Unknown,Transcriptomics,Genomics,Proteomics

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A Novel Human Leiomyoma Tissue Derived Matrix for Cell Culture Studies

ABSTRACT: The composition of the matrix molecules is important in in vitro cell culture experiments of e.g. human cancer invasion and vessel formation. Currently, the mouse Engelbreth-Holm-Swarm (EHS) sarcoma -derived products, such as MatrigelÂ®, are the most commonly used tumor microenvironment mimicking (TMEM) matrices for experimental studies. However, since MatrigelÂ® is non-human in origin, its molecular composition does not accurately simulate human TMEM and we expect myogel to be more natural environment for human cancer cells. The environment may have crucial impact on cell behavior and gene expression. The gene expression of the cells growing on top of myogel compared to those growing on top of plastic were sought for potential differencies. 90 000 HSC-3 cells were cultured in 6-well plates (three replicates) with and without myogel coating. The RNA samples were pooled and the changes in gene expressions were analyzed.

ORGANISM(S): Homo sapiens

SUBMITTER: Pirjo ÃstrÃ¶m

PROVIDER: E-GEOD-68722 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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A novel human leiomyoma tissue derived matrix for cell culture studies.

Salo Tuula T Sutinen Meeri M Hoque Apu Ehsanul E Sundquist Elias E Cervigne Nilva K NK de Oliveira Carine Ervolino CE Akram Saad Ullah SU Ohlmeier Steffen S Suomi Fumi F Eklund Lauri L Juusela Pirjo P Åström Pirjo P Bitu Carolina Cavalcante CC Santala Markku M Savolainen Kalle K Korvala Johanna J Paes Leme Adriana Franco AF Coletta Ricardo D RD

BMC cancer 20151216

<h4>Background</h4>The composition of the matrix molecules is important in in vitro cell culture experiments of e.g. human cancer invasion and vessel formation. Currently, the mouse Engelbreth-Holm-Swarm (EHS) sarcoma-derived products, such as Matrigel®, are the most commonly used tumor microenvironment (TME) mimicking matrices for experimental studies. However, since Matrigel® is non-human in origin, its molecular composition does not accurately simulate human TME. We have previously described ...[more]

PMID: 26673244

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Project description:RNA decay was measured in Prochlorococcus after inhibition of transcription by rifampicin using customized Affymetrix gene expression arrays. RNA turnover plays an important role in the gene regulation of microorganisms and influences their speed of acclimation to environmental changes. We investigated whole-genome RNA stability of Prochlorococcus, a relatively slow-growing marine cyanobacterium doubling approximately once a day, which is extremely abundant in the oceans. Using a combination of microarrays, quantitative RT-PCR and a new algorithm for determining RNA decay rates, we found a median half-life of 2.4 min and a median decay rate of 2.6 min for expressed genes â two-fold faster than that reported for any organism. The shortest transcript half-life (33 seconds) was for a gene of unknown function, while some of the longest (ca. 18 min) were for highly expressed genes. Genes organized in operons displayed intriguing mRNA decay patterns, such as increased stability, and delayed onset of decay with greater distance from the transcriptional start site. The same phenomenon was observed on a single probe resolution for genes greater than 2 kb. We hypothesize that the fast turnover relative to generation time in Prochlorococcus may enable a swift response to environmental changes through rapid recycling of nucleotides, which could be advantageous in nutrient poor oceans. Our growing understanding of RNA half-lives will inform on the modelling of cell processes and help interpret the growing bank of metatranscriptomic studies of wild populations of Prochlorococcus. The surprisingly complex decay patterns of large transcripts reported here, and the method developed to describe them, will open new avenues for the investigation and understanding of RNA decay for all organisms. Prochlorococcus cells were treated with rifampicin, which prevents initiation of new transcripts. Cells were harvested at 0 min (before rifampicin addition), 2.5 min, 5 min, 10 min, 20 min, 40 min and 60 min after rifampicin addition.

Dataset Information

A Novel Human Leiomyoma Tissue Derived Matrix for Cell Culture Studies

Publications

A novel human leiomyoma tissue derived matrix for cell culture studies.

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