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Unknown,Transcriptomics,Genomics,Proteomics

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Determination of transcript abundance before and after serum induction in human HCT-116 colon cancer cell line.

ABSTRACT: Transcriptional regulation of developmentally controlled genes is at the heart of differentiation and organogenesis. In this study, we have performed mRNA transcript abdundance analyses in human cells in response to serum activation signal by RNA-seq. mRNA transcript abundance determined before and after serum activation signals using two biological replicates.

ORGANISM(S): Homo sapiens

SUBMITTER: Alexander Garruss

PROVIDER: E-GEOD-30786 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Dynamic transcriptional events in embryonic stem cells mediated by the super elongation complex (SEC).

Lin Chengqi C Garrett Alexander S AS De Kumar Bony B Smith Edwin R ER Gogol Madelaine M Seidel Christopher C Krumlauf Robb R Shilatifard Ali A

Genes & development 20110701 14

Transcriptional regulation of developmentally controlled genes is at the heart of differentiation and organogenesis. In this study, we performed global genomic analyses in murine embryonic stem (ES) cells and in human cells in response to activation signals. We identified an essential role for the ELL (eleven-nineteen lysine-rich leukemia gene)/P-TEFb (positive transcription elongation factor)-containing super elongation complex (SEC) in the regulation of gene expression, including several genes ...[more]

PMID: 21764852

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Super Elongation Complex (SEC) and global genomic analyses in murine embryonic stem (ES) cells and in human cells in response to activation signals.

Project description:Transcriptional regulation of developmentally controlled genes is at the heart of differentiation and organogenesis. In this study, we have performed global genomic analyses in murine embryonic stem (ES) cells and in human cells in response to activation signals. We have identified an essential role for the ELL/P-TEFbcontaining Super Elongation Complex (SEC) in the regulation of gene expression including several genes bearing paused RNA polymerase II (Pol II). Paused Pol II has been proposed to be associated with loci that respond rapidly to environmental stimuli. However, our studies in ES cells have also identified a requirement for SEC at genes without preloaded Pol II, which also respond dynamically to differentiation signals. Our findings suggest that SEC is a major class of active P-TEFb-containing complexes required for transcriptional activation in response to environmental cues such as differentiation signals. Examination of ELL2, AFF4, and Pol II before and after activation signals in two cell types.

2011-07-19 | E-GEOD-30267 | biostudies-arrayexpress

Expression data from Che-1 (AATF) depleted HCT 116 cell line

Project description:Che-1 is a RNA Polymerase II binding protein involved in the regulation of gene transcription. Che-1 emerges as an important adaptor that connects transcriptional regulation, cell-cycle progression, checkpoint control, and apoptosis. We have observed that Che-1 depletion sensitizes cells to chemotherapy. We used microarrays analysis to investigate classes of genes regulated by Che-1. Total RNA was extracted from control and Che-1 depleted HCT 116 cells 48 hours after transient transfection of siRNA.

2013-03-12 | E-GEOD-45009 | biostudies-arrayexpress

RNA-seq of the human colorectal adenocarcinoma cell line HCT-116 treated with 5-aza-2’-deoxycytidine

Project description:We performed poly(A)+ stranded RNA-seq of a panel of the human colorectal adenocarcinoma cell line HCT-116 treated with 5-aza-2’-deoxycytidine. In parallel, we determined the genomic location and DNA methylation levels of human full-length LINE-1 elements (L1) from the same samples using bs-ATLAS-seq (E-MTAB-12240). To link DNA methylation and L1 expression, we used cell pellets from the same cell culture to perform both RNA-seq and bs-ATLAS-seq.

2023-09-21 | E-MTAB-12245 | biostudies-arrayexpress

GM-CSF induced gene-regulation in human monocytes

Project description:Human and murine studies showed that granulocyte macrophage colony-stimulating factor (GM-CSF) exerts beneficial effects in intestinal inflammation. To explore whether GM-CSF mediates its effects via monocytes, we analyzed effects of GM-CSF on monocytes in vitro and assessed the immunomodulatory potential of GM-CSF-activated monocytes (GMaM). We used microarray technology and functional assays to characterize GMaM in vitro and used a mouse model of colitis to study GMaM functions in vivo. Peripheral blood monocytes where cultured 16 h with media containing AB serum (control monocytes) or media containing 10 ng/mL GM-CSF and AB serum (GM-CSF activated monocytes). In three independent experiments, total RNA from GMaM and control monocytes was isolated and processed for microarray hybridization.

2014-11-27 | E-GEOD-63662 | biostudies-arrayexpress

Targeting the Scaffold Protein Plectin by an Organometallic as a Strategy to Inhibit Tumour Invasiveness- whole cell lysate of HCT 116 epithelial cells, Ru-OH-2 normal pull down 4h

Project description:The inability of determining direct molecular targets of metal-based therapeutic agents beyond the platinum class is one of the major bottlenecks in their development. Here, we employ an integrated chemical proteomics and response profiling approach to identify and validate plestatins, based on an organometallic ruthenium(II) scaffold, as selective plectin-targeting agents. Plectin is a giant scaffold protein involved in controlling cytoarchitecture. Subcytotoxic concentrations of plestatins induce drastic morphological phenotypes on the microtubule (MT) network accompanied by a global down-regulation of translational activity. Plecstatins possess anti-invasive properties in tumour spheroids and also display tumour-inhibiting effects in vivo after oral administration. The ability of plecstatins to alter the MT network via plectin represents a unique mechanism to target MTs and shows promise as an anticancer strategy. Ru-OH-2 is an analogue of plecstatin-3 displaying an ancillary hydrogen bond donor instead of a hydrogen bond acceptor.

2022-03-01 | PXD010318 | Pride

Targeting the Scaffold Protein Plectin by an Organometallic as a Strategy to Inhibit Tumour Invasiveness- whole cell lysate of HCT 116 epithelial cells, Ru-OH-2 competitive pull down 4h

2022-03-01 | PXD010319 | Pride

Spatial SILAC Regorafenib Treated Bottom-up Proteomic Analysis

Project description:Developing effective model systems to evaluate new potential chemotherapeutic reagents is critical. Three-dimensional cell cultures, such as spheroids, aid in bridging the gap between commonly used monolayer cell cultures and significantly more complex and expensive animal models. Spheroid model systems contain pathophysiological and chemical gradients similar to an in vivo tumor, which ultimately form distinct cellular subpopulations. In the spatial SILAC model, labels are pulsed into the spheroid at discrete time windows during development. These media pulses result in labeled proteins in distinct regions of the spheroid, which allows for tracing of quantitative proteomic changes to be correlated to different cellular subregions. In this study, we use the Spatial SILAC model to evaluate the proteomic response of a colon carcinoma spheroid to the multikinase inhibitor Regorafenib. We determined regorafenib to be an effective kinase inhibitor which significantly altered whole spheroid proliferation and resulted in increased apoptosis when the signal was averaged for all cells in the culture. However, when regorafenib treatment is more closely examined among the cellular subpopulations, drastic differences are observed for how the drug impacted the proteome of the necrotic spheroid core and the proliferating outer regions. Whole spheroid and outer region analysis shows that regorafenib treatment inhibited critical pathways such as mTOR signaling, ERK/MAPK signaling, and colorectal cancer metastasis signaling. However, analysis of the core shows that regorafenib had an entirely different effect, including upregulation of MAPK1 and KRAS, possibly indicating drug resistance within these late apoptotic cells. Ultimately, these combinatory studies can be used to further understanding of drug metabolism is different cellular subpopulations and provide valuable information to ultimately improve the accuracy of therapeutic testing.

2024-08-09 | PXD038958 | Pride

Methylation profiling of human colorectal carcinoma cells after inhibition of DNMT3B

Project description:Array-based analysis of genome-wide DNA methylation changes in colorectal carcinoma cells after inhibition of DNA methyltransferase 3B (DNMT3B)

2012-03-01 | E-MTAB-719 | biostudies-arrayexpress

Optimized siRNAs with a minimal off-target effect facilitate the screening of essential genes in cancer cells

Project description:siRNAs with dN are a promising and easy approach to characterize essential genes by minimizing the off-target effect in cancer cells. mRNA profiles of HCT 116 cells after the transfection of siRNAs or blank control by deep sequencing, using HiSeq 2000

2015-07-01 | E-GEOD-62968 | biostudies-arrayexpress

RNAi knock down of mSin3a-b and SBTB4 in human colon carcinoma cell line HCT116

Project description:Efffects of silencing ZBTB4, mSin3a/mSin3b on HCT 116 human colon carcinoma cell lines for 48 hours

2008-03-31 | E-MEXP-1509 | biostudies-arrayexpress