Devices for molecular genetics
NextSeq
- Manufacturer: Ilumina
- In CLIP since 2015
- The NextSeq Series desktop sequencing system provides exome, transcriptome and targeted sequencing
- Uses fluorescently labeled nucleotides to detect single bases as they are incorporated into growing DNA strands
- Produces up to 400M reads in single workflow with read length 75-150bp
Ion Personal Genome Machine® (PGM™) Sequencer
- Manufacturer: Life Technologies
- In CLIP since 2012
- This new generation benchtop sequencer works on the massively parallel sequencing principle. During sequencing, this system detects hydrogen ions that are released after nucleotide is incorporated into the DNA string. Information obtained this way is then converted into digital form.
- Works with 3 types of semiconductor chips. Using the biggest chip, up to 1 Gb of sequencing data can be generated within several hours.
- Produces reads 35 - 400 bp long with a 99 % accuracy
- We would like to use this system for a detection of minimal residual disease based on Ig/TCR rearrangements
Agilent 2100 Bioanalyzer
- In CLIP since 2005 and another unit since 2009
- We use this system to locate new targets for a detection of minimal residual disease in patients with acute lymphoblastic leukemia
LightCycler480 II
- Manufacturer: Roche
- Has been in CLIP since several years
- We use LightCycler480 II for searching for point mutations that increase the probability of thrombophilic disease
TaqMan 7500 Fast Real Time PCR System
- Manufacturer: Applied Biosystems
- We have 3 units in CLIP: 3 units since 2008, 1 unit since 2013
- They are used for a detection of minimal residual disease in acute lymphoblastic and myeloid leukemias
iCycler iQ Multicolor Real-Time PCR Detection System
- Manufacturer: Bio-Rad
- We have 3 units in CLIP
- We use them for a detection of minimal residual disease in acute lymphoblastic andy myeloid leukemias
Cytometric devices
3 flow cytometers:
BD FACS Lyric
- 3 lasers, 13 fluorescence channels - SW: BD FACSuite
- Violet (405 nm) - 488/45, 528/45, 606/36, 715/50, 755LP
- Blue (488 nm) - 527/32, 586/42, 700/54, 783/56
- Red (640 nm) - 660/10, 720/30, 783/56
- Is used mostly for measuring for routine diagnostics
BD FACS LSR II
- This modification allows us to measure
- Up to 4 lasers, 17 fluorescence parameters - SW: BD FACSDiva
- Violet (405 nm) - 450/50, 536/26, 586/42, 605/15, 655/30, 710/40, 780/40 - Omicron-Laserage Laserprodukte GmbH, Rodgau, Germany
- Blue (488 nm) - 530/30, 576/26, 615/20, 695/40, 780/60
- Yellow (561 nm) - 586/15, 615/20, 780/60 - Coherent, Santa Clara, CA, USA
- Red (633nm) - 660/20, 710/50, 780/60 - OBIS, Coherent, Santa Clara, CA, USA
- Manufacturer: BD Bioscience, San Jose, CA, USA
- In CLIP since 2006
- Is used for research measurement of experimental samples, e.g. measuring amounts of DNA, cerebrospinal fluid, PNH, EMA
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BD FACS Celesta
- 3 lasers, 12 fluorescence channels - SW: BD FACSDiva
- Violet (405 nm) - 450/50, 525/50, 610/20, 670/30, 780/60
- Blue (488 nm) - 530/30, 575/25, 695/40, 780/60
- Red (640 nm) - 670/30, 730/45, 780/60
- Is used for research measurement of experimental samples
Spectral cytometer:
Cytek Aurora
- 4 lasers - SW: SpectroFlo
- UV (355 nm) - 16 channels, 365 - 829 nm
- Violet (405 nm) - 16 channels, 420-826 nm
- Blue (488 nm) - 14 channels, 498 - 829 nm
- Red (640 nm) - 8 channels, 652 - 829 nm
- Is used for research measurement of experimental samples
Mass cytometer:
CyTOF 2
- SW: CyTOF
- Allows detection of up to 120 parameters (non-radioactive metal isotope tags): http://youtu.be/TCxk_30cTL4
- Manufacturer: DVS Sciences/Fluidigm
- In CLIP since 2015
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Sorter:
BD FACS Aria III
- 3 lasers:
- Violet (405 nm)
- Blue (405 nm)
- Diodový Red (637 nm) - OBIS, Coherent, Santa Clara, CA, USA
- Thanks to this configuration, the device is able to measure 11 fluorescence parameters
- Manufacturer: BD Bioscience, San Jose, CA, USA
- In CLIP since 2011
- FACS Aria III is used mainly for sorting of lymphocytic subpopulations
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