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Transcriptome and chromatin accessibility in oral squamous carcinoma with human plasma-like medium culture (RNA-Seq)

ABSTRACT: In recent years, human plasma like medium (HPLM) have been developed that mimic the conditions of the human physiology. In comparison with conventional cell culture medium, cell culture in HPLM had extensive effects on cellular metabolism, including metabolome, redox status, and glucose utilization. However, molecular mechanisms underlying HPLM effects on human cells are only partly understood. Transcriptome and chromatin accessibilities are important regulators of cell states and implicate in a variety of biological processes. We habituated three oral cancer cell lines such as SAS, HSC-3, and HSC-4 in HPLM and evaluated cell growth and drug sensitivity. We perform transcriptome analysis between HPLM and conventional culture condition in HSC-3 cells by mRNA-seq.

ORGANISM(S): Homo sapiens

PROVIDER: GSE256193 | GEO | 2024/02/21

REPOSITORIES: GEO

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Transcriptome and chromatin accessibility in oral squamous carcinoma with human plasma-like medium culture (ATAC-Seq)

Project description:In recent years, human plasma like medium (HPLM) have been developed that mimic the conditions of the human physiology. In comparison with conventional cell culture medium, cell culture in HPLM had extensive effects on cellular metabolism, including metabolome, redox status, and glucose utilization. However, molecular mechanisms underlying HPLM effects on human cells are only partly understood. Transcriptome and chromatin accessibilities are important regulators of cell states and implicate in a variety of biological processes. We habituated three oral cancer cell lines such as SAS, HSC-3, and HSC-4 in HPLM and evaluated cell growth and drug sensitivity. We perform epigenetic analysis between HPLM and conventional culture condition in HSC-3 cells by ATAC-seq.

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Medium-dependent gene-expression profiling of the human K562 chronic myeloid leukemia cell line

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Molecular characterization of hematopoietic stem cells after in vitro amplification on biomimetic 3D PDMS cell culture scaffoldsMolecular characterization of hematopoietic stem cells after in vitro amplification on biomimetic 3D PDMS cell culture scaffolds

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MYCT1 CONTROLS ENVIRONMENTAL SENSING IN HUMAN HEMATOPOIETIC STEM CELLS

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2024-04-15 | PXD042257 | Pride

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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).

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A platform for efficient establishment and drug response profiling of high-grade serous ovarian cancer organoids

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Single cell transcriptome sequencing of expanded human hematopoieic stem/progenitor cells cultured in PCL-PVAc-PEG based 3a medium and StemSpan with UM171/SR-1 medium.

Project description:We demonstrated that chemically difined PCL-PVAc-PEG based 3a medium was superior to conventional StemSpan besed medium in expansion of human hematopoietic stem cells. In fact, more phenotypic HSCs (CD34+EPCR+CD90+CD45RA-ITGA3+) were expanded in our culture condition and higher donor chmerism was achieved in transplantation assay using humanized mice. But detail transcriptome profiles of expanded HSCs was unknown and therefore single-cell RNA sequencing was done to reveal it. As a result, expanded cells in our medium had more HSPC featured cells. Interestingly, erythroid/megakaryocyte progenitors was more expanded in our condition. On the other hands, other culture condition made more myeloid progenitor cells but few HSPC featured cells. This result support the idea that our new medium are able to selectively expand HSCs.

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