|
| 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.
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| |
|
| 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 |
| E-mail(s) |
Wendy.Huang@med.nyu.edu
|
| 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)
|
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| This SubSeries is part of SuperSeries: |
| GSE70110 |
DDX5 and its associated lncRNA Rmrp modulate Th17 cell effector functions |
|
| Relations |
| BioProject |
PRJNA298543 |
| SRA |
SRP064770 |
| 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 |
| GSE73912_Th17_ChIRP_RMRP_RM262.bw |
88.6 Mb |
(ftp)(http) |
BW |
| GSE73912_Th17_ChIRP_RMRP_RM262_Input.bw |
374.0 Mb |
(ftp)(http) |
BW |
| GSE73912_Th17_ChIRP_RMRP_WT.bw |
54.4 Mb |
(ftp)(http) |
BW |
| GSE73912_Th17_ChIRP_RMRP_WT_DDX5ko.bw |
36.4 Mb |
(ftp)(http) |
BW |
| GSE73912_Th17_ChIRP_RMRP_WT_DDX5ko_Input.bw |
230.4 Mb |
(ftp)(http) |
BW |
| GSE73912_Th17_ChIRP_RMRP_WT_Input.bw |
276.6 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Processed data are available on Series record |
| Raw data are available in SRA |
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