Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA Sequencing Analyzes Chondrocyte Transcriptomes of Wild-type, miR-26a -/- and Cartilage-specific miR-23a/b clusters Knockout Mice

ABSTRACT: To reveal the potential regulation target genes of miR-26a and miR-23a/b clusters in articular chondrocytes, we performed RNA-seq using RNA samples from cultured chondrocytes, which were primarily isolated from 3-week-old wild-type, miR-26a -/- or miR-23a/b cluster flox/flox;Col2a1-cre mice. Single-read libraries were prepared and sequenced by Illumina Nextseq 500. Proteins from the same sample were extracted for LC-MS/MS analysis. After data processing, differential expressed genes were screened out for exploring potential miRNA regulation targets.

ORGANISM(S): Mus musculus

PROVIDER: GSE197363 | GEO | 2023/01/25

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Mouse Articular chondrocyte LC-MSMS of wild-type, miR-26a -/- and cartilage-specific miR-23ab clusters knockout mice

Project description:To reveal the potential regulation target genes of miR-26a and miR-23a/b clusters in articular chondrocytes, we performed a multi-omics analysis of LC-MSMS and RNA-seq using cultured chondrocytes samples, which were primarily isolated from 3-week-old wild-type, miR-26a -/- (with or without miR-26a mimic transfection afterwards) or miR-23a/b cluster flox/flox;Col2a1-cre mice. For LC-MSMS, protein from TRIZOL reagent was extracted, nanoLC-MSMS was performed. An expression list was made to further explore the regulation targets of miR-26a and miR-23a/b clusters.

2023-01-25 | PXD031868 | Pride

Discovering the miR-26a/targetome in prostate cancer cells

Project description:In this work, we showed that the re-expression of miR-26a in DU-145 prostate cancer cells restored the tumor suppressor activity of miR-26a. To discover the genes and pathways elicited by miR-26a re-expression, we used the miRNA pull out assay to capture and the Next Generation Sequencing to identify the miR-26a targets. Data showed that: i) miR-26a captured both non-coding and coding RNAs; ii) 46% of transcripts were putative miR-26a targets according to target prediction algorithms; iii) 21 pathways were significantly enriched and the “Pathway in Cancer” was among those comprising the largest number of genes, including BIRC5 that we experimentally validated. Accordingly, the detection of cell proliferation-related events showed that miR-26a exerted its tumor suppressor activity at several levels, by decreasing the survival, impairing the migration of tumor cells and by inducing both apoptosis and cell cycle block. In conclusion, we showed that the collection of miR-26a interacting transcripts (miR-26a/targetome) represented a fruitful platform to decipher the miR-26a-dependent gene expression networks. In perspective the availability of miRNA-specific and tumor-specific targetomes will allow the discovery of new druggable tumor genes and pathways.

2017-04-04 | GSE85306 | GEO

Transcription profiling by array of hMADS cells transfected with miR-26a

Project description:Human multipotent adipose-derived stem (hMADS) cells were transfected at confluence with miR-26a or miR-C (non-targeting control microRNA) and cells were harvested two days later (=d0) to identify mRNAs that are downregulated by miR-26a versus miR-C, as such mRNAs could be direct miR-26a targets.

2013-11-25 | E-MARS-28 | biostudies-arrayexpress

MiR-26a targets EphA2 to resist intracellular Listeria monocytogenes in macrophages

Project description:We performed transcriptome analyses of miR-26a-overexpressing RAW264.7 cells (RAW264.7.miR-26a.OE) and NC-plasmid-transfected RAW264.7 cells (RAW264.7.NC), using RNA-seq . We identified 121 genes that were downregulated in RAW264.7.miR-26a.OE cells compared with RAW264.7.NC cells. Among the downregulated genes, we identified four putative target genes, using TargetScan (www.targetscan.org), including EphA2, Map3k9, Nhsl1, and Otud1, which all contain a putative miR-26a seed sequence.

2022-06-01 | GSE149842 | GEO

Trastuzumab produces therapeutic actions by upregulating miR-26a and miR-30b in breast cancer cells

Project description:Objective: Trastuzumab has been used for the treatment of HER2-positive breast cancer (BC). However, a subset of BC patients exhibited resistance to trastuzumab therapy. Thus, clarifying the molecular mechanism of trastuzumab treatment will be beneficial to improve the treatment of HER2-positive BC patients. In this study, we identified trastuzumab-responsive microRNAs that are involved in the therapeutic effects of trastuzumab. Methods and results: RNA samples were obtained from HER2-positive (SKBR3 and BT474) and HER2-negetive (MCF7 and MDA-MB-231) cells with and without trastuzumab treatment for 6 days. Next, we conducted a microRNA profiling analysis using these samples to screen those microRNAs that were up- or downregulated only in HER2-positive cells. This analysis identified miR-26a and miR-30b as trastuzumab-inducible microRNAs. Transfecting miR-26a and miR-30b induced cell growth suppression in the BC cells by 40% and 32%, respectively. A cell cycle analysis showed that these microRNAs induced G1 arrest in HER2-positive BC cells as trastuzumab did. An Annexin-V assay revealed that miR-26a but not miR-30b induced apoptosis in HER2-positive BC cells. Using the prediction algorithms for microRNA targets, we identified cyclin E2 (CCNE2) as a target gene of miR-30b. A luciferase-based reporter assay demonstrated that miR-30b post-transcriptionally reduced 27% (p=0.005) of the gene expression by interacting with two binding sites in the 3’-UTR of CCNE2. Conclusion: In BC cells, trastuzumab modulated the expression of a subset of microRNAs, including miR-26a and miR-30b. The upregulation of miR-30b by trastuzumab may play a biological role in trastuzumab-induced cell growth inhibition by targeting CCNE2.

2012-06-03 | GSE38415 | GEO

Trastuzumab produces therapeutic actions by upregulating miR-26a and miR-30b in breast cancer cells

2012-06-02 | E-GEOD-38415 | biostudies-arrayexpress

Transcription profiling by array of hMADS cells transfected with miR-26a and induced to differentiate into adipocytes

Project description:Human multipotent adipose-derived stem (hMADS) cells were transfected at confluence with miR-26a or miR-C (non-targeting control microRNA). Two days later (=d0), adipocyte differentiation was induced. At d9 after start of differentiation, cells were harvested to identify mRNAs that are down- and upregulated by miR-26a versus miR-C.

2013-11-25 | E-MARS-29 | biostudies-arrayexpress

The change of mRNA expression in murine immortalized podocyte after miR-26a silencing

Project description:The change of mRNA expression in murine immortalized podocyte were analyzed after miR-26a silencing. These results provide a basical information of molecular pathology in podocyte biology. Mouse podocytes immortalized by temperature sensitive SV40 were used. Podocyte cultures grown at 33 °C were trypsinized and then cultured with RPMI-1640 without antibiotics in 24-well plates at 60–70% confluence for 2 days. On day 3, an anti-miR negative control (40 pmol) or the miR-26a miRNA inhibitor (40 pmol) was transfected to podocytes. The cells were analyzed after culturing for 24 hour.

2014-10-01 | E-GEOD-51210 | biostudies-arrayexpress

RNA-sequencing (RNA-seq) in breast cancer cell lines after ectopic manipulation of miR-26a expression

Project description:RNA sequencing technology has been carried out in order to evaluate mRNA expression changes after manipulation of miR-26a in both MCF-7 and MDA-MB-231 breast cancer cell lines. To evaluate the entire set of genes modulated by miR-26a in breast cancer, we performed RNA-seq after ectopic manipulation of this miRNA. We over-expressed miR-26a in MCF-7 epithelial cancer cell lines and also reduced its activity by stably transfecting MDA-MB-231 mesenchymal-like cancer cell lines with a specific sponge vector. GO terms and pathway enriched analysis of the transcripts that significantly change upon miR-26 ectopic manipulation implicates miR-26ab in cell cycle, apoptosis, cell spreading and cell adhesion in breast cancer

2016-06-30 | E-GEOD-43726 | biostudies-arrayexpress

Investigation of ssc-miR-23a genetic variants

Project description:Genetic variation of miR-23a in sows

2022-04-17 | PRJEB52348 | EVA