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PROVIDER: PRJNA820468 | ENA |
REPOSITORIES: ENA
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Project description:The objective of the study was to examine the gene expression changes in glioma cell line U87 and U251 with LAMP2A knockdown. There were 15 samples in total- U87-1, U87-2, U87-3, U87-1812-1, U87-1812-2, U87-1812-3, U251-1, U251-2, U251-3, U251-1812-1, U251-1812-2, U251-1812-3, U251-1813-1, U251-1813-2, and U251-1813-3. U87-1 to U87-3 and U251--1 to U251-3 were used as the control groups (CON). U87-1812-1 to U871812-3, U251-1812-1 to U251-1812-3, and U251-1813-1 to U251-1813-3 were used as the experimental groups (shLAMP2A-1 and shLAMP2A-2). The total RNA of each sample was extracted from the stable transfected glioma cells by using TRIzol reagent. Then the RNA samples were processed for high throughput transcriptome sequencing on Illumina HiSeq 3000 platform. There were two types of libraries: the circRNA, mRNA, and lncRNA were all constructed by removing rRNA (one library, three types of RNA were analyzed together), and the insert fragment was about 300bp; the small RNA was constructed and analyzed separately, mainly microRNA of about 22bp. Results: among 60612 cleaned mRNAs, 781 were differentially expressed in U87-1812 group compared with U87 group, 146 were differentially expressed in U251-1812 group compared with U251 group, 43 were differentially expressed in U251-1813 group compared with U251 group (padj ≤ 0.05 and expression change ≥2 fold). The differential expressed genes distributed in all chromosomes. Functional annotation with GO and KEGG enrichment revealed the top functional groups including inflammation, DNA replication, cell adhesion, TNF, IL17, and axon guidance signaling pathways.
2024-07-15 | GSE270618 | GEO
Project description:The genes that are differentially expressed in ADAR3 expressing cells compared to control U87 cells were identified.
2022-03-20 | GSE198547 | GEO
Project description:Study on differentially expressed genes in the WT1 overexpressed group and the control group by RNA-seq
| PRJNA598831 | ENA
Project description:Enforced expression of miRNAs in cells leads to down-regulation of several mRNAs, which harbour binding sites in their 3'UTRs for the overexpressed miRNA and represent potential target genes of the miRNA We transfected unedited miR-376a* (376a*A) and edited miR-376a* (376a*G) into U87 cells to identify transcripts down-regulated by each in comparison to control miRNA transfection. The aim was to identify target genes directly subject to regulation by miR-376a*A and by miR-376a*G U87 cells (100,000) were transfected with 50 nM of miR-376a*A, miR-376a*G or miR-control. Following incubation for 24 hours, total RNA was isolated from transfected cells. For each (miR-376a*A or miR-376a*G), genes differentially expressed upon miRNA transfection were determined based on comparison with miR-control-transfected samples. Biological triplicates were used for each sample type.
2012-05-31 | E-GEOD-34455 | biostudies-arrayexpress
Project description:High-throughput sequencing identified differentially expressed RNAs between MALAT1 knockdown C3H10 adipocyte and control cells
| PRJNA658520 | ENA
Project description:PD-L1 Inhibitor Regulates the miR-33a-5p/PTEN Signaling Pathway and Can Be Targeted to Sensitize Glioblastomas to Radiation. Glioblastoma (GBM) is the most common and lethal brain tumor in adults. Ionizing radiation (IR) is a standard treatment for GBM patients and results in DNA damage. However, the clinical efficacy of IR is limited due to therapeutic resistance. The programmed death ligand 1 (PD-L1) blockade has a shown the potential to increase the efficacy of radiotherapy by inhibiting DNA damage and repair responses. The miR-33a-5p is an essential microRNA that promotes GBM growth and self-renewal. In this study, we investigated whether a PD-L1 inhibitor (a small molecule inhibitor) exerted radio-sensitive effects to impart an anti-tumor function in GBM cells by modulating miR-33a-5p. U87 MG cells and U251 cells were pretreated with PD-L1 inhibitor. The PD-L1 inhibitor-induced radio-sensitivity in these cells was assessed by assaying cellular apoptosis, clonogenic survival assays, and migration. TargetScan and luciferase assay showed that miR-33a-5p targeted the phosphatase and tensin homolog (PTEN) 3' untranslated region. The expression level of PTEN was measured by western blotting, and was also silenced using small interfering RNAs. The levels of DNA damage following radiation was measured by the presence of γ-H2AX foci, cell cycle, and the mRNA of the DNA damage-related genes, BRCA1, NBS1, RAD50, and MRE11. Our results demonstrated that the PD-L1 inhibitor significantly decreased the expression of the target gene, miR-33a-5p. In addition, pretreatment of U87 MG and U251 cells with the PD-L1 inhibitor increased radio-sensitivity, as indicated by increased apoptosis, while decreased survival and migration of GBM cells. Mir-33a-5p overexpression or silencing PTEN in U87 MG and U251 cells significantly attenuated PD-L1 radiosensitive effect. Additionally, PD-L1 inhibitor treatment suppressed the expression of the DNA damage response-related genes, BRCA1, NBS1, RAD50, and MRE11. Our results demonstrated a novel role for the PD-L1 inhibitor in inducing radio- sensitivity in GBM cells, where inhibiting miR-33a-5p, leading to PTEN activated, and inducing DNA damage was crucial for antitumor immunotherapies to treat GBM.
2020-04-21 | E-MTAB-9007 | biostudies-arrayexpress
Project description:Whole gene methylation profiles of U87 and U251 glioma cells before and after artesunate treatment, Infinium MethylationEPIC BeadChip, samples including 3 U87 cell normal group, 3 U251 cell normal group, 3 artesunate treated U87 cell group, U251 cell group was treated with 3 artesunate.
2022-10-18 | GSE215784 | GEO
Project description:This study aimed to investigate the microRNA expression profile of mechnically strained human periodontal ligament-derived stem cells, and SurePrint G3 Human v16 miRNA Array (Agilent) was employed as a screening platform. We discovered 39 differentially expressed microRNAs between the stretched and the static control group.
2014-09-28 | GSE41337 | GEO
Project description:Purpose: The aim was to find the differentially expressed genes between the WT1 overexpressed group and the control group Methods:Hacat cell was transfected with WT1 overexpressed plasmids and blank plasmids, then RNA from both groups of cells was sequenced. The data obtained from the sequencing is called raw reads, and then the raw reads are subject to quality control QC. After the quality control is passed, the filtered clean reads are compared to the reference genome, This was followed by gene Quantitative analysis, gene expression level based analyses, and more in depth mining analyses such as GO functional significance enrichment analysis and pathway significance enrichment analysis for the selected differentially expressed genes between samples. Conclusions:Our study was the first to analyze the transcriptome of Hacat cells overexpressing WT1 generated by RNA-seq technique and to conduct biological replication. Six samples were measured using BGISEQ-500 platform, and the average output of each sample was 21.89 m. The average ratio of sample to genome was 94.81% . A total of 17,693 genes were detected. A total of 181 differentially expressed genes between the two groups were analyzed by GO and Kegg.
2023-01-03 | GSE142985 | GEO