Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

34 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

A Dictyostelium SH2 domain adaptor protein required for correct DIF-1 signaling and pattern formation

ABSTRACT: When developing in the light slug formation in LrrB null (lrrB-) mutants is delayed, relative to the parental strain, and the slugs are highly defective in phototaxis and thermotaxis. In the dark the mutant arrests development as an elongated mound, in a novel process we term dark stalling. The developmental and phototaxis defects are cell autonomous and marker analysis shows that the pstO prestalk sub-region of the slug is aberrant in the lrrB- mutant. Expression profiling reveals many other alterations in gene expression in lrrB- slugs compared to the wild-type parental Ax2 line, including greatly reduced expression of the ecmB gene.

ORGANISM(S): Dictyostelium discoideum

SUBMITTER: Gareth Bloomfield

PROVIDER: E-TABM-1090 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

A Dictyostelium SH2 adaptor protein required for correct DIF-1 signaling and pattern formation.

Sugden Christopher C Ross Susan S Annesley Sarah J SJ Cole Christian C Bloomfield Gareth G Ivens Alasdair A Skelton Jason J Fisher Paul R PR Barton Geoffrey G Williams Jeffrey G JG

Developmental biology 20110321 2

Dictyostelium is the only non-metazoan with functionally analyzed SH2 domains and studying them can give insights into their evolution and wider potential. LrrB has a novel domain configuration with leucine-rich repeat, 14-3-3 and SH2 protein-protein interaction modules. It is required for the correct expression of several specific genes in early development and here we characterize its role in later, multicellular development. During development in the light, slug formation in LrrB null (lrrB-) ...[more]

PMID: 21396932

Similar Datasets

Influence of Slug/SNAI2 on global gene expression in CRC cells and tumors

Project description:To establish the role of Slug in CRC, we created a genetic CRC model for Slug expression. As parental cells, we selected HT-29 cells that display a pronounced epithelial phe-notype. HT-29 cells were transfected with Slug, and two stable Slug-expressing clones. (Slug1, Slug2) were isolated. As transfection control, we used HT-29 cells transfected with empty vector (control). To characterize the influence of Slug on gene ex-pression, transcriptome analysis was performed for the four HT-29 cell lines as well as for the corresponding tumor xenografts. Global expression profiling showed that Slug-overexpressing cells and tumors were clustered together while the parental and control cells and tumors formed a separate cluster. Next, a two-step analysis was carried out. First, a subtractive analysis was carried out comparing the gene profiles of Slug-expressing cells and tumors with the corresponding parental/control samples. Genes were considered to be significantly upregulated by Slug if the fold change (FC) was greater than +2 and downregulated if the fold change was less than −2 with p-values (false dis-covery rates) less than 0.01

2022-06-11 | E-MTAB-11812 | biostudies-arrayexpress

Expression analysis of HepG2, HepG2-slug and HepG2-slug on Matrigel

Project description:Investigation of whole genome gene expression level changes in hepatocellular carcinoma cell line hepG2 in regular culture, hepG2-slug in regular culture and hepG2-slug on Matrigel. Whole genome gene expression level changes have been compared in hepatocellular carcinoma cell line hepG2 in regular culture, hepG2-slug in regular culture and hepG2-slug on Matrigel. Roche NimbleGen micro-array analysis was employed to assess global genome expression in HepG2 in regular culture, HepG2-slug in regular culture and HepG2-slug on Matrigel. The results demonstrated that the up-regulated genes and the down-regulated genes increased significantly when HepG2-slug cells with VM forming ablity were cultured on Matrigel and formed VM.

2012-09-21 | E-GEOD-41026 | biostudies-arrayexpress

Combined proteomic and transcriptomic analysis of Arion vulgaris

Project description:The Spanish slug, Arion vulgaris, is considered one of the hundred most invasive species in Central Europe. The lack of natural predators can refer to the potential toxicity of slugs. However, no transcriptomic or proteomic study has been done so far in Arion vulgaris. In this study, we present the first investigation of expression profile in Arion vulgaris at the protein level. Two-dimensional (2D) gel electrophoresis and nano-LC-ESI-MS/MS were used to resolve and identify proteins from slug mantel and slug eggs. To facilitate proteomics in non-model organisms, mRNA-derived protein database was used for protein identification.

2016-03-22 | PXD002078 | Pride

Expression data of mammary epithelial cells during the epithelial-mesenchymal transition

Project description:The EMT program allows epithelial cells to become endowed with motility, invasiveness and stem cell traits. We investigated difference in signaling networks that are differentially utilized in EMTed and non-EMTed cells, thereby identifying therapeutic targets that are unique to EMT/cancer stem cells. We expressed the EMT transcription factors, Twist, Snail and Slug in HMLE human mammary epithelial cells, and compared their gene expression with parental cells. We identified kinases that are more differentially regulated between the epithelial and mesenchymal cell state.

2013-09-09 | E-GEOD-43495 | biostudies-arrayexpress

Proteomic profiling of the extracellular matrix (slime sheath) of Dictyostelium discoideum

Project description:Dictyostelium discoideum has historically served as a model system for cell and developmental biology, but recently it has gained increasing attention as a model for the study of human diseases. The extracellular matrix (ECM) of this eukaryotic microbe serves multiple essential functions during development. It not only provides structural integrity to the moving multicellular pseudoplasmodium, or slug, it also provides components that regulate cell motlity and differentiation. An LC/MS/MS analysis of slug ECM revealed the presence of a large number of proteins in two wild-type strains, NC4 and WS380B. GO annotation identified proteins involved in binding, as well as proteins that modulate metabolic processes, cell movement, and multicellular development. In addition, this proteomic analysis identified numerous expected, as well as unexpected components.

2015-07-22 | PXD002040 | Pride

CHD chromatin remodelers regulate separate gene sets and distinct stages of Dictyostelium development

Project description:We utilized RNA-seq to profile expression levels in wild type AX2 cells and three mutants for the CHD family of ATP-dependent chromatin remodellers in Dictyostelium discoideum. Total RNA was polyA enriched and sequenced at two stages of development: in the growth stage (0H) and in 5H cAMP pulsed cells (5H). All mutants analysed were also in the AX2 background. Looking at mRNA levels in AX2, chdA-, chdB- and chdC-.

2014-01-03 | E-GEOD-47222 | biostudies-arrayexpress

Slug overexpression

Project description:This SuperSeries is composed of the following subset Series: GSE41026: Expression analysis of HepG2, HepG2-slug and HepG2-slug on Matrigel GSE41027: Chip-chip from HepG2 cells and HepG2 cells with slug overexpression Refer to individual Series

2012-09-21 | E-GEOD-41028 | biostudies-arrayexpress

The invasion promoter Slug is a critical cell cycle regulator

Project description:Background: The well-characterized function of the transcriptional repressor, Slug, is to promote EMT and tumor invasion/metastasis by down-regulating E-cadherin expression. In this study, we investigated the significance of Slug during the S phase. Method: Slug mRNA expression was isolated from thymidine-arrested CL1-5/AS2neo (control) and CL1-5/AS2neo-Slug-WT stable cells. The Agilent oligonucleotide microarray analysis was performed to identify Slug downstream genes. Results: Overexpression of Slug inhibited lung [3H]-thymidine incorporation and delayed S phase progression. By using Agilent microarray we have identified panel of genes altered by Slug overexpression. Slug can down-regulate target genes about cell cycle networks for DNA replication, DNA replication checkpoint and genomic stability, such as TOP1, ORC4, RFC3, and Rad17. Conclusions: the multifaceted role of Slug in cancer progression by controlling the epithelial-mesenchymal transition and genome stability. Two-condition experiment, Vector vs. Slug overexpression cells. The cDNAs encoding full-length human Slug were amplified and subcloned into lentiviral pLKO_AS2.neo which generated full-length Slug. Vector control or Slug lentivirus were transduced into CL1-5 cells and Gentamycin was used to select stable cells.

2012-02-09 | E-GEOD-35617 | biostudies-arrayexpress

Analysis of gene expression change due to knockdown of Slug expression in a basal-subtype breast cancer cell line, MCFDCIS.

Project description:Analysis of gene expression change due to knockdown of Slug expression in a basal-subtype breast cancer cell line, MCFDCIS. Total RNA isolated from MCFDCIS cells transfected with control or Slug specific siRNA.

2016-08-11 | E-GEOD-72011 | biostudies-arrayexpress

DcgA knock-out experiment in Dictyostelium discoideum

Project description:Four replicates of DcgA gene knockout D. discoideum clones were sequenced together with four replicates of random integrant clones. All clones were from the same AX2 strain.

2017-02-01 | E-MTAB-3829 | 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