SimCT specifications

Information


Unique identifier OMICS_29177
Name SimCT
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Perl
Computer skills Advanced
Version 0.012
Stability Stable
Maintained Yes

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Maintainers


  • person_outline CracTools <>
  • person_outline Nicolas Philippe <>

Additional information


http://cractools.gforge.inria.fr/softwares/simba/

Publication for SimCT

SimCT in publications

 (9)
PMCID: 5638914
PMID: 29026134
DOI: 10.1038/s41598-017-13298-z

[…] for retrovirus packaging, hek293t cells were seeded in 6 cm dishes. at 70% confluence, full growth medium was replaced by dmem without penicillin/streptomycin. next, 2.75 μg lentiviral vector (plko-simct1, plko.1 empty vector, sigma-aldrich), 0.75 μg of the two packaging plasmids (prsv-rev, pmdlg/prre, addgene plasmids # 12253, 12251) and 0.75 μg envelope plasmid (pmd2.g, addgene plasmid # […]

PMCID: 5090896
PMID: 27822312
DOI: 10.1186/s13040-016-0112-6

[…] the fusim tool [], though the pipeline does not simulate rna-seq data including chimeras, it only provides their associated sequences. the simulated data generator is packaged in a tools called simct (not yet published) that can easily integrate new complex chimeric events., we have developed a benchmark pipeline (fig. ) using the above genome simulation procedure along with i) […]

PMCID: 4956219
PMID: 27441625
DOI: 10.1371/journal.pone.0154102

[…] from santa-cruz was employed, against mct1(sc-37235) and mct4(sc-45892), with lipofectamine rnaimax reagent, catalog#1377–100, invitrogen, accordingly to the manufacturer´s protocol. in brief, 10nm simct1 or simct4, together with 1 ug plasmid, coding for a red fluorescent protein ptomato (cat#632532, clontech, us), to monitor transfection efficiency, was introduced into c666-1 cells seeded one […]

PMCID: 5190039
PMID: 27224918
DOI: 10.18632/oncotarget.9523

[…] proliferation and lactate uptake (figure ). western blot results confirmed that silencing of mcts selectively decreased the mcts expression in gc cell lines (figure ). as mcts were knocked down by simct1, 2, or 4 after 72 h, cell proliferation was significantly decreased in snu668 and snu216 cell lines, which highly expressed mct1, 2, and 4 as compared with expression levels seen […]

PMCID: 4998054
PMID: 26219007
DOI: 10.1120/jacmp.v16i4.5416

[…] is shown in ., it is important to note that, in the fsrs treatment using both immobilization systems, a new reference alignrt image is acquired after the patient setup is finalized based on cbct/simct alignment on bony landmarks. the original roi drawn on dicom surface from simct is automatically mapped to the new reference image, serving as a skin surrogate of the tumor position […]


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SimCT institution(s)
SeqOne, IRMB, CHRU de Montpellier - Hopital St Eloi, Montpellier, France; Institute of Computational Biology, Montpellier, Montpellier, France; University Lille, CNRS, Centrale Lille, Inria, UMR 9189 - CRIStAL - Centre de Recherche en Informatique Signal et Automatique de Lille, Lille, France; University Bordeaux, Inserm, BMGIC, U1035, Bordeaux, France
SimCT funding source(s)
Supported by the Fondation pour la Recherche Médicale (FRM, BIOINFO2013 call, grant noDBI20131228566), SATT AxLR, la Région Occitanie, and Montpellier Métropole Méditerranée. Institute of Computational Biology, Investissement d’Avenir.

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