Dataset Information

Brd4 regulates the homeostasis of CD8+ T-lymphocytes and their proliferation in response to antigen stimulation [RNA-seq]

ABSTRACT: Purpose: The goals of this study are to compare the differentially expressed genes between in wild type and Brd4-/- CD8+T cells. Methods: RNA extracted from wild type and Brd4-/- CD8+T cells was used to generate RNA-seq library，followed by sequencing. Results: In naïve CD8+T cells, Brd4 deletion casued 956 downregulated genes and 841 upregulated genes. In in vitro-activated CD8+T cells（18hr），Brd4 deletion resulted in 1182 downregulated genes and 789 upregulated genes. Importantly，we noticed that Brd4 is required for the migration- and glucose-related genes. expression Conclusions: Our study represents the first detailed analysis of transcriptomes in wild type and Brd4-/- CD8+T cells. Our results show that Brd4 deletion resulted in more downregulated genes exceeding the upregulated genes and the downregulation of many migration- and glucose-ralated genes. We conclude that Brd4-mediated gene expresssion program promotes glucose metabolism and cell migartion.

ORGANISM(S): Mus musculus

PROVIDER: GSE179491 | GEO | 2021/09/15

REPOSITORIES: GEO

ACCESS DATA

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Project description:Purpose: To investigate the expression profiles of genes regulated by bHLH6, we performed RNA-seq analysis using bHLH6 OV, spx4, and wild type treated with high and low P Methods: Roots and shoots mRNA profiles of 7-day-old bHLH6 OV, spx4, and wild-type (WT) rice seedlings treated with 200 μM or 10 μM Pi for 2 weeks three biological replicates were generated by deep sequencing using the NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA). The mapped reads of each sample were assembled by Hisat2 (v2.0.5). qRT–PCR validation was performed using SYBR Green assays Results: RNA-seq data confirmed that in shoots, 4,694 genes were upregulated and 4,126 were downregulated in bHLH6 OV lines compared with wild type under high-P conditions.Among the differentially expressed genes, 1,805 (38.5%) were upregulated in wild type under low-P conditions, whereas 1,598 (38.7%) of the downregulated genes were downregulated in wild type under low-P conditions, suggesting that bHLH6 overexpression upregulates a subset of PSI genes. In total, 971 genes were upregulated and 853 genes were downregulated in spx4 compared to wild type in high-P conditions. Among these upregulated genes, 371 (38.2%) were also upregulated in shoots of bHLH6 OV plants compared to in wild type; 456 (53.4%) of the downregulated genes were also downregulated in shoots of bHLH6 OV compared with wild type. In roots, 311 (10.5%) out of the 2,969 upregulated genes in bHLH6 OV lines under high-P conditions were also upregulated in wild type under low-P conditions; 501 (19.1%) out of the 2,628 downregulated genes in bHLH6 OV were also downregulated in wild type under low-P conditions. However, 313 (60.2%) out of the 520 genes upregulated in spx4 in roots were also upregulated in bHLH6 OV lines compared to in wild type, whereas 497 (54.6%) out of 910 the downregulated genes were also downregulated in bHLH6 OV compared to in wild type. To validate the RNA-seq results, we selected the upregulated PT and PAP (PURPLE ACID PHOSPHATASE) genes for expression analysis using RT-qPCR. The expression levels of PT2, PT10, PAP10a, and PAP21b were considerably higher in roots of bHLH6 OV plants than in those of wild type and bhlh6 mutants, whereas the expression of SPX2 was much lower in bHLH6 OV plants than in wild type Conclusion: our study is the first to analyze in detail the bHLH6 transcriptome produced by rna-seq technology and perform biological replication. Our results suggest that bHLH6 mediates the regulation of Pi homeostasis by SPX4. Our results advance the current understanding of the Pi-signaling regulatory network and will potentially contribute to the genetic improvement of crop P efficiency.

Project description:To investigate the glucose regulatory system in Saccharomyces cerevisiae, we conducted a time-course in which glucose-depleted wildtype (WT) cells were inoculated into fresh media (SC, 2% glucose). Their subsequent transcriptional output was monitored over a period of five hours by DNA microarrays: samples for gene expression profiling were taken immediately after, as well as 3, 7.5, 15, 30, 60, 110, 150, and 300 minutes after inoculation into fresh medium. Transcripts upregulated are involved in translational processes such as the GO biological processes “ribosome biogenesis” and “ribosome localization”. Transcripts downregulated are enriched for the GO biological processes “cellular respiration” and various metabolism related processes. The time-course was used to verify the physiological relevance of gene expression profiles determined for individual deletions of glucose regulatory system components. Importantly, transcripts up- or downregulated in WT cells upon the addition of glucose are similarly up- or downregulated in deletion mutants that each lack a component of the glucose regulatory system. RNA isolated from a large amount of wt yeast from a single culture was used as a common reference. This common reference was used for each separate hybridization and used in the statistical analysis to obtain an average expression-profile for each deletion mutant relative to the wt. Two independent cultures were hybridized on two separate microarrays. For the first hybridization the Cy5 (red) labeled cRNA from the deletion mutant is hybridized together with the Cy3 (green) labeled cRNA from the common reference. For the replicate hybridization, the labels are swapped. Each gene is represented twice on the microarray, resulting in four measurements per mutant. Two overnight WT cultures were used to inoculate 50 ml cultures at an OD600 of 0.15. These were depleted of glucose by growing for 24 hours and were used the next day to inoculate 500 ml cultures in fresh medium to an OD600 of 0.15. Samples for expression profiling were taken immediately after, as well as 3, 7.5, 15, 30, 60, 110, 150, and 300 minutes after inoculation into fresh medium.

Dataset Information

Brd4 regulates the homeostasis of CD8+ T-lymphocytes and their proliferation in response to antigen stimulation [RNA-seq]

Dataset's files

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets