The NGS platform UniTO uses state-of-the-art Illumina sequencers.

Illumina NextSeq 1000

 

The Illumina NextSeq 1000 System was purchased with the financial support of Regione Piemonte – Bando INFRA-P

The Illumina NextSeq 1000 System uses patterned flow cells that offer the highest cluster density flow cell of any on-market NGS system. It features a novel super resolution optics system that is optimized to increase cluster brightness, reduce channel cross-talk, and improve signal-to-noise ratio. It provides flexible output from 30 Gb up to 120 Gb. The NextSeq 1000 System can support a broad range of applications like small whole-genome sequencing, whole exome sequencing and single-cell RNA sequencing.

More information about NextSeq 1000

Illumina NextSeq 500

 

The Illumina NextSeq 500 System was purchased with the financial support of Compagnia di San Paolo

The Illumina NextSeq 500 System is a desktop sequencer with power and flexibility to carry out applications such as targeted sequencing (amplicon-based, gene panel), exome sequencing, whole transcriptome sequencing, mRNA sequencing, and methylation sequencing. At high output, up to 800 million paired end reads can be generated (at 150 bp read length) to produce up to 120 Gb of data in 29 hours.

More information about: NextSeq 500 

Illumina MiSeq

 
The Illumina MiSeq System was purchased with the financial support of Compagnia di San Paolo.

The Illumina MiSeq System is a versatile and cost-effective platform for smaller sequencing projects. It is suitable for applications such as targeted resequencing, metagenomics, small genome sequencing, targeted gene expression profiling, and more. MiSeq reagents enable up to 15 Gb of output with 25 million sequencing reads and 2 × 300 bp read lengths.

More information about: Illumina MiSeq

Quantification and quality control

• Qubit 4.0
• TapeStation 4150 Agilent

Fragmentation

• Bioruptor Pico Diagenode

Server

• Cluster TERA-X-CLS-013

TapeStation 4150 Agilent, Bioruptor Pico Diagenode and server Cluster TERA-X-CLS-013 were purchased with the financial support of Regione Piemonte - Bando INFRA-P.

• Support on experimental design
• Support on sample preparation
• Support on data analysis
• Data analysis

The NGS platform UniTO offers the access to a single part of the service:

• Library preparation
• Sequencing
• Use of Illumina Systems under the supervision of the technical staff.

• Sample delivery (purified DNA, purified RNA, cells, tissue)

• Quantification and Quality control of starting material (DNA, RNA)

• Library preparation

• Quality control of libraries

• High throughput sequencing on Illumina platform

• Demultiplexing

• Quality control of sequencing

Prof. Salvatore Oliviero
the responsible of the platform
salvatore.oliviero@unito.it

Dr. Francesca Anselmi
francesca.anselmi@unito.it
the person in charge of the platform

Dr. Anna Krepelova
anna.krepelova@unito.it
the person in charge of the platform

For information, quotes and booking services please contact the persons in charge, with whom sample preparation and delivery will be arranged.

For numerous and repeated analysis, agreements with external public or private subjects are possible. In such agreements the type of services offered and the relative expected costs are specified.
Digital data will be sent via e-mail or transferred to a storage device.

Data analysis is performed on request.

Scientific publications in the last 5 years

Del Giudice M, Foster JG, Peirone S, Rissone A, Caizzi L, Gaudino F, Parlato
C, Anselmi F, Arkell R, Guarrera S, Oliviero S, Basso G, Rajan P, Cereda M.
FOXA1 regulates alternative splicing in prostate cancer. Cell Rep. 2022 Sep
27;40(13):111404. doi: 10.1016/j.celrep.2022.111404.
 
Gigliotti CL, Boggio E, Favero F, Incarnato D, Santoro C, Oliviero S, Rojo
JM, Zucchelli S, Persichetti F, Baldanzi G, Dianzani U, Corà D. Specific
transcriptional programs differentiate ICOS from CD28 costimulatory signaling in
human Naïve CD4⁺ T cells. Front Immunol. 2022 Sep 5;13:915963. doi:
10.3389/fimmu.2022.915963.
 
Astanina E, Doronzo G, Corà D, Neri F, Oliviero S, Genova T, Mussano F,
Middonti E, Vallariello E, Cencioni C, Valdembri D, Serini G, Limana F, Foglio
E, Ballabio A, Bussolino F. The TFEB-TGIF1 axis regulates EMT in mouse
epicardial cells. Nat Commun. 2022 Sep 3;13(1):5191. doi:
10.1038/s41467-022-32855-3.
 
Divisato G, Chiariello AM, Esposito A, Zoppoli P, Zambelli F, Elia MA, Pesole
G, Incarnato D, Passaro F, Piscitelli S, Oliviero S, Nicodemi M, Parisi S, Russo
T. Hmga2 protein loss alters nuclear envelope and 3D chromatin structure. BMC
Biol. 2022 Aug 2;20(1):171. doi: 10.1186/s12915-022-01375-3.
 
Houshmand M, Vitale N, Orso F, Cignetti A, Molineris I, Gaidano V, Sainas S,
Giorgis M, Boschi D, Fava C, Passoni A, Gai M, Geuna M, Sora F, Iurlo A,
Abruzzese E, Breccia M, Mulas O, Caocci G, Castagnetti F, Taverna D, Oliviero S,
Pane F, Lolli ML, Circosta P, Saglio G. Dihydroorotate dehydrogenase inhibition
reveals metabolic vulnerability in chronic myeloid leukemia. Cell Death Dis.
2022 Jun 30;13(6):576. doi: 10.1038/s41419-022-05028-9.
 
Elia I, Realini G, Di Mauro V, Borghi S, Bottoni L, Tornambè S, Vitiello L,
Weiss SJ, Chiariello M, Tamburrini A, Oliviero S, Neri F, Orlandini M, Galvagni
F. SNAI1 is upregulated during muscle regeneration and represses FGF21 and ATF3
expression by directly binding their promoters. FASEB J. 2022 Jul;36(7):e22401.
doi: 10.1096/fj.202200215R.
 
Avalle L, Raggi L, Monteleone E, Savino A, Viavattene D, Statello L, Camperi
A, Stabile SA, Salemme V, De Marzo N, Marino F, Guglielmi C, Lobascio A, Zanini
C, Forni M, Incarnato D, Defilippi P, Oliviero S, Poli V. STAT3 induces breast
cancer growth via ANGPTL4, MMP13 and STC1 secretion by cancer associated
fibroblasts. Oncogene. 2022 Mar;41(10):1456-1467. doi:
10.1038/s41388-021-02172-y.
 
 Shafaroudi AM, Sharifi-Zarchi A, Rahmani S, Nafissi N, Mowla SJ, Lauria A,
Oliviero S, Matin MM. Expression and Function of C1orf132 Long-Noncoding
RNA in Breast Cancer Cell Lines and Tissues. Int J Mol Sci. 2021 Jun
23;22(13):6768. doi: 10.3390/ijms22136768.
 
Fujimura Y, Watanabe M, Ohno K, Kobayashi Y, Takashima S, Nakamura H, Kosumi
H, Wang Y, Mai Y, Lauria A, Proserpio V, Ujiie H, Iwata H, Nishie W, Nagayama M,
Oliviero S, Donati G, Shimizu H, Natsuga K. Hair follicle stem cell progeny heal
blisters while pausing skin development. EMBO Rep. 2021 Jul 5;22(7):e50882. doi:
10.15252/embr.202050882.
 
Ho JS, Di Tullio F, Schwarz M, Low D, Incarnato D, Gay F, Tabaglio T, Zhang
J, Wollmann H, Chen L, An O, Chan THM, Hall Hickman A, Zheng S, Roudko V, Chen
S, Karz A, Ahmed M, He HH, Greenbaum BD, Oliviero S, Serresi M, Gargiulo G, Mann
KM, Hernando E, Mulholland D, Marazzi I, Wee DKB, Guccione E. HNRNPM controls
circRNA biogenesis and splicing fidelity to sustain cancer cell fitness. Elife.
2021 Jun 2;10:e59654. doi: 10.7554/eLife.59654.
 
 Morandi E, Manfredonia I, Simon LM, Anselmi F, van Hemert MJ, Oliviero S,
Incarnato D. Genome-scale deconvolution of RNA structure ensembles. Nat Methods.
2021 Mar;18(3):249-252. doi: 10.1038/s41592-021-01075-w.
 
Malavasi F, Faini AC, Morandi F, Castella B, Incarnato D, Oliviero S,
Horenstein AL, Massaia M, van de Donk NWCJ, Richardson PG. Molecular dynamics of
targeting CD38 in multiple myeloma. Br J Haematol. 2021 May;193(3):581-591. doi:
10.1111/bjh.17329.
 
Betto RM, Diamante L, Perrera V, Audano M, Rapelli S, Lauria A, Incarnato D,
Arboit M, Pedretti S, Rigoni G, Guerineau V, Touboul D, Stirparo GG, Lohoff T,
Boroviak T, Grumati P, Soriano ME, Nichols J, Mitro N, Oliviero S, Martello G.
Metabolic control of DNA methylation in naive pluripotent cells. Nat Genet. 2021
Feb;53(2):215-229. doi: 10.1038/s41588-020-00770-2.
 
Bertacchi M, Romano AL, Loubat A, Tran Mau-Them F, Willems M, Faivre L, Khau
van Kien P, Perrin L, Devillard F, Sorlin A, Kuentz P, Philippe C, Garde A, Neri
F, Di Giaimo R, Oliviero S, Cappello S, D'Incerti L, Frassoni C, Studer M. NR2F1
regulates regional progenitor dynamics in the mouse neocortex and cortical
gyrification in BBSOAS patients. EMBO J. 2020 Jul 1;39(13):e104163. doi:
10.15252/embj.2019104163.
 
Di Timoteo G, Dattilo D, Centrón-Broco A, Colantoni A, Guarnacci M, Rossi F,
Incarnato D, Oliviero S, Fatica A, Morlando M, Bozzoni I. Modulation of circRNA
Metabolism by m⁶A Modification. Cell Rep. 2020 May 12;31(6):107641.
doi: 10.1016/j.celrep.2020.107641.
 
Zorzan I, Pellegrini M, Arboit M, Incarnato D, Maldotti M, Forcato M,
Tagliazucchi GM, Carbognin E, Montagner M, Oliviero S, Martello G. The
transcriptional regulator ZNF398 mediates pluripotency and epithelial character
downstream of TGF-beta in human PSCs. Nat Commun. 2020 May 12;11(1):2364. doi:
10.1038/s41467-020-16205-9.
  
Managò A, Audrito V, Mazzola F, Sorci L, Gaudino F, Gizzi K, Vitale N,
Incarnato D, Minazzato G, Ianniello A, Varriale A, D'Auria S, Mengozzi G,
Politano G, Oliviero S, Raffaelli N, Deaglio S. Extracellular nicotinate
phosphoribosyltransferase binds Toll like receptor 4 and mediates inflammation.
Nat Commun. 2019 Sep 11;10(1):4116. doi: 10.1038/s41467-019-12055-2.
  
Simon LM, Morandi E, Luganini A, Gribaudo G, Martinez-Sobrido L, Turner DH,
Oliviero S, Incarnato D. In vivo analysis of influenza A mRNA secondary
structures identifies critical regulatory motifs. Nucleic Acids Res. 2019 Jul
26;47(13):7003-7017. doi: 10.1093/nar/gkz318.
 
Grassi E, Santoro R, Umbach A, Grosso A, Oliviero S, Neri F, Conti L, Ala U,
Provero P, DiCunto F, Merlo GR. Choice of Alternative Polyadenylation Sites,
Mediated by the RNA-Binding Protein Elavl3, Plays a Role in Differentiation of
Inhibitory Neuronal Progenitors. Front Cell Neurosci. 2019 Jan 10;12:518. doi:
10.3389/fncel.2018.00518.
 
Doronzo G, Astanina E, Corà D, Chiabotto G, Comunanza V, Noghero A, Neri F,
Puliafito A, Primo L, Spampanato C, Settembre C, Ballabio A, Camussi G, Oliviero
S, Bussolino F. TFEB controls vascular development by regulating the
proliferation of endothelial cells. EMBO J. 2019 Feb 1;38(3):e98250. doi:
10.15252/embj.201798250.
  
Brossa A, Papadimitriou E, Collino F, Incarnato D, Oliviero S, Camussi G,
Bussolati B. Role of CD133 Molecule in Wnt Response and Renal Repair. Stem Cells
Transl Med. 2018 Mar;7(3):283-294. doi: 10.1002/sctm.17-0158.