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Comparative gene expression profiling of serum-free and FBS treated adherent primary pancreatic TIC cultures

ABSTRACT: To induce a differentiated phenotype, primary pancreatic TIC cultures were grown in 10% FBS containing conditions. To analyze gene expression changes upon induction of a differentiated phenotype, total RNA of cells cultured in FBS containing conditions and parallel control cells cultured under serum-free conditions was isolated and comparative gene expression profiling was performed.

ORGANISM(S): Homo sapiens

PROVIDER: GSE59118 | GEO | 2017/05/16

SECONDARY ACCESSION(S): PRJNA254461

REPOSITORIES: GEO

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Comparative gene expression profiling of serum-free and FBS treated adherent primary pancreatic TIC cultures

Project description:To induce a differentiated phenotype, primary pancreatic TIC cultures were grown in 10% FBS containing conditions. To analyze gene expression changes upon induction of a differentiated phenotype, total RNA of cells cultured in FBS containing conditions and parallel control cells cultured under serum-free conditions was isolated and comparative gene expression profiling was performed. RNA was obtained from four different patient derived cultures grown in serum-free or 10% FBS containing culture medium at passage 3 and passage 8

2017-05-16 | E-GEOD-59118 | biostudies-arrayexpress

Comparative gene expression profiling of serum-free and FBS treated colorectal TIC cultures

Project description:To induce a differentiated phenotype, primary colorectal TIC cultures were grown in 10% FBS containing conditions. To analyze gene expression changes upon induction of a differentiated phenotype, total RNA of cells cultured in FBS containing conditions and control cells cultured under serum-free conditions was isolated and comparative gene expression profiling was performed.

2016-08-20 | GSE72543 | GEO

Comparative gene expression profiling of serum-free and FBS treated colorectal TIC cultures

2016-08-20 | E-GEOD-72543 | biostudies-arrayexpress

Simple differentiation method using FBS identifies DUSP6 as a marker for fine-tuning of FGF-ERK signaling activity in human pluripotent stem cells

Project description:Assessment of differentiation potential is a basic requirement to obtain qualified human pluripotent stem cells (hPSCs). Here, we report a simple differentiation method using fetal bovine serum (FBS) to estimate differentiation potential and propensity of hPSCs. PluriTest using RNA-sequencing showed that cells differentiated after treatment with 5% FBS. Expression patterns of three germ layer markers revealed that cells cultured in Knockout Serum Replacement-containing medium (KSR) with mouse feeder cells had higher differentiation potential than cells cultured in a chemically defined medium (E8) with recombinant matrix proteins, especially into the mesoderm and endoderm lineages. Analysis of differentially expressed genes between KSR and E8 identified DUSP6 as a marker for where cells had been cultured. Expression of DUSP6 correlated with FGF-ERK signaling activity. Fine-tuning of FGF-ERK signaling activity to a range that can shut down DUSP6 transcription but sustain NANOG transcription partially increased the differentiation potential. Our data suggest that differentiation with 5% FBS is good to estimate differentiation potential and propensity at the early stage, and that DUSP6 is an excellent marker to monitor ERK signaling activity.

2020-02-18 | GSE135799 | GEO

Effects of spheroid and adherent growth conditions in ovarian cancer

Project description:Purpose: To understand the changes in RNA expression in tumor-initiating cell (TIC) (spheroid) and non-TIC populations (adherent) in ovarian cancer. Methods: OV90 cells were grown in adherent (non-TIC) or spheroid (TIC) conditions. Total RNA was extracted from each condition and RNAseq was performed and analysed for differential gene expression between the conditions.

2020-10-03 | GSE158949 | GEO

Quantification of Tic-Toc subunits in gun1

Project description:Quantification of Tic-Toc subunits in the wild type and gun1-101 mutants in the control conditions and treated with lincomycin or norflurazon to determine if there are differences between genotypes.

2019-04-23 | PXD013005 | Pride

Effects of RELA and RELB in spheroid and adherent ovarian cancer

Project description:Purpose: To understand the role of NF-kB signaling in tumor-initiating cell (TIC) and non-TIC populations in ovarian cancer. Methods: OV90 cells with inducible shRNA against RelA and RelB, and a non-targeting shRNA control were induced by doxycycline treatment and were grown in adherent (non-TIC) or spheroid (TIC) conditions. Total RNA was extracted from each condtion and RNAseq was performed and analysed for differential gene expression between the conditions.

2023-04-28 | GSE230678 | GEO

Genomic alteration in MRC5-derived induced pluripotent stem (MRC5-iPS) cell line, Tic

Project description:Disease-specific induced pluripotent stem (iPS) cells have been used for a model to analyze pathogenesis of the disease. We generated iPS cells derived from a fibroblastic cell line of ataxia telangiectasia (AT-iPS cells). In analysis of AT-iPS cells, the human wild-type iPS cell line (MRC5-iPS) was generated and cultured in the same conditions as the diseased iPS cell lines. It is an ideal control cell line for the disease and patient-specific iPS cell lines. Because MRC5-iPS cells exhibited considerable chromosomal abnormalities in vitro, we performed a structural alteration analysis by using a SNP genotyping array for MRC5-iPS cell line, Tic, at passage 15, passage 30, and passage 37. The parental MRC-5 fibroblast cells and MRC-iPS 25 (Tic) were subjected to Illumina HumanCytoSNP-12 v2.1 BeadChip analysis.

2013-07-23 | E-GEOD-49082 | biostudies-arrayexpress

Examination of the effect of exosome in FBS on myogenic differentiation

Project description:we performed Next-generation sequencing analyses with C2C12 cells in growing conditions with 10% of FBS, or in differentiating conditions with 0.2% of FBS or 2% of horse serum with or without added exosomes

2022-03-31 | GSE193702 | GEO

The effect of FBS and cyclic mechanical stretch on serum starved mesenchymal stem cells

Project description:Purpose: Cyclic mechanical stretch (CMS) promoted proliferation of serum starved mesenchymal stem cells (MSCs) by inhibiting miR-337 expression, similar to FBS. In order to reveal the underlying mechanisms of both CMS and FBS on MSC activation, as well as the regulatory role of miR-337, this research performed high-throughput RNA sequencing (RNA-seq) on MSCs isolated from both wild-type (ET)- and miR-337 knockout- (miR-337-/-) rats. Methods: MSCs isolated form 2-month-old wild-type (WT) and miR-337 knockout (-/-) rats and cultured in vitro to passage 3. After serum starvation for 8h, MSCs were treated with FBS or 10% CMS for another 24h before deep sequencing in triplicate, using Illumina GAIIx. The sequence reads that passed quality filters were analyzed at the transcript isoform level. Results: Using an optimized data analysis workflow, we mapped about 40 million sequence reads per sample. We identified 2472 differentially expressed genes (DEGs) between CMS-stimulated vs. SSt conditions, 2468 DEGs FBS-treated vs. SSt groups. However, only 97 DEGs were identified between CMS and FBS groups, indicating that CMS and FBS groups are more similar to each other and both CMS and FBS groups are quite different from the SSt group. Analysis of DEGs between CMS- or FBS-treated and SSt -treated group revealed that CMS and FBS stimulation activated similar biological processes, of which, PI3K-Akt-mTOR pathway was highly enriched. However, PI3K-Akt-mTOR pathway was not enriched in miR-337-/- MSCs, indicating constitutive activation of this pathway. Conclusions: Our RNA-seq data revealed that both CMS and FBS activates quiescent MSCs through regulating similar genes and pathways. miR-337 is one of the main factors that regulate MSC activation by targeting PI3K-Akt pathway.

2021-12-02 | GSE189845 | GEO

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