Single-cell RNA-seq uncovers dynamic processes and critical regulators in mouse spermatogenesis

Transcriptome analysis of highly purified mouse spermatogenic cell populations: gene expression signatures switch from meiotic-to postmeiotic-related processes at pachytene stage

(2016) Irene da Cruz et al.   BMC GENOMICS

Retinoid signaling controls spermatogonial differentiation by regulating expression of replication-dependent core histone genes

(2016) Yao Chen et al.   DEVELOPMENT

The ribosome-engaged landscape of alternative splicing

(2016) Robert J Weatheritt et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Mouse Genome Database (MGD)-2017: community knowledge resource for the laboratory mouse

(2016) Judith A. Blake et al.   NUCLEIC ACIDS RESEARCH

Spermatogenesis: The Commitment to Meiosis

(2016) Michael D. Griswold   PHYSIOLOGICAL REVIEWS

MRG15 is required for pre-mRNA splicing and spermatogenesis

(2016) Naoki Iwamori et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A DNA topoisomerase VI-like complex initiates meiotic recombination

(2016) N. Vrielynck et al.   SCIENCE

The TopoVIB-Like protein family is required for meiotic DNA double-strand break formation

(2016) T. Robert et al.   SCIENCE

The ribosome-engaged landscape of alternative splicing

(2016) Robert J Weatheritt et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization

(2015) Guangchuang Yu et al.   BIOINFORMATICS

The Transcriptome and DNA Methylome Landscapes of Human Primordial Germ Cells

(2015) Fan Guo et al.   CELL

DNA Demethylation Dynamics in the Human Prenatal Germline

(2015) Sofia Gkountela et al.   CELL

A Unique Gene Regulatory Network Resets the Human Germline Epigenome for Development

(2015) Walfred W.C. Tang et al.   CELL

Spatial reconstruction of single-cell gene expression data

(2015) Rahul Satija et al.   NATURE BIOTECHNOLOGY

Fourteen babies born after round spermatid injection into human oocytes

(2015) Atsushi Tanaka et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Recombination, Pairing, and Synapsis of Homologs during Meiosis

(2015) Denise Zickler et al.   Cold Spring Harbor Perspectives in Biology

RFX2 Is a Major Transcriptional Regulator of Spermiogenesis

(2015) W. Stephen Kistler et al.   PLoS Genetics

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

High-Resolution Profiling of Novel Transcribed Regions During Rat Spermatogenesis1

(2014) Frédéric Chalmel et al.   BIOLOGY OF REPRODUCTION

Integrated transcriptome analysis of mouse spermatogenesis

(2014) Gennady Margolin et al.   BMC GENOMICS

A Highly Conserved Program of Neuronal Microexons Is Misregulated in Autistic Brains

(2014) Manuel Irimia et al.   CELL

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

(2014) Simone Picelli et al.   Nature Protocols

AnimalTFDB 2.0: a resource for expression, prediction and functional study of animal transcription factors

(2014) Hong-Mei Zhang et al.   NUCLEIC ACIDS RESEARCH

RAN-Binding Protein 9 is Involved in Alternative Splicing and is Critical for Male Germ Cell Development and Male Fertility

(2014) Jianqiang Bao et al.   PLoS Genetics

Initiation of Meiotic Recombination: How and Where? Conservation and Specificities Among Eukaryotes

(2013) Bernard de Massy   Annual Review of Genetics

Turning a Spermatogenic Wave into a Tsunami: Synchronizing Murine Spermatogenesis Using WIN 18,4461

(2013) Cathryn A. Hogarth et al.   BIOLOGY OF REPRODUCTION

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

(2013) Simone Picelli et al.   NATURE METHODS

The splicing landscape is globally reprogrammed during male meiosis

(2013) Ralf Schmid et al.   NUCLEIC ACIDS RESEARCH

Taf7l cooperates with Trf2 to regulate spermiogenesis

(2013) H. Zhou et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Connecting cis-elements and trans-factors with mechanisms of developmental regulation of mRNA translation in meiotic and haploid mammalian spermatogenic cells

(2013) Kenneth C Kleene   REPRODUCTION

Cellular Source and Mechanisms of High Transcriptome Complexity in the Mammalian Testis

(2013) Magali Soumillon et al.   Cell Reports

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

(2012) H. Thorvaldsdottir et al.   BRIEFINGS IN BIOINFORMATICS

GENCODE: The reference human genome annotation for The ENCODE Project

(2012) J. Harrow et al.   GENOME RESEARCH

HnRNPL as a key factor in spermatogenesis: Lesson from functional proteomic studies of azoospermia patients with sertoli cell only syndrome

(2012) Jingping Li et al.   Journal of Proteomics

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

Retinol dehydrogenase 10 is indispensible for spermatogenesis in juvenile males

(2012) M.-H. Tong et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Distinct Properties of the XY Pseudoautosomal Region Crucial for Male Meiosis

(2011) L. Kauppi et al.   SCIENCE

Unique Aspects of Transcription Regulation in Male Germ Cells

(2011) H. White-Cooper et al.   Cold Spring Harbor Perspectives in Biology

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

Surfing the wave, cycle, life history, and genes/proteins expressed by testicular germ cells. Part 1: Background to spermatogenesis, spermatogonia, and spermatocytes

(2009) Louis Hermo et al.   MICROSCOPY RESEARCH AND TECHNIQUE

ToppGene Suite for gene list enrichment analysis and candidate gene prioritization

(2009) J. Chen et al.   NUCLEIC ACIDS RESEARCH

The mouse X chromosome is enriched for multicopy testis genes showing postmeiotic expression

(2008) Jacob L Mueller et al.   NATURE GENETICS

Stage-specific gene expression is a fundamental characteristic of rat spermatogenic cells and Sertoli cells

(2008) D. S. Johnston et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA