The Instituto de Neurociencias (IN) Omics Facility is a platform for Genomic and Transcriptomic analysis that provides services and training to both IN and external users. This core facility includes a set of state-of-the-art equipment that allows to perform a great variety of techniques including Cell Sorting (populations and single cell), Single Cell platform, QPCR, DNA and RNA quality control, Library construction, DNA sonication, Bioinformatics platform for data analysis and storage. Genomic and Transcriptomic issues from fixed cells, disaggregated living tissues, cell cultures and cellular organelles can be analyzed.

The service also counts with high-performance workstations and software packages for data analysis.

omicsLab Countless
omicsLab SingleCellg
omicsLab Rack
omicsLab Mastercyclerg
omicsLab Diagenode
omicsLab FlowCabinet
omicsLab Bioanalyser

Services offered:

  • Technical assistance for the use of all the devices and equipment provided in the facility.
  • Coaching/training for experimental design.
  • Assistance in the processing and analysis of data using the facility’s provided, and freely available software.
  • Guidance in the development of single cell protocols.
  • Equipment and devices maintenance.
  • Workshop organization and displays related to omics issues, as well as new technologies.
  • Participation in outreach activities.

Facility requests:
General communication, questions, appointment inquiries and training requests will preferably be set up by email: omics@umh.es

FACS (Fluorescence activated cell sorter)

BD FACS Aria III

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 FACS Melody

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.

Single cell applications

Chromium controller 10X Genomics

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.

PCR

Eppendorf Mastercycler Pro S

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.

QPCR

Applied Biosystems QuantStudio 3

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….

DNA and RNA Quantification and Quality control

Agilent 2100 Bioanalizer

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.

Sonication

Diagenode Bioruptor pico

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.

Cell count

Invitrogen Countess II FL Automated Cell Counter

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.

Biological safety Cabinet

MSC-Advantage class II Biological Safety Cabinet

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

Computing platform

Computing platform


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.

General operational considerations of the Omics Facility:

1. General communication, questions, appointment inquiries, and training requests will be preferably stablished by email to: omics@umh.es.

2. The Principal Investigator is ultimately responsible for the correct use of the Facility’s equipment by any member of his/her team.

3. Users must read and be aware of the basic instructions for the correct use of each equipment he/she manipulates, as well as for the rules applicable in each case.

4. It is mandatory for new users to receive the corresponding training by the Facility’s personnel before using any equipment. Moreover, during the first session they should be supervised by the Facility’s personnel or an experimented user.

5. Microscopes and workstations will be always booked through the web page: intranet equipment reservation.

6. Cancellation of a booked session the same day that the equipment will be used, is not possible. However, an email may be sent to omics@umh.es, in order to make use of the slot. Canceling bookings prior to one day can be done through the web page.

7. It is forbidden to browse Internet, software installation/deletion or the use of external storage devices in any Facility’s computer.

8. Any user booking a slot is responsible for the equipment during that time.

9. Working area should be kept clean, particularly after finalizing the session.

10. If you have uncertainties regarding the use of any equipment, no matter how simple may seem, ask for help to the personnel without any hesitation.

omicsbooked

Booking, except for the Invitrogen Countess II FL and MSC-Advantage Class II Biological Safety Cabinet, must be done via intranet at:
Access

Invitrogen Countess II FL and MSC-Advantage Class II Biological Safety Cabinet bookings must be done through the Omics Facility personnel: omics@umh.es

Table 1. Price list (€)

Services   CSIC/UMH   Universidades OPI’s Entidades privadas
Citometría y Sorting
FacsAriaIII sorter

127,5 €/hora 153,75 €/hora 218,75 €/hora
FacsMelody sorter

127,5 €/hora 153,75 €/hora 218,75 €/hora
Genómica de célula única
Librería scRNA-seq

200 €/librería 280 €/librería 360 €/librería
Librería scATAC-seq

150 €/librería 210 €/librería 270 €/librería
L. Multiomics scATAC-RNA-seq

250 €/librería 310 €/librería 370 €/librería
Control de calidad (QC) Bioanalyzer 2100 Agilent
DNA high sensitivity run

60 €/chip 75 €/chip 120 €/chip
RNA Pico chip run

45 €/chip 60 €/chip 100 €/chip
Library Quality control

60 €/chip 75 €/chip 120 €/chip
Real Time PCR (QuantStudio 3 Applied biosystems)
Acceso a QuantStudio 3

6,99 €/hora 10 €/hora 20 €/hora


The Omics Facility is located on the ground floor, southeast corner of the IN and organized as follows:

  • Room 012 : Omics Facility
  • Room 010 : Computational Analysis

omicas loc

Scientific Director:
José Pascual López-Atalaya
jose.lopez@umh.es »
+34 965 23 37 44

CalerEscribanox

Technical Manager: Antonio Javier Caler Escribano
acaler@umh.es »
+34 965 91 92 18

RECURSO2

Specialized Technician:
Jose Mulet Soler
jmulet@umh.es »
+34 965 91 92 18

General communication, questions, appointment inquiries, and training requests will be preferably set up by email to: omics@umh.es (Omics facility) or bioinformatics@umh.es (Computational analysis).

Application form for external users: Application Form

Omics Facility
Instituto de Neurociencias
Universidad Miguel Hernández – CSIC
Campus de San Juan
Sant Joan d’Alacant
Alicante | España

Tel. + 34 965 23 37 00
(ext. service 9218)