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Poly A+ RNA sequencing of quiescent and early serum stimulated WI-38s

ABSTRACT: poly A+ RNA sequencing of quiescent and early serum stimulated WI-38s

PROVIDER: PRJNA604619 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR11007920_1.fastq.gz	Fastqsanger.gz
	SRR11007920_2.fastq.gz	Fastqsanger.gz
	SRR11007921_1.fastq.gz	Fastqsanger.gz
	SRR11007921_2.fastq.gz	Fastqsanger.gz
	SRR11007922_1.fastq.gz	Fastqsanger.gz

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poly A+ RNA sequencing of quiescent and early serum stimulated WI-38s

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poly A+ RNA sequencing of quiescent and early serum stimulated control and MIR222HG-depleted WI-38s

Project description:We performed paired-end poly A+ RNA sequencing using total RNA isolated from serum-starved and serum-released (6-hour) control and MIR222HG-depleted WI-38 cells

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poly A+ RNA sequencing of quiescent and early serum stimulated control and MIR222HG-depleted WI-38s

Project description:poly A+ RNA sequencing of quiescent and early serum stimulated control and MIR222HG-depleted WI-38s

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Response of quiescent human fibroblasts to different growth factors and serum

Project description:Quiescent human fibroblasts (2091 and Wi-38) were stimulated with different growth factors and serum. Cells were collected at 6 different time points followed by global transcriptional profiling. Keywords: time course, growth factor response, cell line comparison

2006-04-12 | GSE3901 | GEO

Global mapping of polyadenylation site use in proliferating and quiescent (contact-inhibited and serum-starved) cells

Project description:Purpose: To determine genes that undergo alternative polyadenylation in proliferating versus quiescent fibroblasts. Methods: Three different biological replicates (fibroblast strains, 10-1, 12-1, and 12-2) were used for generating proliferating and quiescent (7-day contact inhibited and 7-day serum-starved) cells. RNA extracted from these cells were used for library preparation. cDNA fragments were enriched for the junction between the poly(A) site and the end of the 3' UTR using a modified high throughput sequencing protocol (GnomeGen). cDNA libraries were created according to Gnome-Gen RNA-seq library preparation kit for RNA profiling except Amgen Ampure XP beads were used instead of the Gnome-gen size selector product to remove ligation reaction products before proceeding to the reverse transcription step. The libraries were sequenced on an Illumina HiSeq 2000 instrument. The sequencing reaction wasa run for 147 cycles. Reads from pol(A) enriched cDNA libraries were aligned to the genome using the STAR alignment algorithm after the computational removal of untemplated adenosines. Results: Polyadenylation site selection was significantly altered in approximately 10% of genes in quiescent compared with proliferating fibroblasts. Contact inhibited and serum starved fibroblasts had similar polyadenylation site selection profiles. Conclusions: Quiescence is associated with changes in polyadenylation site selection.

2018-07-19 | GSE117337 | GEO

Role of PI3K pathway in serum/growth factor response of quiescent fibroblasts

Project description:PI-3K inhibitor (LY294002) was added to quiescent fibroblasts 30 minutes prior growth factor/serum treatments. The role of PI-3K pathway was thus monitored by comparing with untreated samples. Keywords: time course, growth factor response, cell line comparison

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Transcriptomic datat of senescence WI-38 cell

Project description:Senescence in WI-38 cell context was induce by RASv12 over expression Cellular senescence is a permanent cell cycle arrest that is triggered by cancer- initiating or promoting events in mammalian cells and is now considered a major tumour suppressor mechanism. Here, we did a transcriptomic analysis and compared WI-38 contol wich is a human fibroblaste cell line and WI-38 that overexpressed RASv12 a G protein that induce senescence. The goal of our project is to compare transciptomic profile of human growing fibroblast (WI-38 control) and senescent human fibroblast (WI-38 OERAS)

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Macrophages stimulated with LPS and Poly (I:C)

Project description:The aim of the current study was to investigate the response of in vitro differentiated trout macrophages, a primary cell culture system widely used in fish immunology research, to lipopolysaccharide (LPS) and to the analog viral ds(RNA) Poly I:C. To that end we have used a salmonid-specific microarray platform enriched with immune-related genes. The results clearly suggest that the molecular mechanisms involved in the response of macrophages to LPS and Poly (I:C) are specific in some signaling pathways related to cell communication, signal transduction and kinase cascades. Nevertheless, macrophages stimulated with bacterial or viral PAMPs also activate common transcription factors.

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Project description:The focus of this study was to investigate the response of cultured rainbow trout erythrocytes to lipopolysaccharide (LPS) and to the analog viral dsRNA Poly(I:C) using a salmonid-specific microarray platform enriched with immune-related genes. Although the transcriptomic response measured as the total number of differentially expressed genes was higher in LPS, the intensity response, in terms of genes with a FC>2, was greater in Poly(I:C) treated cells. These two treatments shared the regulation of some genes, but not alls followed the same pattern. Over representation of Gene Ontology functional categories showed us that Poly(I:C) treatment produced a immune response whereas LPS stimulation affect biological processes specially. Trout erythrocytes were isolated from blood by twice Ficoll 1.007 density gradient centrifugations. For primary cell culture, erythrocytes were resuspended in DMEM (PAA Laboratories) supplemented with 10% heat-inactivated fetal bovine serum (FBS, PAA Laboratories) and the antibiotic Primocin (100 μg/ml, Invivogen) at a density of 7.5x106 cells/ml in six well cell culture plates (NUNC) and cultured at 18 ºC and 5% CO2. Erythrocytes were stimulated with LPS from E. coli (serotype 026:B6, Sigma) and Poly(I:C) (Invivogen) at 50 μg/ml, each treatment had their own control plate. All culture plates were incubated for 24h. Total RNA was extracted from the cultures using 1 ml of Tri Reagent (Sigma) following the manufacturer’s instructions with minor modifications. Quantity and integrity was analyzed by Experion RNA StdSens Analysis Kit (Bio-Rad). The design of the microarray posses 1818 genes printed in six replicates each, including random clones from common and subtracted cDNA libraries which were compared with known vertebrate proteins using blastx. The platform was enriched in immune-related genes.

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