Transcription profiling of mouse migrating cell bodies vs pseudopodia fibronectin
Ontology highlight
ABSTRACT:
ORGANISM(S): Mus musculus
SUBMITTER: Stavroula Mili
PROVIDER: E-GEOD-10227 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:The goal of the study was to identify on a genome-wide scale RNAs that are enriched at the leading edge of migrating cells. For this, we employed a fractionation method in which serum-starved cells are first plated and allowed to spread on a microporous filter. Addition of LPA at the bottom side of the filter induces the cells to polarize and extend pseudopodial protrusions. These protruding pseudopodia can then be physically isolated from the bottom surface of the filter and their contents compared with the remaining cell bodies, which are isolated from the upper surface of the filter. Experiment Overall Design: We analyzed two independent pseudopodia samples (05-61_PS_A and 06-04_PS_A) and two independent cell body samples (05-61_CB_A and 06-04_CB_A)
2008-04-05 | E-GEOD-10226 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the following subset Series:; GSE10226: Analysis of RNA distribution between pseudopodia and cell bodies in response to LPA stimulation; GSE10227: Analysis of RNA distribution between pseudopodia and cell bodies in response to Fibronectin Experiment Overall Design: Refer to individual Series
2008-04-05 | E-GEOD-10230 | biostudies-arrayexpress
Project description:The goal of the study was to identify on a genome-wide scale RNAs that are enriched at the leading edge of migrating cells. For this, we employed a fractionation method in which cells are plated on a microporous filter whose bottom side only is coated with fibronectin. The cells thus polarize and extend pseudopodial protrusions towards the bottom surface. These protruding pseudopodia can then be physically isolated from the bottom surface of the filter and their contents compared with the remaining cell bodies, which are isolated from the upper surface of the filter. Keywords: comparative RNA distribution
2008-03-18 | GSE10227 | GEO
Project description:The goal of the study was to identify on a genome-wide scale RNAs that are enriched at the leading edge of migrating cells. For this, we employed a fractionation method in which serum-starved cells are first plated and allowed to spread on a microporous filter. Addition of LPA at the bottom side of the filter induces the cells to polarize and extend pseudopodial protrusions. These protruding pseudopodia can then be physically isolated from the bottom surface of the filter and their contents compared with the remaining cell bodies, which are isolated from the upper surface of the filter. Keywords: comparative RNA distribution
2008-03-18 | GSE10226 | GEO
Project description:mRNA trafficking and local protein translation are associated with protrusive cellular domains, such as neuronal growth cones, and deregulated control of protein translation is associated with tumor malignancy. We show here that activated RhoA, but not Rac1, is enriched in pseudopodia of MSV-MDCK-INV tumor cells and that Rho, Rho kinase (ROCK) and myosin II regulate the microtubule-independent targeting of RNA to these tumor cell domains. ROCK inhibition does not affect pseudopodial actin turnover but significantly reduces the dynamics of pseudopodial RNA turnover. Gene array analysis shows that 7.3% of the total genes analyzed exhibited a greater than 1.6-fold difference between the pseudopod and cell body fractions. Of these, only 13.2% (261 genes) are enriched in pseudopodia, suggesting that only a limited number of total cellular mRNAs are enriched in tumor cell protrusions. Comparison of the tumor pseudopod mRNA cohort and a cohort of mRNAs enriched in neuronal processes identified tumor pseudopod-specific signaling networks that were defined by expression of M-Ras and the Shp2 protein phosphatase. Pseudopod expression of M-Ras and Shp2 mRNA were diminished by ROCK inhibition linking pseudopodial Rho/ROCK activation to the localized expression of specific mRNAs. Pseudopodial enrichment for mRNAs involved in protein translation and signaling suggests that local mRNA translation regulates pseudopodial expression of less stable signaling molecules as well as the cellular machinery to translate these mRNAs. mRNA trafficking and local protein translation are associated with protrusive cellular domains, such as neuronal growth cones, and deregulated control of protein translation is associated with tumor malignancy. We show here that activated RhoA, but not Rac1, is enriched in pseudopodia of MSV-MDCK-INV tumor cells and that Rho, Rho kinase (ROCK) and myosin II regulate the microtubule-independent targeting of RNA to these tumor cell domains. ROCK inhibition does not affect pseudopodial actin turnover but significantly reduces the dynamics of pseudopodial RNA turnover. Gene array analysis shows that 7.3% of the total genes analyzed exhibited a greater than 1.6-fold difference between the pseudopod and cell body fractions. Of these, only 13.2% (261 genes) are enriched in pseudopodia, suggesting that only a limited number of total cellular mRNAs are enriched in tumor cell protrusions. Comparison of the tumor pseudopod mRNA cohort and a cohort of mRNAs enriched in neuronal processes identified tumor pseudopod-specific signaling networks that were defined by expression of M-Ras and the Shp2 protein phosphatase. Pseudopod expression of M-Ras and Shp2 mRNA were diminished by ROCK inhibition linking pseudopodial Rho/ROCK activation to the localized expression of specific mRNAs. Pseudopodial enrichment for mRNAs involved in protein translation and signaling suggests that local mRNA translation regulates pseudopodial expression of less stable signaling molecules as well as the cellular machinery to translate these mRNAs. Pseudopodial Rho/ROCK activation may impact on tumor cell migration and metastasis by stimulating the pseudopodial translocation of mRNAs and thereby regulating the expression of local signaling cascades. Keywords: tumor cells, protrusive cellular domains, pseudopodia vs cell body, RNA trafficking Pseudopod purification- Pseudopodia purification was performed as previously described (Jia et al, J. Biol. Chem. 280, 30564-73, 2005). Briefly, 107 MSV-MDCK-INV cells were plated on 100 mm 1um pore filters mounted between two 3-3.5â custom-made washers (Boulons Plus, Anjou, QC) in a 100 mm Falcon Petri dish and the exterior sealed with agarose to prevent cell leakage to the bottom of the filter. After 24 hours culture, the filter was washed 4 times with cold PBS containing 0.1 mM Ca2+ and 1 mM Mg2+ and the top (cell bodies) and bottom (pseudopodia) of the filter scraped with a glass cover slip in ice-cold lysis buffer (20 mM Tris-HCl pH 7.6, 0.5% NP-40, 250 mM NaCl, 3 mM EDTA, 3 mM EGTA containing freshly added 2 mM DTT, 0.5 mM PMSF, 1 mM sodium vanadate, 2.5 mM sodium fluoride and 1uM leupeptin). Affymetrix gene array- GeneChips were processed at the London Regional Genomics Centre (Robarts Research Institute, London, Ontario, Canada; http://www.lrge.ca). Six Affymetrix canine arrays (3 pseudopodia, 3 cell body) were scanned with the Affymetrix GeneChip Scanner 3000 and signal intensities for genes generated with GCOS1.2 (Affymetrix Inc., Santa Clara, CA) using default values for statistical expression algorithm parameters, a target signal of 150 for all probe sets and a normalization value of 1. To determine significant differences in gene expression levels between pseudopodia and cell body samples, 1 way-ANOVA was performed using Partek Pro (St. Louis, MO). Significantly modulated genes were defined as those with absolute log2 fold change greater than 0.7. Genes were summarized together using hierarchical clustering by Z score normalized data crossing all 6 samples.
2010-05-18 | E-GEOD-13253 | biostudies-arrayexpress
Project description:Analysis of bacterial fraction collected on GF/F filters post pre-filtration on 1um filter. 15L were filtered from Bering Strait (BSt) surface water and Chukchi Sea (station 2) bottom waters.
2019-01-25 | PXD006472 | Pride
Project description:For the studies of cell migration in various micro-environments, self-assembled monolayer surfaces presenting adhesive ligand, RGD peptide, were used for the assay. Presentation of RGD ligands was based on the immobilization reaction with alkanethiols on a gold surface. There were differences in cell morphology and migration according to the ligand affinity (linear vs. cyclic RGD) and manner of ligand presentation (dynamic vs. non-dynamic). In dynamic surface experiment, cells initially grown on the fibronectin-coated patterns were exposed to either linear or cyclic RGD while in non-dynamic surface experiment cells interacted with the immobilized RGD from the beginning. Goal was to compare how the affinity and spatio-temporal exposure of ligand affect the overall transcriptional profiling. Five conditioned surfaces were prepared by chemical treatment for cell culture: Fibronectin, Dynamic linear RGD, Dynamic cyclic RGD, Non-dynamic linear RGD, and Non-dynamic cyclic RGD surfaces. Reference: cells cultured in standard tissue culture flasks. Biological replicates: triplicates for each experiment (each surface was 1.25 cm x 1.25 cm and three surfaces were used for each condition). When reached 70-80% of confluency, cells from the triplicates were pooled and harvested for RNA extraction. Hybridization replicates: 4 replicates for each condition.
2014-10-15 | E-GEOD-62304 | biostudies-arrayexpress
Project description:Sample preparation is a crucial step in bottom-up proteomics. Analytical performances of bottom-up proteomics can be improved by the miniaturization of sample preparation steps. Many microfluidic devices are proposed in the field of proteomics. But many of them are not capable of handling complex sample and do not integrate the processing and digestion steps. We propose a ChipFilter Proteolysis (CFP) microfluidic device derived from the Filter Aided Sample Preparation FASP method for the miniaturization of protein processing and digestion steps in bottom-up proteomics. The microchip has two reaction chambers of 0.6 µL volume separated by a protein filtration membrane in regenerated cellulose. Cell lysis, protein concentration and rapid chemical and enzymatic treatment can be performed in our microfluidic device. Complex proteomic samples like yeast protein extract have already been analyzed with our microchip. Compared to the traditional FASP method, our microfluidic device offers a better proteome coverage with ten times less starting material and eight times quicker protocol.
2020-04-29 | PXD018066 | Pride
Project description:Sample preparation is a crucial step in bottom-up proteomics. Analytical performances of bottom-up proteomics can be improved by the miniaturization of sample preparation steps. Many microfluidic devices are proposed in the field of proteomics. But many of them are not capable of handling complex sample and do not integrate the processing and digestion steps. We propose a ChipFilter Proteolysis (CFP) microfluidic device derived from the Filter Aided Sample Preparation FASP method for the miniaturization of protein processing and digestion steps in bottom-up proteomics. The microchip has two reaction chambers of 0.6 µL volume separated by a protein filtration membrane in regenerated cellulose. Cell lysis, protein concentration and rapid chemical and enzymatic treatment can be performed in our microfluidic device. Complex proteomic samples like yeast protein extract have already been analyzed with our microchip. Compared to the traditional FASP method, our microfluidic device offers a better proteome coverage with ten times less starting material and eight times quicker protocol.
2020-04-29 | PXD016742 | Pride
Project description:Microbial Mat Metagenome from Zacaton Surface Filter
| PRJNA38467 | ENA