Omics and gene analysis

BD FACS Discover S8 with BD CellView™ Image Technology and BD SpectralFX Technology. BD CellView™ Image Technology expands the power of cell analysis and sorting by combining flow cytometry data with spatial and morphological insights. BD SpectralFX Technology expands panel size and flexibility with 78 fluorescent detectors across five lasers (349nm; 405nm; 488nm; 561nm; 637nm) with algorithmically optimized bandpass filters.

FACS Aria III has four laser lines (Near Violet 375nm; Blue 488nm;
Yellow/Green 561nm and Red 633nm) which allows covering the entire
electromagnetic spectrum for applications of both endogenous fluorescence
(fluorescent proteins such as gfp, cherry, tomato …), as well as
antibodies conjugated to fluorophores. The fluidics and optical systems are
precisely integrated to maximize signal detection. It is also equipped with
a temperature control system between 4 and 37 degrees Celsius for both the
sample and the cell collection tube.

BD FACSMelody is a last generation cell sorter which allows cell purification
of both cell populations and single cell. It is equipped with three laser
lines (Violet 405nm; Blue 488nm and Yellow /Green 561nm) for applications of
both endogenous fluorescence (fluorescent proteins such as gfp, cherry, tomato
…), as well as antibodies conjugated to fluorophores. It is also equipped
with a temperature control system between 4 and 37 degrees Celsius for both
the sample and the cell collection tube.

FlowJo™ Software is the leading platform for single-cell flow cytometry analysis that helps you interpret your data quickly and effectively with accessible features for immunophenotyping, cell cycle analysis, proliferation, kinetics studies, quantitative population comparison, high-dimensional analysis and more. FlowJo documentation: https://docs.flowjo.com/flowjo/

Chromium X is 10X Genomics’ most advanced instrument, offering compatibility with all 10x Genomics single cell assays. Chromium X instrument efficiently and reliably handle cell partitioning so you can easily take on a wide range of projects, from pilot studies to large-scale or multi-site projects. 10X Genomics’ comprehensive portfolio lets you profile fresh, frozen, and fixed samples (even FFPE) and capture multiple molecular readouts, including gene expression, chromatin accessibility, proteins, immune clonotype, and CRISPR perturbation screens.

It combines large partition numbers with a massively diverse barcode library
to generate >100,000 barcode-containing partitions in a matter of minutes
and allows a user to run any Chromium Solution, from genome to single cell
analysis (Single cell gene expression, Single cell ATAC…). It allows working
with different types of samples that range from high molecular weight (HMW)
DNA, individual cells, cells labeled using Feature Barcoding technology,
nuclei, nuclei treated with transposase, or cell Beads.

MERSCOPE is a high-resolution in situ spatial genomics platform that enables users to map transcripts across 1 cm² of tissue on a single slide, offering a tissue-wide view of up to 1000 custom genes at single-cell resolution.

The Mastercycler® pro S offers ultimate flexibility for your PCR applications.
Equipped with a silver block, operate in various configurations, and use any
plate, tube, or strip you want. All formats come with gradient SteadySlope®
technology to ensure heating and cooling ramp rates remain consistent. With
the vapo.protect technology, evaporation is kept to a minimum.

Applied Biosystems QuantStudio 3 Real-Time PCR System is a simple and
affordable real-time PCR solution designed for users with all levels of
experience. Get connected to your data easier than before with a real-time PCR
systems that offers an interactive touch screen and the option to choose Web
browser-based software enabled through the Thermo Fisher Cloud. It offers
improved data accuracy and sensitivity for a broad range of applications, such
as analyses of gene expression, microRNAs and noncoding RNAs, SNP genotyping,
copy number variation, mutation detection….

The 2100 Bioanalyzer system is an established automated electrophoresis tool
for the sample quality control of biomolecules. It provides highly precise
analytical evaluation of various samples types in many workflows, including
next generation sequencing (NGS), gene expression, biopharmaceutical, and gene
editing research, and delivers objective assessment of sizing, quantitation,
integrity and purity from DNA, RNA, and proteins. Minimal sample volumes are
required for an accurate result, and the data may be exported in a many
different formats for ease-of-use.

The Bioruptor® Pico is the latest innovation in shearing and represents a new
breakthrough as an all-in-one shearing system optimized for shearing
micro-volumes of 5 μl to larger volumes of up to 2 ml. The built-in cooling
system (Bioruptor® Cooler) ensures high precision temperature control
resulting in higher quality samples. Ideal for DNA shearing for
Next-Generation-Sequencing (5 – 100 µl), Chromatin shearing (10 µl – 2 ml),
RNA shearing, Protein extraction from tissues and cells, FFPE DNA extraction
and Protein aggregation studies.

Countess II FL Automated Cell Counter is a benchtop assay platform equipped
with state-of-the-art optics, full autofocus, and image analysis software for
rapid assessment of cells in suspension. With three-channel
flexibility—brightfield, researchers can count cells, evaluate apoptosis, and
measure cell viability.

It allows working in an environment free of biological contamination for the preparation of delicate samples such as RNA, cDNA libraries….

The computing platform provides researchers at Instituto de Neurociencias and external organizations with high-performance computing resources for next-generation sequencing (NGS) data processing and analysis.

Server main features and configuration:

• CPU: 4 Cores Intel(R) Xeon(R) CPU E7-8870 v4 @ 2.10GHz -> 80 cores with HyperThreading [160 Threads] with 200MB cache storage L3.
• RAM: 2TB 2400MHz -> Registered 1600MHz.
• SSD: 4TB in parity RAID5 (4 SSD x 1TB each).

Dedicated NAS:

• HDD: 22.6TB available (8 6TB HDD configured in parity RAID 6 plus 1 hot spare disk).
• CPU AMD GX-420MC SOC @ 2.0 GHz -> 4 cores, [4 Threads].
• RAM: 4GB.