Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

29 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Microarray analyses of cDNA expressions of long-term-cultured breast cancer stem cells in comparison with TV-circRGPD6-treated group and si-circRGPD6 group

ABSTRACT: RNA extraction and microarray analysis total RNA from long-term-cultured breast cancer stem cells of TV-circRGPD6-treated group and si-circRGPD6 group. Microarray experiments were conducted according to the manufacturer's instructions. To select the differentially expressed genes, we used threshold values of ≥ 2 and ≤2-fold change and a Benjamini-Hochberg corrected p value of 0.05. The data was Log2 transformed and median centered by genes using the Adjust Data function of Cluster 3.0 software then further analyzed with hierarchical clustering with average linkage (genes which value more than 100 were evaluated).

INSTRUMENT(S): GeneSpring software V12 (Agilent).

ORGANISM(S): Homo sapiens

SUBMITTER: Xiaoti Lin

PROVIDER: E-MTAB-7557 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Microarray analyses of microRNA expressions of long-term-cultured breast cancer stem cells in comparison with TV-circRGPD6-treated group and si-circRGPD6 group

Project description:RNA extraction and microarray analysis total RNA from long-term-cultured breast cancer stem cells of TV-circRGPD6-treated group and si-circRGPD6 group.The miRNA profiling was performed using Agilent miRNA array. Microarray experiments were conducted according to the manufacturer's instructions. To select the differentially expressed genes, we used threshold values of ≥ 2 and ≤2-fold change and a Benjamini-Hochberg corrected p value of 0.05. The data was Log2 transformed and median centered by genes using the Adjust Data function of Cluster 3.0 software then further analyzed with hierarchical clustering with average linkage (genes which value more than 100 were evaluated).

2022-02-13 | E-MTAB-7556 | biostudies-arrayexpress

Antagonizing miR-128 abrogates chemoresistance-associated metastasis and is therapeutic in non-small cell lung cancer [miRNA]

Project description:This experiment is designed to screen miRNAs that are deregulated during chemoresistance-associated metastasis of lung cancer cells. Chemoresistant metastatic in vivo tumor model of A549-luc-Vector cells was established after four rounds of cisplatin (CDDP) treatments compared to corresponding control solvent treatments. Upon examining profiles of miRNA expression differential between tumor-derived cultured cells from the Ctrl-4th and CDDP-4th treatments, most markedly upregulated and downregulated miRNAs in chemoresistant, metastatic A549-luc-CDDP-4th cells were identified. In order to establish a chemoresistant in vivo tumor model, after inoculation of A549-luc-Vector cells, cisplatin (CDDP) or control solvent was intraperitoneally (i.p.) injected six rounds in a two-week period and cells were isolated from corresponding resultant tumors, cultured and re-transplanted into syngeneic mice to receive the next round of treatment. In our experimental model, human lung cancer xenografts developed chemoresistance in the third round of CDDP treatment (CDDP-3rd) and chemoresistance-associated metastases following the fourth round of treatment. Tumor-derived cultured cells from Ctrl-4th and CDDP (cisplatin)-4th treatment were subjected to miRNA array (Agilent-031181 human miRNA (8*60k) V16.0) analysis, with two biological replications for each treatment.

2015-04-10 | E-GEOD-67727 | biostudies-arrayexpress

Antagonizing miR-128 abrogates chemoresistance-associated metastasis and is therapeutic in non-small cell lung cancer

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2015-04-10 | E-GEOD-67729 | biostudies-arrayexpress

Microarray analyses of microRNA expressions in comparison with immortal healthy mammary epithelial cells, breast cancer cells, and long-term-cultured breast cancer stem cells

Project description:RNA extraction and microarray analysis total RNA from immortalized normal mammary epithelial cells (184A1, MCF-12A), breast cancer cells (MDA-MB-231, MCF-7, MDA-MB-468, SK-BR-3), BCSC (MDA-MB-231SC, MCF-7SC, XM322, XM607). MDA-MB-231SC and MCF-7SC originating from breast cancer cell lines; XM322 and XM607 derived from clinical specimens which had been described in previous submission (E-MTAB-5057). The miRNA profiling was performed using Agilent miRNA array. Microarray experiments were conducted according to the manufacturer's instructions. To select the differentially expressed genes, we used threshold values of ≥ 2 and ≤ −2-fold change and a Benjamini-Hochberg corrected p value of 0.05. The data was Log2 transformed and median centered by genes using the Adjust Data function of Cluster 3.0 software then further analyzed with hierarchical clustering with average linkage (genes which value more than 100 were evaluated).

2017-12-01 | E-MTAB-5584 | biostudies-arrayexpress

PAPERCLIP identifies novel microRNA targets and provides insights into mRNA alternative polyadenylation

Project description:Accurate and precise annotation of the 3â² untranslated regions (3â² UTRs) is critical in understanding how mRNA stability, localization and translational efficiency are regulated by microRNAs (miRNAs) and RNA-binding proteins (RBPs). Here we describe a novel method, PAPERCLIP (Poly(A) binding Protein-mediated mRNA 3Â´End Retrieval by CrossLinking ImmunoPrecipitation), which shows high specificity for the mRNA 3â² ends and compares favorably to existing 3â² end mapping methods including direct RNA sequencing in performance. PAPERCLIP protocol and RNA-Seq on human cell lines and mouse whole brain cortex.

2016-02-19 | E-GEOD-66092 | biostudies-arrayexpress

Global Transcriptional Analysis of Nuclear Reprogramming in the Transition from MEFs to iPSCs

Project description:Here, we focused on the intermediate stages of SCR by comparing the somatic cell line induced by OCT4, SOX2, and KLF4 (OSK) for 7 days with mouse embryonic fibroblasts (MEFs), iPSCs, and embryonic stem cells (ESCs). Transcriptional profiles of these four cell lines were analyzed by microarray, and we found that the transition process from day 7 to the formation of iPSCs is crucial for SCR and that the reverse expression patterns can provide more candidate markers to distinguish ESCs and somatic cells iPSC. Data confirmed that the viral infection results in defense innate immunity, DNA damage, and apoptosis in MEFs, which slows down cell proliferation and immortalization to inhibit SCR. Although SCR is initiated by OSK, the p53 signaling pathway can affect the transcriptional regulatory networks through cell cycle and genomic instability as a powerful core node. MEFs were derived from embryonic day 13.5 C57BL6 mice embryos. Cell line day7 is MEF induced by OCT4, SOX2, and KLF4 (OSK) for 7 days with mouse embryonic fibroblasts (MEFs), iPSCs, and embryonic stem cells (ESCs).

2012-10-01 | E-GEOD-37397 | biostudies-arrayexpress

miR-182 induced gene expression alteration in glioma cells

Project description:This experiment is designed to evaluate gene expression alteration following miR-182 transfection in glioma cells. We find a significant elevation of NF kappa B transcriptional targets. Total RNA were extracted from SNB-19 glioma cells transfected with miR-182 mimic oligo or miRNA mimic negative control 36 hours after transfection, two biological replications for each treatment.

2011-11-15 | E-GEOD-33293 | biostudies-arrayexpress

Gene expression profile of the SV40-immortalized human corneal epithelial cells

Project description:Microarray was used to study global gene expression of a cell culture model based on SV40-immortalized human corneal epithelial (iHCE) cells. The gene expression profile of the cell line was compared to the normal human corneal epithelium. Affymetrix HG-U133A GeneChipsÂ® were used for microarray experiments and results were validated by performing RT-qPCR for selected genes. iHCE was found to over- and under-express 22 % and 14 % of the annotated genes, respectively. The results of this study suggest that differences between iHCE cells and normal corneal epithelium are substantial and therefore the use of these cells in corneal research should be considered with caution. SV40-immortalized human corneal epithelial (iHCE) cells were cultured on collagen coated permeable supports for one week using standard culture conditions. Subsequently the apical medium was removed and culturing was continued at the air-liquid interface which allows cells to stratify. Trans-epithelial electrical resistance was followed and total RNA was extracted from cultures with resistance > 300 Î© x cm2. RNA was amplified, labeled with biotin, fragmented and hybridized to the HG-U133A GeneChipsÂ® (Affymetrix) according to the protocol of the manufacturer. Three separate experiments with samples from three independent culture batches (iHCE1, iHCE2, iHCE3) were performed. The Global gene expression profile of iHCE was compared to previously published human corneal epithelial tissue (GSE5543) data.

2010-07-29 | E-GEOD-22539 | biostudies-arrayexpress

AEG-1 silencing induced gene expression alteration in glioma cells

Project description:This experiment is designed to evaluate gene expression alteration following AEG-1 (MTDH) silencing in glioma cells. AEG-1 is found to be a potential regulator through interaction with other transcription factor. We intended to investigate the enriched transcription factor dependent downstream gene sets regulated by AEG-1 form the differential expressed genes we obtained from AEG-1 silencing. Total RNA were extracted from U87MG glioma cells stably silencing AEG-1 and correspondent pSuper Retro vector cells respectively. Passage 5 of the indicated cells after infection and selection were harvested for RNA extraction.

2011-07-12 | E-GEOD-29952 | biostudies-arrayexpress

Expression data at each site in colon cancer

Project description:Colon cancer invade to depper layer and the expression of major molecules at cancer front change. But the screening of expression changing at cancer front has not be adequtely clarified. We compared gene expression at cancer front with it at cancer center. We got cancer cells from cancer front(F) and cancer center(C) by lasermicrodissection.

2016-01-06 | E-GEOD-65480 | 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