Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Next Generation Sequencing Facilitates Quantitative Analysis of SW480 cells and HPSE-knockdown SW480 cells Transcriptomes

ABSTRACT: Heparanase (HPSE), the only known mammalian endoglycosidase responsible for heparan sulfate cleavage, is a multi-faceted protein affecting multiple malignant behaviors in cancer cells. The goals of this study are to compare the mRNA transcriptome differences between SW480 cells and HPSE-knockdown SW480 cells. Methods: mRNA profiles of SW480 cells and HPSE-knockdown SW480 cells were generated by deep sequencing, in triplicate, using Illumina.

ORGANISM(S): Homo sapiens

PROVIDER: GSE126504 | GEO | 2019/02/14

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

mRNA-seq of SW480 USP22 knockdown cells

Project description:mRNA-seq of SW480 USP22 knockdown cells

| PRJEB33859 | ENA

Ezrin knockdown in SW480

Project description:Analysis of SW480 cells following knockdown of Ezrin using RNAi. Ezrin is a protein that regulate the organization of cytoskeleton. Ezrin KD SW480 was used to study the role of ezrin in colon cancer. Keywords: ezrin, colon cancer, migration

2008-04-29 | GSE11279 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of SW480 cells and HPSE-knockdown SW480 cells Transcriptomes

Project description:Next Generation Sequencing Facilitates Quantitative Analysis of SW480 cells and HPSE-knockdown SW480 cells Transcriptomes

| PRJNA522246 | ENA

mRNA-seq of SW480 USP22 knockdown cells

Project description:This analysis identifies genes which are affected in SW480 cells upon siRNA-mediated USP22 knockdown

2019-12-05 | E-MTAB-8214 | biostudies-arrayexpress

Expression data from SW480 cells with Gankyrin knockdown

Project description:We performed genome-wide screening using SW480 cells with Gankyrin knockdown on an Affymetrix gene expression array to identify the transcriptional targets of Gankyrin. Transcriptional profiling with samples from SW480 cells that were infected with control or gankyrin shRNA. Two condition experiment: control shRNA (three replicates) and NFIL3 shRNA (three replicates)

2013-02-04 | E-GEOD-44029 | biostudies-arrayexpress

Expression data from SW480 cells with Gankyrin knockdown

Project description:we performed genome-wide screening using SW480 cells with Gankyrin knockdown on an Affymetrix gene expression array to identify the transcriptional targets of Gankyrin

2013-02-04 | GSE44029 | GEO

SW480 cells undergoes postmitotic neuron-like differentiation in response to EZH2 knockdown

Project description:Formerly we found that combined inhibition of class I HDACs, DNMTs, EZH2 and LSD1 with chemical inhibitors in a variety of cancer cells caused neuronal differentiation. Our recent study demonstrated that functional knockdown of EZH2 alone in SW480 cells can also lead to significant neuronal differentiation. We used microarray to analyze global gene expression change in SW480 cells after neuronal differentiation induced by EZH2 knockdown.

2018-12-31 | GSE118593 | GEO

Systems-wide RNAi analysis of different chr13 genes in colorectal cancer cell line (SW480)

Project description:Expression profiles were generated for eight genes located on chromosome 13 following RNAi to enable the determination of gene specific LOF RNAi signatures in the colorectal cancer cell line SW480. Triplicate transfections of SW480 cells were performed using two different siRNA duplexes corresponding to each gene target in 6-well plates using the same protocol scaled 30-fold. RNA was purified 72 hrs after transfection. RNA was also purified from negative control siRNA-transfected cells (AllStar siNegative (siNEG), Qiagen). Reduction in target mRNA levels was confirmed by real-time PCR prior to the array analysis.

2013-04-05 | E-GEOD-33824 | biostudies-arrayexpress

Expression data from adult mice pulmonary endothelial cells

Project description:Sepsis patients are at increased risk for hospital-acquired pulmonary infections, potentially due to post-septic immunosuppression known as the compensatory anti-inflammatory response syndrome (CARS). CARS has been attributed to leukocyte dysfunction, with an unclear role for endothelial cells. The pulmonary circulation is lined by an endothelial glycocalyx, a heparan sulfate-rich layer essential to pulmonary homeostasis. Heparan sulfate degradation occurs early in sepsis, leading to lung injury. Endothelial synthesis of new heparan sulfates subsequently allows for glycocalyx reconstitution and endothelial recovery. We hypothesized that remodeling of the reconstituted endothelial glycocalyx, mediated by alterations in the endothelial machinery responsible for heparan sulfate synthesis, contributes to CARS. Our experimental animal model of CARS recapitulated post-septic immunosuppression, coincidentally with structural remodeling of endothelial glycocalyx heparan sulfate. We used microarray to identify which heparan sulfate modifying enzyme is responsible for the remodeling of post-septic reconstituted glycocalyx, characterized with enrichment of heparan sulfate disaccharides sulfated at the 6-O position of glucosamine.

2019-04-14 | GSE129775 | GEO

Examine differential expression of sulf-1 and sulf-2, enzymes involved in heparan sulfate biosynthesis

Project description:Our specific aim is to examine differential expression of sulf-1 and sulf-2, enzymes involved in heparan sulfate biosynthesis, as well as Wnt ligands and Wnt signaling mediators during corneal wound healing using a mouse corneal scratch model. The specific structural features of heparan sulfate underlie its role in modulating cellular responses to growth factors such as the Wnts. Heparan sulfate 6-O-endosulfatases (sulf-1 and sulf-2) remove 6-O sulfate group from trisulfated disaccharides present on heparan sulfate chains. Our preliminary results suggest that sulf-1 is upregulated at the protein level in the epithelial cells of wounded mouse corneas, as compared to the undamaged contralateral eye. Modulation of heparan sulfate proteoglycan expression and/or structural modifications of its chains might be an important aspect of the regulation of epithelial cell migration and proliferation during wound healing.

2011-04-29 | GSE28931 | GEO

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