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Next Generation Sequencing Analysis of human primary airway smooth muscle cells treated with IL17A or DEX or both combined.

ABSTRACT: Purpose: The goals of this study is to identify IL17A-induced transcripts differentially regulated by DEX in hASMCs. Methods:Primary hASMCs were treated for 4 hours with IL17A or DEX or both combined. mRNA profiles were generated by deep sequencing using Illumina GAIIx. Each treatment has 3 biological replicates. Results: Using an optimized data analysis workflow, we mapped about 40 million sequence reads per sample (>97% clean reads) to the human genome (build mm9) and identified 48,162 transcripts in hASMC samples. Conclusions: Our study showed that DEX regulated IL17A targt genes in both synergistic and suppressive manner in hASMCs. This is the first detailed analysis of transcriptoms of hASMCs in response to IL17A and DEX.

ORGANISM(S): Homo sapiens

PROVIDER: GSE135730 | GEO | 2020/04/06

REPOSITORIES: GEO

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Project description:Purpose: The goals of this study are screening the putative target genes regulated by OsNF-YA5 using DEX(dexamethason) inducible system. Methods: 10-day-old GOS2::OsNF-YA5-GR plants grown on MS solid media were treated with 50 μM dexamethasone (DEX) solution containing 0.02% (w/v) Silwet L-77. For mock treatments, 0.02% Silwet L-77 was sprayed into rice plants. To minimize the effect by the treatment, plants were pre-treated with 0.02% Silwet L-77 3 hours before DEX treatment). Total RNAs were extracted using the RNeasy plant mini kit (Qiagen, USA) according to the manufacturer’s instruction. cDNA libraries were prepared using the TruSeq RNA Sample Prep kit (v2) (Macrogen, Korea). Single-end sequences were obtained using IRGSP (v 1.0) and raw sequence reads were trimmed to remove adaptor sequence, and those with a quality lower than Q20 were removed using the Trimmomatic 0.32 software (Bolger et al., 2014). To map the reads to reference genome, all reads were assembled with annotated genes from the Rap-DB database [http://rapdb.dna.affrc.go.jp; IRGSP (v 1.0)] using TopHat software (https://ccb.jhu.edu/software/tophat/index.shtml). After mapping reads to a reference genome, differentially expressed genes (DEGs) were selected using a cut-off change of at least 2-fold change (DEX/mock) and Student’s t-test (P < 0.1). The selected DEGs were grouped by hierarchical clustering analysis (Complete Linkage). Results: RNA sequencing analysis revealed that 81 (3 hr DEX treatment) and 88 (9 hr DEX treatment) genes were up-regulated. In comparison, 61 (3 hr DEX treatment) and 45 (9 hr DEX treatment) genes were down-regulated in GOS2:OsNF-YA5-GR transgenic plants by DEX treatment compared to mock treatment. Among 161 up-regulated genes, 71 genes (44%) were also up-regulated in N starvation conditions. GO term analysis of up-regulated genes revealed that 59-76% of genes were involved in the metabolic process, and 10%-12% were transporter (Extended Data Fig. 4c). These results suggested that OsNF-YA5 regulated the genes involved in the metabolic process. Conclusions: OsNF-YA5 positively regulated the genes involved in the nitrogen metabolic process including amino acid and nitrate/peptide transporters.

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Next Generation Sequencing Analysis of human primary airway smooth muscle cells treated with IL17A or DEX or both combined.

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