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RNA sequencing to study transcriptomic changes in DLD-1 (colorectal adenocarcinoma) cells exposed to soft polyacrylamide matrices (~2 kPa and ~55 kPa) for short time scale of 90 minutes

ABSTRACT: RNA sequencing to study transcriptomic changes in DLD-1 (colorectal adenocarcinoma) cells exposed to soft polyacrylamide matrices (~2 kPa and ~55 kPa) for short time scale of 90 minutes

PROVIDER: PRJNA429111 | ENA |

REPOSITORIES: ENA

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RNA sequencing to study transcriptomic changes in DLD-1 (colorectal adenocarcinoma) cells exposed to soft polyacrylamide matrices (~2 kPa and ~55 kPa) for short time scale of 90 minutes

Project description:Aim: To examine transcriptional changes in DLD-1 cells exposed to softer matrices (2 kPa and 55 kPa) and identify the chromosomes that are enriched with maximmally deregulated genes Methods: DLD-1 cells (otherwise growing on stiff tissue culture plastic substrates) were exposed to softer matrices for 90 minutes and to collagen coated glass coverslips (served as control) served as control) Results: RNA sequencing revealed nearly equivalent transcriptional deregulation in cells on both the polyacrylamide matrices (783 genes up and 872 genes down on 2 kPa, 649 genes up and 783 genes down on 55 kPa) when compared to cells on glass. Additionally, GO classification revealed that unique sets of transcriptionally deregulated genes (log fold≥2) belonged to pathways associated with transcription regulation, chromatin organization, cell cycle and DNA damage/repair Results: We identified chromosomes 1, 2, 3, 6, 7, 10, 12, 14, 17 and 19 to be maximally enriched with the deregulated genes on softer matrices (log fold≥2), while chromosomes 13, 18 and 21 showed minimal enrichment of deregulated genes. We also examined the spatial organization of chromosome 1, 18 and 19 territories in cells on softer matrices (using 3D-FISH) and observed that these chromosomes were mislocalized away from their conserved nuclear locations Conclusions: Our study reports the transcriptomic changes in DLD-1 cells upon lowering of extracellular substrate stiffnes and its impact on the spatial positioning of chromosome territories

2018-04-05 | GSE108907 | GEO

3dpf untreated zebrafish larvae vs. 3dpf zebrafish larvae treated with 20mM PTZ for 30 minutes and 90 minutes

Project description:Transcriptional profiling of 3dpf wild type zebrafish larvae treated with 20mM PTZ for 30 and 90 minutes compared with 3dpf wild type control untreated zebrafish larvae.

2017-02-24 | GSE95312 | GEO

mRNA sequencing analysis of transcripts from CA1 regions 90 minutes after Long-Term Potentiation was induced

Project description:Purpose: Study the differentially expressed genes in hippocampal rat CA1 regions 90 minutes after Long-Term Potentiation (LTP) was induced using field recordings Methods: hippocampal rat CA1 region mRNA profiles of control (unstimulated) and 90 minutes after LTPwas induced (LTP 90) were generated by deep sequencing. A pool of approximately 10 CA1 regions collected from at least 3 different animals were used. The seq library was prepared using TruSeq RNA Sample Prep Kit v2 protocol (Illumina, CA, USA). For the RNA-Seq data analysis Tophat 2.0.13, bowtie 2.1.0 , samtool 0.1.7 and cufflinks 1.3.0 were used. The rn5-bowtie2 index was generated with the command 'bowtie2-build rn5.fa rn5'. The 'rn5.fa'-file was downloaded from the UCSC genome browser. The mm10-bowtie2 index was downloaded from http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml. RefSeq geneTracks and GTF-files for the rn5 and mm10 genome assembly were downloaded from UCSC genome browser. Common gene ids in the GTF-files were matched to individual transcript_ids using the corresponding official symbols obtained from the geneTracks files. Conclusions: Our study illustrates the nature of the different transcripts in acute rat hippocampal slices after LTP 90 minutes was induced using field electrophysiology and compares them with control, unstimulated slices. Thius allowed us to identify wich genes are modulated in the hippocampus in order to promote and sustain LTP.

2018-10-02 | GSE120712 | GEO

RNAseq analysis of genes activated 90 minutes, or 7 days post irradiation or untreated cells with knockdown of NFKBIA

Project description:Goal of the study was to investigate genes regulated differentially after 90 minutes versus 7 days after irradiation. 7 day time point corresponds to cellular senescence. U2OS cells were irradiated with 20 Gy and harvested either 90 minutes or 7 days. In addition cells were left untreated (control) or had knockdown of NFKBIA (protein name Ikappa B alpha). Ikappa B alpha is the main inhibitor of the transcription factor NFkappa B. NFkappa B regulates transcription of many factors constituting the SASP (senescence associated secretory phenotype).

2020-09-30 | GSE158743 | GEO

Next Generation Sequencing on HMEC-1 or HUVEC residing on SOFT or STIFF matrices

Project description:Purpose: Endothelial cells respond to changes in subendothelial stiffness altering their proliferation, migration and barrier integrity but whether that is due to transcriptional reprogramming was largely unknown. Using RNA-Sequencing, we performed gene expression profiling for two endothelial cell types grown on soft or stiff matrices: primary human umbilical vein endothelial cells (HUVEC) and immortalized human microvascular endothelial cells (HMEC-1), to understand whether subendothelial stiffness-dependent changes in endothelial cell mechanics are due to transcriptional regulation. Methods and Results: By analyzing the differentially expressed genes between all samples we found that endothelial cell type rather that subendothelial stiffness is the primary determinant of the endothelial cell transcriptome. Both cell types respond to changes in their subendothelial stiffness by increasing the traction stresses they exert on stiffer as opposed to softer matrices, however it is apparently not the endothelial cell transcriptome that regulates this universal biomechanical response to subendothelial stiffness. Only a handful of genes were differentially expressed in each cell type in a stiffness-dependent manner, and none were shared between the two cell types examined. In contrast, thousands of genes were differentially regulated in HUVEC as compared to HMEC-1. HUVEC (but not HMEC-1) upregulate expression of TGF-2 on stiffer matrices, and also enhance their endogenous TGF-2 expression and their cell-matrix traction stresses in response to application of exogenous TGF-2. Conclusions: Altogether, these findings provide insights into the relationship between subendothelial stiffness, endothelial mechanics and variation of the transcriptome between distinct endothelial cell types, and reveal that subendothelial stiffness while critically impacting endothelial cell mechanics is minimally altering their transcriptome.

2019-07-31 | GSE135123 | GEO

Expression data from placenta harvested from WT and Pth-null fetuses treated 90 minutes prior with saline or PTH (1-84)

Project description:Parathyroid hormone (PTH) plays an essential role in regulating calcium and bone homeostasis in the adult, but whether PTH is required at all for regulating fetal-placental mineral homeostasis is uncertain. To address this we treated Pth-null mice in utero with 1 nmol PTH (1-84) or saline and examined placental calcium transfer 90 minutes later. It was found that placental calcium transfer increased in Pth-null fetuses treated with PTH as compared to Pth-null fetuses treated with saline. Subsequently, to determine the effect of PTH treatment on placental gene expression, in a separate experiment, 90 minutes after the fetal injections the placentas were removed for subsequent RNA extraction and microarray analysis.

2010-03-01 | GSE16983 | GEO

Next Generation Sequencing on HMEC-1 or HUVEC residing on SOFT or STIFF matrices

Project description:Next Generation Sequencing on HMEC-1 or HUVEC residing on SOFT or STIFF matrices

| PRJNA557476 | ENA

Transcription profiling of yeast to determine polysome-associated mRNAs after 90 minutes of mRNA mistranslation induction

Project description:Polysome-associated transcriptome analysis in cells after 90 minutes of mistranslation induction comparing with a pool of mRNAs existent in cells without induction at several time points (Reference)

2010-02-01 | E-MTAB-166 | biostudies-arrayexpress

Ectopic expression of AP4 in human colorectal cancer cells DLD-1 for different times

Project description:To characterize the transcriptome of the transcription factor AP4 DLD-1 cells were infected with AP4 coding viruses for different periods of time. Adenovirus amplification and purification was performed as previously described (He et al., 1998). The minimal amount of virus needed to reach more than 90% infection efficiency was determined by monitoring GFP signals with fluorescence microscopy. DLD-1 cells were infected in serum-free medium with adenovirus for 3 hours. After removal an equal amount of medium containing 20% FBS was added.

2013-05-31 | GSE46578 | GEO

HMGA2-driven gene expression in human colorectal DLD-1 cells.

Project description:Gene expression analysis of stable HMGA2-overexpressing DLD-1 cells (DLD-1-HMGA2) and its control cells (DLD-1-Vector).

2019-08-29 | GSE136544 | GEO