RNA-seq of YAP's role in hDPCs
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE148287 | GEO | 2023/04/08
REPOSITORIES: GEO
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Project description:We report the application of RNA sequencing technology for high-throughput profiling of gene expression in YAP2SA-lentivirus-infected adult human dental pulp stromal cells (hDPCs).To overexpress YAP2SA in hDPCs we transfected cells with YAP2SA-lentivirus. Cells were derived from a 18~22-year-old healthy male human donor. Total mRNA was collected using TRIzol ® (Invitrogen, CA, USA) solution. Then all the extraction procedures were conducted according to manufacture’s instructions for RNA extraction from homogenized tissues. After quality checks they were subjected to the high-throughput RNA-sequencing. Every group consists of 3 replicates which were from 3 independent experimental repeats.
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2022-10-10 | GSE145960 | GEO
Project description:YAP knockdown in HUVEC elicits proliferation and cell cycle preogression defects. YAP deficient cells caused arrest in G1 and defects in S-phase entry. The microarray analysis was conducted to identify potential YAP targets that are involved in HUVEC cell cycle regulation mRNA samples were collected from siRNA treated HUVECs 30 hour after transfection. Four biological replicates were used for each condition: control (RISC-free) and knockdown (siYAP#1 and siYAP#2)
2014-10-17 | E-GEOD-61989 | biostudies-arrayexpress
Project description:We report the application of RNA sequencing technology for high-throughput profiling of gene expression in Wnt7b overexpressing bone and wide-type bones.To increase Wnt7b in bone we crossed 9.6kb DMP1-Cre mice and R26-Wnt7b mice. 9.6kb DMP1-Cre; R26-Wnt7b mice were set as OE mice meanwhile their littermates of R26-Wnt7b were controls (Ctrl). Owing to heterozygotes and homozygotes of OE mice didn’t show any different phenotypes all OE mice used in this study were homozygotes. Total mRNA of femur was collected from 8-week-old OE and Ctrl mice respectively. Fresh femur samples without soft tissues were rapidly collected within 2 min after euthanasia. And then samples were immediately transported into a sterile 10cm culture dish containing cold PBS, followed with articular cartilage removal via sterile lancets within 5 min, being flushed 3 times using sterile cold PBS to remove marrow cells and being chopped into 2~5mm fragments using sterile scissors. About 200mg bone fragments were collected into a sterile mortal containing 1ml liquid nitrogen and then were crushed and homogenized using a sterile pestle within 5 min, followed by a sterile scalpel until the tissue was adequately homogenized. Homogenized samples were collected into a 2-ml sterile tube, followed with 1 ml TRIzol ® (Invitrogen, CA, USA) solution added. Then all the extraction procedures were conducted according to manufacture’s instructions for RNA extraction from homogenized tissues. After quality checks they were subjected to the high-throughput RNA-sequencing. Every group consists of 3 replicates which were from 3 different mice.
2020-12-06 | GSE116628 | GEO
Project description:Purpose: To compare the transcriptional changes of genes in dental pulp tissues with different degrees of inflammatory severity and investigate the role of RAD54B in inflamed human dental pulp cells (hDPCs) Methods: Normal, carious, and pulpitis human dental pulp tissues were collected. Total RNA extracted were subjected to RNA-sequencing and gene expression profiles were further studied by Gene Ontology (GO) and KEGG pathway analysis. DEGs (differentially expressed genes) in homologous recombination repair (HRR) were validated with qRT-PCR. The expression of RAD54B and TNF-α in human dental pulp tissues was detected by immunohistochemistry. HDPCs were cultured and RAD54B level in hDPCs was detected after LPS stimulation using western blot. CCK-8 was applied to investigate the cell proliferation of hDPCs transfected with negative control (Nc) small interfering RNA (siRNA), RAD54B siRNA, P53 siRNA or both siRNAs with or without LPS stimulation. Flow cytometry was applied to detect the cell cycle distribution, and western blot and immunofluorescence were utilized to analyze the expression of RAD54B, P53 and P21 under the above treatments. One-way and two-way ANOVA followed by LSD posttest were used for statistical analysis. Results: RNA-sequencing results identified DEGs among three groups. KEGG pathway analysis revealed enrichment of DEGs in Replication and Repair pathway. HRR and non-homologous end joining (NHEJ) components were further verified and qRT-PCR results were basically consistent with the sequencing data. RAD54B, a HRR accessory factor highly expressed in carious and pulpitis tissues compared to normal pulp, was chosen as our gene of interest. High RAD54B expression was confirmed in inflamed human dental pulp tissues and LPS-stimulated hDPCs. Upon RAD54B knockdown, P53 and P21 expressions in hDPCs were upregulated whereas the cell proliferation was significantly downregulated, accompanied with increased G2/M phase arrest. After inhibiting P53 expression in RAD54B-knockdown hDPCs, P21 expression and cell proliferation were reversed. Conclusions: Gene expression profiles of normal, carious and pulpitis human dental pulp tissues were revealed. HRR components was elucidated to function in dental pulp inflammation. Among HRR DEGs, RAD54B could regulate the cell proliferation of inflamed hDPCs via P53/P21 signaling. This research not only deepens our understanding of dental pulp inflammation but also provides a new insight to clarify the underlying mechanisms.
2023-09-02 | GSE198359 | GEO
Project description:Purpose: To investigate the signal crosstalk between IRF3 and YAP, RNA-sequencing (RNA-seq) was performed to analyze the genome-wide changes by the knockdown of IRF3 or YAP in HGC-27 cells. Methods: Total RNA was extracted from HGC-27 cell after transfection with negative control siRNA (n.c.), IRF3 siRNA (siIRF3) or YAP siRNA (siYAP). Then total RNA was quality controlled and quantified using an Agilent 2100 Bioanalyzer. After converting to cDNA and building library, high-throughput sequencing was performed using the Illumina HiSeq 2500 platform. Results: Approximately one thousand transcripts showed differential expression between the siIRF3/siYAP and n.c., with a Fold-change>=2 and q-value <= 0.05. Gene ontology (GO) and gene set enrichment analysis (GSEA) showed a significant negative enrichment of YAP target genes identified by three independent studies in IRF3-knockdown condition. Conclusions: We conclude that RNA-seq based transcriptome characterization would provide a framework for understanding the signal crosstalk between IRF3 and YAP.
2018-08-01 | GSE102112 | GEO
Project description:Purpose: To investigate the signal crosstalk between IRF3 and YAP, RNA-sequencing (RNA-seq) was performed to analyze the genome-wide changes by the knockdown of IRF3 or YAP in HGC-27 cells. Methods: Total RNA was extracted from HGC-27 cell after transfection with negative control siRNA (n.c.), IRF3 siRNA (siIRF3) or YAP siRNA (siYAP). Then total RNA was quality controlled and quantified using an Agilent 2100 Bioanalyzer. After converting to cDNA and building library, high-throughput sequencing was performed using the Illumina HiSeq 2500 platform. Results: Approximately approximately one thousand transcripts showed differential expression between the siIRF3/siYAP and n.c., with a Fold-change>=2 and q-value <= 0.05. Gene ontology (GO) and gene set enrichment analysis (GSEA) showed a significant negative enrichment of YAP target genes identified by three independent studies in IRF3-knockdown condition. Conclusions: We conclude that RNA-seq based transcriptome characterization would provide a framework for understanding the signal crosstalk between IRF3 and YAP.
2018-01-10 | GSE109028 | GEO
Project description:We found that heat stress induces a strong and rapid YAP dephosphorylation and activation. To determin what is the physiological functions of YAP in response to heat stress, we performed RNA-SEQ analysis on siCon and siYAP/TAZ knockdown tumor cells with or without heat shock. Results indicated that 95% of heat inducible genes is blocked (83% completely and 12% partially) by YAP/TAZ knockdown in the B16-OVA melanoma cells whereas only 5% of heat inducible genes were unaffected, supporting a previously unrecognized prominent role of YAP/TAZ in the expression of the heat shock transcriptome and cell survival.
2020-09-05 | GSE133251 | GEO
Project description:To investigate the role of YAP/TAZ as b-catenin inhibitors, we compared the expression profiles of Rex1GFPd2 ES cells transfected with siControl#1, siControl#2, siYAP/TAZ#1, siYAP/TAZ#2 and cultured in 2i medium or PD-only medium
2014-06-26 | GSE55622 | GEO
Project description:Human dental pulp cells (hDPCs) are one of the promising resources for regenerative medicine and tissue engineering, including derivation of induced pluripotent stem cells (iPSCs). However, our current protocol uses reagents of animal origin, mainly fetal bovine serum (FBS) with potential risk of infectious diseases and unwanted immunogenicity. This time, we designed a chemically defined protocol to isolate and maintain the growth and differentiation potentials of hDPCs.
2014-12-25 | GSE59493 | GEO