Cargando…

Intrinsic bias estimation for improved analysis of bulk and single-cell chromatin accessibility profiles using SELMA

Genome-wide profiling of chromatin accessibility by DNase-seq or ATAC-seq has been widely used to identify regulatory DNA elements and transcription factor binding sites. However, enzymatic DNA cleavage exhibits intrinsic sequence biases that confound chromatin accessibility profiling data analysis....

Descripción completa

Detalles Bibliográficos
Autores principales:	Hu, Shengen Shawn, Liu, Lin, Li, Qi, Ma, Wenjing, Guertin, Michael J., Meyer, Clifford A., Deng, Ke, Zhang, Tingting, Zang, Chongzhi
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	Nature Publishing Group UK 2022
Materias:	Article
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9492688/ https://www.ncbi.nlm.nih.gov/pubmed/36130957 http://dx.doi.org/10.1038/s41467-022-33194-z

Ejemplares similares

Selma /
por: Bauer, Jutta
Publicado: (2009)

Analysis of optimized DNase-seq reveals intrinsic bias in transcription factor footprint identification
por: He, Housheng Hansen, et al.
Publicado: (2013)

Mortuary Statistics of the City of Selma
Publicado: (1874)

Selma and Lois DeBakey: Icons of Medical Preservation
por: Reznick, Jeffrey S.
Publicado: (2022)

High-dimensional genomic data bias correction and data integration using MANCIE
por: Zang, Chongzhi, et al.
Publicado: (2016)

Universal correction of enzymatic sequence bias reveals molecular signatures of protein/DNA interactions
por: Martins, André L, et al.
Publicado: (2018)

Single-cell chromatin profiling of the primitive gut tube reveals regulatory dynamics underlying lineage fate decisions
por: Smith, Ryan J., et al.
Publicado: (2022)

Cistrome Data Browser: a data portal for ChIP-Seq and chromatin accessibility data in human and mouse
por: Mei, Shenglin, et al.
Publicado: (2017)

Temporal trends and predictors of perfluoroalkyl substances serum levels in Swedish pregnant women in the SELMA study
por: Shu, Huan, et al.
Publicado: (2018)

Inherited DNA methylation primes the establishment of accessible chromatin during genome activation
por: Liu, Guifen, et al.
Publicado: (2018)

Single-nucleus chromatin accessibility profiling highlights regulatory mechanisms of coronary artery disease risk
por: Turner, Adam W., et al.
Publicado: (2022)

Maternal nutrition during mid-pregnancy and children’s body composition at 7 years of age in the SELMA study
por: Svensson, Katherine, et al.
Publicado: (2023)

Extracting physical characteristics of higher-order chromatin structures from 3D image data
por: Lamberti, William Franz, et al.
Publicado: (2022)

Protocol for bulk and single-nuclei chromatin accessibility quantification in mouse liver tissue
por: Korenfeld, Noga, et al.
Publicado: (2023)

Persistent organic pollutants, pre-pregnancy use of combined oral contraceptives, age, and time-to-pregnancy in the SELMA cohort
por: Björvang, Richelle D., et al.
Publicado: (2020)

BART3D: inferring transcriptional regulators associated with differential chromatin interactions from Hi-C data
por: Wang, Zhenjia, et al.
Publicado: (2021)

Prenatal exposures to mixtures of endocrine disrupting chemicals and children’s weight trajectory up to age 5.5 in the SELMA study
por: Svensson, Katherine, et al.
Publicado: (2021)

Tcf1 preprograms the mobilization of glycolysis in central memory CD8(+) T cells during recall responses
por: Shan, Qiang, et al.
Publicado: (2022)

The development of a Simplified, Effective, Labour Monitoring-to-Action (SELMA) tool for Better Outcomes in Labour Difficulty (BOLD): study protocol
por: Souza, João Paulo, et al.
Publicado: (2015)

A Smartphone-Based Health Care Chatbot to Promote Self-Management of Chronic Pain (SELMA): Pilot Randomized Controlled Trial
por: Hauser-Ulrich, Sandra, et al.
Publicado: (2020)

High Temperature SELMA: Evolution of DNA-Supported Oligomannose Clusters Which Are Tightly Recognized by HIV bnAb 2G12
por: Temme, J. Sebastian, et al.
Publicado: (2014)

Intrinsic Bulk Quantum Oscillations in a Bulk Unconventional Insulator SmB(6)
por: Hartstein, Máté, et al.
Publicado: (2020)

Molecular Heterogeneity of Glucose-6-Phosphate Dehydrogenase Deficiency in Burkina Faso: G-6-PD Betica Selma and Santamaria in People with Symptomatic Malaria in Ouagadougou
por: Ouattara, Abdoul Karim, et al.
Publicado: (2016)

Report on the Relation of the Druggist to the Physician: Read at the Semi-Annual Meeting of the Dallas County Medical Association, Held at Selma, Ala., November 14th, 1871
por: Rosser, H. N.
Publicado: (1871)

NF-E2, FLI1 and RUNX1 collaborate at areas of dynamic chromatin to activate transcription in mature mouse megakaryocytes
por: Zang, Chongzhi, et al.
Publicado: (2016)

On Accounting for Sequence-Specific Bias in Genome-Wide Chromatin Accessibility Experiments: Recent Advances and Contradictions
por: Madrigal, Pedro
Publicado: (2015)

Chromatin Accessibility Data Sets Show Bias Due to Sequence Specificity of the DNase I Enzyme
por: Koohy, Hashem, et al.
Publicado: (2013)

Towards the Better: Intrinsic Property Amelioration in Bulk Metallic Glasses
por: Sarac, Baran, et al.
Publicado: (2016)

TRPS1 modulates chromatin accessibility to regulate estrogen receptor (ER) binding and ER target gene expression in luminal breast cancer cells
por: Scott, Thomas G., et al.
Publicado: (2023)

Chromatin Landscape Dictates HSF Binding to Target DNA Elements
por: Guertin, Michael J., et al.
Publicado: (2010)

Biases in bulk: DNA metabarcoding of marine communities and the methodology involved
por: van der Loos, Luna M., et al.
Publicado: (2020)

Leukaemia cell of origin identified by chromatin landscape of bulk tumour cells
por: George, Joshy, et al.
Publicado: (2016)

The Chromatin Accessibility Landscape of Adult Rat
por: Yuan, Yue, et al.
Publicado: (2021)

Chromatin-accessibility estimation from single-cell ATAC-seq data with scOpen
por: Li, Zhijian, et al.
Publicado: (2021)

ASTER: accurately estimating the number of cell types in single-cell chromatin accessibility data
por: Chen, Shengquan, et al.
Publicado: (2022)

Two sources of bias explain errors in facial age estimation
por: Clifford, Colin W. G., et al.
Publicado: (2018)

Regulation of the Boundaries of Accessible Chromatin
por: Chai, Xiaoran, et al.
Publicado: (2013)

Heparanase Modulates Chromatin Accessibility
por: Li, Honglian, et al.
Publicado: (2023)

Exchange Bias Demonstrated in Bulk Nanocomposites Processed by High-Pressure Torsion
por: Zawodzki, Michael, et al.
Publicado: (2023)

Chromatin accessibility profiling in Neurospora crassa reveals molecular features associated with accessible and inaccessible chromatin
por: Ferraro, Aileen R., et al.
Publicado: (2021)

Cannot write session to /tmp/vufind_sessions/sess_ojf27cdnv3fu45ni685aeko91p