Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNAi profiling of human MCF-7 cells depleted for SIRT1

ABSTRACT: SIRT1 is a nuclear NAD+-dependent protein deacetylase. Expression microarray analysis was used to study the effect of SIRT1 knockdown on gene expression in MCF-7 breast cancer cells. Experiment Overall Design: SIRT1 stable knockdown was achieved using two retroviral shRNA constructs. An shRNA directed against Luciferase was used to generate the Luc control cells. Three independent biological replicates with matching Luc controls were analyzed using Affymetrix U133A 2.0 microarrays. Experiment Overall Design: These 6 samples were part of a 15-sample microarray analysis (GSE12971) examining expression regulation by SIRT1, PARP-1, PARG and macroH2A. All 15 samples were included for the following data normalization steps: data sets obtained using the GCOS software were grouped based on date of experiment and adjusted for batch effect using the parametric empirical Bayes method (Combat R); all values < 0.01 were adjusted to 0.01; the data were log2 transformed, median centered for each array, and median centered for each gene.

ORGANISM(S): Homo sapiens

SUBMITTER: Kraus Lee

PROVIDER: S-ECPF-GEOD-13459 | biostudies-other |

REPOSITORIES: biostudies-other

ACCESS DATA

Json Xml

Similar Datasets

RNAi profiling of human MCF-7 cells depleted for NMNAT1

Project description:"NMNAT1 is a nuclear enzyme in the mammalian NAD+ salvage pathway. Expression microarray analysis was used to study the effect of NMNAT1 knockdown on gene expression in MCF-7 breast cancer cells. Experiment Overall Design: NMNAT1 stable knockdown was achieved using a retroviral shRNA construct. An shRNA directed against Luciferase was used to generate the Luc control cells. Three independent cell populations with matching Luc controls were prepared for the expression analysis. Each cell population was treated with either vehicle control (ethanol) or estradiol (E2) for 3 hours before harvest of RNA samples. Four samples in one replicate (LUC2 CON, LUC2 E2, NMNAT2 CON and NMNAT2 E2) were hybridized to Affymetrix U133 Plus 2.0 arrays, while the other two replicates of eight samples were hybridized to Affymetrix U133A 2.0 arrays. Experiment Overall Design: All 12 samples were included for the following data normalization steps: common probe sets on both U133A 2.0 and U133 Plus 2.0 platforms were selected; within each sample group hybridized to the same microarray platform, the signal values were log2 transformed, median centered for each array, and median centered for each gene; the data sets were further adjusted using the parametric empirical Bayes method (Combat R) to eliminate batch effect caused by the different array platforms."

| S-ECPF-GEOD-13458 | biostudies-other

RNAi profiling of human MCF-7 cells depleted for NAMPT knockdown

Project description:NAMPT is an enzyme in the mammalian NAD+ salvage pathway. Expression microarray analysis was used to study the effect of NAMPT knockdown on gene expression in MCF-7 breast cancer cells. Experiment Overall Design: Stable knockdown of NAMPT was achieved using a retroviral shRNA construct. An shRNA directed against Luciferase was used to generate the Luc control cells. Three independent biological replicates with matching Luc controls were analyzed using Affymetrix U133 A2.0 microarrays.

| S-ECPF-GEOD-13449 | biostudies-other

RNAi profiling of human MCF-7 cells depleted for SIRT1

Project description:SIRT1 is a nuclear NAD+-dependent protein deacetylase. Expression microarray analysis was used to study the effect of SIRT1 knockdown on gene expression in MCF-7 breast cancer cells. Experiment Overall Design: SIRT1 stable knockdown was achieved using two retroviral shRNA constructs. An shRNA directed against Luciferase was used to generate the Luc control cells. Three independent biological replicates with matching Luc controls were analyzed using Affymetrix U133A 2.0 microarrays. Experiment Overall Design: These 6 samples were part of a 15-sample microarray analysis (GSE12971) examining expression regulation by SIRT1, PARP-1, PARG and macroH2A. All 15 samples were included for the following data normalization steps: data sets obtained using the GCOS software were grouped based on date of experiment and adjusted for batch effect using the parametric empirical Bayes method (Combat R); all values < 0.01 were adjusted to 0.01; the data were log2 transformed, median centered for each array, and median centered for each gene.

2009-06-08 | E-GEOD-13459 | biostudies-arrayexpress

RNAi profiling of human MCF-7 cells depleted for NMNAT1

Project description:NMNAT1 is a nuclear enzyme in the mammalian NAD+ salvage pathway. Expression microarray analysis was used to study the effect of NMNAT1 knockdown on gene expression in MCF-7 breast cancer cells. Experiment Overall Design: NMNAT1 stable knockdown was achieved using a retroviral shRNA construct. An shRNA directed against Luciferase was used to generate the Luc control cells. Three independent cell populations with matching Luc controls were prepared for the expression analysis. Each cell population was treated with either vehicle control (ethanol) or estradiol (E2) for 3 hours before harvest of RNA samples. Four samples in one replicate (LUC2 CON, LUC2 E2, NMNAT2 CON and NMNAT2 E2) were hybridized to Affymetrix U133 Plus 2.0 arrays, while the other two replicates of eight samples were hybridized to Affymetrix U133A 2.0 arrays. Experiment Overall Design: All 12 samples were included for the following data normalization steps: common probe sets on both U133A 2.0 and U133 Plus 2.0 platforms were selected; within each sample group hybridized to the same microarray platform, the signal values were log2 transformed, median centered for each array, and median centered for each gene; the data sets were further adjusted using the parametric empirical Bayes method (Combat R) to eliminate batch effect caused by the different array platforms.

2009-06-05 | E-GEOD-13458 | biostudies-arrayexpress

RNAi profiling of human MCF-7 cells depleted for NAMPT knockdown

2009-06-08 | E-GEOD-13449 | biostudies-arrayexpress

Transcription profiling of human MCF-7 and MCF-7-14 cells

Project description:We investigated the differentially expressed genes between MCF-7 and MCF-7-14, and estimated the similarities of expression profiles between MCF-7-14 and MDA-MB-231. We identified genes differentially expressed between non-invasive/non-metastatic and invasive/metastatic breast cancer cells. Experiment Overall Design: We performed microarray analysis as following design: MCF-7 versus MCF-7-14 versus MDA-MB-231 cells.

| S-ECPF-GEOD-18903 | biostudies-other

Profiling essential genes in human mammary cells by multiplex RNAi screening.

Project description:By virtue of their accumulated genetic alterations, tumor cells may acquire vulnerabilities that create opportunities for therapeutic intervention. We have devised a massively parallel strategy for screening short hairpin RNA (shRNA) collections for stable loss-of-function phenotypes. We assayed from 6000 to 20,000 shRNAs simultaneously to identify genes important for the proliferation and survival of five cell lines derived from human mammary tissue. Lethal shRNAs common to these cell lines targeted many known cell-cycle regulatory networks. Cell line-specific sensitivities to suppression of protein complexes and biological pathways also emerged, and these could be validated by RNA interference (RNAi) and pharmacologically. These studies establish a practical platform for genome-scale screening of complex phenotypes in mammalian cells and demonstrate that RNAi can be used to expose genotype-specific sensitivities.

| S-EPMC2981861 | biostudies-literature

Transcription profiling of MCF-7 Human Breast Cancer Cells

Project description:SOX genes encode a family of high-mobility group transcription factors that play critical roles in organogenesis. Virtually all members of SOX family have been found to be deregulated in tumors of various origins. However, little is known about the cellular and molecular behaviours involved in the oncogenic potential of SOX proteins. Cell culture experiments, tissue analysis, and molecular profiling revealed that SOX2 promotes cell proliferation and tumorigenesis through its transcription regulation of cell cycle related genes in breast cancer cells Experiment Overall Design: To delineate the molecular mechanism underlying the cell proliferation and tumorigenic properties of SOX2, we investigated the gene expression profile in MCF-7 cells. Briefly, MCF-7 cells were transfected with pcDNA3.1 and Human SOX2 expression constructs respectively. 24 hours after transfection, total RNA collected from control and SOX2-overexpressing MCF-7 cells was used to probe Human Genome GeneChip array U133 Plus 2.0

| S-ECPF-GEOD-11330 | biostudies-other

Expression data for Control and SMRT-Depleted MCF-7 Cells

Project description:Estrogens are an important regulator of breast cancer disease progression, and they function by binding the estrogen receptor--alpha (ER-alpha) to regulate changes in gene expression. ER-alpha is able to both activate and inhibit gene transcription in a gene-specific manner and do so by binding target DNA sequences and recruiting coactivators and corepressors which can modulate the chromatin environment. Silencing mediator of retinoic acid and thyroid hormone receptor (SMRT) is known to act as coactivator and corepressor of ER-alpha in a gene-specific manner. We used a microarray analysis to examine the gene expression changes that occur when the coregulator SMRT is depleted from the ER-alpha positive MCF-7 breast cancer cell line. We sought to determine the genes that are regulated by depletion of the coregulator SMRT using Affymetrix Human Gene 1.0 ST Array. To this end, we transfected MCF-7 cells with control siRNA or SMRT-targeting siRNA for 48 h and treated for an additional 4 or 24 h with vehicle (0.1% EtOH) or 1 nM estradiol (E2). A total of 24 samples were analyzed, separated into eight groups each with three experimental replicates in each group, siControl-Veh 4 h, siControl -E2 4 h, siSMRT-Veh 4 h, siSMRT-E2 4 h, siControl-Veh 24 h, siControl-E2 24 h, siSMRT-Veh 24 h, siSMRT-E2 24 h.

| S-ECPF-GEOD-57935 | biostudies-other

RNAi profiling of human MDA-MB-231 cells knocked down for RhoGDIbeta

Project description:RhoGDIbeta (ARHGDIB) is often expressed in tumor cells. It negatively regulates Rho-GTPases, but may have other functions as well. To analyze its effect on gene expression, RhoGDIbeta was suppressed by RNA interference in MDA-MB-231 breast cancer cells and changes in gene expression monitored by cDNA microarrays. Experiment Overall Design: MDA-MB-231 cells were either transfected with a RhoGDIbeta-specific siRNA or a control siRNA (siLuc), grown for three days, harvested and lysed for total RNA isolation. RNA was subjected to cDNA microarray analysis by using Affymetrix chip HG-U133A. A total of three independent transfection experiments were performed. The samples obtained from experiments 1, 2 and 3 were designated as siLuc_rep1, siLuc_rep2, siLuc_rep3 (siLuc transfected) and siARH_rep1, siARH_rep2, siARH_rep3 (siRhoGDIbeta transfected), respectively.

| S-ECPF-GEOD-8087 | biostudies-other

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