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Title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type, DDX5 knockout, RORc knockout, RmrpG262T knockin T helper 17 cell Transcriptomes [RNA-seq]      
keywords:
Transcriptome or Gene expression
ID:
PRJNA287657
description:
Purpose: The goals of this study are to compare in vitro polarized T helper 17 cell transcriptome profiling (RNA-seq) in different genetic background. Methods: Th17 mRNA profiles of 96hrs in vitro cultured T helper 17 cells from wild-type and mutant mice were generated by deep sequencing, using Illumina RapidRun. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) and TopHat followed by CuffDiff. qRT–PCR validation was performed using SYBR Green assays. Results: Among the 325 genes that were significantly dysregulated in DDX5-deficient T cells, approximately 40% were previously identified as RORγt targets in Th17 cells. 96 RORγt-dependent Th17 cell genes co-regulated by Rmrp together with DDX5. Conclusions: Our study suggest that the DDX5-Rmrp axis is critical for expression of a critical subset of the RORγt transcriptional targets in Th17 cells. Overall design: mRNA profiles of 96hr in vitro cultured Th17 from wild type (WT) and mutant mice were generated by deep sequencing using Illumina RapidRun.
accesstypes:
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landingpage: http://www.ncbi.nlm.nih.gov/bioproject/PRJNA287657
authentication:
none
authorization:
none
ID:
pmid:26675721
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
  • T32 CA009161/CA/NCI NIH HHS/United States

  • P30 CA016087/CA/NCI NIH HHS/United States

  • R01AI080885/AI/NIAID NIH HHS/United States

  • R01HG004361/HG/NHGRI NIH HHS/United States

  • P50-HG007735/HG/NHGRI NIH HHS/United States

  • R01DK103358/DK/NIDDK NIH HHS/United States

  • R01 AI121436/AI/NIAID NIH HHS/United States

  • R01 DK101520/DK/NIDDK NIH HHS/United States

  • Howard Hughes Medical Institute/United States

  • 1F30CA189514-01/CA/NCI NIH HHS/United States

  • T32 AI100853/AI/NIAID NIH HHS/United States

  • F30 CA189514/CA/NCI NIH HHS/United States

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