metadata: run_metadata: 57 rows where technology = "10x" and tissue

57 rows where technology = "10x" and tissue_curation = "Gonad"

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.treatmentprotocol	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
29187	29187	SRR8176747	SRX4996876	SRS4031879	SRP480945	PRJNA1055160	Single cell RNA seq of Juvenile Zebrafish Gonads from the Nadia Strain	PRJNA1055160	Other	We used single cell RNA Seq 10x Genomics Chromium to profile the transcriptomes of undifferentiated ZZ and ZW gonads at 19 dpf and immature ZZ and ZW gonads at 30 dpf	pubmed:38529407	Nadia 19dpf ZZ Gonad Single Cell RNA Seq	Nadia 19dpf ZZ Gonad Single Cell RNA Seq	strain:Nadia\|age:19 dpf provider:John H. Postlethwait University of Oregon\|genotype:ZZ\|BioSampleModel:Model organism or animal									scRNA Seq of Danio rerio: Nadia 19dpf ZZ gonad	Nadia 19dpf ZZ gonad	Nadia 19dpf ZZ gonad	A single cell suspension was prepared from the pooled gonads of five individuals. The sequencing library was prepared with the Chromium Single Cell 3 Library & Gel Bead Kit v2 10x Genomics.		RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	NextSeq 500	SRP480945	loader:fastq load.py			15090036999.0	107021539.0	zz 19NAmale I1 001.fastq.gz	0:8 1:133	A:4154103253;C:3402890354;G:3765557416;T:3755723849;N:11762127	8	133			4154103253	3402890354	3765557416	3755723849	11762127	SRX4996876	SRS4031879	SRA807619	University of Oregon\|Institute of Neuroscience	University of Oregon												T	B	sc-like readlen	illumina	nextseq	unknown	poly_a	unknown	sc	single_cell_droplet	10x	United States	2018-11-08	Larval	Larval	Gonad	Reproductive System
29188	29188	SRR8176753	SRX4996870	SRS4031878	SRP480945	PRJNA1055160	Single cell RNA seq of Juvenile Zebrafish Gonads from the Nadia Strain	PRJNA1055160	Other	We used single cell RNA Seq 10x Genomics Chromium to profile the transcriptomes of undifferentiated ZZ and ZW gonads at 19 dpf and immature ZZ and ZW gonads at 30 dpf	pubmed:38529407	Nadia 30dpf ZZ Gonad Single Cell RNA Seq	Nadia 30dpf ZZ Gonad Single Cell RNA Seq	strain:Nadia\|age:30 dpf provider:John H. Postlethwait University of Oregon\|genotype:ZZ\|BioSampleModel:Model organism or animal									scRNA Seq of Danio rerio: Nadia 30dpf ZZ gonad	Nadia 30dpf ZZ gonad	Nadia 30dpf ZZ gonad	A single cell suspension was prepared from the pooled gonads of five individuals. The sequencing library was prepared with the Chromium Single Cell 3 Library & Gel Bead Kit v2 10x Genomics.		RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	NextSeq 500	SRP480945	loader:fastq load.py			23587173438.0	167284918.0	1 I1 001.fastq.gz	0:8 1:133	A:6732844252;C:4934497997;G:5685086026;T:6219863789;N:14881374	8	133			6732844252	4934497997	5685086026	6219863789	14881374	SRX4996870	SRS4031878	SRA807619	University of Oregon\|Institute of Neuroscience	University of Oregon												T	B	sc-like readlen	illumina	nextseq	unknown	poly_a	unknown	sc	single_cell_droplet	10x	United States	2018-11-08	Juvenile	Juvenile	Gonad	Reproductive System
29189	29189	SRR8176754	SRX4996869	SRS4031877	SRP480945	PRJNA1055160	Single cell RNA seq of Juvenile Zebrafish Gonads from the Nadia Strain	PRJNA1055160	Other	We used single cell RNA Seq 10x Genomics Chromium to profile the transcriptomes of undifferentiated ZZ and ZW gonads at 19 dpf and immature ZZ and ZW gonads at 30 dpf	pubmed:38529407	Nadia 30dpf ZW Gonad Single Cell RNA Seq	Nadia 30dpf ZW Gonad Single Cell RNA Seq	strain:Nadia\|age:30 dpf provider:John H. Postlethwait University of Oregon\|genotype:ZW\|BioSampleModel:Model organism or animal									scRNA Seq of Danio rerio: Nadia 30dpf ZW gonad	Nadia 30dpf ZW gonad	Nadia 30dpf ZW gonad	A single cell suspension was prepared from the pooled gonads of five individuals. The sequencing library was prepared with the Chromium Single Cell 3 Library & Gel Bead Kit v2 10x Genomics.		RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	NextSeq 500	SRP480945	loader:fastq load.py			43358808480.0	307509280.0	2 I1 001.fastq.gz	0:8 1:133	A:12290612367;C:8880655083;G:10261318751;T:11898771792;N:27450487	8	133			12290612367	8880655083	10261318751	11898771792	27450487	SRX4996869	SRS4031877	SRA807619	University of Oregon\|Institute of Neuroscience	University of Oregon												T	B	sc-like readlen	illumina	nextseq	unknown	poly_a	unknown	sc	single_cell_droplet	10x	United States	2018-11-08	Juvenile	Juvenile	Gonad	Reproductive System
29190	29190	SRR8176756	SRX4996867	SRS4031876	SRP480945	PRJNA1055160	Single cell RNA seq of Juvenile Zebrafish Gonads from the Nadia Strain	PRJNA1055160	Other	We used single cell RNA Seq 10x Genomics Chromium to profile the transcriptomes of undifferentiated ZZ and ZW gonads at 19 dpf and immature ZZ and ZW gonads at 30 dpf	pubmed:38529407	Nadia 19dpf ZW Gonad Single Cell RNA Seq	Nadia 19dpf ZW Gonad Single Cell RNA Seq	strain:Nadia\|age:19 dpf provider:John H. Postlethwait University of Oregon\|genotype:ZW\|BioSampleModel:Model organism or animal									scRNA Seq of Danio rerio: Nadia 19dpf ZW gonad	Nadia 19dpf ZW gonad	Nadia 19dpf ZW gonad	A single cell suspension was prepared from the pooled gonads of five individuals. The sequencing library was prepared with the Chromium Single Cell 3 Library & Gel Bead Kit v2 10x Genomics.		RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	NextSeq 500	SRP480945	loader:fastq load.py			17141425554.0	121570394.0	zw 19NAfem I1 001.fastq.gz	0:8 1:133	A:4656207219;C:3824531650;G:4322736498;T:4324676442;N:13273745	8	133			4656207219	3824531650	4322736498	4324676442	13273745	SRX4996867	SRS4031876	SRA807619	University of Oregon\|Institute of Neuroscience	University of Oregon												T	B	sc-like readlen	illumina	nextseq	unknown	poly_a	unknown	sc	single_cell_droplet	10x	United States	2018-11-08	Larval	Larval	Gonad	Reproductive System
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
67758	67758	SRR17262950	SRX13441050	SRS11340479	SRP351377	PRJNA789855	Single cell transcriptome reveals insights into the development and function of the zebrafish ovary	GSE191137	Transcriptome Analysis	Zebrafish are an established research organism that has made many contributions to our understanding of vertebrate tissue and organ development yet there are still significant gaps in our understanding of the genes that regulate gonad development sex and reproduction. Unlike the development of many organs such as the brain and heart that form during the first few days of development zebrafish gonads do not begin to form until the larval stage =5 dpf. Thus forward genetic screens have identified very few genes required for gonad development. In addition bulk RNA sequencing studies which identify genes expressed in the gonads do not have the resolution necessary to define minor cell populations that may play significant roles in development and function of these organs. To overcome these limitations we have used single cell RNA sequencing to determine the transcriptomes of cells isolated from juvenile zebrafish ovaries. This resulted in the profiles of 10 658 germ cells and 14 431 somatic cells. Our germ cell data represents all developmental stages from germline stem cells to early meiotic oocytes. Our somatic cell data represents all known somatic cell types including follicle cells theca cells and interstitial stromal cells. Further analysis revealed an unexpected number of cell subpopulations within these broadly defined cell types. To further define their functional significance we determined the location of these cell subpopulations within the ovary. Finally for select examples we used gene knockout experiments to determine the role of newly identified genes. Our results reveal novel insights into ovarian development and function and the sequencing information will provide a valuable resource for future studies. Overall design: Single cell RNA sequencing of 40 dpf zebrafish ovaries	pubmed:35588359	40 dpf zebrafish ovaries cells zx4	GSM5739896	tissue:40 dpf zebrafish ovaries\|cell type:Ovary cells\|genotype:AB wildtype	40 dpf zebrafish ovaries cells zx4	A General Transfer Format GTF gene annotation filerelease 96 for the GRCz11 zebrafish genome was downloaded from Ensembl Genome Browser and filtered using the “mkgtf” function in Cell Ranger v3.0.2; 10x Genomic to retain the following attributes: protein coding lincRNA and antisense. A genome reference file was generated with Cell Ranger’s “mkref” function using the GRCz11 zebrafish genome obtained from the Ensembl Genome Browser with alternative loci scaffolds removed and the filtered GTF file. GRCz11 zebrafish genome FASTQ file from Ensembl Genome Browser with alternative loci scaffolds removed and the filtered GTF file described above were used to generate the count file using the “count” function in Cell Ranger v3.0.2; 10x Genomic. “expect cells” was setted to 10000 based on estimated cell recovery. Genome build: GRCz11 Supplementary files format and content: Filtered or raw matrix files generated from Cell Ranger in one zip file.	40 dpf zebrafish ovaries		Somatic ovary cells were dissociated using a modification of Elkouby and Mullins 2016. 40 pairs of 40 dpf ovaries were dissected from Tgpiwil1:egfp transgenic fish Leu et al. 2010 were dissected and stored in a LoBind tube containing 2mL of L15. Tissues were minced with microdissection scissors into < 1 mm pieces. post the tissue had settled to the bottom of the tube the media was replaced with 5mL of digestive enzyme mixture 3 mg/mL collagenase I Cat.No. C0130; Sigma Aldrich 3 mg/mL collagenase II Cat.No. C6885; Sigma Aldrich and 1.6 mg/mL hyaluronidase Cat.No. H4272; Sigma Aldrich in L15 and incubated on an orbital rotator at room temperature . The suspension was monitored every 10 mins until a minimal number of cell clumps were observed 30 min.. Cells were centrifuged for 3 mins at 300 x g and resuspended in 5 mL of 5x TrypLE Cat.No. A1217701; Thermo Fisher in L15 and incubated on an orbital rotator at room temperature for 15 min. The trypsin reaction was stopped by adding 500 µL of 2.8 mg/mL trypsin inhibitor in L15 and incubated on an orbital rotator at room temperature for 1 min. The cell suspension was then added to 25 ml of L15 in a 50 ml conical tube to dilute the trypsin and centrifuged for 3 min at 300 x g. The cell pellet was resuspended and washed two times with 5 mL of L15 using a P1000 pipette and centrifuged for 3 mins at 300 x g. The cell pellet was then resuspended and filtered as described above. Single cell RNA sequencing libraries were prepared by the UC Davis DNA Technologies core. Briefly barcoded 3’ single cell libraries were prepared from dissociated cell suspensions or sorted cells using the Chromium Single Cell 3’ Library and Gel Bead kit V3 10X Genomics for sequencing according to the manufacturer’s recommendations. All libraries were targeted at 10 000 cell recovery and were amplified using 11 cycles. The cDNA and library fragment size distribution was verified via micro capillary gel electrophoresis on a Bioanalyzer 2100 Agilent. The libraries were quantified by fluorometry on …	Zebrafish husbandry was performed as previously described Westerfield 2000.	cell type:Ovary cells\|genotype:AB wildtype	GSM5739896	GSM5739896: 40 dpf zebrafish ovaries cells zx4; Danio rerio; ssRNA seq	GSM5739896 r1	GSM5739896	1	Somatic ovary cells were dissociated using a modification of Elkouby and Mullins 2016. 40 pairs of 40 dpf ovaries were dissected from Tgpiwil1:egfp transgenic fish Leu et al. 2010 were dissected and stored in a LoBind tube containing 2mL of L15. Tissues were minced with microdissection scissors into < 1 mm pieces. post the tissue had settled to the bottom of the tube the media was replaced with 5mL of digestive enzyme mixture 3 mg/mL collagenase I Cat.No. C0130; Sigma Aldrich 3 mg/mL collagenase II Cat.No. C6885; Sigma Aldrich and 1.6 mg/mL hyaluronidase Cat.No. H4272; Sigma Aldrich in L15 and incubated on an orbital rotator at room temperature . The suspension was monitored every 10 mins until a minimal number of cell clumps were observed 30 min.. Cells were centrifuged for 3 mins at 300 x g and resuspended in 5 mL of 5x TrypLE Cat.No. A1217701; Thermo Fisher in L15 and incubated on an orbital rotator at room temperature for 15 min. The trypsin reaction was stopped by adding 500 µL of 2.8 mg/mL trypsin inhibitor in L15 and incubated on an orbital rotator at room temperature for 1 min. The cell suspension was then added to 25 ml of L15 in a 50 ml conical tube to dilute the trypsin and centrifuged for 3 min at 300 x g. The cell pellet was resuspended and washed two times with 5 mL of L15 using a P1000 pipette and centrifuged for 3 mins at 300 x g. The cell pellet was then resuspended and filtered as described above. Single cell RNA sequencing libraries were prepared by the UC Davis DNA Technologies core. Briefly barcoded three prime single cell libraries were prepared from dissociated cell suspensions or sorted cells using the Chromium Single Cell three prime Library and Gel Bead kit V3 10X Genomics for sequencing according to the manufacturer's recommendations. All libraries were targeted at 10 000 cell recovery and were amplified using 11 cycles. The cDNA and library fragment size distribution was verified via micro capillary gel electrophoresis on a Bioanalyzer 2100 Agilent. The libraries were quantified …	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP351377		40dpf_ova_2_S1_L001_R1_001.fastq.gz 40dpf_ova_2_S1_L001_R2_001.fastq.gz	fastq fastq	109199255578.0	361586939.0	GSM5739896 r1	0:151 1:151	A:26889567766;C:19012911507;G:17705256458;T:45580417154;N:11102693	151	151			26889567766	19012911507	17705256458	45580417154	11102693	SRX13441050	SRS11340479	SRA1345465	Bruce Draper Lab, Molecular and Cellular Biology, University of California, Davis	Bruce Draper Lab, Molecular and Cellular Biology, University of California, Davis	2	0.00012	0.84311	5e-05	0.10842	0.99997	0.78486	1.0	0.53946	151	151	T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-12-17	Juvenile	Juvenile	Gonad	Reproductive System
67759	67759	SRR17262951	SRX13441049	SRS11340478	SRP351377	PRJNA789855	Single cell transcriptome reveals insights into the development and function of the zebrafish ovary	GSE191137	Transcriptome Analysis	Zebrafish are an established research organism that has made many contributions to our understanding of vertebrate tissue and organ development yet there are still significant gaps in our understanding of the genes that regulate gonad development sex and reproduction. Unlike the development of many organs such as the brain and heart that form during the first few days of development zebrafish gonads do not begin to form until the larval stage =5 dpf. Thus forward genetic screens have identified very few genes required for gonad development. In addition bulk RNA sequencing studies which identify genes expressed in the gonads do not have the resolution necessary to define minor cell populations that may play significant roles in development and function of these organs. To overcome these limitations we have used single cell RNA sequencing to determine the transcriptomes of cells isolated from juvenile zebrafish ovaries. This resulted in the profiles of 10 658 germ cells and 14 431 somatic cells. Our germ cell data represents all developmental stages from germline stem cells to early meiotic oocytes. Our somatic cell data represents all known somatic cell types including follicle cells theca cells and interstitial stromal cells. Further analysis revealed an unexpected number of cell subpopulations within these broadly defined cell types. To further define their functional significance we determined the location of these cell subpopulations within the ovary. Finally for select examples we used gene knockout experiments to determine the role of newly identified genes. Our results reveal novel insights into ovarian development and function and the sequencing information will provide a valuable resource for future studies. Overall design: Single cell RNA sequencing of 40 dpf zebrafish ovaries	pubmed:35588359	40 dpf zebrafish ovaries cells zx2	GSM5739895	tissue:40 dpf zebrafish ovaries\|cell type:Ovary cells\|genotype:AB wildtype	40 dpf zebrafish ovaries cells zx2	A General Transfer Format GTF gene annotation filerelease 96 for the GRCz11 zebrafish genome was downloaded from Ensembl Genome Browser and filtered using the “mkgtf” function in Cell Ranger v3.0.2; 10x Genomic to retain the following attributes: protein coding lincRNA and antisense. A genome reference file was generated with Cell Ranger’s “mkref” function using the GRCz11 zebrafish genome obtained from the Ensembl Genome Browser with alternative loci scaffolds removed and the filtered GTF file. GRCz11 zebrafish genome FASTQ file from Ensembl Genome Browser with alternative loci scaffolds removed and the filtered GTF file described above were used to generate the count file using the “count” function in Cell Ranger v3.0.2; 10x Genomic. “expect cells” was setted to 10000 based on estimated cell recovery. Genome build: GRCz11 Supplementary files format and content: Filtered or raw matrix files generated from Cell Ranger in one zip file.	40 dpf zebrafish ovaries		Somatic ovary cells were dissociated using a modification of Elkouby and Mullins 2016. 40 pairs of 40 dpf ovaries were dissected from Tgpiwil1:egfp transgenic fish Leu et al. 2010 were dissected and stored in a LoBind tube containing 2mL of L15. Tissues were minced with microdissection scissors into < 1 mm pieces. post the tissue had settled to the bottom of the tube the media was replaced with 5mL of digestive enzyme mixture 3 mg/mL collagenase I Cat.No. C0130; Sigma Aldrich 3 mg/mL collagenase II Cat.No. C6885; Sigma Aldrich and 1.6 mg/mL hyaluronidase Cat.No. H4272; Sigma Aldrich in L15 and incubated on an orbital rotator at room temperature . The suspension was monitored every 10 mins until a minimal number of cell clumps were observed 30 min.. Cells were centrifuged for 3 mins at 300 x g and resuspended in 5 mL of 5x TrypLE Cat.No. A1217701; Thermo Fisher in L15 and incubated on an orbital rotator at room temperature for 15 min. The trypsin reaction was stopped by adding 500 µL of 2.8 mg/mL trypsin inhibitor in L15 and incubated on an orbital rotator at room temperature for 1 min. The cell suspension was then added to 25 ml of L15 in a 50 ml conical tube to dilute the trypsin and centrifuged for 3 min at 300 x g. The cell pellet was resuspended and washed two times with 5 mL of L15 using a P1000 pipette and centrifuged for 3 mins at 300 x g. The cell pellet was then resuspended and filtered as described above. Single cell RNA sequencing libraries were prepared by the UC Davis DNA Technologies core. Briefly barcoded 3’ single cell libraries were prepared from dissociated cell suspensions or sorted cells using the Chromium Single Cell 3’ Library and Gel Bead kit V3 10X Genomics for sequencing according to the manufacturer’s recommendations. All libraries were targeted at 10 000 cell recovery and were amplified using 11 cycles. The cDNA and library fragment size distribution was verified via micro capillary gel electrophoresis on a Bioanalyzer 2100 Agilent. The libraries were quantified by fluorometry on …	Zebrafish husbandry was performed as previously described Westerfield 2000.	cell type:Ovary cells\|genotype:AB wildtype	GSM5739895	GSM5739895: 40 dpf zebrafish ovaries cells zx2; Danio rerio; ssRNA seq	GSM5739895 r1	GSM5739895	1	Somatic ovary cells were dissociated using a modification of Elkouby and Mullins 2016. 40 pairs of 40 dpf ovaries were dissected from Tgpiwil1:egfp transgenic fish Leu et al. 2010 were dissected and stored in a LoBind tube containing 2mL of L15. Tissues were minced with microdissection scissors into < 1 mm pieces. post the tissue had settled to the bottom of the tube the media was replaced with 5mL of digestive enzyme mixture 3 mg/mL collagenase I Cat.No. C0130; Sigma Aldrich 3 mg/mL collagenase II Cat.No. C6885; Sigma Aldrich and 1.6 mg/mL hyaluronidase Cat.No. H4272; Sigma Aldrich in L15 and incubated on an orbital rotator at room temperature . The suspension was monitored every 10 mins until a minimal number of cell clumps were observed 30 min.. Cells were centrifuged for 3 mins at 300 x g and resuspended in 5 mL of 5x TrypLE Cat.No. A1217701; Thermo Fisher in L15 and incubated on an orbital rotator at room temperature for 15 min. The trypsin reaction was stopped by adding 500 µL of 2.8 mg/mL trypsin inhibitor in L15 and incubated on an orbital rotator at room temperature for 1 min. The cell suspension was then added to 25 ml of L15 in a 50 ml conical tube to dilute the trypsin and centrifuged for 3 min at 300 x g. The cell pellet was resuspended and washed two times with 5 mL of L15 using a P1000 pipette and centrifuged for 3 mins at 300 x g. The cell pellet was then resuspended and filtered as described above. Single cell RNA sequencing libraries were prepared by the UC Davis DNA Technologies core. Briefly barcoded three prime single cell libraries were prepared from dissociated cell suspensions or sorted cells using the Chromium Single Cell three prime Library and Gel Bead kit V3 10X Genomics for sequencing according to the manufacturer's recommendations. All libraries were targeted at 10 000 cell recovery and were amplified using 11 cycles. The cDNA and library fragment size distribution was verified via micro capillary gel electrophoresis on a Bioanalyzer 2100 Agilent. The libraries were quantified …	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP351377		40dpf_ova_1_S146_L004_R2_001.fastq.gz 40dpf_ova_1_S146_L004_R1_001.fastq.gz	fastq fastq	109753922368.0	363423584.0	GSM5739895 r1	0:151 1:151	A:26550231612;C:18985464266;G:18837331344;T:45367377509;N:13517637	151	151			26550231612	18985464266	18837331344	45367377509	13517637	SRX13441049	SRS11340478	SRA1345465	Bruce Draper Lab, Molecular and Cellular Biology, University of California, Davis	Bruce Draper Lab, Molecular and Cellular Biology, University of California, Davis	2	9e-05	0.84548	8e-05	0.09287	1.0	0.78589		0.54454	151	151	T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-12-17	Juvenile	Juvenile	Gonad	Reproductive System
67760	67760	SRR17262952	SRX13441048	SRS11340477	SRP351377	PRJNA789855	Single cell transcriptome reveals insights into the development and function of the zebrafish ovary	GSE191137	Transcriptome Analysis	Zebrafish are an established research organism that has made many contributions to our understanding of vertebrate tissue and organ development yet there are still significant gaps in our understanding of the genes that regulate gonad development sex and reproduction. Unlike the development of many organs such as the brain and heart that form during the first few days of development zebrafish gonads do not begin to form until the larval stage =5 dpf. Thus forward genetic screens have identified very few genes required for gonad development. In addition bulk RNA sequencing studies which identify genes expressed in the gonads do not have the resolution necessary to define minor cell populations that may play significant roles in development and function of these organs. To overcome these limitations we have used single cell RNA sequencing to determine the transcriptomes of cells isolated from juvenile zebrafish ovaries. This resulted in the profiles of 10 658 germ cells and 14 431 somatic cells. Our germ cell data represents all developmental stages from germline stem cells to early meiotic oocytes. Our somatic cell data represents all known somatic cell types including follicle cells theca cells and interstitial stromal cells. Further analysis revealed an unexpected number of cell subpopulations within these broadly defined cell types. To further define their functional significance we determined the location of these cell subpopulations within the ovary. Finally for select examples we used gene knockout experiments to determine the role of newly identified genes. Our results reveal novel insights into ovarian development and function and the sequencing information will provide a valuable resource for future studies. Overall design: Single cell RNA sequencing of 40 dpf zebrafish ovaries	pubmed:35588359	40 dpf zebrafish ovaries cells sorted germ cells	GSM5739894	tissue:40 dpf zebrafish ovaries\|cell type:Germ cells\|genotype:AB wildtype	40 dpf zebrafish ovaries cells sorted germ cells	A General Transfer Format GTF gene annotation filerelease 96 for the GRCz11 zebrafish genome was downloaded from Ensembl Genome Browser and filtered using the “mkgtf” function in Cell Ranger v3.0.2; 10x Genomic to retain the following attributes: protein coding lincRNA and antisense. A genome reference file was generated with Cell Ranger’s “mkref” function using the GRCz11 zebrafish genome obtained from the Ensembl Genome Browser with alternative loci scaffolds removed and the filtered GTF file. GRCz11 zebrafish genome FASTQ file from Ensembl Genome Browser with alternative loci scaffolds removed and the filtered GTF file described above were used to generate the count file using the “count” function in Cell Ranger v3.0.2; 10x Genomic. “expect cells” was setted to 10000 based on estimated cell recovery. Genome build: GRCz11 Supplementary files format and content: Filtered or raw matrix files generated from Cell Ranger in one zip file.	40 dpf zebrafish ovaries		Germ cells were dissociated from the somatic gonad using a modification of Blokhina et al. 2019. 40 pairs of 40 dpf ovaries were dissected from Tgpiwil1:egfpuc02 transgenic fish Leu et al. 2010 and stored in a LoBind tube Cat.No. 0030108302; Eppendorf containing 2 mL of L15 mediumCat.No. L5520; Sigma Aldrich. The tissue was minced with small scissors into <1 mm pieces. 200 µL of 20 mg/mL of type 2 collagenase in L15 Cat.No. NC9870009; Worthington were added and incubated on an orbital rotator at 28°C for 35 min. The cell suspension was then gently passed through a 23g needle five times to break up large cell clumps. 200 µL of 7 mg/mL trypsin Cat.No. LS003708; Worthington in L15 were added and incubated on an orbital rotator for 10 min or until a minimal amount of cell clumps was observed. The trypsin reaction was stopped by adding 500 µL of 20 mg/mL trypsin Inhibitor Cat.No. 100612; MP Biomedicals in L15. The cells were centrifuged for 3 min at 300 x g and the supernatant carefully removed. The cells were then resuspended and washed two times with 5 mL of L15 using a P1000 pipette tip and then centrifuged for 3 min at 300 x g. Cells were then resuspended in 1 mL L15 and filtered through a 100 µm nylon filter Cat.No. 431752; Corning and then through a 40 µm nylon filter Cat.No. 431750; Corning to remove cell clumps. The filtrate was centrifuged for 3 min at 300 x g and resuspended in 1 mL of 50 mg/mL BSA Cat.No. A8806; Sigma Aldrich in Phosphate Buffered Saline. Cell viability and number were assessed using propidium iodine Cat. No. P1304MP; Thermo Fisher and Hoechst 33342 Cat.No. H3570; Thermo Fisher staining on a Fuchs Rosenthal hemocytometer Cat.No. DHC F01; Incyto. Following cell dissociation of Tgpiwil1:egfp transgenic ovaries GFP+ germ cells were sorted using a MoFlo Astrios EQ Cell Sorter Beckman Coulter with a 70 µm nozzle. Cells were sorted using side scatter and GFP purify to identify single germ cells. Single cell RNA sequencing libraries were prepared by the UC Davis DNA Technologies core. Briefly…	Zebrafish husbandry was performed as previously described Westerfield 2000.	cell type:Germ cells\|genotype:AB wildtype	GSM5739894	GSM5739894: 40 dpf zebrafish ovaries cells sorted germ cells; Danio rerio; ssRNA seq	GSM5739894 r1	GSM5739894	1	Germ cells were dissociated from the somatic gonad using a modification of Blokhina et al. 2019. 40 pairs of 40 dpf ovaries were dissected from Tgpiwil1:egfpuc02 transgenic fish Leu et al. 2010 and stored in a LoBind tube Cat.No. 0030108302; Eppendorf containing 2 mL of L15 mediumCat.No. L5520; Sigma Aldrich. The tissue was minced with small scissors into <1 mm pieces. 200 µL of 20 mg/mL of type 2 collagenase in L15 Cat.No. NC9870009; Worthington were added and incubated on an orbital rotator at 28°C for 35 min. The cell suspension was then gently passed through a 23g needle five times to break up large cell clumps. 200 µL of 7 mg/mL trypsin Cat.No. LS003708; Worthington in L15 were added and incubated on an orbital rotator for 10 min or until a minimal amount of cell clumps was observed. The trypsin reaction was stopped by adding 500 µL of 20 mg/mL trypsin Inhibitor Cat.No. 100612; MP Biomedicals in L15. The cells were centrifuged for 3 min at 300 x g and the supernatant carefully removed. The cells were then resuspended and washed two times with 5 mL of L15 using a P1000 pipette tip and then centrifuged for 3 min at 300 x g. Cells were then resuspended in 1 mL L15 and filtered through a 100 µm nylon filter Cat.No. 431752; Corning and then through a 40 µm nylon filter Cat.No. 431750; Corning to remove cell clumps. The filtrate was centrifuged for 3 min at 300 x g and resuspended in 1 mL of 50 mg/mL BSA Cat.No. A8806; Sigma Aldrich in Phosphate Buffered Saline. Cell viability and number were assessed using propidium iodine Cat. No. P1304MP; Thermo Fisher and Hoechst 33342 Cat.No. H3570; Thermo Fisher staining on a Fuchs Rosenthal hemocytometer Cat.No. DHC F01; Incyto. Following cell dissociation of Tgpiwil1:egfp transgenic ovaries GFP+ germ cells were sorted using a MoFlo Astrios EQ Cell Sorter Beckman Coulter with a 70 µm nozzle. Cells were sorted using side scatter and GFP purify to identify single germ cells. Single cell RNA sequencing libraries were prepared by the UC Davis DNA Technologies core. Briefly…	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 4000	SRP351377		40d_Germ_S67_L007_R1_001.fastq.gz 40d_Germ_S67_L007_R2_001.fastq.gz	fastq fastq	97157899800.0	321714900.0	GSM5739894 r1	0:151 1:151	A:25130180865;C:15016964022;G:17255588720;T:39751154898;N:4011295	151	151			25130180865	15016964022	17255588720	39751154898	4011295	SRX13441048	SRS11340477	SRA1345465	Bruce Draper Lab, Molecular and Cellular Biology, University of California, Davis	Bruce Draper Lab, Molecular and Cellular Biology, University of California, Davis	2	0.00058	0.83872	0.00016	0.05616	0.99989	0.77873	0.4	0.51521	151	151	T	B	mate1 technical by mapping diff	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-12-17	Juvenile	Juvenile	Gonad	Reproductive System
68139	68139	SRR17630961	SRX13799339	SRS11681628	SRP355202	PRJNA797655	Toxicotranscriptomics of single cell RNA Seq and conventional RNA Seq in TCDD exposed testicular tissue	GSE193758	Transcriptome Analysis	Spermatogenesis is a dynamic tightly conserved process that is susceptible to environmental contaminants. Exposure to environmental contaminants such as 2 3 7 8 tetrachlorodibenzo p dioxin TCDD is believed to be a cause of idiopathic male infertility. To understand TCDD induced disruption of spermatogenesis at the single cell level we profiled adult zebrafish testes with and without xxx life exposure to TCDD. Secondly to investigate the potential for technical artifacts in scRNA seq we compared bulk sequenced and scRNA seq paired samples from control and TCDD exposed samples and included an intact control fish to account for dissociation induced artifacts. We found scRNA seq and bulk seq of dissociated testes produced markedly different profiles both toxicologically and transcriptomically. Through scRNA seq we found TCDD exposure induces mid late germ cell apoptosis while increasing the population of spermatogonial stem cells. Bulk seq on the same cells returned results of immune dysregulation. The transcriptome was unequally detected by scRNA seq and bulk seq with scRNA seq biased towards detecting longer and more abundant transcripts but this was not mediated by TCDD exposure. Overall design: Zebrafish were exposed to 50 pg/mL TCDD or vehicle solution for 1 hour during sexual differentiation and maturation. Adult testes were dissected for toxicotranscriptomic analysis. Samples were prepared by dissociation for scRNA seq remained intact for bulk seq or were dissociated for bulk seq.	pubmed:35615540;pubmed:35799832	scRNA seq TCDD testes rep 2	GSM5820556	tissue:testes\|strain:AB\|treatment:50 pg/mL TCDD in 0.1% DMSO\|sample preparation:dissociated cell suspension	scRNA seq TCDD testes rep 2	Reads were aligned and tabulated by individual cells in each sample using Cell Ranger 6.01 Count data was imported to Seurat version 4.0.4 for quality control QC filtering clustering dimensionality reduction visualization and differential gene expression Each sample was filtered to cells containing at least 500 features with clusters requiring a minimum of 30 cells. Samples were merged prior to normalization and clustering resolution 0.3. Differentially expressed genes between conditions for each cluster were identified using the "FindMarkers" function Genome build: Zebrafish May 2017 GRCz11/danRer11 Assembly Supplementary files format and content: xlsx; read counts and DEGs; Cell Ranger output matrices 10X SC TCDD DEG clusters: 10X Single cell cluster DEGs GEO CDxCI read counts DEGs: Control dissociated cells compared to Control intact cells GEO CPxCB read counts DEGs: Control psuedo bulk seq compared to Control dissociated cells for bulk seq GEO TBxCB read counts DEGs: TCDD dissociated cells compared to Control dissociated cells GEO TPxCP read counts DEGs: TCDD psuedo bulk seq compared to Control psuedo bulk seq GEO TPxTB read counts DEGs: TCDD psuedo bulk seq compared to TCDD dissociated cells bulk seq	testes	Experimental fish Sample 4 and 5 were exposed to 1 hour of TCDD at xxx and 7 wpf allowed to mature and testes were harvested as adults.	Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform and sequenced on a NovaSeq.	Zebrafish were maintained on a 14:10h light/dark cycle with temperatures maintained at 27°C– 30°C. Fish were fed twice daily. Fish were raised in beakers with daily water changes. Animal use protocols were approved by the Institutional Animal Care and Use Committees at Wayne State University and the University of Wisconsin Madison according to the National Institutes of Health Guide to the Care and Use of Laboratory Animals Protocol No. M00489.	strain:AB\|treatment:50 pg/mL TCDD in 0.1% DMSO\|sample preparation:dissociated cell suspension	GSM5820556	GSM5820556: scRNA seq TCDD testes rep 2; Danio rerio; RNA Seq	GSM5820556 r1	GSM5820556	1	Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform and sequenced on a NovaSeq.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP355202	loader:fastq load.py	SC_T2_S5_L001_I1_001.fastq.gz SC_T2_S5_L001_R1_001.fastq.gz SC_T2_S5_L001_R2_001.fastq.gz	fastq fastq fastq	11262679659.0	88682517.0	GSM5820556 r1	0:8 1:28 2:91	A:2329833844;C:1736580490;G:2028746154;T:1974513391;N:435168	8	28	91		2329833844	1736580490	2028746154	1974513391	435168	SRX13799339	SRS11681628	SRA1357269	University of Florida	University of Florida	1	0.89663		0.23137		0.75166		0.55299		91		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2022-01-15	Juvenile	Juvenile	Gonad	Reproductive System
68140	68140	SRR17630962	SRX13799339	SRS11681628	SRP355202	PRJNA797655	Toxicotranscriptomics of single cell RNA Seq and conventional RNA Seq in TCDD exposed testicular tissue	GSE193758	Transcriptome Analysis	Spermatogenesis is a dynamic tightly conserved process that is susceptible to environmental contaminants. Exposure to environmental contaminants such as 2 3 7 8 tetrachlorodibenzo p dioxin TCDD is believed to be a cause of idiopathic male infertility. To understand TCDD induced disruption of spermatogenesis at the single cell level we profiled adult zebrafish testes with and without xxx life exposure to TCDD. Secondly to investigate the potential for technical artifacts in scRNA seq we compared bulk sequenced and scRNA seq paired samples from control and TCDD exposed samples and included an intact control fish to account for dissociation induced artifacts. We found scRNA seq and bulk seq of dissociated testes produced markedly different profiles both toxicologically and transcriptomically. Through scRNA seq we found TCDD exposure induces mid late germ cell apoptosis while increasing the population of spermatogonial stem cells. Bulk seq on the same cells returned results of immune dysregulation. The transcriptome was unequally detected by scRNA seq and bulk seq with scRNA seq biased towards detecting longer and more abundant transcripts but this was not mediated by TCDD exposure. Overall design: Zebrafish were exposed to 50 pg/mL TCDD or vehicle solution for 1 hour during sexual differentiation and maturation. Adult testes were dissected for toxicotranscriptomic analysis. Samples were prepared by dissociation for scRNA seq remained intact for bulk seq or were dissociated for bulk seq.	pubmed:35615540;pubmed:35799832	scRNA seq TCDD testes rep 2	GSM5820556	tissue:testes\|strain:AB\|treatment:50 pg/mL TCDD in 0.1% DMSO\|sample preparation:dissociated cell suspension	scRNA seq TCDD testes rep 2	Reads were aligned and tabulated by individual cells in each sample using Cell Ranger 6.01 Count data was imported to Seurat version 4.0.4 for quality control QC filtering clustering dimensionality reduction visualization and differential gene expression Each sample was filtered to cells containing at least 500 features with clusters requiring a minimum of 30 cells. Samples were merged prior to normalization and clustering resolution 0.3. Differentially expressed genes between conditions for each cluster were identified using the "FindMarkers" function Genome build: Zebrafish May 2017 GRCz11/danRer11 Assembly Supplementary files format and content: xlsx; read counts and DEGs; Cell Ranger output matrices 10X SC TCDD DEG clusters: 10X Single cell cluster DEGs GEO CDxCI read counts DEGs: Control dissociated cells compared to Control intact cells GEO CPxCB read counts DEGs: Control psuedo bulk seq compared to Control dissociated cells for bulk seq GEO TBxCB read counts DEGs: TCDD dissociated cells compared to Control dissociated cells GEO TPxCP read counts DEGs: TCDD psuedo bulk seq compared to Control psuedo bulk seq GEO TPxTB read counts DEGs: TCDD psuedo bulk seq compared to TCDD dissociated cells bulk seq	testes	Experimental fish Sample 4 and 5 were exposed to 1 hour of TCDD at xxx and 7 wpf allowed to mature and testes were harvested as adults.	Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform and sequenced on a NovaSeq.	Zebrafish were maintained on a 14:10h light/dark cycle with temperatures maintained at 27°C– 30°C. Fish were fed twice daily. Fish were raised in beakers with daily water changes. Animal use protocols were approved by the Institutional Animal Care and Use Committees at Wayne State University and the University of Wisconsin Madison according to the National Institutes of Health Guide to the Care and Use of Laboratory Animals Protocol No. M00489.	strain:AB\|treatment:50 pg/mL TCDD in 0.1% DMSO\|sample preparation:dissociated cell suspension	GSM5820556	GSM5820556: scRNA seq TCDD testes rep 2; Danio rerio; RNA Seq	GSM5820556 r1	GSM5820556	1	Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform and sequenced on a NovaSeq.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP355202	loader:fastq load.py	SC_T2_S5_L002_I1_001.fastq.gz SC_T2_S5_L002_R1_001.fastq.gz SC_T2_S5_L002_R2_001.fastq.gz	fastq fastq fastq	11384315052.0	89640276.0	GSM5820556 r2	0:8 1:28 2:91	A:2351124750;C:1758531934;G:2054452297;T:1992620872;N:535263	8	28	91		2351124750	1758531934	2054452297	1992620872	535263	SRX13799339	SRS11681628	SRA1357269	University of Florida	University of Florida	1	0.89836		0.23263		0.7543		0.55738		91		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2022-01-15	Juvenile	Juvenile	Gonad	Reproductive System
68141	68141	SRR17630963	SRX13799338	SRS11681627	SRP355202	PRJNA797655	Toxicotranscriptomics of single cell RNA Seq and conventional RNA Seq in TCDD exposed testicular tissue	GSE193758	Transcriptome Analysis	Spermatogenesis is a dynamic tightly conserved process that is susceptible to environmental contaminants. Exposure to environmental contaminants such as 2 3 7 8 tetrachlorodibenzo p dioxin TCDD is believed to be a cause of idiopathic male infertility. To understand TCDD induced disruption of spermatogenesis at the single cell level we profiled adult zebrafish testes with and without xxx life exposure to TCDD. Secondly to investigate the potential for technical artifacts in scRNA seq we compared bulk sequenced and scRNA seq paired samples from control and TCDD exposed samples and included an intact control fish to account for dissociation induced artifacts. We found scRNA seq and bulk seq of dissociated testes produced markedly different profiles both toxicologically and transcriptomically. Through scRNA seq we found TCDD exposure induces mid late germ cell apoptosis while increasing the population of spermatogonial stem cells. Bulk seq on the same cells returned results of immune dysregulation. The transcriptome was unequally detected by scRNA seq and bulk seq with scRNA seq biased towards detecting longer and more abundant transcripts but this was not mediated by TCDD exposure. Overall design: Zebrafish were exposed to 50 pg/mL TCDD or vehicle solution for 1 hour during sexual differentiation and maturation. Adult testes were dissected for toxicotranscriptomic analysis. Samples were prepared by dissociation for scRNA seq remained intact for bulk seq or were dissociated for bulk seq.	pubmed:35615540;pubmed:35799832	scRNA seq TCDD testes rep 1	GSM5820555	tissue:testes\|strain:AB\|treatment:50 pg/mL TCDD in 0.1% DMSO\|sample preparation:dissociated cell suspension	scRNA seq TCDD testes rep 1	Reads were aligned and tabulated by individual cells in each sample using Cell Ranger 6.01 Count data was imported to Seurat version 4.0.4 for quality control QC filtering clustering dimensionality reduction visualization and differential gene expression Each sample was filtered to cells containing at least 500 features with clusters requiring a minimum of 30 cells. Samples were merged prior to normalization and clustering resolution 0.3. Differentially expressed genes between conditions for each cluster were identified using the "FindMarkers" function Genome build: Zebrafish May 2017 GRCz11/danRer11 Assembly Supplementary files format and content: xlsx; read counts and DEGs; Cell Ranger output matrices 10X SC TCDD DEG clusters: 10X Single cell cluster DEGs GEO CDxCI read counts DEGs: Control dissociated cells compared to Control intact cells GEO CPxCB read counts DEGs: Control psuedo bulk seq compared to Control dissociated cells for bulk seq GEO TBxCB read counts DEGs: TCDD dissociated cells compared to Control dissociated cells GEO TPxCP read counts DEGs: TCDD psuedo bulk seq compared to Control psuedo bulk seq GEO TPxTB read counts DEGs: TCDD psuedo bulk seq compared to TCDD dissociated cells bulk seq	testes	Experimental fish Sample 4 and 5 were exposed to 1 hour of TCDD at xxx and 7 wpf allowed to mature and testes were harvested as adults.	Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform and sequenced on a NovaSeq.	Zebrafish were maintained on a 14:10h light/dark cycle with temperatures maintained at 27°C– 30°C. Fish were fed twice daily. Fish were raised in beakers with daily water changes. Animal use protocols were approved by the Institutional Animal Care and Use Committees at Wayne State University and the University of Wisconsin Madison according to the National Institutes of Health Guide to the Care and Use of Laboratory Animals Protocol No. M00489.	strain:AB\|treatment:50 pg/mL TCDD in 0.1% DMSO\|sample preparation:dissociated cell suspension	GSM5820555	GSM5820555: scRNA seq TCDD testes rep 1; Danio rerio; RNA Seq	GSM5820555 r1	GSM5820555	1	Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform and sequenced on a NovaSeq.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP355202	loader:fastq load.py	SC_T1_S4_L001_I1_001.fastq.gz SC_T1_S4_L001_R1_001.fastq.gz SC_T1_S4_L001_R2_001.fastq.gz	fastq fastq fastq	10978768873.0	86446999.0	GSM5820555 r1	0:8 1:28 2:91	A:2363149906;C:1616901304;G:1945888469;T:1940298056;N:439174	8	28	91		2363149906	1616901304	1945888469	1940298056	439174	SRX13799338	SRS11681627	SRA1357269	University of Florida	University of Florida	1	0.87562		0.208		0.75511		0.5329		91		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2022-01-15	Juvenile	Juvenile	Gonad	Reproductive System
68142	68142	SRR17630964	SRX13799338	SRS11681627	SRP355202	PRJNA797655	Toxicotranscriptomics of single cell RNA Seq and conventional RNA Seq in TCDD exposed testicular tissue	GSE193758	Transcriptome Analysis	Spermatogenesis is a dynamic tightly conserved process that is susceptible to environmental contaminants. Exposure to environmental contaminants such as 2 3 7 8 tetrachlorodibenzo p dioxin TCDD is believed to be a cause of idiopathic male infertility. To understand TCDD induced disruption of spermatogenesis at the single cell level we profiled adult zebrafish testes with and without xxx life exposure to TCDD. Secondly to investigate the potential for technical artifacts in scRNA seq we compared bulk sequenced and scRNA seq paired samples from control and TCDD exposed samples and included an intact control fish to account for dissociation induced artifacts. We found scRNA seq and bulk seq of dissociated testes produced markedly different profiles both toxicologically and transcriptomically. Through scRNA seq we found TCDD exposure induces mid late germ cell apoptosis while increasing the population of spermatogonial stem cells. Bulk seq on the same cells returned results of immune dysregulation. The transcriptome was unequally detected by scRNA seq and bulk seq with scRNA seq biased towards detecting longer and more abundant transcripts but this was not mediated by TCDD exposure. Overall design: Zebrafish were exposed to 50 pg/mL TCDD or vehicle solution for 1 hour during sexual differentiation and maturation. Adult testes were dissected for toxicotranscriptomic analysis. Samples were prepared by dissociation for scRNA seq remained intact for bulk seq or were dissociated for bulk seq.	pubmed:35615540;pubmed:35799832	scRNA seq TCDD testes rep 1	GSM5820555	tissue:testes\|strain:AB\|treatment:50 pg/mL TCDD in 0.1% DMSO\|sample preparation:dissociated cell suspension	scRNA seq TCDD testes rep 1	Reads were aligned and tabulated by individual cells in each sample using Cell Ranger 6.01 Count data was imported to Seurat version 4.0.4 for quality control QC filtering clustering dimensionality reduction visualization and differential gene expression Each sample was filtered to cells containing at least 500 features with clusters requiring a minimum of 30 cells. Samples were merged prior to normalization and clustering resolution 0.3. Differentially expressed genes between conditions for each cluster were identified using the "FindMarkers" function Genome build: Zebrafish May 2017 GRCz11/danRer11 Assembly Supplementary files format and content: xlsx; read counts and DEGs; Cell Ranger output matrices 10X SC TCDD DEG clusters: 10X Single cell cluster DEGs GEO CDxCI read counts DEGs: Control dissociated cells compared to Control intact cells GEO CPxCB read counts DEGs: Control psuedo bulk seq compared to Control dissociated cells for bulk seq GEO TBxCB read counts DEGs: TCDD dissociated cells compared to Control dissociated cells GEO TPxCP read counts DEGs: TCDD psuedo bulk seq compared to Control psuedo bulk seq GEO TPxTB read counts DEGs: TCDD psuedo bulk seq compared to TCDD dissociated cells bulk seq	testes	Experimental fish Sample 4 and 5 were exposed to 1 hour of TCDD at xxx and 7 wpf allowed to mature and testes were harvested as adults.	Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform and sequenced on a NovaSeq.	Zebrafish were maintained on a 14:10h light/dark cycle with temperatures maintained at 27°C– 30°C. Fish were fed twice daily. Fish were raised in beakers with daily water changes. Animal use protocols were approved by the Institutional Animal Care and Use Committees at Wayne State University and the University of Wisconsin Madison according to the National Institutes of Health Guide to the Care and Use of Laboratory Animals Protocol No. M00489.	strain:AB\|treatment:50 pg/mL TCDD in 0.1% DMSO\|sample preparation:dissociated cell suspension	GSM5820555	GSM5820555: scRNA seq TCDD testes rep 1; Danio rerio; RNA Seq	GSM5820555 r1	GSM5820555	1	Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform and sequenced on a NovaSeq.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP355202	loader:fastq load.py	SC_T1_S4_L002_I1_001.fastq.gz SC_T1_S4_L002_R1_001.fastq.gz SC_T1_S4_L002_R2_001.fastq.gz	fastq fastq fastq	11084990022.0	87283386.0	GSM5820555 r2	0:8 1:28 2:91	A:2382115862;C:1635424114;G:1968060449;T:1956671635;N:516066	8	28	91		2382115862	1635424114	1968060449	1956671635	516066	SRX13799338	SRS11681627	SRA1357269	University of Florida	University of Florida	1	0.8745		0.20808		0.7585		0.52692		91		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2022-01-15	Juvenile	Juvenile	Gonad	Reproductive System
68143	68143	SRR17630965	SRX13799337	SRS11681626	SRP355202	PRJNA797655	Toxicotranscriptomics of single cell RNA Seq and conventional RNA Seq in TCDD exposed testicular tissue	GSE193758	Transcriptome Analysis	Spermatogenesis is a dynamic tightly conserved process that is susceptible to environmental contaminants. Exposure to environmental contaminants such as 2 3 7 8 tetrachlorodibenzo p dioxin TCDD is believed to be a cause of idiopathic male infertility. To understand TCDD induced disruption of spermatogenesis at the single cell level we profiled adult zebrafish testes with and without xxx life exposure to TCDD. Secondly to investigate the potential for technical artifacts in scRNA seq we compared bulk sequenced and scRNA seq paired samples from control and TCDD exposed samples and included an intact control fish to account for dissociation induced artifacts. We found scRNA seq and bulk seq of dissociated testes produced markedly different profiles both toxicologically and transcriptomically. Through scRNA seq we found TCDD exposure induces mid late germ cell apoptosis while increasing the population of spermatogonial stem cells. Bulk seq on the same cells returned results of immune dysregulation. The transcriptome was unequally detected by scRNA seq and bulk seq with scRNA seq biased towards detecting longer and more abundant transcripts but this was not mediated by TCDD exposure. Overall design: Zebrafish were exposed to 50 pg/mL TCDD or vehicle solution for 1 hour during sexual differentiation and maturation. Adult testes were dissected for toxicotranscriptomic analysis. Samples were prepared by dissociation for scRNA seq remained intact for bulk seq or were dissociated for bulk seq.	pubmed:35615540;pubmed:35799832	scRNA seq control testes rep 3	GSM5820554	tissue:testes\|strain:AB\|treatment:50 pg/mL 0.1% DMSO\|sample preparation:dissociated cell suspension	scRNA seq control testes rep 3	Reads were aligned and tabulated by individual cells in each sample using Cell Ranger 6.01 Count data was imported to Seurat version 4.0.4 for quality control QC filtering clustering dimensionality reduction visualization and differential gene expression Each sample was filtered to cells containing at least 500 features with clusters requiring a minimum of 30 cells. Samples were merged prior to normalization and clustering resolution 0.3. Differentially expressed genes between conditions for each cluster were identified using the "FindMarkers" function Genome build: Zebrafish May 2017 GRCz11/danRer11 Assembly Supplementary files format and content: xlsx; read counts and DEGs; Cell Ranger output matrices 10X SC TCDD DEG clusters: 10X Single cell cluster DEGs GEO CDxCI read counts DEGs: Control dissociated cells compared to Control intact cells GEO CPxCB read counts DEGs: Control psuedo bulk seq compared to Control dissociated cells for bulk seq GEO TBxCB read counts DEGs: TCDD dissociated cells compared to Control dissociated cells GEO TPxCP read counts DEGs: TCDD psuedo bulk seq compared to Control psuedo bulk seq GEO TPxTB read counts DEGs: TCDD psuedo bulk seq compared to TCDD dissociated cells bulk seq	testes	Experimental fish Sample 4 and 5 were exposed to 1 hour of TCDD at xxx and 7 wpf allowed to mature and testes were harvested as adults.	Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform and sequenced on a NovaSeq.	Zebrafish were maintained on a 14:10h light/dark cycle with temperatures maintained at 27°C– 30°C. Fish were fed twice daily. Fish were raised in beakers with daily water changes. Animal use protocols were approved by the Institutional Animal Care and Use Committees at Wayne State University and the University of Wisconsin Madison according to the National Institutes of Health Guide to the Care and Use of Laboratory Animals Protocol No. M00489.	strain:AB\|treatment:50 pg/mL 0.1% DMSO\|sample preparation:dissociated cell suspension	GSM5820554	GSM5820554: scRNA seq control testes rep 3; Danio rerio; RNA Seq	GSM5820554 r1	GSM5820554	1	Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform and sequenced on a NovaSeq.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP355202	loader:fastq load.py	SC_C3_S3_L001_I1_001.fastq.gz SC_C3_S3_L001_R1_001.fastq.gz SC_C3_S3_L001_R2_001.fastq.gz	fastq fastq fastq	11736916836.0	92416668.0	GSM5820554 r1	0:8 1:28 2:91	A:2491182657;C:1749727321;G:2001921423;T:2166620469;N:464918	8	28	91		2491182657	1749727321	2001921423	2166620469	464918	SRX13799337	SRS11681626	SRA1357269	University of Florida	University of Florida	1	0.89927		0.17983		0.71601		0.52261		91		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2022-01-15	Juvenile	Juvenile	Gonad	Reproductive System
68144	68144	SRR17630966	SRX13799337	SRS11681626	SRP355202	PRJNA797655	Toxicotranscriptomics of single cell RNA Seq and conventional RNA Seq in TCDD exposed testicular tissue	GSE193758	Transcriptome Analysis	Spermatogenesis is a dynamic tightly conserved process that is susceptible to environmental contaminants. Exposure to environmental contaminants such as 2 3 7 8 tetrachlorodibenzo p dioxin TCDD is believed to be a cause of idiopathic male infertility. To understand TCDD induced disruption of spermatogenesis at the single cell level we profiled adult zebrafish testes with and without xxx life exposure to TCDD. Secondly to investigate the potential for technical artifacts in scRNA seq we compared bulk sequenced and scRNA seq paired samples from control and TCDD exposed samples and included an intact control fish to account for dissociation induced artifacts. We found scRNA seq and bulk seq of dissociated testes produced markedly different profiles both toxicologically and transcriptomically. Through scRNA seq we found TCDD exposure induces mid late germ cell apoptosis while increasing the population of spermatogonial stem cells. Bulk seq on the same cells returned results of immune dysregulation. The transcriptome was unequally detected by scRNA seq and bulk seq with scRNA seq biased towards detecting longer and more abundant transcripts but this was not mediated by TCDD exposure. Overall design: Zebrafish were exposed to 50 pg/mL TCDD or vehicle solution for 1 hour during sexual differentiation and maturation. Adult testes were dissected for toxicotranscriptomic analysis. Samples were prepared by dissociation for scRNA seq remained intact for bulk seq or were dissociated for bulk seq.	pubmed:35615540;pubmed:35799832	scRNA seq control testes rep 3	GSM5820554	tissue:testes\|strain:AB\|treatment:50 pg/mL 0.1% DMSO\|sample preparation:dissociated cell suspension	scRNA seq control testes rep 3	Reads were aligned and tabulated by individual cells in each sample using Cell Ranger 6.01 Count data was imported to Seurat version 4.0.4 for quality control QC filtering clustering dimensionality reduction visualization and differential gene expression Each sample was filtered to cells containing at least 500 features with clusters requiring a minimum of 30 cells. Samples were merged prior to normalization and clustering resolution 0.3. Differentially expressed genes between conditions for each cluster were identified using the "FindMarkers" function Genome build: Zebrafish May 2017 GRCz11/danRer11 Assembly Supplementary files format and content: xlsx; read counts and DEGs; Cell Ranger output matrices 10X SC TCDD DEG clusters: 10X Single cell cluster DEGs GEO CDxCI read counts DEGs: Control dissociated cells compared to Control intact cells GEO CPxCB read counts DEGs: Control psuedo bulk seq compared to Control dissociated cells for bulk seq GEO TBxCB read counts DEGs: TCDD dissociated cells compared to Control dissociated cells GEO TPxCP read counts DEGs: TCDD psuedo bulk seq compared to Control psuedo bulk seq GEO TPxTB read counts DEGs: TCDD psuedo bulk seq compared to TCDD dissociated cells bulk seq	testes	Experimental fish Sample 4 and 5 were exposed to 1 hour of TCDD at xxx and 7 wpf allowed to mature and testes were harvested as adults.	Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform and sequenced on a NovaSeq.	Zebrafish were maintained on a 14:10h light/dark cycle with temperatures maintained at 27°C– 30°C. Fish were fed twice daily. Fish were raised in beakers with daily water changes. Animal use protocols were approved by the Institutional Animal Care and Use Committees at Wayne State University and the University of Wisconsin Madison according to the National Institutes of Health Guide to the Care and Use of Laboratory Animals Protocol No. M00489.	strain:AB\|treatment:50 pg/mL 0.1% DMSO\|sample preparation:dissociated cell suspension	GSM5820554	GSM5820554: scRNA seq control testes rep 3; Danio rerio; RNA Seq	GSM5820554 r1	GSM5820554	1	Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform and sequenced on a NovaSeq.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP355202	loader:fastq load.py	SC_C3_S3_L002_I1_001.fastq.gz SC_C3_S3_L002_R1_001.fastq.gz SC_C3_S3_L002_R2_001.fastq.gz	fastq fastq fastq	11862480339.0	93405357.0	GSM5820554 r2	0:8 1:28 2:91	A:2515246562;C:1770645118;G:2026263526;T:2187182415;N:549866	8	28	91		2515246562	1770645118	2026263526	2187182415	549866	SRX13799337	SRS11681626	SRA1357269	University of Florida	University of Florida	1	0.89922		0.1803		0.71419		0.52093		91		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2022-01-15	Juvenile	Juvenile	Gonad	Reproductive System
68145	68145	SRR17630967	SRX13799336	SRS11681625	SRP355202	PRJNA797655	Toxicotranscriptomics of single cell RNA Seq and conventional RNA Seq in TCDD exposed testicular tissue	GSE193758	Transcriptome Analysis	Spermatogenesis is a dynamic tightly conserved process that is susceptible to environmental contaminants. Exposure to environmental contaminants such as 2 3 7 8 tetrachlorodibenzo p dioxin TCDD is believed to be a cause of idiopathic male infertility. To understand TCDD induced disruption of spermatogenesis at the single cell level we profiled adult zebrafish testes with and without xxx life exposure to TCDD. Secondly to investigate the potential for technical artifacts in scRNA seq we compared bulk sequenced and scRNA seq paired samples from control and TCDD exposed samples and included an intact control fish to account for dissociation induced artifacts. We found scRNA seq and bulk seq of dissociated testes produced markedly different profiles both toxicologically and transcriptomically. Through scRNA seq we found TCDD exposure induces mid late germ cell apoptosis while increasing the population of spermatogonial stem cells. Bulk seq on the same cells returned results of immune dysregulation. The transcriptome was unequally detected by scRNA seq and bulk seq with scRNA seq biased towards detecting longer and more abundant transcripts but this was not mediated by TCDD exposure. Overall design: Zebrafish were exposed to 50 pg/mL TCDD or vehicle solution for 1 hour during sexual differentiation and maturation. Adult testes were dissected for toxicotranscriptomic analysis. Samples were prepared by dissociation for scRNA seq remained intact for bulk seq or were dissociated for bulk seq.	pubmed:35615540;pubmed:35799832	scRNA seq control testes rep 2	GSM5820553	tissue:testes\|strain:AB\|treatment:50 pg/mL 0.1% DMSO\|sample preparation:dissociated cell suspension	scRNA seq control testes rep 2	Reads were aligned and tabulated by individual cells in each sample using Cell Ranger 6.01 Count data was imported to Seurat version 4.0.4 for quality control QC filtering clustering dimensionality reduction visualization and differential gene expression Each sample was filtered to cells containing at least 500 features with clusters requiring a minimum of 30 cells. Samples were merged prior to normalization and clustering resolution 0.3. Differentially expressed genes between conditions for each cluster were identified using the "FindMarkers" function Genome build: Zebrafish May 2017 GRCz11/danRer11 Assembly Supplementary files format and content: xlsx; read counts and DEGs; Cell Ranger output matrices 10X SC TCDD DEG clusters: 10X Single cell cluster DEGs GEO CDxCI read counts DEGs: Control dissociated cells compared to Control intact cells GEO CPxCB read counts DEGs: Control psuedo bulk seq compared to Control dissociated cells for bulk seq GEO TBxCB read counts DEGs: TCDD dissociated cells compared to Control dissociated cells GEO TPxCP read counts DEGs: TCDD psuedo bulk seq compared to Control psuedo bulk seq GEO TPxTB read counts DEGs: TCDD psuedo bulk seq compared to TCDD dissociated cells bulk seq	testes	Experimental fish Sample 4 and 5 were exposed to 1 hour of TCDD at xxx and 7 wpf allowed to mature and testes were harvested as adults.	Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform and sequenced on a NovaSeq.	Zebrafish were maintained on a 14:10h light/dark cycle with temperatures maintained at 27°C– 30°C. Fish were fed twice daily. Fish were raised in beakers with daily water changes. Animal use protocols were approved by the Institutional Animal Care and Use Committees at Wayne State University and the University of Wisconsin Madison according to the National Institutes of Health Guide to the Care and Use of Laboratory Animals Protocol No. M00489.	strain:AB\|treatment:50 pg/mL 0.1% DMSO\|sample preparation:dissociated cell suspension	GSM5820553	GSM5820553: scRNA seq control testes rep 2; Danio rerio; RNA Seq	GSM5820553 r1	GSM5820553	1	Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform and sequenced on a NovaSeq.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP355202	loader:fastq load.py	SC_C2_S2_L001_I1_001.fastq.gz SC_C2_S2_L001_R1_001.fastq.gz SC_C2_S2_L001_R2_001.fastq.gz	fastq fastq fastq	11597196897.0	91316511.0	GSM5820553 r1	0:8 1:28 2:91	A:2441188567;C:1731265684;G:2062239362;T:2074648513;N:460375	8	28	91		2441188567	1731265684	2062239362	2074648513	460375	SRX13799336	SRS11681625	SRA1357269	University of Florida	University of Florida	1	0.87524		0.22302		0.75893		0.55047		91		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2022-01-15	Juvenile	Juvenile	Gonad	Reproductive System
68146	68146	SRR17630968	SRX13799336	SRS11681625	SRP355202	PRJNA797655	Toxicotranscriptomics of single cell RNA Seq and conventional RNA Seq in TCDD exposed testicular tissue	GSE193758	Transcriptome Analysis	Spermatogenesis is a dynamic tightly conserved process that is susceptible to environmental contaminants. Exposure to environmental contaminants such as 2 3 7 8 tetrachlorodibenzo p dioxin TCDD is believed to be a cause of idiopathic male infertility. To understand TCDD induced disruption of spermatogenesis at the single cell level we profiled adult zebrafish testes with and without xxx life exposure to TCDD. Secondly to investigate the potential for technical artifacts in scRNA seq we compared bulk sequenced and scRNA seq paired samples from control and TCDD exposed samples and included an intact control fish to account for dissociation induced artifacts. We found scRNA seq and bulk seq of dissociated testes produced markedly different profiles both toxicologically and transcriptomically. Through scRNA seq we found TCDD exposure induces mid late germ cell apoptosis while increasing the population of spermatogonial stem cells. Bulk seq on the same cells returned results of immune dysregulation. The transcriptome was unequally detected by scRNA seq and bulk seq with scRNA seq biased towards detecting longer and more abundant transcripts but this was not mediated by TCDD exposure. Overall design: Zebrafish were exposed to 50 pg/mL TCDD or vehicle solution for 1 hour during sexual differentiation and maturation. Adult testes were dissected for toxicotranscriptomic analysis. Samples were prepared by dissociation for scRNA seq remained intact for bulk seq or were dissociated for bulk seq.	pubmed:35615540;pubmed:35799832	scRNA seq control testes rep 2	GSM5820553	tissue:testes\|strain:AB\|treatment:50 pg/mL 0.1% DMSO\|sample preparation:dissociated cell suspension	scRNA seq control testes rep 2	Reads were aligned and tabulated by individual cells in each sample using Cell Ranger 6.01 Count data was imported to Seurat version 4.0.4 for quality control QC filtering clustering dimensionality reduction visualization and differential gene expression Each sample was filtered to cells containing at least 500 features with clusters requiring a minimum of 30 cells. Samples were merged prior to normalization and clustering resolution 0.3. Differentially expressed genes between conditions for each cluster were identified using the "FindMarkers" function Genome build: Zebrafish May 2017 GRCz11/danRer11 Assembly Supplementary files format and content: xlsx; read counts and DEGs; Cell Ranger output matrices 10X SC TCDD DEG clusters: 10X Single cell cluster DEGs GEO CDxCI read counts DEGs: Control dissociated cells compared to Control intact cells GEO CPxCB read counts DEGs: Control psuedo bulk seq compared to Control dissociated cells for bulk seq GEO TBxCB read counts DEGs: TCDD dissociated cells compared to Control dissociated cells GEO TPxCP read counts DEGs: TCDD psuedo bulk seq compared to Control psuedo bulk seq GEO TPxTB read counts DEGs: TCDD psuedo bulk seq compared to TCDD dissociated cells bulk seq	testes	Experimental fish Sample 4 and 5 were exposed to 1 hour of TCDD at xxx and 7 wpf allowed to mature and testes were harvested as adults.	Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform and sequenced on a NovaSeq.	Zebrafish were maintained on a 14:10h light/dark cycle with temperatures maintained at 27°C– 30°C. Fish were fed twice daily. Fish were raised in beakers with daily water changes. Animal use protocols were approved by the Institutional Animal Care and Use Committees at Wayne State University and the University of Wisconsin Madison according to the National Institutes of Health Guide to the Care and Use of Laboratory Animals Protocol No. M00489.	strain:AB\|treatment:50 pg/mL 0.1% DMSO\|sample preparation:dissociated cell suspension	GSM5820553	GSM5820553: scRNA seq control testes rep 2; Danio rerio; RNA Seq	GSM5820553 r1	GSM5820553	1	Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform and sequenced on a NovaSeq.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP355202	loader:fastq load.py	SC_C2_S2_L002_I1_001.fastq.gz SC_C2_S2_L002_R1_001.fastq.gz SC_C2_S2_L002_R2_001.fastq.gz	fastq fastq fastq	11724309038.0	92317394.0	GSM5820553 r2	0:8 1:28 2:91	A:2464546352;C:1753014248;G:2088164317;T:2094592155;N:565782	8	28	91		2464546352	1753014248	2088164317	2094592155	565782	SRX13799336	SRS11681625	SRA1357269	University of Florida	University of Florida	1	0.87809		0.22205		0.75272		0.55306		91		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2022-01-15	Juvenile	Juvenile	Gonad	Reproductive System
68147	68147	SRR17630969	SRX13799335	SRS11681624	SRP355202	PRJNA797655	Toxicotranscriptomics of single cell RNA Seq and conventional RNA Seq in TCDD exposed testicular tissue	GSE193758	Transcriptome Analysis	Spermatogenesis is a dynamic tightly conserved process that is susceptible to environmental contaminants. Exposure to environmental contaminants such as 2 3 7 8 tetrachlorodibenzo p dioxin TCDD is believed to be a cause of idiopathic male infertility. To understand TCDD induced disruption of spermatogenesis at the single cell level we profiled adult zebrafish testes with and without xxx life exposure to TCDD. Secondly to investigate the potential for technical artifacts in scRNA seq we compared bulk sequenced and scRNA seq paired samples from control and TCDD exposed samples and included an intact control fish to account for dissociation induced artifacts. We found scRNA seq and bulk seq of dissociated testes produced markedly different profiles both toxicologically and transcriptomically. Through scRNA seq we found TCDD exposure induces mid late germ cell apoptosis while increasing the population of spermatogonial stem cells. Bulk seq on the same cells returned results of immune dysregulation. The transcriptome was unequally detected by scRNA seq and bulk seq with scRNA seq biased towards detecting longer and more abundant transcripts but this was not mediated by TCDD exposure. Overall design: Zebrafish were exposed to 50 pg/mL TCDD or vehicle solution for 1 hour during sexual differentiation and maturation. Adult testes were dissected for toxicotranscriptomic analysis. Samples were prepared by dissociation for scRNA seq remained intact for bulk seq or were dissociated for bulk seq.	pubmed:35615540;pubmed:35799832	scRNA seq control testes rep 1	GSM5820552	tissue:testes\|strain:AB\|treatment:50 pg/mL 0.1% DMSO\|sample preparation:dissociated cell suspension	scRNA seq control testes rep 1	Reads were aligned and tabulated by individual cells in each sample using Cell Ranger 6.01 Count data was imported to Seurat version 4.0.4 for quality control QC filtering clustering dimensionality reduction visualization and differential gene expression Each sample was filtered to cells containing at least 500 features with clusters requiring a minimum of 30 cells. Samples were merged prior to normalization and clustering resolution 0.3. Differentially expressed genes between conditions for each cluster were identified using the "FindMarkers" function Genome build: Zebrafish May 2017 GRCz11/danRer11 Assembly Supplementary files format and content: xlsx; read counts and DEGs; Cell Ranger output matrices 10X SC TCDD DEG clusters: 10X Single cell cluster DEGs GEO CDxCI read counts DEGs: Control dissociated cells compared to Control intact cells GEO CPxCB read counts DEGs: Control psuedo bulk seq compared to Control dissociated cells for bulk seq GEO TBxCB read counts DEGs: TCDD dissociated cells compared to Control dissociated cells GEO TPxCP read counts DEGs: TCDD psuedo bulk seq compared to Control psuedo bulk seq GEO TPxTB read counts DEGs: TCDD psuedo bulk seq compared to TCDD dissociated cells bulk seq	testes	Experimental fish Sample 4 and 5 were exposed to 1 hour of TCDD at xxx and 7 wpf allowed to mature and testes were harvested as adults.	Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform and sequenced on a NovaSeq.	Zebrafish were maintained on a 14:10h light/dark cycle with temperatures maintained at 27°C– 30°C. Fish were fed twice daily. Fish were raised in beakers with daily water changes. Animal use protocols were approved by the Institutional Animal Care and Use Committees at Wayne State University and the University of Wisconsin Madison according to the National Institutes of Health Guide to the Care and Use of Laboratory Animals Protocol No. M00489.	strain:AB\|treatment:50 pg/mL 0.1% DMSO\|sample preparation:dissociated cell suspension	GSM5820552	GSM5820552: scRNA seq control testes rep 1; Danio rerio; RNA Seq	GSM5820552 r1	GSM5820552	1	Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform and sequenced on a NovaSeq.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP355202	loader:fastq load.py	SC_C1_S1_L001_I1_001.fastq.gz SC_C1_S1_L001_R1_001.fastq.gz SC_C1_S1_L001_R2_001.fastq.gz	fastq fastq fastq	11845124392.0	93268696.0	GSM5820552 r1	0:8 1:28 2:91	A:2554285232;C:1757437977;G:2060709302;T:2114543968;N:474857	8	28	91		2554285232	1757437977	2060709302	2114543968	474857	SRX13799335	SRS11681624	SRA1357269	University of Florida	University of Florida	1	0.89006		0.16375		0.74714		0.51816		91		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2022-01-15	Juvenile	Juvenile	Gonad	Reproductive System
68148	68148	SRR17630970	SRX13799335	SRS11681624	SRP355202	PRJNA797655	Toxicotranscriptomics of single cell RNA Seq and conventional RNA Seq in TCDD exposed testicular tissue	GSE193758	Transcriptome Analysis	Spermatogenesis is a dynamic tightly conserved process that is susceptible to environmental contaminants. Exposure to environmental contaminants such as 2 3 7 8 tetrachlorodibenzo p dioxin TCDD is believed to be a cause of idiopathic male infertility. To understand TCDD induced disruption of spermatogenesis at the single cell level we profiled adult zebrafish testes with and without xxx life exposure to TCDD. Secondly to investigate the potential for technical artifacts in scRNA seq we compared bulk sequenced and scRNA seq paired samples from control and TCDD exposed samples and included an intact control fish to account for dissociation induced artifacts. We found scRNA seq and bulk seq of dissociated testes produced markedly different profiles both toxicologically and transcriptomically. Through scRNA seq we found TCDD exposure induces mid late germ cell apoptosis while increasing the population of spermatogonial stem cells. Bulk seq on the same cells returned results of immune dysregulation. The transcriptome was unequally detected by scRNA seq and bulk seq with scRNA seq biased towards detecting longer and more abundant transcripts but this was not mediated by TCDD exposure. Overall design: Zebrafish were exposed to 50 pg/mL TCDD or vehicle solution for 1 hour during sexual differentiation and maturation. Adult testes were dissected for toxicotranscriptomic analysis. Samples were prepared by dissociation for scRNA seq remained intact for bulk seq or were dissociated for bulk seq.	pubmed:35615540;pubmed:35799832	scRNA seq control testes rep 1	GSM5820552	tissue:testes\|strain:AB\|treatment:50 pg/mL 0.1% DMSO\|sample preparation:dissociated cell suspension	scRNA seq control testes rep 1	Reads were aligned and tabulated by individual cells in each sample using Cell Ranger 6.01 Count data was imported to Seurat version 4.0.4 for quality control QC filtering clustering dimensionality reduction visualization and differential gene expression Each sample was filtered to cells containing at least 500 features with clusters requiring a minimum of 30 cells. Samples were merged prior to normalization and clustering resolution 0.3. Differentially expressed genes between conditions for each cluster were identified using the "FindMarkers" function Genome build: Zebrafish May 2017 GRCz11/danRer11 Assembly Supplementary files format and content: xlsx; read counts and DEGs; Cell Ranger output matrices 10X SC TCDD DEG clusters: 10X Single cell cluster DEGs GEO CDxCI read counts DEGs: Control dissociated cells compared to Control intact cells GEO CPxCB read counts DEGs: Control psuedo bulk seq compared to Control dissociated cells for bulk seq GEO TBxCB read counts DEGs: TCDD dissociated cells compared to Control dissociated cells GEO TPxCP read counts DEGs: TCDD psuedo bulk seq compared to Control psuedo bulk seq GEO TPxTB read counts DEGs: TCDD psuedo bulk seq compared to TCDD dissociated cells bulk seq	testes	Experimental fish Sample 4 and 5 were exposed to 1 hour of TCDD at xxx and 7 wpf allowed to mature and testes were harvested as adults.	Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform and sequenced on a NovaSeq.	Zebrafish were maintained on a 14:10h light/dark cycle with temperatures maintained at 27°C– 30°C. Fish were fed twice daily. Fish were raised in beakers with daily water changes. Animal use protocols were approved by the Institutional Animal Care and Use Committees at Wayne State University and the University of Wisconsin Madison according to the National Institutes of Health Guide to the Care and Use of Laboratory Animals Protocol No. M00489.	strain:AB\|treatment:50 pg/mL 0.1% DMSO\|sample preparation:dissociated cell suspension	GSM5820552	GSM5820552: scRNA seq control testes rep 1; Danio rerio; RNA Seq	GSM5820552 r1	GSM5820552	1	Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform and sequenced on a NovaSeq.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP355202	loader:fastq load.py	SC_C1_S1_L002_I1_001.fastq.gz SC_C1_S1_L002_R1_001.fastq.gz SC_C1_S1_L002_R2_001.fastq.gz	fastq fastq fastq	11974253293.0	94285459.0	GSM5820552 r2	0:8 1:28 2:91	A:2577816465;C:1779883368;G:2086781140;T:2134925822;N:569974	8	28	91		2577816465	1779883368	2086781140	2134925822	569974	SRX13799335	SRS11681624	SRA1357269	University of Florida	University of Florida	1	0.89007		0.16458		0.74986		0.52005		91		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2022-01-15	Juvenile	Juvenile	Gonad	Reproductive System
68149	68149	SRR17630939	SRX13799350	SRS11681639	SRP355202	PRJNA797655	Toxicotranscriptomics of single cell RNA Seq and conventional RNA Seq in TCDD exposed testicular tissue	GSE193758	Transcriptome Analysis	Spermatogenesis is a dynamic tightly conserved process that is susceptible to environmental contaminants. Exposure to environmental contaminants such as 2 3 7 8 tetrachlorodibenzo p dioxin TCDD is believed to be a cause of idiopathic male infertility. To understand TCDD induced disruption of spermatogenesis at the single cell level we profiled adult zebrafish testes with and without xxx life exposure to TCDD. Secondly to investigate the potential for technical artifacts in scRNA seq we compared bulk sequenced and scRNA seq paired samples from control and TCDD exposed samples and included an intact control fish to account for dissociation induced artifacts. We found scRNA seq and bulk seq of dissociated testes produced markedly different profiles both toxicologically and transcriptomically. Through scRNA seq we found TCDD exposure induces mid late germ cell apoptosis while increasing the population of spermatogonial stem cells. Bulk seq on the same cells returned results of immune dysregulation. The transcriptome was unequally detected by scRNA seq and bulk seq with scRNA seq biased towards detecting longer and more abundant transcripts but this was not mediated by TCDD exposure. Overall design: Zebrafish were exposed to 50 pg/mL TCDD or vehicle solution for 1 hour during sexual differentiation and maturation. Adult testes were dissected for toxicotranscriptomic analysis. Samples were prepared by dissociation for scRNA seq remained intact for bulk seq or were dissociated for bulk seq.	pubmed:35615540;pubmed:35799832	dissociated bulk seq control testes rep 3 compared to intact control testes	GSM5820567	tissue:testes\|strain:AB\|treatment:50 pg/mL 0.1% DMSO\|sample preparation:dissociated cell suspension	dissociated bulk seq control testes rep 3 compared to intact control testes	Reads were aligned and tabulated by individual cells in each sample using Cell Ranger 6.01 Count data was imported to Seurat version 4.0.4 for quality control QC filtering clustering dimensionality reduction visualization and differential gene expression Each sample was filtered to cells containing at least 500 features with clusters requiring a minimum of 30 cells. Samples were merged prior to normalization and clustering resolution 0.3. Differentially expressed genes between conditions for each cluster were identified using the "FindMarkers" function Genome build: Zebrafish May 2017 GRCz11/danRer11 Assembly Supplementary files format and content: xlsx; read counts and DEGs; Cell Ranger output matrices 10X SC TCDD DEG clusters: 10X Single cell cluster DEGs GEO CDxCI read counts DEGs: Control dissociated cells compared to Control intact cells GEO CPxCB read counts DEGs: Control psuedo bulk seq compared to Control dissociated cells for bulk seq GEO TBxCB read counts DEGs: TCDD dissociated cells compared to Control dissociated cells GEO TPxCP read counts DEGs: TCDD psuedo bulk seq compared to Control psuedo bulk seq GEO TPxTB read counts DEGs: TCDD psuedo bulk seq compared to TCDD dissociated cells bulk seq	testes	Experimental fish Sample 4 and 5 were exposed to 1 hour of TCDD at xxx and 7 wpf allowed to mature and testes were harvested as adults.	Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform and sequenced on a NovaSeq.	Zebrafish were maintained on a 14:10h light/dark cycle with temperatures maintained at 27°C– 30°C. Fish were fed twice daily. Fish were raised in beakers with daily water changes. Animal use protocols were approved by the Institutional Animal Care and Use Committees at Wayne State University and the University of Wisconsin Madison according to the National Institutes of Health Guide to the Care and Use of Laboratory Animals Protocol No. M00489.	strain:AB\|treatment:50 pg/mL 0.1% DMSO\|sample preparation:dissociated cell suspension	GSM5820567	GSM5820567: dissociated bulk seq control testes rep 3 compared to intact control testes; Danio rerio; RNA Seq	GSM5820567 r1	GSM5820567	1	Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform and sequenced on a NovaSeq.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP355202		I_C3_S14_L001_R1_001.fastq.gz	fastq	1847371623.0	36222973.0	GSM5820567 r1	0:51 1:0	A:535632392;C:366862698;G:429979337;T:514873991;N:23205	51	0			535632392	366862698	429979337	514873991	23205	SRX13799350	SRS11681639	SRA1357269	University of Florida	University of Florida	1	0.87212		0.1857		0.69372		0.56886		51		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2022-01-15	Juvenile	Juvenile	Gonad	Reproductive System
68150	68150	SRR17630940	SRX13799350	SRS11681639	SRP355202	PRJNA797655	Toxicotranscriptomics of single cell RNA Seq and conventional RNA Seq in TCDD exposed testicular tissue	GSE193758	Transcriptome Analysis	Spermatogenesis is a dynamic tightly conserved process that is susceptible to environmental contaminants. Exposure to environmental contaminants such as 2 3 7 8 tetrachlorodibenzo p dioxin TCDD is believed to be a cause of idiopathic male infertility. To understand TCDD induced disruption of spermatogenesis at the single cell level we profiled adult zebrafish testes with and without xxx life exposure to TCDD. Secondly to investigate the potential for technical artifacts in scRNA seq we compared bulk sequenced and scRNA seq paired samples from control and TCDD exposed samples and included an intact control fish to account for dissociation induced artifacts. We found scRNA seq and bulk seq of dissociated testes produced markedly different profiles both toxicologically and transcriptomically. Through scRNA seq we found TCDD exposure induces mid late germ cell apoptosis while increasing the population of spermatogonial stem cells. Bulk seq on the same cells returned results of immune dysregulation. The transcriptome was unequally detected by scRNA seq and bulk seq with scRNA seq biased towards detecting longer and more abundant transcripts but this was not mediated by TCDD exposure. Overall design: Zebrafish were exposed to 50 pg/mL TCDD or vehicle solution for 1 hour during sexual differentiation and maturation. Adult testes were dissected for toxicotranscriptomic analysis. Samples were prepared by dissociation for scRNA seq remained intact for bulk seq or were dissociated for bulk seq.	pubmed:35615540;pubmed:35799832	dissociated bulk seq control testes rep 3 compared to intact control testes	GSM5820567	tissue:testes\|strain:AB\|treatment:50 pg/mL 0.1% DMSO\|sample preparation:dissociated cell suspension	dissociated bulk seq control testes rep 3 compared to intact control testes	Reads were aligned and tabulated by individual cells in each sample using Cell Ranger 6.01 Count data was imported to Seurat version 4.0.4 for quality control QC filtering clustering dimensionality reduction visualization and differential gene expression Each sample was filtered to cells containing at least 500 features with clusters requiring a minimum of 30 cells. Samples were merged prior to normalization and clustering resolution 0.3. Differentially expressed genes between conditions for each cluster were identified using the "FindMarkers" function Genome build: Zebrafish May 2017 GRCz11/danRer11 Assembly Supplementary files format and content: xlsx; read counts and DEGs; Cell Ranger output matrices 10X SC TCDD DEG clusters: 10X Single cell cluster DEGs GEO CDxCI read counts DEGs: Control dissociated cells compared to Control intact cells GEO CPxCB read counts DEGs: Control psuedo bulk seq compared to Control dissociated cells for bulk seq GEO TBxCB read counts DEGs: TCDD dissociated cells compared to Control dissociated cells GEO TPxCP read counts DEGs: TCDD psuedo bulk seq compared to Control psuedo bulk seq GEO TPxTB read counts DEGs: TCDD psuedo bulk seq compared to TCDD dissociated cells bulk seq	testes	Experimental fish Sample 4 and 5 were exposed to 1 hour of TCDD at xxx and 7 wpf allowed to mature and testes were harvested as adults.	Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform and sequenced on a NovaSeq.	Zebrafish were maintained on a 14:10h light/dark cycle with temperatures maintained at 27°C– 30°C. Fish were fed twice daily. Fish were raised in beakers with daily water changes. Animal use protocols were approved by the Institutional Animal Care and Use Committees at Wayne State University and the University of Wisconsin Madison according to the National Institutes of Health Guide to the Care and Use of Laboratory Animals Protocol No. M00489.	strain:AB\|treatment:50 pg/mL 0.1% DMSO\|sample preparation:dissociated cell suspension	GSM5820567	GSM5820567: dissociated bulk seq control testes rep 3 compared to intact control testes; Danio rerio; RNA Seq	GSM5820567 r1	GSM5820567	1	Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform and sequenced on a NovaSeq.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP355202		I_C3_S14_L002_R1_001.fastq.gz	fastq	1823230824.0	35749624.0	GSM5820567 r2	0:51 1:0	A:529009592;C:361883074;G:424030274;T:508289743;N:18141	51	0			529009592	361883074	424030274	508289743	18141	SRX13799350	SRS11681639	SRA1357269	University of Florida	University of Florida	1	0.8708		0.18714		0.6955		0.5716		51		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2022-01-15	Juvenile	Juvenile	Gonad	Reproductive System
68151	68151	SRR17630941	SRX13799349	SRS11681638	SRP355202	PRJNA797655	Toxicotranscriptomics of single cell RNA Seq and conventional RNA Seq in TCDD exposed testicular tissue	GSE193758	Transcriptome Analysis	Spermatogenesis is a dynamic tightly conserved process that is susceptible to environmental contaminants. Exposure to environmental contaminants such as 2 3 7 8 tetrachlorodibenzo p dioxin TCDD is believed to be a cause of idiopathic male infertility. To understand TCDD induced disruption of spermatogenesis at the single cell level we profiled adult zebrafish testes with and without xxx life exposure to TCDD. Secondly to investigate the potential for technical artifacts in scRNA seq we compared bulk sequenced and scRNA seq paired samples from control and TCDD exposed samples and included an intact control fish to account for dissociation induced artifacts. We found scRNA seq and bulk seq of dissociated testes produced markedly different profiles both toxicologically and transcriptomically. Through scRNA seq we found TCDD exposure induces mid late germ cell apoptosis while increasing the population of spermatogonial stem cells. Bulk seq on the same cells returned results of immune dysregulation. The transcriptome was unequally detected by scRNA seq and bulk seq with scRNA seq biased towards detecting longer and more abundant transcripts but this was not mediated by TCDD exposure. Overall design: Zebrafish were exposed to 50 pg/mL TCDD or vehicle solution for 1 hour during sexual differentiation and maturation. Adult testes were dissected for toxicotranscriptomic analysis. Samples were prepared by dissociation for scRNA seq remained intact for bulk seq or were dissociated for bulk seq.	pubmed:35615540;pubmed:35799832	dissociated bulk seq control testes rep 2 compared to intact control testes	GSM5820566	tissue:testes\|strain:AB\|treatment:50 pg/mL 0.1% DMSO\|sample preparation:dissociated cell suspension	dissociated bulk seq control testes rep 2 compared to intact control testes	Reads were aligned and tabulated by individual cells in each sample using Cell Ranger 6.01 Count data was imported to Seurat version 4.0.4 for quality control QC filtering clustering dimensionality reduction visualization and differential gene expression Each sample was filtered to cells containing at least 500 features with clusters requiring a minimum of 30 cells. Samples were merged prior to normalization and clustering resolution 0.3. Differentially expressed genes between conditions for each cluster were identified using the "FindMarkers" function Genome build: Zebrafish May 2017 GRCz11/danRer11 Assembly Supplementary files format and content: xlsx; read counts and DEGs; Cell Ranger output matrices 10X SC TCDD DEG clusters: 10X Single cell cluster DEGs GEO CDxCI read counts DEGs: Control dissociated cells compared to Control intact cells GEO CPxCB read counts DEGs: Control psuedo bulk seq compared to Control dissociated cells for bulk seq GEO TBxCB read counts DEGs: TCDD dissociated cells compared to Control dissociated cells GEO TPxCP read counts DEGs: TCDD psuedo bulk seq compared to Control psuedo bulk seq GEO TPxTB read counts DEGs: TCDD psuedo bulk seq compared to TCDD dissociated cells bulk seq	testes	Experimental fish Sample 4 and 5 were exposed to 1 hour of TCDD at xxx and 7 wpf allowed to mature and testes were harvested as adults.	Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform and sequenced on a NovaSeq.	Zebrafish were maintained on a 14:10h light/dark cycle with temperatures maintained at 27°C– 30°C. Fish were fed twice daily. Fish were raised in beakers with daily water changes. Animal use protocols were approved by the Institutional Animal Care and Use Committees at Wayne State University and the University of Wisconsin Madison according to the National Institutes of Health Guide to the Care and Use of Laboratory Animals Protocol No. M00489.	strain:AB\|treatment:50 pg/mL 0.1% DMSO\|sample preparation:dissociated cell suspension	GSM5820566	GSM5820566: dissociated bulk seq control testes rep 2 compared to intact control testes; Danio rerio; RNA Seq	GSM5820566 r1	GSM5820566	1	Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform and sequenced on a NovaSeq.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP355202		I_C2_S13_L001_R1_001.fastq.gz	fastq	536561208.0	10520808.0	GSM5820566 r1	0:51 1:0	A:163430759;C:106016694;G:122059136;T:145048023;N:6596	51	0			163430759	106016694	122059136	145048023	6596	SRX13799349	SRS11681638	SRA1357269	University of Florida	University of Florida	1	0.83573		0.2005		0.71056		0.52825		51		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2022-01-15	Juvenile	Juvenile	Gonad	Reproductive System
68152	68152	SRR17630942	SRX13799349	SRS11681638	SRP355202	PRJNA797655	Toxicotranscriptomics of single cell RNA Seq and conventional RNA Seq in TCDD exposed testicular tissue	GSE193758	Transcriptome Analysis	Spermatogenesis is a dynamic tightly conserved process that is susceptible to environmental contaminants. Exposure to environmental contaminants such as 2 3 7 8 tetrachlorodibenzo p dioxin TCDD is believed to be a cause of idiopathic male infertility. To understand TCDD induced disruption of spermatogenesis at the single cell level we profiled adult zebrafish testes with and without xxx life exposure to TCDD. Secondly to investigate the potential for technical artifacts in scRNA seq we compared bulk sequenced and scRNA seq paired samples from control and TCDD exposed samples and included an intact control fish to account for dissociation induced artifacts. We found scRNA seq and bulk seq of dissociated testes produced markedly different profiles both toxicologically and transcriptomically. Through scRNA seq we found TCDD exposure induces mid late germ cell apoptosis while increasing the population of spermatogonial stem cells. Bulk seq on the same cells returned results of immune dysregulation. The transcriptome was unequally detected by scRNA seq and bulk seq with scRNA seq biased towards detecting longer and more abundant transcripts but this was not mediated by TCDD exposure. Overall design: Zebrafish were exposed to 50 pg/mL TCDD or vehicle solution for 1 hour during sexual differentiation and maturation. Adult testes were dissected for toxicotranscriptomic analysis. Samples were prepared by dissociation for scRNA seq remained intact for bulk seq or were dissociated for bulk seq.	pubmed:35615540;pubmed:35799832	dissociated bulk seq control testes rep 2 compared to intact control testes	GSM5820566	tissue:testes\|strain:AB\|treatment:50 pg/mL 0.1% DMSO\|sample preparation:dissociated cell suspension	dissociated bulk seq control testes rep 2 compared to intact control testes	Reads were aligned and tabulated by individual cells in each sample using Cell Ranger 6.01 Count data was imported to Seurat version 4.0.4 for quality control QC filtering clustering dimensionality reduction visualization and differential gene expression Each sample was filtered to cells containing at least 500 features with clusters requiring a minimum of 30 cells. Samples were merged prior to normalization and clustering resolution 0.3. Differentially expressed genes between conditions for each cluster were identified using the "FindMarkers" function Genome build: Zebrafish May 2017 GRCz11/danRer11 Assembly Supplementary files format and content: xlsx; read counts and DEGs; Cell Ranger output matrices 10X SC TCDD DEG clusters: 10X Single cell cluster DEGs GEO CDxCI read counts DEGs: Control dissociated cells compared to Control intact cells GEO CPxCB read counts DEGs: Control psuedo bulk seq compared to Control dissociated cells for bulk seq GEO TBxCB read counts DEGs: TCDD dissociated cells compared to Control dissociated cells GEO TPxCP read counts DEGs: TCDD psuedo bulk seq compared to Control psuedo bulk seq GEO TPxTB read counts DEGs: TCDD psuedo bulk seq compared to TCDD dissociated cells bulk seq	testes	Experimental fish Sample 4 and 5 were exposed to 1 hour of TCDD at xxx and 7 wpf allowed to mature and testes were harvested as adults.	Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform and sequenced on a NovaSeq.	Zebrafish were maintained on a 14:10h light/dark cycle with temperatures maintained at 27°C– 30°C. Fish were fed twice daily. Fish were raised in beakers with daily water changes. Animal use protocols were approved by the Institutional Animal Care and Use Committees at Wayne State University and the University of Wisconsin Madison according to the National Institutes of Health Guide to the Care and Use of Laboratory Animals Protocol No. M00489.	strain:AB\|treatment:50 pg/mL 0.1% DMSO\|sample preparation:dissociated cell suspension	GSM5820566	GSM5820566: dissociated bulk seq control testes rep 2 compared to intact control testes; Danio rerio; RNA Seq	GSM5820566 r1	GSM5820566	1	Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform and sequenced on a NovaSeq.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP355202		I_C2_S13_L002_R1_001.fastq.gz	fastq	530978238.0	10411338.0	GSM5820566 r2	0:51 1:0	A:161875304;C:104815309;G:120705456;T:143576873;N:5296	51	0			161875304	104815309	120705456	143576873	5296	SRX13799349	SRS11681638	SRA1357269	University of Florida	University of Florida	1	0.83663		0.19964		0.71104		0.54143		51		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2022-01-15	Juvenile	Juvenile	Gonad	Reproductive System
68153	68153	SRR17630943	SRX13799348	SRS11681637	SRP355202	PRJNA797655	Toxicotranscriptomics of single cell RNA Seq and conventional RNA Seq in TCDD exposed testicular tissue	GSE193758	Transcriptome Analysis	Spermatogenesis is a dynamic tightly conserved process that is susceptible to environmental contaminants. Exposure to environmental contaminants such as 2 3 7 8 tetrachlorodibenzo p dioxin TCDD is believed to be a cause of idiopathic male infertility. To understand TCDD induced disruption of spermatogenesis at the single cell level we profiled adult zebrafish testes with and without xxx life exposure to TCDD. Secondly to investigate the potential for technical artifacts in scRNA seq we compared bulk sequenced and scRNA seq paired samples from control and TCDD exposed samples and included an intact control fish to account for dissociation induced artifacts. We found scRNA seq and bulk seq of dissociated testes produced markedly different profiles both toxicologically and transcriptomically. Through scRNA seq we found TCDD exposure induces mid late germ cell apoptosis while increasing the population of spermatogonial stem cells. Bulk seq on the same cells returned results of immune dysregulation. The transcriptome was unequally detected by scRNA seq and bulk seq with scRNA seq biased towards detecting longer and more abundant transcripts but this was not mediated by TCDD exposure. Overall design: Zebrafish were exposed to 50 pg/mL TCDD or vehicle solution for 1 hour during sexual differentiation and maturation. Adult testes were dissected for toxicotranscriptomic analysis. Samples were prepared by dissociation for scRNA seq remained intact for bulk seq or were dissociated for bulk seq.	pubmed:35615540;pubmed:35799832	dissociated bulk seq control testes rep 1 compared to intact control testes	GSM5820565	tissue:testes\|strain:AB\|treatment:50 pg/mL 0.1% DMSO\|sample preparation:dissociated cell suspension	dissociated bulk seq control testes rep 1 compared to intact control testes	Reads were aligned and tabulated by individual cells in each sample using Cell Ranger 6.01 Count data was imported to Seurat version 4.0.4 for quality control QC filtering clustering dimensionality reduction visualization and differential gene expression Each sample was filtered to cells containing at least 500 features with clusters requiring a minimum of 30 cells. Samples were merged prior to normalization and clustering resolution 0.3. Differentially expressed genes between conditions for each cluster were identified using the "FindMarkers" function Genome build: Zebrafish May 2017 GRCz11/danRer11 Assembly Supplementary files format and content: xlsx; read counts and DEGs; Cell Ranger output matrices 10X SC TCDD DEG clusters: 10X Single cell cluster DEGs GEO CDxCI read counts DEGs: Control dissociated cells compared to Control intact cells GEO CPxCB read counts DEGs: Control psuedo bulk seq compared to Control dissociated cells for bulk seq GEO TBxCB read counts DEGs: TCDD dissociated cells compared to Control dissociated cells GEO TPxCP read counts DEGs: TCDD psuedo bulk seq compared to Control psuedo bulk seq GEO TPxTB read counts DEGs: TCDD psuedo bulk seq compared to TCDD dissociated cells bulk seq	testes	Experimental fish Sample 4 and 5 were exposed to 1 hour of TCDD at xxx and 7 wpf allowed to mature and testes were harvested as adults.	Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform and sequenced on a NovaSeq.	Zebrafish were maintained on a 14:10h light/dark cycle with temperatures maintained at 27°C– 30°C. Fish were fed twice daily. Fish were raised in beakers with daily water changes. Animal use protocols were approved by the Institutional Animal Care and Use Committees at Wayne State University and the University of Wisconsin Madison according to the National Institutes of Health Guide to the Care and Use of Laboratory Animals Protocol No. M00489.	strain:AB\|treatment:50 pg/mL 0.1% DMSO\|sample preparation:dissociated cell suspension	GSM5820565	GSM5820565: dissociated bulk seq control testes rep 1 compared to intact control testes; Danio rerio; RNA Seq	GSM5820565 r1	GSM5820565	1	Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform and sequenced on a NovaSeq.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP355202		I_C1_S12_L001_R1_001.fastq.gz	fastq	523779282.0	10270182.0	GSM5820565 r1	0:51 1:0	A:155891194;C:103400919;G:120028554;T:144451616;N:6999	51	0			155891194	103400919	120028554	144451616	6999	SRX13799348	SRS11681637	SRA1357269	University of Florida	University of Florida	1	0.85957		0.19557		0.69501		0.56637		51		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2022-01-15	Juvenile	Juvenile	Gonad	Reproductive System
68154	68154	SRR17630944	SRX13799348	SRS11681637	SRP355202	PRJNA797655	Toxicotranscriptomics of single cell RNA Seq and conventional RNA Seq in TCDD exposed testicular tissue	GSE193758	Transcriptome Analysis	Spermatogenesis is a dynamic tightly conserved process that is susceptible to environmental contaminants. Exposure to environmental contaminants such as 2 3 7 8 tetrachlorodibenzo p dioxin TCDD is believed to be a cause of idiopathic male infertility. To understand TCDD induced disruption of spermatogenesis at the single cell level we profiled adult zebrafish testes with and without xxx life exposure to TCDD. Secondly to investigate the potential for technical artifacts in scRNA seq we compared bulk sequenced and scRNA seq paired samples from control and TCDD exposed samples and included an intact control fish to account for dissociation induced artifacts. We found scRNA seq and bulk seq of dissociated testes produced markedly different profiles both toxicologically and transcriptomically. Through scRNA seq we found TCDD exposure induces mid late germ cell apoptosis while increasing the population of spermatogonial stem cells. Bulk seq on the same cells returned results of immune dysregulation. The transcriptome was unequally detected by scRNA seq and bulk seq with scRNA seq biased towards detecting longer and more abundant transcripts but this was not mediated by TCDD exposure. Overall design: Zebrafish were exposed to 50 pg/mL TCDD or vehicle solution for 1 hour during sexual differentiation and maturation. Adult testes were dissected for toxicotranscriptomic analysis. Samples were prepared by dissociation for scRNA seq remained intact for bulk seq or were dissociated for bulk seq.	pubmed:35615540;pubmed:35799832	dissociated bulk seq control testes rep 1 compared to intact control testes	GSM5820565	tissue:testes\|strain:AB\|treatment:50 pg/mL 0.1% DMSO\|sample preparation:dissociated cell suspension	dissociated bulk seq control testes rep 1 compared to intact control testes	Reads were aligned and tabulated by individual cells in each sample using Cell Ranger 6.01 Count data was imported to Seurat version 4.0.4 for quality control QC filtering clustering dimensionality reduction visualization and differential gene expression Each sample was filtered to cells containing at least 500 features with clusters requiring a minimum of 30 cells. Samples were merged prior to normalization and clustering resolution 0.3. Differentially expressed genes between conditions for each cluster were identified using the "FindMarkers" function Genome build: Zebrafish May 2017 GRCz11/danRer11 Assembly Supplementary files format and content: xlsx; read counts and DEGs; Cell Ranger output matrices 10X SC TCDD DEG clusters: 10X Single cell cluster DEGs GEO CDxCI read counts DEGs: Control dissociated cells compared to Control intact cells GEO CPxCB read counts DEGs: Control psuedo bulk seq compared to Control dissociated cells for bulk seq GEO TBxCB read counts DEGs: TCDD dissociated cells compared to Control dissociated cells GEO TPxCP read counts DEGs: TCDD psuedo bulk seq compared to Control psuedo bulk seq GEO TPxTB read counts DEGs: TCDD psuedo bulk seq compared to TCDD dissociated cells bulk seq	testes	Experimental fish Sample 4 and 5 were exposed to 1 hour of TCDD at xxx and 7 wpf allowed to mature and testes were harvested as adults.	Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform and sequenced on a NovaSeq.	Zebrafish were maintained on a 14:10h light/dark cycle with temperatures maintained at 27°C– 30°C. Fish were fed twice daily. Fish were raised in beakers with daily water changes. Animal use protocols were approved by the Institutional Animal Care and Use Committees at Wayne State University and the University of Wisconsin Madison according to the National Institutes of Health Guide to the Care and Use of Laboratory Animals Protocol No. M00489.	strain:AB\|treatment:50 pg/mL 0.1% DMSO\|sample preparation:dissociated cell suspension	GSM5820565	GSM5820565: dissociated bulk seq control testes rep 1 compared to intact control testes; Danio rerio; RNA Seq	GSM5820565 r1	GSM5820565	1	Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform and sequenced on a NovaSeq.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP355202		I_C1_S12_L002_R1_001.fastq.gz	fastq	516901983.0	10135333.0	GSM5820565 r2	0:51 1:0	A:153923180;C:101966413;G:118359254;T:142647450;N:5686	51	0			153923180	101966413	118359254	142647450	5686	SRX13799348	SRS11681637	SRA1357269	University of Florida	University of Florida	1	0.85795		0.19403		0.69627		0.57159		51		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2022-01-15	Juvenile	Juvenile	Gonad	Reproductive System
68155	68155	SRR17630945	SRX13799347	SRS11681636	SRP355202	PRJNA797655	Toxicotranscriptomics of single cell RNA Seq and conventional RNA Seq in TCDD exposed testicular tissue	GSE193758	Transcriptome Analysis	Spermatogenesis is a dynamic tightly conserved process that is susceptible to environmental contaminants. Exposure to environmental contaminants such as 2 3 7 8 tetrachlorodibenzo p dioxin TCDD is believed to be a cause of idiopathic male infertility. To understand TCDD induced disruption of spermatogenesis at the single cell level we profiled adult zebrafish testes with and without xxx life exposure to TCDD. Secondly to investigate the potential for technical artifacts in scRNA seq we compared bulk sequenced and scRNA seq paired samples from control and TCDD exposed samples and included an intact control fish to account for dissociation induced artifacts. We found scRNA seq and bulk seq of dissociated testes produced markedly different profiles both toxicologically and transcriptomically. Through scRNA seq we found TCDD exposure induces mid late germ cell apoptosis while increasing the population of spermatogonial stem cells. Bulk seq on the same cells returned results of immune dysregulation. The transcriptome was unequally detected by scRNA seq and bulk seq with scRNA seq biased towards detecting longer and more abundant transcripts but this was not mediated by TCDD exposure. Overall design: Zebrafish were exposed to 50 pg/mL TCDD or vehicle solution for 1 hour during sexual differentiation and maturation. Adult testes were dissected for toxicotranscriptomic analysis. Samples were prepared by dissociation for scRNA seq remained intact for bulk seq or were dissociated for bulk seq.	pubmed:35615540;pubmed:35799832	bulk seq intact control testes rep 3	GSM5820564	tissue:testes\|strain:AB\|treatment:50 pg/mL 0.1% DMSO\|sample preparation:non dissociated intact testes	bulk seq intact control testes rep 3	Reads were aligned and tabulated by individual cells in each sample using Cell Ranger 6.01 Count data was imported to Seurat version 4.0.4 for quality control QC filtering clustering dimensionality reduction visualization and differential gene expression Each sample was filtered to cells containing at least 500 features with clusters requiring a minimum of 30 cells. Samples were merged prior to normalization and clustering resolution 0.3. Differentially expressed genes between conditions for each cluster were identified using the "FindMarkers" function Genome build: Zebrafish May 2017 GRCz11/danRer11 Assembly Supplementary files format and content: xlsx; read counts and DEGs; Cell Ranger output matrices 10X SC TCDD DEG clusters: 10X Single cell cluster DEGs GEO CDxCI read counts DEGs: Control dissociated cells compared to Control intact cells GEO CPxCB read counts DEGs: Control psuedo bulk seq compared to Control dissociated cells for bulk seq GEO TBxCB read counts DEGs: TCDD dissociated cells compared to Control dissociated cells GEO TPxCP read counts DEGs: TCDD psuedo bulk seq compared to Control psuedo bulk seq GEO TPxTB read counts DEGs: TCDD psuedo bulk seq compared to TCDD dissociated cells bulk seq	testes	Experimental fish Sample 4 and 5 were exposed to 1 hour of TCDD at xxx and 7 wpf allowed to mature and testes were harvested as adults.	Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform and sequenced on a NovaSeq.	Zebrafish were maintained on a 14:10h light/dark cycle with temperatures maintained at 27°C– 30°C. Fish were fed twice daily. Fish were raised in beakers with daily water changes. Animal use protocols were approved by the Institutional Animal Care and Use Committees at Wayne State University and the University of Wisconsin Madison according to the National Institutes of Health Guide to the Care and Use of Laboratory Animals Protocol No. M00489.	strain:AB\|treatment:50 pg/mL 0.1% DMSO\|sample preparation:non dissociated intact testes	GSM5820564	GSM5820564: bulk seq intact control testes rep 3; Danio rerio; RNA Seq	GSM5820564 r1	GSM5820564	1	Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform and sequenced on a NovaSeq.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP355202		D_C3_S16_L001_R1_001.fastq.gz	fastq	1673456880.0	32812880.0	GSM5820564 r1	0:51 1:0	A:496655744;C:334242155;G:387205466;T:455330132;N:23383	51	0			496655744	334242155	387205466	455330132	23383	SRX13799347	SRS11681636	SRA1357269	University of Florida	University of Florida	1	0.8707		0.22045		0.71078		0.60605		51		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2022-01-15	Juvenile	Juvenile	Gonad	Reproductive System
68156	68156	SRR17630946	SRX13799347	SRS11681636	SRP355202	PRJNA797655	Toxicotranscriptomics of single cell RNA Seq and conventional RNA Seq in TCDD exposed testicular tissue	GSE193758	Transcriptome Analysis	Spermatogenesis is a dynamic tightly conserved process that is susceptible to environmental contaminants. Exposure to environmental contaminants such as 2 3 7 8 tetrachlorodibenzo p dioxin TCDD is believed to be a cause of idiopathic male infertility. To understand TCDD induced disruption of spermatogenesis at the single cell level we profiled adult zebrafish testes with and without xxx life exposure to TCDD. Secondly to investigate the potential for technical artifacts in scRNA seq we compared bulk sequenced and scRNA seq paired samples from control and TCDD exposed samples and included an intact control fish to account for dissociation induced artifacts. We found scRNA seq and bulk seq of dissociated testes produced markedly different profiles both toxicologically and transcriptomically. Through scRNA seq we found TCDD exposure induces mid late germ cell apoptosis while increasing the population of spermatogonial stem cells. Bulk seq on the same cells returned results of immune dysregulation. The transcriptome was unequally detected by scRNA seq and bulk seq with scRNA seq biased towards detecting longer and more abundant transcripts but this was not mediated by TCDD exposure. Overall design: Zebrafish were exposed to 50 pg/mL TCDD or vehicle solution for 1 hour during sexual differentiation and maturation. Adult testes were dissected for toxicotranscriptomic analysis. Samples were prepared by dissociation for scRNA seq remained intact for bulk seq or were dissociated for bulk seq.	pubmed:35615540;pubmed:35799832	bulk seq intact control testes rep 3	GSM5820564	tissue:testes\|strain:AB\|treatment:50 pg/mL 0.1% DMSO\|sample preparation:non dissociated intact testes	bulk seq intact control testes rep 3	Reads were aligned and tabulated by individual cells in each sample using Cell Ranger 6.01 Count data was imported to Seurat version 4.0.4 for quality control QC filtering clustering dimensionality reduction visualization and differential gene expression Each sample was filtered to cells containing at least 500 features with clusters requiring a minimum of 30 cells. Samples were merged prior to normalization and clustering resolution 0.3. Differentially expressed genes between conditions for each cluster were identified using the "FindMarkers" function Genome build: Zebrafish May 2017 GRCz11/danRer11 Assembly Supplementary files format and content: xlsx; read counts and DEGs; Cell Ranger output matrices 10X SC TCDD DEG clusters: 10X Single cell cluster DEGs GEO CDxCI read counts DEGs: Control dissociated cells compared to Control intact cells GEO CPxCB read counts DEGs: Control psuedo bulk seq compared to Control dissociated cells for bulk seq GEO TBxCB read counts DEGs: TCDD dissociated cells compared to Control dissociated cells GEO TPxCP read counts DEGs: TCDD psuedo bulk seq compared to Control psuedo bulk seq GEO TPxTB read counts DEGs: TCDD psuedo bulk seq compared to TCDD dissociated cells bulk seq	testes	Experimental fish Sample 4 and 5 were exposed to 1 hour of TCDD at xxx and 7 wpf allowed to mature and testes were harvested as adults.	Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform and sequenced on a NovaSeq.	Zebrafish were maintained on a 14:10h light/dark cycle with temperatures maintained at 27°C– 30°C. Fish were fed twice daily. Fish were raised in beakers with daily water changes. Animal use protocols were approved by the Institutional Animal Care and Use Committees at Wayne State University and the University of Wisconsin Madison according to the National Institutes of Health Guide to the Care and Use of Laboratory Animals Protocol No. M00489.	strain:AB\|treatment:50 pg/mL 0.1% DMSO\|sample preparation:non dissociated intact testes	GSM5820564	GSM5820564: bulk seq intact control testes rep 3; Danio rerio; RNA Seq	GSM5820564 r1	GSM5820564	1	Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform and sequenced on a NovaSeq.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP355202		D_C3_S16_L002_R1_001.fastq.gz	fastq	1647184587.0	32297737.0	GSM5820564 r2	0:51 1:0	A:489182217;C:328774657;G:380849646;T:448358863;N:19204	51	0			489182217	328774657	380849646	448358863	19204	SRX13799347	SRS11681636	SRA1357269	University of Florida	University of Florida	1	0.87032		0.22081		0.71261		0.60917		51		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2022-01-15	Juvenile	Juvenile	Gonad	Reproductive System
68157	68157	SRR17630947	SRX13799346	SRS11681635	SRP355202	PRJNA797655	Toxicotranscriptomics of single cell RNA Seq and conventional RNA Seq in TCDD exposed testicular tissue	GSE193758	Transcriptome Analysis	Spermatogenesis is a dynamic tightly conserved process that is susceptible to environmental contaminants. Exposure to environmental contaminants such as 2 3 7 8 tetrachlorodibenzo p dioxin TCDD is believed to be a cause of idiopathic male infertility. To understand TCDD induced disruption of spermatogenesis at the single cell level we profiled adult zebrafish testes with and without xxx life exposure to TCDD. Secondly to investigate the potential for technical artifacts in scRNA seq we compared bulk sequenced and scRNA seq paired samples from control and TCDD exposed samples and included an intact control fish to account for dissociation induced artifacts. We found scRNA seq and bulk seq of dissociated testes produced markedly different profiles both toxicologically and transcriptomically. Through scRNA seq we found TCDD exposure induces mid late germ cell apoptosis while increasing the population of spermatogonial stem cells. Bulk seq on the same cells returned results of immune dysregulation. The transcriptome was unequally detected by scRNA seq and bulk seq with scRNA seq biased towards detecting longer and more abundant transcripts but this was not mediated by TCDD exposure. Overall design: Zebrafish were exposed to 50 pg/mL TCDD or vehicle solution for 1 hour during sexual differentiation and maturation. Adult testes were dissected for toxicotranscriptomic analysis. Samples were prepared by dissociation for scRNA seq remained intact for bulk seq or were dissociated for bulk seq.	pubmed:35615540;pubmed:35799832	bulk seq TCDD testes rep 2to be compared to scRNA seq TCDD testes	GSM5820561	tissue:testes\|strain:AB\|treatment:50 pg/mL TCDD in 0.1% DMSO\|sample preparation:dissociated cell suspension	bulk seq TCDD testes rep 2to be compared to scRNA seq TCDD testes	Reads were aligned and tabulated by individual cells in each sample using Cell Ranger 6.01 Count data was imported to Seurat version 4.0.4 for quality control QC filtering clustering dimensionality reduction visualization and differential gene expression Each sample was filtered to cells containing at least 500 features with clusters requiring a minimum of 30 cells. Samples were merged prior to normalization and clustering resolution 0.3. Differentially expressed genes between conditions for each cluster were identified using the "FindMarkers" function Genome build: Zebrafish May 2017 GRCz11/danRer11 Assembly Supplementary files format and content: xlsx; read counts and DEGs; Cell Ranger output matrices 10X SC TCDD DEG clusters: 10X Single cell cluster DEGs GEO CDxCI read counts DEGs: Control dissociated cells compared to Control intact cells GEO CPxCB read counts DEGs: Control psuedo bulk seq compared to Control dissociated cells for bulk seq GEO TBxCB read counts DEGs: TCDD dissociated cells compared to Control dissociated cells GEO TPxCP read counts DEGs: TCDD psuedo bulk seq compared to Control psuedo bulk seq GEO TPxTB read counts DEGs: TCDD psuedo bulk seq compared to TCDD dissociated cells bulk seq	testes	Experimental fish Sample 4 and 5 were exposed to 1 hour of TCDD at xxx and 7 wpf allowed to mature and testes were harvested as adults.	Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform and sequenced on a NovaSeq.	Zebrafish were maintained on a 14:10h light/dark cycle with temperatures maintained at 27°C– 30°C. Fish were fed twice daily. Fish were raised in beakers with daily water changes. Animal use protocols were approved by the Institutional Animal Care and Use Committees at Wayne State University and the University of Wisconsin Madison according to the National Institutes of Health Guide to the Care and Use of Laboratory Animals Protocol No. M00489.	strain:AB\|treatment:50 pg/mL TCDD in 0.1% DMSO\|sample preparation:dissociated cell suspension	GSM5820561	GSM5820561: bulk seq TCDD testes rep 2to be compared to scRNA seq TCDD testes; Danio rerio; RNA Seq	GSM5820561 r1	GSM5820561	1	Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform and sequenced on a NovaSeq.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP355202		BS_T2_S7_L001_R1_001.fastq.gz	fastq	1583815608.0	31055208.0	GSM5820561 r1	0:51 1:0	A:447529477;C:312467507;G:374130013;T:449667219;N:21392	51	0			447529477	312467507	374130013	449667219	21392	SRX13799346	SRS11681635	SRA1357269	University of Florida	University of Florida	1	0.86982		0.25275		0.70774		0.5721		51		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2022-01-15	Juvenile	Juvenile	Gonad	Reproductive System
68158	68158	SRR17630948	SRX13799346	SRS11681635	SRP355202	PRJNA797655	Toxicotranscriptomics of single cell RNA Seq and conventional RNA Seq in TCDD exposed testicular tissue	GSE193758	Transcriptome Analysis	Spermatogenesis is a dynamic tightly conserved process that is susceptible to environmental contaminants. Exposure to environmental contaminants such as 2 3 7 8 tetrachlorodibenzo p dioxin TCDD is believed to be a cause of idiopathic male infertility. To understand TCDD induced disruption of spermatogenesis at the single cell level we profiled adult zebrafish testes with and without xxx life exposure to TCDD. Secondly to investigate the potential for technical artifacts in scRNA seq we compared bulk sequenced and scRNA seq paired samples from control and TCDD exposed samples and included an intact control fish to account for dissociation induced artifacts. We found scRNA seq and bulk seq of dissociated testes produced markedly different profiles both toxicologically and transcriptomically. Through scRNA seq we found TCDD exposure induces mid late germ cell apoptosis while increasing the population of spermatogonial stem cells. Bulk seq on the same cells returned results of immune dysregulation. The transcriptome was unequally detected by scRNA seq and bulk seq with scRNA seq biased towards detecting longer and more abundant transcripts but this was not mediated by TCDD exposure. Overall design: Zebrafish were exposed to 50 pg/mL TCDD or vehicle solution for 1 hour during sexual differentiation and maturation. Adult testes were dissected for toxicotranscriptomic analysis. Samples were prepared by dissociation for scRNA seq remained intact for bulk seq or were dissociated for bulk seq.	pubmed:35615540;pubmed:35799832	bulk seq TCDD testes rep 2to be compared to scRNA seq TCDD testes	GSM5820561	tissue:testes\|strain:AB\|treatment:50 pg/mL TCDD in 0.1% DMSO\|sample preparation:dissociated cell suspension	bulk seq TCDD testes rep 2to be compared to scRNA seq TCDD testes	Reads were aligned and tabulated by individual cells in each sample using Cell Ranger 6.01 Count data was imported to Seurat version 4.0.4 for quality control QC filtering clustering dimensionality reduction visualization and differential gene expression Each sample was filtered to cells containing at least 500 features with clusters requiring a minimum of 30 cells. Samples were merged prior to normalization and clustering resolution 0.3. Differentially expressed genes between conditions for each cluster were identified using the "FindMarkers" function Genome build: Zebrafish May 2017 GRCz11/danRer11 Assembly Supplementary files format and content: xlsx; read counts and DEGs; Cell Ranger output matrices 10X SC TCDD DEG clusters: 10X Single cell cluster DEGs GEO CDxCI read counts DEGs: Control dissociated cells compared to Control intact cells GEO CPxCB read counts DEGs: Control psuedo bulk seq compared to Control dissociated cells for bulk seq GEO TBxCB read counts DEGs: TCDD dissociated cells compared to Control dissociated cells GEO TPxCP read counts DEGs: TCDD psuedo bulk seq compared to Control psuedo bulk seq GEO TPxTB read counts DEGs: TCDD psuedo bulk seq compared to TCDD dissociated cells bulk seq	testes	Experimental fish Sample 4 and 5 were exposed to 1 hour of TCDD at xxx and 7 wpf allowed to mature and testes were harvested as adults.	Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform and sequenced on a NovaSeq.	Zebrafish were maintained on a 14:10h light/dark cycle with temperatures maintained at 27°C– 30°C. Fish were fed twice daily. Fish were raised in beakers with daily water changes. Animal use protocols were approved by the Institutional Animal Care and Use Committees at Wayne State University and the University of Wisconsin Madison according to the National Institutes of Health Guide to the Care and Use of Laboratory Animals Protocol No. M00489.	strain:AB\|treatment:50 pg/mL TCDD in 0.1% DMSO\|sample preparation:dissociated cell suspension	GSM5820561	GSM5820561: bulk seq TCDD testes rep 2to be compared to scRNA seq TCDD testes; Danio rerio; RNA Seq	GSM5820561 r1	GSM5820561	1	Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform and sequenced on a NovaSeq.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP355202		BS_T2_S7_L002_R1_001.fastq.gz	fastq	1564087941.0	30668391.0	GSM5820561 r2	0:51 1:0	A:442209708;C:308400147;G:369229792;T:444230646;N:17648	51	0			442209708	308400147	369229792	444230646	17648	SRX13799346	SRS11681635	SRA1357269	University of Florida	University of Florida	1	0.87035		0.2527		0.70682		0.57673		51		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2022-01-15	Juvenile	Juvenile	Gonad	Reproductive System
68159	68159	SRR17630949	SRX13799345	SRS11681634	SRP355202	PRJNA797655	Toxicotranscriptomics of single cell RNA Seq and conventional RNA Seq in TCDD exposed testicular tissue	GSE193758	Transcriptome Analysis	Spermatogenesis is a dynamic tightly conserved process that is susceptible to environmental contaminants. Exposure to environmental contaminants such as 2 3 7 8 tetrachlorodibenzo p dioxin TCDD is believed to be a cause of idiopathic male infertility. To understand TCDD induced disruption of spermatogenesis at the single cell level we profiled adult zebrafish testes with and without xxx life exposure to TCDD. Secondly to investigate the potential for technical artifacts in scRNA seq we compared bulk sequenced and scRNA seq paired samples from control and TCDD exposed samples and included an intact control fish to account for dissociation induced artifacts. We found scRNA seq and bulk seq of dissociated testes produced markedly different profiles both toxicologically and transcriptomically. Through scRNA seq we found TCDD exposure induces mid late germ cell apoptosis while increasing the population of spermatogonial stem cells. Bulk seq on the same cells returned results of immune dysregulation. The transcriptome was unequally detected by scRNA seq and bulk seq with scRNA seq biased towards detecting longer and more abundant transcripts but this was not mediated by TCDD exposure. Overall design: Zebrafish were exposed to 50 pg/mL TCDD or vehicle solution for 1 hour during sexual differentiation and maturation. Adult testes were dissected for toxicotranscriptomic analysis. Samples were prepared by dissociation for scRNA seq remained intact for bulk seq or were dissociated for bulk seq.	pubmed:35615540;pubmed:35799832	bulk seq intact control testes rep 2	GSM5820563	tissue:testes\|strain:AB\|treatment:50 pg/mL 0.1% DMSO\|sample preparation:non dissociated intact testes	bulk seq intact control testes rep 2	Reads were aligned and tabulated by individual cells in each sample using Cell Ranger 6.01 Count data was imported to Seurat version 4.0.4 for quality control QC filtering clustering dimensionality reduction visualization and differential gene expression Each sample was filtered to cells containing at least 500 features with clusters requiring a minimum of 30 cells. Samples were merged prior to normalization and clustering resolution 0.3. Differentially expressed genes between conditions for each cluster were identified using the "FindMarkers" function Genome build: Zebrafish May 2017 GRCz11/danRer11 Assembly Supplementary files format and content: xlsx; read counts and DEGs; Cell Ranger output matrices 10X SC TCDD DEG clusters: 10X Single cell cluster DEGs GEO CDxCI read counts DEGs: Control dissociated cells compared to Control intact cells GEO CPxCB read counts DEGs: Control psuedo bulk seq compared to Control dissociated cells for bulk seq GEO TBxCB read counts DEGs: TCDD dissociated cells compared to Control dissociated cells GEO TPxCP read counts DEGs: TCDD psuedo bulk seq compared to Control psuedo bulk seq GEO TPxTB read counts DEGs: TCDD psuedo bulk seq compared to TCDD dissociated cells bulk seq	testes	Experimental fish Sample 4 and 5 were exposed to 1 hour of TCDD at xxx and 7 wpf allowed to mature and testes were harvested as adults.	Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform and sequenced on a NovaSeq.	Zebrafish were maintained on a 14:10h light/dark cycle with temperatures maintained at 27°C– 30°C. Fish were fed twice daily. Fish were raised in beakers with daily water changes. Animal use protocols were approved by the Institutional Animal Care and Use Committees at Wayne State University and the University of Wisconsin Madison according to the National Institutes of Health Guide to the Care and Use of Laboratory Animals Protocol No. M00489.	strain:AB\|treatment:50 pg/mL 0.1% DMSO\|sample preparation:non dissociated intact testes	GSM5820563	GSM5820563: bulk seq intact control testes rep 2; Danio rerio; RNA Seq	GSM5820563 r1	GSM5820563	1	Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform and sequenced on a NovaSeq.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP355202		D_C2_S15_L001_R1_001.fastq.gz	fastq	1493724669.0	29288719.0	GSM5820563 r1	0:51 1:0	A:445588125;C:289131502;G:340459665;T:418525850;N:19527	51	0			445588125	289131502	340459665	418525850	19527	SRX13799345	SRS11681634	SRA1357269	University of Florida	University of Florida	1	0.85779		0.20343		0.69887		0.56808		51		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2022-01-15	Juvenile	Juvenile	Gonad	Reproductive System
68160	68160	SRR17630950	SRX13799345	SRS11681634	SRP355202	PRJNA797655	Toxicotranscriptomics of single cell RNA Seq and conventional RNA Seq in TCDD exposed testicular tissue	GSE193758	Transcriptome Analysis	Spermatogenesis is a dynamic tightly conserved process that is susceptible to environmental contaminants. Exposure to environmental contaminants such as 2 3 7 8 tetrachlorodibenzo p dioxin TCDD is believed to be a cause of idiopathic male infertility. To understand TCDD induced disruption of spermatogenesis at the single cell level we profiled adult zebrafish testes with and without xxx life exposure to TCDD. Secondly to investigate the potential for technical artifacts in scRNA seq we compared bulk sequenced and scRNA seq paired samples from control and TCDD exposed samples and included an intact control fish to account for dissociation induced artifacts. We found scRNA seq and bulk seq of dissociated testes produced markedly different profiles both toxicologically and transcriptomically. Through scRNA seq we found TCDD exposure induces mid late germ cell apoptosis while increasing the population of spermatogonial stem cells. Bulk seq on the same cells returned results of immune dysregulation. The transcriptome was unequally detected by scRNA seq and bulk seq with scRNA seq biased towards detecting longer and more abundant transcripts but this was not mediated by TCDD exposure. Overall design: Zebrafish were exposed to 50 pg/mL TCDD or vehicle solution for 1 hour during sexual differentiation and maturation. Adult testes were dissected for toxicotranscriptomic analysis. Samples were prepared by dissociation for scRNA seq remained intact for bulk seq or were dissociated for bulk seq.	pubmed:35615540;pubmed:35799832	bulk seq intact control testes rep 2	GSM5820563	tissue:testes\|strain:AB\|treatment:50 pg/mL 0.1% DMSO\|sample preparation:non dissociated intact testes	bulk seq intact control testes rep 2	Reads were aligned and tabulated by individual cells in each sample using Cell Ranger 6.01 Count data was imported to Seurat version 4.0.4 for quality control QC filtering clustering dimensionality reduction visualization and differential gene expression Each sample was filtered to cells containing at least 500 features with clusters requiring a minimum of 30 cells. Samples were merged prior to normalization and clustering resolution 0.3. Differentially expressed genes between conditions for each cluster were identified using the "FindMarkers" function Genome build: Zebrafish May 2017 GRCz11/danRer11 Assembly Supplementary files format and content: xlsx; read counts and DEGs; Cell Ranger output matrices 10X SC TCDD DEG clusters: 10X Single cell cluster DEGs GEO CDxCI read counts DEGs: Control dissociated cells compared to Control intact cells GEO CPxCB read counts DEGs: Control psuedo bulk seq compared to Control dissociated cells for bulk seq GEO TBxCB read counts DEGs: TCDD dissociated cells compared to Control dissociated cells GEO TPxCP read counts DEGs: TCDD psuedo bulk seq compared to Control psuedo bulk seq GEO TPxTB read counts DEGs: TCDD psuedo bulk seq compared to TCDD dissociated cells bulk seq	testes	Experimental fish Sample 4 and 5 were exposed to 1 hour of TCDD at xxx and 7 wpf allowed to mature and testes were harvested as adults.	Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform and sequenced on a NovaSeq.	Zebrafish were maintained on a 14:10h light/dark cycle with temperatures maintained at 27°C– 30°C. Fish were fed twice daily. Fish were raised in beakers with daily water changes. Animal use protocols were approved by the Institutional Animal Care and Use Committees at Wayne State University and the University of Wisconsin Madison according to the National Institutes of Health Guide to the Care and Use of Laboratory Animals Protocol No. M00489.	strain:AB\|treatment:50 pg/mL 0.1% DMSO\|sample preparation:non dissociated intact testes	GSM5820563	GSM5820563: bulk seq intact control testes rep 2; Danio rerio; RNA Seq	GSM5820563 r1	GSM5820563	1	Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform and sequenced on a NovaSeq.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP355202		D_C2_S15_L002_R1_001.fastq.gz	fastq	1475012565.0	28921815.0	GSM5820563 r2	0:51 1:0	A:440339743;C:285301590;G:335922618;T:413432380;N:16234	51	0			440339743	285301590	335922618	413432380	16234	SRX13799345	SRS11681634	SRA1357269	University of Florida	University of Florida	1	0.85783		0.20221		0.70102		0.57116		51		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2022-01-15	Juvenile	Juvenile	Gonad	Reproductive System
68161	68161	SRR17630957	SRX13799344	SRS11681633	SRP355202	PRJNA797655	Toxicotranscriptomics of single cell RNA Seq and conventional RNA Seq in TCDD exposed testicular tissue	GSE193758	Transcriptome Analysis	Spermatogenesis is a dynamic tightly conserved process that is susceptible to environmental contaminants. Exposure to environmental contaminants such as 2 3 7 8 tetrachlorodibenzo p dioxin TCDD is believed to be a cause of idiopathic male infertility. To understand TCDD induced disruption of spermatogenesis at the single cell level we profiled adult zebrafish testes with and without xxx life exposure to TCDD. Secondly to investigate the potential for technical artifacts in scRNA seq we compared bulk sequenced and scRNA seq paired samples from control and TCDD exposed samples and included an intact control fish to account for dissociation induced artifacts. We found scRNA seq and bulk seq of dissociated testes produced markedly different profiles both toxicologically and transcriptomically. Through scRNA seq we found TCDD exposure induces mid late germ cell apoptosis while increasing the population of spermatogonial stem cells. Bulk seq on the same cells returned results of immune dysregulation. The transcriptome was unequally detected by scRNA seq and bulk seq with scRNA seq biased towards detecting longer and more abundant transcripts but this was not mediated by TCDD exposure. Overall design: Zebrafish were exposed to 50 pg/mL TCDD or vehicle solution for 1 hour during sexual differentiation and maturation. Adult testes were dissected for toxicotranscriptomic analysis. Samples were prepared by dissociation for scRNA seq remained intact for bulk seq or were dissociated for bulk seq.	pubmed:35615540;pubmed:35799832	bulk seq intact control testes rep 1	GSM5820562	tissue:testes\|strain:AB\|treatment:50 pg/mL 0.1% DMSO\|sample preparation:non dissociated intact testes	bulk seq intact control testes rep 1	Reads were aligned and tabulated by individual cells in each sample using Cell Ranger 6.01 Count data was imported to Seurat version 4.0.4 for quality control QC filtering clustering dimensionality reduction visualization and differential gene expression Each sample was filtered to cells containing at least 500 features with clusters requiring a minimum of 30 cells. Samples were merged prior to normalization and clustering resolution 0.3. Differentially expressed genes between conditions for each cluster were identified using the "FindMarkers" function Genome build: Zebrafish May 2017 GRCz11/danRer11 Assembly Supplementary files format and content: xlsx; read counts and DEGs; Cell Ranger output matrices 10X SC TCDD DEG clusters: 10X Single cell cluster DEGs GEO CDxCI read counts DEGs: Control dissociated cells compared to Control intact cells GEO CPxCB read counts DEGs: Control psuedo bulk seq compared to Control dissociated cells for bulk seq GEO TBxCB read counts DEGs: TCDD dissociated cells compared to Control dissociated cells GEO TPxCP read counts DEGs: TCDD psuedo bulk seq compared to Control psuedo bulk seq GEO TPxTB read counts DEGs: TCDD psuedo bulk seq compared to TCDD dissociated cells bulk seq	testes	Experimental fish Sample 4 and 5 were exposed to 1 hour of TCDD at xxx and 7 wpf allowed to mature and testes were harvested as adults.	Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform and sequenced on a NovaSeq.	Zebrafish were maintained on a 14:10h light/dark cycle with temperatures maintained at 27°C– 30°C. Fish were fed twice daily. Fish were raised in beakers with daily water changes. Animal use protocols were approved by the Institutional Animal Care and Use Committees at Wayne State University and the University of Wisconsin Madison according to the National Institutes of Health Guide to the Care and Use of Laboratory Animals Protocol No. M00489.	strain:AB\|treatment:50 pg/mL 0.1% DMSO\|sample preparation:non dissociated intact testes	GSM5820562	GSM5820562: bulk seq intact control testes rep 1; Danio rerio; RNA Seq	GSM5820562 r1	GSM5820562	1	Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform and sequenced on a NovaSeq.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP355202		D_C1_S2_L001_R1_001.fastq.gz	fastq	1783515696.0	34970896.0	GSM5820562 r1	0:51 1:0	A:503613569;C:361648917;G:420357217;T:497872153;N:23840	51	0			503613569	361648917	420357217	497872153	23840	SRX13799344	SRS11681633	SRA1357269	University of Florida	University of Florida	1	0.88797		0.22692		0.69522		0.57676		51		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2022-01-15	Juvenile	Juvenile	Gonad	Reproductive System
68162	68162	SRR17630958	SRX13799344	SRS11681633	SRP355202	PRJNA797655	Toxicotranscriptomics of single cell RNA Seq and conventional RNA Seq in TCDD exposed testicular tissue	GSE193758	Transcriptome Analysis	Spermatogenesis is a dynamic tightly conserved process that is susceptible to environmental contaminants. Exposure to environmental contaminants such as 2 3 7 8 tetrachlorodibenzo p dioxin TCDD is believed to be a cause of idiopathic male infertility. To understand TCDD induced disruption of spermatogenesis at the single cell level we profiled adult zebrafish testes with and without xxx life exposure to TCDD. Secondly to investigate the potential for technical artifacts in scRNA seq we compared bulk sequenced and scRNA seq paired samples from control and TCDD exposed samples and included an intact control fish to account for dissociation induced artifacts. We found scRNA seq and bulk seq of dissociated testes produced markedly different profiles both toxicologically and transcriptomically. Through scRNA seq we found TCDD exposure induces mid late germ cell apoptosis while increasing the population of spermatogonial stem cells. Bulk seq on the same cells returned results of immune dysregulation. The transcriptome was unequally detected by scRNA seq and bulk seq with scRNA seq biased towards detecting longer and more abundant transcripts but this was not mediated by TCDD exposure. Overall design: Zebrafish were exposed to 50 pg/mL TCDD or vehicle solution for 1 hour during sexual differentiation and maturation. Adult testes were dissected for toxicotranscriptomic analysis. Samples were prepared by dissociation for scRNA seq remained intact for bulk seq or were dissociated for bulk seq.	pubmed:35615540;pubmed:35799832	bulk seq intact control testes rep 1	GSM5820562	tissue:testes\|strain:AB\|treatment:50 pg/mL 0.1% DMSO\|sample preparation:non dissociated intact testes	bulk seq intact control testes rep 1	Reads were aligned and tabulated by individual cells in each sample using Cell Ranger 6.01 Count data was imported to Seurat version 4.0.4 for quality control QC filtering clustering dimensionality reduction visualization and differential gene expression Each sample was filtered to cells containing at least 500 features with clusters requiring a minimum of 30 cells. Samples were merged prior to normalization and clustering resolution 0.3. Differentially expressed genes between conditions for each cluster were identified using the "FindMarkers" function Genome build: Zebrafish May 2017 GRCz11/danRer11 Assembly Supplementary files format and content: xlsx; read counts and DEGs; Cell Ranger output matrices 10X SC TCDD DEG clusters: 10X Single cell cluster DEGs GEO CDxCI read counts DEGs: Control dissociated cells compared to Control intact cells GEO CPxCB read counts DEGs: Control psuedo bulk seq compared to Control dissociated cells for bulk seq GEO TBxCB read counts DEGs: TCDD dissociated cells compared to Control dissociated cells GEO TPxCP read counts DEGs: TCDD psuedo bulk seq compared to Control psuedo bulk seq GEO TPxTB read counts DEGs: TCDD psuedo bulk seq compared to TCDD dissociated cells bulk seq	testes	Experimental fish Sample 4 and 5 were exposed to 1 hour of TCDD at xxx and 7 wpf allowed to mature and testes were harvested as adults.	Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform and sequenced on a NovaSeq.	Zebrafish were maintained on a 14:10h light/dark cycle with temperatures maintained at 27°C– 30°C. Fish were fed twice daily. Fish were raised in beakers with daily water changes. Animal use protocols were approved by the Institutional Animal Care and Use Committees at Wayne State University and the University of Wisconsin Madison according to the National Institutes of Health Guide to the Care and Use of Laboratory Animals Protocol No. M00489.	strain:AB\|treatment:50 pg/mL 0.1% DMSO\|sample preparation:non dissociated intact testes	GSM5820562	GSM5820562: bulk seq intact control testes rep 1; Danio rerio; RNA Seq	GSM5820562 r1	GSM5820562	1	Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform and sequenced on a NovaSeq.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP355202		D_C1_S2_L002_R1_001.fastq.gz	fastq	1758067563.0	34471913.0	GSM5820562 r2	0:51 1:0	A:496669418;C:356271536;G:414028881;T:491077933;N:19795	51	0			496669418	356271536	414028881	491077933	19795	SRX13799344	SRS11681633	SRA1357269	University of Florida	University of Florida	1	0.88843		0.22792		0.69619		0.57488		51		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2022-01-15	Juvenile	Juvenile	Gonad	Reproductive System
68163	68163	SRR17630951	SRX13799343	SRS11681632	SRP355202	PRJNA797655	Toxicotranscriptomics of single cell RNA Seq and conventional RNA Seq in TCDD exposed testicular tissue	GSE193758	Transcriptome Analysis	Spermatogenesis is a dynamic tightly conserved process that is susceptible to environmental contaminants. Exposure to environmental contaminants such as 2 3 7 8 tetrachlorodibenzo p dioxin TCDD is believed to be a cause of idiopathic male infertility. To understand TCDD induced disruption of spermatogenesis at the single cell level we profiled adult zebrafish testes with and without xxx life exposure to TCDD. Secondly to investigate the potential for technical artifacts in scRNA seq we compared bulk sequenced and scRNA seq paired samples from control and TCDD exposed samples and included an intact control fish to account for dissociation induced artifacts. We found scRNA seq and bulk seq of dissociated testes produced markedly different profiles both toxicologically and transcriptomically. Through scRNA seq we found TCDD exposure induces mid late germ cell apoptosis while increasing the population of spermatogonial stem cells. Bulk seq on the same cells returned results of immune dysregulation. The transcriptome was unequally detected by scRNA seq and bulk seq with scRNA seq biased towards detecting longer and more abundant transcripts but this was not mediated by TCDD exposure. Overall design: Zebrafish were exposed to 50 pg/mL TCDD or vehicle solution for 1 hour during sexual differentiation and maturation. Adult testes were dissected for toxicotranscriptomic analysis. Samples were prepared by dissociation for scRNA seq remained intact for bulk seq or were dissociated for bulk seq.	pubmed:35615540;pubmed:35799832	bulk seq TCDD testes rep 1 to be compared to scRNA seq TCDD testes	GSM5820560	tissue:testes\|strain:AB\|treatment:50 pg/mL TCDD in 0.1% DMSO\|sample preparation:dissociated cell suspension	bulk seq TCDD testes rep 1 to be compared to scRNA seq TCDD testes	Reads were aligned and tabulated by individual cells in each sample using Cell Ranger 6.01 Count data was imported to Seurat version 4.0.4 for quality control QC filtering clustering dimensionality reduction visualization and differential gene expression Each sample was filtered to cells containing at least 500 features with clusters requiring a minimum of 30 cells. Samples were merged prior to normalization and clustering resolution 0.3. Differentially expressed genes between conditions for each cluster were identified using the "FindMarkers" function Genome build: Zebrafish May 2017 GRCz11/danRer11 Assembly Supplementary files format and content: xlsx; read counts and DEGs; Cell Ranger output matrices 10X SC TCDD DEG clusters: 10X Single cell cluster DEGs GEO CDxCI read counts DEGs: Control dissociated cells compared to Control intact cells GEO CPxCB read counts DEGs: Control psuedo bulk seq compared to Control dissociated cells for bulk seq GEO TBxCB read counts DEGs: TCDD dissociated cells compared to Control dissociated cells GEO TPxCP read counts DEGs: TCDD psuedo bulk seq compared to Control psuedo bulk seq GEO TPxTB read counts DEGs: TCDD psuedo bulk seq compared to TCDD dissociated cells bulk seq	testes	Experimental fish Sample 4 and 5 were exposed to 1 hour of TCDD at xxx and 7 wpf allowed to mature and testes were harvested as adults.	Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform and sequenced on a NovaSeq.	Zebrafish were maintained on a 14:10h light/dark cycle with temperatures maintained at 27°C– 30°C. Fish were fed twice daily. Fish were raised in beakers with daily water changes. Animal use protocols were approved by the Institutional Animal Care and Use Committees at Wayne State University and the University of Wisconsin Madison according to the National Institutes of Health Guide to the Care and Use of Laboratory Animals Protocol No. M00489.	strain:AB\|treatment:50 pg/mL TCDD in 0.1% DMSO\|sample preparation:dissociated cell suspension	GSM5820560	GSM5820560: bulk seq TCDD testes rep 1 to be compared to scRNA seq TCDD testes; Danio rerio; RNA Seq	GSM5820560 r1	GSM5820560	1	Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform and sequenced on a NovaSeq.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP355202		BS_T1_S6_L001_R1_001.fastq.gz	fastq	3525780042.0	69132942.0	GSM5820560 r1	0:51 1:0	A:1025376436;C:691776192;G:829134506;T:979443851;N:49057	51	0			1025376436	691776192	829134506	979443851	49057	SRX13799343	SRS11681632	SRA1357269	University of Florida	University of Florida	1	0.86505		0.30929		0.72074		0.6373		51		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2022-01-15	Juvenile	Juvenile	Gonad	Reproductive System
68164	68164	SRR17630952	SRX13799343	SRS11681632	SRP355202	PRJNA797655	Toxicotranscriptomics of single cell RNA Seq and conventional RNA Seq in TCDD exposed testicular tissue	GSE193758	Transcriptome Analysis	Spermatogenesis is a dynamic tightly conserved process that is susceptible to environmental contaminants. Exposure to environmental contaminants such as 2 3 7 8 tetrachlorodibenzo p dioxin TCDD is believed to be a cause of idiopathic male infertility. To understand TCDD induced disruption of spermatogenesis at the single cell level we profiled adult zebrafish testes with and without xxx life exposure to TCDD. Secondly to investigate the potential for technical artifacts in scRNA seq we compared bulk sequenced and scRNA seq paired samples from control and TCDD exposed samples and included an intact control fish to account for dissociation induced artifacts. We found scRNA seq and bulk seq of dissociated testes produced markedly different profiles both toxicologically and transcriptomically. Through scRNA seq we found TCDD exposure induces mid late germ cell apoptosis while increasing the population of spermatogonial stem cells. Bulk seq on the same cells returned results of immune dysregulation. The transcriptome was unequally detected by scRNA seq and bulk seq with scRNA seq biased towards detecting longer and more abundant transcripts but this was not mediated by TCDD exposure. Overall design: Zebrafish were exposed to 50 pg/mL TCDD or vehicle solution for 1 hour during sexual differentiation and maturation. Adult testes were dissected for toxicotranscriptomic analysis. Samples were prepared by dissociation for scRNA seq remained intact for bulk seq or were dissociated for bulk seq.	pubmed:35615540;pubmed:35799832	bulk seq TCDD testes rep 1 to be compared to scRNA seq TCDD testes	GSM5820560	tissue:testes\|strain:AB\|treatment:50 pg/mL TCDD in 0.1% DMSO\|sample preparation:dissociated cell suspension	bulk seq TCDD testes rep 1 to be compared to scRNA seq TCDD testes	Reads were aligned and tabulated by individual cells in each sample using Cell Ranger 6.01 Count data was imported to Seurat version 4.0.4 for quality control QC filtering clustering dimensionality reduction visualization and differential gene expression Each sample was filtered to cells containing at least 500 features with clusters requiring a minimum of 30 cells. Samples were merged prior to normalization and clustering resolution 0.3. Differentially expressed genes between conditions for each cluster were identified using the "FindMarkers" function Genome build: Zebrafish May 2017 GRCz11/danRer11 Assembly Supplementary files format and content: xlsx; read counts and DEGs; Cell Ranger output matrices 10X SC TCDD DEG clusters: 10X Single cell cluster DEGs GEO CDxCI read counts DEGs: Control dissociated cells compared to Control intact cells GEO CPxCB read counts DEGs: Control psuedo bulk seq compared to Control dissociated cells for bulk seq GEO TBxCB read counts DEGs: TCDD dissociated cells compared to Control dissociated cells GEO TPxCP read counts DEGs: TCDD psuedo bulk seq compared to Control psuedo bulk seq GEO TPxTB read counts DEGs: TCDD psuedo bulk seq compared to TCDD dissociated cells bulk seq	testes	Experimental fish Sample 4 and 5 were exposed to 1 hour of TCDD at xxx and 7 wpf allowed to mature and testes were harvested as adults.	Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform and sequenced on a NovaSeq.	Zebrafish were maintained on a 14:10h light/dark cycle with temperatures maintained at 27°C– 30°C. Fish were fed twice daily. Fish were raised in beakers with daily water changes. Animal use protocols were approved by the Institutional Animal Care and Use Committees at Wayne State University and the University of Wisconsin Madison according to the National Institutes of Health Guide to the Care and Use of Laboratory Animals Protocol No. M00489.	strain:AB\|treatment:50 pg/mL TCDD in 0.1% DMSO\|sample preparation:dissociated cell suspension	GSM5820560	GSM5820560: bulk seq TCDD testes rep 1 to be compared to scRNA seq TCDD testes; Danio rerio; RNA Seq	GSM5820560 r1	GSM5820560	1	Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform and sequenced on a NovaSeq.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP355202		BS_T1_S6_L002_R1_001.fastq.gz	fastq	3479799156.0	68231356.0	GSM5820560 r2	0:51 1:0	A:1012622841;C:682305804;G:817948602;T:966881210;N:40699	51	0			1012622841	682305804	817948602	966881210	40699	SRX13799343	SRS11681632	SRA1357269	University of Florida	University of Florida	1	0.86392		0.30933		0.71863		0.63706		51		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2022-01-15	Juvenile	Juvenile	Gonad	Reproductive System
68165	68165	SRR17630953	SRX13799342	SRS11681631	SRP355202	PRJNA797655	Toxicotranscriptomics of single cell RNA Seq and conventional RNA Seq in TCDD exposed testicular tissue	GSE193758	Transcriptome Analysis	Spermatogenesis is a dynamic tightly conserved process that is susceptible to environmental contaminants. Exposure to environmental contaminants such as 2 3 7 8 tetrachlorodibenzo p dioxin TCDD is believed to be a cause of idiopathic male infertility. To understand TCDD induced disruption of spermatogenesis at the single cell level we profiled adult zebrafish testes with and without xxx life exposure to TCDD. Secondly to investigate the potential for technical artifacts in scRNA seq we compared bulk sequenced and scRNA seq paired samples from control and TCDD exposed samples and included an intact control fish to account for dissociation induced artifacts. We found scRNA seq and bulk seq of dissociated testes produced markedly different profiles both toxicologically and transcriptomically. Through scRNA seq we found TCDD exposure induces mid late germ cell apoptosis while increasing the population of spermatogonial stem cells. Bulk seq on the same cells returned results of immune dysregulation. The transcriptome was unequally detected by scRNA seq and bulk seq with scRNA seq biased towards detecting longer and more abundant transcripts but this was not mediated by TCDD exposure. Overall design: Zebrafish were exposed to 50 pg/mL TCDD or vehicle solution for 1 hour during sexual differentiation and maturation. Adult testes were dissected for toxicotranscriptomic analysis. Samples were prepared by dissociation for scRNA seq remained intact for bulk seq or were dissociated for bulk seq.	pubmed:35615540;pubmed:35799832	bulk seq control testes rep 2 to be compared to scRNA seq control testes	GSM5820558	tissue:testes\|strain:AB\|treatment:50 pg/mL 0.1% DMSO\|sample preparation:dissociated cell suspension	bulk seq control testes rep 2 to be compared to scRNA seq control testes	Reads were aligned and tabulated by individual cells in each sample using Cell Ranger 6.01 Count data was imported to Seurat version 4.0.4 for quality control QC filtering clustering dimensionality reduction visualization and differential gene expression Each sample was filtered to cells containing at least 500 features with clusters requiring a minimum of 30 cells. Samples were merged prior to normalization and clustering resolution 0.3. Differentially expressed genes between conditions for each cluster were identified using the "FindMarkers" function Genome build: Zebrafish May 2017 GRCz11/danRer11 Assembly Supplementary files format and content: xlsx; read counts and DEGs; Cell Ranger output matrices 10X SC TCDD DEG clusters: 10X Single cell cluster DEGs GEO CDxCI read counts DEGs: Control dissociated cells compared to Control intact cells GEO CPxCB read counts DEGs: Control psuedo bulk seq compared to Control dissociated cells for bulk seq GEO TBxCB read counts DEGs: TCDD dissociated cells compared to Control dissociated cells GEO TPxCP read counts DEGs: TCDD psuedo bulk seq compared to Control psuedo bulk seq GEO TPxTB read counts DEGs: TCDD psuedo bulk seq compared to TCDD dissociated cells bulk seq	testes	Experimental fish Sample 4 and 5 were exposed to 1 hour of TCDD at xxx and 7 wpf allowed to mature and testes were harvested as adults.	Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform and sequenced on a NovaSeq.	Zebrafish were maintained on a 14:10h light/dark cycle with temperatures maintained at 27°C– 30°C. Fish were fed twice daily. Fish were raised in beakers with daily water changes. Animal use protocols were approved by the Institutional Animal Care and Use Committees at Wayne State University and the University of Wisconsin Madison according to the National Institutes of Health Guide to the Care and Use of Laboratory Animals Protocol No. M00489.	strain:AB\|treatment:50 pg/mL 0.1% DMSO\|sample preparation:dissociated cell suspension	GSM5820558	GSM5820558: bulk seq control testes rep 2 to be compared to scRNA seq control testes; Danio rerio; RNA Seq	GSM5820558 r1	GSM5820558	1	Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform and sequenced on a NovaSeq.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP355202		BS_C2_S8_L001_R1_001.fastq.gz	fastq	1264687137.0	24797787.0	GSM5820558 r1	0:51 1:0	A:361072135;C:254984535;G:302043978;T:346569617;N:16872	51	0			361072135	254984535	302043978	346569617	16872	SRX13799342	SRS11681631	SRA1357269	University of Florida	University of Florida	1	0.86972		0.31888		0.71561		0.6242		51		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2022-01-15	Juvenile	Juvenile	Gonad	Reproductive System
68166	68166	SRR17630954	SRX13799342	SRS11681631	SRP355202	PRJNA797655	Toxicotranscriptomics of single cell RNA Seq and conventional RNA Seq in TCDD exposed testicular tissue	GSE193758	Transcriptome Analysis	Spermatogenesis is a dynamic tightly conserved process that is susceptible to environmental contaminants. Exposure to environmental contaminants such as 2 3 7 8 tetrachlorodibenzo p dioxin TCDD is believed to be a cause of idiopathic male infertility. To understand TCDD induced disruption of spermatogenesis at the single cell level we profiled adult zebrafish testes with and without xxx life exposure to TCDD. Secondly to investigate the potential for technical artifacts in scRNA seq we compared bulk sequenced and scRNA seq paired samples from control and TCDD exposed samples and included an intact control fish to account for dissociation induced artifacts. We found scRNA seq and bulk seq of dissociated testes produced markedly different profiles both toxicologically and transcriptomically. Through scRNA seq we found TCDD exposure induces mid late germ cell apoptosis while increasing the population of spermatogonial stem cells. Bulk seq on the same cells returned results of immune dysregulation. The transcriptome was unequally detected by scRNA seq and bulk seq with scRNA seq biased towards detecting longer and more abundant transcripts but this was not mediated by TCDD exposure. Overall design: Zebrafish were exposed to 50 pg/mL TCDD or vehicle solution for 1 hour during sexual differentiation and maturation. Adult testes were dissected for toxicotranscriptomic analysis. Samples were prepared by dissociation for scRNA seq remained intact for bulk seq or were dissociated for bulk seq.	pubmed:35615540;pubmed:35799832	bulk seq control testes rep 2 to be compared to scRNA seq control testes	GSM5820558	tissue:testes\|strain:AB\|treatment:50 pg/mL 0.1% DMSO\|sample preparation:dissociated cell suspension	bulk seq control testes rep 2 to be compared to scRNA seq control testes	Reads were aligned and tabulated by individual cells in each sample using Cell Ranger 6.01 Count data was imported to Seurat version 4.0.4 for quality control QC filtering clustering dimensionality reduction visualization and differential gene expression Each sample was filtered to cells containing at least 500 features with clusters requiring a minimum of 30 cells. Samples were merged prior to normalization and clustering resolution 0.3. Differentially expressed genes between conditions for each cluster were identified using the "FindMarkers" function Genome build: Zebrafish May 2017 GRCz11/danRer11 Assembly Supplementary files format and content: xlsx; read counts and DEGs; Cell Ranger output matrices 10X SC TCDD DEG clusters: 10X Single cell cluster DEGs GEO CDxCI read counts DEGs: Control dissociated cells compared to Control intact cells GEO CPxCB read counts DEGs: Control psuedo bulk seq compared to Control dissociated cells for bulk seq GEO TBxCB read counts DEGs: TCDD dissociated cells compared to Control dissociated cells GEO TPxCP read counts DEGs: TCDD psuedo bulk seq compared to Control psuedo bulk seq GEO TPxTB read counts DEGs: TCDD psuedo bulk seq compared to TCDD dissociated cells bulk seq	testes	Experimental fish Sample 4 and 5 were exposed to 1 hour of TCDD at xxx and 7 wpf allowed to mature and testes were harvested as adults.	Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform and sequenced on a NovaSeq.	Zebrafish were maintained on a 14:10h light/dark cycle with temperatures maintained at 27°C– 30°C. Fish were fed twice daily. Fish were raised in beakers with daily water changes. Animal use protocols were approved by the Institutional Animal Care and Use Committees at Wayne State University and the University of Wisconsin Madison according to the National Institutes of Health Guide to the Care and Use of Laboratory Animals Protocol No. M00489.	strain:AB\|treatment:50 pg/mL 0.1% DMSO\|sample preparation:dissociated cell suspension	GSM5820558	GSM5820558: bulk seq control testes rep 2 to be compared to scRNA seq control testes; Danio rerio; RNA Seq	GSM5820558 r1	GSM5820558	1	Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform and sequenced on a NovaSeq.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP355202		BS_C2_S8_L002_R1_001.fastq.gz	fastq	1247134620.0	24453620.0	GSM5820558 r2	0:51 1:0	A:356333809;C:251264657;G:297639103;T:341883185;N:13866	51	0			356333809	251264657	297639103	341883185	13866	SRX13799342	SRS11681631	SRA1357269	University of Florida	University of Florida	1	0.8683		0.31544		0.71332		0.62605		51		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2022-01-15	Juvenile	Juvenile	Gonad	Reproductive System
68167	68167	SRR17630955	SRX13799341	SRS11681630	SRP355202	PRJNA797655	Toxicotranscriptomics of single cell RNA Seq and conventional RNA Seq in TCDD exposed testicular tissue	GSE193758	Transcriptome Analysis	Spermatogenesis is a dynamic tightly conserved process that is susceptible to environmental contaminants. Exposure to environmental contaminants such as 2 3 7 8 tetrachlorodibenzo p dioxin TCDD is believed to be a cause of idiopathic male infertility. To understand TCDD induced disruption of spermatogenesis at the single cell level we profiled adult zebrafish testes with and without xxx life exposure to TCDD. Secondly to investigate the potential for technical artifacts in scRNA seq we compared bulk sequenced and scRNA seq paired samples from control and TCDD exposed samples and included an intact control fish to account for dissociation induced artifacts. We found scRNA seq and bulk seq of dissociated testes produced markedly different profiles both toxicologically and transcriptomically. Through scRNA seq we found TCDD exposure induces mid late germ cell apoptosis while increasing the population of spermatogonial stem cells. Bulk seq on the same cells returned results of immune dysregulation. The transcriptome was unequally detected by scRNA seq and bulk seq with scRNA seq biased towards detecting longer and more abundant transcripts but this was not mediated by TCDD exposure. Overall design: Zebrafish were exposed to 50 pg/mL TCDD or vehicle solution for 1 hour during sexual differentiation and maturation. Adult testes were dissected for toxicotranscriptomic analysis. Samples were prepared by dissociation for scRNA seq remained intact for bulk seq or were dissociated for bulk seq.	pubmed:35615540;pubmed:35799832	bulk seq control testes rep 3 to be compared to scRNA seq control testes	GSM5820559	tissue:testes\|strain:AB\|treatment:50 pg/mL 0.1% DMSO\|sample preparation:dissociated cell suspension	bulk seq control testes rep 3 to be compared to scRNA seq control testes	Reads were aligned and tabulated by individual cells in each sample using Cell Ranger 6.01 Count data was imported to Seurat version 4.0.4 for quality control QC filtering clustering dimensionality reduction visualization and differential gene expression Each sample was filtered to cells containing at least 500 features with clusters requiring a minimum of 30 cells. Samples were merged prior to normalization and clustering resolution 0.3. Differentially expressed genes between conditions for each cluster were identified using the "FindMarkers" function Genome build: Zebrafish May 2017 GRCz11/danRer11 Assembly Supplementary files format and content: xlsx; read counts and DEGs; Cell Ranger output matrices 10X SC TCDD DEG clusters: 10X Single cell cluster DEGs GEO CDxCI read counts DEGs: Control dissociated cells compared to Control intact cells GEO CPxCB read counts DEGs: Control psuedo bulk seq compared to Control dissociated cells for bulk seq GEO TBxCB read counts DEGs: TCDD dissociated cells compared to Control dissociated cells GEO TPxCP read counts DEGs: TCDD psuedo bulk seq compared to Control psuedo bulk seq GEO TPxTB read counts DEGs: TCDD psuedo bulk seq compared to TCDD dissociated cells bulk seq	testes	Experimental fish Sample 4 and 5 were exposed to 1 hour of TCDD at xxx and 7 wpf allowed to mature and testes were harvested as adults.	Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform and sequenced on a NovaSeq.	Zebrafish were maintained on a 14:10h light/dark cycle with temperatures maintained at 27°C– 30°C. Fish were fed twice daily. Fish were raised in beakers with daily water changes. Animal use protocols were approved by the Institutional Animal Care and Use Committees at Wayne State University and the University of Wisconsin Madison according to the National Institutes of Health Guide to the Care and Use of Laboratory Animals Protocol No. M00489.	strain:AB\|treatment:50 pg/mL 0.1% DMSO\|sample preparation:dissociated cell suspension	GSM5820559	GSM5820559: bulk seq control testes rep 3 to be compared to scRNA seq control testes; Danio rerio; RNA Seq	GSM5820559 r1	GSM5820559	1	Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform and sequenced on a NovaSeq.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP355202		BS_C3_S5_L001_R1_001.fastq.gz	fastq	1298470557.0	25460207.0	GSM5820559 r1	0:51 1:0	A:370125548;C:258465981;G:307735443;T:362125609;N:17976	51	0			370125548	258465981	307735443	362125609	17976	SRX13799341	SRS11681630	SRA1357269	University of Florida	University of Florida	1	0.87017		0.23168		0.7049		0.43404		51		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2022-01-15	Juvenile	Juvenile	Gonad	Reproductive System
68168	68168	SRR17630956	SRX13799341	SRS11681630	SRP355202	PRJNA797655	Toxicotranscriptomics of single cell RNA Seq and conventional RNA Seq in TCDD exposed testicular tissue	GSE193758	Transcriptome Analysis	Spermatogenesis is a dynamic tightly conserved process that is susceptible to environmental contaminants. Exposure to environmental contaminants such as 2 3 7 8 tetrachlorodibenzo p dioxin TCDD is believed to be a cause of idiopathic male infertility. To understand TCDD induced disruption of spermatogenesis at the single cell level we profiled adult zebrafish testes with and without xxx life exposure to TCDD. Secondly to investigate the potential for technical artifacts in scRNA seq we compared bulk sequenced and scRNA seq paired samples from control and TCDD exposed samples and included an intact control fish to account for dissociation induced artifacts. We found scRNA seq and bulk seq of dissociated testes produced markedly different profiles both toxicologically and transcriptomically. Through scRNA seq we found TCDD exposure induces mid late germ cell apoptosis while increasing the population of spermatogonial stem cells. Bulk seq on the same cells returned results of immune dysregulation. The transcriptome was unequally detected by scRNA seq and bulk seq with scRNA seq biased towards detecting longer and more abundant transcripts but this was not mediated by TCDD exposure. Overall design: Zebrafish were exposed to 50 pg/mL TCDD or vehicle solution for 1 hour during sexual differentiation and maturation. Adult testes were dissected for toxicotranscriptomic analysis. Samples were prepared by dissociation for scRNA seq remained intact for bulk seq or were dissociated for bulk seq.	pubmed:35615540;pubmed:35799832	bulk seq control testes rep 3 to be compared to scRNA seq control testes	GSM5820559	tissue:testes\|strain:AB\|treatment:50 pg/mL 0.1% DMSO\|sample preparation:dissociated cell suspension	bulk seq control testes rep 3 to be compared to scRNA seq control testes	Reads were aligned and tabulated by individual cells in each sample using Cell Ranger 6.01 Count data was imported to Seurat version 4.0.4 for quality control QC filtering clustering dimensionality reduction visualization and differential gene expression Each sample was filtered to cells containing at least 500 features with clusters requiring a minimum of 30 cells. Samples were merged prior to normalization and clustering resolution 0.3. Differentially expressed genes between conditions for each cluster were identified using the "FindMarkers" function Genome build: Zebrafish May 2017 GRCz11/danRer11 Assembly Supplementary files format and content: xlsx; read counts and DEGs; Cell Ranger output matrices 10X SC TCDD DEG clusters: 10X Single cell cluster DEGs GEO CDxCI read counts DEGs: Control dissociated cells compared to Control intact cells GEO CPxCB read counts DEGs: Control psuedo bulk seq compared to Control dissociated cells for bulk seq GEO TBxCB read counts DEGs: TCDD dissociated cells compared to Control dissociated cells GEO TPxCP read counts DEGs: TCDD psuedo bulk seq compared to Control psuedo bulk seq GEO TPxTB read counts DEGs: TCDD psuedo bulk seq compared to TCDD dissociated cells bulk seq	testes	Experimental fish Sample 4 and 5 were exposed to 1 hour of TCDD at xxx and 7 wpf allowed to mature and testes were harvested as adults.	Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform and sequenced on a NovaSeq.	Zebrafish were maintained on a 14:10h light/dark cycle with temperatures maintained at 27°C– 30°C. Fish were fed twice daily. Fish were raised in beakers with daily water changes. Animal use protocols were approved by the Institutional Animal Care and Use Committees at Wayne State University and the University of Wisconsin Madison according to the National Institutes of Health Guide to the Care and Use of Laboratory Animals Protocol No. M00489.	strain:AB\|treatment:50 pg/mL 0.1% DMSO\|sample preparation:dissociated cell suspension	GSM5820559	GSM5820559: bulk seq control testes rep 3 to be compared to scRNA seq control testes; Danio rerio; RNA Seq	GSM5820559 r1	GSM5820559	1	Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform and sequenced on a NovaSeq.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP355202		BS_C3_S5_L002_R1_001.fastq.gz	fastq	1282277445.0	25142695.0	GSM5820559 r2	0:51 1:0	A:365706822;C:255117242;G:303741803;T:357696714;N:14864	51	0			365706822	255117242	303741803	357696714	14864	SRX13799341	SRS11681630	SRA1357269	University of Florida	University of Florida	1	0.86967		0.23412		0.70447		0.60084		51		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2022-01-15	Juvenile	Juvenile	Gonad	Reproductive System
68169	68169	SRR17630959	SRX13799340	SRS11681629	SRP355202	PRJNA797655	Toxicotranscriptomics of single cell RNA Seq and conventional RNA Seq in TCDD exposed testicular tissue	GSE193758	Transcriptome Analysis	Spermatogenesis is a dynamic tightly conserved process that is susceptible to environmental contaminants. Exposure to environmental contaminants such as 2 3 7 8 tetrachlorodibenzo p dioxin TCDD is believed to be a cause of idiopathic male infertility. To understand TCDD induced disruption of spermatogenesis at the single cell level we profiled adult zebrafish testes with and without xxx life exposure to TCDD. Secondly to investigate the potential for technical artifacts in scRNA seq we compared bulk sequenced and scRNA seq paired samples from control and TCDD exposed samples and included an intact control fish to account for dissociation induced artifacts. We found scRNA seq and bulk seq of dissociated testes produced markedly different profiles both toxicologically and transcriptomically. Through scRNA seq we found TCDD exposure induces mid late germ cell apoptosis while increasing the population of spermatogonial stem cells. Bulk seq on the same cells returned results of immune dysregulation. The transcriptome was unequally detected by scRNA seq and bulk seq with scRNA seq biased towards detecting longer and more abundant transcripts but this was not mediated by TCDD exposure. Overall design: Zebrafish were exposed to 50 pg/mL TCDD or vehicle solution for 1 hour during sexual differentiation and maturation. Adult testes were dissected for toxicotranscriptomic analysis. Samples were prepared by dissociation for scRNA seq remained intact for bulk seq or were dissociated for bulk seq.	pubmed:35615540;pubmed:35799832	bulk seq control testes rep 1 to be compared to scRNA seq control testes	GSM5820557	tissue:testes\|strain:AB\|treatment:50 pg/mL 0.1% DMSO\|sample preparation:dissociated cell suspension	bulk seq control testes rep 1 to be compared to scRNA seq control testes	Reads were aligned and tabulated by individual cells in each sample using Cell Ranger 6.01 Count data was imported to Seurat version 4.0.4 for quality control QC filtering clustering dimensionality reduction visualization and differential gene expression Each sample was filtered to cells containing at least 500 features with clusters requiring a minimum of 30 cells. Samples were merged prior to normalization and clustering resolution 0.3. Differentially expressed genes between conditions for each cluster were identified using the "FindMarkers" function Genome build: Zebrafish May 2017 GRCz11/danRer11 Assembly Supplementary files format and content: xlsx; read counts and DEGs; Cell Ranger output matrices 10X SC TCDD DEG clusters: 10X Single cell cluster DEGs GEO CDxCI read counts DEGs: Control dissociated cells compared to Control intact cells GEO CPxCB read counts DEGs: Control psuedo bulk seq compared to Control dissociated cells for bulk seq GEO TBxCB read counts DEGs: TCDD dissociated cells compared to Control dissociated cells GEO TPxCP read counts DEGs: TCDD psuedo bulk seq compared to Control psuedo bulk seq GEO TPxTB read counts DEGs: TCDD psuedo bulk seq compared to TCDD dissociated cells bulk seq	testes	Experimental fish Sample 4 and 5 were exposed to 1 hour of TCDD at xxx and 7 wpf allowed to mature and testes were harvested as adults.	Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform and sequenced on a NovaSeq.	Zebrafish were maintained on a 14:10h light/dark cycle with temperatures maintained at 27°C– 30°C. Fish were fed twice daily. Fish were raised in beakers with daily water changes. Animal use protocols were approved by the Institutional Animal Care and Use Committees at Wayne State University and the University of Wisconsin Madison according to the National Institutes of Health Guide to the Care and Use of Laboratory Animals Protocol No. M00489.	strain:AB\|treatment:50 pg/mL 0.1% DMSO\|sample preparation:dissociated cell suspension	GSM5820557	GSM5820557: bulk seq control testes rep 1 to be compared to scRNA seq control testes; Danio rerio; RNA Seq	GSM5820557 r1	GSM5820557	1	Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform and sequenced on a NovaSeq.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP355202		BS_C1_S4_L001_R1_001.fastq.gz	fastq	363711651.0	7131601.0	GSM5820557 r1	0:51 1:0	A:101645255;C:77359657;G:89895787;T:94805817;N:5135	51	0			101645255	77359657	89895787	94805817	5135	SRX13799340	SRS11681629	SRA1357269	University of Florida	University of Florida	1	0.86049		0.29611		0.72293		0.54071		51		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2022-01-15	Juvenile	Juvenile	Gonad	Reproductive System
68170	68170	SRR17630960	SRX13799340	SRS11681629	SRP355202	PRJNA797655	Toxicotranscriptomics of single cell RNA Seq and conventional RNA Seq in TCDD exposed testicular tissue	GSE193758	Transcriptome Analysis	Spermatogenesis is a dynamic tightly conserved process that is susceptible to environmental contaminants. Exposure to environmental contaminants such as 2 3 7 8 tetrachlorodibenzo p dioxin TCDD is believed to be a cause of idiopathic male infertility. To understand TCDD induced disruption of spermatogenesis at the single cell level we profiled adult zebrafish testes with and without xxx life exposure to TCDD. Secondly to investigate the potential for technical artifacts in scRNA seq we compared bulk sequenced and scRNA seq paired samples from control and TCDD exposed samples and included an intact control fish to account for dissociation induced artifacts. We found scRNA seq and bulk seq of dissociated testes produced markedly different profiles both toxicologically and transcriptomically. Through scRNA seq we found TCDD exposure induces mid late germ cell apoptosis while increasing the population of spermatogonial stem cells. Bulk seq on the same cells returned results of immune dysregulation. The transcriptome was unequally detected by scRNA seq and bulk seq with scRNA seq biased towards detecting longer and more abundant transcripts but this was not mediated by TCDD exposure. Overall design: Zebrafish were exposed to 50 pg/mL TCDD or vehicle solution for 1 hour during sexual differentiation and maturation. Adult testes were dissected for toxicotranscriptomic analysis. Samples were prepared by dissociation for scRNA seq remained intact for bulk seq or were dissociated for bulk seq.	pubmed:35615540;pubmed:35799832	bulk seq control testes rep 1 to be compared to scRNA seq control testes	GSM5820557	tissue:testes\|strain:AB\|treatment:50 pg/mL 0.1% DMSO\|sample preparation:dissociated cell suspension	bulk seq control testes rep 1 to be compared to scRNA seq control testes	Reads were aligned and tabulated by individual cells in each sample using Cell Ranger 6.01 Count data was imported to Seurat version 4.0.4 for quality control QC filtering clustering dimensionality reduction visualization and differential gene expression Each sample was filtered to cells containing at least 500 features with clusters requiring a minimum of 30 cells. Samples were merged prior to normalization and clustering resolution 0.3. Differentially expressed genes between conditions for each cluster were identified using the "FindMarkers" function Genome build: Zebrafish May 2017 GRCz11/danRer11 Assembly Supplementary files format and content: xlsx; read counts and DEGs; Cell Ranger output matrices 10X SC TCDD DEG clusters: 10X Single cell cluster DEGs GEO CDxCI read counts DEGs: Control dissociated cells compared to Control intact cells GEO CPxCB read counts DEGs: Control psuedo bulk seq compared to Control dissociated cells for bulk seq GEO TBxCB read counts DEGs: TCDD dissociated cells compared to Control dissociated cells GEO TPxCP read counts DEGs: TCDD psuedo bulk seq compared to Control psuedo bulk seq GEO TPxTB read counts DEGs: TCDD psuedo bulk seq compared to TCDD dissociated cells bulk seq	testes	Experimental fish Sample 4 and 5 were exposed to 1 hour of TCDD at xxx and 7 wpf allowed to mature and testes were harvested as adults.	Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform and sequenced on a NovaSeq.	Zebrafish were maintained on a 14:10h light/dark cycle with temperatures maintained at 27°C– 30°C. Fish were fed twice daily. Fish were raised in beakers with daily water changes. Animal use protocols were approved by the Institutional Animal Care and Use Committees at Wayne State University and the University of Wisconsin Madison according to the National Institutes of Health Guide to the Care and Use of Laboratory Animals Protocol No. M00489.	strain:AB\|treatment:50 pg/mL 0.1% DMSO\|sample preparation:dissociated cell suspension	GSM5820557	GSM5820557: bulk seq control testes rep 1 to be compared to scRNA seq control testes; Danio rerio; RNA Seq	GSM5820557 r1	GSM5820557	1	Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform and sequenced on a NovaSeq.	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000	SRP355202		BS_C1_S4_L002_R1_001.fastq.gz	fastq	358349460.0	7026460.0	GSM5820557 r2	0:51 1:0	A:100176173;C:76199709;G:88532838;T:93436578;N:4162	51	0			100176173	76199709	88532838	93436578	4162	SRX13799340	SRS11681629	SRA1357269	University of Florida	University of Florida	1	0.86034		0.29588		0.72346		0.54277		51		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2022-01-15	Juvenile	Juvenile	Gonad	Reproductive System

Advanced export

JSON shape: default, array, newline-delimited

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");;