A comparative analysis of library prep approaches for sequencing low input translatome samples

Simultaneous Transcriptional and Epigenomic Profiling from Specific Cell Types within Heterogeneous Tissues In Vivo

(2017) Hyun Cheol Roh et al.   Cell Reports

Gfi1Cre mice have early onset progressive hearing loss and induce recombination in numerous inner ear non-hair cells

(2017) Maggie Matern et al.   Scientific Reports

Methods to analyze cell type-specific gene expression profiles from heterogeneous cell populations

(2016) Jane Jung et al.   Animal Cells and Systems

Dynamic Axonal Translation in Developing and Mature Visual Circuits

(2016) Toshiaki Shigeoka et al.   CELL

The impact of amplification on differential expression analyses by RNA-seq

(2016) Swati Parekh et al.   Scientific Reports

Cell type-specific gene expression profiling in brain tissue: comparison between TRAP, LCM and RNA-seq

(2015) TaeHyun Kim et al.   BMB Reports

Evaluating whole transcriptome amplification for gene profiling experiments using RNA-Seq

(2015) Sheena L Faherty et al.   BMC BIOTECHNOLOGY

Does FACS perturb gene expression?

(2015) Graham M. Richardson et al.   CYTOMETRY PART A

Single‐cell transcriptomes reveal characteristic features of human pancreatic islet cell types

(2015) Jin Li et al.   EMBO REPORTS

Ribosome profiling reveals the what, when, where and how of protein synthesis

(2015) Gloria A. Brar et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Low-cost, low-input RNA-seq protocols perform nearly as well as high-input protocols

(2015) Peter A. Combs et al.   PeerJ

Comprehensive analysis of gene expression in human retina and supporting tissues

(2014) Mingyao Li et al.   HUMAN MOLECULAR GENETICS

How deep is enough in single-cell RNA-seq?

(2014) Aaron M Streets et al.   NATURE BIOTECHNOLOGY

Visualizing samples with box plots

(2014) Martin Krzywinski et al.   NATURE METHODS

Full-length RNA-seq from single cells using Smart-seq2

(2014) Simone Picelli et al.   Nature Protocols

Comparative analysis of RNA sequencing methods for degraded or low-input samples

(2013) Xian Adiconis et al.   NATURE METHODS

Quantitative assessment of single-cell RNA-sequencing methods

(2013) Angela R Wu et al.   NATURE METHODS

Smart-seq2 for sensitive full-length transcriptome profiling in single cells

(2013) Simone Picelli et al.   NATURE METHODS

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

Cell Type–Specific Transcriptome Analysis Reveals a Major Role for Zeb1 and miR-200b in Mouse Inner Ear Morphogenesis

(2011) Ronna Hertzano et al.   PLoS Genetics

Ergatis: a web interface and scalable software system for bioinformatics workflows

(2010) J. Orvis et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Gfi1-Cre knock-in mouse line: A tool for inner ear hair cell-specific gene deletion

(2010) Hua Yang et al.   GENESIS

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

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Comprehensive comparative analysis of strand-specific RNA sequencing methods

(2010) Joshua Z Levin et al.   NATURE METHODS

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

Cell-Type Specific Gene Expression Signature in Liver Underlies Response to Interferon Therapy in Chronic Hepatitis C Infection

(2009) Limin Chen et al.   GASTROENTEROLOGY

Cell-type-specific isolation of ribosome-associated mRNA from complex tissues

(2009) E. Sanz et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Application of a Translational Profiling Approach for the Comparative Analysis of CNS Cell Types

(2008) Joseph P. Doyle et al.   CELL

A Translational Profiling Approach for the Molecular Characterization of CNS Cell Types

(2008) Myriam Heiman et al.   CELL

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS