Unknown,Transcriptomics,Genomics,Proteomics

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Transcription profiling of mouse brain and kidney Sense-antisense transcript comparison


ABSTRACT: Comparison of sense (forward probes) and antisense (reverse probes on U74 v1 gene arrays) transcripts in mouse kidney and brain. Positive calls related to antisense transcripts were compared to the cognate signals on the 430 version of mouse genome arrays to obtain genes that co expressed sense and antisense transcripts. This had to be done manually because divergent probe IDs on the two chip generations. Experiment Overall Design: The first Affymetrix U74 mouse gene chips contains reversely oriented probe sets. These probes will hybridize to natural antisense transcripts that overlap with the sense transcript in the cognate area. Affymetrix provided a mask to identify the reverse probes. Positive calls with these reverse probes will give an estimate of the antisense transcriptome in that particular tissue. Comparison of the reversely oriented probes with correctly annotated probes will reveal the expression ratio of sense and antisense transcripts.

ORGANISM(S): Mus musculus

SUBMITTER: Andreas Werner 

PROVIDER: E-GEOD-6106 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Expression profiling of antisense transcripts on DNA arrays.

Werner Andreas A   Schmutzler Gabriele G   Carlile Mark M   Miles Colin G CG   Peters Heiko H  

Physiological genomics 20061114 3


The majority of mouse genes are estimated to undergo bidirectional transcription; however, their tissue-specific distribution patterns and physiological significance are largely unknown. This is in part due to the lack of methodology to routinely assess the expression of natural antisense transcripts (NATs) on a large scale. Here we tested whether commercial DNA arrays can be used to monitor antisense transcription in mouse kidney and brain. We took advantage of the reversely annotated oligonucl  ...[more]

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