BioProject

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. More...

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. Overall design: 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. Less...