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run_metadata: 33648

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rowid run.accession experiment.accession sample.accession study.accession bioproject study.title study.alias study.type study.abstract study.attributes study.PMIDs sample.description sample.title sample.alias sample.centername sample.attributes GEOsample.title GEOsample.dataprocessing GEOsample.source GEOsample.treatmentprotocol GEOsample.extractprotocol GEOsample.growthprotocol GEOsample.characteristics GEOsample.accession experiment.title experiment.alias experiment.library_name experiment.design_description experiment.library_construction_protocol experiment.attributes experiment.library_strategy experiment.library_source experiment.library_selection experiment.library_layout experiment.platform experiment.instrument_model experiment.spot_descriptor experiment.study_ref run.title run.attributes run.filename run.semantic_name run.total_bases run.total_spots run.alias run.read_lengths run.base_counts run.r1_length run.r2_length run.r3_length run.r4_length run.Acount run.Ccount run.Gcount run.Tcount run.Ncount run.experiment run.pool_member submission.accession submission.srasource submission.bioprojectsource seqdetective.n_mates seqdetective.mapping_rate.mate1 seqdetective.mapping_rate.mate2 seqdetective.nofeature_rate.mate1 seqdetective.nofeature_rate.mate2 seqdetective.sparsity.mate1 seqdetective.sparsity.mate2 seqdetective.pos_strand_rate.mate1 seqdetective.pos_strand_rate.mate2 seqdetective.readlen.mate1 seqdetective.readlen.mate2 seqdetective.judgement.mate1 seqdetective.judgement.mate2 seqdetective.judgement.reason platform_family instrument_generation read_bias selection_class prep_kit sc_or_bulk tech_class technology tech_variant submission.bioprojectsource.country earliest_date devstage_curation devstage_curation_coarse tissue_curation tissue_curation_coarse
33648 SRR30329369 SRX25789571 SRS22421015 SRP527811 PRJNA1150539 Germ cell progression through zebrafish spermatogenesis declines with age GSE275361 Transcriptome Analysis Vertebrate spermatogonial stem cells maintain sperm production over the lifetime of an animal but fertility declines with age. While morphological studies have informed our understanding of typical spermatogenesis the molecular and cellular mechanisms underlying the maintenance and decline of spermatogenesis are not yet understood. We used single cell RNA sequencing to generate a developmental atlas of the aging zebrafish testis. All testes contained spermatogonia but we observed a progressive decline in spermatogenesis that correlates with age. Testes from some older males only contained spermatogonia and a reduced population of spermatocytes. Spermatogonia in older males are transcriptionally distinct from spermatogonia in testes capable of robust spermatogenesis. Immune cells including macrophages and lymphocytes drastically increase in abundance in testes that cannot complete spermatogenesis. Our developmental atlas reveals the cellular changes as the testis ages and defines a molecular roadmap for the regulation of spermatogenesis. Overall design: scRNA seq of dissected zebrafish testes from 5 12 20 22 and 27 month individuals   pubmed:39470160   mo5 fish1 rep1 GSM8475554   source name:Testis|tissue:Testis|age:5 month|geo loc name:missing|collection date:missing mo5 fish1 rep1 Single cell RNA seq reads were processed with Cellranger from 10X Genomics with the default settings using GRCz11 v4.3.2 reference Lawson et al. 2020 for zebrafish read alignments. Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files Testis   post euthanasia by immersion in ice cold water testes were dissected from fish and immediately placed in a dissociation solution of 440 µL 1X Hank’s Balanced Salt Solution HBSS 50 µL 10% pluronic F 68 and 10 µL 0.26U/mL liberase TM. Tissue was incubated at 37°C for approximately 45 minutes while rotating at 750 rpm in an Eppendorf Thermomixer. The dissociation reaction was stopped by adding 1% bovine serum albumin BSA in 500 µL cold HBSS. The cell suspensions were filtered through a 40 µm cell strainer. Cells were pelleted in a 4°C centrifuge at 200g for 5 minutes washed with 0.5% BSA in 500 µL cold HBSS pelleted again and resuspended in 0.5% BSA in 500 µL cold HBSS. Single cell RNA sequencing libraries were prepared by the University of Utah High Throughput Genomics Shared Resource using the 10X Genomics Next GEM Single Cell 3’ Gene Expression Library prep v3.1 with UDI. Libraries were sequenced with the NovaSeq Reagent Kit v1.5 150x150 bp Sequencing. Libraries were constructed according to the manufacturer's protocol 10X chromium controller Wild type Tübingen zebrafish were used for all experiments. Ages of animals are noted in sample title and age metadata. All zebrafish work was performed at University of Utah’s CBRZ zebrafish facility. This study was conducted under the approval of the Office of Institutional Animal Care and Use Committee IACUC no. 20 07013 of the University of Utah’s animal care and use program. tissue:Testis|age:5 month GSM8475554 GSM8475554: mo5 fish1 rep1; Danio rerio; RNA Seq GSM8475554 r1 GSM8475554 1 post euthanasia by immersion in ice cold water testes were dissected from fish and immediately placed in a dissociation solution of 440 µL 1X Hank's Balanced Salt Solution HBSS 50 µL 10% pluronic F 68 and 10 µL 0.26U/mL liberase TM. Tissue was incubated at 37°C for approximately 45 minutes while rotating at 750 rpm in an Eppendorf Thermomixer. The dissociation reaction was stopped by adding 1% bovine serum albumin BSA in 500 µL cold HBSS. The cell suspensions were filtered through a 40 µm cell strainer. Cells were pelleted in a 4°C centrifuge at 200g for 5 minutes washed with 0.5% BSA in 500 µL cold HBSS pelleted again and resuspended in 0.5% BSA in 500 µL cold HBSS. Single cell RNA sequencing libraries were prepared by the University of Utah High Throughput Genomics Shared Resource using the 10X Genomics Next GEM Single Cell three prime Gene Expression Library prep v3.1 with UDI. Libraries were sequenced with the NovaSeq Reagent Kit v1.5 150x150 bp Sequencing. Libraries were constructed according to the manufacturer's protocol 10X chromium controller   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP527811   loader:fastq load.py 19779X1_220608_A00421_0445_BHVGF7DSX3_S2_L003_R2_001.fastq.gz 19779X1_220608_A00421_0445_BHVGF7DSX3_S2_L003_R1_001.fastq.gz 19779X1_220608_A00421_0445_BHVGF7DSX3_S2_L003_I2_001.fastq.gz 19779X1_220608_A00421_0445_BHVGF7DSX3_S2_L003_I1_001.fastq.gz fastq fastq fastq fastq 76667132916.0 387207742.0 GSM8475554 r1 0:10 1:10 2:28 3:150 A:17411509978;C:12112655410;G:13713621582;T:14843326531;N:47799 10 10 28 150 17411509978 12112655410 13713621582 14843326531 47799 SRX25789571 SRS22421015 SRA1952802 Gagnon, Biology, University of Utah Gagnon, Biology, University of Utah 1 0.92205   0.21455   0.69952   0.51581   150   B   usable mapping rate illumina novaseq_era 3prime cdna_unspecified unknown sc single_cell_droplet 10x   United States 2024-08-21 Adult Adult Gonad Reproductive System