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RNA sequencing of HECTD3 knockdown during TNFalpha stimulation in primary HUVEC cells

ABSTRACT: RNA sequencing of HECTD3 knockdown during TNFalpha stimulation in primary HUVEC cells

PROVIDER: PRJNA832954 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR18961300_1.fastq.gz	Fastqsanger.gz
	SRR18961300_2.fastq.gz	Fastqsanger.gz
	SRR18961301_1.fastq.gz	Fastqsanger.gz
	SRR18961301_2.fastq.gz	Fastqsanger.gz
	SRR18961294_1.fastq.gz	Fastqsanger.gz

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Interaction effects of knockdown of PML and TNFalpha treatment in HUVEC cells

2013-01-10 | GSE35000 | GEO

Interaction effects of knockdown of PML and TNFalpha treatment in HUVEC cells

Project description:To study the interaction effects between promyelocytic leukemia (PML) gene knockdown and tumor necrosis factor-alpha (TNFalpha) signaling in human umbilical vein endothelial cells (HUVECs), we transfected control or two independent PML siRNAs into HUVEC cells without or with 20 ng/mL TNFalpha treatment for 20 h. The total RNA was extracted for gene expression microarray analyses. The experiment is a 3x2 two-factor design. One factor is siRNA and it has three levels (siCtrl, siPML1, siPML2). siCtrl is RISC-inducing non-targeting control siRNA. siPML1 and siPML2 designate two independent siRNAs against the PML gene. Two independent siRNAs were used to eliminate the off-target effects of siRNA. The other factor is TNFalpha treatment (20 ng/mL for 20 h) and it has two levels: Untreated (U) or Treated (T). Each sample has technical duplicates.

2013-01-10 | E-GEOD-35000 | biostudies-arrayexpress

RNA sequencing of HECTD3 knockdown during TNFalpha stimulation in primary HUVEC cells

Project description:We isolated and validated primary HUVECs from the neonatal umbilical cord vein, and performed genome-wide expression analysis to profile differentially expressed genes in control and HECTD3-KD HUVECs treated with or without TNFα for 2 hours. Compared with control HUVECs, 59 genes showed lower expression in HECTD3-KD HUVECs in response to TNFα. Most of them are NF-κB target genes, including adhesion molecules SELE (E-selectin), ICAM-1, and VCAM-1.

2022-06-29 | GSE201759 | GEO

Stimulation of HUVEC by BMP9/10

Project description:Stimulation of HUVEC by BMP9/10

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Project description:The experiment studied the effect of knockdown WTAP in HUVEC. two control samples and two WTAP knockdown samples. Keywords: other

2005-11-30 | GSE2327 | GEO

Comparison of primary vs immortalized HUVEC

Project description:Comparison of primary vs immortalized HUVEC

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Expression data from HUVEC with YAP siRNA knockdown

2014-10-17 | GSE61989 | GEO

siRNA profiling of human HUVEC cells after WTAP knockdown

Project description:The experiment studied the effect of knockdown WTAP in HUVEC. two control samples and two WTAP knockdown samples.

2008-06-12 | E-GEOD-2327 | biostudies-arrayexpress

Expression data from HUVEC with YAP siRNA knockdown

Project description:YAP knockdown in HUVEC elicits proliferation and cell cycle preogression defects. YAP deficient cells caused arrest in G1 and defects in S-phase entry. The microarray analysis was conducted to identify potential YAP targets that are involved in HUVEC cell cycle regulation mRNA samples were collected from siRNA treated HUVECs 30 hour after transfection. Four biological replicates were used for each condition: control (RISC-free) and knockdown (siYAP#1 and siYAP#2)

2014-10-17 | E-GEOD-61989 | biostudies-arrayexpress

TNFalpha signaling primes chromatin for NF-kappaB binding and induces rapid and widespread nucleosome repositioning

Project description:Background The rearrangement of nucleosomes along the DNA fiber profoundly affects gene expression, but little is known about how signaling reshapes the chromatin landscape, in 3D space and over time, to allow the establishment of new transcriptional programs. Results Using micrococcal nuclease treatment and high-throughput sequencing, we map genome-wide changes in nucleosome positioning in primary human endothelial cells stimulated with tumour necrosis factor alpha (TNFalpha) - a proinflammatory cytokine that signals through nuclear factor kappaB (NF-kappaB). Within 10 minutes, nucleosomes reposition at regions both proximal and distal to NF-kappaB binding sites, before the transcription factor quantitatively binds thereon. Similarly, in long TNFalpha-responsive genes, repositioning precedes transcription by pioneering elongating polymerases and appears to nucleate from intragenic enhancer clusters resembling super-enhancers. By 30 minutes, widespread repositioning occurs throughout Mbp-long chromosomal segments, with consequential effects on 3D structure, detected using chromosome conformation capture. Conclusions Whilst nucleosome repositioning is viewed as a local phenomenon, our results point to effects occurring over multiple scales. Here, we present data in support of a TNFalpha-induced priming mechanism, mostly independent of NF-kappaB binding and/or elongating RNA polymerases, leading to a plastic network of interactions that affects DNA accessibility over large domains. MNase-Seq of HUVEC cells after stimulation with TNFÎ± for 0, 10 or 30 min. Biological replicates for 0 and 30 min.

2014-11-05 | E-GEOD-53343 | biostudies-arrayexpress

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