A Powerful Method for Transcriptional Profiling of Specific Cell Types in Eukaryotes: Laser-Assisted Microdissection and RNA Sequencing

A tissue-specific landscape of sense/antisense transcription in the mouse intestine

(2011) Ulrich C Klostermeier et al.   BMC GENOMICS

Meiosis-specific gene discovery in plants: RNA-Seq applied to isolated Arabidopsis male meiocytes

(2011) Changbin Chen et al.   BMC PLANT BIOLOGY

Maternal Epigenetic Pathways Control Parental Contributions to Arabidopsis Early Embryogenesis

(2011) Daphné Autran et al.   CELL

De Novo Assembly of Chickpea Transcriptome Using Short Reads for Gene Discovery and Marker Identification

(2011) R. Garg et al.   DNA RESEARCH

Whole-transcriptome RNAseq analysis from minute amount of total RNA

(2011) Muhammad A. Tariq et al.   NUCLEIC ACIDS RESEARCH

Transcriptome Analysis of the Arabidopsis Megaspore Mother Cell Uncovers the Importance of RNA Helicases for Plant Germline Development

(2011) Anja Schmidt et al.   PLOS BIOLOGY

Rnnotator: an automated de novo transcriptome assembly pipeline from stranded RNA-Seq reads

(2010) Jeffrey Martin et al.   BMC GENOMICS

MicroRNAs prevent precocious gene expression and enable pattern formation during plant embryogenesis

(2010) M. D. Nodine et al.   GENES & DEVELOPMENT

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

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

A scaling normalization method for differential expression analysis of RNA-seq data

(2010) Mark D Robinson et al.   GENOME BIOLOGY

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

Transcript length bias in RNA-seq data confounds systems biology

(2009) Alicia Oshlack et al.   Biology Direct

Genome-wide mapping of alternative splicing in Arabidopsis thaliana

(2009) S. A. Filichkin et al.   GENOME RESEARCH

Defensin-like polypeptide LUREs are pollen tube attractants secreted from synergid cells

(2009) Satohiro Okuda et al.   NATURE

mRNA-Seq whole-transcriptome analysis of a single cell

(2009) Fuchou Tang et al.   NATURE METHODS

Extensive Demethylation of Repetitive Elements During Seed Development Underlies Gene Imprinting

(2009) M. Gehring et al.   SCIENCE

Genome-Wide Demethylation of Arabidopsis Endosperm

(2009) T.-F. Hsieh et al.   SCIENCE

Microdissection of Shoot Meristem Functional Domains

(2009) Lionel Brooks et al.   PLoS Genetics

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

Highly Integrated Single-Base Resolution Maps of the Epigenome in Arabidopsis

(2008) Ryan Lister et al.   CELL

RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays

(2008) J. C. Marioni et al.   GENOME RESEARCH

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

The Transcriptional Landscape of the Yeast Genome Defined by RNA Sequencing

(2008) U. Nagalakshmi et al.   SCIENCE