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Series GSE41444 Query DataSets for GSE41444
Status Public on Dec 20, 2012
Title Airn transcriptional overlap but not its lncRNA products induce imprinted Igf2r silencing.
Organism Mus musculus
Experiment type Expression profiling by genome tiling array
Summary To test if the imprinted long non-coding RNA (lncRNA) Airn transcription or its product silences the protein-coding Igf2r gene, we shortened the endogenous lncRNA to four different lengths by inserting polyadenylation (polyA) cassettes on the paternal chromosome via homologous recombination in ES cells.
ES cell differentiation was used to recapitulate the developmental onset of Airn and Igf2r imprinted expression and polyA cassettes inserted before (T3, T16, T27) or after (T31, T51) the Igf2r promoter successfully truncated Airn, with the exception of T27.
RNA hybridization to a tiling array (MIRTA) demonstrated loss of Airn upstream of the Igf2r promoter (except T27) and absence of novel spliced variants in all truncation alleles.

To further test the transcriptional overlap model we moved the Airn promoter ~700bp before the Igf2r TSS in ES cells that lack an endogenous paternal Airn promoter and called this cell line FAP (Forward-Airn-Promoter).
RNA hybridization to a tiling array (MIRTA) demonstrated that the moved Airn promoter expresses Airn in wildtype orientation and terminates at the wildtype 3' end.
Overall design ES cell lines expressing different Airn variants were differentiated on gelatinized dishes after feeder cell depletion and LIF withdrawal by 0.27µM retinoic acid for 5 days and Airn length was assayed.
Contributor(s) Latos PA, Pauler FM, Koerner MV, Şenergin HB, Barlow DP
Citation(s) 23239737
Submission date Oct 10, 2012
Last update date Dec 22, 2012
Contact name Florian M Pauler
Phone +43 2243 9000-7434
Organization name IST Austria
Lab Simon Hippenmeyer
Street address Am Campus 1
City Klosterneuburg
ZIP/Postal code 3400
Country Austria
Platforms (1)
GPL11618 NimbleGen custom Mouse MIRTA Array
Samples (7)
GSM1017448 Airn wildtype
GSM1017449 Airn 3kb truncation
GSM1017450 Airn 16kb truncation
BioProject PRJNA177027

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
GSE41444_RAW.tar 122.7 Mb (http)(custom) TAR (of PAIR, TXT)
Processed data included within Sample table
Processed data provided as supplementary file

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