Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

66 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

MiRNA expression profile in breast cancer cells

ABSTRACT: We performed microRNA sequencing (miRNA-seq) according to Illumina sequencing protocols. Total RNA extracted from MCF-7 cells expressing human ER-beta in absence of estrogen stimuli was subjected to size selection labrary preparation ond retrotranscribed. Obtained DNA was sequenced with the Illumina/Solexa Genome Analyzer (GAIIX).

INSTRUMENT(S): Illumina Genome Analyzer IIx

ORGANISM(S): Homo sapiens

SUBMITTER: Maria Rosaria De Filippo

PROVIDER: E-MTAB-2085 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

ChIP-Seq of human MCF-7 cells with ER-alpha and ER-beta anitbodies following estrogen treatment

Project description:We performed chromatin immunoprecipitation (ChIP) with overnight with antibodies against the C-terminus (HC-20, from Santa Cruz Biotechnology, Europe) or the N-terminus (anti-Estrogen Receptor 18-32, from SigmaAldrich, Italy) of human ER-alpha with or without estrogen treatment for 45 minutes on TAP-ER-beta cells, and the immunoprecipitated DNA was sequenced with the Illumina/Solexa Genome Analyzer. (Note: Raw data files not provided by submitter)

2010-12-01 | E-MTAB-345 | biostudies-arrayexpress

ChIP-Seq of human MCF-7 cells with ER-alpha anitbody following estrogen treatment

Project description:We performed chromatin immunoprecipitation (ChIP) with two polyclonal anti-ERalpha antibodies directed against the N- and C-terminus of the protein, with or without estrogen treatment for 45 minutes of MCF-7 cells, and the immunoprecipitated DNA was sequenced with the Illumina/Solexa Genome Analyzer.

2010-01-11 | E-MTAB-131 | biostudies-arrayexpress

Transcription profiling by array of human MCF-7 cells with ER-beta tagged with TAP-tag at the C-term or N-term or expressing ER-alpha tagged

Project description:MCF-7 TET Off cells (MCF-7 wt) were used to produce stable clones expressing ER-beta tagged with TAP-tag respectively at the C-term and at the N-term (C-TAP-ER-beta and N-TAP-ER-beta) or expressing ER-alpha tagged (C-TAP-ER-alpha). All were grown in Dulbecco's modified Eagle's medium (DMEM). Then cells were lysed and RNA extracted were pooled. For mRNA expression profiling, 500 ng total RNA were reverse transcribed and used for synthesis of cDNA and biotinylated cRNA. Finally cRNA were hybridized for 18 hours on Illumina HumanHT-12 v3.0 BeadChips and after scanning, data analysis was performed.

2011-10-11 | E-TABM-1052 | biostudies-arrayexpress

Gene expression profile in breast cancer cell lines using miRNA over-expression

Project description:MCF-7 TET Off cells (MCF-7 wt) were used to produce stable clones expressing ER-beta tagged with TAP-tag at the C-term (C-TAP-ER-beta). All cells were grown in Dulbecco's modified Eagle's medium (DMEM), starved by using DMEM w/o phenol red and 5% Dextran Coated Charcoal stripped serum (DCC-FBS) for 5 days. Cells were transfected wiyh hsa-miR-30a-5p Mimics and with tha negative control Scramble both at concentration of 5 and 10 nM. Biological replicate were lysed and RNA extracted were pooled 24 hrs after transfectiions. For mRNA expression profiling, 500 ng total RNA were reverse transcribed and used for synthesis of cDNA and biotinylated cRNA. Finally cRNA were hybridized for 19 hours on Illumina HumanHT-12 v4.0 BeadChips and after scanning, data analysis was performed.

2014-02-07 | E-MTAB-1493 | biostudies-arrayexpress

Gene expression profile in a breast cancer cell line upon hormonal treatments

Project description:MCF-7 TET Off cells (MCF-7 wt) were used to produce stable clones expressing ER-alpha tagged with TAP-tag at the C-term (C-TAP-ER-alpha). All cells were grown in Dulbecco's modified Eagle's medium (DMEM), starved by using DMEM w/o phenol red and 5% Dextran Coated Charcoal stripped serum (DCC-FBS) for 5 days. Cells were stimulated with 17 beta Estradiol (E2), 4-idrossi-tamoxifen (Tam), raloxifene (Ral) and Fulvestrant (ICI) at the concentration of 10-8M for 12 hours or with vehicle Ethanol. Biological replicate were lysed and RNA extracted were pooled. For mRNA expression profiling, 500 ng total RNA were reverse transcribed and used for synthesis of cDNA and biotinylated cRNA. Finally cRNA were hybridized for 19 hours on Illumina HumanHT-12 v4.0 BeadChips and after scanning, data analysis was performed.

2012-06-25 | E-MTAB-1196 | biostudies-arrayexpress

Transcription profiling by array of human MCF-7 breast cell clones expressing ER-beta tagged with TAP-tag at the C-terminal or N-terminal

Project description:MCF-7 TET Off cells (MCF-7 wt) were used to produce stable clones expressing ER-beta tagged with TAP-tag respectively at the C-term and at the N-term (C-TAP-ER-beta and N-TAP-ER-beta) or expressing ER-alpha tagged (C-TAP-ER-alpha) as previously described.Cells were cultured in standard growth conditions, then were lysed and RNA was extracted using TRIzol method.Total RNA were fluorescently labelled, amplified and hybridized in triplicate (MCF7-TAP and C-TAP-ER-alpha) and in duplicate (C-TAP-ER-beta_A, C-TAP-ER-beta_B, N-TAP-ER-beta) for 18 hours on Illumina v2 MicroRNA Expression BeadChips and after scanning, analysis was performed with GenomeStudio v.2010.1 software, for quality control and miRNA expression analysis.

2011-10-11 | E-TABM-1053 | biostudies-arrayexpress

MicroRNA profiling by array of human MCF-7 breast cancer cells with ER-beta tagged at the C-terminal or N-terminal and treated with 17-beta-estradiol

Project description:Human estrogen-responsive breast cancer cell line MCF-7 TET Off (MCF-7 wt) were used to produce stable clones expressing ER-beta tagged with TAP-tag respectively at the C-term and at the N-term (C-TAP-ER-beta and N-TAP-ER-beta) or expressing ER-alpha tagged (C-TAP-ER-alpha) as previously described.(C-TAP-ER-beta, N-TAP-ER-beta, C-TAP-ER-alpha) were treated with 10nM of17-beta-estradiol, or vehicle (ETOH). miRNA expression was analyzed on total RNA extracted before or after 6, 12, 24, and 72 hours hormonal stimulation. Total RNA was fluorescently labelled, amplified in triplicate, to be, than, pooled for the Hybridization.Each pool, were hybridized for 18 hours on Illumina v2 MicroRNA Expression BeadChips, and after scanning, analysis was performed with GenomeStudio v.2010.1 software, for quality control and miRNA expression analysis.

2011-07-29 | E-TABM-1055 | biostudies-arrayexpress

The nuclear receptor ERbeta engages AGO2 in regulation of gene transcription, RNA splicing and RISC loading. Part 4

Project description:The RNA-binding protein Argonaute 2 (AGO2) is a key effector of RNA-silencing pathways It exerts a pivotal role in microRNA maturation and activity, and can modulate chromatin remodeling, transcriptional gene regulation and RNA splicing. The Estrogen Receptor beta (ERβ) is endowed with oncosuppressive activities, antagonizing hormone-induced carcinogenesis and inhibiting growth and oncogenic functions in luminal-like breast cancers (BCs), where its expression correlates with a better prognosis of the disease. Applying interaction proteomics coupled to mass spectrometry (MS) to characterize nuclear factors cooperating with ERβ in gene regulation, we identify AGO2 as a novel partner of ERβ in human BC cells. ERβ-AGO2 association was confirmed in vitro and in vivo both in the nucleus and in cytoplasm and is shown to be RNA-mediated. ChIP-Seq demonstrates AGO2 association to a large number of ERβ binding sites, and total and nascent RNA-Seq in ERβ+ vs ERβ- cells, and before and after AGO2 knock-down in ERβ+ cells, reveals a widespread involvement of this factor in ERβ-mediated regulation of gene transcription rate and RNA splicing. Moreover, isolation and sequencing by RIP-Seq of ERβ-associated long and small RNAs in the cytoplasm suggests involvement of the nuclear receptor in RISC loading, indicating that it may able to control directly also mRNA translation efficiency and stability.These results demonstrate that AGO2 can act as a pleiotropic functional partner of ERβ, indicating that both factors are endowed with multiple roles in the control of key cellular functions.

2017-04-25 | E-MTAB-4363 | biostudies-arrayexpress

Gene expression profile in breast cancer cells

Project description:Human estrogen-responsive breast cancer cell line MCF-7 wt were used to produce stable clones expressing ER-beta tagged with TAP-tag respectively at the C-term and at the N-term (Ct-ER-beta and Nt-ER-beta) as previously described. MCF7 wt and beta clone cells were cultured in steroid-free medium for 5 days and then were treated with 10nM of 17-beta-estradiol, or vehicle (ETOH). RNA was extracted after 2h, 4h and 8h of stimulation with 17-ß-estradiol 10 nM (+E2) or ethanol vehicle . Total RNA extracted by Ct-ER-beta and Nt-ER-beta cells were pooled (TAP-ER-beta). For mRNA expression profiling, 500 ng total RNA were reverse transcribed and used for synthesis of cDNA and biotinylated cRNA. Finally cRNA were hybridized for 18 hours on Illumina HumanHT-12 v3.0 BeadChips and after scanning, data analysis was performed.

2011-07-29 | E-TABM-1051 | biostudies-arrayexpress

A Pyrazolo[3,4-d]Pyrimidine compound (a Fyn inhibitor) induces apoptosis and cell death in Large Granular Lymphocyte Leukemia cells

Project description:KHYG1 cell line (NK leukemia) were treated with a new compound, a pyrazolo[3,4-d]Pyrimidine. This compound induces apoptosis and cell death in this cell line. The mechanisms of apoptosis and cell death were investigated. A gene expression profile was used as support.

2016-10-03 | E-MTAB-4536 | 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