ArticleBMC genomics2014
Integrated transcriptome analysis of mouse spermatogenesis.
Article in BMC genomics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 90 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
90 citing papers in PubMed, 155 citations in OpenAlex.
- Germline organoids develop in vitro from embryonic Taeniopygia guttata (zebra finch) cultures.Scientific reports · 2026Article
- Stable isotope labelling mass spectrometry analysis of isolated mouse sperm.Biology of reproduction · 2026Article
- PAN2 maintains mRNA poly(A) tail homeostasis and regulates translation during spermiogenesis in mice.Nature communications · 2026Article
- Effectiveness of Multivitamins vs Folic Acid on Prevention of Neural Tube Defects in Mouse Genetic Models and Human Organoids.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Effect of Alternative Splicing Euchromatic Histone Lysine Methyltransferase 2 (Animals : an open access journal from MDPI · 2025Article
- A dynamic transcriptional cell atlas of testes development after birth in Hu sheep.BMC biology · 2025Article
- Genome-wide transcriptional silencing and mRNA stabilization allow the coordinated expression of the meiotic program in mice.Nucleic acids research · 2025Article
- Evolutionary innovations in germline biology of placental mammals identified by transcriptomics of first-wave spermatogenesis in opossum.Developmental cell · 2025Article
- Insights from the single-cell level: lineage trajectory and somatic-germline interactions during spermatogenesis in dwarf surfclam Mulinia lateralis.BMC genomics · 2025Article
- A germline PAF1 paralog complex ensures cell type-specific gene expression.Genes & development · 2024Article
- Positive Selection Drives the Evolution of the Structural Maintenance of Chromosomes (SMC) Complexes.Genes · 2024Article
- Uncovering a multitude of stage-specific splice variants and putative protein isoforms generated along mouse spermatogenesis.BMC genomics · 2024Article
- Purification by STA-PUT Technique of Male Germ Cells from Single Mouse and RNA-Extraction for Transcriptomic Analysis.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Genomic analysis reveals a cryptic pangolin species.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- A pumpless monolayer microfluidic device based on mesenchymal stem cell-conditioned medium promotes neonatal mouse in vitro spermatogenesis.Stem cell research & therapy · 2023Article
- An ancient testis-specific IQ motif-containing H gene regulates specific transcript isoform expression during spermatogenesis.Development (Cambridge, England) · 2023Article
- A-MYB and BRDT-dependent RNA Polymerase II pause release orchestrates transcriptional regulation in mammalian meiosis.Nature communications · 2023Article
- Chromatin Remodeling via Retinoic Acid Action during Murine Spermatogonial Development.Life (Basel, Switzerland) · 2023Article
- Ectopic expression of meiotic cohesin generates chromosome instability in cancer cell line.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Mesenchymal stem cells promote spermatogonial stem/progenitor cell pool and spermatogenesis in neonatal mice in vitro.Scientific reports · 2022Article
30 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors at 3 institutions in 1 country.
Funding
Abstract
backgroundDifferentiation of primordial germ cells into mature spermatozoa proceeds through multiple stages, one of the most important of which is meiosis. Meiotic recombination is in turn a key part of meiosis. To achieve the highly specialized and diverse functions necessary for the successful completion of meiosis and the generation of spermatozoa thousands of genes are coordinately regulated through spermatogenesis. A complete and unbiased characterization of the transcriptome dynamics of spermatogenesis is, however, still lacking.
resultsIn order to characterize gene expression during spermatogenesis we sequenced eight mRNA samples from testes of juvenile mice from 6 to 38 days post partum. Using gene expression clustering we defined over 1,000 novel meiotically-expressed genes. We also developed a computational de-convolution approach and used it to estimate cell type-specific gene expression in pre-meiotic, meiotic and post-meiotic cells. In addition, we detected 13,000 novel alternative splicing events around 40% of which preserve an open reading frame, and found experimental support for 159 computational gene predictions. A comparison of RNA polymerase II (Pol II) ChIP-Seq signals with RNA-Seq coverage shows that gene expression correlates well with Pol II signals, both at promoters and along the gene body. However, we observe numerous instances of non-canonical promoter usage, as well as intergenic Pol II peaks that potentially delineate unannotated promoters, enhancers or small RNA clusters.
conclusionsHere we provide a comprehensive analysis of gene expression throughout mouse meiosis and spermatogenesis. Importantly, we find over a thousand of novel meiotic genes and over 5,000 novel potentially coding isoforms. These data should be a valuable resource for future studies of meiosis and spermatogenesis in mammals.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.