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Caco-2 cells: 21-days differentiated cells maintained with the low density protocol (LD cells) vs 21-days differentiated cells maintained with the high density protocol (HD cells)

ABSTRACT: Transcriptional profile of 21-days differentiated LD Caco-2 cells compared to 21-days differentiated HD Caco-2 cells. Goal was to find some differences in the genome profile of the LD and HD Caco-2 cells that could be addressed to the different protocols used for the line maintenance.

ORGANISM(S): Homo sapiens

PROVIDER: GSE21518 | GEO | 2011/04/25

SECONDARY ACCESSION(S): PRJNA125965

REPOSITORIES: GEO

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Caco-2 cells: 21-days differentiated cells maintained with the low density protocol (LD cells) vs 21-days differentiated cells maintained with the high density protocol (HD cells)

Project description:Transcriptional profile of 21-days differentiated LD Caco-2 cells compared to 21-days differentiated HD Caco-2 cells. Goal was to find some differences in the genome profile of the LD and HD Caco-2 cells that could be addressed to the different protocols used for the line maintenance. Two-condition experiment: 21-days differentiated Caco-2 cells maintained with the LD protocol and 21-days differentiated Caco-2 cells maintained with the HD protocol. Dye-swap technical replicates.

2011-04-25 | E-GEOD-21518 | biostudies-arrayexpress

Caco-2 cells: cycling vs 21-days differentiated cells

2011-04-25 | GSE21519 | GEO

Caco-2 cells: cycling vs 21-days differentiated cells

Project description:Transcriptional profile of 21-days differentiated Caco-2 cells compared to Caco-2 cycling cells. Goal was to demonstrate the ability of Caco-2 cells to express most of the markers typical of differentiated enterocytes. A novel protocol of line maintenance was used. Two-condition experiment: cycling Caco-2 cells and 21-days differentiated Caco-2 cells. Two biological replicates of each condition in dye-swap configuration

2011-04-25 | E-GEOD-21519 | biostudies-arrayexpress

Comparison of transcriptome of high differentiation-inducible murine erythroleukemia cells and low differentiation-inducible murine erythroleukemia cells

Project description:Murine erythroleukemia (MEL) cells are differentiated by dimethyl sulfoxide (DMSOM-oM-<M-^I, hexamethylene bisacetamide (HMBAM-oM-<M-^I or trichostatin A (TSAM-oM-<M-^I treatment. We selsected high differentiation-inducible (HD) and low differentiation-inducible (LD)-MEL cells by recloning of original MEL cells. We screened erythroid differentiation related-genes to compare transcriptome of HD and LD-MEL cells. HD-MEL cells and LD-MEL cells were cultured 6, 12, 24, or 36 hours with 1.0% DMSO, 3.0 mM HMBA, or 15 nM TSA. The RNA of HD-MEL cells and LD-MEL cells were compare same time points of each drug treatment. The expression ratio (HD/LD) was calculated by average of technical quadruplicate microarray experiments includes two dye-swaps.

2013-04-23 | E-GEOD-40754 | biostudies-arrayexpress

Comparison of transcriptome of high differentiation-inducible murine erythroleukemia cells and low differentiation-inducible murine erythroleukemia cells

Project description:Murine erythroleukemia (MEL) cells are differentiated by dimethyl sulfoxide (DMSO）, hexamethylene bisacetamide (HMBA） or trichostatin A (TSA） treatment. We selsected high differentiation-inducible (HD) and low differentiation-inducible (LD)-MEL cells by recloning of original MEL cells. We screened erythroid differentiation related-genes to compare transcriptome of HD and LD-MEL cells.

2013-04-23 | GSE40754 | GEO

Identification of candidate genes affecting juvenile wood density in Pinus radiata

Project description:Wood density is a foundamental quality trait for structural timber, bioenergy and pulp industries. We investigated genes differentially transcribed in radiate pine juvneile trees with distinct wood density using cDNA microarrays. Radiata pine trees were selected from a progeny trial planted at Flynn, Australia. Based on the gravitical measurement of wood cores, 12 families with highest and lowest density each were selected, representing two groups of trees with contrasting wood density. One individual with higher or lower density were further sampled in each selected family. Developing xylem tissues of selected trees were sampled in autumn (April) when latewood (LW) was formed. The xylem tissues were scraped at breast height with a sharp chisel after the bark was removed. Wood cores of the sampled trees were further measured using SilviScan 2. Total RNA extracted from ten developing xylem tissues with confirmed distinct density in each tree group were pooled into two bulks (five trees each), and the two bulks of HD were compared with two LD bulks in the microarray experiment (named the bulk experiment). Six developing xylem tissues with the most distinct density from each tree group were further chosen. Six xylem tissues with HD were individually compared with bulked six xylem tissues with LD in the second microarray experiment (named individual experiment). These two different pooling strategies can partly minimize the genetic variation among different genotypes. Dye swaps were applied in each biological replicate.

2012-08-02 | E-GEOD-32086 | biostudies-arrayexpress

Two distinct extracellular protein signatures released by a single cell type identified by LC-MS/MS

Project description:Cells secrete extracellular RNA (exRNA) to their surrounding environment and exRNA has been found in many body fluids such as blood, breast milk and cerebrospinal fluid. However, there are conflicting results regarding the nature of exRNA. Here, we have separated two distinct exRNA profiles released by mast cells, here termed high-density (HD) and low-density (LD) exRNA. The exRNA in both fractions was characterized by microarray and next-generation sequencing. Both exRNA fractions contained mRNA and miRNA, and the mRNAs in the LD exRNA correlated closely with the cellular mRNA, whereas the HD mRNA did not. Furthermore, the HD exRNA was enriched in lincRNA, antisense RNA, vault RNA, snoRNA, and snRNA with little or no evidence of full-length 18S and 28S rRNA. The LD exRNA was enriched in mitochondrial rRNA, mitochondrial tRNA, tRNA, piRNA, Y RNA, and full-length 18S and 28S rRNA. The proteomes of the HD and LD exRNA-containing fractions were determined with LC-MS/MS and analysed with Gene Ontology term finder, which showed that both proteomes were associated with extracellular vesicles. Additionally, the proteins in the HD fractions tended to be associated with the nucleus and ribosomes, whereas the LD fraction proteome tended to be associated with the mitochondrion. We show that the two exRNA signatures released by a single cell type can be separated by floatation on a density gradient. These results show that cells can release multiple types of exRNA with substantial differences in RNA species content. This is important for any future studies determining the nature and function of exRNA released from different cells under different conditions.

2018-10-26 | PXD004931 | Pride

Transcription profiling of CaCo-2 cells differentiated to M cells - establishing and characterizing a cell culture model for M cells

Project description:M cells are special cells in the epithelium of the small intestinal bowel and play an important role during the initiation of a primary, fast immune response. On a Costar-Transwell filter cells of a colon adeno carcinoma cell line (Caco-2) are growing until differentiation. Then on the other side of the Caco cell layer lymphocytes from human venous blood are added. Pores in the filter membrane allow contact between lymphocytes and Caco cells. Therefore some cells of the Caco cell layer are differentiating to "M cell like" cells, showing the morpholgy and function of natural M cells. Experiment Overall Design: Two replicates of non-induced filter-grown Caco cells and three replicates of lymphocyte-induced filter-grown Caco cells (including lymphocyte expression) for the identification of regulated genes; one experiment of bottle-grown Caco cells and one experiment of bottle-grown lymphocytes for baseline expression profiling and control reasons.

2008-06-12 | E-GEOD-3054 | biostudies-arrayexpress

Two distinct extracellular RNA signatures released by a single cell type identified by microarray and next-generation sequencing [miRNA]

Project description:Cells secrete extracellular RNA (exRNA) to their surrounding environment and exRNA has been found in many body fluids such as blood, breast milk and cerebrospinal fluid. However, there are conflicting results regarding the nature of exRNA. Here, we have separated two distinct exRNA profiles released by mast cells, here termed high-density (HD) and low-density (LD) exRNA. The exRNA in both fractions was characterized by microarray and next-generation sequencing. Both exRNA fractions contained mRNA and miRNA, and the mRNAs in the LD exRNA correlated closely with the cellular mRNA, whereas the HD mRNA did not. Furthermore, the HD exRNA was enriched in lincRNA, antisense RNA, vault RNA, snoRNA, and snRNA with little or no evidence of full-length 18S and 28S rRNA. The LD exRNA was enriched in mitochondrial rRNA, mitochondrial tRNA, tRNA, piRNA, Y RNA, and full-length 18S and 28S rRNA. The proteomes of the HD and LD exRNA-containing fractions were determined with LC-MS/MS and analysed with Gene Ontology term finder, which showed that both proteomes were associated with the term extracellular vesicles and electron microscopy suggests that at least a part of the exRNA is associated with exosome-like extracellular vesicles. Additionally, the proteins in the HD fractions tended to be associated with the nucleus and ribosomes, whereas the LD fraction proteome tended to be associated with the mitochondrion. We show that the two exRNA signatures released by a single cell type can be separated by floatation on a density gradient. These results show that cells can release multiple types of exRNA with substantial differences in RNA species content. This is important for any future studies determining the nature and function of exRNA released from different cells under different conditions.

2016-10-31 | GSE88754 | GEO

Two distinct extracellular RNA signatures released by a single cell type identified by microarray and next-generation sequencing [total RNA]

Project description:Cells secrete extracellular RNA (exRNA) to their surrounding environment and exRNA has been found in many body fluids such as blood, breast milk and cerebrospinal fluid. However, there are conflicting results regarding the nature of exRNA. Here, we have separated two distinct exRNA profiles released by mast cells, here termed high-density (HD) and low-density (LD) exRNA. The exRNA in both fractions was characterized by microarray and next-generation sequencing. Both exRNA fractions contained mRNA and miRNA, and the mRNAs in the LD exRNA correlated closely with the cellular mRNA, whereas the HD mRNA did not. Furthermore, the HD exRNA was enriched in lincRNA, antisense RNA, vault RNA, snoRNA, and snRNA with little or no evidence of full-length 18S and 28S rRNA. The LD exRNA was enriched in mitochondrial rRNA, mitochondrial tRNA, tRNA, piRNA, Y RNA, and full-length 18S and 28S rRNA. The proteomes of the HD and LD exRNA-containing fractions were determined with LC-MS/MS and analysed with Gene Ontology term finder, which showed that both proteomes were associated with the term extracellular vesicles and electron microscopy suggests that at least a part of the exRNA is associated with exosome-like extracellular vesicles. Additionally, the proteins in the HD fractions tended to be associated with the nucleus and ribosomes, whereas the LD fraction proteome tended to be associated with the mitochondrion. We show that the two exRNA signatures released by a single cell type can be separated by floatation on a density gradient. These results show that cells can release multiple types of exRNA with substantial differences in RNA species content. This is important for any future studies determining the nature and function of exRNA released from different cells under different conditions.

2016-10-31 | GSE88753 | GEO

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