metadata: run_metadata: 21 rows where experiment.library_source = "TRANSCRIPTOMIC SINGLE CELL", experiment.library_strategy = "RNA-Seq" and tissue_curation

21 rows where experiment.library_source = "TRANSCRIPTOMIC SINGLE CELL", experiment.library_strategy = "RNA-Seq" and tissue_curation_coarse = "Reproductive System"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.PMIDs	sample.title	sample.alias	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	GEOsample.extractprotocol	GEOsample.growthprotocol	GEOsample.characteristics	GEOsample.accession	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_construction_protocol	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.study_ref	run.attributes	run.filename	run.semantic_name	run.total_bases	run.total_spots	run.alias	run.read_lengths	run.base_counts	run.r1_length	run.r2_length	run.r3_length	run.r4_length	run.Acount	run.Ccount	run.Gcount	run.Tcount	run.Ncount	run.experiment	run.pool_member	submission.accession	submission.srasource	submission.bioprojectsource	seqdetective.n_mates	seqdetective.mapping_rate.mate1	seqdetective.mapping_rate.mate2	seqdetective.nofeature_rate.mate1	seqdetective.nofeature_rate.mate2	seqdetective.sparsity.mate1	seqdetective.sparsity.mate2	seqdetective.pos_strand_rate.mate1	seqdetective.pos_strand_rate.mate2	seqdetective.readlen.mate1	seqdetective.readlen.mate2	seqdetective.judgement.mate1	seqdetective.judgement.mate2	seqdetective.judgement.reason	platform_family	instrument_generation	read_bias	selection_class	prep_kit	sc_or_bulk	tech_class	technology	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
33631	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	pubmed:39470160	mo27 fish4 rep2	GSM8475571	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	post euthanasia by immersion in ice cold water testes were dissected from fish and immediately placed in a dissociation solution of 440 µL 1X Hank’s Balanced Salt Solution HBSS 50 µL 10% pluronic F 68 and 10 µL 0.26U/mL liberase TM. Tissue was incubated at 37°C for approximately 45 minutes while rotating at 750 rpm in an Eppendorf Thermomixer. The dissociation reaction was stopped by adding 1% bovine serum albumin BSA in 500 µL cold HBSS. The cell suspensions were filtered through a 40 µm cell strainer. Cells were pelleted in a 4°C centrifuge at 200g for 5 minutes washed with 0.5% BSA in 500 µL cold HBSS pelleted again and resuspended in 0.5% BSA in 500 µL cold HBSS. Single cell RNA sequencing libraries were prepared by the University of Utah High Throughput Genomics Shared Resource using the 10X Genomics Next GEM Single Cell 3’ Gene Expression Library prep v3.1 with UDI. Libraries were sequenced with the NovaSeq Reagent Kit v1.5 150x150 bp Sequencing. Libraries were constructed according to the manufacturer's protocol 10X chromium controller	Wild type Tübingen zebrafish were used for all experiments. Ages of animals are noted in sample title and age metadata. All zebrafish work was performed at University of Utah’s CBRZ zebrafish facility. This study was conducted under the approval of the Office of Institutional Animal Care and Use Committee IACUC no. 20 07013 of the University of Utah’s animal care and use program.	tissue:Testis\|age: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 µL 1X Hank's Balanced Salt Solution HBSS 50 µL 10% pluronic F 68 and 10 µL 0.26U/mL liberase TM. Tissue was incubated at 37°C for approximately 45 minutes while rotating at 750 rpm in an Eppendorf Thermomixer. The dissociation reaction was stopped by adding 1% bovine serum albumin BSA in 500 µL cold HBSS. The cell suspensions were filtered through a 40 µm cell strainer. Cells were pelleted in a 4°C centrifuge at 200g for 5 minutes washed with 0.5% BSA in 500 µL cold HBSS pelleted again and resuspended in 0.5% BSA in 500 µL cold HBSS. Single cell RNA sequencing libraries were prepared by the University of Utah High Throughput Genomics Shared Resource using the 10X Genomics Next GEM Single Cell three prime Gene Expression Library prep v3.1 with UDI. Libraries were sequenced with the NovaSeq Reagent Kit v1.5 150x150 bp Sequencing. Libraries were constructed according to the manufacturer's protocol 10X chromium controller	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP527811	loader:fastq load.py	23822X4_20240226_LH00227_0052_A22HJWLLT3_S8_L003_I1_001.fastq.gz 23822X4_20240226_LH00227_0052_A22HJWLLT3_S8_L003_I2_001.fastq.gz 23822X4_20240226_LH00227_0052_A22HJWLLT3_S8_L003_R1_001.fastq.gz 23822X4_20240226_LH00227_0052_A22HJWLLT3_S8_L003_R2_001.fastq.gz	fastq fastq fastq fastq	62332746910.0	328067089.0	GSM8475571 r1	0:6 1:6 2:28 3:150	A:14114753316;C:10050790836;G:11058814166;T:13983250670;N:2454362	6	6	28	150	14114753316	10050790836	11058814166	13983250670	2454362	SRX25789588	SRS22421035	SRA1952802	Gagnon, Biology, University of Utah	Gagnon, Biology, University of Utah	1	0.854		0.31359		0.74659		0.69085		150		B		usable mapping rate	illumina	novaseq_era	3prime	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-08-21	Adult	Adult	Gonad	Reproductive System
33632	33632	SRR30329353	SRX25789587	SRS22421034	SRP527811	PRJNA1150539	Germ cell progression through zebrafish spermatogenesis declines with age	GSE275361	Transcriptome Analysis	Vertebrate spermatogonial stem cells maintain sperm production over the lifetime of an animal but fertility declines with age. While morphological studies have informed our understanding of typical spermatogenesis the molecular and cellular mechanisms underlying the maintenance and decline of spermatogenesis are not yet understood. We used single cell RNA sequencing to generate a developmental atlas of the aging zebrafish testis. All testes contained spermatogonia but we observed a progressive decline in spermatogenesis that correlates with age. Testes from some older males only contained spermatogonia and a reduced population of spermatocytes. Spermatogonia in older males are transcriptionally distinct from spermatogonia in testes capable of robust spermatogenesis. Immune cells including macrophages and lymphocytes drastically increase in abundance in testes that cannot complete spermatogenesis. Our developmental atlas reveals the cellular changes as the testis ages and defines a molecular roadmap for the regulation of spermatogenesis. Overall design: scRNA seq of dissected zebrafish testes from 5 12 20 22 and 27 month individuals	pubmed:39470160	mo27 fish4 rep1	GSM8475570	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	post euthanasia by immersion in ice cold water testes were dissected from fish and immediately placed in a dissociation solution of 440 µL 1X Hank’s Balanced Salt Solution HBSS 50 µL 10% pluronic F 68 and 10 µL 0.26U/mL liberase TM. Tissue was incubated at 37°C for approximately 45 minutes while rotating at 750 rpm in an Eppendorf Thermomixer. The dissociation reaction was stopped by adding 1% bovine serum albumin BSA in 500 µL cold HBSS. The cell suspensions were filtered through a 40 µm cell strainer. Cells were pelleted in a 4°C centrifuge at 200g for 5 minutes washed with 0.5% BSA in 500 µL cold HBSS pelleted again and resuspended in 0.5% BSA in 500 µL cold HBSS. Single cell RNA sequencing libraries were prepared by the University of Utah High Throughput Genomics Shared Resource using the 10X Genomics Next GEM Single Cell 3’ Gene Expression Library prep v3.1 with UDI. Libraries were sequenced with the NovaSeq Reagent Kit v1.5 150x150 bp Sequencing. Libraries were constructed according to the manufacturer's protocol 10X chromium controller	Wild type Tübingen zebrafish were used for all experiments. Ages of animals are noted in sample title and age metadata. All zebrafish work was performed at University of Utah’s CBRZ zebrafish facility. This study was conducted under the approval of the Office of Institutional Animal Care and Use Committee IACUC no. 20 07013 of the University of Utah’s animal care and use program.	tissue:Testis\|age: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 µL 1X Hank's Balanced Salt Solution HBSS 50 µL 10% pluronic F 68 and 10 µL 0.26U/mL liberase TM. Tissue was incubated at 37°C for approximately 45 minutes while rotating at 750 rpm in an Eppendorf Thermomixer. The dissociation reaction was stopped by adding 1% bovine serum albumin BSA in 500 µL cold HBSS. The cell suspensions were filtered through a 40 µm cell strainer. Cells were pelleted in a 4°C centrifuge at 200g for 5 minutes washed with 0.5% BSA in 500 µL cold HBSS pelleted again and resuspended in 0.5% BSA in 500 µL cold HBSS. Single cell RNA sequencing libraries were prepared by the University of Utah High Throughput Genomics Shared Resource using the 10X Genomics Next GEM Single Cell three prime Gene Expression Library prep v3.1 with UDI. Libraries were sequenced with the NovaSeq Reagent Kit v1.5 150x150 bp Sequencing. Libraries were constructed according to the manufacturer's protocol 10X chromium controller	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP527811	loader:fastq load.py	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		0.30845		0.7543		0.68115		150		B		usable mapping rate	illumina	novaseq_era	3prime	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-08-21	Adult	Adult	Gonad	Reproductive System
33633	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	pubmed:39470160	mo27 fish3 rep2	GSM8475569	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	post euthanasia by immersion in ice cold water testes were dissected from fish and immediately placed in a dissociation solution of 440 µL 1X Hank’s Balanced Salt Solution HBSS 50 µL 10% pluronic F 68 and 10 µL 0.26U/mL liberase TM. Tissue was incubated at 37°C for approximately 45 minutes while rotating at 750 rpm in an Eppendorf Thermomixer. The dissociation reaction was stopped by adding 1% bovine serum albumin BSA in 500 µL cold HBSS. The cell suspensions were filtered through a 40 µm cell strainer. Cells were pelleted in a 4°C centrifuge at 200g for 5 minutes washed with 0.5% BSA in 500 µL cold HBSS pelleted again and resuspended in 0.5% BSA in 500 µL cold HBSS. Single cell RNA sequencing libraries were prepared by the University of Utah High Throughput Genomics Shared Resource using the 10X Genomics Next GEM Single Cell 3’ Gene Expression Library prep v3.1 with UDI. Libraries were sequenced with the NovaSeq Reagent Kit v1.5 150x150 bp Sequencing. Libraries were constructed according to the manufacturer's protocol 10X chromium controller	Wild type Tübingen zebrafish were used for all experiments. Ages of animals are noted in sample title and age metadata. All zebrafish work was performed at University of Utah’s CBRZ zebrafish facility. This study was conducted under the approval of the Office of Institutional Animal Care and Use Committee IACUC no. 20 07013 of the University of Utah’s animal care and use program.	tissue:Testis\|age: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 µL 1X Hank's Balanced Salt Solution HBSS 50 µL 10% pluronic F 68 and 10 µL 0.26U/mL liberase TM. Tissue was incubated at 37°C for approximately 45 minutes while rotating at 750 rpm in an Eppendorf Thermomixer. The dissociation reaction was stopped by adding 1% bovine serum albumin BSA in 500 µL cold HBSS. The cell suspensions were filtered through a 40 µm cell strainer. Cells were pelleted in a 4°C centrifuge at 200g for 5 minutes washed with 0.5% BSA in 500 µL cold HBSS pelleted again and resuspended in 0.5% BSA in 500 µL cold HBSS. Single cell RNA sequencing libraries were prepared by the University of Utah High Throughput Genomics Shared Resource using the 10X Genomics Next GEM Single Cell three prime Gene Expression Library prep v3.1 with UDI. Libraries were sequenced with the NovaSeq Reagent Kit v1.5 150x150 bp Sequencing. Libraries were constructed according to the manufacturer's protocol 10X chromium controller	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP527811	loader:fastq load.py	23822X2_20240226_LH00227_0052_A22HJWLLT3_S6_L003_R2_001.fastq.gz 23822X2_20240226_LH00227_0052_A22HJWLLT3_S6_L003_R1_001.fastq.gz 23822X2_20240226_LH00227_0052_A22HJWLLT3_S6_L003_I2_001.fastq.gz 23822X2_20240226_LH00227_0052_A22HJWLLT3_S6_L003_I1_001.fastq.gz	fastq fastq fastq fastq	47201245520.0	248427608.0	GSM8475569 r1	0:6 1:6 2:28 3:150	A:10398745837;C:7966730578;G:8916412008;T:9980276803;N:1975974	6	6	28	150	10398745837	7966730578	8916412008	9980276803	1975974	SRX25789586	SRS22421033	SRA1952802	Gagnon, Biology, University of Utah	Gagnon, Biology, University of Utah	1	0.87941		0.25226		0.76045		0.55073		150		B		usable mapping rate	illumina	novaseq_era	3prime	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-08-21	Adult	Adult	Gonad	Reproductive System
33634	33634	SRR30329357	SRX25789585	SRS22421029	SRP527811	PRJNA1150539	Germ cell progression through zebrafish spermatogenesis declines with age	GSE275361	Transcriptome Analysis	Vertebrate spermatogonial stem cells maintain sperm production over the lifetime of an animal but fertility declines with age. While morphological studies have informed our understanding of typical spermatogenesis the molecular and cellular mechanisms underlying the maintenance and decline of spermatogenesis are not yet understood. We used single cell RNA sequencing to generate a developmental atlas of the aging zebrafish testis. All testes contained spermatogonia but we observed a progressive decline in spermatogenesis that correlates with age. Testes from some older males only contained spermatogonia and a reduced population of spermatocytes. Spermatogonia in older males are transcriptionally distinct from spermatogonia in testes capable of robust spermatogenesis. Immune cells including macrophages and lymphocytes drastically increase in abundance in testes that cannot complete spermatogenesis. Our developmental atlas reveals the cellular changes as the testis ages and defines a molecular roadmap for the regulation of spermatogenesis. Overall design: scRNA seq of dissected zebrafish testes from 5 12 20 22 and 27 month individuals	pubmed:39470160	mo27 fish3 rep1	GSM8475568	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	post euthanasia by immersion in ice cold water testes were dissected from fish and immediately placed in a dissociation solution of 440 µL 1X Hank’s Balanced Salt Solution HBSS 50 µL 10% pluronic F 68 and 10 µL 0.26U/mL liberase TM. Tissue was incubated at 37°C for approximately 45 minutes while rotating at 750 rpm in an Eppendorf Thermomixer. The dissociation reaction was stopped by adding 1% bovine serum albumin BSA in 500 µL cold HBSS. The cell suspensions were filtered through a 40 µm cell strainer. Cells were pelleted in a 4°C centrifuge at 200g for 5 minutes washed with 0.5% BSA in 500 µL cold HBSS pelleted again and resuspended in 0.5% BSA in 500 µL cold HBSS. Single cell RNA sequencing libraries were prepared by the University of Utah High Throughput Genomics Shared Resource using the 10X Genomics Next GEM Single Cell 3’ Gene Expression Library prep v3.1 with UDI. Libraries were sequenced with the NovaSeq Reagent Kit v1.5 150x150 bp Sequencing. Libraries were constructed according to the manufacturer's protocol 10X chromium controller	Wild type Tübingen zebrafish were used for all experiments. Ages of animals are noted in sample title and age metadata. All zebrafish work was performed at University of Utah’s CBRZ zebrafish facility. This study was conducted under the approval of the Office of Institutional Animal Care and Use Committee IACUC no. 20 07013 of the University of Utah’s animal care and use program.	tissue:Testis\|age: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 µL 1X Hank's Balanced Salt Solution HBSS 50 µL 10% pluronic F 68 and 10 µL 0.26U/mL liberase TM. Tissue was incubated at 37°C for approximately 45 minutes while rotating at 750 rpm in an Eppendorf Thermomixer. The dissociation reaction was stopped by adding 1% bovine serum albumin BSA in 500 µL cold HBSS. The cell suspensions were filtered through a 40 µm cell strainer. Cells were pelleted in a 4°C centrifuge at 200g for 5 minutes washed with 0.5% BSA in 500 µL cold HBSS pelleted again and resuspended in 0.5% BSA in 500 µL cold HBSS. Single cell RNA sequencing libraries were prepared by the University of Utah High Throughput Genomics Shared Resource using the 10X Genomics Next GEM Single Cell three prime Gene Expression Library prep v3.1 with UDI. Libraries were sequenced with the NovaSeq Reagent Kit v1.5 150x150 bp Sequencing. Libraries were constructed according to the manufacturer's protocol 10X chromium controller	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP527811	loader:fastq load.py	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		0.23873		0.76688		0.66783		150		B		usable mapping rate	illumina	novaseq_era	3prime	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-08-21	Adult	Adult	Gonad	Reproductive System
33635	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	pubmed:39470160	mo27 fish2 rep1	GSM8475567	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	post euthanasia by immersion in ice cold water testes were dissected from fish and immediately placed in a dissociation solution of 440 µL 1X Hank’s Balanced Salt Solution HBSS 50 µL 10% pluronic F 68 and 10 µL 0.26U/mL liberase TM. Tissue was incubated at 37°C for approximately 45 minutes while rotating at 750 rpm in an Eppendorf Thermomixer. The dissociation reaction was stopped by adding 1% bovine serum albumin BSA in 500 µL cold HBSS. The cell suspensions were filtered through a 40 µm cell strainer. Cells were pelleted in a 4°C centrifuge at 200g for 5 minutes washed with 0.5% BSA in 500 µL cold HBSS pelleted again and resuspended in 0.5% BSA in 500 µL cold HBSS. Single cell RNA sequencing libraries were prepared by the University of Utah High Throughput Genomics Shared Resource using the 10X Genomics Next GEM Single Cell 3’ Gene Expression Library prep v3.1 with UDI. Libraries were sequenced with the NovaSeq Reagent Kit v1.5 150x150 bp Sequencing. Libraries were constructed according to the manufacturer's protocol 10X chromium controller	Wild type Tübingen zebrafish were used for all experiments. Ages of animals are noted in sample title and age metadata. All zebrafish work was performed at University of Utah’s CBRZ zebrafish facility. This study was conducted under the approval of the Office of Institutional Animal Care and Use Committee IACUC no. 20 07013 of the University of Utah’s animal care and use program.	tissue:Testis\|age: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 µL 1X Hank's Balanced Salt Solution HBSS 50 µL 10% pluronic F 68 and 10 µL 0.26U/mL liberase TM. Tissue was incubated at 37°C for approximately 45 minutes while rotating at 750 rpm in an Eppendorf Thermomixer. The dissociation reaction was stopped by adding 1% bovine serum albumin BSA in 500 µL cold HBSS. The cell suspensions were filtered through a 40 µm cell strainer. Cells were pelleted in a 4°C centrifuge at 200g for 5 minutes washed with 0.5% BSA in 500 µL cold HBSS pelleted again and resuspended in 0.5% BSA in 500 µL cold HBSS. Single cell RNA sequencing libraries were prepared by the University of Utah High Throughput Genomics Shared Resource using the 10X Genomics Next GEM Single Cell three prime Gene Expression Library prep v3.1 with UDI. Libraries were sequenced with the NovaSeq Reagent Kit v1.5 150x150 bp Sequencing. Libraries were constructed according to the manufacturer's protocol 10X chromium controller	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP527811	loader:fastq load.py	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		0.10879		0.74671		0.53003		150		B		usable mapping rate	illumina	novaseq_era	3prime	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-08-21	Adult	Adult	Gonad	Reproductive System
33636	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	pubmed:39470160	mo27 fish1 rep1	GSM8475566	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	post euthanasia by immersion in ice cold water testes were dissected from fish and immediately placed in a dissociation solution of 440 µL 1X Hank’s Balanced Salt Solution HBSS 50 µL 10% pluronic F 68 and 10 µL 0.26U/mL liberase TM. Tissue was incubated at 37°C for approximately 45 minutes while rotating at 750 rpm in an Eppendorf Thermomixer. The dissociation reaction was stopped by adding 1% bovine serum albumin BSA in 500 µL cold HBSS. The cell suspensions were filtered through a 40 µm cell strainer. Cells were pelleted in a 4°C centrifuge at 200g for 5 minutes washed with 0.5% BSA in 500 µL cold HBSS pelleted again and resuspended in 0.5% BSA in 500 µL cold HBSS. Single cell RNA sequencing libraries were prepared by the University of Utah High Throughput Genomics Shared Resource using the 10X Genomics Next GEM Single Cell 3’ Gene Expression Library prep v3.1 with UDI. Libraries were sequenced with the NovaSeq Reagent Kit v1.5 150x150 bp Sequencing. Libraries were constructed according to the manufacturer's protocol 10X chromium controller	Wild type Tübingen zebrafish were used for all experiments. Ages of animals are noted in sample title and age metadata. All zebrafish work was performed at University of Utah’s CBRZ zebrafish facility. This study was conducted under the approval of the Office of Institutional Animal Care and Use Committee IACUC no. 20 07013 of the University of Utah’s animal care and use program.	tissue:Testis\|age: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 µL 1X Hank's Balanced Salt Solution HBSS 50 µL 10% pluronic F 68 and 10 µL 0.26U/mL liberase TM. Tissue was incubated at 37°C for approximately 45 minutes while rotating at 750 rpm in an Eppendorf Thermomixer. The dissociation reaction was stopped by adding 1% bovine serum albumin BSA in 500 µL cold HBSS. The cell suspensions were filtered through a 40 µm cell strainer. Cells were pelleted in a 4°C centrifuge at 200g for 5 minutes washed with 0.5% BSA in 500 µL cold HBSS pelleted again and resuspended in 0.5% BSA in 500 µL cold HBSS. Single cell RNA sequencing libraries were prepared by the University of Utah High Throughput Genomics Shared Resource using the 10X Genomics Next GEM Single Cell three prime Gene Expression Library prep v3.1 with UDI. Libraries were sequenced with the NovaSeq Reagent Kit v1.5 150x150 bp Sequencing. Libraries were constructed according to the manufacturer's protocol 10X chromium controller	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP527811	loader:fastq load.py	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		0.1044		0.77571		0.55175		150		B		usable mapping rate	illumina	novaseq_era	3prime	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-08-21	Adult	Adult	Gonad	Reproductive System
33637	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	pubmed:39470160	mo22 fish1 rep2	GSM8475565	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	post euthanasia by immersion in ice cold water testes were dissected from fish and immediately placed in a dissociation solution of 440 µL 1X Hank’s Balanced Salt Solution HBSS 50 µL 10% pluronic F 68 and 10 µL 0.26U/mL liberase TM. Tissue was incubated at 37°C for approximately 45 minutes while rotating at 750 rpm in an Eppendorf Thermomixer. The dissociation reaction was stopped by adding 1% bovine serum albumin BSA in 500 µL cold HBSS. The cell suspensions were filtered through a 40 µm cell strainer. Cells were pelleted in a 4°C centrifuge at 200g for 5 minutes washed with 0.5% BSA in 500 µL cold HBSS pelleted again and resuspended in 0.5% BSA in 500 µL cold HBSS. Single cell RNA sequencing libraries were prepared by the University of Utah High Throughput Genomics Shared Resource using the 10X Genomics Next GEM Single Cell 3’ Gene Expression Library prep v3.1 with UDI. Libraries were sequenced with the NovaSeq Reagent Kit v1.5 150x150 bp Sequencing. Libraries were constructed according to the manufacturer's protocol 10X chromium controller	Wild type Tübingen zebrafish were used for all experiments. Ages of animals are noted in sample title and age metadata. All zebrafish work was performed at University of Utah’s CBRZ zebrafish facility. This study was conducted under the approval of the Office of Institutional Animal Care and Use Committee IACUC no. 20 07013 of the University of Utah’s animal care and use program.	tissue:Testis\|age: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 µL 1X Hank's Balanced Salt Solution HBSS 50 µL 10% pluronic F 68 and 10 µL 0.26U/mL liberase TM. Tissue was incubated at 37°C for approximately 45 minutes while rotating at 750 rpm in an Eppendorf Thermomixer. The dissociation reaction was stopped by adding 1% bovine serum albumin BSA in 500 µL cold HBSS. The cell suspensions were filtered through a 40 µm cell strainer. Cells were pelleted in a 4°C centrifuge at 200g for 5 minutes washed with 0.5% BSA in 500 µL cold HBSS pelleted again and resuspended in 0.5% BSA in 500 µL cold HBSS. Single cell RNA sequencing libraries were prepared by the University of Utah High Throughput Genomics Shared Resource using the 10X Genomics Next GEM Single Cell three prime Gene Expression Library prep v3.1 with UDI. Libraries were sequenced with the NovaSeq Reagent Kit v1.5 150x150 bp Sequencing. Libraries were constructed according to the manufacturer's protocol 10X chromium controller	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP527811	loader:fastq load.py	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		0.15397		0.72354		0.51746		150		B		usable mapping rate	illumina	novaseq_era	3prime	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-08-21	Adult	Adult	Gonad	Reproductive System
33638	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	pubmed:39470160	mo22 fish1 rep1	GSM8475564	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	post euthanasia by immersion in ice cold water testes were dissected from fish and immediately placed in a dissociation solution of 440 µL 1X Hank’s Balanced Salt Solution HBSS 50 µL 10% pluronic F 68 and 10 µL 0.26U/mL liberase TM. Tissue was incubated at 37°C for approximately 45 minutes while rotating at 750 rpm in an Eppendorf Thermomixer. The dissociation reaction was stopped by adding 1% bovine serum albumin BSA in 500 µL cold HBSS. The cell suspensions were filtered through a 40 µm cell strainer. Cells were pelleted in a 4°C centrifuge at 200g for 5 minutes washed with 0.5% BSA in 500 µL cold HBSS pelleted again and resuspended in 0.5% BSA in 500 µL cold HBSS. Single cell RNA sequencing libraries were prepared by the University of Utah High Throughput Genomics Shared Resource using the 10X Genomics Next GEM Single Cell 3’ Gene Expression Library prep v3.1 with UDI. Libraries were sequenced with the NovaSeq Reagent Kit v1.5 150x150 bp Sequencing. Libraries were constructed according to the manufacturer's protocol 10X chromium controller	Wild type Tübingen zebrafish were used for all experiments. Ages of animals are noted in sample title and age metadata. All zebrafish work was performed at University of Utah’s CBRZ zebrafish facility. This study was conducted under the approval of the Office of Institutional Animal Care and Use Committee IACUC no. 20 07013 of the University of Utah’s animal care and use program.	tissue:Testis\|age: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 µL 1X Hank's Balanced Salt Solution HBSS 50 µL 10% pluronic F 68 and 10 µL 0.26U/mL liberase TM. Tissue was incubated at 37°C for approximately 45 minutes while rotating at 750 rpm in an Eppendorf Thermomixer. The dissociation reaction was stopped by adding 1% bovine serum albumin BSA in 500 µL cold HBSS. The cell suspensions were filtered through a 40 µm cell strainer. Cells were pelleted in a 4°C centrifuge at 200g for 5 minutes washed with 0.5% BSA in 500 µL cold HBSS pelleted again and resuspended in 0.5% BSA in 500 µL cold HBSS. Single cell RNA sequencing libraries were prepared by the University of Utah High Throughput Genomics Shared Resource using the 10X Genomics Next GEM Single Cell three prime Gene Expression Library prep v3.1 with UDI. Libraries were sequenced with the NovaSeq Reagent Kit v1.5 150x150 bp Sequencing. Libraries were constructed according to the manufacturer's protocol 10X chromium controller	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP527811	loader:fastq load.py	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		0.16024		0.71526		0.51211		150		B		usable mapping rate	illumina	novaseq_era	3prime	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-08-21	Adult	Adult	Gonad	Reproductive System
33639	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	pubmed:39470160	mo20 fish1 rep2	GSM8475563	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	post euthanasia by immersion in ice cold water testes were dissected from fish and immediately placed in a dissociation solution of 440 µL 1X Hank’s Balanced Salt Solution HBSS 50 µL 10% pluronic F 68 and 10 µL 0.26U/mL liberase TM. Tissue was incubated at 37°C for approximately 45 minutes while rotating at 750 rpm in an Eppendorf Thermomixer. The dissociation reaction was stopped by adding 1% bovine serum albumin BSA in 500 µL cold HBSS. The cell suspensions were filtered through a 40 µm cell strainer. Cells were pelleted in a 4°C centrifuge at 200g for 5 minutes washed with 0.5% BSA in 500 µL cold HBSS pelleted again and resuspended in 0.5% BSA in 500 µL cold HBSS. Single cell RNA sequencing libraries were prepared by the University of Utah High Throughput Genomics Shared Resource using the 10X Genomics Next GEM Single Cell 3’ Gene Expression Library prep v3.1 with UDI. Libraries were sequenced with the NovaSeq Reagent Kit v1.5 150x150 bp Sequencing. Libraries were constructed according to the manufacturer's protocol 10X chromium controller	Wild type Tübingen zebrafish were used for all experiments. Ages of animals are noted in sample title and age metadata. All zebrafish work was performed at University of Utah’s CBRZ zebrafish facility. This study was conducted under the approval of the Office of Institutional Animal Care and Use Committee IACUC no. 20 07013 of the University of Utah’s animal care and use program.	tissue:Testis\|age: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 µL 1X Hank's Balanced Salt Solution HBSS 50 µL 10% pluronic F 68 and 10 µL 0.26U/mL liberase TM. Tissue was incubated at 37°C for approximately 45 minutes while rotating at 750 rpm in an Eppendorf Thermomixer. The dissociation reaction was stopped by adding 1% bovine serum albumin BSA in 500 µL cold HBSS. The cell suspensions were filtered through a 40 µm cell strainer. Cells were pelleted in a 4°C centrifuge at 200g for 5 minutes washed with 0.5% BSA in 500 µL cold HBSS pelleted again and resuspended in 0.5% BSA in 500 µL cold HBSS. Single cell RNA sequencing libraries were prepared by the University of Utah High Throughput Genomics Shared Resource using the 10X Genomics Next GEM Single Cell three prime Gene Expression Library prep v3.1 with UDI. Libraries were sequenced with the NovaSeq Reagent Kit v1.5 150x150 bp Sequencing. Libraries were constructed according to the manufacturer's protocol 10X chromium controller	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP527811	loader:fastq load.py	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		0.15438		0.73888		0.52949		150		B		usable mapping rate	illumina	novaseq_era	3prime	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-08-21	Adult	Adult	Gonad	Reproductive System
33640	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	pubmed:39470160	mo20 fish1 rep1	GSM8475562	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	post euthanasia by immersion in ice cold water testes were dissected from fish and immediately placed in a dissociation solution of 440 µL 1X Hank’s Balanced Salt Solution HBSS 50 µL 10% pluronic F 68 and 10 µL 0.26U/mL liberase TM. Tissue was incubated at 37°C for approximately 45 minutes while rotating at 750 rpm in an Eppendorf Thermomixer. The dissociation reaction was stopped by adding 1% bovine serum albumin BSA in 500 µL cold HBSS. The cell suspensions were filtered through a 40 µm cell strainer. Cells were pelleted in a 4°C centrifuge at 200g for 5 minutes washed with 0.5% BSA in 500 µL cold HBSS pelleted again and resuspended in 0.5% BSA in 500 µL cold HBSS. Single cell RNA sequencing libraries were prepared by the University of Utah High Throughput Genomics Shared Resource using the 10X Genomics Next GEM Single Cell 3’ Gene Expression Library prep v3.1 with UDI. Libraries were sequenced with the NovaSeq Reagent Kit v1.5 150x150 bp Sequencing. Libraries were constructed according to the manufacturer's protocol 10X chromium controller	Wild type Tübingen zebrafish were used for all experiments. Ages of animals are noted in sample title and age metadata. All zebrafish work was performed at University of Utah’s CBRZ zebrafish facility. This study was conducted under the approval of the Office of Institutional Animal Care and Use Committee IACUC no. 20 07013 of the University of Utah’s animal care and use program.	tissue:Testis\|age: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 µL 1X Hank's Balanced Salt Solution HBSS 50 µL 10% pluronic F 68 and 10 µL 0.26U/mL liberase TM. Tissue was incubated at 37°C for approximately 45 minutes while rotating at 750 rpm in an Eppendorf Thermomixer. The dissociation reaction was stopped by adding 1% bovine serum albumin BSA in 500 µL cold HBSS. The cell suspensions were filtered through a 40 µm cell strainer. Cells were pelleted in a 4°C centrifuge at 200g for 5 minutes washed with 0.5% BSA in 500 µL cold HBSS pelleted again and resuspended in 0.5% BSA in 500 µL cold HBSS. Single cell RNA sequencing libraries were prepared by the University of Utah High Throughput Genomics Shared Resource using the 10X Genomics Next GEM Single Cell three prime Gene Expression Library prep v3.1 with UDI. Libraries were sequenced with the NovaSeq Reagent Kit v1.5 150x150 bp Sequencing. Libraries were constructed according to the manufacturer's protocol 10X chromium controller	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP527811	loader:fastq load.py	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		0.14351		0.74513		0.52838		150		B		usable mapping rate	illumina	novaseq_era	3prime	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-08-21	Adult	Adult	Gonad	Reproductive System
33641	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	pubmed:39470160	mo12 fish2 rep1	GSM8475561	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	post euthanasia by immersion in ice cold water testes were dissected from fish and immediately placed in a dissociation solution of 440 µL 1X Hank’s Balanced Salt Solution HBSS 50 µL 10% pluronic F 68 and 10 µL 0.26U/mL liberase TM. Tissue was incubated at 37°C for approximately 45 minutes while rotating at 750 rpm in an Eppendorf Thermomixer. The dissociation reaction was stopped by adding 1% bovine serum albumin BSA in 500 µL cold HBSS. The cell suspensions were filtered through a 40 µm cell strainer. Cells were pelleted in a 4°C centrifuge at 200g for 5 minutes washed with 0.5% BSA in 500 µL cold HBSS pelleted again and resuspended in 0.5% BSA in 500 µL cold HBSS. Single cell RNA sequencing libraries were prepared by the University of Utah High Throughput Genomics Shared Resource using the 10X Genomics Next GEM Single Cell 3’ Gene Expression Library prep v3.1 with UDI. Libraries were sequenced with the NovaSeq Reagent Kit v1.5 150x150 bp Sequencing. Libraries were constructed according to the manufacturer's protocol 10X chromium controller	Wild type Tübingen zebrafish were used for all experiments. Ages of animals are noted in sample title and age metadata. All zebrafish work was performed at University of Utah’s CBRZ zebrafish facility. This study was conducted under the approval of the Office of Institutional Animal Care and Use Committee IACUC no. 20 07013 of the University of Utah’s animal care and use program.	tissue:Testis\|age: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 µL 1X Hank's Balanced Salt Solution HBSS 50 µL 10% pluronic F 68 and 10 µL 0.26U/mL liberase TM. Tissue was incubated at 37°C for approximately 45 minutes while rotating at 750 rpm in an Eppendorf Thermomixer. The dissociation reaction was stopped by adding 1% bovine serum albumin BSA in 500 µL cold HBSS. The cell suspensions were filtered through a 40 µm cell strainer. Cells were pelleted in a 4°C centrifuge at 200g for 5 minutes washed with 0.5% BSA in 500 µL cold HBSS pelleted again and resuspended in 0.5% BSA in 500 µL cold HBSS. Single cell RNA sequencing libraries were prepared by the University of Utah High Throughput Genomics Shared Resource using the 10X Genomics Next GEM Single Cell three prime Gene Expression Library prep v3.1 with UDI. Libraries were sequenced with the NovaSeq Reagent Kit v1.5 150x150 bp Sequencing. Libraries were constructed according to the manufacturer's protocol 10X chromium controller	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP527811	loader:fastq load.py	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		6603266449	4452149795	4932656681	6015543518	1625857	SRX25789578	SRS22421027	SRA1952802	Gagnon, Biology, University of Utah	Gagnon, Biology, University of Utah	1	0.923		0.08981		0.74446		0.49211		100		B		usable mapping rate	illumina	novaseq_era	3prime	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-08-21	Adult	Adult	Gonad	Reproductive System
33642	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	pubmed:39470160	mo12 fish1 rep1	GSM8475560	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	post euthanasia by immersion in ice cold water testes were dissected from fish and immediately placed in a dissociation solution of 440 µL 1X Hank’s Balanced Salt Solution HBSS 50 µL 10% pluronic F 68 and 10 µL 0.26U/mL liberase TM. Tissue was incubated at 37°C for approximately 45 minutes while rotating at 750 rpm in an Eppendorf Thermomixer. The dissociation reaction was stopped by adding 1% bovine serum albumin BSA in 500 µL cold HBSS. The cell suspensions were filtered through a 40 µm cell strainer. Cells were pelleted in a 4°C centrifuge at 200g for 5 minutes washed with 0.5% BSA in 500 µL cold HBSS pelleted again and resuspended in 0.5% BSA in 500 µL cold HBSS. Single cell RNA sequencing libraries were prepared by the University of Utah High Throughput Genomics Shared Resource using the 10X Genomics Next GEM Single Cell 3’ Gene Expression Library prep v3.1 with UDI. Libraries were sequenced with the NovaSeq Reagent Kit v1.5 150x150 bp Sequencing. Libraries were constructed according to the manufacturer's protocol 10X chromium controller	Wild type Tübingen zebrafish were used for all experiments. Ages of animals are noted in sample title and age metadata. All zebrafish work was performed at University of Utah’s CBRZ zebrafish facility. This study was conducted under the approval of the Office of Institutional Animal Care and Use Committee IACUC no. 20 07013 of the University of Utah’s animal care and use program.	tissue:Testis\|age: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 µL 1X Hank's Balanced Salt Solution HBSS 50 µL 10% pluronic F 68 and 10 µL 0.26U/mL liberase TM. Tissue was incubated at 37°C for approximately 45 minutes while rotating at 750 rpm in an Eppendorf Thermomixer. The dissociation reaction was stopped by adding 1% bovine serum albumin BSA in 500 µL cold HBSS. The cell suspensions were filtered through a 40 µm cell strainer. Cells were pelleted in a 4°C centrifuge at 200g for 5 minutes washed with 0.5% BSA in 500 µL cold HBSS pelleted again and resuspended in 0.5% BSA in 500 µL cold HBSS. Single cell RNA sequencing libraries were prepared by the University of Utah High Throughput Genomics Shared Resource using the 10X Genomics Next GEM Single Cell three prime Gene Expression Library prep v3.1 with UDI. Libraries were sequenced with the NovaSeq Reagent Kit v1.5 150x150 bp Sequencing. Libraries were constructed according to the manufacturer's protocol 10X chromium controller	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP527811	loader:fastq load.py	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		5596266137	3743379083	4132198708	5092012085	1370687	SRX25789577	SRS22421019	SRA1952802	Gagnon, Biology, University of Utah	Gagnon, Biology, University of Utah	1	0.92275		0.09038		0.74572		0.48557		100		B		usable mapping rate	illumina	novaseq_era	3prime	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-08-21	Adult	Adult	Gonad	Reproductive System
33643	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	pubmed:39470160	mo5 fish2 rep3	GSM8475559	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	post euthanasia by immersion in ice cold water testes were dissected from fish and immediately placed in a dissociation solution of 440 µL 1X Hank’s Balanced Salt Solution HBSS 50 µL 10% pluronic F 68 and 10 µL 0.26U/mL liberase TM. Tissue was incubated at 37°C for approximately 45 minutes while rotating at 750 rpm in an Eppendorf Thermomixer. The dissociation reaction was stopped by adding 1% bovine serum albumin BSA in 500 µL cold HBSS. The cell suspensions were filtered through a 40 µm cell strainer. Cells were pelleted in a 4°C centrifuge at 200g for 5 minutes washed with 0.5% BSA in 500 µL cold HBSS pelleted again and resuspended in 0.5% BSA in 500 µL cold HBSS. Single cell RNA sequencing libraries were prepared by the University of Utah High Throughput Genomics Shared Resource using the 10X Genomics Next GEM Single Cell 3’ Gene Expression Library prep v3.1 with UDI. Libraries were sequenced with the NovaSeq Reagent Kit v1.5 150x150 bp Sequencing. Libraries were constructed according to the manufacturer's protocol 10X chromium controller	Wild type Tübingen zebrafish were used for all experiments. Ages of animals are noted in sample title and age metadata. All zebrafish work was performed at University of Utah’s CBRZ zebrafish facility. This study was conducted under the approval of the Office of Institutional Animal Care and Use Committee IACUC no. 20 07013 of the University of Utah’s animal care and use program.	tissue:Testis\|age:5 month	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 µL 1X Hank's Balanced Salt Solution HBSS 50 µL 10% pluronic F 68 and 10 µL 0.26U/mL liberase TM. Tissue was incubated at 37°C for approximately 45 minutes while rotating at 750 rpm in an Eppendorf Thermomixer. The dissociation reaction was stopped by adding 1% bovine serum albumin BSA in 500 µL cold HBSS. The cell suspensions were filtered through a 40 µm cell strainer. Cells were pelleted in a 4°C centrifuge at 200g for 5 minutes washed with 0.5% BSA in 500 µL cold HBSS pelleted again and resuspended in 0.5% BSA in 500 µL cold HBSS. Single cell RNA sequencing libraries were prepared by the University of Utah High Throughput Genomics Shared Resource using the 10X Genomics Next GEM Single Cell three prime Gene Expression Library prep v3.1 with UDI. Libraries were sequenced with the NovaSeq Reagent Kit v1.5 150x150 bp Sequencing. Libraries were constructed according to the manufacturer's protocol 10X chromium controller	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP527811	loader:fastq load.py	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		0.18284		0.70709		0.49769		150		B		usable mapping rate	illumina	novaseq_era	3prime	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-08-21	Adult	Adult	Gonad	Reproductive System
33644	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	pubmed:39470160	mo5 fish2 rep2	GSM8475558	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	post euthanasia by immersion in ice cold water testes were dissected from fish and immediately placed in a dissociation solution of 440 µL 1X Hank’s Balanced Salt Solution HBSS 50 µL 10% pluronic F 68 and 10 µL 0.26U/mL liberase TM. Tissue was incubated at 37°C for approximately 45 minutes while rotating at 750 rpm in an Eppendorf Thermomixer. The dissociation reaction was stopped by adding 1% bovine serum albumin BSA in 500 µL cold HBSS. The cell suspensions were filtered through a 40 µm cell strainer. Cells were pelleted in a 4°C centrifuge at 200g for 5 minutes washed with 0.5% BSA in 500 µL cold HBSS pelleted again and resuspended in 0.5% BSA in 500 µL cold HBSS. Single cell RNA sequencing libraries were prepared by the University of Utah High Throughput Genomics Shared Resource using the 10X Genomics Next GEM Single Cell 3’ Gene Expression Library prep v3.1 with UDI. Libraries were sequenced with the NovaSeq Reagent Kit v1.5 150x150 bp Sequencing. Libraries were constructed according to the manufacturer's protocol 10X chromium controller	Wild type Tübingen zebrafish were used for all experiments. Ages of animals are noted in sample title and age metadata. All zebrafish work was performed at University of Utah’s CBRZ zebrafish facility. This study was conducted under the approval of the Office of Institutional Animal Care and Use Committee IACUC no. 20 07013 of the University of Utah’s animal care and use program.	tissue:Testis\|age:5 month	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 µL 1X Hank's Balanced Salt Solution HBSS 50 µL 10% pluronic F 68 and 10 µL 0.26U/mL liberase TM. Tissue was incubated at 37°C for approximately 45 minutes while rotating at 750 rpm in an Eppendorf Thermomixer. The dissociation reaction was stopped by adding 1% bovine serum albumin BSA in 500 µL cold HBSS. The cell suspensions were filtered through a 40 µm cell strainer. Cells were pelleted in a 4°C centrifuge at 200g for 5 minutes washed with 0.5% BSA in 500 µL cold HBSS pelleted again and resuspended in 0.5% BSA in 500 µL cold HBSS. Single cell RNA sequencing libraries were prepared by the University of Utah High Throughput Genomics Shared Resource using the 10X Genomics Next GEM Single Cell three prime Gene Expression Library prep v3.1 with UDI. Libraries were sequenced with the NovaSeq Reagent Kit v1.5 150x150 bp Sequencing. Libraries were constructed according to the manufacturer's protocol 10X chromium controller	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP527811	loader:fastq load.py	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		0.20483		0.70475		0.49687		150		B		usable mapping rate	illumina	novaseq_era	3prime	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-08-21	Adult	Adult	Gonad	Reproductive System
33645	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	pubmed:39470160	mo5 fish2 rep1	GSM8475557	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	post euthanasia by immersion in ice cold water testes were dissected from fish and immediately placed in a dissociation solution of 440 µL 1X Hank’s Balanced Salt Solution HBSS 50 µL 10% pluronic F 68 and 10 µL 0.26U/mL liberase TM. Tissue was incubated at 37°C for approximately 45 minutes while rotating at 750 rpm in an Eppendorf Thermomixer. The dissociation reaction was stopped by adding 1% bovine serum albumin BSA in 500 µL cold HBSS. The cell suspensions were filtered through a 40 µm cell strainer. Cells were pelleted in a 4°C centrifuge at 200g for 5 minutes washed with 0.5% BSA in 500 µL cold HBSS pelleted again and resuspended in 0.5% BSA in 500 µL cold HBSS. Single cell RNA sequencing libraries were prepared by the University of Utah High Throughput Genomics Shared Resource using the 10X Genomics Next GEM Single Cell 3’ Gene Expression Library prep v3.1 with UDI. Libraries were sequenced with the NovaSeq Reagent Kit v1.5 150x150 bp Sequencing. Libraries were constructed according to the manufacturer's protocol 10X chromium controller	Wild type Tübingen zebrafish were used for all experiments. Ages of animals are noted in sample title and age metadata. All zebrafish work was performed at University of Utah’s CBRZ zebrafish facility. This study was conducted under the approval of the Office of Institutional Animal Care and Use Committee IACUC no. 20 07013 of the University of Utah’s animal care and use program.	tissue:Testis\|age:5 month	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 µL 1X Hank's Balanced Salt Solution HBSS 50 µL 10% pluronic F 68 and 10 µL 0.26U/mL liberase TM. Tissue was incubated at 37°C for approximately 45 minutes while rotating at 750 rpm in an Eppendorf Thermomixer. The dissociation reaction was stopped by adding 1% bovine serum albumin BSA in 500 µL cold HBSS. The cell suspensions were filtered through a 40 µm cell strainer. Cells were pelleted in a 4°C centrifuge at 200g for 5 minutes washed with 0.5% BSA in 500 µL cold HBSS pelleted again and resuspended in 0.5% BSA in 500 µL cold HBSS. Single cell RNA sequencing libraries were prepared by the University of Utah High Throughput Genomics Shared Resource using the 10X Genomics Next GEM Single Cell three prime Gene Expression Library prep v3.1 with UDI. Libraries were sequenced with the NovaSeq Reagent Kit v1.5 150x150 bp Sequencing. Libraries were constructed according to the manufacturer's protocol 10X chromium controller	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP527811	loader:fastq load.py	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		0.20357		0.70307		0.4898		150		B		usable mapping rate	illumina	novaseq_era	3prime	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-08-21	Adult	Adult	Gonad	Reproductive System
33646	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	pubmed:39470160	mo5 fish1 rep3	GSM8475556	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	post euthanasia by immersion in ice cold water testes were dissected from fish and immediately placed in a dissociation solution of 440 µL 1X Hank’s Balanced Salt Solution HBSS 50 µL 10% pluronic F 68 and 10 µL 0.26U/mL liberase TM. Tissue was incubated at 37°C for approximately 45 minutes while rotating at 750 rpm in an Eppendorf Thermomixer. The dissociation reaction was stopped by adding 1% bovine serum albumin BSA in 500 µL cold HBSS. The cell suspensions were filtered through a 40 µm cell strainer. Cells were pelleted in a 4°C centrifuge at 200g for 5 minutes washed with 0.5% BSA in 500 µL cold HBSS pelleted again and resuspended in 0.5% BSA in 500 µL cold HBSS. Single cell RNA sequencing libraries were prepared by the University of Utah High Throughput Genomics Shared Resource using the 10X Genomics Next GEM Single Cell 3’ Gene Expression Library prep v3.1 with UDI. Libraries were sequenced with the NovaSeq Reagent Kit v1.5 150x150 bp Sequencing. Libraries were constructed according to the manufacturer's protocol 10X chromium controller	Wild type Tübingen zebrafish were used for all experiments. Ages of animals are noted in sample title and age metadata. All zebrafish work was performed at University of Utah’s CBRZ zebrafish facility. This study was conducted under the approval of the Office of Institutional Animal Care and Use Committee IACUC no. 20 07013 of the University of Utah’s animal care and use program.	tissue:Testis\|age:5 month	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 µL 1X Hank's Balanced Salt Solution HBSS 50 µL 10% pluronic F 68 and 10 µL 0.26U/mL liberase TM. Tissue was incubated at 37°C for approximately 45 minutes while rotating at 750 rpm in an Eppendorf Thermomixer. The dissociation reaction was stopped by adding 1% bovine serum albumin BSA in 500 µL cold HBSS. The cell suspensions were filtered through a 40 µm cell strainer. Cells were pelleted in a 4°C centrifuge at 200g for 5 minutes washed with 0.5% BSA in 500 µL cold HBSS pelleted again and resuspended in 0.5% BSA in 500 µL cold HBSS. Single cell RNA sequencing libraries were prepared by the University of Utah High Throughput Genomics Shared Resource using the 10X Genomics Next GEM Single Cell three prime Gene Expression Library prep v3.1 with UDI. Libraries were sequenced with the NovaSeq Reagent Kit v1.5 150x150 bp Sequencing. Libraries were constructed according to the manufacturer's protocol 10X chromium controller	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP527811	loader:fastq load.py	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		0.20924		0.70427		0.51976		150		B		usable mapping rate	illumina	novaseq_era	3prime	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-08-21	Adult	Adult	Gonad	Reproductive System
33647	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	pubmed:39470160	mo5 fish1 rep2	GSM8475555	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	post euthanasia by immersion in ice cold water testes were dissected from fish and immediately placed in a dissociation solution of 440 µL 1X Hank’s Balanced Salt Solution HBSS 50 µL 10% pluronic F 68 and 10 µL 0.26U/mL liberase TM. Tissue was incubated at 37°C for approximately 45 minutes while rotating at 750 rpm in an Eppendorf Thermomixer. The dissociation reaction was stopped by adding 1% bovine serum albumin BSA in 500 µL cold HBSS. The cell suspensions were filtered through a 40 µm cell strainer. Cells were pelleted in a 4°C centrifuge at 200g for 5 minutes washed with 0.5% BSA in 500 µL cold HBSS pelleted again and resuspended in 0.5% BSA in 500 µL cold HBSS. Single cell RNA sequencing libraries were prepared by the University of Utah High Throughput Genomics Shared Resource using the 10X Genomics Next GEM Single Cell 3’ Gene Expression Library prep v3.1 with UDI. Libraries were sequenced with the NovaSeq Reagent Kit v1.5 150x150 bp Sequencing. Libraries were constructed according to the manufacturer's protocol 10X chromium controller	Wild type Tübingen zebrafish were used for all experiments. Ages of animals are noted in sample title and age metadata. All zebrafish work was performed at University of Utah’s CBRZ zebrafish facility. This study was conducted under the approval of the Office of Institutional Animal Care and Use Committee IACUC no. 20 07013 of the University of Utah’s animal care and use program.	tissue:Testis\|age:5 month	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 µL 1X Hank's Balanced Salt Solution HBSS 50 µL 10% pluronic F 68 and 10 µL 0.26U/mL liberase TM. Tissue was incubated at 37°C for approximately 45 minutes while rotating at 750 rpm in an Eppendorf Thermomixer. The dissociation reaction was stopped by adding 1% bovine serum albumin BSA in 500 µL cold HBSS. The cell suspensions were filtered through a 40 µm cell strainer. Cells were pelleted in a 4°C centrifuge at 200g for 5 minutes washed with 0.5% BSA in 500 µL cold HBSS pelleted again and resuspended in 0.5% BSA in 500 µL cold HBSS. Single cell RNA sequencing libraries were prepared by the University of Utah High Throughput Genomics Shared Resource using the 10X Genomics Next GEM Single Cell three prime Gene Expression Library prep v3.1 with UDI. Libraries were sequenced with the NovaSeq Reagent Kit v1.5 150x150 bp Sequencing. Libraries were constructed according to the manufacturer's protocol 10X chromium controller	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP527811	loader:fastq load.py	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		0.2152		0.70007		0.51331		150		B		usable mapping rate	illumina	novaseq_era	3prime	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-08-21	Adult	Adult	Gonad	Reproductive System
33648	33648	SRR30329369	SRX25789571	SRS22421015	SRP527811	PRJNA1150539	Germ cell progression through zebrafish spermatogenesis declines with age	GSE275361	Transcriptome Analysis	Vertebrate spermatogonial stem cells maintain sperm production over the lifetime of an animal but fertility declines with age. While morphological studies have informed our understanding of typical spermatogenesis the molecular and cellular mechanisms underlying the maintenance and decline of spermatogenesis are not yet understood. We used single cell RNA sequencing to generate a developmental atlas of the aging zebrafish testis. All testes contained spermatogonia but we observed a progressive decline in spermatogenesis that correlates with age. Testes from some older males only contained spermatogonia and a reduced population of spermatocytes. Spermatogonia in older males are transcriptionally distinct from spermatogonia in testes capable of robust spermatogenesis. Immune cells including macrophages and lymphocytes drastically increase in abundance in testes that cannot complete spermatogenesis. Our developmental atlas reveals the cellular changes as the testis ages and defines a molecular roadmap for the regulation of spermatogenesis. Overall design: scRNA seq of dissected zebrafish testes from 5 12 20 22 and 27 month individuals	pubmed:39470160	mo5 fish1 rep1	GSM8475554	source name:Testis\|tissue:Testis\|age:5 month\|geo loc name:missing\|collection date:missing	mo5 fish1 rep1	Single cell RNA seq reads were processed with Cellranger from 10X Genomics with the default settings using GRCz11 v4.3.2 reference Lawson et al. 2020 for zebrafish read alignments. Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files	Testis	post euthanasia by immersion in ice cold water testes were dissected from fish and immediately placed in a dissociation solution of 440 µL 1X Hank’s Balanced Salt Solution HBSS 50 µL 10% pluronic F 68 and 10 µL 0.26U/mL liberase TM. Tissue was incubated at 37°C for approximately 45 minutes while rotating at 750 rpm in an Eppendorf Thermomixer. The dissociation reaction was stopped by adding 1% bovine serum albumin BSA in 500 µL cold HBSS. The cell suspensions were filtered through a 40 µm cell strainer. Cells were pelleted in a 4°C centrifuge at 200g for 5 minutes washed with 0.5% BSA in 500 µL cold HBSS pelleted again and resuspended in 0.5% BSA in 500 µL cold HBSS. Single cell RNA sequencing libraries were prepared by the University of Utah High Throughput Genomics Shared Resource using the 10X Genomics Next GEM Single Cell 3’ Gene Expression Library prep v3.1 with UDI. Libraries were sequenced with the NovaSeq Reagent Kit v1.5 150x150 bp Sequencing. Libraries were constructed according to the manufacturer's protocol 10X chromium controller	Wild type Tübingen zebrafish were used for all experiments. Ages of animals are noted in sample title and age metadata. All zebrafish work was performed at University of Utah’s CBRZ zebrafish facility. This study was conducted under the approval of the Office of Institutional Animal Care and Use Committee IACUC no. 20 07013 of the University of Utah’s animal care and use program.	tissue:Testis\|age:5 month	GSM8475554	GSM8475554: mo5 fish1 rep1; Danio rerio; RNA Seq	GSM8475554 r1	GSM8475554	1	post euthanasia by immersion in ice cold water testes were dissected from fish and immediately placed in a dissociation solution of 440 µL 1X Hank's Balanced Salt Solution HBSS 50 µL 10% pluronic F 68 and 10 µL 0.26U/mL liberase TM. Tissue was incubated at 37°C for approximately 45 minutes while rotating at 750 rpm in an Eppendorf Thermomixer. The dissociation reaction was stopped by adding 1% bovine serum albumin BSA in 500 µL cold HBSS. The cell suspensions were filtered through a 40 µm cell strainer. Cells were pelleted in a 4°C centrifuge at 200g for 5 minutes washed with 0.5% BSA in 500 µL cold HBSS pelleted again and resuspended in 0.5% BSA in 500 µL cold HBSS. Single cell RNA sequencing libraries were prepared by the University of Utah High Throughput Genomics Shared Resource using the 10X Genomics Next GEM Single Cell three prime Gene Expression Library prep v3.1 with UDI. Libraries were sequenced with the NovaSeq Reagent Kit v1.5 150x150 bp Sequencing. Libraries were constructed according to the manufacturer's protocol 10X chromium controller	RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP527811	loader:fastq load.py	19779X1_220608_A00421_0445_BHVGF7DSX3_S2_L003_R2_001.fastq.gz 19779X1_220608_A00421_0445_BHVGF7DSX3_S2_L003_R1_001.fastq.gz 19779X1_220608_A00421_0445_BHVGF7DSX3_S2_L003_I2_001.fastq.gz 19779X1_220608_A00421_0445_BHVGF7DSX3_S2_L003_I1_001.fastq.gz	fastq fastq fastq fastq	76667132916.0	387207742.0	GSM8475554 r1	0:10 1:10 2:28 3:150	A:17411509978;C:12112655410;G:13713621582;T:14843326531;N:47799	10	10	28	150	17411509978	12112655410	13713621582	14843326531	47799	SRX25789571	SRS22421015	SRA1952802	Gagnon, Biology, University of Utah	Gagnon, Biology, University of Utah	1	0.92205		0.21455		0.69952		0.51581		150		B		usable mapping rate	illumina	novaseq_era	3prime	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2024-08-21	Adult	Adult	Gonad	Reproductive System
68777	68777	SRR18188990	SRX14335888	SRS12150682	SRP362100	PRJNA811725	Single cell sequencing of zebra fish primordial germ cell	PRJNA811725	Other	Based on the transcriptome we constructed long non coding RNA lncRNA profile of zebrafish primordial germ cells PGCs to further discern functional lncRNA that might play role in PGCs development.			GC9	strain:kop:EGFP 3 primeUTR nanos primordial germ cell transgenic line\|isolate:Based on green fluorescence single PGC was distinctively identified and picked out using a capillary tube\|age:5hpf\|dev stage:30% 50% epiboly\|sex:not applicable\|tissue:primordial germ cell\|cell type:primordial germ cell\|replicate:replicate3\|BioSampleModel:Model organism or animal								3pgc	3 3pgc	3 3pgc	primordial germ cell from 5 hpf zebrafish embryos		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	RANDOM	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP362100		GC9_R1.fq.gz GC9_R2.fq.gz	fastq fastq	16392678600.0	54642262.0	GC9 R1.fq.gz	0:150 1:150	A:4548403510;C:3786937912;G:3801036342;T:4255236177;N:1064659	150	150			4548403510	3786937912	3801036342	4255236177	1064659	SRX14335888	SRS12150682	SRA1379556	Sun-Yat sen University\|School of Marine Science	Sun-Yat sen University	2	0.92711	0.93044	0.08622	0.08652	0.79693	0.80306	0.58096	0.58168	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_generic	generic-scrnaseq-only	China	2022-03-02	Multi-stage	Embryo	Gonad	Reproductive System
68778	68778	SRR18188991	SRX14335887	SRS12150683	SRP362100	PRJNA811725	Single cell sequencing of zebra fish primordial germ cell	PRJNA811725	Other	Based on the transcriptome we constructed long non coding RNA lncRNA profile of zebrafish primordial germ cells PGCs to further discern functional lncRNA that might play role in PGCs development.			GC4	strain:kop:EGFP 3 primeUTR nanos primordial germ cell transgenic line\|isolate:Based on green fluorescence single PGC was distinctively identified and picked out using a capillary tube\|age:5hpf\|dev stage:30% 50% epiboly\|sex:not applicable\|tissue:primordial germ cell\|cell type:primordial germ cell\|replicate:replicate2\|BioSampleModel:Model organism or animal								2pgc	2 2pgc	2 2pgc	primordial germ cell from 5 hpf zebrafish embryos		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	RANDOM	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP362100		GC4_R1.fq.gz GC4_R2.fq.gz	fastq fastq	14471348700.0	48237829.0	GC4 R1.fq.gz	0:150 1:150	A:4127039158;C:3211803959;G:3224340004;T:3907215356;N:950223	150	150			4127039158	3211803959	3224340004	3907215356	950223	SRX14335887	SRS12150683	SRA1379556	Sun-Yat sen University\|School of Marine Science	Sun-Yat sen University	2	0.91951	0.91886	0.14001	0.14043	0.75777	0.76605	0.55643	0.55313	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_generic	generic-scrnaseq-only	China	2022-03-02	Multi-stage	Embryo	Gonad	Reproductive System
68779	68779	SRR18188992	SRX14335886	SRS12150681	SRP362100	PRJNA811725	Single cell sequencing of zebra fish primordial germ cell	PRJNA811725	Other	Based on the transcriptome we constructed long non coding RNA lncRNA profile of zebrafish primordial germ cells PGCs to further discern functional lncRNA that might play role in PGCs development.			GC1	strain:kop:EGFP 3 primeUTR nanos primordial germ cell transgenic line\|isolate:Based on green fluorescence single PGC was distinctively identified and picked out using a capillary tube\|age:5hpf\|dev stage:30% 50% epiboly\|sex:not applicable\|tissue:primordial germ cell\|cell type:primordial germ cell\|replicate:replicate1\|BioSampleModel:Model organism or animal								1pgc	1 1pgc	1 1pgc	primordial germ cell from 5 hpf zebrafish embryos		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	RANDOM	PAIRED	ILLUMINA	Illumina HiSeq 2500	SRP362100		GC1_R1.fq.gz GC1_R2.fq.gz	fastq fastq	18801698100.0	62672327.0	GC1 R1.fq.gz	0:150 1:150	A:5242992703;C:4310290517;G:4334163362;T:4913025193;N:1226325	150	150			5242992703	4310290517	4334163362	4913025193	1226325	SRX14335886	SRS12150681	SRA1379556	Sun-Yat sen University\|School of Marine Science	Sun-Yat sen University	2	0.93192	0.93277	0.09532	0.09559	0.78358	0.7906	0.5661	0.56344	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	random_priming	unknown	sc	single_cell_generic	generic-scrnaseq-only	China	2022-03-02	Multi-stage	Embryo	Gonad	Reproductive System

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CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;