{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_layout = \"PAIRED\", experiment.library_source = \"TRANSCRIPTOMIC SINGLE CELL\" and tissue_curation_coarse = \"Reproductive System\"", "rows": [[33631, "SRR30329352", "SRX25789588", "SRS22421035", "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", null, "pubmed:39470160", null, "mo27 fish4 rep2", "GSM8475571", null, "source name:Testis|tissue:Testis|age:27 month|geo loc name:missing|collection date:missing", "mo27 fish4 rep2", "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", null, "post euthanasia by immersion in ice cold water  testes were dissected from fish and immediately placed in a dissociation solution of 440 \u00b5L 1X Hank\u2019s Balanced Salt Solution HBSS  50 \u00b5L 10% pluronic F 68  and 10 \u00b5L 0.26U/mL liberase TM. Tissue was incubated at 37\u00b0C 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 \u00b5L cold HBSS. The cell suspensions were filtered through a 40 \u00b5m cell strainer. Cells were pelleted in a 4\u00b0C centrifuge at 200g for 5 minutes  washed with 0.5% BSA in 500 \u00b5L cold HBSS  pelleted again and resuspended in 0.5% BSA in 500 \u00b5L 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\u2019 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 T\u00fcbingen 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\u2019s 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\u2019s animal care and use program.", "tissue:Testis|age:27 month", "GSM8475571", "GSM8475571: mo27 fish4 rep2; Danio rerio; RNA Seq", "GSM8475571 r1", "GSM8475571", "1", "post euthanasia by immersion in ice cold water  testes were dissected from fish and immediately placed in a dissociation solution of 440 \u00b5L 1X Hank's Balanced Salt Solution HBSS  50 \u00b5L 10% pluronic F 68  and 10 \u00b5L 0.26U/mL liberase TM. Tissue was incubated at 37\u00b0C 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 \u00b5L cold HBSS. The cell suspensions were filtered through a 40 \u00b5m cell strainer. Cells were pelleted in a 4\u00b0C centrifuge at 200g for 5 minutes  washed with 0.5% BSA in 500 \u00b5L cold HBSS  pelleted again and resuspended in 0.5% BSA in 500 \u00b5L 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. 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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", null, "pubmed:39470160", null, "mo27 fish4 rep1", "GSM8475570", null, "source name:Testis|tissue:Testis|age:27 month|geo loc name:missing|collection date:missing", "mo27 fish4 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", null, "post euthanasia by immersion in ice cold water  testes were dissected from fish and immediately placed in a dissociation solution of 440 \u00b5L 1X Hank\u2019s Balanced Salt Solution HBSS  50 \u00b5L 10% pluronic F 68  and 10 \u00b5L 0.26U/mL liberase TM. Tissue was incubated at 37\u00b0C 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 \u00b5L cold HBSS. The cell suspensions were filtered through a 40 \u00b5m cell strainer. Cells were pelleted in a 4\u00b0C centrifuge at 200g for 5 minutes  washed with 0.5% BSA in 500 \u00b5L cold HBSS  pelleted again and resuspended in 0.5% BSA in 500 \u00b5L 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\u2019 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 T\u00fcbingen 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\u2019s 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\u2019s animal care and use program.", "tissue:Testis|age:27 month", "GSM8475570", "GSM8475570: mo27 fish4 rep1; Danio rerio; RNA Seq", "GSM8475570 r1", "GSM8475570", "1", "post euthanasia by immersion in ice cold water  testes were dissected from fish and immediately placed in a dissociation solution of 440 \u00b5L 1X Hank's Balanced Salt Solution HBSS  50 \u00b5L 10% pluronic F 68  and 10 \u00b5L 0.26U/mL liberase TM. Tissue was incubated at 37\u00b0C 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 \u00b5L cold HBSS. The cell suspensions were filtered through a 40 \u00b5m cell strainer. Cells were pelleted in a 4\u00b0C centrifuge at 200g for 5 minutes  washed with 0.5% BSA in 500 \u00b5L cold HBSS  pelleted again and resuspended in 0.5% BSA in 500 \u00b5L 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", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP527811", null, "loader:fastq load.py", "23822X3_20240226_LH00227_0052_A22HJWLLT3_S7_L003_I1_001.fastq.gz 23822X3_20240226_LH00227_0052_A22HJWLLT3_S7_L003_I2_001.fastq.gz 23822X3_20240226_LH00227_0052_A22HJWLLT3_S7_L003_R1_001.fastq.gz 23822X3_20240226_LH00227_0052_A22HJWLLT3_S7_L003_R2_001.fastq.gz", "fastq fastq fastq fastq", 68435798090.0, 360188411.0, "GSM8475570 r1", "0:6 1:6 2:28 3:150", "A:15473213482;C:11152077954;G:12263658125;T:15136431378;N:2880711", 6, 6, 28, 150, 15473213482, 11152077954, 12263658125, 15136431378, 2880711, "SRX25789587", "SRS22421034", "SRA1952802", "Gagnon, Biology, University of Utah", "Gagnon, Biology, University of Utah", 1, 0.85213, null, 0.30845, null, 0.7543, null, 0.68115, null, 150, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-08-21", "Adult", "Adult", "Gonad", "Reproductive System"], [33633, "SRR30329354", "SRX25789586", "SRS22421033", "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", null, "pubmed:39470160", null, "mo27 fish3 rep2", "GSM8475569", null, "source name:Testis|tissue:Testis|age:27 month|geo loc name:missing|collection date:missing", "mo27 fish3 rep2", "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", null, "post euthanasia by immersion in ice cold water  testes were dissected from fish and immediately placed in a dissociation solution of 440 \u00b5L 1X Hank\u2019s Balanced Salt Solution HBSS  50 \u00b5L 10% pluronic F 68  and 10 \u00b5L 0.26U/mL liberase TM. Tissue was incubated at 37\u00b0C 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 \u00b5L cold HBSS. The cell suspensions were filtered through a 40 \u00b5m cell strainer. Cells were pelleted in a 4\u00b0C centrifuge at 200g for 5 minutes  washed with 0.5% BSA in 500 \u00b5L cold HBSS  pelleted again and resuspended in 0.5% BSA in 500 \u00b5L 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\u2019 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 T\u00fcbingen 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\u2019s 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\u2019s animal care and use program.", "tissue:Testis|age:27 month", "GSM8475569", "GSM8475569: mo27 fish3 rep2; Danio rerio; RNA Seq", "GSM8475569 r1", "GSM8475569", "1", "post euthanasia by immersion in ice cold water  testes were dissected from fish and immediately placed in a dissociation solution of 440 \u00b5L 1X Hank's Balanced Salt Solution HBSS  50 \u00b5L 10% pluronic F 68  and 10 \u00b5L 0.26U/mL liberase TM. Tissue was incubated at 37\u00b0C 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 \u00b5L cold HBSS. The cell suspensions were filtered through a 40 \u00b5m cell strainer. Cells were pelleted in a 4\u00b0C centrifuge at 200g for 5 minutes  washed with 0.5% BSA in 500 \u00b5L cold HBSS  pelleted again and resuspended in 0.5% BSA in 500 \u00b5L 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. 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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", null, "pubmed:39470160", null, "mo27 fish3 rep1", "GSM8475568", null, "source name:Testis|tissue:Testis|age:27 month|geo loc name:missing|collection date:missing", "mo27 fish3 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", null, "post euthanasia by immersion in ice cold water  testes were dissected from fish and immediately placed in a dissociation solution of 440 \u00b5L 1X Hank\u2019s Balanced Salt Solution HBSS  50 \u00b5L 10% pluronic F 68  and 10 \u00b5L 0.26U/mL liberase TM. Tissue was incubated at 37\u00b0C 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 \u00b5L cold HBSS. The cell suspensions were filtered through a 40 \u00b5m cell strainer. Cells were pelleted in a 4\u00b0C centrifuge at 200g for 5 minutes  washed with 0.5% BSA in 500 \u00b5L cold HBSS  pelleted again and resuspended in 0.5% BSA in 500 \u00b5L 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\u2019 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 T\u00fcbingen 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\u2019s 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\u2019s animal care and use program.", "tissue:Testis|age:27 month", "GSM8475568", "GSM8475568: mo27 fish3 rep1; Danio rerio; RNA Seq", "GSM8475568 r1", "GSM8475568", "1", "post euthanasia by immersion in ice cold water  testes were dissected from fish and immediately placed in a dissociation solution of 440 \u00b5L 1X Hank's Balanced Salt Solution HBSS  50 \u00b5L 10% pluronic F 68  and 10 \u00b5L 0.26U/mL liberase TM. Tissue was incubated at 37\u00b0C 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 \u00b5L cold HBSS. The cell suspensions were filtered through a 40 \u00b5m cell strainer. Cells were pelleted in a 4\u00b0C centrifuge at 200g for 5 minutes  washed with 0.5% BSA in 500 \u00b5L cold HBSS  pelleted again and resuspended in 0.5% BSA in 500 \u00b5L 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", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP527811", null, "loader:fastq load.py", "23822X1_20240226_LH00227_0052_A22HJWLLT3_S5_L003_R2_001.fastq.gz 23822X1_20240226_LH00227_0052_A22HJWLLT3_S5_L003_R1_001.fastq.gz 23822X1_20240226_LH00227_0052_A22HJWLLT3_S5_L003_I2_001.fastq.gz 23822X1_20240226_LH00227_0052_A22HJWLLT3_S5_L003_I1_001.fastq.gz", "fastq fastq fastq fastq", 50530978990.0, 265952521.0, "GSM8475568 r1", "0:6 1:6 2:28 3:150", "A:10826041411;C:8852230501;G:9916508585;T:10296022501;N:2075152", 6, 6, 28, 150, 10826041411, 8852230501, 9916508585, 10296022501, 2075152, "SRX25789585", "SRS22421029", "SRA1952802", "Gagnon, Biology, University of Utah", "Gagnon, Biology, University of Utah", 1, 0.89468, null, 0.23873, null, 0.76688, null, 0.66783, null, 150, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-08-21", "Adult", "Adult", "Gonad", "Reproductive System"], [33635, "SRR30329355", "SRX25789584", "SRS22421032", "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", null, "pubmed:39470160", null, "mo27 fish2 rep1", "GSM8475567", null, "source name:Testis|tissue:Testis|age:27 month|geo loc name:missing|collection date:missing", "mo27 fish2 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", null, "post euthanasia by immersion in ice cold water  testes were dissected from fish and immediately placed in a dissociation solution of 440 \u00b5L 1X Hank\u2019s Balanced Salt Solution HBSS  50 \u00b5L 10% pluronic F 68  and 10 \u00b5L 0.26U/mL liberase TM. Tissue was incubated at 37\u00b0C 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 \u00b5L cold HBSS. The cell suspensions were filtered through a 40 \u00b5m cell strainer. Cells were pelleted in a 4\u00b0C centrifuge at 200g for 5 minutes  washed with 0.5% BSA in 500 \u00b5L cold HBSS  pelleted again and resuspended in 0.5% BSA in 500 \u00b5L 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\u2019 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 T\u00fcbingen 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\u2019s 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\u2019s animal care and use program.", "tissue:Testis|age:27 month", "GSM8475567", "GSM8475567: mo27 fish2 rep1; Danio rerio; RNA Seq", "GSM8475567 r1", "GSM8475567", "1", "post euthanasia by immersion in ice cold water  testes were dissected from fish and immediately placed in a dissociation solution of 440 \u00b5L 1X Hank's Balanced Salt Solution HBSS  50 \u00b5L 10% pluronic F 68  and 10 \u00b5L 0.26U/mL liberase TM. Tissue was incubated at 37\u00b0C 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 \u00b5L cold HBSS. The cell suspensions were filtered through a 40 \u00b5m cell strainer. Cells were pelleted in a 4\u00b0C centrifuge at 200g for 5 minutes  washed with 0.5% BSA in 500 \u00b5L cold HBSS  pelleted again and resuspended in 0.5% BSA in 500 \u00b5L 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", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP527811", null, "loader:fastq load.py", "19226X4_211001_A00421_0374_BHMGTFDSX2_S4_L004_I1_001.fastq.gz 19226X4_211001_A00421_0374_BHMGTFDSX2_S4_L004_I2_001.fastq.gz 19226X4_211001_A00421_0374_BHMGTFDSX2_S4_L004_R1_001.fastq.gz 19226X4_211001_A00421_0374_BHMGTFDSX2_S4_L004_R2_001.fastq.gz", "fastq fastq fastq fastq", 61159613328.0, 308886936.0, "GSM8475567 r1", "0:10 1:10 2:28 3:150", "A:13534358992;C:9743134047;G:11041233192;T:12013610107;N:704062", 10, 10, 28, 150, 13534358992, 9743134047, 11041233192, 12013610107, 704062, "SRX25789584", "SRS22421032", "SRA1952802", "Gagnon, Biology, University of Utah", "Gagnon, Biology, University of Utah", 1, 0.89529, null, 0.10879, null, 0.74671, null, 0.53003, null, 150, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-08-21", "Adult", "Adult", "Gonad", "Reproductive System"], [33636, "SRR30329356", "SRX25789583", "SRS22421031", "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", null, "pubmed:39470160", null, "mo27 fish1 rep1", "GSM8475566", null, "source name:Testis|tissue:Testis|age:27 month|geo loc name:missing|collection date:missing", "mo27 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", null, "post euthanasia by immersion in ice cold water  testes were dissected from fish and immediately placed in a dissociation solution of 440 \u00b5L 1X Hank\u2019s Balanced Salt Solution HBSS  50 \u00b5L 10% pluronic F 68  and 10 \u00b5L 0.26U/mL liberase TM. Tissue was incubated at 37\u00b0C 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 \u00b5L cold HBSS. The cell suspensions were filtered through a 40 \u00b5m cell strainer. Cells were pelleted in a 4\u00b0C centrifuge at 200g for 5 minutes  washed with 0.5% BSA in 500 \u00b5L cold HBSS  pelleted again and resuspended in 0.5% BSA in 500 \u00b5L 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\u2019 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 T\u00fcbingen 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\u2019s 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\u2019s animal care and use program.", "tissue:Testis|age:27 month", "GSM8475566", "GSM8475566: mo27 fish1 rep1; Danio rerio; RNA Seq", "GSM8475566 r1", "GSM8475566", "1", "post euthanasia by immersion in ice cold water  testes were dissected from fish and immediately placed in a dissociation solution of 440 \u00b5L 1X Hank's Balanced Salt Solution HBSS  50 \u00b5L 10% pluronic F 68  and 10 \u00b5L 0.26U/mL liberase TM. Tissue was incubated at 37\u00b0C 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 \u00b5L cold HBSS. The cell suspensions were filtered through a 40 \u00b5m cell strainer. Cells were pelleted in a 4\u00b0C centrifuge at 200g for 5 minutes  washed with 0.5% BSA in 500 \u00b5L cold HBSS  pelleted again and resuspended in 0.5% BSA in 500 \u00b5L 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", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP527811", null, "loader:fastq load.py", "19226X3_211001_A00421_0374_BHMGTFDSX2_S3_L004_R2_001.fastq.gz 19226X3_211001_A00421_0374_BHMGTFDSX2_S3_L004_R1_001.fastq.gz 19226X3_211001_A00421_0374_BHMGTFDSX2_S3_L004_I2_001.fastq.gz 19226X3_211001_A00421_0374_BHMGTFDSX2_S3_L004_I1_001.fastq.gz", "fastq fastq fastq fastq", 81122109948.0, 409707626.0, "GSM8475566 r1", "0:10 1:10 2:28 3:150", "A:18515219377;C:12708263135;G:14580444363;T:15651262388;N:954637", 10, 10, 28, 150, 18515219377, 12708263135, 14580444363, 15651262388, 954637, "SRX25789583", "SRS22421031", "SRA1952802", "Gagnon, Biology, University of Utah", "Gagnon, Biology, University of Utah", 1, 0.88948, null, 0.1044, null, 0.77571, null, 0.55175, null, 150, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-08-21", "Adult", "Adult", "Gonad", "Reproductive System"], [33637, "SRR30329358", "SRX25789582", "SRS22421030", "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", null, "pubmed:39470160", null, "mo22 fish1 rep2", "GSM8475565", null, "source name:Testis|tissue:Testis|age:22 month|geo loc name:missing|collection date:missing", "mo22 fish1 rep2", "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", null, "post euthanasia by immersion in ice cold water  testes were dissected from fish and immediately placed in a dissociation solution of 440 \u00b5L 1X Hank\u2019s Balanced Salt Solution HBSS  50 \u00b5L 10% pluronic F 68  and 10 \u00b5L 0.26U/mL liberase TM. Tissue was incubated at 37\u00b0C 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 \u00b5L cold HBSS. The cell suspensions were filtered through a 40 \u00b5m cell strainer. Cells were pelleted in a 4\u00b0C centrifuge at 200g for 5 minutes  washed with 0.5% BSA in 500 \u00b5L cold HBSS  pelleted again and resuspended in 0.5% BSA in 500 \u00b5L 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\u2019 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 T\u00fcbingen 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\u2019s 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\u2019s animal care and use program.", "tissue:Testis|age:22 month", "GSM8475565", "GSM8475565: mo22 fish1 rep2; Danio rerio; RNA Seq", "GSM8475565 r1", "GSM8475565", "1", "post euthanasia by immersion in ice cold water  testes were dissected from fish and immediately placed in a dissociation solution of 440 \u00b5L 1X Hank's Balanced Salt Solution HBSS  50 \u00b5L 10% pluronic F 68  and 10 \u00b5L 0.26U/mL liberase TM. Tissue was incubated at 37\u00b0C 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 \u00b5L cold HBSS. The cell suspensions were filtered through a 40 \u00b5m cell strainer. Cells were pelleted in a 4\u00b0C centrifuge at 200g for 5 minutes  washed with 0.5% BSA in 500 \u00b5L cold HBSS  pelleted again and resuspended in 0.5% BSA in 500 \u00b5L 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", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP527811", null, "loader:fastq load.py", "18827X3_210414_A00421_0315_BH225KDSX2_S3_L004_I1_001.fastq.gz 18827X3_210414_A00421_0315_BH225KDSX2_S3_L004_I2_001.fastq.gz 18827X3_210414_A00421_0315_BH225KDSX2_S3_L004_R1_001.fastq.gz 18827X3_210414_A00421_0315_BH225KDSX2_S3_L004_R2_001.fastq.gz", "fastq fastq fastq fastq", 71619246666.0, 361713367.0, "GSM8475565 r1", "0:10 1:10 2:28 3:150", "A:16269086558;C:11392726801;G:12707460817;T:13887610399;N:120475", 10, 10, 28, 150, 16269086558, 11392726801, 12707460817, 13887610399, 120475, "SRX25789582", "SRS22421030", "SRA1952802", "Gagnon, Biology, University of Utah", "Gagnon, Biology, University of Utah", 1, 0.91983, null, 0.15397, null, 0.72354, null, 0.51746, null, 150, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-08-21", "Adult", "Adult", "Gonad", "Reproductive System"], [33638, "SRR30329359", "SRX25789581", "SRS22421026", "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", null, "pubmed:39470160", null, "mo22 fish1 rep1", "GSM8475564", null, "source name:Testis|tissue:Testis|age:22 month|geo loc name:missing|collection date:missing", "mo22 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", null, "post euthanasia by immersion in ice cold water  testes were dissected from fish and immediately placed in a dissociation solution of 440 \u00b5L 1X Hank\u2019s Balanced Salt Solution HBSS  50 \u00b5L 10% pluronic F 68  and 10 \u00b5L 0.26U/mL liberase TM. Tissue was incubated at 37\u00b0C 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 \u00b5L cold HBSS. The cell suspensions were filtered through a 40 \u00b5m cell strainer. Cells were pelleted in a 4\u00b0C centrifuge at 200g for 5 minutes  washed with 0.5% BSA in 500 \u00b5L cold HBSS  pelleted again and resuspended in 0.5% BSA in 500 \u00b5L 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\u2019 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 T\u00fcbingen 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\u2019s 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\u2019s animal care and use program.", "tissue:Testis|age:22 month", "GSM8475564", "GSM8475564: mo22 fish1 rep1; Danio rerio; RNA Seq", "GSM8475564 r1", "GSM8475564", "1", "post euthanasia by immersion in ice cold water  testes were dissected from fish and immediately placed in a dissociation solution of 440 \u00b5L 1X Hank's Balanced Salt Solution HBSS  50 \u00b5L 10% pluronic F 68  and 10 \u00b5L 0.26U/mL liberase TM. Tissue was incubated at 37\u00b0C 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 \u00b5L cold HBSS. The cell suspensions were filtered through a 40 \u00b5m cell strainer. Cells were pelleted in a 4\u00b0C centrifuge at 200g for 5 minutes  washed with 0.5% BSA in 500 \u00b5L cold HBSS  pelleted again and resuspended in 0.5% BSA in 500 \u00b5L 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", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP527811", null, "loader:fastq load.py", "18827X1_210414_A00421_0315_BH225KDSX2_S1_L004_R2_001.fastq.gz 18827X1_210414_A00421_0315_BH225KDSX2_S1_L004_R1_001.fastq.gz 18827X1_210414_A00421_0315_BH225KDSX2_S1_L004_I2_001.fastq.gz 18827X1_210414_A00421_0315_BH225KDSX2_S1_L004_I1_001.fastq.gz", "fastq fastq fastq fastq", 75353487858.0, 380573171.0, "GSM8475564 r1", "0:10 1:10 2:28 3:150", "A:17277856526;C:11721380902;G:13064732269;T:15021876455;N:129498", 10, 10, 28, 150, 17277856526, 11721380902, 13064732269, 15021876455, 129498, "SRX25789581", "SRS22421026", "SRA1952802", "Gagnon, Biology, University of Utah", "Gagnon, Biology, University of Utah", 1, 0.91525, null, 0.16024, null, 0.71526, null, 0.51211, null, 150, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-08-21", "Adult", "Adult", "Gonad", "Reproductive System"], [33639, "SRR30329362", "SRX25789580", "SRS22421025", "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", null, "pubmed:39470160", null, "mo20 fish1 rep2", "GSM8475563", null, "source name:Testis|tissue:Testis|age:20 month|geo loc name:missing|collection date:missing", "mo20 fish1 rep2", "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", null, "post euthanasia by immersion in ice cold water  testes were dissected from fish and immediately placed in a dissociation solution of 440 \u00b5L 1X Hank\u2019s Balanced Salt Solution HBSS  50 \u00b5L 10% pluronic F 68  and 10 \u00b5L 0.26U/mL liberase TM. Tissue was incubated at 37\u00b0C 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 \u00b5L cold HBSS. The cell suspensions were filtered through a 40 \u00b5m cell strainer. Cells were pelleted in a 4\u00b0C centrifuge at 200g for 5 minutes  washed with 0.5% BSA in 500 \u00b5L cold HBSS  pelleted again and resuspended in 0.5% BSA in 500 \u00b5L 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\u2019 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 T\u00fcbingen 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\u2019s 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\u2019s animal care and use program.", "tissue:Testis|age:20 month", "GSM8475563", "GSM8475563: mo20 fish1 rep2; Danio rerio; RNA Seq", "GSM8475563 r1", "GSM8475563", "1", "post euthanasia by immersion in ice cold water  testes were dissected from fish and immediately placed in a dissociation solution of 440 \u00b5L 1X Hank's Balanced Salt Solution HBSS  50 \u00b5L 10% pluronic F 68  and 10 \u00b5L 0.26U/mL liberase TM. Tissue was incubated at 37\u00b0C 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 \u00b5L cold HBSS. The cell suspensions were filtered through a 40 \u00b5m cell strainer. Cells were pelleted in a 4\u00b0C centrifuge at 200g for 5 minutes  washed with 0.5% BSA in 500 \u00b5L cold HBSS  pelleted again and resuspended in 0.5% BSA in 500 \u00b5L 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", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP527811", null, "loader:fastq load.py", "18827X4_210414_A00421_0315_BH225KDSX2_S4_L004_I1_001.fastq.gz 18827X4_210414_A00421_0315_BH225KDSX2_S4_L004_I2_001.fastq.gz 18827X4_210414_A00421_0315_BH225KDSX2_S4_L004_R1_001.fastq.gz 18827X4_210414_A00421_0315_BH225KDSX2_S4_L004_R2_001.fastq.gz", "fastq fastq fastq fastq", 66564197766.0, 336182817.0, "GSM8475563 r1", "0:10 1:10 2:28 3:150", "A:15385982034;C:10396224096;G:11708098438;T:12937004162;N:113820", 10, 10, 28, 150, 15385982034, 10396224096, 11708098438, 12937004162, 113820, "SRX25789580", "SRS22421025", "SRA1952802", "Gagnon, Biology, University of Utah", "Gagnon, Biology, University of Utah", 1, 0.90394, null, 0.15438, null, 0.73888, null, 0.52949, null, 150, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-08-21", "Adult", "Adult", "Gonad", "Reproductive System"], [33640, "SRR30329360", "SRX25789579", "SRS22421023", "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", null, "pubmed:39470160", null, "mo20 fish1 rep1", "GSM8475562", null, "source name:Testis|tissue:Testis|age:20 month|geo loc name:missing|collection date:missing", "mo20 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", null, "post euthanasia by immersion in ice cold water  testes were dissected from fish and immediately placed in a dissociation solution of 440 \u00b5L 1X Hank\u2019s Balanced Salt Solution HBSS  50 \u00b5L 10% pluronic F 68  and 10 \u00b5L 0.26U/mL liberase TM. Tissue was incubated at 37\u00b0C 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 \u00b5L cold HBSS. The cell suspensions were filtered through a 40 \u00b5m cell strainer. Cells were pelleted in a 4\u00b0C centrifuge at 200g for 5 minutes  washed with 0.5% BSA in 500 \u00b5L cold HBSS  pelleted again and resuspended in 0.5% BSA in 500 \u00b5L 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\u2019 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 T\u00fcbingen 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\u2019s 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\u2019s animal care and use program.", "tissue:Testis|age:20 month", "GSM8475562", "GSM8475562: mo20 fish1 rep1; Danio rerio; RNA Seq", "GSM8475562 r1", "GSM8475562", "1", "post euthanasia by immersion in ice cold water  testes were dissected from fish and immediately placed in a dissociation solution of 440 \u00b5L 1X Hank's Balanced Salt Solution HBSS  50 \u00b5L 10% pluronic F 68  and 10 \u00b5L 0.26U/mL liberase TM. Tissue was incubated at 37\u00b0C 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 \u00b5L cold HBSS. The cell suspensions were filtered through a 40 \u00b5m cell strainer. Cells were pelleted in a 4\u00b0C centrifuge at 200g for 5 minutes  washed with 0.5% BSA in 500 \u00b5L cold HBSS  pelleted again and resuspended in 0.5% BSA in 500 \u00b5L 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", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP527811", null, "loader:fastq load.py", "18827X2_210414_A00421_0315_BH225KDSX2_S2_L004_R2_001.fastq.gz 18827X2_210414_A00421_0315_BH225KDSX2_S2_L004_R1_001.fastq.gz 18827X2_210414_A00421_0315_BH225KDSX2_S2_L004_I2_001.fastq.gz 18827X2_210414_A00421_0315_BH225KDSX2_S2_L004_I1_001.fastq.gz", "fastq fastq fastq fastq", 76196757582.0, 384832109.0, "GSM8475562 r1", "0:10 1:10 2:28 3:150", "A:17603147649;C:11925253793;G:13442889985;T:14753395348;N:129575", 10, 10, 28, 150, 17603147649, 11925253793, 13442889985, 14753395348, 129575, "SRX25789579", "SRS22421023", "SRA1952802", "Gagnon, Biology, University of Utah", "Gagnon, Biology, University of Utah", 1, 0.90462, null, 0.14351, null, 0.74513, null, 0.52838, null, 150, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-08-21", "Adult", "Adult", "Gonad", "Reproductive System"], [33641, "SRR30329361", "SRX25789578", "SRS22421027", "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", null, "pubmed:39470160", null, "mo12 fish2 rep1", "GSM8475561", null, "source name:Testis|tissue:Testis|age:12 month|geo loc name:missing|collection date:missing", "mo12 fish2 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", null, "post euthanasia by immersion in ice cold water  testes were dissected from fish and immediately placed in a dissociation solution of 440 \u00b5L 1X Hank\u2019s Balanced Salt Solution HBSS  50 \u00b5L 10% pluronic F 68  and 10 \u00b5L 0.26U/mL liberase TM. Tissue was incubated at 37\u00b0C 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 \u00b5L cold HBSS. The cell suspensions were filtered through a 40 \u00b5m cell strainer. Cells were pelleted in a 4\u00b0C centrifuge at 200g for 5 minutes  washed with 0.5% BSA in 500 \u00b5L cold HBSS  pelleted again and resuspended in 0.5% BSA in 500 \u00b5L 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\u2019 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 T\u00fcbingen 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\u2019s 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\u2019s animal care and use program.", "tissue:Testis|age:12 month", "GSM8475561", "GSM8475561: mo12 fish2 rep1; Danio rerio; RNA Seq", "GSM8475561 r1", "GSM8475561", "1", "post euthanasia by immersion in ice cold water  testes were dissected from fish and immediately placed in a dissociation solution of 440 \u00b5L 1X Hank's Balanced Salt Solution HBSS  50 \u00b5L 10% pluronic F 68  and 10 \u00b5L 0.26U/mL liberase TM. Tissue was incubated at 37\u00b0C 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 \u00b5L cold HBSS. The cell suspensions were filtered through a 40 \u00b5m cell strainer. Cells were pelleted in a 4\u00b0C centrifuge at 200g for 5 minutes  washed with 0.5% BSA in 500 \u00b5L cold HBSS  pelleted again and resuspended in 0.5% BSA in 500 \u00b5L 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", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP527811", null, "loader:fastq load.py", "15756X4_S4_L001_I1_001.fastq.gz 15756X4_S4_L001_R1_001.fastq.gz 15756X4_S4_L001_R2_001.fastq.gz", "fastq fastq fastq", 29487024682.0, 220052423.0, "GSM8475561 r1", "0:8 1:26 2:100", "A:6603266449;C:4452149795;G:4932656681;T:6015543518;N:1625857", 8, 26, 100, null, 6603266449, 4452149795, 4932656681, 6015543518, 1625857, "SRX25789578", "SRS22421027", "SRA1952802", "Gagnon, Biology, University of Utah", "Gagnon, Biology, University of Utah", 1, 0.923, null, 0.08981, null, 0.74446, null, 0.49211, null, 100, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-08-21", "Adult", "Adult", "Gonad", "Reproductive System"], [33642, "SRR30329363", "SRX25789577", "SRS22421019", "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", null, "pubmed:39470160", null, "mo12 fish1 rep1", "GSM8475560", null, "source name:Testis|tissue:Testis|age:12 month|geo loc name:missing|collection date:missing", "mo12 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", null, "post euthanasia by immersion in ice cold water  testes were dissected from fish and immediately placed in a dissociation solution of 440 \u00b5L 1X Hank\u2019s Balanced Salt Solution HBSS  50 \u00b5L 10% pluronic F 68  and 10 \u00b5L 0.26U/mL liberase TM. Tissue was incubated at 37\u00b0C 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 \u00b5L cold HBSS. The cell suspensions were filtered through a 40 \u00b5m cell strainer. Cells were pelleted in a 4\u00b0C centrifuge at 200g for 5 minutes  washed with 0.5% BSA in 500 \u00b5L cold HBSS  pelleted again and resuspended in 0.5% BSA in 500 \u00b5L 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\u2019 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 T\u00fcbingen 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\u2019s 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\u2019s animal care and use program.", "tissue:Testis|age:12 month", "GSM8475560", "GSM8475560: mo12 fish1 rep1; Danio rerio; RNA Seq", "GSM8475560 r1", "GSM8475560", "1", "post euthanasia by immersion in ice cold water  testes were dissected from fish and immediately placed in a dissociation solution of 440 \u00b5L 1X Hank's Balanced Salt Solution HBSS  50 \u00b5L 10% pluronic F 68  and 10 \u00b5L 0.26U/mL liberase TM. Tissue was incubated at 37\u00b0C 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 \u00b5L cold HBSS. The cell suspensions were filtered through a 40 \u00b5m cell strainer. Cells were pelleted in a 4\u00b0C centrifuge at 200g for 5 minutes  washed with 0.5% BSA in 500 \u00b5L cold HBSS  pelleted again and resuspended in 0.5% BSA in 500 \u00b5L 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", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP527811", null, "loader:fastq load.py", "15756X3_S3_L001_R2_001.fastq.gz 15756X3_S3_L001_R1_001.fastq.gz 15756X3_S3_L001_I1_001.fastq.gz", "fastq fastq fastq", 24877403778.0, 185652267.0, "GSM8475560 r1", "0:8 1:26 2:100", "A:5596266137;C:3743379083;G:4132198708;T:5092012085;N:1370687", 8, 26, 100, null, 5596266137, 3743379083, 4132198708, 5092012085, 1370687, "SRX25789577", "SRS22421019", "SRA1952802", "Gagnon, Biology, University of Utah", "Gagnon, Biology, University of Utah", 1, 0.92275, null, 0.09038, null, 0.74572, null, 0.48557, null, 100, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-08-21", "Adult", "Adult", "Gonad", "Reproductive System"], [33643, "SRR30329364", "SRX25789576", "SRS22421017", "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", null, "pubmed:39470160", null, "mo5 fish2 rep3", "GSM8475559", null, "source name:Testis|tissue:Testis|age:5 month|geo loc name:missing|collection date:missing", "mo5 fish2 rep3", "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", null, "post euthanasia by immersion in ice cold water  testes were dissected from fish and immediately placed in a dissociation solution of 440 \u00b5L 1X Hank\u2019s Balanced Salt Solution HBSS  50 \u00b5L 10% pluronic F 68  and 10 \u00b5L 0.26U/mL liberase TM. Tissue was incubated at 37\u00b0C 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 \u00b5L cold HBSS. The cell suspensions were filtered through a 40 \u00b5m cell strainer. Cells were pelleted in a 4\u00b0C centrifuge at 200g for 5 minutes  washed with 0.5% BSA in 500 \u00b5L cold HBSS  pelleted again and resuspended in 0.5% BSA in 500 \u00b5L 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\u2019 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 T\u00fcbingen 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\u2019s 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\u2019s animal care and use program.", "tissue:Testis|age:5 month", "GSM8475559", "GSM8475559: mo5 fish2 rep3; Danio rerio; RNA Seq", "GSM8475559 r1", "GSM8475559", "1", "post euthanasia by immersion in ice cold water  testes were dissected from fish and immediately placed in a dissociation solution of 440 \u00b5L 1X Hank's Balanced Salt Solution HBSS  50 \u00b5L 10% pluronic F 68  and 10 \u00b5L 0.26U/mL liberase TM. Tissue was incubated at 37\u00b0C 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 \u00b5L cold HBSS. The cell suspensions were filtered through a 40 \u00b5m cell strainer. Cells were pelleted in a 4\u00b0C centrifuge at 200g for 5 minutes  washed with 0.5% BSA in 500 \u00b5L cold HBSS  pelleted again and resuspended in 0.5% BSA in 500 \u00b5L 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", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP527811", null, "loader:fastq load.py", "19779X6_220608_A00421_0445_BHVGF7DSX3_S7_L003_R2_001.fastq.gz 19779X6_220608_A00421_0445_BHVGF7DSX3_S7_L003_R1_001.fastq.gz 19779X6_220608_A00421_0445_BHVGF7DSX3_S7_L003_I2_001.fastq.gz 19779X6_220608_A00421_0445_BHVGF7DSX3_S7_L003_I1_001.fastq.gz", "fastq fastq fastq fastq", 68519376288.0, 346057456.0, "GSM8475559 r1", "0:10 1:10 2:28 3:150", "A:15372037903;C:10806459023;G:12028186552;T:13701892692;N:42230", 10, 10, 28, 150, 15372037903, 10806459023, 12028186552, 13701892692, 42230, "SRX25789576", "SRS22421017", "SRA1952802", "Gagnon, Biology, University of Utah", "Gagnon, Biology, University of Utah", 1, 0.93821, null, 0.18284, null, 0.70709, null, 0.49769, null, 150, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-08-21", "Adult", "Adult", "Gonad", "Reproductive System"], [33644, "SRR30329367", "SRX25789575", "SRS22421028", "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", null, "pubmed:39470160", null, "mo5 fish2 rep2", "GSM8475558", null, "source name:Testis|tissue:Testis|age:5 month|geo loc name:missing|collection date:missing", "mo5 fish2 rep2", "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", null, "post euthanasia by immersion in ice cold water  testes were dissected from fish and immediately placed in a dissociation solution of 440 \u00b5L 1X Hank\u2019s Balanced Salt Solution HBSS  50 \u00b5L 10% pluronic F 68  and 10 \u00b5L 0.26U/mL liberase TM. Tissue was incubated at 37\u00b0C 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 \u00b5L cold HBSS. The cell suspensions were filtered through a 40 \u00b5m cell strainer. Cells were pelleted in a 4\u00b0C centrifuge at 200g for 5 minutes  washed with 0.5% BSA in 500 \u00b5L cold HBSS  pelleted again and resuspended in 0.5% BSA in 500 \u00b5L 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\u2019 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 T\u00fcbingen 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\u2019s 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\u2019s animal care and use program.", "tissue:Testis|age:5 month", "GSM8475558", "GSM8475558: mo5 fish2 rep2; Danio rerio; RNA Seq", "GSM8475558 r1", "GSM8475558", "1", "post euthanasia by immersion in ice cold water  testes were dissected from fish and immediately placed in a dissociation solution of 440 \u00b5L 1X Hank's Balanced Salt Solution HBSS  50 \u00b5L 10% pluronic F 68  and 10 \u00b5L 0.26U/mL liberase TM. Tissue was incubated at 37\u00b0C 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 \u00b5L cold HBSS. The cell suspensions were filtered through a 40 \u00b5m cell strainer. Cells were pelleted in a 4\u00b0C centrifuge at 200g for 5 minutes  washed with 0.5% BSA in 500 \u00b5L cold HBSS  pelleted again and resuspended in 0.5% BSA in 500 \u00b5L 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", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP527811", null, "loader:fastq load.py", "19779X5_220608_A00421_0445_BHVGF7DSX3_S6_L003_I1_001.fastq.gz 19779X5_220608_A00421_0445_BHVGF7DSX3_S6_L003_I2_001.fastq.gz 19779X5_220608_A00421_0445_BHVGF7DSX3_S6_L003_R1_001.fastq.gz 19779X5_220608_A00421_0445_BHVGF7DSX3_S6_L003_R2_001.fastq.gz", "fastq fastq fastq fastq", 67592651346.0, 341377027.0, "GSM8475558 r1", "0:10 1:10 2:28 3:150", "A:15408420726;C:10264745865;G:11496692817;T:14036653315;N:41327", 10, 10, 28, 150, 15408420726, 10264745865, 11496692817, 14036653315, 41327, "SRX25789575", "SRS22421028", "SRA1952802", "Gagnon, Biology, University of Utah", "Gagnon, Biology, University of Utah", 1, 0.93225, null, 0.20483, null, 0.70475, null, 0.49687, null, 150, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-08-21", "Adult", "Adult", "Gonad", "Reproductive System"], [33645, "SRR30329365", "SRX25789574", "SRS22421024", "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", null, "pubmed:39470160", null, "mo5 fish2 rep1", "GSM8475557", null, "source name:Testis|tissue:Testis|age:5 month|geo loc name:missing|collection date:missing", "mo5 fish2 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", null, "post euthanasia by immersion in ice cold water  testes were dissected from fish and immediately placed in a dissociation solution of 440 \u00b5L 1X Hank\u2019s Balanced Salt Solution HBSS  50 \u00b5L 10% pluronic F 68  and 10 \u00b5L 0.26U/mL liberase TM. Tissue was incubated at 37\u00b0C 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 \u00b5L cold HBSS. The cell suspensions were filtered through a 40 \u00b5m cell strainer. Cells were pelleted in a 4\u00b0C centrifuge at 200g for 5 minutes  washed with 0.5% BSA in 500 \u00b5L cold HBSS  pelleted again and resuspended in 0.5% BSA in 500 \u00b5L 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\u2019 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 T\u00fcbingen 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\u2019s 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\u2019s animal care and use program.", "tissue:Testis|age:5 month", "GSM8475557", "GSM8475557: mo5 fish2 rep1; Danio rerio; RNA Seq", "GSM8475557 r1", "GSM8475557", "1", "post euthanasia by immersion in ice cold water  testes were dissected from fish and immediately placed in a dissociation solution of 440 \u00b5L 1X Hank's Balanced Salt Solution HBSS  50 \u00b5L 10% pluronic F 68  and 10 \u00b5L 0.26U/mL liberase TM. Tissue was incubated at 37\u00b0C 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 \u00b5L cold HBSS. The cell suspensions were filtered through a 40 \u00b5m cell strainer. Cells were pelleted in a 4\u00b0C centrifuge at 200g for 5 minutes  washed with 0.5% BSA in 500 \u00b5L cold HBSS  pelleted again and resuspended in 0.5% BSA in 500 \u00b5L 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", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP527811", null, "loader:fastq load.py", "19779X4_220608_A00421_0445_BHVGF7DSX3_S5_L003_I1_001.fastq.gz 19779X4_220608_A00421_0445_BHVGF7DSX3_S5_L003_I2_001.fastq.gz 19779X4_220608_A00421_0445_BHVGF7DSX3_S5_L003_R1_001.fastq.gz 19779X4_220608_A00421_0445_BHVGF7DSX3_S5_L003_R2_001.fastq.gz", "fastq fastq fastq fastq", 82593431316.0, 417138542.0, "GSM8475557 r1", "0:10 1:10 2:28 3:150", "A:18738302033;C:12676748417;G:14156436045;T:16999244279;N:50526", 10, 10, 28, 150, 18738302033, 12676748417, 14156436045, 16999244279, 50526, "SRX25789574", "SRS22421024", "SRA1952802", "Gagnon, Biology, University of Utah", "Gagnon, Biology, University of Utah", 1, 0.93364, null, 0.20357, null, 0.70307, null, 0.4898, null, 150, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-08-21", "Adult", "Adult", "Gonad", "Reproductive System"], [33646, "SRR30329366", "SRX25789573", "SRS22421016", "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", null, "pubmed:39470160", null, "mo5 fish1 rep3", "GSM8475556", null, "source name:Testis|tissue:Testis|age:5 month|geo loc name:missing|collection date:missing", "mo5 fish1 rep3", "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", null, "post euthanasia by immersion in ice cold water  testes were dissected from fish and immediately placed in a dissociation solution of 440 \u00b5L 1X Hank\u2019s Balanced Salt Solution HBSS  50 \u00b5L 10% pluronic F 68  and 10 \u00b5L 0.26U/mL liberase TM. Tissue was incubated at 37\u00b0C 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 \u00b5L cold HBSS. The cell suspensions were filtered through a 40 \u00b5m cell strainer. Cells were pelleted in a 4\u00b0C centrifuge at 200g for 5 minutes  washed with 0.5% BSA in 500 \u00b5L cold HBSS  pelleted again and resuspended in 0.5% BSA in 500 \u00b5L 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\u2019 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 T\u00fcbingen 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\u2019s 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\u2019s animal care and use program.", "tissue:Testis|age:5 month", "GSM8475556", "GSM8475556: mo5 fish1 rep3; Danio rerio; RNA Seq", "GSM8475556 r1", "GSM8475556", "1", "post euthanasia by immersion in ice cold water  testes were dissected from fish and immediately placed in a dissociation solution of 440 \u00b5L 1X Hank's Balanced Salt Solution HBSS  50 \u00b5L 10% pluronic F 68  and 10 \u00b5L 0.26U/mL liberase TM. Tissue was incubated at 37\u00b0C 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 \u00b5L cold HBSS. The cell suspensions were filtered through a 40 \u00b5m cell strainer. Cells were pelleted in a 4\u00b0C centrifuge at 200g for 5 minutes  washed with 0.5% BSA in 500 \u00b5L cold HBSS  pelleted again and resuspended in 0.5% BSA in 500 \u00b5L 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", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP527811", null, "loader:fastq load.py", "19779X3_220608_A00421_0445_BHVGF7DSX3_S4_L003_R2_001.fastq.gz 19779X3_220608_A00421_0445_BHVGF7DSX3_S4_L003_R1_001.fastq.gz 19779X3_220608_A00421_0445_BHVGF7DSX3_S4_L003_I2_001.fastq.gz 19779X3_220608_A00421_0445_BHVGF7DSX3_S4_L003_I1_001.fastq.gz", "fastq fastq fastq fastq", 73957673592.0, 373523604.0, "GSM8475556 r1", "0:10 1:10 2:28 3:150", "A:16641674848;C:11574088141;G:12922095601;T:14890636198;N:45812", 10, 10, 28, 150, 16641674848, 11574088141, 12922095601, 14890636198, 45812, "SRX25789573", "SRS22421016", "SRA1952802", "Gagnon, Biology, University of Utah", "Gagnon, Biology, University of Utah", 1, 0.92791, null, 0.20924, null, 0.70427, null, 0.51976, null, 150, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-08-21", "Adult", "Adult", "Gonad", "Reproductive System"], [33647, "SRR30329368", "SRX25789572", "SRS22421014", "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", null, "pubmed:39470160", null, "mo5 fish1 rep2", "GSM8475555", null, "source name:Testis|tissue:Testis|age:5 month|geo loc name:missing|collection date:missing", "mo5 fish1 rep2", "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", null, "post euthanasia by immersion in ice cold water  testes were dissected from fish and immediately placed in a dissociation solution of 440 \u00b5L 1X Hank\u2019s Balanced Salt Solution HBSS  50 \u00b5L 10% pluronic F 68  and 10 \u00b5L 0.26U/mL liberase TM. Tissue was incubated at 37\u00b0C 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 \u00b5L cold HBSS. The cell suspensions were filtered through a 40 \u00b5m cell strainer. Cells were pelleted in a 4\u00b0C centrifuge at 200g for 5 minutes  washed with 0.5% BSA in 500 \u00b5L cold HBSS  pelleted again and resuspended in 0.5% BSA in 500 \u00b5L 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\u2019 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 T\u00fcbingen 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\u2019s 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\u2019s animal care and use program.", "tissue:Testis|age:5 month", "GSM8475555", "GSM8475555: mo5 fish1 rep2; Danio rerio; RNA Seq", "GSM8475555 r1", "GSM8475555", "1", "post euthanasia by immersion in ice cold water  testes were dissected from fish and immediately placed in a dissociation solution of 440 \u00b5L 1X Hank's Balanced Salt Solution HBSS  50 \u00b5L 10% pluronic F 68  and 10 \u00b5L 0.26U/mL liberase TM. Tissue was incubated at 37\u00b0C 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 \u00b5L cold HBSS. The cell suspensions were filtered through a 40 \u00b5m cell strainer. Cells were pelleted in a 4\u00b0C centrifuge at 200g for 5 minutes  washed with 0.5% BSA in 500 \u00b5L cold HBSS  pelleted again and resuspended in 0.5% BSA in 500 \u00b5L 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", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP527811", null, "loader:fastq load.py", "19779X2_220608_A00421_0445_BHVGF7DSX3_S3_L003_R2_001.fastq.gz 19779X2_220608_A00421_0445_BHVGF7DSX3_S3_L003_R1_001.fastq.gz 19779X2_220608_A00421_0445_BHVGF7DSX3_S3_L003_I2_001.fastq.gz 19779X2_220608_A00421_0445_BHVGF7DSX3_S3_L003_I1_001.fastq.gz", "fastq fastq fastq fastq", 81431066970.0, 411268015.0, "GSM8475555 r1", "0:10 1:10 2:28 3:150", "A:18341504843;C:12608734527;G:14017359094;T:16722553528;N:50258", 10, 10, 28, 150, 18341504843, 12608734527, 14017359094, 16722553528, 50258, "SRX25789572", "SRS22421014", "SRA1952802", "Gagnon, Biology, University of Utah", "Gagnon, Biology, University of Utah", 1, 0.93012, null, 0.2152, null, 0.70007, null, 0.51331, null, 150, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-08-21", "Adult", "Adult", "Gonad", "Reproductive System"], [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", null, "pubmed:39470160", null, "mo5 fish1 rep1", "GSM8475554", null, "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", null, "post euthanasia by immersion in ice cold water  testes were dissected from fish and immediately placed in a dissociation solution of 440 \u00b5L 1X Hank\u2019s Balanced Salt Solution HBSS  50 \u00b5L 10% pluronic F 68  and 10 \u00b5L 0.26U/mL liberase TM. Tissue was incubated at 37\u00b0C 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 \u00b5L cold HBSS. The cell suspensions were filtered through a 40 \u00b5m cell strainer. Cells were pelleted in a 4\u00b0C centrifuge at 200g for 5 minutes  washed with 0.5% BSA in 500 \u00b5L cold HBSS  pelleted again and resuspended in 0.5% BSA in 500 \u00b5L 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\u2019 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 T\u00fcbingen 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\u2019s 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\u2019s 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 \u00b5L 1X Hank's Balanced Salt Solution HBSS  50 \u00b5L 10% pluronic F 68  and 10 \u00b5L 0.26U/mL liberase TM. Tissue was incubated at 37\u00b0C 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 \u00b5L cold HBSS. The cell suspensions were filtered through a 40 \u00b5m cell strainer. Cells were pelleted in a 4\u00b0C centrifuge at 200g for 5 minutes  washed with 0.5% BSA in 500 \u00b5L cold HBSS  pelleted again and resuspended in 0.5% BSA in 500 \u00b5L 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", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP527811", null, "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, null, 0.21455, null, 0.69952, null, 0.51581, null, 150, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", 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