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Series GSE73912 Query DataSets for GSE73912
Status Public on Dec 21, 2015
Title Next Generation Sequencing Facilitates Quantitative Analysis of RNAs bound by DDX5 and RORgt in cultured T helper 17 cell [ChIRP-Seq]
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Purpose: The goals of this study are to compare RNAs bound by DDX5 and RORgt in cultured T helper 17 cell in wildtype background.
Methods: Th17 mRNA profiles of 48hrs in vitro cultured T helper 17 cells from wild-type mice were generated by deep sequencing, using Illumina HighSeq. 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 3444 RefSeq non-coding RNAs and 46449 NONCODE non-coding RNAs, 2533 were found to be expressed in Th17 cells (FPKM>1). 210 of them were enriched in DDX5 pull-down and 119 of them were enriched in RORgt pull-down.
Conclusions: Our study suggest that a subset of 31 ncRNAs were co-enriched in DDX5 and RORgt pull-down.
Overall design DDX5 or RORgt-associated-RNA profiles of 48hr in vitro cultured Th17 from wild type (WT) mice were generated by deep sequencing using Illumina HighSeq
Contributor(s) Huang W, Littman DR
Citation(s) 26675721
Submission date Oct 11, 2015
Last update date May 15, 2019
Contact name Wendy Huang
Organization name NYU School of Medicine
Lab Littman Lab
Street address 540 First Ave Skirball 2-14
City New York
ZIP/Postal code 10016
Country USA
Platforms (1)
GPL19057 Illumina NextSeq 500 (Mus musculus)
Samples (9)
GSM1905753 Th17_ChIRP_RMRP_RM262_Even
GSM1905754 Th17_ChIRP_RMRP_RM262_Input
GSM1905755 Th17_ChIRP_RMRP_RM262_Odd
This SubSeries is part of SuperSeries:
GSE70110 DDX5 and its associated lncRNA Rmrp modulate Th17 cell effector functions
BioProject PRJNA298543
SRA SRP064770

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Supplementary file Size Download File type/resource
GSE73912_RMRP_ChIRPseq_DDX5ko_overlapPeaks.bed.gz 25.7 Kb (ftp)(http) BED
GSE73912_RMRP_ChIRPseq_RM262_overlapPeaks.bed.gz 52.8 Kb (ftp)(http) BED
GSE73912_RMRP_ChIRPseq_WT_overlapPeaks.bed.gz 60.7 Kb (ftp)(http) BED 88.6 Mb (ftp)(http) BW 374.0 Mb (ftp)(http) BW 54.4 Mb (ftp)(http) BW 36.4 Mb (ftp)(http) BW 230.4 Mb (ftp)(http) BW 276.6 Mb (ftp)(http) BW
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Raw data are available in SRA

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