Collection of mouse ES cell lines engineered for the forced induction of transcription factors (part B)
Ontology highlight
ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE31374 | GEO | 2011/11/10
SECONDARY ACCESSION(S): PRJNA154149
REPOSITORIES: GEO
Similar Datasets
Project description:Here we report the generation of 84 mouse ES cell lines with doxycycline-controllable transcription factors (TFs) which, together with the previous 53 lines, cover 7 - 10% of all TFs encoded in the mouse genome. Global gene expression profiles of all 137 lines after the induction of TFs for 48 hrs can associate each TF with the direction of ES cell differentiation, regulatory pathways, and mouse phonotypes. These cell lines and microarray data provide the building blocks for a variety of future biomedical research applications as a community resource.
2011-11-10 | GSE30917 | GEO
Project description:Here we report the generation of 84 mouse ES cell lines with doxycycline-controllable transcription factors (TFs) which, together with the previous 53 lines, cover 7 - 10% of all TFs encoded in the mouse genome. Global gene expression profiles of all 137 lines after the induction of TFs for 48 hrs can associate each TF with the direction of ES cell differentiation, regulatory pathways, and mouse phonotypes. These cell lines and microarray data provide the building blocks for a variety of future biomedical research applications as a community resource. This set of data uses Universal Mouse Reference on the Cy5 channel. ES cells (passage 25) were cultured in the standard LIF+ medium with Dox+ on a gelatin-coated dish through the experiments. Cells from each cell line were split into 6 wells and the media was changed 24 hr after cell plating: 3 wells with Dox+ medium, and 3 wells with Dox- medium to induce transgenic TFs. Dox was removed via washing 3 times with PBS at 3 hour intervals. Total RNA was isolated by TRIzol (Invitrogen) after 48 hr, and two replications were used for real time qPCR and for microarray hybridization. RNA samples were labeled using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent). For most TFs, we hybridized a Cy3-CTP labeled sample from Dox- medium together with a Cy5-CTP labeled sample from Dox+ medium. But for 7 TFs, we labeled samples from Dox- and Dox+ with Cy3, and hybridized them independently with a Cy5-labeled reference target, which is a mixture of Stratagene Universal Mouse Reference RNA and MC1 cells RNA (this method requires a double number of arrays). Analysis showed that both methods produce results of comparable quality.
2011-11-10 | E-GEOD-30917 | biostudies-arrayexpress
Project description:Here we report the generation of 84 mouse ES cell lines with doxycycline-controllable transcription factors (TFs) which, together with the previous 53 lines, cover 7 - 10% of all TFs encoded in the mouse genome. Global gene expression profiles of all 137 lines after the induction of TFs for 48 hrs can associate each TF with the direction of ES cell differentiation, regulatory pathways, and mouse phonotypes. These cell lines and microarray data provide the building blocks for a variety of future biomedical research applications as a community resource. This set of data does not use Universal Mouse Reference on Cy5 channel. ES cells (passage 25) were cultured in the standard LIF+ medium with Dox+ on a gelatin-coated dish through the experiments. Cells from each cell line were split into 6 wells and the media was changed 24 hr after cell plating: 3 wells with Dox+ medium, and 3 wells with Dox- medium to induce transgenic TFs. Dox was removed via washing 3 times with PBS at 3 hours intervals. Total RNA was isolated by TRIzol (Invitrogen) after 48 hr, and two replications were used for real time qPCR (see primers in Supplementary Table S2) and for microarray hybridization. RNA samples were labeled with total RNA by Low RNA Input Fluorescent Linear Amplification Kit (Agilent). For most TFs, we hybridized Cy3-CTP labeled sample from Dox- medium together with Cy5-CTP labeled sample from Dox+ medium. But for 7 TFs we labeled samples from Dox- and Dox+ with Cy3, and hybridized them independently with Cy5-labeled reference target, which is a mixture of Stratagene Universal Mouse Reference RNA and MC1 cells RNA (this method requires a double number of arrays). Analysis showed that both methods produce results of comparable quality. The arrays are for 2 channel agilent 44K. We used treated two channels are two separate arrays, and normalized them with an quantile method described in the data processing sections. So we used one supplemental file for two samples (Cy3 and Cy5, or ch1 and ch2). Supplementary 'processed data' file linked below.
2011-11-10 | E-GEOD-31374 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the following subset Series: GSE30917: Collection of mouse ES cell lines engineered for the forced induction of transcription factors (part A) GSE31374: Collection of mouse ES cell lines engineered for the forced induction of transcription factors (part B) Refer to individual Series
2011-11-10 | E-GEOD-31381 | biostudies-arrayexpress
Project description:A network of transcription factors (TFs) determines cell identity, but identity can be altered by overexpressing a combination of TFs. In principle, this opens the possibility of achieving one of the goals of regenerative medicine generating the desired differentiated cells from pluripotent stem cells, such as embryonic stem (ES) cells and induced pluripotent stem (iPS) cells. However, choosing and verifying combinations of TFs for specific cell differentiation has been daunting due to a large number of possible combinations of ~2,000 TFs. Here we report an unbiased systematic approach identifying individual TFs that can direct efficient and rapid specific lineage differentiation. We start from a correlation matrix of global gene expression responses to the induction of single TFs and global gene expression profiles of a variety of tissues and organs. Based on the correlation matrix, we select TFs as examples and show that their overexpression differentiates ES cells into cells of specific organs, as predicted: Sfpi1 for blood cells, Hnf4a or Foxa1 for hepatocytes, and Ascl1 for neurons. Furthermore, we show that transfection of synthetic mRNAs of Sfpi1, Hnf4a, or Ascl1 generate correspondingly specific target cells. These results demonstrate both the wide-ranging utility of this approach to identify potent TFs for cell differentiation, and also the unanticipated capacity of single TFs to directly guide differentiation to specific lineage fates. Previously, we generated the global gene expression profiles obtained by overexpressing single TFs using the NIA mouse ES cell bank, which consists of 137 mouse ES cell lines carrying a doxycycline-regulatable TF. We then generated the correlation matrix by comparing TF-induced gene expression profiles and the expression profiles of a variety of cell types. TFs predicted by the correlation matrix for specific cell differentiation were selected and subjected to the detailed differentiation assays. ES cell lines were cultured in the GMEM with 1% FBS, 10% knockout serum (invitrogen), and LIF (Millipore). To induce differentiation, ES cell lines were cultured in the differentiation medium (DM) [(alpha minimal essential medium, aMEM) supplemented with 10% fetal calf serum and 5 × 10–5 M 2-mercaptoethanol] with or without doxycycline (1 g/ml). The following organ-specific cell culture media were also used: StemPro-34 Serum Free Media (invitrogen) for blood cells, Hepatocyte culture media kit (BD Biosciences) for hepatocytes, and NeuroCult differentiation kit (StemCell Technologies Inc) for neurons.
2014-03-14 | E-GEOD-43971 | biostudies-arrayexpress
Project description:Controlled induction of individual transcription factors (TFs) in embryonic stem cells (ESCs) with subsequent global gene expression profiling is a promising approach for identification of downstream genes regulated by these TFs in a relatively promiscuous epigenetic background. Here we generated and characterized mouse ESCs clones with 49 doxycycline-controllable TFs as a continuation of the NIA Mouse ESC Bank project. Together with the previous clone libraries, the project now comprises 186 TFs (ca. 10% of all TFs in the genome). Induction of individual TFs shifts the transcriptome towards specific differentiation fates (e.g., neural for Myt1, St18; fibroblasts and osteoblasts for Pitx1, Pitx2, Barhl2, and Lmx1a; thymocytes for Myb; lymph nodes and spleen for Etv2 and Plac1, and ovary for Pitx1, Pitx2, and Dmrtc2). Gene set enrichment analysis for expression profile change after induction of TFs provides additional information on the functions and phenotypes associated with these TFs. These data could facilitate methods for generating various types of cells in regenerative medicine as well as ameliorating pathogenic phenotypes in gene therapy. Dox- overexpressing transcription factor vs. Dox+ (control).
2016-07-21 | E-GEOD-72350 | biostudies-arrayexpress
Project description:The developmental potential of human pluripotent stem cells suggests that they can produce disease-relevant cell types for biomedical research. However, substantial variation has been reported among pluripotent cell lines, which could affect their utility and clinical safety. Such cell-line specific differences must be better understood before one can confidently use embryonic stem (ES) or induced pluripotent stem (iPS) cells in translational research. Towards this goal we have established genome-wide reference maps of DNA methylation and gene expression for 20 previously derived human ES lines and 12 human iPS cell lines, and we have measured the in vitro differentiation propensity of these cell lines. This resource enabled us to assess the epigenetic and transcriptional similarity of ES and iPS cells and to predict the differentiation efficiency of individual cell lines. The combination of assays yields a scorecard for quick and comprehensive characterization of pluripotent cell lines. We used microarrays to compare the gene expression profiles between human ES cell lines, iPS cell lines, fibroblasts and embryoid bodies, and to identify cell-line specific outlier genes.
2011-02-03 | GSE25970 | GEO
Project description:Controlled induction of individual transcription factors (TFs) in embryonic stem cells (ESCs) with subsequent global gene expression profiling is a promising approach for identification of downstream genes regulated by these TFs in a relatively promiscuous epigenetic background. Here we generated and characterized mouse ESCs clones with 49 doxycycline-controllable TFs as a continuation of the NIA Mouse ESC Bank project. Together with the previous clone libraries, the project now comprises 186 TFs (ca. 10% of all TFs in the genome). Induction of individual TFs shifts the transcriptome towards specific differentiation fates (e.g., neural for Myt1, St18; fibroblasts and osteoblasts for Pitx1, Pitx2, Barhl2, and Lmx1a; thymocytes for Myb; lymph nodes and spleen for Etv2 and Plac1, and ovary for Pitx1, Pitx2, and Dmrtc2). Gene set enrichment analysis for expression profile change after induction of TFs provides additional information on the functions and phenotypes associated with these TFs. These data could facilitate methods for generating various types of cells in regenerative medicine as well as ameliorating pathogenic phenotypes in gene therapy.
2016-07-21 | GSE72350 | GEO
Project description:Elastin-like polypeptides (ELPs) are promising for biomedical applications due to their unique thermos-responsive and elastic properties. ELP-based biomaterial has been produced through enzymatic crosslinking of modified ELPs. We investigated the role of elastin like polypeptide in cardiomyocyte proliferation and differentiation in mouse ES cells
2024-02-12 | GSE145623 | GEO
Project description:Recent genetic evidence has revealed microRNA-137 (miR-137) as a risk gene in schizophrenia and autism spectrum disorder (ASD), and the following cellular studies have demonstrated the importance of miR-137 in regulating neurogenesis. We have generated miR-137 knockout mice which display behaviors that resemble some symptoms of these two diseases. To investigate the underlying molecular mechanism, we performed comprehensive analyses of the entire RNA and protein molecules of the miR-137 mouse brains. The dataset uploaded here is the raw data of the mass spectrometry-based whole proteome analysis of the six miR-137 mouse brains: wild-type, heterozygous (miR-137+/–) and homozygous (miR-137–/–) from two different litters. The tandem mass tag (TMT) methodology was employed in this proteomics analysis for the quantitation. The sample channels are: 128C (miR-137+/+, litter 1), 129N (miR-137+/–, litter 1), 129C (miR-137–/–, litter 1), 130N (miR-137+/+, litter 2), 130C (miR-137+/–, litter 2), and 131N (miR-137–/–, litter 2).
2018-10-17 | PXD003874 | Pride