characteristics.text: ERC000011
characteristics.characteristic: ENA-CHECKLIST
characteristics.text: 2018-04-04T17:01:59Z
characteristics.characteristic: ENA-FIRST-PUBLIC
characteristics.text: 2018-04-03T18:56:46Z
characteristics.characteristic: ENA-LAST-UPDATE
characteristics.text: SAMEA1052992
characteristics.characteristic: External Id
characteristics.text: LUMC
characteristics.characteristic: INSDC center name
characteristics.text: 2018-04-04T17:01:59Z
characteristics.characteristic: INSDC first public
characteristics.text: 2018-04-03T18:56:46Z
characteristics.characteristic: INSDC last update
characteristics.text: public
characteristics.characteristic: INSDC status
characteristics.text: ERS2358659
characteristics.characteristic: SRA accession
characteristics.text: E-MTAB-6640:PTEC_NF3
characteristics.characteristic: Submitter Id
characteristics.text: ArrayExpress
characteristics.ontologyTerms: http://www.ebi.ac.uk/efo/EFO_0009737
characteristics.characteristic: broker name
characteristics.text: immortalized cell line
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/CL_0000002
characteristics.characteristic: cell line
characteristics.text: epithelial cell of proximal tubule
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/CL_0002306
characteristics.characteristic: cell type
characteristics.text: house mouse
characteristics.characteristic: common name
characteristics.text: Protocols: Proximal tubular epithelial cells (PTECs) were exposed to laminar fluid shear stress (1.9 dyn/cm2) in a cone-plate device. The cone-plate device was designed for 3.5 cm cell culture dishes (Greiner Bio-One). Cells were grown on collagen-I (Advanced BioMatrix; #5005) coated dishes until confluence, followed by 24 hr serum starvation, before the start of the treatment to exclude effects of serum-derived growth-factors and to synchronize cells and cilia formation. Culture dishes were placed in the cone-plate flow system and incubated at 37°C and 5% CO2. The confluent cell monolayer of 9.6 cm2 was subjected to constant laminar (Re = 0.3) fluid shear stress for 6 hours, using 2 ml serum-free DMEM/F-12 medium containing penicillin-streptomycin, with viscosity (μ) of 0.0078 dyn s/cm2, a cone with an angle (α) of 2° and a velocity (ω) of 80 rpm, generating a fluid shear stress (τ = μω/α) of 1.9 dyn/cm2. Static control cells were incubated for the same time in equal amounts of serum-free DMEM/F12 medium containing penicillin-streptomycin at 37°C and 5% CO2. Total RNA was isolated from fluid shear stress treated PTECs or static controls (n = 4) using TRI Reagent (Sigma-Aldrich; #T9424) and purified using Nucleospin RNA Clean-up (Macherey-Nagel; #740948) according to manufacturer’s protocols. Illumina mRNA-Seq Sample Prep Kit was used to process the samples according to the manufacturer’s protocol. Briefly, mRNA was isolated from total RNA using the oligo-dT magnetic beads. After fragmentation of the mRNA, a cDNA synthesis was performed. This was used for ligation with the sequencing adapters and PCR amplification of the resulting product. The quality and yield after sample preparation was measured with a DNA 1000 Lab-on-a-Chip. The size of the resulting products was consistent with expected size distribution (a broad peak between 300-500 bp).
characteristics.characteristic: description
characteristics.text: normal
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/PATO_0000461
characteristics.characteristic: disease
characteristics.text: wild type genotype
characteristics.ontologyTerms: http://www.ebi.ac.uk/efo/EFO_0005168
characteristics.characteristic: genotype
characteristics.text: Mus musculus
characteristics.characteristic: organism
characteristics.text: Mus musculus
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/NCBITaxon_10090
characteristics.characteristic: organism
characteristics.text: kidney
characteristics.characteristic: organism part
characteristics.text: Mus musculus
characteristics.characteristic: scientific_name
characteristics.text: PTEC_NF3
characteristics.characteristic: title