Gene Expression
Nebulas
Gene Expression NebulasSummary: The human testis undergoes dramatic developmental and structural changes during puberty, including proliferation and maturation of niche/somatic cells, and the onset of spermatogenesis. Here, we profiled and analyzed single-cell transcriptomes of ~10,000 testicular cells from four boys spanning puberty, and compared to infants and adults. During puberty, undifferentiated spermatogonia first expand and then differentiate, prior to gametogenesis. Notably, we identify a common pre-pubertal progenitor for Leydig and myoid cells, and reveal candidate factors/pathways for pubertal differentiation. Furthermore, pre-pubertal Sertoli cells form two states that differ in mitochondrial/metabolic transcription, which converge to a single mature population during puberty. Roles for testosterone in Sertoli cell maturation, antimicrobial peptide secretion and spermatogonial differentiation are revealed through analyses of testosterone-suppressed transgender female testis and via in vitro seminiferous tubule culturing. Overall, our transcriptional atlas of the developing human testis provides major insights into developmental changes and key factors/pathways that accompany male puberty.
Overall Design: Single-cell RNA-seq of testicular cells from different ages of boys in puberty. Testosterone-suppressed transgender female testis samples are included.
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| Growth Protocol: | - |
| Treatment Protocol: | - |
| Extract Protocol: | Testicular tissues were firstly minced into small pieces mechanically, and subject to trypsin digestion for ~25 min at 37 C. Cell suspension was centrifuged and resuspended in cold PBS buffer with 0.4% of BSA at the concentration of ~1000/ul, which then was loaded onto the 10X Chromium Controller using Chromium Single Cell 3' v2 reagents. |
| Library Construction Protocol: | Sequencing library was prepared following the manufacturer's instructions (10X Genomics), with 13 cycles used for cDNA amplification and 12 cycles for library amplification, which was then sequenced on a 26 X 100 cycle paired-end run via a Illumina 2500 instrument. Each sample was sequenced in one separate sequencing lane. |
| Molecule Type: | poly(A)+ RNA |
| Library Source: | |
| Library Layout: | PAIRED |
| Library Strand: | Forward |
| Platform: | ILLUMINA |
| Instrument Model: | Illumina HiSeq 2500 |
| Strand-Specific: | Specific |
| Data Resource | GEN Sample ID | GEN Dataset ID | Project ID | BioProject ID | Sample ID | Sample Name | BioSample ID | Sample Accession | Experiment Accession | Release Date | Submission Date | Update Date | Species | Race | Ethnicity | Age | Age Unit | Gender | Source Name | Tissue | Cell Type | Cell Subtype | Cell Line | Disease | Disease State | Development Stage | Mutation | Phenotype | Case Detail | Control Detail | Growth Protocol | Treatment Protocol | Extract Protocol | Library Construction Protocol | Molecule Type | Library Layout | Strand-Specific | Library Strand | Spike-In | Strategy | Platform | Instrument Model | Cell Number | Reads Number | Gbases | AvgSpotLen1 | AvgSpotLen2 | Uniq Mapping Rate | Multiple Mapping Rate | Coverage Rate |
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