chipseq statistics

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Protocols

chipseq specifications

Information


Unique identifier OMICS_17147
Name chipseq
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License Artistic License version 2.0
Computer skills Advanced
Version 1.30.0
Stability Stable
Requirements
methods, stats, BiocGenerics, IRanges, GenomicRanges, ShortRead, lattice, BSgenome, R(>=2.10), GenomicFeatures, S4Vectors(>=0.17.25), IRanges(>=2.13.12), GenomicRanges(>=1.31.8), BiocGenerics(>=0.1.0), TxDb.Mmusculus.UCSC.mm9.knownGene
Maintained Yes

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chipseq citations

 (14)
library_books

Matrix stiffness controls lymphatic vessel formation through regulation of a GATA2 dependent transcriptional program

2018
Nat Commun
PMCID: 5904183
PMID: 29666442
DOI: 10.1038/s41467-018-03959-6

[…] pression (Fig. ). This was dependent on GATA2, since GATA2 silencing abrogated soft matrix-induced VEGFR3 upregulation (Fig. ).To determine if GATA2 directly regulates VEGFR3 expression, we performed ChIPseq in human dermal LECs. One pronounced peak within a region covering the FLT4 gene (encoding VEGFR3) and up to 50 kb upstream of the FLT4 promoter was identified (Fig. , Supplementary Fig. ). Th […]

call_split

Pharmacological targeting of the transcription factor SOX18 delays breast cancer in mice

2017
eLife
PMCID: 5283831
PMID: 28137359
DOI: 10.7554/eLife.21221.028
call_split See protocol

[…] Following IP, DNA amplification was performed using TruSeq ChIPseq kit (Illumina, IP-202–1012), using 0.5 µM of the universal reverse PCR primer and the forward PCR primer containing the index sequence of choice in 50 µL 1 x NEBNext High-Fidelity PCR Master M […]

library_books

TCGA Workflow: Analyze cancer genomics and epigenomics data using Bioconductor packages

2016
F1000Res
PMCID: 5302158
PMID: 28232861
DOI: 10.5256/f1000research.9601.r14695

[…] ype of file. The data downloaded is a processed data from an integrative Analysis of 111 reference human epigenomes . 1 library (AnnotationHub) 2 library (pbapply) 3 #–––––––––––––––––– Working with ChipSeq data ––––––––––––––– 4 # Step 1: download histone marks for a brain samples. 5 #–––––––––––––––––––––––––––––––––––––––––––––––––––––––––––– 6 ah = AnnotationHub() # loading annotation hub dat […]

library_books

Bio TDS: bioscience query tool discovery system

2016
Nucleic Acids Res
PMCID: 5210639
PMID: 27924016
DOI: 10.1093/nar/gkw940

[…] one of the tools repositories that has been integrated into the Bio-TDS is SEQAnswer-Wiki SEQ, the most relevant tools repository for the High Throughput Sequencing (HTS) community (e.g. NGS, RNASeq, ChipSeq) (,). […]

library_books

IL 4 orchestrates STAT6 mediated DNA demethylation leading to dendritic cell differentiation

2016
Genome Biol
PMCID: 4711003
PMID: 26758199
DOI: 10.1186/s13059-015-0863-2

[…] tone marks H3K9me3 (Abcam, ab8898) and H3K27me3 (Millipore 07-449). Human IgG was used as a negative control. Primer sequences were designed to contain predicted or known TF binding (from TRANSFAC or ChIPseq data) as close as possible to the CpG undergoing methylation changes. Primer sequences are shown in Additional file . Three biological replicates of the experiments were performed. […]

library_books

Stromal SLIT2 impacts on pancreatic cancer associated neural remodeling

2015
PMCID: 4669755
PMID: 25590802
DOI: 10.1038/cddis.2014.557

[…] Individual Affymetrix files were parsed and normalized with GCRMA using Affy and GCRMA packages with Bioconductor 3.0 (http://www.bioconductor.org/packages/release/bioc/html/chipseq.html). Differential analysis was performed with the SAM method (MeV, version 4.8.1) after application of a variance (top 20% of transcripts were kept). FDR was fixed to 6%, and 1001 genes were […]

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