Protocols

iSmaRT specifications

Information


Unique identifier OMICS_14669
Name iSmaRT
Alternative name integrative Small RNA Tool-kit
Software type Pipeline/Workflow
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS
Programming languages Python
Computer skills Medium
Stability Stable
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Giorgio Giurato

Publication for integrative Small RNA Tool-kit

iSmaRT citations

 (2)
library_books

The nuclear receptor ERβ engages AGO2 in regulation of gene transcription, RNA splicing and RISC loading

2017
Genome Biol
PMCID: 5634881
PMID: 29017520
DOI: 10.1186/s13059-017-1321-0

[…] e Ct-ERβ IPβ group, and those that, when compared to wild type, showed a ratio (Ct-ERβ EF/wild-type EF) ≥ 4, or showing a negative EF in wild-type IPβ vs input. Small RNA-Seq data were analyzed using iSmaRT [] with standard parameters, using miRBase v20 as reference track. miRNAs showing EF > 1 and p value ≤ 0.05 were considered for further analysis. To select ERβ-specific enriched miRNAs, those w […]

call_split

Genetic characterization of trh positive Vibrio spp. isolated from Norway

2013
PMCID: 3872308
PMID: 24400227
DOI: 10.3389/fcimb.2013.00107
call_split See protocol

[…] he PCR running conditions were: an initial denaturation of 95°C for 4 min, 35 cycles of 94°C for 1 min, 50°C for 1 min and 72°C for 2 min, and a final elongation step of 72°C for 1.5 min in a Bio-Rad Ismart cycler (BioRad, Hercules, CA). Reference V. parahaemolyticus isolate AQ4037 (trh1+) was used as positive control. Reference V. parahaemolyticus isolate 222 (trh–) was used as negative control. […]

iSmaRT institution(s)
Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry ‘Scuola Medica Salernitana’, University of Salerno, Baronissi, Italy; Genomix4Life, University of Salerno, Baronissi, Italy; Institute for Biomedical Technologies, National Research Council, Segrate, Italy
iSmaRT funding source(s)
Supported by: Italian Association for Cancer Research (AIRC, Grant IG-17426), National Research Council (CNR Flagship Projects EPIGEN and InterOmics), Ministry of Health (Garnts GR-201102347781 and GR-2011-02350476) and Genomix4Life Srl.

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