Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1125111 | ENA |
REPOSITORIES: ENA
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Project description:Muscle larva of a parasitic nematode Trichinella spp. lives a portion of muscle fiber transformed to a nurse cell (NC). The NC is formed from miss-differentiated muscle satellite cells which have fused with a parasite-invaded degenerating myofiber. Though originating from muscle cells, the NC is of non-muscular type.The NC is multinuclear and hypertrophic. Molecular mechanism of the NC development remains largely unknown. The microarray project was aimed at characterization of the NC transcriptome. The NCs were isolated by enzymatic digestion from infected mouse striated muscles. Murine C2C12 myogenic cell line (ATCC) was cultured in vitro. Differentiation of myoblasts into myotubes was carried out for 6 days in a high-glucose DMEM supplemented with 2% heat-inactivated horse serum, on the plates covered with laminin and collagen IV.The NC transcriptome was referred to the transcriptomes of C2C12 myoblasts and C2C12 myotubes in two sets of camparative expression microarray hybridization experiments, NC vs myoblasts and NC vs myotubes, respectively.
2022-07-26 | E-MTAB-12042 | biostudies-arrayexpress
Project description:CircRNA-sequencing in HBx-overexpressing (HBx-oe) and NC (negative control) HepG2 cells
2022-10-18 | GSE215232 | GEO
Project description:We evaluate the effects of CNN3 on myogenesis and further explored its potential molecular mechanisms. C2C12 cells were transfected with siRNA CNN3 and its NC control siRNA. Total mRNA was extracted from cells using TRIZOL reagent in accordance with the manufacturer’ protocol. And transcriptomes of CNN3 gene silenced C2C12 cells was detected by RNA-Seq.
2021-06-01 | GSE164407 | GEO
Project description:Metastatic melanoma is the most aggressive skin cancer and associated with a poor prognosis. Targeted therapy is one of the most important treatments for patients with BRAFV600E-mutated advanced melanoma. However, the development of resistance to this treatment compromises its therapeutic success. Increasing evidence has indicated that NC-associated genes play important roles in tumor progress and drug resistance. Our previous study showed that FOXD1 is a neural crest (NC)-associated gene that has high expression levels both in NC cells and melanoma and that it could regulate melanoma migration and invasion. Here, we found that the FOXD1-CTGF axis is important for melanoma resistance. The connective tissue growth factor (CTGF) was identified as a direct downstream factor of FOXD1 using microarray assay. In detail, when we compared the microarray data from FOXD1 OE and control groups, we found that the expression level of CTGF was also higher in FOXD1 OE cells (FC=1.97).
2021-03-29 | GSE162973 | GEO
Project description:NCI-H446 control (NC) and MTA1-overexpressing (OE) cells
| PRJNA579765 | ENA
Project description:In order to investigate the role of FOXA2 in the occurrence and development, we infected gallbladder cancer cells with recombinant lentivirus to construct FOXA2 overexpression SGC-996. We then performed gene expression profiling analysis using data obtained from RNA-seq of 6 different gallbladder cancer cells from SGC-996-NC or SGC-996-OE groups.
2023-09-29 | GSE239351 | GEO
Project description:In the current study, to figure out the regulation pattern of TfR1, we knocked down TFRC expression level by shRNA in HeLa cells. RNA-sequencing (RNA-seq) was used to analyze the global transcript level and alternative splicing (AS) on knockdown-treated (KD) and normal control (NC) cell samples. 629 differentially expressed genes (DEGs) were identified between OE and NC, and Gene ontology (GO) and KEGG analysis for DEGs were carried out. It was found that multiple DEGs were involved in O-glycan processing, protein modification, response to hypoxia and ATP catabolic process, indicating the down-regulated expression of TfR1 extensively disturbed cell physiology.
2022-05-08 | GSE131598 | GEO
Project description:The transferrin receptor 1 (TfR1), encoded by TFRC gene, is the gatekeeper of cellular iron uptake for cells. A variety of molecular mechanisms are at work to tightly regulate TfR1 expression, and abnormal TfR1 expression was associated with diseases. In the current study, to figure out the regulation pattern of TfR1, we cloned and overexpressed human TFRC gene in HeLa cells. RNA-sequencing (RNA-seq) was used to analyze the global transcript level on overexpression-treated (OE) and normal control (NC) cell samples. 1669 differentially expressed genes (DEGs) were identified between OE and NC, and Gene ontology (GO) analysis for DEGs were carried out. It was found that lots of DEGs were associated with ion transmembrane transport and immunity. Moreover, the network was constructed on basis of DEGs regulating ion transport and immunity, the results revealed that TFRC was the node gene of the network, further suggesting that precisely controlled TfR1 expression might be not only essential for iron homeostasis, but also globally important for cell physiology, including ion transport and immunity.
2021-08-27 | GSE130048 | GEO
Project description:In this study, we used ChIP-seq to map Six4 binding profile in different C2C12 cell lines 24 hours after differentiation (T24). We performed ChIP-seq using two different antibodies: anti-Flag antibody in Flag-Six4 C2C12 cell line or in parental C2C12 cells; a custom-made anti-Six4 antibody in shNS C2C12 cell line (a control cell line) or shSix4 C2C12 (C2C12 with stable Six4 knockdown using short hairpin RNA). We also performed ChIP-seq in parental C2C12 cells using normal rabbit IgG. We were able to identify Six4-bound loci in C2C12 T24 that were recognized by two different antibodies and showed a decrease in peak intensity in shSix4 C2C12 compared to shNS C2C12 cells. We established a C2C12 cell line with stable Six4 knockdown by short hairpin RNA (shSix4) vs. a control cell line (shNS). We also established a C2C12 cell line with stable expression of Flag-Six4-myc by infection of retroviruses expressing pBABE-Flag-Six4-myc (Flag-Six4 C2C12) vs. parental C2C12. We differentiate these cells for 24 hours before using them for ChIP-seq.
2015-12-31 | E-GEOD-66901 | biostudies-arrayexpress