Results 41 to 50 of about 459,773 (306)

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

, 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

diffReps: detecting differential chromatin modification sites from ChIP-seq data with biological replicates. [PDF]

PLoS ONE, 2013
ChIP-seq is increasingly being used for genome-wide profiling of histone modification marks. It is of particular importance to compare ChIP-seq data of two different conditions, such as disease vs.
Li Shen, Ning-Yi Shao, Xiaochuan Liu, Ian Maze, Jian Feng, Eric J Nestler   +5 more
doaj   +1 more source

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

, 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

SMARTcleaner: identify and clean off-target signals in SMART ChIP-seq analysis

BMC Bioinformatics, 2018
Background Noises and artifacts may arise in several steps of the next-generation sequencing (NGS) process. Recently, an NGS library preparation method called SMART, or Switching Mechanism At the 5′ end of the RNA Transcript, is introduced to prepare ...
Dejian Zhao, Deyou Zheng
doaj   +1 more source

Profiling chromatin regulatory landscape: insights into the development of ChIP-seq and ATAC-seq

Molecular Biomedicine, 2020
Chromatin regulatory landscape plays a critical role in many disease processes and embryo development. Epigenome sequencing technologies such as chromatin immunoprecipitation sequencing (ChIP-seq) and assay for transposase-accessible chromatin with high ...
Shaoqian Ma, Yongyou Zhang
doaj   +1 more source

Investigating transcription factor dynamics in health and disease using FRAP

FEBS Letters, EarlyView.
FRAP analysis of GFP‐tagged transcription factors reveals how molecular mobility and target engagement change in response to drug treatment. By combining live‐cell imaging, quantitative model fitting, and statistical analysis, this approach uncovers transcription factor dynamics linked to disease mechanisms, providing a powerful framework for ...
Kannan Govindaraj, Carolina Vazquez Garzon, Jose Joaquin Velasco, Janine N. Post   +3 more
wiley   +1 more source

ENCODE-DCC/chip-seq-pipeline2: v1.6.0

, 2020
Conda users should update pipeline's environment. However, reinstalling is always recommended since we added GNU utils to the installer. # To update env $ bash scripts/update_conda_env.sh # To re-install env $ bash scripts/uninstall_conda_env.sh $ bash ...
Paul L. Maurizio, Meenakshi Kagda, annashcherbina, J. Seth Strattan, Jin Lee   +4 more
core   +1 more source

Tissue-Specific In Vivo Biotin Chromatin Immunoprecipitation with Sequencing in Zebrafish and Chicken

STAR Protocols, 2020
Summary: Chromatin immunoprecipitation with sequencing (ChIP-seq) has been instrumental in understanding transcription factor (TF) binding during gene regulation.
Martyna Lukoseviciute, Irving T.C. Ling, Upeka Senanayake, Ivan Candido-Ferreira, Gunes Taylor, Ruth M. Williams, Tatjana Sauka-Spengler   +6 more
doaj   +1 more source

Circular RNA expression landscapes in myelodysplastic neoplasms: Associations with mutational signatures and disease progression

Molecular Oncology, EarlyView.
In this explorative study, the abundance of circular RNA molecules in bone marrow stem cells was found to be elevated in patients with high‐risk myelodysplastic neoplasms, and to be associated with an increased risk of progression to acute myeloid leukemia.
Eileen Wedge, Morten Tulstrup, Gabriele Todisco, Pedro Moura, Christophe Côme, Jakob Werner Hansen, Jakob Schmidt Jespersen, Balthasar Schlotmann, Maria Creignou, Mette Dahl, Claudia Schöllkopf, Klas Raaschou‐Jensen, Krister Wennerberg, Bo Porse, Joachim Weischenfeldt, Eva Hellström‐Lindberg, Lasse Sommer Kristensen, Kirsten Grønbæk   +17 more
wiley   +1 more source

ChIP-seq analysis of ZHX3.

, 2022
(A) ChIP-seq analysis showing the distribution of ZHX3 around target gene loci in proliferating IMR-90 cells. TSS, transcription start site; TES, transcription end site.
Naoki Tani (504791), Tomoaki Koga (35204), Tomoka Igata (12009374), Hiroshi Tanaka (3087), Mitsuyoshi Nakao (12822), Seonghyeon Hong (12009380), Kan Etoh (12009377)   +6 more
core   +1 more source