Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

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

ABSTRACT: 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.

ORGANISM(S): Homo sapiens

PROVIDER: GSE111928 | GEO | 2020/03/30

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

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.

2022-08-19 | GSE211351 | GEO

NtrBC as a regulator of adaptive lifestyles and virulence

Project description:When comparing dNtrB and dNtrC to WT, we identified 790 and 1184 dysregulated genes, respectively. Genes were considered dysregulated if the absolute log2 fold change was greater than 1.5 and an adjusted p value of < 0.05. The large number of commonly DE genes indicated NtrB and C act as a cognate pair. Most notably, there were several dysregulated genes involved in nitrogen and carbon metabolic processes.

2020-04-16 | GSE145591 | GEO

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.

2013-02-16 | GSE43750 | GEO

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.

2009-10-15 | GSE13210 | GEO

miRNA-Seq analysis of parental human leukemia K562 and clonal etoposide resistant K562 (designated K/VP.5) cell lines.

Project description:We report that ~300 mature miRNAs were detected in these cells. 73 miRNAs were overexpressed (fold change > 2; adjusted P-value < 0.05) and 14 were underexpressed (fold change > 2; adjusted P-value < 0.05) in K/VP.5 compared to K562 cells.

2020-01-31 | GSE141687 | GEO

Probe level meta analysis of microarray data to understand the role of retrotransposable elements in myelination.

Project description:This study aim to understand the role of retrotransposable elements in myelination Raw data with accession number GSE11218 and GSE5940 (using Affymetrix expresion GeneChIP Rat Genome 230 2.0 and 230A, respectively) were extracted fromm GEO. Probe level information was extracted using R library rat2302probe (for Rat genome 230 2.0) and rae230aprobe (for rat genome 230A). Unique probe sequence in 230 2.0 and 230A platform were retained and the intersect probes (90507 in number) between two platforms were used for analysis. Background subtracted raw data were quantile normalized. Probes for which intensity were greater than. sample median level in at least half the arrays for one experimental condition in. a dataset were considered present; absent probes were removed. Further differentially expressed probbes between OL and OPC were identified by using R Bioconductor package 'limma'. P-values were adjusted to correct for multiple testing using FDR (Benjamini-Hochberg). Probes for which the difference between groups were > or = 2 fold and the adjusted P-value<0.05 were considered differentially expressed.

2024-02-14 | GSE245032 | GEO

Transcriptome analysis of total RNA in the Raji B cell line

Project description:RNA-seq was performed for total RNA in the Raji B cell line

2018-10-29 | GSE111880 | GEO

Direct long-read RNA sequencing of Raji cells

Project description:To identify full-length cap-to-poly(A) mRNA isoforms of CD20 and rule out reverse transcription artifacts which are common in cDNA-seq approaches, long-read Oxford Nanopore direct RNA sequencing was performed on the Raji cell line.

2023-12-08 | GSE243920 | GEO

FHL3 overexpression microarray

Project description:To investigate the target genes of FHL3 in glioma cells, we conducted a gene expression microarray analysis to identify novel FHL3 regulating genes. The FHL3 overexpressed T98G glioma cells l were used as the experiments model. We conservatively established a minimum of 2-fold difference between FHL3 and control group, with an FDR-adjusted P value of less than 0.05, and identified 285 up-regulated and 420 down-regulated genes that met the threshold in all microarray analyses of 3 independent groups.

2018-02-02 | GSE109988 | GEO

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

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

| PRJNA438589 | ENA