Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

56 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Ago2 associated gene transcripts in two Hodgkin lymphoma cell lines

ABSTRACT: The aim of the study is to identify miRNA targets in Hodgkin lymphoma cell lines. By immunoprecipitation of wild type Ago2, it is expected to pull down the Ago2 associated gene transcripts. Through microarray analysis, the Ago2 associated gene transcripts identified are expected to be miRNA targets. Keywords: Ribonucleoprotein Immunoprecipitation - Gene Chip (RIP-Chip) RNA isolated from the Ago2 immunoprecipitated (IP) fraction is hybridized against the RNA from total cell lysate (T) fraction. The experiment is performed in two independent Hodgkin lymphoma cell lines, L1236 and L428. In addition, RNA of flow through (FT) fraction of L1236 is hybridized against RNA of total cell lysate (T) fraction of L1236 to demonstrate the specificity/enrichment seen in the IP fraction and not in the FT fraction. All hybridizations is done with a dye swap design.

ORGANISM(S): Homo sapiens

SUBMITTER: Bart-Jan Kroesen

PROVIDER: E-GEOD-14409 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

A high throughput experimental approach to identify miRNA targets in human cells.

Tan Lu Ping LP Seinen Erwin E Duns Gerben G de Jong Debora D Sibon Ody C M OC Poppema Sibrand S Kroesen Bart-Jan BJ Kok Klaas K van den Berg Anke A

Nucleic acids research 20090904 20

The study of human microRNAs is seriously hampered by the lack of proper tools allowing genome-wide identification of miRNA targets. We performed Ribonucleoprotein ImmunoPrecipitation-gene Chip (RIP-Chip) using antibodies against wild-type human Ago2 in untreated Hodgkin lymphoma (HL) cell lines. Ten to thirty percent of the gene transcripts from the genome were enriched in the Ago2-IP fraction of untreated cells, representing the HL miRNA-targetome. In silico analysis indicated that approximate ...[more]

PMID: 19734348

Similar Datasets

Overexpression of miR-155 enhances B-cell lymphoma growth by targeting TBRG1

Project description:MYC regulates the expression of multiple microRNA (miRNA) genes and defines the Burkitt lymphoma (BL) miRNA signature. Here, we investigate the role of the MYC-regulated miRNAs by gain- and loss-of-function analysis. Overexpression of 5 miRNAs that were significantly downregulated by MYC resulted in strong (miR-150, miR-26a, miR-26b) and mild (miR-29a, let-7a) impaired cell growth. Overexpression of miR-155 increased proliferation of BL cells. By RNA immunoprecipitation of Argonaute 2 in BL cells with and without miR-155 we identified 54 miR-155 target genes. Using an shRNA approach we identified TBRG1 (NIAM1) as a miR-155 target gene that copied the miR-155-induced phenotype upon its inhibition. Analysis of TBRG1 protein expression and miR-155 levels in primary cases of B-cell lymphoma revealed that miR-155 levels are significantly lower in TBRG1 positive cases suggesting that TBRG1 is also regulated by miR-155 in primary B-cell lymphoma. Our data demonstrate that overexpression of individual MYC-repressed miRNAs has a strong suppressive effect on BL cell growth, whereas overexpression of miR-155 enhances B-cell lymphoma growth by targeting the tumor suppressor gene TBRG1. Gene expression profile was performed in ST486 Burkitt lymphoma cell line in 4 samples: ST486 EV (empty MXW-PGK-IRES-GFP vector) total cell lysate, ST486 EV Ago2-IP, ST486 miR-155 (ST486 with ectopic miR-155) total cell lysate, ST486 miR-155 Ago2-IP.

2015-02-20 | E-GEOD-64484 | biostudies-arrayexpress

Identification of miRNA targets in breast cancer cells (Ago2-IP)

Project description:miRNAs regulate mRNA stability and translation through the action of the RNAi-induced silencing complex. In this study, we systematically identified endogenous miRNA target genes by using AGO2 immunoprecipitation (AGO2-IP) and microarray analyses in two breast cancer cell lines, MCF7 and MDA-MB-231, representing luminal and basal-like breast cancer, respectively. The expression levels of ~70% of the AGO2-IP mRNAs were increased by DROSHA or DICER1 knockdown. In addition, integrated analysis of miRNA expression profiles, mRNA-AGO2 interaction, and the 3'-UTR of mRNAs revealed that >60% of the AGO2-IP mRNAs were putative targets of the fifty most abundantly expressed miRNAs. To identify mRNAs associated with AGO2, cell lysate was precleaned with control IgG and immunoprecipitated with anti-human Ago2 (Clone 2E12-1C9, Abnova). Total RNA from cell lysate or coimmunoprecipitated with AGO2 was extracted with Trizol and subjected to microarray analysis, with three biological repeats for each experimental condition.

2013-10-21 | E-GEOD-48158 | biostudies-arrayexpress

miR-17 seed family specific targets in two Hodgkin lymphoma cell lines

Project description:The aim of the study is to identify miRNA specific targets in Hodgkin lymphoma cell lines. By immunoprecipitation (IP) of wild type Ago2, Ago2 associated gene transcripts (ie miRNA targets) are coimmunoprecipitated. In cells transfected with anti-miR-17/20/93/106, the miR-17 seed family specific targets are not coimmunoprecipitated with Ago2. With microarray analysis, signal intensities of probes associated with Ago2 from untransfected and anti-miRNA transfected cells are compared. Gene transcripts that are depleted from the Ago2-IP fraction upon miRNA inhibition (ie miRNA specific targets) are identified.

2009-10-13 | GSE16053 | GEO

Profiling of Argonaute (AGO) 2-associated sRNAs after infection of bacterial pathogen Pseudomonas syringae

Project description:Transgenic Arabidopsis plants (AGO2::HA:AGO2) were treated with either mock (10 mM MgCl2) or Pseudomonas syringae pv. tomato (Pst) expressing avrRpt2 (R2) at a concentration of 2 x 107 cfu/ml for 14 hours. sRNAs associated with AGO1 and AGO2 were co-immunoprecipitated using antibodies against either AGO1 (AGO1-IP), or HA (hemagglutinin) (AGO2-IP). As controls, we also gel-purified the 18-28 nt fraction of the total RNAs from an AGO2 mutant (ago2-1). The co-immunoprecipitated or gel-purified RNAs were cloned and sequenced by Illumina deep sequencing. Examination of AGO-associated sRNAs in pathogen-treated or control plants

2011-05-10 | E-GEOD-26161 | biostudies-arrayexpress

Ago2 associated gene transcripts in two Hodgkin lymphoma cell lines

Project description:The aim of the study is to identify miRNA targets in Hodgkin lymphoma cell lines. By immunoprecipitation of wild type Ago2, it is expected to pull down the Ago2 associated gene transcripts. Through microarray analysis, the Ago2 associated gene transcripts identified are expected to be miRNA targets. Keywords: Ribonucleoprotein Immunoprecipitation - Gene Chip (RIP-Chip)

2009-09-21 | GSE14409 | GEO

JAK/STAT blockade in cHL

Project description:Here we investigated the effects of JAK/STAT pharmacological inhibition on cHL cell models using ruxolitinib, a JAK 1/2 inhibitor. We use five classical Hodgkin lymphoma cell lines: L428, L1236, L540, KMH2, L591

2021-10-15 | GSE185818 | GEO

A nuclear role for the Argonaute protein AGO2 in mammalian gametogenesis

Project description:The reduced sperm count observed in Ago2 cKO mice implies that AGO2 has non-redundant functions in the male germ line. Because AGO2 is a key protein in the RNA interference (RNAi) pathway, we first postulated that AGO2 loss disrupts normal transcriptional and translational dynamics of target mRNAs relevant to sperm maturation. To address this hypothesis, we took advantage of the apparently normal spermatogenesis in Ago2 cKO mice, which allowed us to purify matched meiotic and post-meiotic germ cells from Ago2 cKO and wild type controls. We examined changes in the transcriptome and proteome of these two spermatogenic stages in Ago2 cKO relative to control mice using RNA-seq and quantitative mass spectrometry (MS). To further examine if the changes in mRNA and protein levels detected in Ago2 cKO germ cells was due to a loss of regulation by the canonical AGO2-miRNA pathway, we characterized AGO2 protein interactors by AGO2 immunoprecipitation-mass spectrometry (IP-MS) in cytoplasmic and nuclear fractions of post-meiotic cells

2022-08-01 | PXD027935 | Pride

Mouse adult testes: Total RNA vs. IP RNA

Project description:RNAs that are enriched in AGO2 Immunoprecipitated (IP) products or PIWIL1 IP products were identified from mouse(BALB/C) adult testes by examine the ratio of total RNA signal intensity to AGO2 IP RNA or PIWIL1 IP RNA signal intensity. Two-condition experiment,Total RNA extracted from mouse adult testes vs. AGO2 IP RNA extracted from mouse adult testes and total RNA extracted from mouse adult testes vs. PIWIL1 IP RNA extracted from mouse adult testes.

2013-04-01 | E-GEOD-27582 | biostudies-arrayexpress

Ago2-bound short RNAs in HeLaS3 cell line

Project description:Characterization of AGO2 bound short RNAs from nuclear extracts of HeLaS3 cell line. Nuclei were isolated from HeLaS3 cells; a fraction of Nuclear lysates was harvsted and sequenced as the 'input' samples. The rest of nuclear lysates were Immunoprecipitated using AGO2 monoclonal antibodies or Isotype matched IgG. Following immunoprecipitation, RNA was extracted from AGO2 or control IgG IP for short RNA sequencing. Two independent biological replicates were carried out.

2015-05-17 | E-MTAB-2084 | biostudies-arrayexpress

AGO2 bound short RNAs in Jurkat cell line

Project description:Characterization of AGO2 bound short RNAs from nuclear extracts of Jurkat cell line. Nuclei were isolated from cells; a fraction of Nuclear lysates was harvested and sequenced as the input samples. The rest of nuclear lysates were Immunoprecipitated using AGO2 monoclonal antibodies or Isotype matched IgG. Following immunoprecipitation, RNA was extracted from AGO2 or control IgG IP for short RNA sequencing. Two independent biological replicates were carried out.

2015-05-17 | E-MTAB-2104 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data