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Modulation of the cancer cell transcriptome by culture media formulations and cell density

ABSTRACT: We investigated how varying the composition of cell culture formulations and growing cancer cells at different densities might affect tumor cells genotype. Specifically, we compared gene expression profiles generated by human MDA-MB-231 human breast cancer cells cultured in different media (MEM, DMEM, or RPMI 1640) containing different concentrations of fetal bovine serum (FBS) or different sera (equine or bovine) that were grown at different cell densities.

ORGANISM(S): Homo sapiens

PROVIDER: GSE61670 | GEO | 2015/06/17

SECONDARY ACCESSION(S): PRJNA261801

REPOSITORIES: GEO

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Modulation of the cancer cell transcriptome by culture media formulations and cell density

Project description:We investigated how varying the composition of cell culture formulations and growing cancer cells at different densities might affect tumor cells genotype. Specifically, we compared gene expression profiles generated by human MDA-MB-231 human breast cancer cells cultured in different media (MEM, DMEM, or RPMI 1640) containing different concentrations of fetal bovine serum (FBS) or different sera (equine or bovine) that were grown at different cell densities. We have 6 different group (1. MDA-MB-231; MEM-10% FBS-90% confluence (MEM-1 and MEM-2). 2. MDA-MB-231; DMEM-10% FBS-90% confluence (DMEM-1 and DMEM-2). 3. MDA-MB-231; RPMI1640-10% FBS-90% confluence (RPMI-1 and RPMI-2) 4. MDA-MB-231; MEM-10% Horse serum-90% confluence (Horse-1 and Horse-2). 5. MDA-MB-231; MEM-0.1% FBS-90% confluence (FBS0.1-1 and FBS0.1-2). 6. MDA-MB-231; MEM-10% FBS-50% confluence (Con50-1 and Con50-2). Each group has duplicated. We analyzed; 1. Cell density (90% vs 50% confluence). 2. FBS concentration (10% FBS vs 0.1% FBS). 3. Sera (10% FBS vs 10% Horse serum). 4. Media (MEM vs DMEM vs RPMI1640)

2015-06-17 | E-GEOD-61670 | biostudies-arrayexpress

Project description:This study was undertaken to compare efficacy of MJC13 and the classic AR antagonist flutamide. Both compounds modulate endogenous AR target gene expression in Prostate cancer cells in a similar fashion despite different mechanisms of action. LNCaP cells were seeded within 6-well dishes at density of 1 Ã 100,000 within RPMI 1640 media supplemented with L-glutamine and 10% fetal bovine serum (FBS), day 2 the media replaced with RPMI 1640 media supplemented with L-glutamine and 10% charcoal-stripped FBS, day 3 the cells were treated with DMSO (control), 10nM DHT, 1Î¼M Flutamide, 1Î¼M Flutamide + 10nM DHT, 30Î¼M MJC13, or 30Î¼M MJC13 + 10nM DHT for 24 hours, after which total RNA was isolated.

2015-12-31 | E-GEOD-65562 | biostudies-arrayexpress

Innate immune responses in the alveolar space to different formulations of SDI RNA

Project description:The aim of this experiment was to analyse the innate immune response in alveolar cells after different nanoparticle formulations are delivered intranasally in 50 µl PBS with or without 1 µg Sendai virus Defective Interfering RNA

2021-11-22 | GSE183892 | GEO

Transcriptional profile in TECs

Project description:Cortical 1.4C18 and medullary 3.10 TEC lines (mTEC) were cultured in 10% fetal bovine serum-supplemented RPMI 1640 medium at 37 ?C in a 5% CO2 atmosphere. Confluent cultures of 3.10 mTEC cell line were cultured during 72 h in RPMI medium as above mentioned and total RNA was extracted using the mirVana kitM-. (Ambion, Austin, TX, USA).

2011-08-31 | E-MEXP-3214 | biostudies-arrayexpress

Targeting tumor-intrinsic SLC16A3 to enhance anti-PD-1 efficacy via tumor immune microenvironment reprogramming

Project description:To study the impacts of glycolytic states of tumor cells, we took advantage of different in vitro culture systems and established demanded glycolysis states in B16F10 cells. B16F10 cells were maintained with either RPMI-1640 or DMEM mediums to maintain different metabolic models.

2023-07-07 | GSE233834 | GEO

To investigate whether recover DNMT3A expression permitted adult beta cell of βRapKO establishing proper transcriptome

Project description:Murine islets were isolated from 8-week-old WT and βRapKO mice and initially recovered in 1640 RPMI supplemented with 10% serum, 11.1mM glucose overnight. Then islets were transfected with Lenti-GFP or Lenti-Dnmt3a for 24 hours, following cultured in 1640 RPMI medium for 48 hours.Islets were harvested and stored in -80°C for preparation for RNA sequencing.

2019-06-01 | GSE130910 | GEO

MHP vaccine formulations

Project description:System immunology characterization of novel vaccine formulations for Mycoplasma hyopneumoniae bacterins

| PRJEB30361 | ENA

Human plasma-like medium improves T lymphocyte activation

Project description:T lymphocytes are critical effectors of the immune system and the ability to study their behavior in synthetic media in vitro has facilitated major discoveries in their development, function, and fate. Recently, it has been shown that the constituents in human plasma differ markedly from commonly used synthetic media and these differences have important effects on cell physiology. We therefore compared T lymphocyte activation in human plasma-like medium (HPLM) to RPMI conventional medium both with and without serum. We found that HPLM and RPMI induced vastly different transcriptional programs, especially for transcripts encoding proteins involved in activation, proliferation and metabolism, in human peripheral blood T cells after T cell receptor (TCR) stimulation. We also found that in dialyzed fetal bovine serum (dFBS), HPLM supports a stronger response to TCR engagement compared to RPMI. In reconstruction experiments, we demonstrated that this activation difference is due to RPMI being hypocalcemic relative to the in vivo milieu and that addition of calcium chloride to RPMI can improve human T lymphocyte activation. Thus, we conclude that investigators should be cognizant of differences between commonly used media formulations and the in vivo environment since this could profoundly affect their experimental results and that physiologic media is a valuable new way to study immune cells in culture

2020-01-21 | GSE135936 | GEO

RNA-seq analysis of the effect of BSA and NaOH added to standard culturing medium on THP-1 macrophages

Project description:The data is supplementary to the RNA-seq analysis of LPS and palmitate stimulation of THP-1 macrophages (E-MTAB-6064), where palmitate for the cell treatment was dissolved in sodium hydroxide and coupled with BSA at a molar ratio 7.5:1. Here we stimulated THP-1 macrophages with the corresponding concentration of BSA (4%) and NaOH (0.4 mM) in the presence of 10 nM phorbol 12-myristate 13-acetate (PMA) for 24 hours added to the standard RPMI 1640 medium with 10% fetal bovine serum (FBS) to estimate the effects and compared them with unstimulated THP-1 macrophages cultured in RPMI 1640 medium with 10% FBS and 10nM PMA.

2019-05-17 | E-MTAB-6439 | biostudies-arrayexpress

GSK-inhibitor treatment in IMR32 neuroblastoma cell line

Project description:Cells were cultured in RPMI 1640 (Gibco), supplemented with 10% fetal bovine serum (FBS) (Gibco), 2mM L-glutamine (Gibco) and 1% Penicillin-Streptomycin solution (Gibco). IMR32 cells were treated as follows; untreated control, 24h 1uM azakenpaullone, 24h 1uM BIO or 24h 28mM LiCl with biological duplicates.

2014-10-01 | E-MTAB-1684 | biostudies-arrayexpress

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