Genomics Core Facility

Genomics Core Facility works on the most up-to-date apparatus for nucleic acids manipulation and analysis. We strive to make able to take advantage of the equipment to all interested research group, serving full support in operation and substantive help in the preparation of material for analysis. If interested please contact as via on-line form.

Next Generation Sequencing Systems

Illumina NovaSeq 6000

The very high-throughput, the most cost-effective and flexible sequencer in Illumina porfolio High scalability: 65-3000 Gb/run 800M-10B reads/run up to 2×250 bp read length Very high quality (tipically ≥ 95% of bases higher than Q37 at 2×100 bp) High speed of sequencing: 13-48 h Can run two flow cells in parallel at once

Illumina NextSeq 500

The mid-throughput sequencer for a wide range of application Scalability: 20-120 Gb/run 130-400M reads/run up to 2×150 bp read length High quality (tipically ≥ 90% of bases higher than Q30 at 2×75bp) High speed of sequencing: 11-29 h

Illumina MiSeq

The relatively low-throughput sequencer for small projects, amplicon or test sequencing runs High scalability of low-throughput runs: 0.3-15 Gb/run 1-25M reads/run The longest read length: up to 2×300 bp read length High speed of sequencing: 6-56 h

Systems for Automatic Reaction Preparation

Freedom EVO 150/8

Automatic pipetting station for reaction set up Two types of robotic arm: 8 – tip pipetting arm (LiHA) and labware movement arm (ROMA) Scalability with mutliple format and size of robotic carrieres – from 384-well plates to reservoirs for hundreds of ml Wide range of modules for liquid manipulation and carrying out reactions Heating system Fluorometric system Magnetic separation module

Nucleic acids quality and quantity assessment

TapeStation 2200

Nucleic acid and proteins quality control automated system based on electrophoresis on tapes High sesnsitivity – from 10 pg for DNA , 200 pg for RNA, 5 ng for protein High resolution – up to 5 bp for DNA/RNA and 0.5 kDa for protein Broad range of different reagents for: DNA (from 30bp to genomic) total RNA and mRNA protein (up to 200 kDa) High flexibility  – from one sample at a time

BioAnalyzer 2100

Nucleic acid quality control automated system based on electrophoresis on chips Very high sensitivity – from 5 pg for DNA , 50 pg for RNA, 0.3 ng for protein High resolution – up to 5 bp for DNA/RNA and 0.5 kDa for protein Broad range of different reagents for: DNA (from 30 bp to 10 kbp) total RNA and mRNA small RNA protein (up to 250 kDa) 11-12 samples at a time

LightCycler 480

Real-time PCR system High-throughput system – 384-well plate format Nucleic acids quantity and quality assessment for: relative expression analysis genotyping sequence specific detection PCR amplification optimization sequencing libraries relative concentration measurements

Nucleic acids preparation 

Covaris S220

Ultra-focused, very precised sonication system with cooling Very high repeatability assured by: ultra-focused sound wave external cooling system water degassing vessel construction High precision of very equal physical fragmentation to particular size of DNA High efficiency of cell disruption and chromatin fragmentation

Covaris M220

Ultra-focused, very precised sonication system  Very high repeatability assured by: ultra-focused sound wave internal temperature control system vessel construction High precision of very equal physical fragmentation to particular size of DNA High efficiency of cell disruption and chromatin fragmentation

Cooperation or orders in Genomics Core Facility CeNT UW is equivalent to acceptance of the following rules. Please read the regulations before starting the consultation and starting work.

General rules for the use of the CeNT UW
Genomics Core Facility

I. General provisions

1. The equipment is localized in room 03.231 and 05.101-05.115 in the CeNT I building.

2. Genomics Core Facility  personnel: 
   

   Jeffrey Palatini (head) (e-mail: j.palatini@cent.uw.edu.pl); 

   Sample Processing Section:
   Dorota Adamska (e-mail: d.adamska@cent.uw.edu.pl);
   Michał Szeląg (e-mail: m.szelag@cent.uw.edu.pl); 
   Bioinformatics Section:
   dr Krzysztof Goryca (e-mail: k.goryca@cent.uw.edu.pl);

3. Direct use of the equipment is restricted to the personnel of the Genomics Core Facility.

4. Users are requested to submit a brief description of the planned experiment and/or data analysis proposal by filling an electronic form. The project description is the basis for consultations scheduling, obtaining acceptance for the experiment from the Sample Processing Section and/or Bioinformatics Section, and enables them to plan sequencing and data analysis, respectively.

5. Users are requested to accept the preliminary cost estimate before starting the sample processing or data analysis.  

6. Users are obliged to familiarize themselves with these rules.

II. Project submission

1. The submissions of experiment and data analysis proposals are made through the Genomics Core Facility website:
   “https://cent.uw.edu.pl/en/core-facilities/genomics-core-facility/”

2. By accepting the terms and conditions the Users declare that the samples and data provided have not been obtained in violation of applicable law, as well as their further processing requested by the Genomics Core Facility personnel is fully legal.

III. Sample preparation

1. Users submitting DNA/RNA samples must provide nucleic acid quality and quantity data or request such an analysis to be carried out by the Genomics Core Facility. Samples that do not meet quality requirements as specified by the selected sequencing library preparation protocol will be processed only upon written consent, wherein the User agrees that no guarantee is given for the successful library construction and the full costs of the library construction attempts (including the unsuccessful ones) are to be fully covered by the User.

2. Users submitting DNA libraries are required to follow sample preparation protocol approved by the head of the Sample Processing Section. They must also present data on the quality of the libraries delivered (results from Agilent Bioanalyzer or equivalent instrument) or request the quality analysis to be carried out by the Genomics Core Facility. Any modification (e.g. resulted from a human error) should be reported before the libraries are handed over for sequencing. The Genomics Core Facility bears no responsibility for the quality of results obtained, based on sequencing User-delivered libraries.

3. Users submitting sequencing data for analysis should deliver data in BCL, FASTQ, or BAM format.

IV. Provided services

1. The services are rendered, based on the initial consultation (see Collaboration Guide) and according to the written cost estimate provided to and accepted by the User.

2. The Genomics Core Facility personnel is responsible for scheduling the services. Generally, User requests are being processed on a first come, first served basis. However, the personnel reserves the right to queue the samples provided, according to the availability of measurement time and sequencing consumables, unless the User agrees to bear the full costs of the sequencing process, as estimated by the Genomics Core Facility personnel.

3. The general services offered by the Genomics Core Facility include:
   • Consulting services (help with designing the experiment, customizing sample preparation protocols, data interpretation);
   • Sample processing (eg. DNA/RNA quality assessment, DNA library preparation);
   • Sequencing run set up and raw data preprocessing (FASTQ generation, demultiplexing and basic quality report);
   • Data analysis (basic processing as well as tailored analysis and data visualization are available).

4. The services rendered are described on the Genomics Core Facility website and individually adjusted in accordance with experiment-specific modifications of the standard protocols and additional services requested (e.g. sample quality control, data analysis).

5. A consultation is expected to precede any sample processing and/or data analysis (see Collaboration Guide). As a result of the consultation, an optimal analytical strategy is agreed upon and the estimated cost of services (calculated based on the Pricelist) is provided in a written form and explained.

6. The Genomics Core Facility personnel reserves the right to reject requests for the provision of services in objectively justified cases. In the event of a refusal, a constructive feedback will be provided to both the User who had requested the service, and to the appropriate head of the respective laboratory (where applicable). 

V. Libraries storage, data storage & security

1. The results will be made available to the User in an adequate form::
   • Report on the methodology and work results (for Sample processing service);
   • Raw, demultiplexed data with basic quality report (for Sequencing service);
   • Full report with a summary addressing the User’s expectances (for data analysis service).

2. Users are expected to collect data within 14 days from the time the results became available to them. After that time, access to the data will require intervention of the head of the lab, from which the project originated.

3. The samples and libraries remained will be stored for 6 months and provided to the User on demand or may be subjected to further sequencing on separate sequencing request.

4. Raw data will be stored on a server for a duration of 6 moths. On request, they will be made available to the User.

5. Additional storage time of libraries or raw data requires written request from the User within 6 months from making results available to them and may result in storage cost covering by the User.

VI. Publication of data

1. Acknowledgment: For basic analyses, where a minimal intellectual contribution from the Genomics Core Facility personnel has been requested, their work should be clearly identified in the acknowledgments section of resulting publications with marked Research Resources ID (RRID:SCR_022718). Sequences and data analysis reports will be provided along with a generic statement about the instrumentation and the software utilized.

2. Co-authorship: When a significant intellectual contribution from the Genomics Core Facility personnel has been requested and delivered, their work must be acknowledged by naming them as co-authors of resulting publications. This is a default mode of agreement for projects involving the development of new sequencing and data analysis approaches and methods or projects requiring complex data processing and/or mining. A selection of publication-ready figures and an input into writing of the relevant sections of the paper will be provided by the Genomics Core Facility personnel.

Collaboration guide

The method of contacting us can be found in the Contact tab, and all the necessary documents in the Attachments tab.

To facilitate the transfer of all the information needed to start cooperation with us, we have prepared a form for you. When initiating contact, we encourage you to complete it.
 

Contact Form

Questions and information not covered by the form should be provide by e-mail or by phone: 

Samples preparation and sequencing
Dorota Adamska (e-mail: d.adamska@cent.uw.edu.pl), +48 22 55 43628

Bioinformatic analysis
dr Krzysztof Goryca (e-mail: k.goryca@cent.uw.edu.pl), +48 22 55 43681