Ontology highlight
ABSTRACT:
PROVIDER: PRJNA726719 | ENA |
REPOSITORIES: ENA
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Project description:Purpose: The RF/6A chorioretinal cell line originally isolated from a fetal rhesus macaque in 1968 is widely used to model human retinal and choroidal endothelial cells in cell culture. We sought to determine the extent to which this line possesses endothelial cell-specific characteristics. Methods: RF/6A cells obtained from American Type Culture Collection were subjected to next-generation RNA sequencing. Transcriptomic-based cell type profiling was conducted using xCell. Validation of endothelial cell-specific marker expression was conducted by qRT-PCR and western blotting. Functional assays of acetylated low density lipoprotein uptake, TNF-?-induced adhesion molecule expression, shear stress alignment, and endothelial tube formation were assessed. Results: RF/6A transcriptomic profiles obtained de novo or from a publically available repository did not correspond to endothelial gene expression signatures. Expression of established endothelial markers (PECAM1, CDH5, KDR, VWF, ICAM2, ENG, or TEK) were very low or undetectable in RF/6A compared to primary human umbilical vein endothelial cells. Compared to primary endothelial cells, RF/6A were unable to uptake acetylated LDL, exhibit induction of E-selectin in response to TNF-? treatment, align in the direction of shear stress, or form regular capillary-like tubes in Matrigel. Conclusions: RF/6A do not exhibit key endothelial cell characteristics or behaviors. Therefore, caution should be employed in designing and interpreting studies using these cells as surrogates for choroidal or retinal endothelial cells.
2018-12-06 | GSE113674 | GEO
Project description:HCC cell line, Huh-7 cells and HCC-LM3 cells, was transfected with sh-WDR4-2 or sh-NC for 48hr to knockdown WDR4 expression, and check the downstream mRNA changes.
2021-07-07 | GSE169394 | GEO
Project description:RF/6A Chorioretinal Cells do not Display Key Endothelial Phenotypes
| PRJNA453564 | ENA
Project description:Endothelial cell is the major cell type that senses and transduces mechanosignal generated by shear stress. We have recently shown that Hippo/YAP pathway is a mechanosensitive pathway that is critical for maintaining endothelial cell homeostasis. However, the transcritpional targets and biological functions of YAP in endothelial cells remain largely unknown. To evaluate YAP-dependent gene expression in endothelial cells, we performed RNA-sequencing in YAP depleted (by transfection with by YAP siRNA) and overexpressed (by infection with YAP-S127A catalytically active adenovirus) human endothelial cells. We observed that YAP critically regulates endothelial function by modulating multiple atherosclerosis-related genes. Our study provides mechanistic insights into the question how YAP regulates endothelial function and atherosclerosis by modulating endothelial transcriptional profile.
2017-10-03 | GSE87554 | GEO
Project description:Age-related macular degeneration (AMD) is a common, blinding disease of the elderly in which macular photoreceptor cells, retinal pigment epithelium, and choriocapillaris endothelial cells ultimately degenerate. Recent studies have found that degeneration of the choriocapillaris occurs early in this disease and that this endothelial cell dropout is concomitant with increased deposition of the complement membrane attack complex (MAC) at the choroidal endothelium. However, the impact of MAC injury to choroidal endothelial cells is poorly understood. To model this event in vitro, and to study the downstream consequences of MAC injury, endothelial cells were exposed to complement from human serum, compared to heat inactivated serum which lacks complement components. Cells exposed to complement components in human serum showed increased labeling with antibodies directed against the MAC, time and dose dependent cell death as assessed by lactate dehydrogenase assay, and increased permeability. RNA-Seq analysis following complement injury revealed increased expression of genes associated with angiogenesis including matrix metalloproteases (MMPs) 3 and 9, and VEGF-A. The MAC-induced increase in MMP9 RNA expression was validated using C5 depleted serum compared to C5 reconstitited serum. Increased levels of MMP9 were also determined using Western blot and zymography. These data suggest that, in addition to cell lysis, complement attack on choroidal endothelial cells promotes an angiogenic phenotype in surviving cells. RNA-Seq of RF/6A (cultured choroidal endothelial cells from Rhesus macaque) treated with either 50% heat-inactivated human serum ([CONTROL], n=3) or 50% normal human serum (active complement membrane attack complex [MAC], n=3)
2015-11-04 | E-GEOD-70806 | biostudies-arrayexpress
Project description:Label-Free Quantitation of Differentially Expressed Proteins in Sh-QKI6 and sh-NC
2022-06-09 | PXD027013 | Pride
Project description:We report the transcriptome sequencing results of the mouse mastocytoma cell line P815. After ESR1-specific shRNA vectors (SH) or the negative control vectors (NC) were transfected, the transcriptome in P815 after estrogen stimulation. We also detected the transcriptome of P815 cells after estrogen stimulation with the administration of estrogen receptor inhibitors Tamoxifen and ICI-182780.
2021-09-14 | GSE181773 | GEO
Project description:Osteosarcoma (OS) is one of the leading causes of cancer mortality in children and teenagers. Patients with OS have been shown to have a poor prognosis and may suffer from potential distant metastasis. Emerging evidence has revealed that circular RNAs (circRNAs) are involved in OS progression. In this paper, we aim to explore the function of hsa_circ_0000073 in the progression of OS. OS cells transfected with sh‐NC or sh-circ_0000073 were enrolled in this study.We used microarray analysis to identify the mRNA expression in the cells.
2021-08-24 | GSE176373 | GEO
Project description:Total RNA was extracted from HepG2 cells with sh-NC (n = 3) or sh-LINC01977 (n = 3). RNA samples were analyzed by RNA sequencing based on the manufacturer’s protocols. Briefly, Illumina HiSeq 4000 platform was used to sequence the RNA samples for the subsequent generation of raw data. R package was utilized to select genes with significantly differential expression based on fold change ≥2.0 and P≤0.05 between sh-NC and sh-LINC01977 cells. KEGG pathway and GSEA enrichment analysis were used for functional pathway analysis.
2023-05-24 | GSE227449 | GEO
Project description:We report the application of size selection of small RNA species isolated from Jjhan cells harboring the human herpesvirus 6A genome. We ammassed >3.4million reads of sequence from three different sources: Normal Brain cell total RNA, Jjhan total RNA and HHV-6A BAC transfected Jjhan total RNA. Sequences were mapped to the HHV-6A Uganda 1102 strain genome (GenBank: X83413.1) with no less than 100% match for reads >20nt and <23nt. The resulting pool of candidates was mapped to the HHV-6A genome.
2015-01-09 | GSE62233 | GEO