Cargando…

Measure transcript integrity using RNA-seq data

BACKGROUND: Stored biological samples with pathology information and medical records are invaluable resources for translational medical research. However, RNAs extracted from the archived clinical tissues are often substantially degraded. RNA degradation distorts the RNA-seq read coverage in a gene-...

Descripción completa

Detalles Bibliográficos
Autores principales:	Wang, Liguo, Nie, Jinfu, Sicotte, Hugues, Li, Ying, Eckel-Passow, Jeanette E., Dasari, Surendra, Vedell, Peter T., Barman, Poulami, Wang, Liewei, Weinshiboum, Richard, Jen, Jin, Huang, Haojie, Kohli, Manish, Kocher, Jean-Pierre A.
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	BioMed Central 2016
Materias:	Methodology Article
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4739097/ https://www.ncbi.nlm.nih.gov/pubmed/26842848 http://dx.doi.org/10.1186/s12859-016-0922-z

Ejemplares similares

Determining the frequency of pathogenic germline variants from exome sequencing in patients with castrate-resistant prostate cancer
por: Hart, Steven N, et al.
Publicado: (2016)

Mutational Landscapes of Sequential Prostate Metastases and Matched Patient Derived Xenografts during Enzalutamide Therapy
por: Kohli, Manish, et al.
Publicado: (2015)

A Prospective Correlation of Tissue Histopathology With Nucleic Acid Yield in Metastatic Castration-Resistant Prostate Cancer Biopsy Specimens
por: Jimenez, Rafael E., et al.
Publicado: (2019)

TSPYL Family Regulates CYP17A1 and CYP3A4 Expression: Potential Mechanism Contributing to Abiraterone Response in Metastatic Castration‐Resistant Prostate Cancer
por: Qin, Sisi, et al.
Publicado: (2017)

SNPPicker: High quality tag SNP selection across multiple populations
por: Sicotte, Hugues, et al.
Publicado: (2011)

GLOSSI: a method to assess the association of genetic loci-sets with complex diseases
por: Chai, High-Seng, et al.
Publicado: (2009)

Exome sequencing reveals frequent deleterious germline variants in cancer susceptibility genes in women with invasive breast cancer undergoing neoadjuvant chemotherapy
por: Ellingson, Marissa S., et al.
Publicado: (2015)

Identification of factors associated with duplicate rate in ChIP-seq data
por: Tian, Shulan, et al.
Publicado: (2019)

Molecular Profile Changes in Patients with Castrate-Resistant Prostate Cancer Pre- and Post-Abiraterone/Prednisone Treatment
por: Sicotte, Hugues, et al.
Publicado: (2022)

XL-DNase-seq: improved footprinting of dynamic transcription factors
por: Oh, Kyu-Seon, et al.
Publicado: (2019)

CPAT: Coding-Potential Assessment Tool using an alignment-free logistic regression model
por: Wang, Liguo, et al.
Publicado: (2013)

Androgen receptor splice variants bind to constitutively open chromatin and promote abiraterone-resistant growth of prostate cancer
por: He, Yundong, et al.
Publicado: (2018)

CircularLogo: A lightweight web application to visualize intra-motif dependencies
por: Ye, Zhenqing, et al.
Publicado: (2017)

DeLTa-Seq: direct-lysate targeted RNA-Seq from crude tissue lysate
por: Kashima, Makoto, et al.
Publicado: (2022)

Protocol to apply spike-in ChIP-seq to capture massive histone acetylation in human cells
por: Wu, Di, et al.
Publicado: (2021)

Gene set analysis controlling for length bias in RNA-seq experiments
por: Ren, Xing, et al.
Publicado: (2017)

Quality assessment metrics for whole genome gene expression profiling of paraffin embedded samples
por: Mahoney, Douglas W, et al.
Publicado: (2013)

On Differential Gene Expression Using RNA-Seq Data
por: Lee, Juhee, et al.
Publicado: (2011)

Butt-seq: a new method for facile profiling of transcription
por: Yu, Albert D., et al.
Publicado: (2023)

MIRA-seq for DNA methylation analysis of CpG islands
por: Jung, Marc, et al.
Publicado: (2015)

Glioma: interaction of acquired and germline genetics
por: Eckel-Passow, Jeanette E., et al.
Publicado: (2021)

RNA-seq assistant: machine learning based methods to identify more transcriptional regulated genes
por: Wang, Likai, et al.
Publicado: (2018)

Plasma cell-free DNA–based predictors of response to abiraterone acetate/prednisone and prognostic factors in metastatic castration-resistant prostate cancer
por: Du, Meijun, et al.
Publicado: (2020)

Identifying Cell Type-Specific Transcription Factors by Integrating ChIP-seq and eQTL Data–Application to Monocyte Gene Regulation
por: Choudhury, Mudra, et al.
Publicado: (2016)

Nonparametric Tests for Differential Histone Enrichment with ChIP-Seq Data
por: Wu, Qian, et al.
Publicado: (2015)

INC-Seq: accurate single molecule reads using nanopore sequencing
por: Li, Chenhao, et al.
Publicado: (2016)

Purification of nanogram-range immunoprecipitated DNA in ChIP-seq application
por: Zhong, Jian, et al.
Publicado: (2017)

An iteration normalization and test method for differential expression analysis of RNA-seq data
por: Zhou, Yan, et al.
Publicado: (2014)

K-seq, an affordable, reliable, and open Klenow NGS-based genotyping technology
por: Ziarsolo, Peio, et al.
Publicado: (2021)

A new pipeline for structural characterization and classification of RNA-Seq microbiome data
por: Racedo, Sebastian, et al.
Publicado: (2021)

Comparative performance of the BGISEQ-500 and Illumina HiSeq4000 sequencing platforms for transcriptome analysis in plants
por: Zhu, Fu-Yuan, et al.
Publicado: (2018)

MUREN: a robust and multi-reference approach of RNA-seq transcript normalization
por: Feng, Yance, et al.
Publicado: (2021)

DNA methylation signature predicts cancer response to demethylation agents from profiling diverse cancer cell lines
por: Sun, Zhifu, et al.
Publicado: (2022)

Grouped False-Discovery Rate for Removing the Gene-Set-Level Bias of RNA-seq
por: Yang, Tae Young, et al.
Publicado: (2013)

ATAC-seq normalization method can significantly affect differential accessibility analysis and interpretation
por: Reske, Jake J., et al.
Publicado: (2020)

Comparative analysis on the expression of L1 loci using various RNA-Seq preparations
por: Kaul, Tiffany, et al.
Publicado: (2020)

Using DenseFly algorithm for cell searching on massive scRNA-seq datasets
por: Chen, Yixin, et al.
Publicado: (2020)

Concurrent mapping of multiple epigenetic marks and co-occupancy using ACT2-seq
por: Carter, Benjamin, et al.
Publicado: (2021)

An optimized approach for multiplexing single-nuclear ATAC-seq using oligonucleotide-conjugated antibodies
por: Bera, Betelehem Solomon, et al.
Publicado: (2023)

Elimination of PCR duplicates in RNA-seq and small RNA-seq using unique molecular identifiers
por: Fu, Yu, et al.
Publicado: (2018)

Cannot write session to /tmp/vufind_sessions/sess_bq27f13r9s9vjdr89mos71f39s