Full-Service Sequencing Workflow (End-to-end Sequencing)
The SCF provides comprehensive, end-to-end services for sequencing and bioinformatics data analysis projects, which include experimental design, sample quality checks, nucleic acids extraction, library preparation and QC, sequencing, and data analysis. See below for more details on these services.
We also offer these services individually as you require.
Sequencing of User-Supplied Libraries
We also offer sequencing-only services for user-prepared libraries on the Illumina NextSeq2000 platform. A variety of flow cell kits are available to accommodate different read lengths and output requirements.
All submitted libraries undergo quality assessment, including concentration measurement and size distribution analysis. If quality issues are detected – such as the presence of adapter dimers or excess primers – we may recommend additional cleanup before sequencing.
Each library requires a unique index (barcode) for pooling in the same sequencing run. Standard Illumina sequencing services include ‘demultiplexing’ of the dataset and distributing FASTQ files based on the Illumina index reads that capture library barcode information. If libraries are submitted as separate samples, the core facility will handle the pooling. Pooling may require a consultation to determine the most appropriate approach.
Library Preparation
The core facility offers comprehensive services, not only sequencing with user-supplied libraries but also full project support, including library preparation according to standard protocols for whole exome sequencing, reduced representation bisulfite sequencing, and transcriptome sequencing. We are open to discussing other/custom protocols and applications.
Sample Preparation and Sequencing Support
- DNA/RNA extraction and sample clean-up
Our protocols are optimized for DNA/RNA extraction from various sources with different types, quantities, and qualities. Samples with evidence of impurities may need to undergo clean-up before library preparation. If submitted DNA or RNA does not meet the required purity standards, we will recommend performing clean-up using commercial columns or magnetic beads.
- DNA/RNA size QC and quantification
This service will assess the size profile and concentration of RNA or DNA samples, libraries, or pools with the Agilent TapeStation 4150 instrument and Qubit fluorometer. The core facility provides both size profiling and quality assessment, including RNA integrity (degree of degradation), genomic DNA contamination of RNA, the average size of libraries, and genomic DNA samples. The results will include the library concentration and size distribution profile, and quantitative metrics for detected peaks.
Sequencing (Self-Service)
The SCF offers self-service sequencing for experienced users who wish to run their own libraries on the NextSeq2000 platform. Access to the instrument requires prior training and approval by SCF staff. This option is intended for users who are familiar with library preparation and sequencing workflows and prefer to manage their own sample processing. Users are responsible for preparing and quantifying their libraries, ensuring appropriate indexing, and providing a ready-to-sequence pool. Flow cells and reagents must be booked in advance through our scheduling system. Data output will be made available via demultiplexed FASTQ files. SCF staff are available for consultation as needed, but hands-on support is limited for self-service runs.
Data analysis
In collaboration with the Armenian Bioinformatics Institute’s Bioinformatics Core Facility and IMB’s Bioinformatics Group, SCF provides a wide range of data analysis services: sequencing data processing, data quality control, and statistical and bioinformatics analysis (in collaboration with the Armenian Institute of Bioinformatics). Examples of advanced analysis include, but are not limited to differential expression, variant calling, (differential) DNA methylation analysis․