Comparison of transcriptome profiles of human embryo cultured in either closed or standard incubator
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ABSTRACT: Measuring transcriptomic profiles of human embryos cultured in time-lapse imaging (TLI) incubator and standard incubator (SI) is crucial for studying whether the closed culture system has a positive impact on embryos. Here we used RNA-sequencing (RNA-Seq) to characterize and compare the gene expression profiles of TLI and SI cultured 8-cell embryos with the same quality grade. A total of 580,952,620 fragments were sequenced for zygote, SI and TLI groups. The global transcriptomic profiles of embryos from TLI group were similar to SI group, with a high distinct to zygotes. However, wo also detected 539 genes showing differential expression between the TLI and SI group with false discovery rate (FDR) < 0.05. Using GO enrichment analysis, we found that the high expressed genes in SI tend to execute functions, including transcription, RNA splicing and DNA repair, and the high expressed genes in TLI were enriched in the cell differentiation and methyltransferase activity pathway. This study provides the first comparison between SI and TLI via transcriptome analysis, and will serve as a basis for assessing the safety of TLI application in assisted reproductive technology.
Project description:Much research has been conducted to determine how hair regeneration is regulated, as this could provide therapeutic, cosmetic, and even psychological interventions for hair loss. The current study focused on the hair growth effect and effective utilization of fatty oil obtained from Bryde's whales through high-throughput DNA microarray approach in conjunction with immunohistochemical observations. The research also examined the mechanisms and factors involved in hair growth. In an experiment using female C57BL/6J mice, the vehicle control group (VC: propylene glycol: ethanol: water), the positive control group (MXD: 3% minoxidil), and the experimental group (WO: 20% Whale Oil) were topically applied to the back of the mouse. The results showed that 3% MXD and 20% WO were more effective than VC in promoting hair growth, especially 20% WO. Furthermore, in hematoxylin and eosin-stained skin tissue, an increase in the number of hair follicles and subcutaneous tissue thickness was observed with 20% WO. Whole-genome transcriptomic analysis also showed that 20% WO may have lower stress- and inflammation-related responses than 3% MXD. Therefore, whale oil can be expected to be used as a safe hair growth agent.
Project description:ILC3s from the spleen (SP) and small intestine (SI) have been shown to be phenotypically and functional different. Intestinal factors are likely to regulate transcriptional profiles and thereby function of ILC3s. The goal of this study is to analyze if SI ILC3s acquire a SP-similar transcriptional profile after in vitro culture. Therefore transcriptional profiles of cultured SI ILC3s were compared to freshly isolated ILC3s of the murine SP and the SI by RNA seq technology. Cell suspension were generated from both organs and ILC3s (CD117+, Thy1.2+, KLRG1-, lin- (CD3, CD8, CD11b, CD11c, CD19, B220, Gr-1, TCRβ, TCRγδ, TER-119, NK1.1)) were sort purified. SI ILC3 were cultured for 7 days in vitro with IL-2, IL-7 and SCF. RNA was isolated and RNA sequencing was done using Ilumina Hiseq 2500 system and NuGEN Ovation RNA Seq System V2, with biological replicates. We show that intestinal ILC3 acquire a splenic-similar transcriptional profile after in vitro culture.
Project description:Purpose: to find the potential down-stream target gene of circFAM120A Methods: mRNA profiles of decidualized human endometrial stromal cells (hESCs) after down-regulated FAM120A and control using siRNA were generated by NGS and compared by bioinformatics analysis Results: we sequenced 26414 mRNAs in hESCs between the si-NC and si-circFAM120A groups and identified 242 differentially expressed mRNAs, between which 161 were downregulated and 81 were up-regulated in si-circFAM120A group Conclusions: Our study represents the detailed analysis of decidualized hESCs transcriptomes between si-NC and si-circFAM120A groups.
Project description:Oral administration of Si-based agents produces large amounts of hydrogen under alkaline conditions in the intestinal tract. Hydrogen removes reactive oxygen species and reduces oxidative stress. It is also known that oxidative stress is involved in the progression of renal fibrosis. We reported that oral administration of Si- based agent suppressed renal fibrosis using UUO model. mRNA expression in Sham group, UUO group, and UUO+Si group was evaluated by RNA-seq and functional analysis, and found that fibrosis-related Gene ontology and Pathways related to fibrosis were suppressed by the Si-based agent.
Project description:To understand the role of DPPA2 in epigenetic memory during X-Chromosome reactivation (XCR) we employed inducible Xist hybrid female embryonic stem cell line (TX1072, hybrid Bl6/Cast). Wild type or Dppa2 knockout TX1072 cells were cultured, in three or two independent biological replicates, respectively, in presence of DOX (1ug/ml) for 6 days to induce Xist overexpression and X-Chomosome inactivation (XCI) on the Bl6 allele. DOX was then washed out to silence Xist and XCR was followed in a time-series at 1, 3 or 7 days after DOX removal. Cell pellets were harvested at the following timepoints: -DOX, +DOX, 1d D-wo, 3d D-wo and 7d D-wo. RNA was extracted and 250 ng used for PolyA mRNA library preparation and Next generation sequencing.
Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of transfected NC K1 cells and transfected si-NEAT1_2 K1 cells. The goals of this study are to analysis the different mRNA expression between transfected NC K1 cells and transfected si-NEAT1_2 K1 cells. Quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to evaluate protocols for optimal high-throughput data analysis. We performed mRNA-seq in the NEAT1_2 knockdown group and NC group in the K1 cell line. We found that after knockdown of NEAT1_2, 615 mRNAs were upregulated and 2364 mRNAs were downregulated.
Project description:A bovine oligo microarray platform (GPL7053) was used to evidence differences in gene expression profiles from eight (8) lymphocytes samples from prednisolone-treated cows and seven (7) from control animals at two sampling times (T1 and T2). T-test found 539 up-regulated and 368 down-regulated transcripts at T1 sampling time (31 days treatment) and 768 up-regulated and 648 down-regulated transcripts at T2 sampling time (6 days after drug withdrawal) in the prednisolone-treated animal group respect to the controls.
Project description:Primary liver cancer (PLC) is the third largest contributor to cancer mortality in the world. PLC is a heterogeneous disease that encompasses several biologically distinct subtypes including hepatocellular carcinoma (HCC), intrahepatic cholangiocarcinoma (ICC) and combined hepatocellular-cholangiocarcinoma (CHC). The cells were cultured in DMEM medium supplemented with 10% fetal bovine serum and 1% antibiotic-antimitotic solution. The HCC cell line LM3 and ICCA cell line RBE were transfected using Lipofectamine 3000 reagent following the manufacturer’s protocol and incubated for 48h for further analysis. The gene expression profiles were analyzed of LM3 and RBE cells transfected with si-FENDRR or si-NC to assess effect of FENDRR on genetic expressions of PLC.