Results 51 to 60 of about 152,412 (174)

ChIP-seq Analysis in R (CSAR): An R package for the statistical detection of protein-bound genomic regions [PDF]

, 2011
Background In vivo detection of protein-bound genomic regions can be achieved by combining chromatin-immunoprecipitation with next-generation sequencing technology (ChIP-seq). The large amount of sequence data produced by this method needs to be analyzed
Muino, J.M., Angenent, G.C., Krajewski Pawel, Angenent Gerco C, Roeland CHJ van Ham, Pawel Krajewski, Muiño Jose M, Ham, R.C.H.J., van, Kaufmann, K., van Ham Roeland CHJ, Jose M Muiño, Kaufmann Kerstin, van Ham, R.C.H.J., Krajewski, P., Kerstin Kaufmann, Gerco C Angenent   +15 more
core   +1 more source

N6-Methyladenosine METTL3 Modulates the Proliferation and Apoptosis of Lens Epithelial Cells in Diabetic Cataract

Molecular Therapy: Nucleic Acids, 2020
N6-methyladenosine (m6A) is the most prevalent eukaryotic messenger RNA modification. Diabetic cataract (DC) is caused by high glucose (HG) in diabetes mellitus. However, the regulatory mechanism of m6A in the DC pathogenesis is poorly understood.
Jun Yang, Jingshu Liu, Shaozhen Zhao, Fang Tian   +3 more
doaj   +1 more source

Comprehensive Epitranscriptome Analysis from MeRIP-seq Data with exomePeak2

Genomics, Proteomics & Bioinformatics
Abstract As the most abundant internal RNA modification, N  6-methyladenosine (m6A) affects the fate of RNA through various mechanisms and regulates essential biological processes. In this study, we developed exomePeak2, a novel computational tool for the comprehensive analysis of the m6A epitranscriptome using data generated by ...
Jingxian, Zhou, Zhen, Wei, Di, Zhen, Yue, Wang, Jionglong, Su, Frans, Coenen, Guifang, Jia, Daniel J, Rigden, Jia, Meng   +8 more
openaire   +2 more sources

MeRIP-seq/scRNA-seq Code

These are the codes for MeRIP-seq/scRNA-seq analysis used in the paper titled "METTL3-Driven RNA Modifications: A Key Mechanism and Potential Therapeutic Target in Pancreatic Acinar Cell Carcinoma in Mice". The relevant GEO accession numbers are as follows: GSE305529, GSE305530.
Tatekawa, Shotaro, Hara, Tomoaki, Meng, Sikun, Sato, Tetsuya, Ishii, Hideshi   +4 more
openaire   +3 more sources

PRI-CAT: a web-tool for the analysis, storage and visualization of plant ChIP-seq experiments. [PDF]

, 2011
Although several tools for the analysis of ChIP-seq data have been published recently, there is a growing demand, in particular in the plant research community, for computational resources with which such data can be processed, analyzed, stored ...
Muino, J.M., Marlous Hoogstraat, Dijk, A.D.J., van, Roeland C. H. J. van Ham, Ham, R.C.H.J., van, van Dijk, A.D.J., van Ham, R.C.H.J., Jose M. Muiño, Aalt D. J. van Dijk, Hoogstraat, M.   +9 more
core   +1 more source

Ferroptosis Suppression by the M6A Reader IGF2BP1 Underlies Gemcitabine Resistance in Pancreatic Ductal Adenocarcinoma

Advanced Science, EarlyView.
IGF2BP1 promotes gemcitabine resistance in pancreatic cancer by stabilizing m6A‐modified FTH1 transcripts and protecting them in stress granules, thereby suppressing ferroptosis. Pharmacological inhibition of IGF2BP1 disrupts this protective pathway, restores ferroptotic sensitivity, and enhances gemcitabine efficacy in resistant tumors.
Ying‐Qin Zhu, Yue Huang, Jing‐Yuan Ye, Si‐Yuan Lu, Zhi‐De Liu, Ming‐Jian Ma, De‐Liang Fang, Zi‐Yi Zhao, Jin‐Zhao Xie, Jiao Chen, Xiao‐Yu Yin   +10 more
wiley   +1 more source

N6-methyladenosine modification of THBS1 induced by affluent WTAP promotes Graves’ ophthalmopathy progression through glycolysis to affect Th17/Treg balance

Autoimmunity
Graves’ ophthalmopathy (GO) obvious manifestation is the imbalance of Th17/Treg. N6-methyladenosine (m6A) methylation is an important regulator of Th17/Treg balance.
Lin-na Li, Jie-man Wu, Zong-ji Zheng, Shu-xian Li, Meng-yi Cai, Meng-chen Zou   +5 more
doaj   +1 more source

Direct RNA sequencing reveals m6A modifications on adenovirus RNA are necessary for efficient splicing

Nature Communications, 2020
Adenovirus transcripts contain N6-methyladenosine (m6A) modification. Here the authors profile m6A modification sites on adenovirus mRNAs using Illumina meRIP-Seq and nanopore direct RNA sequencing, and showcase a role for m6A in splicing of viral late ...
Alexander M. Price, Katharina E. Hayer, Alexa B. R. McIntyre, Nandan S. Gokhale, Jonathan S. Abebe, Ashley N. Della Fera, Christopher E. Mason, Stacy M. Horner, Angus C. Wilson, Daniel P. Depledge, Matthew D. Weitzman   +10 more
doaj   +1 more source

bigwig files for meRIP Illumina sequencing

, 2020
meRIP-seq data aligned to hg19 and Ad5 virus. All samples are seperated by coverage going to the forward and reverse strand.RNA-seq data is also aligned to hg19 and the Ad5 virus simultaneously. All bigwig show the raw coverage without any normalization.
Katharina Hayer (8393328)
core   +1 more source

Differential expression analysis for sequence count data [PDF]

, 2010
*Motivation:* High-throughput nucleotide sequencing provides quantitative readouts in assays for RNA expression (RNA-Seq), protein-DNA binding (ChIP-Seq) or cell counting (barcode sequencing).
Simon Anders, Wolfgang Huber, Klawonn, Frank   +2 more
core   +1 more source