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Series GSE53212 Query DataSets for GSE53212
Status Public on Jan 01, 2014
Title Nanog Independent Reprogramming to iPSCs with Canonical Factors
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary It has been suggested that the transcription factor Nanog is essential for the establishment of pluripotency during the derivation of embryonic stem (ES) cells and induced pluripotent stem (iPS) cells. However, successful reprogramming to pluripotency with a growing list of divergent transcription factors, at ever increasing efficiencies, suggests that there may be many distinct routes to a pluripotent state. Here, we have investigated whether Nanog is necessary for reprogramming murine fibroblasts under highly efficient conditions using the canonical reprogramming factors Oct4, Sox2, Klf4 and cMyc. In agreement with prior results, the efficiency of reprogramming Nanog-/- fibroblasts was significantly lower than that of control fibroblasts. However, in contrast to previous findings, we were able to reproducibly generate iPS cells from Nanog-/- fibroblasts that effectively contributed to chimeric mice. Thus while Nanog may be an important mediator of reprogramming it is not required for establishing pluripotency in the mouse, even under standard conditions. In order to further evaluate the equivalency of Nanog null iPSC to nanog null ESCs, we have performed RNAseq on two independent nanog null iPSC lines, as well as Nanog Null ESC, WT ESC and iPSCs as well as MEFs. As a negativve control for reprogramming we have analyzed a partially reprogrammed iPSC line.
 
Overall design 2-4 biological replicates each of 7 conditions (WT MEFs, WT ESC, WT iPSC, WT partially reprogrammed iPSC (piPS), Nanog null ESC, Nanog null iPSC clone G2 and Nanog null iPSC clone G5)
 
Contributor(s) Davis-Dusenbery BN, Eggan K
Citation(s) 24527385
Submission date Dec 11, 2013
Last update date May 15, 2019
Contact name Brandi Nicole Davis-Dusenbery
Organization name Harvard University
Department SCRB
Lab Kevin Eggan Laboratory
Street address 7 Divinity Ave
City Cambridge
State/province Massachusetts
ZIP/Postal code 02125
Country USA
 
Platforms (2)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
Samples (17)
GSM1287734 WT ESC -1
GSM1287735 WT ESC -2
GSM1287736 iPSC -1
Relations
BioProject PRJNA231119
SRA SRP033700

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE53212_FPKM_matrix.txt.gz 1.9 Mb (ftp)(http) TXT
GSE53212_RAW.tar 6.9 Mb (http)(custom) TAR (of TXT)
Raw data are available in SRA
Processed data provided as supplementary file
Processed data is available on Series record

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