Determination of dosage compensation of the mammalian X chromosome by RNA-seq is dependent on analytical approach

Rsx is a metatherian RNA with Xist-like properties in X-chromosome inactivation

(2012) Jennifer Grant et al.   NATURE

Mammalian X chromosome inactivation evolved as a dosage-compensation mechanism for dosage-sensitive genes on the X chromosome

(2012) E. Pessia et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Identification of novel transcripts in annotated genomes using RNA-Seq

(2011) A. Roberts et al.   BIOINFORMATICS

General lack of global dosage compensation in ZZ/ZW systems? Broadening the perspective with RNA-seq

(2011) Jochen BW Wolf et al.   BMC GENOMICS

SOME INCONVENIENT TRUTHS ABOUT SEX CHROMOSOME DOSAGE COMPENSATION AND THE POTENTIAL ROLE OF SEXUAL CONFLICT

(2011) Judith E. Mank et al.   EVOLUTION

Getting a Full Dose? Reconsidering Sex Chromosome Dosage Compensation in the Silkworm, Bombyx mori

(2011) James R. Walters et al.   Genome Biology and Evolution

RNA-sequence analysis of human B-cells

(2011) J. M. Toung et al.   GENOME RESEARCH

Differential expression in RNA-seq: A matter of depth

(2011) S. Tarazona et al.   GENOME RESEARCH

Evolutionary diversity and developmental regulation of X-chromosome inactivation

(2011) Martin Escamilla-Del-Arenal et al.   HUMAN GENETICS

Mouse genomic variation and its effect on phenotypes and gene regulation

(2011) Thomas M. Keane et al.   NATURE

Relative overexpression of X-linked genes in mouse embryonic stem cells is consistent with Ohno's hypothesis

(2011) Hong Lin et al.   NATURE GENETICS

Evidence for dosage compensation between the X chromosome and autosomes in mammals

(2011) Peter V Kharchenko et al.   NATURE GENETICS

Evidence for compensatory upregulation of expressed X-linked genes in mammals, Caenorhabditis elegans and Drosophila melanogaster

(2011) Xinxian Deng et al.   NATURE GENETICS

Widespread RNA and DNA Sequence Differences in the Human Transcriptome

(2011) M. Li et al.   SCIENCE

Hyperexpression of the X Chromosome in Both Sexes Results in Extensive Female Bias of X-Linked Genes in the Flour Beetle

(2010) Eldon G. Prince et al.   Genome Biology and Evolution

Sex bias and dosage compensation in the zebra finch versus chicken genomes: General and specialized patterns among birds

(2010) Y. Itoh et al.   GENOME RESEARCH

A comparison between ribo-minus RNA-sequencing and polyA-selected RNA-sequencing

(2010) Peng Cui et al.   GENOMICS

Female-Biased Expression on the X Chromosome as a Key Step in Sex Chromosome Evolution in Threespine Sticklebacks

(2010) Erica H. Leder et al.   MOLECULAR BIOLOGY AND EVOLUTION

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

RNA sequencing shows no dosage compensation of the active X-chromosome

(2010) Yuanyan Xiong et al.   NATURE GENETICS

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

Current-generation high-throughput sequencing: deepening insights into mammalian transcriptomes

(2009) B. J. Blencowe et al.   GENES & DEVELOPMENT

Lessons from X-chromosome inactivation: long ncRNA as guides and tethers to the epigenome

(2009) J. T. Lee   GENES & DEVELOPMENT

The gene balance hypothesis: implications for gene regulation, quantitative traits and evolution

(2009) James A. Birchler et al.   NEW PHYTOLOGIST

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

All dosage compensation is local: Gene-by-gene regulation of sex-biased expression on the chicken Z chromosome

(2008) J E Mank et al.   HEREDITY

Alternative isoform regulation in human tissue transcriptomes

(2008) Eric T. Wang et al.   NATURE

Stem cell transcriptome profiling via massive-scale mRNA sequencing

(2008) Nicole Cloonan et al.   NATURE METHODS

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS