Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Searching for target genes of miR-429 in HCCLM3 cells

ABSTRACT: miRNAs are an class of small noncoding RNAs and about 21-25 nucleotides in length. miRNAs inhibit the translation or induce mRNA degradation by binding to the 3’ UTR of target mRNAs and have been identified as the tumor promoters or suppressors regulating the progression of cancers. miR-429, which is a member of an evolutionarily conserved family of miRNAs that includes miR-200b, miR-200a, miR-200c and miR-141, is expressed in various epithelial tissues. Our goal is to search the possible target genes of miR-429 in human liver cancer cell line HCCLM3. We analyzed possible target genes of miR-429 by identifying the shared genes among the down-regulated genes in epithelial cell adhesion molecule (EpCAM) negative HCCLM3 cells which treated with miR-429 mimics and the up-regulated genes in EpCAM positive HCCLM3 cells which treated with Antagomir-429.

ORGANISM(S): Homo sapiens

PROVIDER: GSE53092 | GEO | 2014/12/31

SECONDARY ACCESSION(S): PRJNA230997

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Homo sapiens

Project description:Searching for target genes of miR-429 in HCCLM3 cells

| PRJNA230997 | ENA

Functional and evolutionary significance of human microRNA seed region mutations [miR-429]

Project description:MicroRNAs (miRNAs) are small non-coding RNAs that play a central role in the regulation of gene expression at the post transcriptional and/or translational level thus impacting various biological processes. Dysregulation of miRNAs could affect processes associated with progression of a variety of diseases including cancer. Majority of miRNA targeting in animals involves a 7-nt M-bM-^@M-^\seed regionM-bM-^@M-^] mapping to positions 2-8 at the moleculeM-bM-^@M-^Ys 5' end. The importance of this 7 nt sequence to miRNA function is evidenced by the fact that the seed region sequence of many miRNAs is highly conserved within and between species. In this study, we computationally and experimentally explore the functional significance of sequence variation within the seed region of human miRNAs. Our results indicate that change of a single nt within the 7-nt seed region changes the spectrum of targeted mRNAs significantly meanwhile further nt changes have little to no additional effect. This high functional cost of even a single nucleotide change within the seed region of miRNAs explains why the seed sequence is highly conserved among many miRNA families both within and between species and could help clarify the likely mechanisms underlying the evolution of miRNA regulatory control. mRNAs were collected from 3 miR-429 treated and 3 negative control miRNA treated HEY ovarian cancer cell samples. mRNA expression was captured on Affymetrix U133 Plus 2 chips. To compare mRNA expression pattern between the miR-429 treated cells and the negative control treated cells, present/absent calls were generated using MAS5, while signals were calculated using GCRMA and then log2 transformed. Expression of differentially expressed genes or down regulated miRanda-mirSVR predicted miRNA target genes was compared between miRNA treated samples.

2015-01-30 | E-GEOD-56967 | biostudies-arrayexpress

The miR-200b/200a/429 cluster prevents metastasis and induces dormancy in murine claudin-low mammary tumor cells

Project description:The miR-200 family of microRNAs consisting of miR-141, miR-200a, miR-200b, miR-200c and miR-429 are key regulators of breast cancer progression. The miR200 family maintains mammary epithelial identity and downregulation of miR-200 expression drives the epithelial-to-mesenchymal transition. Re-expression of one or more miR-200 family members in tumor cells with mesenchymal characteristics may restore the epithelial phenotype and alter growth and metastatic potential. To test this, the miR-200b/200a/429 cluster was re-expressed in a murine claudin-low mammary tumor cell line, RJ423

2018-10-31 | GSE113162 | GEO

Effect of CTHRC1 knockdown on gene expression of HCCLM3 cells

Project description:Collagen triple helix repeat containing 1 (CTHRC1) has been found to be up-regulated in many human solid tumors. In this study, we investigated the changes of gene expression by comparing CTHRC1-siRNA and Scramble-siRNA control in hepatocellular carcinoma cell line HCCLM3, which has high expression levels of CTHRC1. Differential gene expression was assessed by Affymetrix microarray experiments for 2 samples: CTHRC1-siRNA-treated HCCLM3 cells and Scramble-siRNA-treated HCCLM3 cells.

2012-04-22 | E-GEOD-37208 | biostudies-arrayexpress

Expression data from mir-429 transfected HEY cells in a time-point series (0hr-HEY, 24hrs, 48hrs and 144hrs)

Project description:HEY cells display a mesenchymal phenotype (elongated). After a 48hr transfection with mir-429 their phenotype changes to an epithelial-like (cuboidal)

2018-02-27 | GSE111139 | GEO

HCC Cell lines: MHCC97L vs. Huh7 and HCCLM3

Project description:To identify genes associated with HCC invasiveness and metastasis, a hybridization-based microarray assay was used to analyze three cell lines with increasing metastatic potentials, Huh7,MHCC97L, and HCCLM3

2017-04-12 | GSE97626 | GEO

CLEAR-CLIP on murine keratinocytes grown in culture

Project description:The objective of this study was to identify miR-200 family member target sites. Of note, CLEAR-CLIP captures all miRNAs, not one family specifically. So data for all miRNAs is included. CLEAR-CLIP on murine keratinocytes grown in culture. Keratinocytes were either wild type, miR-200 family double knock out or miR-200b/miR-200a/miR-429 cluster inducible.

2018-03-16 | GSE102716 | GEO

RNA-seq of CCDC137-APOBEC1 expressing HCCLM3 cells [APOBEC1-seq]

Project description:We established GFP/CCDC137-APOBEC1 transfected HCCLM3 cells.Then doxycycline was added to induce the expression of GFP/CCDC137-APOBEC1.We then performed gene expression profiling analysis using RNA obtained from GFP/CCDC137-APOBEC1 overexpressing HCCLM3 cells with or without doxycycline treatment.

2023-07-01 | GSE217914 | GEO

p53-regulated networks of protein, mRNA, miRNA and lncRNA expression revealed by integrated pSILAC and NGS analyses

Project description:We determined the effect of p53 activation on de novo protein synthesis using quantitative proteomics of newly synthesized proteins (pulsed stable isotope labeling with amino acids in cell culture, pSILAC) in combination with mRNA and non-coding RNA expression analyses by next generation sequencing (RNA-, miR-Seq) in the colorectal cancer (CRC) cell line SW480. Furthermore, genome-wide DNA binding of p53 was analyzed by chromatin-immunoprecipitation (ChIP-Seq). Thereby, we identified differentially regulated mRNAs (1258 up, 415 down), miRNAs (111 up, 95 down), lncRNAs (270 up, 123 down) and proteins (542 up, 569 down). Changes in mRNA and protein expression levels showed a positive correlation (r = 0.50, p < 0.0001). More transcriptionally induced genes displayed occupied p53 binding sites (4.3% mRNAs, 7.2% miRNAs, 6.3% lncRNAs, 5.9% proteins) than repressed genes (2.4% mRNAs, 3.2% miRNAs, 0.8% lncRNAs, 1.9% proteins), suggesting indirect mechanisms of repression. Around 50% of the downregulated proteins displayed seed-matching sequences of p53-induced miRNAs in the corresponding 3â??-UTRs. Moreover, proteins repressed by p53 significantly overlapped with those previously shown to be repressed by miR-34a. We confirmed upregulation of the novel direct p53 target genes LINC01021, MDFI, ST14 and miR-486 and showed that ectopic LINC01021 expression inhibited proliferation in SW480 cells. Furthermore, HMGB1, KLF12 and CIT mRNAs were confirmed as direct targets of the p53-induced miR-34a, miR-205 and miR-486-5p, respectively. In line with the loss of p53 function during tumor progression, elevated expression of HMGB1, KLF12 and CIT was detected in advanced stages of cancer. This study provides new insights and a comprehensive catalogue of p53-mediated regulations and p53 DNA binding in CRC cells.

2016-05-24 | MSV000079767 | MassIVE

Alcaligenaceae bacterium 429

Project description:Alcaligenaceae sp. 429 genome sequencing and assembly

| PRJNA530183 | ENA