Mus musculus
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA288290 | ENA |
REPOSITORIES: ENA
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Project description:We investigated the role of amino acid to maintain HSC function. To identify essential amino acids for HSCs, CD34-KSL cells were cultured in single amino acids deficient medium. And cultured cells were transplanted into lethally irradiated mice. Then, the donor chimerism and lineage contribution was estimated. Surprisingly, HSC proliferation was prevented in valine and cysteine deficient medium in vitro. Donor cells cultured in these medium were also not engrafted. To elucidate the effects and influences of cysteine and valine in HSCs, we performed global gene expression profiling experiments by RNA-sequencing analysis. Gene sets categorized with cell cycle, mitosis, cell division or DNA replication were strongly down-regulated in both valine- or cysteine-depleted conditions These results imply distinctive amino-acid metabolism involved in HSC division. Gene expression profiles of ten thousand HSCs cultured in cysteine or valine deficient medium for 24 hours were compared with that of HSCs cultured in complete medium by using RNA-sequencing analysis
2016-06-26 | E-GEOD-70307 | biostudies-arrayexpress
Project description:We investigated the role of amino acid to maintain HSC function. To identify essential amino acids for HSCs, CD34-KSL cells were cultured in single amino acids deficient medium. And cultured cells were transplanted into lethally irradiated mice. Then, the donor chimerism and lineage contribution was estimated. Surprisingly, HSC proliferation was prevented in valine and cysteine deficient medium in vitro. Donor cells cultured in these medium were also not engrafted. To elucidate the effects and influences of cysteine and valine in HSCs, we performed global gene expression profiling experiments by RNA-sequencing analysis. Gene sets categorized with cell cycle, mitosis, cell division or DNA replication were strongly down-regulated in both valine- or cysteine-depleted conditions These results imply distinctive amino-acid metabolism involved in HSC division.
2016-06-26 | GSE70307 | GEO
Project description:First experiment: Cells were cultured in sulfur amino acid-free DMEM supplemented with 0.1 mM methionine + 0.1 mM cysteine (complete) or supplemented only with 0.1 mM methionine (cysteine-free). Cells were cultured in either medium for 42 h (Long + Cys; Long -Cys) or in cysteine-free medium for 36 h followed by 6 h in complete medium (Short +Cys) Second experiment: C3A/HepG2 cells were cultured in sulfur amino acid-free DMEM supplemented with 0.1 mM Met and 0.1 mM Cys (complete) or supplemented only with 0.1 mM Met (cysteine-devoid). Cells were cultured in complete medium for 42 h (Long +Cys) or in complete medium for 36 h followed by cysteine-devoid medium for 6 h (Short -Cys). Keywords: amino acid deprivation
2007-12-13 | GSE9517 | GEO
Project description:First experiment: Cells were cultured in sulfur amino acid-free DMEM supplemented with 0.1 mM methionine + 0.1 mM cysteine (complete) or supplemented only with 0.1 mM methionine (cysteine-free). Cells were cultured in either medium for 42 h (Long + Cys; Long -Cys) or in cysteine-free medium for 36 h followed by 6 h in complete medium (Short +Cys); Second experiment: C3A/HepG2 cells were cultured in sulfur amino acid-free DMEM supplemented with 0.1 mM Met and 0.1 mM Cys (complete) or supplemented only with 0.1 mM Met (cysteine-devoid). Cells were cultured in complete medium for 42 h (Long +Cys) or in complete medium for 36 h followed by cysteine-devoid medium for 6 h (Short -Cys). Experiment Overall Design: First experiment: Three plates of cells were cultured under each condition. Cells were cultured in sulfur amino acid-free DMEM supplemented with 0.1 mM methionine + 0.1 mM cysteine (complete) or supplemented only with 0.1 mM methionine (cysteine-free). Cells were cultured in either medium for 42 h (Long + Cys; Long -Cys) or in cysteine-free medium for 36 h followed by 6 h in complete medium (Short +Cys). Experiment Overall Design: Second experiment: C3A/HepG2 cells were cultured in sulfur amino acid-free DMEM supplemented with 0.1 mM Met and 0.1 mM Cys (complete) or supplemented only with 0.1 mM Met (cysteine-devoid). Cells were cultured in complete medium for 42 h (Long +Cys) or in complete medium for 36 h followed by cysteine-devoid medium for 6 h (Short -Cys).
2008-06-16 | E-GEOD-9517 | biostudies-arrayexpress
Project description:Purpose: The goal of this study is to examine gene expression regulation at the transcriptional and translational levels in response to various forms of nutrient deprivation, and whether there are differences between isogenic transformed and non-transformed cells. Mehods: We apply high-throughput sequencing of ribosome footprints (ribosome profiling) and poly(A) RNA (RNA sequencing) in an isogenic pair of transformed (tamoxifen-treated) and non-transformed (ethanol control) MCF10A-ER-Src cells subjected to the metabolic stresses that differentially affect global protein synthesis (Figure 1): deprivation of glutamine (for 30min and 4 hours), glucose (4hours), cysteine/cystine (4hours) or leucine/isoleucine/valine (brach-chain aminoacids - BCAA) (4hours). The same experiments were also performed in transformed ER-Src MCF10A treated with torin1 (500nM) for 4 hours. Results: Genome-wide translational profiling of glutamine deprived ER-Src MCF10A cells (for 30 minutes) shows increased translation of uORFs-containing mRNAs and down-regulation of ribosomal protein mRNAs, which is followed by increased translation and transcription of cytokine and inflammatory mRNAs (after 4 hours of glutamine deprivation). The transcription and translation of inflammatory and cytokine mRNAs is also stimulated in response to 4 hours deprivation of glucose, cysteine/cystine and BCAA, with the extent of stimulation correlating with the i) decrease in global protein synthesis and ii) down-regulation of all translationally-repressed mRNAs or ribosomal protein mRNAs. Conclusions: Pro-inflammatory gene expression is associated with translational repression in response to short-term nutrient deprivation.
2018-07-01 | GSE114794 | GEO
Project description:Human myometrial cells taken from biopsies of pre-menopausal non-cancerous non-pregnant uteri were cultured in complete MEM D-valine medium plus 10% FCS, and stably-transfected with the pcDNA3.1/V5-His TOPO vector (Invitrogen) harbouring either CREB, CREM alpha, CREM tau2alpha, ATF2, ATF2-small gene or a control empty-vector. Total RNA was extracted using TRI-reagent (Sigma) and RNeasy columns (Qiagen), and 10 ug used in target preparation for array hybridization. Keywords: other
2004-02-21 | GSE1059 | GEO
Project description:<p>In order to create a melanocyte-specific eQTL resource, we obtained primary human melanocyte cultures isolated from foreskin of 106 healthy newborn males predominantly of European descent. Melanocytes were cultured in lot-matched culture medium in randomized batches to minimize variability that could be introduced by culturing conditions. RNA sequencing and direct SNP genotyping of these samples produced an average of ~87.9 million reads (paired-end, stranded, 126bps), and ~713,000 SNP genotypes, respectively.</p>
| phs001500 | dbGaP
Project description:Aim of the study was to characterize at a molecular level (changes in transcriptomes) the crosstalk between tumor hepatocytes and activated hepatic stellate cells (HSC) in liver cancer. This was adressed by using a coculture model system of HepaRG cell line (tumor hepatocytes, human), and LX2 cell line (HSC, human). By using genome-wide expression profiling, we demonstrated that hepatocyte-HSC crosstalk is bidirectional and results in the deregulation of functionally relevant gene networks. HepaRG and LX2 cells were cultured alone in serum- and DMSO-free William's E medium or together using 1 M-BM-5m pore size transwell inserts which allow diffusion of media components but prevent cell migration (BD Biosciences, San Jose, CA). Triplicate experiments were performed: HepaRG (culture versus coculture), LX2 (culture versus coculture).
2012-05-31 | E-GEOD-32565 | biostudies-arrayexpress
Project description:Previous data suggest that 2-cysteine peroxiredoxin, cyclophilin 20-3 and the cysteine synthase complex work as a dynamically interacting module (here named COPS-module) and are involved in stress response. In this study we performed global transcriptome analyses to investigate the responses to short-term high light in wildtype and mutants deficient in each protein of COPS-module. The global transcriptomic response in leaves to 6 h high light in Col.0 and mutants deficient in each protein of COPS-module.
2017-07-31 | GSE94327 | GEO
Project description:Recent functional genomics and genome-scale modeling approaches indicated that B12 production in Lactobacillus reuteri could be improved by medium optimization. Here we show that a series of systematic single amino acid omissions could significantly modulate the production of B12 from nearly undetectable levels (by isoleucine omission) to 20-fold higher than previously reported through omission of cysteine. We analyzed by cDNA microarray experiments the transcriptional response of L. reuteri to the medium lacking cysteine. These results supported the observed high B12 production and provided new avenues for future improvement of production of vitamin B12. Keywords: cell type comparison
2008-10-31 | GSE13391 | GEO