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Real time quantitative PCR analysis of serum circulating miRNAs from patients with head and neck tumors. [exp1]

ABSTRACT: The samples were drawn from patients with diagnosed oropharyngeal cancer treated with irradiation. We used blood samples (10ml) collected from patients 7 days after receiving 20Gy dose of irradiation. Blood was centrifuged for 10 min, after which serum was aspirated, aliquoted in RNAse-free tubes, stored at −80°C until required for further processing and did not undergo more than two freeze-thaw cycles. MicroRNA was extracted from 200 μL serum using miRCURY RNA Isolation kit (Qiagen) following the manufacturer’s protocol and stored at −80°C.

ORGANISM(S): Homo sapiens

PROVIDER: GSE143489 | GEO | 2020/01/13

REPOSITORIES: GEO

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Real time quantitative PCR analysis of serum circulating miRNAs from patients with head and neck tumors. [exp2]

Project description:The samples were drawn from patients with diagnosed oropharyngeal cancer. We used blood samples (10ml) collected from patients after diagnosis, before treatment. Blood was centrifuged for 10 min, after which serum was aspirated, aliquoted in RNAse-free tubes, stored at −80°C until required for further processing and did not undergo more than two freeze-thaw cycles. MicroRNA was extracted from 200 μL serum using miRCURY RNA Isolation kit (Qiagen) following the manufacturer’s protocol and stored at −80°C.

2020-01-13 | GSE143490 | GEO

ChIP-Seq of DNA lesions from irradiated and non-irradiated HaCaT cells

Project description:This study aims to investigate the binding DNA lesions of AIM2 in HaCaT cells exposed to 0Gy and 20Gy by ChIP-Seq. In this study, HaCaT cells were maintained in DMEM. All culture media were supplemented with 10% fetal bovine serum (FBS; Biological Industries, Kibbutz Beit-Haemek, Israel). Cells were grown at 37 °C in 5% CO2 incubators. Cells were exposed to 20Gy of ionizing radiation using X-ray linear accelerator (Rad Source, Suwanee, GA) at a fixed dose rate of 1.15 Gy/min.Four hours after irradiation, specific antibody against AIM2 was used to pull down AIM2 and the binding DNA lesions, which was then analyzed through ChIP-Seq.

2022-12-31 | GSE205250 | GEO

Exon level expression profile of MCF7 cells with p53β splice variant knocked out 4hr post 20gy irradiation

Project description:In order to explore the funciton of p53β splice variant in DNA damage response, we utilized CRISPR-cas9 genome editing technique to specifically knock out this variant in MCF7 cells. Microarray analysis is then performed to compare gene expression before and after 20gy irradiation in these cells.

2017-08-31 | GSE84813 | GEO

Transcriptome analysis between wild-type and DM1-affected fibroblast.

Project description:Human skin fibroblast cell lines from 3 normal individuals and 3 individuals with DM1 in one pedigree were obtained from the biobank of Shanghai East Hospital. Human skin fibroblast cells were grown in DMEM (Life Technologies), NaPyr, GlutaMAX, β-mercaptoethanol and 10% foetal bovine serum (FBS) supplemented medium as previously described (Richner et al. 2015). Cells were collected after 80% confluency with TRIzol reagent and stored at -80℃ for RNA-seq and RT-PCR.

2022-11-16 | GSE211497 | GEO

Gene expression profile of wild-type MCF10-A or rho0 MCF10-A cells after cellular irradiation

Project description:Goal is to uncover genes that fail to be activated by cellular irradiation when mitochondrial DNA is depleted in MCF10-A. To this end we delivered 20gy of ionizing radiation at 0.8gy/minute and waited 6 days. Total RNA was collected and DE genes were compared between wild-type irradiated cells and rho0 irradiated cells.

2021-02-24 | GSE164980 | GEO

2 doses of ionising radiations (x-rays) -Transcriptomic analysis of effects of ionising radiation on Arabidopsis thaliana.

Project description:au09-03_gamma-irradiation - 2 doses of ionising radiations (x-rays) - Metabolic pathways involved in the response of plants to ionising radiation treatment. - Arabidopsis thaliana (Col-0) seeds were grown in Petri dishes under sterile conditions until they had 2-rosette-leaves (on average 10 days). Then they received a dose of 10 or 40 gray of X-ray (Faxitron HP). Plant were harvested 2 and 26 hours after irradiation, immediatly frozen and stored at -80°C until RNA extraction (Rneasy plant mini Kit, Qiagen) . Experiment was carried in duplicates and a non irradiated control was done for each time.

2012-02-25 | GSE35942 | GEO

To investigate whether recover DNMT3A expression permitted adult beta cell of βRapKO establishing proper transcriptome

Project description:Murine islets were isolated from 8-week-old WT and βRapKO mice and initially recovered in 1640 RPMI supplemented with 10% serum, 11.1mM glucose overnight. Then islets were transfected with Lenti-GFP or Lenti-Dnmt3a for 24 hours, following cultured in 1640 RPMI medium for 48 hours.Islets were harvested and stored in -80°C for preparation for RNA sequencing.

2019-06-01 | GSE130910 | GEO

Transcriptional responses in various normal mouse tissues after 24 h following 4 MV photon beam irradiation using three partial body irradiation set-ups

Project description:Female BALB/c nude mice (n=3/group) were subjected to partial body irradiation under anesthesia using 2 Gy external photon (4 MV, nominal) irradiation. In group A, the collum (i.e. the thyroid) was irradiated; in group B, thorax+abdomen were irradiated, and in group C, collum+thorax+abdomen were irradiated. The control group (n=5) was anesthetized but not irradiated. At 24 h after treatment, the kidneys, liver, lungs, spleen, and thyroid were excised, flash-frozen, and stored at -80°C. Total RNA was extracted from homogenized tissue samples (kidney cortex and kidney medulla were treated separately) and subjected to expression analysis using RNA microarray technology.

2016-03-31 | GSE66372 | GEO

Expression profiling of mice exposed to multiwalled carbon nanotubes

Project description:Mice were aspirated with multiwalled carbon nanotubes in four doses ranging from 10 µg to 80 µg, plus control, and sacrificed after 1, 7, 28, and 56 days. RNA was extracted from the lungs and expression profilling by microarray was performed.

2012-06-26 | GSE29042 | GEO

Photobiomodulation by blue light induces a dose dependent biphasic proliferation curve in human keratinocytes [exp1]

Project description:Photobiomodulation (PBM) with blue light induces a biphasic dose response curve in proliferation of immortalized human keratinocytes (HaCaT), with a maximum proliferative effect reached with 7.5min (10.35J/cm2). The aim of this study was to test the photobiomodulatory effect of 10.35J/cm2 blue light irradiation on cell proliferation, ROS production and gene expression at different time points after irradiation of HaCaT cells in vitro and to compare the results with the anti-proliferative phase of PBM using blue light with 41.4J/cm2. For 10.35J/cm2 cell proliferation was increased for all measured harvesting time points up to at least 24h after irradiation. ROS concentration was increased 30min after irradiation. However, already 1h after irradiation, cells were able to decrease ROS and stabilize the concentration to the basal level. The sudden increase in ROS was even higher when compared to 41.4J/cm2. However, gene expression analysis did not indicate any sign of apoptosis and even indicated an activation of cell survival mechanisms. Furthermore, comparable to 41.4J/cm2, aryl hydrocarbon receptor (AHR) “battery genes” showed a deregulation after blue light irradiation strengthening the hypothesis of AHR as possible target for blue light irradiation.

2019-10-01 | GSE89083 | GEO

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