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Transcriptomic studies of mouse naïve and Th17 cell from wildtype or DDX5 deficient background [RNA-seq]

ABSTRACT: Transcriptomic studies of mouse naïve and Th17 cell from wildtype or DDX5 deficient background [RNA-seq]

PROVIDER: PRJNA661773 | ENA |

REPOSITORIES: ENA

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Transcriptomic studies of mouse naïve and Th17 cell from wildtype or DDX5 deficient background [RNA-seq]

Project description:Gene expression in naïve and Th17 cell were characterized. We report a notable dynamic change in the expression of genes encoding RNA editing enzymes. Birefly, the transcript encoding ADAR2 (Adarb1) was significantly upregulated in Th17 cells, and the transcript encoding ADAR1 (Adar) was downregulated during the polarization from naive to Th17 cells. The altered expression of RNA editing genes results in the dynamic A-to-I editing in naive and Th17 cells. In addtion, loss of DDX5 dysregulated ADAR2 expression, resulting in altered A-to-I editing on a subset of Th17 transcripts.

2024-12-31 | GSE157578 | GEO

Transcriptomic studies of mouse naïve and Th17 cell from wildtype or Malat1 deficient background

Project description:Transcriptomic studies of mouse naïve and Th17 cell from wildtype or Malat1 deficient background

| PRJNA787542 | ENA

Transcriptomic studies of mouse naïve and Th17 cell from wildtype or Malat1 deficient background

Project description:Long non-coding RNAs (lncRNAs) are critical regulators of mammalian gene programs. Metastasis Associated Lung Adenocarcinoma Transcript 1 (Malat1) is the most abundant lncRNA expressed in intestinal Th17 cells critical for maintaining tissue homeostasis and regulating local inflammation. Here, we report that Malat1 negatively regulates IL-17A and IL-17F productions in intestinal Th17 cells during colitis and contributes to local inflammation. Global RNA interactions with DNA by deep sequencing (GRID-seq) coupled with transcriptomic studies revealed Malat1 is recruited to the Il17a-Il17f super enhancer in Th17 cells, and regulates Il17a-Il17f transcription.

2024-12-31 | GSE190561 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of RNAs bound by DDX5 and RORgt in cultured T helper 17 cell [RIP-seq]

Project description: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: BurrowsâWheeler Aligner (BWA) and TopHat followed by CuffDiff. qRTâPCR 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. 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

2015-12-21 | E-GEOD-70109 | biostudies-arrayexpress

Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type, DDX5 knockout, RORc knockout, RmrpG262T knockin T helper 17 cell Transcriptomes [RNA-seq]

Project 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: BurrowsâWheeler Aligner (BWA) and TopHat followed by CuffDiff. qRTâPCR 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 RORÎ³t targets in Th17 cells. 96 RORÎ³t-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 RORÎ³t transcriptional targets in Th17 cells. mRNA profiles of 96hr in vitro cultured Th17 from wild type (WT) and mutant mice were generated by deep sequencing using Illumina RapidRun.

2015-12-21 | E-GEOD-70108 | biostudies-arrayexpress

GRID-seq studies of mouse naïve and culture Th17 cells from wildtype mice

2024-12-31 | GSE190560 | GEO

GRID-seq studies of mouse naïve and culture Th17 cells from wildtype mice

Project description:GRID-seq studies of mouse naïve and culture Th17 cells from wildtype mice

| PRJNA787543 | ENA

Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type, DDX5 knockout, RORc knockout, RmrpG262T knockin T helper 17 cell Transcriptomes [RNA-seq]

Project 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.

2015-12-21 | GSE70108 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of RNAs bound by DDX5 and RORgt in cultured T helper 17 cell [ChIRP-Seq]

Project description: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.

2015-12-21 | GSE73912 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of RNAs bound by DDX5 and RORgt in cultured T helper 17 cell [RIP-seq]

Project description: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.

2015-12-21 | GSE70109 | GEO

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