Collection of mouse ES cell lines engineered for the forced induction of transcription factors
Ontology highlight
ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE31381 | GEO | 2011/11/10
SECONDARY ACCESSION(S): PRJNA145907
REPOSITORIES: GEO
Similar Datasets
Project description:Here we report the generation and characterization 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 phenotypes. These cell lines and microarray data provide building blocks for a variety of future biomedical research applications as a community resource.
| S-EPMC3240988 | biostudies-literature
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 | GSE31374 | 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.
2011-11-10 | GSE30917 | GEO
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: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: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: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:This SuperSeries is composed of the SubSeries listed below.
2009-10-01 | GSE16375 | GEO
Project description:To decipher the structure and behaviors of the transcription factor (TF) network, we created 50 permanent mouse ES cell lines, in each of which one of the 50 transcription factors tagged with FLAG, is inserted into the doxycycline (dox)-repressible ROSA26 locus. We have obtained time series data for 10 of the transcripts at 24h,48h and 72hr. Expression profiling reveals Cdx2 as the most potent inducer of transcriptome perturbation in ES cells, followed by Esx1, Sox9, Tcf3, Klf4, and Gata3. Immunoprecipitation (IP) with a FLAG-antibody in Cdx2-induced ES cells, identifies NuRD in CDX2-associated protein complexes; and chromatin-IP-sequencing identifies CDX2-binding sites predominantly in genes up-regulated by CDX2. Compendium analyses of Cdx2- and the other TF-inducible ES cells suggest a central role of the POU5F1/SOX2/NANOG protein complex in a swift-acting control mechanism to down-regulate a common set of genes at the beginning of multi-lineage ES cell differentiations. These ES cell lines will be a valuable resource to study biological networks in ES cells and mice. Keywords: dose response design,genetic modification design,individual genetic characteristic design,reference design,replicate design,time series design
2009-10-01 | GSE16148 | GEO