Nascent transcriptional profiling of CEM-C7 ALL cells treated with dexamethasone
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA906631 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR22450585.fastq.gz | Fastqsanger.gz | |||
| SRR22450586.fastq.gz | Fastqsanger.gz | |||
| SRR22450587.fastq.gz | Fastqsanger.gz | |||
| SRR22450588.fastq.gz | Fastqsanger.gz | |||
| SRR22450589.fastq.gz | Fastqsanger.gz |
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Project description:The glucocorticoid receptor (GR) is a transcription factor that localizes to the nucleus and reuglates gene expression upon binding of a glucocorticoid ligand such as dexamethasone. We perform nascent transcriptional profiling of C7 ALL cells following treatment with dexamethasone to evaluate the immediate transcriptional effects of GR. We find 51 dynamic genes (46 activated, 5 repressed) after 1 hour treatment and 141 dynamic genes (70 activated and 71 repressed) after 4 hour treatment. We input RNA polymerase density in pause and gene body regions into a mathematical model designed to quantify rate changes of individual transcriptional steps. We find that dexamethasone treatment primarily activates genes by inducing pause release rate.
2022-12-04 | GSE219041 | GEO
Project description:The beneficial effects of glucocorticoids (GCs) in acute lymphoblastic leukemia (ALL) are based on their ability to induce apoptosis. Omics technologies such as DNA microarray analysis are widely used to study the changes in gene expression and have been successfully implemented in biomarker identification. In addition, time series studies of gene expression enable the identification of correlations between kinetic profiles of glucocorticoid receptor (GR) target genes and diverse modes of transcriptional regulation. This study presents a genome-wide microarray analysis of both our and published Affymetrix HG-U133 Plus 2.0 data in GCs-sensitive and -resistant ALL. GCs-sensitive CCRF-CEM-C7-14 cells were treated with dexamethasone at three time points (0 h, 2 h and 10 h). The treated samples were then compared to the control (0 h). Dexamethasone-treated CCRF-CEM-C7-14 samples were divided into 3 groups based on time points: the untreated control (0 h), 2 h and 10 h.
2012-09-01 | E-GEOD-39338 | biostudies-arrayexpress
Project description:The efficacy of glucocorticoid receptor modulation is well established in Acute Lymphoblastic Leukemia(ALL) but the response remains heterogeneous and limited by emergence of drug resistance. Here we use, two clonally-derived cell lines (CEM-C1 and CEM-C7) from a 3-year-old T-cell ALL patient, as a model system to understand the mechanisms of drug resistance in these cell lines; the clone CEM-C1 is resistant to dexamethasone-induced apoptosis and CEM-C7 is sensitive. We performed ATACseq and RNAseq to query for TF binding motifs present in the open regions of the chromatin and expression levels of TFs that could recognize the identified motifs. We are experimentally validating our hypothesis that depletion of the TFs identified, either singly or in combination, in CEM-C7 cells will cause dexamethasone resistance in CEM-C7 cells.
2021-07-20 | GSE102038 | GEO
Project description:The beneficial effects of glucocorticoids (GCs) in acute lymphoblastic leukemia (ALL) are based on their ability to induce apoptosis. Omics technologies such as DNA microarray analysis are widely used to study the changes in gene expression and have been successfully implemented in biomarker identification. In addition, time series studies of gene expression enable the identification of correlations between kinetic profiles of glucocorticoid receptor (GR) target genes and diverse modes of transcriptional regulation. This study presents a genome-wide microarray analysis of both our and published Affymetrix HG-U133 Plus 2.0 data in GCs-sensitive and -resistant ALL. GCs-sensitive CCRF-CEM-C7-14 cells were treated with dexamethasone at three time points (0 h, 2 h and 10 h). The treated samples were then compared to the control (0 h). The published data used were as follows: GSE2677: GSM51674: B-ALL-24-24h GSM51675: B-ALL-24-6h GSM51676: B-ALL-24-0h GSM51680: B-ALL-17-24h GSM51681: B-ALL-17-8h GSM51682: B-ALL-17-0h GSM51677: B-ALL-13-24h GSM51678: B-ALL-13-8h GSM51679: B-ALL-13-0h GSM51683: B-ALL-31-24h GSM51684: B-ALL-31-6h GSM51685: B-ALL-31-0h GSM51686: B-ALL-32-24h GSM51687: B-ALL-32-6h GSM51688: B-ALL-32-0h GSM51689: B-ALL-33-24h GSM51690: B-ALL-33-6h GSM51691: B-ALL-33-0h GSM51692: B-ALL-37-24h GSM51693: B-ALL-37-6h GSM51694: B-ALL-37-0h GSM51695: B-ALL-38-24h GSM51696: B-ALL-38-6h GSM51697: B-ALL-38-0h GSM51698: B-ALL-40-24h GSM51699: B-ALL-40-6h GSM51700: B-ALL-40-0h GSM51701: B-ALL-43-24h GSM51702: B-ALL-43-6h GSM51703: B-ALL-43-0h GSM51707: T-ALL-25-24h GSM51708: T-ALL-25-6h GSM51709: T-ALL-25-0h GSM51704: T-ALL-20-24h GSM51705: T-ALL-20-8h GSM51706: T-ALL-20-0h GSM51710: T-ALL-2-24h GSM51711: T-ALL-2-8h GSM51712: T-ALL-2-0h GSE2842 GSM60545: S-Line-PreB-6h-EtOH GSM60546: S-Line-PreB-6h-GC GSM60547: S-Line-PreB-24h-GC GSM60542: S-Line-C7H2-6h-EtOH GSM60543: S-Line-C7H2-6h-GC GSM60544: S-Line-C7H2-24h-GC GSM60560: R-Line-CEMC1-6h-EtOH GSM60561: R-Line-CEMC1-6h-GC GSM60562: R-Line-CEMC1-24h-GC GSM60564: R-Line-C7R1-6h-EtOH GSM60566: R-Line-C7R1-6h-GC GSM60576: R-Line-C7R1dim-low-6h-EtOH GSM60578: R-Line-C7R1dim-low-6h-GC GSM60579: R-Line-C7R1dim-low-24h-GC GSM60581: R-Line-PreB-6h-EtOH GSM60583: R-Line-PreB-6h-GC GSM60584: R-Line-PreB-24h-EtOH GSM60586: R-Line-PreB-24h-GC GSM60548: C-Line-CEMC1-ratGR-6h-EtOH GSM60549: C-Line-CEMC1-ratGR-6h-GC GSM60550: C-Line-CEMC1-ratGR-24h-GC GSM60551: C-Line-C7R1dim-high-6h-EtOH GSM60552: C-Line-C7R1dim-high-6h-GC GSM60553: C-Line-C7R1dim-high-24h-GC
2012-09-01 | GSE39338 | GEO
Project description:C7 is a novel lytic cycle inducer of Epstein-Barr virus (EBV) in EBV-positive epithelial cells. To analyze the potential signaling pathways that are activated by C7 for induction of EBV lytic cycle, we performed a RNA sequencing to analyze the RNA expression profiles in AGS-BX1 gastric carcinoma cells before and after treatment with C7.
2018-11-21 | GSE122751 | GEO
Project description:Transcriptional profiling of human CEM cells comparing control untreated CEM cells with either 2h or 4.5h cluvenone-treated CEM cells.
2010-08-11 | GSE23536 | GEO
Project description:We have developed a monoclonal antibody (mAb) C7 that reacts with Als3p and enolase present in Candida albicans cell wall and exerts three anti-Candida activities: candidacidal activity and inhibition of both adhesion and filamentation. To investigate the mode of action of mAb C7 on fungal viability, we examined changes in the genome-wide gene expression profile of C. albicans grown in presence of a subinhibitory concentration of mAb C7 (12.5 µg/ml) by using microarrays. A total of 49 genes were found to be differentially expressed upon treatment with mAb C7. Of these, 28 were found to be up-regulated and 21 down-regulated. The categories of up-regulated genes with the largest number of variations were those involved in iron uptake or related to iron homeostasis (42.86%), while the energy-related group accounted for 38.10% of the down-regulated genes (8/21). Results were validated by real Time PCR. Since these effects resembled those found under iron-limited conditions, the activity of mAb C7 on C. albicans mutants with deletions in key genes implicated in the three iron acquisition systems described in this yeast was also assessed. Only mutants lacking TPK1 and TPK2 genes were less sensitive to the candidacidal effect of mAb C7. FeCl3 or hemin at concentrations ≥ 7.8µM reversed the candidacidal effect of mAb C7 on C. albicans, on a concentration dependent manner. The results presented in this study provide evidence that the candidacidal effect of mAb C7 is related to the blockage of the reductive iron uptake pathway of C. albicans. A saturated culture of C. albicans grown overnight was diluted to an optical density at 600 nm of approximately 0.1 and divided in two aliquots. One of them was used untreated as control and the second one was treated with a subinhibitory concentration (12.5 µg/ml) of monoclonal antibody C7 . Both cultures were incubated for 18 h at 37ºC before harvesting cells. Antibody added and control samples were obtained each time. The experiment was repeated once. Dye-swap technique was used for hybridization and four arrays were analyzed to compare the expresion of over six thousands genes in response to antibody C7.
2010-12-11 | E-GEOD-25969 | biostudies-arrayexpress
Project description:Transcriptional profiling of human CEM cells comparing control untreated CEM cells with either 2h or 4.5h cluvenone-treated CEM cells. Two-timepoint experiment, CEM vs. Cluvenone-Treated CEM (2h and 4.5h). Biological replicates: 4 control, 4 2h-treated, 4 4.5h-treated, independently grown and harvested. Pooled controls. One replicate per array.
2010-08-11 | E-GEOD-23536 | biostudies-arrayexpress
Project description:Lachnospiraceae bacterium c7 strain:c7 Genome sequencing
| PRJNA310131 | ENA
Project description:This SuperSeries is composed of the following subset Series: GSE39335: Expression data from glucocorticoid-treated ALL (BCR-ABL patients) GSE39338: Expression data from glucocorticoid-treated ALL (CCRF-CEM-C7-14 cells) Refer to individual Series
2012-09-01 | E-GEOD-39339 | biostudies-arrayexpress