Genetic researchers study the role that genes and their variants play in disease, and are working to identify the genetic and environmental causes of common illnesses. The results of such studies will lead to advances in disease prevention and treatment. Pharmaceutical innovations are often identified based on our increased understanding of genes; these newer drugs can target focused sites in the body, and may therefore have fewer side effects than more traditional medicines. Moreover, the promise of personalized medicine will require tools for exploring an individual's unique genetic profile. Cell lines are convenient models that can facilitate these studies, but their relevance to the biological systems they are meant to model must be verifiable.
In order to be appropriate models for biological systems, cell lines must be physiologically relevant, and be probed for expression of gene(s) of interest. We have partnered with The European Collection of Authenticated Cell Cultures (ECACC), a part of Public Health England, to provide genomic DNA, RNA and cDNA from most ECACC cell lines to help researchers select the most suitable cell model for their studies. ECACC cell line-derived nucleic acids provide a genomic and transcriptomic snapshot of their corresponding cell line, which can be used to screen lines for genes, expression patterns, or the presence of interesting biomarkers using cost-effective PCR-based methods before deciding to utilize more costly protein-based assays.
Genomic DNA, RNA and cDNA formats are available as standard items on each cell line product page. We additionally provide a range of Human Random Control DNA panels. These comprise 96 control DNA samples (2 mg of DNA at a concentration of 100 ng/mL) supplied in a 96-well plate. Five different panels are available.
We offer high quality, high molecular weight genomic DNA extracted from ECACC cell lines. To ensure the highest quality and reproducibility, extracted DNA is subjected to defined quality control procedures, and all ECACC DNA products are supplied at a standard concentration of 100 ng/μL in 5 µg per tube.
Genomic DNA is extracted from cell lines using an automated extraction system employing silica-coated magnetic bead technology. All DNA is quantified using the A260 absorbance assay and normalized to a standard concentration of 100 ng/µL.
To ensure the highest quality, all ECACC DNA products are subjected to defined quality control procedures which include assays for:
Human Random Control (HRC) DNA is a readily available, cost-effective, and renewable source of authenticated, high quality purified genomic DNA from a control population of 480 randomly selected, non-related UK Caucasian blood donors. DNA is extracted from lymphoblastoid cell lines from single donor blood samples derived by EBV (Epstein-Barr virus) transformation of peripheral blood lymphocytes and is available as a series of five panels. Each panel contains samples from 96 unique individuals in a convenient 96-well format. DNA is provided at a concentration of 100 ng/μL in 10 mM Tris buffer (pH 8.0) with 1mM EDTA. Gender and age at blood collection is available for most samples.
Frozen DNA products should be stored at -20 °C upon receipt if they are not used immediately. Repeated freeze/thawing should be avoided. On receipt of your DNA order, ECACC recommends the following:
We offer high quality RNA prepared from ECACC cell lines. All RNA is quantified using a Nanodrop N1000 spectrophotometer and normalized to a standard concentration of 100 ng/µL. As part of our routine Quality Assurance, a proportion of each batch of RNA is tested for purity using the nucleic acid 260:280 and 260:230 absorbance ratios. RNA size and integrity are measured using agarose gel electrophoresis. RNA is provided in a 5 μg pack size at a concentration of 100 ng/μL.
Agilent Electropherogram showing RNA extracted from an ECACC Cell line. RIN score for this sample was 9.9
Gel electrophoresis of 16 of the RNA samples from ECACC cell lines showing un-degraded RNA with strong 28S ribosomal bands.
Summary of typical quality scores for RNA prepared by ECACC using ECACC cell lines
cDNA (complementary DNA) provides a cost-effective reagent for screening cell lines for gene expression characteristics. This enables selection of the most relevant cell lines for meaningful modeling of biological and disease systems. Researchers can source stable cDNA for pre-screening transcriptomes for expression characteristics.
ECACC scientists use high quality RNA—with RNA Integrity Numbers (RIN) typically above 9.7— to generate cDNA from our diverse range of cell lines. 1-2 x 106 cells are harvested from ECACC cell lines during the log phase of growth, and the RNA extracted before reverse transcription is used to generate single stranded cDNA. Extracted RNA is confirmed to be free of degradation using gel electrophoresis, and the presence of genomic DNA is assessed using PCR primers that recognize intronic sequences. To validate cDNA, PCR is performed using β-actin primers specific for cDNA. These primers do not recognize processed pseudogenes, or intronless copies of the gene within the genome. All cell banks from which cDNA is generated are fully-authenticated and maintained with rigorous process protocols to ensure quality and traceability.
As it’s not possible to quantify total cDNA, ECACC offers a standard single aliquot consisting of 20 µL of cDNA in a 2 mL tube. cDNA is prepared from RNA extracted from cell lines (at log phase growth) and supplied in a 20 µL volume per tube. cDNA should be stored at -80 °C when not in use; we recommend making aliquots of the cDNA after the initial thaw so that repeat freezing and thawing may be avoided.
Agaorose gel electrophoresis of RT-PCR products after RNA extraction and 11st strand cDNA synthesis
Lane 1 — 100bp ladder
Lane 2 — β-actin primers
Lane 3 — NPCC primers
Lane 4 — HMsH2 primers
Lane 5 — XRCC1 primers
Lane 6 — ERCC1 primers
Lane 7 — INRP primers (for gDNA)
Lane 8 — +ve control
Lane 9 — -ve control
Figure 1 (left). The absence of carryover from ECACC cell line genomic DNA is confirmed by using corresponding RNA in a PCR reaction with PCR primers designed to amplify the intronic sequences of a standard, constitutively expressed housekeeping gene. 1 µg of RNA was used as template in a first strand cDNA synthesis reaction using the Qiagen Omniscript® cDNA synthesis kit. Reaction was primed with an anchored oligo dT primer for maximal synthesis of gene sequences. The presence of cDNA was then confirmed by using the cDNA as a template in a PCR reaction with primers that detect exclusively human cDNA sequences, without coamplification of pseudogenes.