for the reprogramming of keratinocytes, suggesting that the kinetics of reprogramming are cell-type dependent. Using our inducible system, we developed a strategy to induce hiPS cell formation at high frequency by generating differentiated cells that contain the viral transgenes in a pattern that enables successful induction of pluripotency. Upon addition of doxycycline to differentiated hiPS-derived cells, we obtained âsecondaryâ hiPS cells at a frequency at least 100-fold greater than the initial conversion. The ability to reprogram cells with high efficiency provides a unique platform to dissect the underlying molecular and biochemical processes that accompany nuclear reprogramming. Experiment Overall Design: Total RNA was isolated from control HUES lines, hBJ (donor line) 4 primary HIPS lines and 1 secondary HIPS line using an RNeasy kit (Qiagen). Samples were processed as independent triplicates. RNA probes for microarray hybridization were prepared and hybridized to Affymetrix HGU133 plus 2 oligonucleotide microarrays. Data was extracted and analyzed using Rosetta Resolver system. During importation, the data was subjected to background correction, intrachip normalization, and the Rosetta Resolver Affymetrix GeneChip error model (Weng et al, 2006). For the generation of intensity plots, genes that showed greater than a two-fold difference in expression value (p<0.01) in HUES8 hES cells and BJ fibroblasts were noted (19,663 probes) and their expression analyzed. A hierarchical clustering was performed.
2008-10-25 | E-GEOD-12390 | biostudies-arrayexpress