Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

12 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Aiolos regulated genes in A549, lung carcinoma cells

ABSTRACT: Analysis of transcriptional profiling change comparing A549 cells expressing control empty vector and A549 cells expressing Aiolos. Results provide insight into molecular mechanisms underlying functional consequence of ectopic expression of Aiolos in solid cancer cells. Two-condition experiment, A549-empty vs. A549-Aiolos cells. Biological replicates: 3 control, 3 transfected, independently grown and harvested. One replicate per array.

ORGANISM(S): Homo sapiens

SUBMITTER: Zhe Liu

PROVIDER: E-GEOD-50812 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

An optimized RNA amplification method for prokaryotic expression profiling analysis

Project description:Conventional prokaryotic RNA labeling method usually requires large amounts of starting materials and tends to generate high background signals. Recently, two novel methods based on amplification systems were introduced. Here, we compared three alternative strategies: direct labeling method, ployadenylation-involved oligo-dT priming amplification method and random priming amplification method (hereafter referred to as DL, PAOD and RPA method in this article) for prokaryotic RNA labeling employing the expression profiling investigation in Escherichia coli (E. coli) heat shock model. To identify an optimal RNA labeling method for prokaryotic microarray analysis, experiments were performed with starting RNA obtained from E.coli growing at control (37Â°C) or heat shock (43Â°C) condition. We employed 0.5 Î¼g of total RNA for a single round of amplification using PAOD and RPA methods coupling to IVT to generate cDNA targets. In addition, an approach using DL method was also performed. Three types of cDNA mixtures containing Cy5-labeled (or Cy3-labeled) control DNA and Cy3-labeled (or Cy5-labeled) DNA targets were hybridized with E.coli microarrays in a dye-swap strategy. Replicate experiments were conducted from the same batch of total RNA to assess technique reproducibility of each approach.

2010-05-15 | E-GEOD-17074 | biostudies-arrayexpress

A Structure-Based Mechanism for DNA Entry into the Cohesin Ring

Project description:The ring-shaped cohesin complex is thought to fulfil its roles in sister chromatid cohesion, genome stability and gene regulation by topologically encircling DNAs. The ring is formed by two Structural Maintenance of Chromosome (SMC) subunits, whose ATPase heads are linked by a kleisin subunit. Additional components, including the Mis4Scc2/NIPL cohesin loader, engage the kleisin. Here, we visualize a DNA gripping intermediate during cohesin loading onto DNA by cryo-electron microscopy. ATP-dependent head engagement creates an interaction surface onto which Mis4Scc2/NIPL clamps the DNA. We use biophysical tools to establish the order of events during cohesin loading. DNA first traverses an N-terminal kleisin gate that was opened by ATP binding and closed again as the loader locks the DNA. Ensuing ATP hydrolysis and head disengagement, assisted by Mis4Scc2/NIPL, will complete DNA entry. A conserved kleisin N-terminal tail guides the DNA on its trajectory to successful topological DNA entry into the cohesin ring.

2020-08-05 | PXD018600 | Pride

A Long Noncoding RNA Acts as a Tumor Promoter in Hepatocellular Carcinoma

Project description:Many long noncoding RNAs are involved in cancer development and progression. Here, we utilized high-throughput microarray to compare the expression difference of transcriptome between the LINC01225 stable knockdown SMCC7721 cells and mock empty plasmid treated SMCC7721 cells; the LINC01225 stable knockdown MHCC97H cells and mock empty plasmid treated MHCC97H cells. These altered genes are involved in tumorigenesis through diverse mechanisms. The present study reveals that LINC01225 functions as a tumor promoter in Hepatocellular Carcinoma. LINC01225 stable knockdown cells were compared to mock empty plasmid treated cells. In addition expression of genes in untreated SMCC7721 cells was detected, we performed a comparison between mock empty plasmid treated SMCC7721 cells and untreated SMCC7721 cells to determine that no confounding factors were brought in. The Agilent human lncRNA+mRNA Array V4.0 were used to perform the analysis.

2017-01-14 | E-MTAB-3833 | biostudies-arrayexpress

Transcription profiling of human adenocarcinoma cell line A549 over-expressing ELMOD2

Project description:ELMOD2 cDNA from the IMAGE clone 3897166 was cloned into the pDsRed-Monomer-N1 expression vector. ELMOD2 was overexpressed in the A549(adenomcarcinoma)cell line and cells transfected with empty vector were considered controls. Transcript profiles were compared with the Affymetrix Hgu133plus2 arrays. Three biological replicates of each condition were included.

2009-12-07 | E-MEXP-1838 | biostudies-arrayexpress

The global gene expression pattern by RCK1 over-expression

Project description:We did transcription profiling on the effect of RCK1 over-expression. rck1 mutant strain was transformed with empty high copy vector pRS425 empty vector), or with RCK1 cloned into pRS425 (the RCK1-overexpressing strain: RCK1 cloned into pRS425). Analysis was performed with rck1 (Empty vector, pRS425) mutant and RCK1 over-expressed cells (pRS425-RCK1). Yeast cells were grown on SD-leu medium. Yeast cells were grown overnight at 30M-BM-0C . The culture was refreshed to 0.2 O.D and grown at 30M-BM-0C for 2h 30min. Cell wall stress was applied by addition of zymolyase to a final concentration of 5 unit/ml . Cells were collected at 2 hours of growth and processed for RNA extraction.

2013-07-31 | E-GEOD-49340 | biostudies-arrayexpress

Genes differentially expressed as a result of Candida albicans SC5314 exposure to pterostilbene

Project description:Transcriptional profiling of Candida albicans comparing pterostilbene treated cells with untreated cells Wild type Candida albicans strain SC5314 was selected to carry out the expression profile microarray. Two-condition experiment, pterostilbene treated vs. untreated cells. Biological replicates: 3 control, 3 pterostilbene treated, independently grown and harvested. One replicate per array.

2014-03-23 | E-GEOD-43690 | biostudies-arrayexpress

ULK1 regulated phosphatases in mouse and human cells

Project description:In the project “ULK1 regulated phosphatases” by Zehan Hu, Devanarayanan Siva Sankar, Björn Stork and Jörn Dengjel two sets of bottom-up MS-based chemical proteomics experiments were performed in which phosphatase complexes were enriched based on their activity using microcystin-LR coupled sepharose beads. (1) Three biological replicates of MEFs (triple labeling) were performed comparing phosphatase activity (36 raw files labeled "2018"). ULK1 MEFs were compared DKO MEFs, both in rapamycin conditions. Empty beads were used as negative control (Ctrl). Following experiments were performed: (2) Three biological replicates of A549 cells (triple labeling) were performed comparing phosphatase activity (30 raw files labeled "A549"). A549 cells in fed conditions (DMEM) were compared to rapamycin treated cells (Rapa). Empty beads were used as negative control (Ctrl).

2021-11-03 | PXD022383 | Pride

miR-1245 induce genomic instability

Project description:This experiment is design to evaluate genomic alteration following stably expression of miR-1245, stably knock down of BRCA2 is setup as a positive control Primary normal breast epithelial cells (NBEC) were collected from the mammoplasty material of a 30-year-old woman at the Department of Plastic Surgery, the First Affiliated Hospital of Sun Yat-sen University (P. R. China), in accordance with rules and regulations concerning ethical issues on research use of human subjects in China, and were cultured in the Keratinocyte serum-free medium (Invitrogen, Carlsbad, CA) supplemented with epithelial growth factor, bovine pituitary extract and antibiotics (120 µg/mL streptomycin and 120 µg/mL penicillin). NBEC were infected with virus produced from retro vector pMSCV-miR1245 or empty pMSCV vector; or pSuper Retro BRCA2 shRNA, or pSuper Retro empty vector. After 2 days infection and 3 days culture, genomic DNA was isolated using the QIAamp DNA Mini Kit (QIAGENE, Valencia, CA). CGH microarray hybridization, data generation and normalization were performed in Shanghai Biochip Corporation.

2011-03-23 | E-GEOD-26715 | biostudies-arrayexpress

Human HEK 293T cells transfected with pEGFP-survivin gene

Project description:Transcriptional profiling of human embryonic kidney 293 cells comparing transfected control pEGFP-C1 (empty vector) with pEGFP (survivin vector). One condition experiment; survivin transfected cell as test sample vs empty vector transfected cell as reference; one dye swap replicate

2014-10-21 | E-GEOD-43817 | biostudies-arrayexpress

Expression data from recoverin positive and negative A549 cell lines

Project description:We compared the transcriptional signatures of recoverin (Rec) negative lung adenocarcinoma A549 cells which had been transfected with a plasmid containing human recoverin cDNA (A549 Rec) or an empty plasmid as a mock control (A549 MOCK).

2023-01-11 | GSE218942 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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