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nucleR specifications

Information


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

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Publication for nucleR

nucleR citations

 (26)
library_books

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

2017
Oncotarget
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 […]

library_books

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

2017
Oncotarget
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 […]

library_books

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

2017
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 […]

library_books

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

2017
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 […]

library_books

Recombination Rate Heterogeneity within Arabidopsis Disease Resistance Genes

2016
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. […]

library_books

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

2016
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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