Dataset Information

Generation of mouse ES cell lines engineered for the forced induction of transcription factors.

ABSTRACT: 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.

SUBMITTER: Correa-Cerro LS

PROVIDER: S-EPMC3240988 | biostudies-literature | 2011

REPOSITORIES: biostudies-literature

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Publications

Generation of mouse ES cell lines engineered for the forced induction of transcription factors.

Correa-Cerro Lina S LS Piao Yulan Y Sharov Alexei A AA Nishiyama Akira A Cadet Jean S JS Yu Hong H Sharova Lioudmila V LV Xin Li L Hoang Hien G HG Thomas Marshall M Qian Yong Y Dudekula Dawood B DB Meyers Emily E Binder Bernard Y BY Mowrer Gregory G Bassey Uwem U Longo Dan L DL Schlessinger David D Ko Minoru S H MS

Scientific reports 20111123

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 var ...[more]

PMID: 22355682

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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.

Dataset Information

Generation of mouse ES cell lines engineered for the forced induction of transcription factors.

Publications

Generation of mouse ES cell lines engineered for the forced induction of transcription factors.

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