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nucleR specifications


Unique identifier OMICS_00511
Name nucleR
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
Computer skills Advanced
Stability Stable
Maintained Yes


No version available

Publication for nucleR

nucleR citations


The expression of cystathionine gamma lyase is regulated by estrogen receptor alpha in human osteoblasts

PMCID: 5731906
PMID: 29254196
DOI: 10.18632/oncotarget.21514

[…] dant non-collagenous proteins in bone matrix [], and COL1, the most abundant protein in bone [].Moreover, cells were positively immunostained for estrogen receptor alpha (ERα) in both cytoplasmic and nucler compartment, but showed only a faint nuclear positivity for estrogen receptor beta (ERβ) (Figure ). The ability of cells to deposit mineralized matrix was evaluated in osteogenic cell culture m […]


Oleate induced PTX3 promotes head and neck squamous cell carcinoma metastasis through the up regulation of vimentin

PMCID: 5522334
PMID: 28489600
DOI: 10.18632/oncotarget.17326

[…] DTT, 0.5 mM PMSF, 2 μg/ml leupeptin, 2 μg/ml pepstatin, 1 mM Sodium vanadate) and incubated on ice for 20 min. The nuclear extract was centrifuged for 10 min at 12,000 g at 4 °C. The supernatant was nucler protein, divided into aliquots, and stored at -70 °C. For detecting the ratios of nuclear and cytoplasmic parts of NF-κB, equal volumes of nuclear and cytoplasmic lysate were subject to western […]


Epstein–Barr virus (EBV) associated epithelial and non epithelial lesions of the oral cavity

PMCID: 5501733
PMID: 28725300
DOI: 10.1016/j.jdsr.2017.01.002

[…] tro transforming effects. Following infection of primary human B cells in vitro, EBV induces their proliferation resulting in the development of lymphoblastoid cell lines (LCLs). The genes of six EBV nucler antigens (EBNA1, 2, 3A, 3B, 3C and EBNA-LP) as well as three latent membrane proteins (LMP-1, 2A and 2B) are expressed in these cells. Likewise, these proteins are expressed in the early phases […]


Intracellular degradation of functionalized carbon nanotube/iron oxide hybrids is modulated by iron via Nrf2 pathway

Sci Rep
PMCID: 5264386
PMID: 28120861
DOI: 10.1038/srep40997

[…] plied Biosystems). Each sample was run in duplicate.Protein quantifications were performed by western blot analysis on cells exposed as described for mRNA quantification. Proteins were extracted with Nucler/Cytosol fractionation Kit (Biovision) according to manufacturer’s protocol. Presence of Hmox1, FerH and RPL19 were analyzed on 50 μg of cytosolic proteins and Nrf2, Bach1 and lamin A on 15 μg o […]


Recombination Rate Heterogeneity within Arabidopsis Disease Resistance Genes

PLoS Genet
PMCID: 4945094
PMID: 27415776
DOI: 10.1371/journal.pgen.1006179

[…] nd subjected to paired-end 100 bp sequencing on a Hi-seq instrument. Reads were mapped using Bowtie2 to the TAIR10 assembly and normalized by library size. Nucleosome occupancy was analysed using the nucleR package []. The MNase-seq fastq files have been uploaded to ArrayExpression accession E-MTAB-4556. […]


Regulation of Budding Yeast CENP A levels Prevents Misincorporation at Promoter Nucleosomes and Transcriptional Defects

PLoS Genet
PMCID: 4794243
PMID: 26982580
DOI: 10.1371/journal.pgen.1005930

[…] ing score > = 30 using samtools []. Mononucleosomes were identified as paired-end reads with insert sizes between 50 bp and 240 bp using R Bioconductor packages GenomicRanges, rtracklayer, Rsamtools, nucleR, and the UCSC SacCer3 reference genome [, –]. ChIP reads were compared to the input reads for each strain using the Dynamic Analysis of Nucleosome and Protein Occupancy by Sequencing, version 2 […]


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nucleR institution(s)
IRB-BSC Joint Research Program on Computational Biology, Institute of Research in Biomedicine, Barcelona, Spain

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