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Determine genes differentially expressed between Raji cells and a subline which is resistant to APTO-253 (Raji/253R)

ABSTRACT: Determine genes differentially expressed between Raji cells and a subline which is resistant to APTO-253 (Raji/253R)

PROVIDER: PRJNA438589 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR6847060.fastq.gz	Fastqsanger.gz
	SRR6847061.fastq.gz	Fastqsanger.gz
	SRR6847062.fastq.gz	Fastqsanger.gz
	SRR6847057.fastq.gz	Fastqsanger.gz
	SRR6847058.fastq.gz	Fastqsanger.gz

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Determine genes differentially expressed between Raji cells and a subline which is resistant to APTO-253 (Raji/253R)

Project description:To obtain further insight into the resistance mechanism, RNA-seq analysis was carried out on 3 independent samples of both the sensitive Raji and resistant Raji/253R cells. A gene-level differential expression analysis was performed by removing all genes with less than 50 reads across all 6 samples as genes with only low level expression can cause irregularities in differential expression analysis. Genes were considered to be differentially expressed if their adjusted p-value was less than the 0.05 level and their fold change was >2 in either direction. Among the 13,791 evaluable genes there were 1,012 that were significantly up-regulated in the Raji/253R cells and 704 genes that were significantly down regulated relative to the parental sensitive Raji cells. The ATP-binding cassette sub-family member ABCG2 was the most up-regulated gene with more than a thousand-fold increase in transcript level. Genes were considered to be differentially expressed if their adjusted p-value was less than the 0.05 level and their fold change was >2 in either direction.

2020-03-30 | GSE111928 | GEO

Differentially expressed genes in radioresistant nasopharyngeal cancer cells

Project description:The NPC parental cell lines were seeded at a density of 1 x 105/T25 flask (30% to 40% confluency) in complete medium. After 24 hours of cell seeding, various doses from 6 to 14 Gy were administered to determine the sublethal dose for each cell line. The radiation was delivered at room temperature at 300 cGy/min with a linear accelerator (2100EX, Varian, VA, USA). To establish RR subclone, the NPC cells were received the sublethal dose of irradiation. After treatment, the surviving cells were selected and cultured to produce first generation of the subline cells. Again, the subline cells were received sublethal dose of irradiation and the surviving cells were cultured to produce next generation of the subline cells. Up to four generations of NPC cells were produced and defined the forth generation cells as RR subclone. Keywords: Parental vs. subclone cell line comparison

2008-05-01 | GSE7817 | GEO

Effect of bryostatin-1 on gene expression profile of Raji cells

Project description:To investigate bryostain's effect on Raji , we performed a whole-transcriptome RNA sequencing experiment for Raji cells treated with Bryostatin and established differntial expression profile comparing to raji treated with DMSO.

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Bradyrhizobium ottawaense strain:USDA 253 | isolate:USDA 253

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Transcription profiling of Bordetella bronchiseptica strains 253 and RB50 to investigate adenylate cyclase toxin (ACT) expression

Project description:Bordetella bronchiseptica is a gram-negative respiratory pathogen that causes a diverse spectrum of respiratory disease in a wide-range of hosts. We sought to determine if strains of B. bronchiseptica differed in virulence using the mouse model of infection. Mean lethal doses (LD50) of different B. bronchiseptica strains varied widely in the murine model. B. bronchiseptica strain 253 had a LD50 that was 10-fold lower than the prototypical and fully sequenced B. bronchiseptica strain RB50. Using whole genomic transcriptome analysis covering 100% of B. bronchisetpctica strain RB50ÃÂÃÂs predicted open reading frames (ORFs), 253 was identified as lacking expression of adenylate cyclase toxin (ACT).

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Gene expression assay from Raji human B cells

Project description:Nuclear RNA from Raji human B cells was hybridized to NimbleGen arrays to quantify gene expression levels.

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Expression of the TM4SF member CD9 on the human Burkitts lymphoma cell line Raji

Project description:Expression of the TM4SF member CD9 on the human Burkitts lymphoma cell line Raji induced increased cell proliferation, motilty and adhesion to fibronectin. CD9 promoted increases in Raji cell proliferation was dependent upon histone deacetyalase (HDAC) activity as treatment with HDAC inhibitors trichostain A or cucurmin attenuated CD9 mediated increases in Raji cell proliferation. Gene expression of Raji cells stably expressing human CD9 via transfection with expression vector PRVCMVCD9 was compared with corresponding Mock transfected cell by microarray analysis using the Affymetrix U133 2.0 platform.

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