Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Ena-DATASET-ErasmusMC-hema-05-05-2020-08:23:09:334-464 - samples

ABSTRACT: RNA was isolated using phenol-chloroform extraction followed by DNase digestion or using the Qiagen Allprep DNA/RNA kit and protocol (Qiagen, #80204). cDNA synthesis was done using the SuperScript II Reverse Transcriptase kit (Invitrogen). Quantitative real-time PCR was performed by using primers as described previously13,21 on the 7500 Fast Real-time PCR System (Applied Biosystems). Relative levels of gene expression were calculated using the ΔΔCt method

PROVIDER: EGAD00001006106 | EGA |

REPOSITORIES: EGA

ACCESS DATA

Json Xml

Similar Datasets

Hyaluronic acid ameliorates the proliferative ability of human amniotic epithelial cells through activation of TGF-β/BMP signaling

Project description:This study investigated the mechanism by which 300 kDa HA (1 mg/mL) promotes the proliferation of hAECs. P1 hAECs in logarithmic growth phase were harvested, inoculated into 6-well plates at 3×105/well, and cultured with 5% CO2 at 37 °C. The medium was changed after 3 days, and then the cells were cultured for 18 or 36 h in the presence and absence of HA (300 kDa, 1 mg/mL). The total RNA was purified using the RNeasy MinElute kit (Qiagen, Valencia, CA, USA) according to the manufacturer’s instructions. cDNA was synthesized using a SuperScript III Reverse Transcriptase Kit (Invitrogen, Shanghai, China). Real-time PCR was conducted, and the 2–∆∆Ct method was used to quantify gene expression levels. The signal was collected by Agilent Feature Extraction software and analyzed by Agilent GeneSpring GX software.

2020-08-28 | GSE157002 | GEO

Real-time quantitative PCR analysis of human low-density (LDNs) and normal-density neutrophils (NDNs)

Project description:NDNs and LDNs were isolated by density gradient centrifugation of PBMCs from 8 patients affected by tubercolosis (TB). In detail, RNA was extracted from NDNs and LDNs by Maxwell® RSC miRNA Tissue kit (Promega, Madison, USA), following manufacturer’s instructions. RNA concentration and quality was measured using NanoDrop 2000 Spectrophotometer (Thermo Fisher Scientific). Total RNA (600 ng) was reverse transcribed using the RT2 First Strand Kit (SABiosciences, Qiagen, UK). 84 human cytokines and chemokines were tested using the RT2 Profiler PCR Array Human Innate & Adaptive Immune Responses array (Qiagen). A semiquantitative real-time RT-PCR was performed using a real-time PCR detection system (QuantStudio 7 Flex Real-Time PCR System, Thermo Fisher Scientific) with a two-step thermal cycling: 95 °C for 10 min, followed by 40 cycles (95 °C for 15 sec, 60 °C for 1 min). Data were analysed using the RT² Profiler PCR Array Qiagen data analysis software, and ACTB and B2M as housekeeping genes.

2019-11-20 | GSE138948 | GEO

Angiogenesis gene expression upon Notch activation in human vascular smooth muscle cells

Project description:VSMCs were cultured on Jag1 or IgG-coated plates as described above. RNA was extracted using RNA isolation kit (Qiagen). Reverse-transcription PCR was done with RNA-to-cDNA kit (Applied Biosystems). cDNA was run on a TaqMan Low-Density Array, human angiogenesis panel (Applied Biosystems , Cat#4378725), amplified on a 7900 HT Fast Real Time PCR system (Applied Biosystems) according to manufacturer’s instructions.

2011-12-01 | GSE34024 | GEO

Real-time quantitative PCR analysis of mouse lungs after exposure to early SARS-CoV-2 bearing 614G, Kappa or Delta variant

Project description:Age-matched K18-hACE2 transgenic mice were passively transferred with human COVID-19 mRNA post-vaccination (post-vac) sera followed by the lethal challenge with different SARS-CoV-2 viruses via intranasal route, including (1) New York-PV09158/2020 (NY) of lineage B.1.3 bearing 614G, (2) Kappa (B.1.617.1) and (3) Delta (B.1.617.2). Mouse lungs were harvested on 5 days post infection (dpi). Total RNA was extracted using QIAgen RNeasy Plus Mini Kit and was reverse transcribed using the High-Capacity cDNA Reverse Transcription Kit (Thermo Fisher Scientific). Resultant cDNA was used as the template along with RT2 SYBR Green ROX qPCR Mastermix (Qiagen) to perform RT² Profiler™ PCR Array Mouse Hypoxia Signaling Pathway (Qiagen) real-time PCR in Stratagene MX3000p qPCR system.

2022-11-21 | GSE193839 | GEO

Real-time quantitative PCR analysis of mouse lungs after exposure to SARS-CoV-2 and variants of concern (VOC)

Project description:Age-matched K18-hACE2 transgenic mice were infected intranasally with different SARS-CoV-2 viruses, including (1) USA-WA1/2020 (WA) of lineage A, (2) New York-PV09158/2020 (NY) of lineage B.1.3, (3) USA/CA_CDC_5574/2020 (CA) of lineage B.1.1.7 and (4) hCoV-19/South Africa/KRISP-EC-K005321/2020 (SA) of lineage B.1.351. Mouse lungs were harvested on 3 days post infection (dpi). Total RNA was extracted using QIAgen RNeasy Plus Mini Kit and was reverse transcribed using the High-Capacity cDNA Reverse Transcription Kit (Thermo Fisher Scientific). Resultant cDNA was used as the template along with RT2 SYBR Green ROX qPCR Mastermix (Qiagen) to perform RT² Profiler™ PCR Array Mouse Hypoxia Signaling Pathway (Qiagen) real-time PCR in Stratagene MX3000p qPCR system.

2021-10-10 | GSE183621 | GEO

Effect of artificial saliva on inflammatory response of oral fibroblasts in an in vitro study

Project description:Real-time quantitative PCR analysis of oral fibroblasts Fibroblasts (HGF-1) was exposed for 120 seconds to human saliva (HS) and two commercially available AS (AS I and AS II). One microgram of RNA was converted in cDNA using RT2 First Strand Kit. 84 genes were analyzed using inflammatory response & Autoimmunity Array RT2 profiler (Qiagen Sabiosciences, Valencia, CA, USA) with buffers supplied by the manufacturer

2016-04-23 | GSE80576 | GEO

MicroRNA profiling in oesophageal adenocarcinoma cell lines and patient serum samples reveals a role for miR-451a in radiation resistance [baseline RT-PCR]

Project description:miRNA was extracted from a range of Oesophageal Adenocarcinoma cell lines using the miRNeasy Mini Kit (Qiagen, #217004, Chadstone, Australia) and RNase-free DNase Set (Qiagen, #79254, Chadstone, Australia). miRNA was reverse transcribed using a Custom OpenArray® miRNA RT pool (Life Technologies cat # A25630) and the TaqMan® microRNA Reverse Transcription Kit (Life Technologies cat # 4366596). cDNA Pre-amplifications were carried out with a Custom OpenArray® PreAmp pool (Life Technologies cat # 4485255) and TaqMan PreAmp Master Mix (Life Technologies cat # 4488593). PCR runs were performed using a QuantStudio™ 12K Flex Real-Time PCR System. Baseline qPCR expression profiling of miRNAs from 8 oesophageal Adenocarcinoma cell lines, prior to treating the cell lines with either 2Gy ionising radiation, 20 µM Cisplatin, or 50 µM 5-fluorouracil (5-FU).

2020-12-15 | GSE161585 | GEO

Malva sylvestris anti-inflammatory activity in oral human cells

Project description:Real-time quantitative PCR analysis of human epithelial cells The activity of Malva sylvestris extract and fractions infected by A. actinomycetemcomitans were investigated using an adapted dual chamber model, oral human epithelial cells were used in the co-culture model. One microgram of RNA was converted in cDNA using RT2 First Strand Kit. 84 genes were analyzed using inflammatory response & Autoimmunity Array RT2 profiler (Qiagen Sabiosciences, Valencia, CA, USA) with buffers supplied by the manufacturer

2015-08-27 | GSE72443 | GEO

GIM mTEC Aire silencing

Project description:We used the TriFectaTM (IDT, Integrated DNA Technologies, Coralville, IA, USA) anti-Aire RNAi sequence (GGAUUCUCUUUAAGGACUACAAUCTAGAUUGUAGUCCUUAAAGAGAAUCCUC) in order to silencing Aire mRNA. Confluent cultures of 3.10 mTEC cell line were transfected with 10nM of anti-Aire siRNA using Hiperfect reagent (Qiagen, GmbH, Hilden, Germany) following manufacturerM-^Rs instructions. After transfection, cells were cultured during 24 h in RPMI medium as above mentioned and total RNA was extracted using the mirVana kitM-. (Ambion, Austin, TX, USA), which served as template for cDNA synthesis. Gene knockdown was confirmed by quantitative reverse transcription PCR (qRT-PCR) using the primers 5_-GCAACTCTGGCCTCAAAGAG-3_ forward and 5_-GGTCTGAATTCCGTTTCCAA-3_ reverse, which allowed amplification of a 120 bp PCR product corresponding to a segment of the Aire cDNA. The cDNA samples were prepared using Superscript II reverse transcriptase (Invitrogen Corporation, Carlsbad, CA, USA) enzyme, as recommended. Expression of the above mentioned genes was quantified using a 7500 Real Time PCR System (Applied Biosystems)

2011-08-31 | E-MEXP-3213 | biostudies-arrayexpress

Transcriptomic Assay of CD8 2012-05-15

Project description:In this study, Genome-wide transcriptomes of CD8+ T cells from HCV/HIV co-infected or mono-infected treatment-naive individuals were analyzed by using microarray assays. Pairwise comparisons were performed and differentially expressed genes were identified followed by quantitative real time PCR (qRT-PCR) validation. To identify the important functional categories, Directed Acyclic Graphs (DAG) from Web-based Gene SeT AnaLysis Toolkit (WebGestalt) was used to find out Gene Ontology (GO) categories with significantly enriched gene numbers. The enriched Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were also obtained by using the similar methods in the same website.

2012-05-17 | E-MEXP-3635 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data