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Fig. 1 | BMC Genomics

Fig. 1

From: Regulatory complexity revealed by integrated cytological and RNA-seq analyses of meiotic substages in mouse spermatocytes

Fig. 1

Decomposition of meiotic cells and gene expression. a Experimental design. Germ cells were isolated from whole testes from each of five juvenile male mice at 8, 10, 12, 14, 16 and 18 dpp. Each sample was analyzed for both cytology and gene expression by RNA-seq. PMCA was developed to identify the meiotic substage-specific transcriptomes. b Cytological classification and cellular populations. Isolated germ cells were immunolabeled for stage-specific maker proteins: STRA8, expressed in differentiating spermatogonia; SYCP3, a component of synaptonemal complex shows meiotic substage-specific labeling morphology; phosphorylated histone H2AFX (γH2AFX), marking DSBs throughout early prophase nuclei and restricted to the XY chromosomes during pachynema and diplonema; and histone HISTH1T, expressed in post-mid-pachytene spermatocytes. Nuclei were counter-stained with DAPI. c Meiotic cell composition during the first wave of spermatogenesis. The contribution by specific germ-cell stages for each developmental time point and mouse is shown, with colors representing specific meiotic substages. Abbreviations: Sp’gonia = spermatogonia, Prelep = pre-leptonema, Early Lep = early leptonema, Lep = leptonema, Late Lep = late leptonema, Zyg = zygonema, Early Pach = early pachynema, Late Pach = late pachynema, Dip = diplonema. d Concordance of expression and cytological data. Principal component 1 (PC1) versus principal component 2 (PC2) from independent PCA of cytological and RNA-seq data. Colors correspond to time points and icon shape corresponds to data type as indicated

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