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Title: Next Generation Sequencing Investigation of altered transcripts in presence of dominant-negative transcription factor      
keywords:
Transcriptome or Gene expression
ID:
PRJNA300871
description:
Purpose:The goals of this study was to determine alterations in expression levels of transcripts downstream of a dominant-negative transcription factor. Quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods was used to confirm the altered expression of targets. Methods: Striatal mRNA profiles of 11-month-old wild-type (WT) and Nestin-Cre X PPAR delta E411P mice were generated by deep sequencing, in triplicate, using Illumina HiSeq 2000. The sequence reads that passed quality filters were analyzed at the transcript isoform level with TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays. Western blots, and immunofluorescence was also used to confirm if altered mRNA levels translated to changes at the protein level. Results: Using data analysis workflow, we mapped sequence reads for each sample to the mouse genome (build mm9) and identified transcripts in the striatum of WT and PPARdelta E411P mice. Conclusions: Our study found multiple transcripts altered in the striatum of the Nestin-Cre x PPAR delta E411P mice as compared to WT striatum, as generated by RNA-SEQ in biologic replicates. Overall design: Striatal mRNA profiles of 11-month-old wild type (WT) and Nestin-Cre X PPAR delta E411P mice were generated by deep sequencing, in triplicate, using Illumina HiSeq2000.
accesstypes:
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landingpage: http://www.ncbi.nlm.nih.gov/bioproject/PRJNA300871
authentication:
none
authorization:
none
ID:
pmid:26642438
name:
Mus musculus
ncbiID:
ncbitax:10090
abbreviation:
NCBI
homePage: http://www.ncbi.nlm.nih.gov
ID:
SCR:006472
name:
National Center for Biotechnology Information
homePage: http://www.ncbi.nlm.nih.gov/bioproject
ID:
SCR:004801
name:
NCBI BioProject
  • R01 AG033082/AG/NIA NIH HHS/United States

  • P01 HL110873/HL/NHLBI NIH HHS/United States

  • F32 NS081964/NS/NINDS NIH HHS/United States

  • R01 HG004659/HG/NHGRI NIH HHS/United States

  • R01 EY022306/EY/NEI NIH HHS/United States

  • R01 NS065874/NS/NINDS NIH HHS/United States

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