Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

46 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Circadian 45h time-course RNA-seq expression profiling of HCT116 cells in WT condition and upon CRISPR/Cas9-mediated knock-out of core-clock genes ARNTL, PER2 and NR1D1

ABSTRACT: A 45h time-course RNA-seq study was performed to analyse the different circadian phenotypes of human colorectal cancer cell line HCT116 WT, HCT116 ARNTL Knockout, HCT116 PER2 Knockout and HCT116 NR1D1 Knockout cells. Samples were taken every 3h starting from 9h after cell synchronization for a period of 45h resulting in 16 time-points for each cell line.

INSTRUMENT(S): NextSeq 500

ORGANISM(S): Homo sapiens

SUBMITTER: Angela Relógio

PROVIDER: E-MTAB-9701 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Up-regulation of IFN-related genes in BRCA2-/- cells

Project description:Microarray-based expression profiling of BRCA2 knockout and isogenic wild type HCT116 human colorectal cancer cells One way ANOVA, single factor comparison of wild type and BRCA2 knockout cells, three CEL files for wild type, three CEL files for BRCA2 knockout

2014-07-01 | E-GEOD-54830 | biostudies-arrayexpress

RNA expression profiling in primary and immortalized human mesothelial cells, and in human vein and microvascular endothelial cells

Project description:Mesothelial cells, which interact with endothelial cells, are widely used in research including cancer and drug development, have not been comprehensively profiled. We therefore performed RNA sequencing of polarized, primary peritoneal (HPMC) and immortalized pleural mesothelial cells (MeT-5A), and compared it to endothelial cells from umbilical vein (HUVEC) and cardiac capillaries (HCMEC).

2023-05-24 | E-MTAB-12021 | biostudies-arrayexpress

Targeted inhibition of ubiquitin signaling reverses the metabolic reprogramming and suppresses Glioblastoma growth

Project description:Glioblastoma (GBM) is the most frequent and aggressive form of primary brain tumor in the adult population, and the high recurrence rate and resistance to current therapeutics urgently demand a better therapy for this disease. Regulation of protein stability by the ubiquitin proteasome system (UPS) represents an important control mechanism of cell growth. Deregulation of UPS is mechanistically linked to the development and progression of a variety of human cancers, including GBM. Thus, UPS system represents a valuable target for GBM treatment. Here, we find that the E3 ligase praja2 selectively marks primary IDH1-wild type GBM. By using an integrated approach, including proteomics, transcriptomics and metabolic profiling, we identify praja2 as a main component of a signaling network that regulates cancer cell growth and metabolism. We show that praja2 binds and regulates the stability of the Kinase Suppressor of Ras 2 (KSR2) and as consequence, the activity of the downstream AMP-dependent protein kinase (AMPK) in GBM cells. By degrading KSR2, praja2 attenuates the oxidative metabolism and promotes the aerobic glycolysis (Warburg effect). Brain delivery of siRNAs targeting praja2 upregulates KSR2 and negatively impacted on GBM growth, reducing the tumor size and significantly improving the survival rate of treated mice. These data highlight the role of praja2 as an essential regulator of cancer cell metabolism, and as a preferential therapeutic target to suppress GBM growth

2022-06-29 | E-MTAB-11137 | biostudies-arrayexpress

The whole transcriptome changes in melanoma cells under dacarbazine treatment

Project description:The experiment was performed to reveal transcriptomic alterations in melanoma cells caused by dacarbazine (DTIC) treatment. Two primary cell cultures were exposed to dacarbazine at a final concentration of 1 mg/mL. The whole transcriptome was investigated in the cells treated with DTIC compared to a negative control group.

2021-04-09 | E-MTAB-10359 | biostudies-arrayexpress

Gene expression profiling of human whole-blood samples before and after the administration of recombinant human erythropoietin

Project description:As part of cross-platform comparisons of microarray and RNA-seq, this current experiment using the Affymetrix Human Transcriptome Array 2.0 aimed to quantify gene-level expression in subjects administered recombinant human erythropoietin over a 10-week protocol for the identification of gene signatures of blood doping. These results were compared to results obtained from other gene expression quantification platforms using the same experimental cohort, including the Illumina HumanHT-12v4 Expression BeadChips (archived in ArrayExpression; E-MTAB-2874), Illumina NextSeq 500 and MGI DNBSEQ-G400RS.

2021-11-04 | E-MTAB-11080 | biostudies-arrayexpress

Genome-wide binding signature of Signal transducer and activator of transcription (STAT) family in colorectal cancer HCT 116 cell

Project description:The excessive and continuous activated Janus kinase/signal transducer and activator of transcription (JAK/STAT) pathway leads to the proliferation and migration of malignant cells resulting in the occurrence and development of almost all of cancers. The defined gene sets specifically activated by different STAT proteins are relied on their genomic accessibility by the interplay of certain STAT proteins with other potential cofactors. However, we have no clue about the status of human activated STAT dimers in the nucleus, as well as the intercrossing modules of synergic, supplementary or competitive relationship among each other in colorectal cancer. In current study, chromatin immunoprecipitation sequencing (ChIP-seq) was conducted to explore the genome-scale binding signatures of STAT1, STAT2, STAT3, STAT5A/B and STAT6 in human HCT-116 CRC cells. Moreover, STAT3 binding on genomic DNA was also investigated in HCT116 cells with NR5A2 knockdown.

2021-11-08 | E-MTAB-11113 | biostudies-arrayexpress

A phase II trial of weekly nab-paclitaxel for progressive and symptomatic desmoid tumors

Project description:The uploaded datasets contains raw data from our research: columns represent patients, rows represent meta data (patients response, type of sarcoma, etc ...) + the raw gene counts.

2022-09-01 | E-MTAB-12163 | biostudies-arrayexpress

The transcriptome-wide alternative polyadenylation alteration in herbal formula YYJD-induced activity in A549 lung adenocarcinoma cells

Project description:The Herbal Formula YYJD inhibit migration and invasion of lung adenocarcinoma cells, we aims to profile a comprehensive alternative polyadenylation (APA) dynamic pattern of Lung Adenocarcinoma Cells under YYJD treatment unsing 3T-seq method.

2019-10-31 | E-MTAB-8151 | biostudies-arrayexpress

miRNA sequencing of rat hearts treated chronically with rofecoxib or its vehicle

Project description:We reported previously that chronic treatment with the Cyclooxygenase-2 inhibitor, rofecoxib, increased acute mortality in rats exposed to ischemia/reperfusion injury (I/R). This manifestation of hidden cardiotoxicity was attributed to the proarrhythmic effect of the drug on the ischemic heart. However, rofecoxib also had beneficial effects on ischemic injury, manifesting as decreased infarct size. In the present study, we aimed to identify molecular changes caused by chronic rofecoxib treatment in the heart. Rats were treated with 5.12 mg/kg rofecoxib or its vehicle for four weeks. Messenger RNA (mRNA), microRNA (miRNA) deep sequencing data, and proteomic datasets of left ventricular tissue samples were used for an unbiased differential expression analysis followed by in silico molecular network analysis and experimental target validation. Using mass spectrometry and filtering criteria, 26 proteins were identified that exhibited pronounced changes in protein expression or phosphorylation due to chronic rofecoxib treatment. The transcriptomic analysis showed mild alterations in the heart´s mRNA- and miRNA expression. The posttranscriptional regulation of mRNAs by miRNAs did not result in differential protein expression. This is the first demonstration that chronic rofecoxib treatment affects posttranslational modification and expression of several proteins in the heart. These are potential off-target effects that could account for the hidden cardiotoxic and/or cardioprotective effects of rofecoxib.

2024-10-30 | E-MTAB-13909 | biostudies-arrayexpress

mRNA sequencing of rat hearts treated chronically with rofecoxib or its vehicle

2024-10-30 | E-MTAB-13913 | biostudies-arrayexpress