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Protocols

Codelink specifications

Information


Unique identifier OMICS_15016
Name Codelink
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.48.0
Stability Stable
Requirements
limma, methods, parallel, R(>=2.10), knitr, genefilter, annotate, Biobase(>=2.17.8), BiocGenerics(>=0.3.2)
Maintained Yes

Taxon


  • Primates
    • Homo sapiens
  • Rodents
    • Mus musculus
    • Rattus norvegicus

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Versioning


No version available

Documentation


Maintainer


  • person_outline Diego Diez <>

Publication for Codelink

Codelink citations

 (264)
library_books

Identification of differentially expressed genes and signaling pathways in ovarian cancer by integrated bioinformatics analysis

2018
PMCID: 5858852
PMID: 29588600
DOI: 10.2147/OTT.S152238

[…] probe sequences of the same target dna. there are various platforms available (http://arrayconsortium.tgen. org/np2/home.do; http://www1.amershambiosciences.com/aptr1x/upp01077.nsf/contentand/codelink_bioarray_system; http://www.affymetrix.com; http://www.illumina.com/prod_expression.htm; and http://www.nimblegen.com; http://www.xeotron.com)., using the keywords “ovarian cancer geo […]

call_split

CD5L Promotes M2 Macrophage Polarization through Autophagy Mediated Upregulation of ID3

2018
PMCID: 5858086
PMID: 29593730
DOI: 10.3389/fimmu.2018.00480
call_split See protocol

[…] crna was generated from 10 µg of total rna by using superscript (invitrogen) and the messageamp ii-biotin (ambion, usa) rna transcription-labeling kit (enzo biochem) crna was hybridized to the codelink™ human whole genome bioarray (applied microarrays) at 37°c for 16 h by using the traymix hybridizer (biotray, france). samples were labeled with cy5 (bionova), and arrays were scanned […]

library_books

Detection of the Malaria causing Plasmodium Parasite in Saliva from Infected Patients using Topoisomerase I Activity as a Biomarker

2018
PMCID: 5841400
PMID: 29515150
DOI: 10.1038/s41598-018-22378-7

[…] outlet the droplets were broken by addition of 25% (v/v) 1 h,1 h,2 h,2h-perfluoro-1-octanol., an amine coupled oligo (amine-rca primer, see table ) was immobilized on nhs-coated microscopy slides (codelink® hd activated slides) as described by the supplier (surmodics)., lysate supplemented with nacl to a final concentration of 500 mm was added to the dna conjugated slides to allow […]

library_books

Differentiated embryo chondrocyte plays a crucial role in DNA damage response via transcriptional regulation under hypoxic conditions

2018
PMCID: 5821451
PMID: 29466367
DOI: 10.1371/journal.pone.0192136

[…] cells were then harvested and stored at -80°c until use., total rna was prepared from frozen cell pellets with a qiagen rneasy® mini kit (qiagen) according to the manufacturer’s instructions., the codelink expression bioarray system (ge healthcare, tokyo, japan) was used as previously described []. briefly, from 1 μg of total rna, double-strand cdna and subsequent biotin-labeled crna […]

library_books

Gene Expression Analysis Reveals Novel Shared Gene Signatures and Candidate Molecular Mechanisms between Pemphigus and Systemic Lupus Erythematosus in CD4+ T Cells

2018
PMCID: 5776326
PMID: 29387060
DOI: 10.3389/fimmu.2017.01992

[…] produced biased results (figure ), the raw files were preprocessed again and an additional normalization step was performed. in detail, raw gene expression profiles were deduced from text files (codelink array) using codelink r package (). using the same package, first, the background was corrected with the “normexp” method and then normalized by the “cyclicloess” method. for affymetrix […]

library_books

Association of miR 548c 5p, miR 7 5p, miR 210 3p, miR 128 3p with recurrence in systemically untreated breast cancer

2018
PMCID: 5823652
PMID: 29507672
DOI: 10.18632/oncotarget.24088

[…] probe-set was purchased from exiqon. the set contains capture-probes for 1212 human mirs based on the mirbase version 16 (http://www.mirbase.org/) []. briefly, the probes were spotted in triplets on codelink hd (surmodics) activated glass slides and post-processed according to the codelink protocol. the mircury power labeling kit (exiqon), mircury lna array hybridization buffer (exiqon) […]


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Codelink institution(s)
Instituto de Investigaciones Biomédicas Alberto Sols, Consejo Superior de Investigaciones Cientificas-Universidad Autonoma de Madrid, Madrid, Spain; Genomics Unit, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
Codelink funding source(s)
Supported by the Programa I3P de la Red de Bioinformática del CSIC (pre-doctoral fellowship), Comunidad de Madrid 08.5/0042/2003 and GR/SAL/0382/2004, MEC BFI2002- 00489 y Red de Centros RCMN (C03/08).

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