metadata: run_metadata: 32 rows where experiment.library_layout = "SINGLE", experiment.library_source = "TRANSCRIPTOMIC" and technology = "10x"

32 rows where experiment.library_layout = "SINGLE", experiment.library_source = "TRANSCRIPTOMIC" and technology = "10x"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.attributes	study.PMIDs	sample.description	sample.title	sample.alias	sample.centername	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	GEOsample.treatmentprotocol	GEOsample.extractprotocol	GEOsample.growthprotocol	GEOsample.characteristics	GEOsample.accession	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_construction_protocol	experiment.attributes	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.spot_descriptor	experiment.study_ref	run.title	run.attributes	run.filename	run.semantic_name	run.total_bases	run.total_spots	run.alias	run.read_lengths	run.base_counts	run.r1_length	run.r2_length	run.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
9166	9166	ERR2788341	ERX2797590	ERS2709706	ERP110806	PRJEB28589	Single cell transcriptional analysis reveals ILC like cells in zebrafish	E-MTAB-7159	Transcriptome Analysis	Transcriptome data from zebrafish single cells from guts from either from Tglck:EGFP rag1 / mutant or wild type zebrafish were isolated and single cell suspensions were prepared as described in protocol section. Three zebrafish per each condition i.e. zebrafish intraperitoneally injected with PBS lyophilised Anisakis simplex or inactivated Vibrio anguillarum were used to collect the total of 12 000 lck+ cells 4000 per zebrafish for 10x experiment.	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 09 11		Protocols: The guts were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. Three zebrafish per each condition i.e. zebrafish intraperitoneally injected with PBS lyophilised Anisakis simplex or inactivated Vibrio anguillarum were used to collect the total of 12 000 lck+ cells 4000 per zebrafish for 10x experiment. Cell were sorted into 1.5 ml Eppendorf tubes containing 20 l 5% FBS in PBS using a BD Influx Index Sorter. Following the sorting cells were spun down and resuspended in ice cold PBS with 0.04% bovine serum albumin at the concentration of 500 cells/μl. Briefly cellular suspension was added to the master mix containing nuclease free water RT Reagent Mix RT Primer Additive A and RT Enzyme Mix. Master mix with cells was transferred to the wells in the row labelled 1 on the Chromium™ Single Cell A Chip 10x Genomics. Single Cell three prime Gel Beads were transferred into the row labelled 2 and Partitioning Oil was transferred into the row labelled 3. The chip was loaded on Chromium™ Controller to generate single cell GEMs. GEM RT was performed in a C1000 Touch Thermal cycler Bio Rad at the following conditions: 53°C for 45 min 85°C for 5 min held at 4°C. Post GEM RT cleanup was performed with DynaBeads MyOne Silane Beads Thermo Fisher Scientific. cDNA was amplified using C1000 Touch Thermal cycler at the following conditions: 98°C for 3 min 12 cycles of 90°C for 15 s 67°C for 20 s and 72°C for 1 min 72°C for 1 min held 4°C. Amplified cDNA was cleaned with the SPRIselect Reagent Kit Beckman Coulter and quality was assessed using 2100 Bioanalyser Agilent. Libraries were constructed using Chromium™ Controller and Chromium™ Single Cell three prime Library & Gel Bead Kit v2 10x Genomics according to the manufacturer's …	5149STDY7292228	SAMEA4890710	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK	ENA FIRST PUBLIC:2018 11 16T17:03:30Z\|ENA LAST UPDATE:2018 09 11T09:38:07Z\|External Id:SAMEA4890710\|INSDC center name:Department of Haematology University of Cambridge Cambridge UK Wellcome Trust Sanger Institute Wellcome Trust Genome Campus Cambridge Wellcome Trust Medical Research Council Cambridge Stem Cell Institute Cambridge UK\|INSDC first public:2018 11 16T17:03:30Z\|INSDC last update:2018 09 11T09:38:07Z\|INSDC status:public\|Submitter Id:E MTAB 7159:5149STDY7292228\|age:6\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:adult\|genotype:Tglck:EGFP\|individual:pool 4\|organism part:intestine\|phenotype:lck positive\|sample name:E MTAB 7159:5149STDY7292228\|scientific name:Danio rerio\|sex:2 female 1 male\|strain:AB									Illumina HiSeq 4000 sequencing; Single cell transcriptional analysis reveals ILC like cells in zebrafish	E MTAB 7159:5149STDY7292228 p	5149STDY7292228 p	Single cell transcriptional analysis reveals ILC like cells in zebrafish	The guts were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. Three zebrafish per each condition i.e. zebrafish intraperitoneally injected with PBS lyophilised Anisakis simplex or inactivated Vibrio anguillarum were used to collect the total of 12 000 lck+ cells 4000 per zebrafish for 10x experiment. Cell were sorted into 1.5 ml Eppendorf tubes containing 20 l 5% FBS in PBS using a BD Influx Index Sorter. Following the sorting cells were spun down and resuspended in ice cold PBS with 0.04% bovine serum albumin at the concentration of 500 cells/μl. Briefly cellular suspension was added to the master mix containing nuclease free water RT Reagent Mix RT Primer Additive A and RT Enzyme Mix. Master mix with cells was transferred to the wells in the row labelled 1 on the Chromium™ Single Cell A Chip 10x Genomics. Single Cell three prime Gel Beads were transferred into the row labelled 2 and Partitioning Oil was transferred into the row labelled 3. The chip was loaded on Chromium™ Controller to generate single cell GEMs. GEM RT was performed in a C1000 Touch Thermal cycler Bio Rad at the following conditions: 53°C for 45 min 85°C for 5 min held at 4°C. Post GEM RT cleanup was performed with DynaBeads MyOne Silane Beads Thermo Fisher Scientific. cDNA was amplified using C1000 Touch Thermal cycler at the following conditions: 98°C for 3 min 12 cycles of 90°C for 15 s 67°C for 20 s and 72°C for 1 min 72°C for 1 min held 4°C. Amplified cDNA was cleaned with the SPRIselect Reagent Kit Beckman Coulter and quality was assessed using 2100 Bioanalyser Agilent. Libraries were constructed using Chromium™ Controller and Chromium™ Single Cell three prime Library & Gel Bead Kit v2 10x Genomics according to the manufacturer's protocol. B…	Experimental Factor: genotype:Tglck:EGFP\|Experimental Factor: infect:n1	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>866</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>434</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP110806	Illumina HiSeq 4000 sequencing; Single cell transcriptional analysis reveals ILC like cells in zebrafish	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 11 16\|options: use QUAL	5149STDY7292228.bam 5149STDY7292228.bam.bai	bam bam	37970494940.0	387454030.0	E MTAB 7159:5149STDY7292228	0:98	A:11476520187;C:7571635167;G:8189594199;T:10701044279;N:31701108	98		11476520187	7571635167	8189594199	10701044279	31701108	ERX2797590	ERS2709706	ERA1594569	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	1	0.87568		0.2122		0.82582		0.5259		98		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United Kingdom	2018-09-11	Adult	Adult	Gut	Digestive System
9167	9167	ERR2788340	ERX2797589	ERS2709705	ERP110806	PRJEB28589	Single cell transcriptional analysis reveals ILC like cells in zebrafish	E-MTAB-7159	Transcriptome Analysis	Transcriptome data from zebrafish single cells from guts from either from Tglck:EGFP rag1 / mutant or wild type zebrafish were isolated and single cell suspensions were prepared as described in protocol section. Three zebrafish per each condition i.e. zebrafish intraperitoneally injected with PBS lyophilised Anisakis simplex or inactivated Vibrio anguillarum were used to collect the total of 12 000 lck+ cells 4000 per zebrafish for 10x experiment.	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 09 11		Protocols: The guts were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. Three zebrafish per each condition i.e. zebrafish intraperitoneally injected with PBS lyophilised Anisakis simplex or inactivated Vibrio anguillarum were used to collect the total of 12 000 lck+ cells 4000 per zebrafish for 10x experiment. Cell were sorted into 1.5 ml Eppendorf tubes containing 20 l 5% FBS in PBS using a BD Influx Index Sorter. Following the sorting cells were spun down and resuspended in ice cold PBS with 0.04% bovine serum albumin at the concentration of 500 cells/μl. Briefly cellular suspension was added to the master mix containing nuclease free water RT Reagent Mix RT Primer Additive A and RT Enzyme Mix. Master mix with cells was transferred to the wells in the row labelled 1 on the Chromium™ Single Cell A Chip 10x Genomics. Single Cell three prime Gel Beads were transferred into the row labelled 2 and Partitioning Oil was transferred into the row labelled 3. The chip was loaded on Chromium™ Controller to generate single cell GEMs. GEM RT was performed in a C1000 Touch Thermal cycler Bio Rad at the following conditions: 53°C for 45 min 85°C for 5 min held at 4°C. Post GEM RT cleanup was performed with DynaBeads MyOne Silane Beads Thermo Fisher Scientific. cDNA was amplified using C1000 Touch Thermal cycler at the following conditions: 98°C for 3 min 12 cycles of 90°C for 15 s 67°C for 20 s and 72°C for 1 min 72°C for 1 min held 4°C. Amplified cDNA was cleaned with the SPRIselect Reagent Kit Beckman Coulter and quality was assessed using 2100 Bioanalyser Agilent. Libraries were constructed using Chromium™ Controller and Chromium™ Single Cell three prime Library & Gel Bead Kit v2 10x Genomics according to the manufacturer's …	5149STDY7274848	SAMEA4890709	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK	ENA FIRST PUBLIC:2018 11 16T17:03:30Z\|ENA LAST UPDATE:2018 09 11T09:38:07Z\|External Id:SAMEA4890709\|INSDC center name:Department of Haematology University of Cambridge Cambridge UK Wellcome Trust Sanger Institute Wellcome Trust Genome Campus Cambridge Wellcome Trust Medical Research Council Cambridge Stem Cell Institute Cambridge UK\|INSDC first public:2018 11 16T17:03:30Z\|INSDC last update:2018 09 11T09:38:07Z\|INSDC status:public\|Submitter Id:E MTAB 7159:5149STDY7274848\|age:4\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:adult\|genotype:Tglck:EGFP; Rag1 homozygous knockout\|individual:pool 3\|organism part:intestine\|phenotype:lck positive\|sample name:E MTAB 7159:5149STDY7274848\|scientific name:Danio rerio\|sex:female\|strain:AB									Illumina HiSeq 4000 sequencing; Single cell transcriptional analysis reveals ILC like cells in zebrafish	E MTAB 7159:5149STDY7274848 p	5149STDY7274848 p	Single cell transcriptional analysis reveals ILC like cells in zebrafish	The guts were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. Three zebrafish per each condition i.e. zebrafish intraperitoneally injected with PBS lyophilised Anisakis simplex or inactivated Vibrio anguillarum were used to collect the total of 12 000 lck+ cells 4000 per zebrafish for 10x experiment. Cell were sorted into 1.5 ml Eppendorf tubes containing 20 l 5% FBS in PBS using a BD Influx Index Sorter. Following the sorting cells were spun down and resuspended in ice cold PBS with 0.04% bovine serum albumin at the concentration of 500 cells/μl. Briefly cellular suspension was added to the master mix containing nuclease free water RT Reagent Mix RT Primer Additive A and RT Enzyme Mix. Master mix with cells was transferred to the wells in the row labelled 1 on the Chromium™ Single Cell A Chip 10x Genomics. Single Cell three prime Gel Beads were transferred into the row labelled 2 and Partitioning Oil was transferred into the row labelled 3. The chip was loaded on Chromium™ Controller to generate single cell GEMs. GEM RT was performed in a C1000 Touch Thermal cycler Bio Rad at the following conditions: 53°C for 45 min 85°C for 5 min held at 4°C. Post GEM RT cleanup was performed with DynaBeads MyOne Silane Beads Thermo Fisher Scientific. cDNA was amplified using C1000 Touch Thermal cycler at the following conditions: 98°C for 3 min 12 cycles of 90°C for 15 s 67°C for 20 s and 72°C for 1 min 72°C for 1 min held 4°C. Amplified cDNA was cleaned with the SPRIselect Reagent Kit Beckman Coulter and quality was assessed using 2100 Bioanalyser Agilent. Libraries were constructed using Chromium™ Controller and Chromium™ Single Cell three prime Library & Gel Bead Kit v2 10x Genomics according to the manufacturer's protocol. B…	Experimental Factor: genotype:Tglck:EGFP; Rag1 homozygous knockout\|Experimental Factor: infect:Vibrio Anguillarum	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>866</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>434</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP110806	Illumina HiSeq 4000 sequencing; Single cell transcriptional analysis reveals ILC like cells in zebrafish	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 11 16\|options: use QUAL	5149STDY7274848.bam 5149STDY7274848.bam.bai	bam bam	34517322840.0	352217580.0	E MTAB 7159:5149STDY7274848	0:98	A:10635243399;C:6658515314;G:7525079510;T:9695995344;N:2489273	98		10635243399	6658515314	7525079510	9695995344	2489273	ERX2797589	ERS2709705	ERA1594569	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	1	0.86206		0.18065		0.83514		0.53609		98		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United Kingdom	2018-09-11	Adult	Adult	Gut	Digestive System
9168	9168	ERR2788339	ERX2797588	ERS2709704	ERP110806	PRJEB28589	Single cell transcriptional analysis reveals ILC like cells in zebrafish	E-MTAB-7159	Transcriptome Analysis	Transcriptome data from zebrafish single cells from guts from either from Tglck:EGFP rag1 / mutant or wild type zebrafish were isolated and single cell suspensions were prepared as described in protocol section. Three zebrafish per each condition i.e. zebrafish intraperitoneally injected with PBS lyophilised Anisakis simplex or inactivated Vibrio anguillarum were used to collect the total of 12 000 lck+ cells 4000 per zebrafish for 10x experiment.	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 09 11		Protocols: The guts were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. Three zebrafish per each condition i.e. zebrafish intraperitoneally injected with PBS lyophilised Anisakis simplex or inactivated Vibrio anguillarum were used to collect the total of 12 000 lck+ cells 4000 per zebrafish for 10x experiment. Cell were sorted into 1.5 ml Eppendorf tubes containing 20 l 5% FBS in PBS using a BD Influx Index Sorter. Following the sorting cells were spun down and resuspended in ice cold PBS with 0.04% bovine serum albumin at the concentration of 500 cells/μl. Briefly cellular suspension was added to the master mix containing nuclease free water RT Reagent Mix RT Primer Additive A and RT Enzyme Mix. Master mix with cells was transferred to the wells in the row labelled 1 on the Chromium™ Single Cell A Chip 10x Genomics. Single Cell three prime Gel Beads were transferred into the row labelled 2 and Partitioning Oil was transferred into the row labelled 3. The chip was loaded on Chromium™ Controller to generate single cell GEMs. GEM RT was performed in a C1000 Touch Thermal cycler Bio Rad at the following conditions: 53°C for 45 min 85°C for 5 min held at 4°C. Post GEM RT cleanup was performed with DynaBeads MyOne Silane Beads Thermo Fisher Scientific. cDNA was amplified using C1000 Touch Thermal cycler at the following conditions: 98°C for 3 min 12 cycles of 90°C for 15 s 67°C for 20 s and 72°C for 1 min 72°C for 1 min held 4°C. Amplified cDNA was cleaned with the SPRIselect Reagent Kit Beckman Coulter and quality was assessed using 2100 Bioanalyser Agilent. Libraries were constructed using Chromium™ Controller and Chromium™ Single Cell three prime Library & Gel Bead Kit v2 10x Genomics according to the manufacturer's …	5149STDY7274847	SAMEA4890708	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK	ENA FIRST PUBLIC:2018 11 16T17:03:30Z\|ENA LAST UPDATE:2018 09 11T09:38:07Z\|External Id:SAMEA4890708\|INSDC center name:Department of Haematology University of Cambridge Cambridge UK Wellcome Trust Sanger Institute Wellcome Trust Genome Campus Cambridge Wellcome Trust Medical Research Council Cambridge Stem Cell Institute Cambridge UK\|INSDC first public:2018 11 16T17:03:30Z\|INSDC last update:2018 09 11T09:38:07Z\|INSDC status:public\|Submitter Id:E MTAB 7159:5149STDY7274847\|age:4\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:adult\|genotype:Tglck:EGFP; Rag1 homozygous knockout\|individual:pool 2\|organism part:intestine\|phenotype:lck positive\|sample name:E MTAB 7159:5149STDY7274847\|scientific name:Danio rerio\|sex:female\|strain:AB									Illumina HiSeq 4000 sequencing; Single cell transcriptional analysis reveals ILC like cells in zebrafish	E MTAB 7159:5149STDY7274847 p	5149STDY7274847 p	Single cell transcriptional analysis reveals ILC like cells in zebrafish	The guts were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. Three zebrafish per each condition i.e. zebrafish intraperitoneally injected with PBS lyophilised Anisakis simplex or inactivated Vibrio anguillarum were used to collect the total of 12 000 lck+ cells 4000 per zebrafish for 10x experiment. Cell were sorted into 1.5 ml Eppendorf tubes containing 20 l 5% FBS in PBS using a BD Influx Index Sorter. Following the sorting cells were spun down and resuspended in ice cold PBS with 0.04% bovine serum albumin at the concentration of 500 cells/μl. Briefly cellular suspension was added to the master mix containing nuclease free water RT Reagent Mix RT Primer Additive A and RT Enzyme Mix. Master mix with cells was transferred to the wells in the row labelled 1 on the Chromium™ Single Cell A Chip 10x Genomics. Single Cell three prime Gel Beads were transferred into the row labelled 2 and Partitioning Oil was transferred into the row labelled 3. The chip was loaded on Chromium™ Controller to generate single cell GEMs. GEM RT was performed in a C1000 Touch Thermal cycler Bio Rad at the following conditions: 53°C for 45 min 85°C for 5 min held at 4°C. Post GEM RT cleanup was performed with DynaBeads MyOne Silane Beads Thermo Fisher Scientific. cDNA was amplified using C1000 Touch Thermal cycler at the following conditions: 98°C for 3 min 12 cycles of 90°C for 15 s 67°C for 20 s and 72°C for 1 min 72°C for 1 min held 4°C. Amplified cDNA was cleaned with the SPRIselect Reagent Kit Beckman Coulter and quality was assessed using 2100 Bioanalyser Agilent. Libraries were constructed using Chromium™ Controller and Chromium™ Single Cell three prime Library & Gel Bead Kit v2 10x Genomics according to the manufacturer's protocol. B…	Experimental Factor: genotype:Tglck:EGFP; Rag1 homozygous knockout\|Experimental Factor: infect:Anisakis simplex	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>866</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>434</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP110806	Illumina HiSeq 4000 sequencing; Single cell transcriptional analysis reveals ILC like cells in zebrafish	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 11 16\|options: use QUAL	5149STDY7274847.bam 5149STDY7274847.bam.bai	bam bam	34467649678.0	351710711.0	E MTAB 7159:5149STDY7274847	0:98	A:10609988948;C:6722093635;G:7464497879;T:9667814950;N:3254266	98		10609988948	6722093635	7464497879	9667814950	3254266	ERX2797588	ERS2709704	ERA1594569	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	1	0.88751		0.21835		0.83771		0.53927		98		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United Kingdom	2018-09-11	Adult	Adult	Gut	Digestive System
9169	9169	ERR2788338	ERX2797587	ERS2709703	ERP110806	PRJEB28589	Single cell transcriptional analysis reveals ILC like cells in zebrafish	E-MTAB-7159	Transcriptome Analysis	Transcriptome data from zebrafish single cells from guts from either from Tglck:EGFP rag1 / mutant or wild type zebrafish were isolated and single cell suspensions were prepared as described in protocol section. Three zebrafish per each condition i.e. zebrafish intraperitoneally injected with PBS lyophilised Anisakis simplex or inactivated Vibrio anguillarum were used to collect the total of 12 000 lck+ cells 4000 per zebrafish for 10x experiment.	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 09 11		Protocols: The guts were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. Three zebrafish per each condition i.e. zebrafish intraperitoneally injected with PBS lyophilised Anisakis simplex or inactivated Vibrio anguillarum were used to collect the total of 12 000 lck+ cells 4000 per zebrafish for 10x experiment. Cell were sorted into 1.5 ml Eppendorf tubes containing 20 l 5% FBS in PBS using a BD Influx Index Sorter. Following the sorting cells were spun down and resuspended in ice cold PBS with 0.04% bovine serum albumin at the concentration of 500 cells/μl. Briefly cellular suspension was added to the master mix containing nuclease free water RT Reagent Mix RT Primer Additive A and RT Enzyme Mix. Master mix with cells was transferred to the wells in the row labelled 1 on the Chromium™ Single Cell A Chip 10x Genomics. Single Cell three prime Gel Beads were transferred into the row labelled 2 and Partitioning Oil was transferred into the row labelled 3. The chip was loaded on Chromium™ Controller to generate single cell GEMs. GEM RT was performed in a C1000 Touch Thermal cycler Bio Rad at the following conditions: 53°C for 45 min 85°C for 5 min held at 4°C. Post GEM RT cleanup was performed with DynaBeads MyOne Silane Beads Thermo Fisher Scientific. cDNA was amplified using C1000 Touch Thermal cycler at the following conditions: 98°C for 3 min 12 cycles of 90°C for 15 s 67°C for 20 s and 72°C for 1 min 72°C for 1 min held 4°C. Amplified cDNA was cleaned with the SPRIselect Reagent Kit Beckman Coulter and quality was assessed using 2100 Bioanalyser Agilent. Libraries were constructed using Chromium™ Controller and Chromium™ Single Cell three prime Library & Gel Bead Kit v2 10x Genomics according to the manufacturer's …	5149STDY7274846	SAMEA4890707	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK	ENA FIRST PUBLIC:2018 11 16T17:03:30Z\|ENA LAST UPDATE:2018 09 11T09:38:07Z\|External Id:SAMEA4890707\|INSDC center name:Department of Haematology University of Cambridge Cambridge UK Wellcome Trust Sanger Institute Wellcome Trust Genome Campus Cambridge Wellcome Trust Medical Research Council Cambridge Stem Cell Institute Cambridge UK\|INSDC first public:2018 11 16T17:03:30Z\|INSDC last update:2018 09 11T09:38:07Z\|INSDC status:public\|Submitter Id:E MTAB 7159:5149STDY7274846\|age:4\|broker name:ArrayExpress\|common name:zebrafish\|developmental stage:adult\|genotype:Tglck:EGFP; Rag1 homozygous knockout\|individual:pool 1\|organism part:intestine\|phenotype:lck positive\|sample name:E MTAB 7159:5149STDY7274846\|scientific name:Danio rerio\|sex:female\|strain:AB									Illumina HiSeq 4000 sequencing; Single cell transcriptional analysis reveals ILC like cells in zebrafish	E MTAB 7159:5149STDY7274846 p	5149STDY7274846 p	Single cell transcriptional analysis reveals ILC like cells in zebrafish	The guts were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. Three zebrafish per each condition i.e. zebrafish intraperitoneally injected with PBS lyophilised Anisakis simplex or inactivated Vibrio anguillarum were used to collect the total of 12 000 lck+ cells 4000 per zebrafish for 10x experiment. Cell were sorted into 1.5 ml Eppendorf tubes containing 20 l 5% FBS in PBS using a BD Influx Index Sorter. Following the sorting cells were spun down and resuspended in ice cold PBS with 0.04% bovine serum albumin at the concentration of 500 cells/μl. Briefly cellular suspension was added to the master mix containing nuclease free water RT Reagent Mix RT Primer Additive A and RT Enzyme Mix. Master mix with cells was transferred to the wells in the row labelled 1 on the Chromium™ Single Cell A Chip 10x Genomics. Single Cell three prime Gel Beads were transferred into the row labelled 2 and Partitioning Oil was transferred into the row labelled 3. The chip was loaded on Chromium™ Controller to generate single cell GEMs. GEM RT was performed in a C1000 Touch Thermal cycler Bio Rad at the following conditions: 53°C for 45 min 85°C for 5 min held at 4°C. Post GEM RT cleanup was performed with DynaBeads MyOne Silane Beads Thermo Fisher Scientific. cDNA was amplified using C1000 Touch Thermal cycler at the following conditions: 98°C for 3 min 12 cycles of 90°C for 15 s 67°C for 20 s and 72°C for 1 min 72°C for 1 min held 4°C. Amplified cDNA was cleaned with the SPRIselect Reagent Kit Beckman Coulter and quality was assessed using 2100 Bioanalyser Agilent. Libraries were constructed using Chromium™ Controller and Chromium™ Single Cell three prime Library & Gel Bead Kit v2 10x Genomics according to the manufacturer's protocol. B…	Experimental Factor: genotype:Tglck:EGFP; Rag1 homozygous knockout\|Experimental Factor: infect:n1	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>866</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>434</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	ERP110806	Illumina HiSeq 4000 sequencing; Single cell transcriptional analysis reveals ILC like cells in zebrafish	ENA FIRST PUBLIC:2018 11 16\|ENA LAST UPDATE:2018 11 16\|options: use QUAL	5149STDY7274846.bam 5149STDY7274846.bam.bai	bam bam	35052538472.0	357678964.0	E MTAB 7159:5149STDY7274846	0:98	A:10698116265;C:6858102477;G:7626019661;T:9866905792;N:3394277	98		10698116265	6858102477	7626019661	9866905792	3394277	ERX2797587	ERS2709703	ERA1594569	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust â€“ Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK\|European Nucleotide Archive	1	0.88916		0.21537		0.83802		0.5336		98		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United Kingdom	2018-09-11	Adult	Adult	Gut	Digestive System
54188	54188	SRR10095964	SRX6828145	SRS5370320	SRP221273	PRJNA564810	A Single Cell Transcriptome Atlas for Zebrafish Development	PRJNA564810	Other	The ability to define cell types and how they change during organogenesis is central to our understanding of animal development and human disease. Despite the crucial nature of this knowledge we have yet to fully characterize all distinct cell types and the gene expression differences that generate cell types during development. To address this knowledge gap we produced an Atlas using single cell RNA sequencing methods to investigate gene expression from the pharyngula to early larval stages in developing zebrafish. Our single cell transcriptome Atlas encompasses transcriptional profiles from 44 102 cells across four days of development using duplicate experiments that confirmed high reproducibility. We annotated 220 identified clusters and highlighted several strategies for interrogating changes in gene expression associated with the development of zebrafish embryos at single cell resolution. Furthermore we highlight the power of this analysis to assign new cell type or developmental stage specific expression information to many genes including those that are currently known only by sequence and/or that lack expression information altogether. The resulting Atlas is a resource of biologists to generate hypotheses for genetic mutant or functional analysis to launch an effort to define the diversity of cell types during zebrafish organogenesis and to examine the transcriptional profiles that produce each cell type over developmental time.					5b		strain:Tgolig2:GFPvu12\|age:5 dpf\|sex:unknown\|tissue:whole embryo\|Replicate name:5b\|BioSampleModel:Model organism or animal									scRNA seq of whole zebrafish embryos	5b	5b	10X v2 chromium cDNA library			RNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 4000		SRP221273		loader:latf load	olig2gfp120hb_S5_L001_R1_001.fastq olig2gfp120hb_S5_L001_R2_001.fastq olig2gfp120hb_S5_L002_R1_001.fastq olig2gfp120hb_S5_L002_R2_001.fastq olig2gfp120hb_S5_L003_R1_001.fastq olig2gfp120hb_S5_L003_R2_001.fastq olig2gfp120hb_S5_L004_R1_001.fastq olig2gfp120hb_S5_L004_R2_001.fastq olig2gfp120hb_S5_L005_R1_001.fastq olig2gfp120hb_S5_L005_R2_001.fastq olig2gfp120hb_S5_L006_R1_001.fastq olig2gfp120hb_S5_L006_R2_001.fastq olig2gfp120hb_S5_L007_R1_001.fastq olig2gfp120hb_S5_L007_R2_001.fastq olig2gfp120hb_S5_L008_R1_001.fastq olig2gfp120hb_S5_L008_R2_001.fastq	fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq	90080193105.0	566542095.0	5b.gz	0:26 1:133	A:25143336916;C:20071432223;G:20537826191;T:24313961041;N:13636734	26	133	25143336916	20071432223	20537826191	24313961041	13636734	SRX6828145	SRS5370320	SRA960102	University of Oregon\|Institute of Neuroscience	University of Oregon	2	0.00976	0.95301	0.00215	0.10077	0.97926	0.77851	0.44407	0.5221	26	133	T	B	sc-like readlen	illumina	hiseq_era	unknown	unknown	unknown	sc	single_cell_droplet	10x	United States	2019-12-10	Larval	Larval	Whole Organism	All anatomical structures
54189	54189	SRR10095965	SRX6828144	SRS5370319	SRP221273	PRJNA564810	A Single Cell Transcriptome Atlas for Zebrafish Development	PRJNA564810	Other	The ability to define cell types and how they change during organogenesis is central to our understanding of animal development and human disease. Despite the crucial nature of this knowledge we have yet to fully characterize all distinct cell types and the gene expression differences that generate cell types during development. To address this knowledge gap we produced an Atlas using single cell RNA sequencing methods to investigate gene expression from the pharyngula to early larval stages in developing zebrafish. Our single cell transcriptome Atlas encompasses transcriptional profiles from 44 102 cells across four days of development using duplicate experiments that confirmed high reproducibility. We annotated 220 identified clusters and highlighted several strategies for interrogating changes in gene expression associated with the development of zebrafish embryos at single cell resolution. Furthermore we highlight the power of this analysis to assign new cell type or developmental stage specific expression information to many genes including those that are currently known only by sequence and/or that lack expression information altogether. The resulting Atlas is a resource of biologists to generate hypotheses for genetic mutant or functional analysis to launch an effort to define the diversity of cell types during zebrafish organogenesis and to examine the transcriptional profiles that produce each cell type over developmental time.					5a		strain:Tgolig2:GFPvu12\|age:5 dpf\|sex:unknown\|tissue:whole embryo\|Replicate name:5a\|BioSampleModel:Model organism or animal									scRNA seq of whole zebrafish embryos	5a	5a	10X v2 chromium cDNA library			RNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 4000		SRP221273		loader:latf load	olig2gfp120ha_S4_L001_R1_001.fastq olig2gfp120ha_S4_L001_R2_001.fastq olig2gfp120ha_S4_L002_R1_001.fastq olig2gfp120ha_S4_L002_R2_001.fastq olig2gfp120ha_S4_L003_R1_001.fastq olig2gfp120ha_S4_L003_R2_001.fastq olig2gfp120ha_S4_L004_R1_001.fastq olig2gfp120ha_S4_L004_R2_001.fastq olig2gfp120ha_S4_L005_R1_001.fastq olig2gfp120ha_S4_L005_R2_001.fastq olig2gfp120ha_S4_L006_R1_001.fastq olig2gfp120ha_S4_L006_R2_001.fastq olig2gfp120ha_S4_L007_R1_001.fastq olig2gfp120ha_S4_L007_R2_001.fastq olig2gfp120ha_S4_L008_R1_001.fastq olig2gfp120ha_S4_L008_R2_001.fastq	fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq	106640540616.0	670695224.0	5a.gz	0:26 1:133	A:29532468637;C:23968826821;G:24791831474;T:28331248539;N:16165145	26	133	29532468637	23968826821	24791831474	28331248539	16165145	SRX6828144	SRS5370319	SRA960102	University of Oregon\|Institute of Neuroscience	University of Oregon	2	0.01014	0.95016	0.00222	0.09527	0.97855	0.78212	0.41929	0.50263	26	133	T	B	sc-like readlen	illumina	hiseq_era	unknown	unknown	unknown	sc	single_cell_droplet	10x	United States	2019-12-10	Larval	Larval	Whole Organism	All anatomical structures
54190	54190	SRR10095966	SRX6828143	SRS5370318	SRP221273	PRJNA564810	A Single Cell Transcriptome Atlas for Zebrafish Development	PRJNA564810	Other	The ability to define cell types and how they change during organogenesis is central to our understanding of animal development and human disease. Despite the crucial nature of this knowledge we have yet to fully characterize all distinct cell types and the gene expression differences that generate cell types during development. To address this knowledge gap we produced an Atlas using single cell RNA sequencing methods to investigate gene expression from the pharyngula to early larval stages in developing zebrafish. Our single cell transcriptome Atlas encompasses transcriptional profiles from 44 102 cells across four days of development using duplicate experiments that confirmed high reproducibility. We annotated 220 identified clusters and highlighted several strategies for interrogating changes in gene expression associated with the development of zebrafish embryos at single cell resolution. Furthermore we highlight the power of this analysis to assign new cell type or developmental stage specific expression information to many genes including those that are currently known only by sequence and/or that lack expression information altogether. The resulting Atlas is a resource of biologists to generate hypotheses for genetic mutant or functional analysis to launch an effort to define the diversity of cell types during zebrafish organogenesis and to examine the transcriptional profiles that produce each cell type over developmental time.					2b		strain:Tgolig2:GFPvu12\|age:2 dpf\|sex:unknown\|tissue:whole embryo\|Replicate name:2b\|BioSampleModel:Model organism or animal									scRNA seq of whole zebrafish embryos	2b	2b	10X v2 chromium cDNA library			RNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 4000		SRP221273		loader:latf load	olig2gfp48ha_S3_L003_R2_001.fastq olig2gfp48ha_S3_L004_R1_001.fastq olig2gfp48ha_S3_L004_R2_001.fastq olig2gfp48ha_S3_L005_R1_001.fastq olig2gfp48ha_S3_L005_R2_001.fastq olig2gfp48ha_S3_L006_R1_001.fastq olig2gfp48ha_S3_L006_R2_001.fastq olig2gfp48ha_S3_L007_R1_001.fastq olig2gfp48ha_S3_L007_R2_001.fastq olig2gfp48ha_S3_L008_R1_001.fastq olig2gfp48ha_S3_L008_R2_001.fastq olig2gfp48ha_S3_L003_R1_001.fastq olig2gfp48ha_S3_L002_R2_001.fastq olig2gfp48ha_S3_L002_R1_001.fastq olig2gfp48ha_S3_L001_R2_001.fastq olig2gfp48ha_S3_L001_R1_001.fastq	fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq	100194025377.0	630151103.0	2b.gz	0:26 1:133	A:27235389395;C:22388810842;G:23041272930;T:27513445748;N:15106462	26	133	27235389395	22388810842	23041272930	27513445748	15106462	SRX6828143	SRS5370318	SRA960102	University of Oregon\|Institute of Neuroscience	University of Oregon	2	0.0127	0.95456	0.00215	0.09469	0.97463	0.79308	0.43287	0.50046	26	133	T	B	sc-like readlen	illumina	hiseq_era	unknown	unknown	unknown	sc	single_cell_droplet	10x	United States	2019-12-10	Hatching	Embryo	Whole Organism	All anatomical structures
54191	54191	SRR10095967	SRX6828142	SRS5370317	SRP221273	PRJNA564810	A Single Cell Transcriptome Atlas for Zebrafish Development	PRJNA564810	Other	The ability to define cell types and how they change during organogenesis is central to our understanding of animal development and human disease. Despite the crucial nature of this knowledge we have yet to fully characterize all distinct cell types and the gene expression differences that generate cell types during development. To address this knowledge gap we produced an Atlas using single cell RNA sequencing methods to investigate gene expression from the pharyngula to early larval stages in developing zebrafish. Our single cell transcriptome Atlas encompasses transcriptional profiles from 44 102 cells across four days of development using duplicate experiments that confirmed high reproducibility. We annotated 220 identified clusters and highlighted several strategies for interrogating changes in gene expression associated with the development of zebrafish embryos at single cell resolution. Furthermore we highlight the power of this analysis to assign new cell type or developmental stage specific expression information to many genes including those that are currently known only by sequence and/or that lack expression information altogether. The resulting Atlas is a resource of biologists to generate hypotheses for genetic mutant or functional analysis to launch an effort to define the diversity of cell types during zebrafish organogenesis and to examine the transcriptional profiles that produce each cell type over developmental time.					2a		strain:Tgelavl3:GCaMP6s\|age:2 dpf\|sex:unknown\|tissue:whole embryo\|Replicate name:2a\|BioSampleModel:Model organism or animal									scRNA seq of whole zebrafish embryos	2a	2a	10X v2 chromium cDNA library			RNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	NextSeq 500		SRP221273		loader:latf load	2a elav_gcamp_48h_S1_L001_R1_001.fastq elav_gcamp_48h_S1_L001_R2_001.fastq elav_gcamp_48h_S1_L002_R1_001.fastq elav_gcamp_48h_S1_L002_R2_001.fastq elav_gcamp_48h_S1_L003_R1_001.fastq elav_gcamp_48h_S1_L003_R2_001.fastq elav_gcamp_48h_S1_L004_R1_001.fastq elav_gcamp_48h_S1_L004_R2_001.fastq	fastq fastq fastq fastq fastq fastq fastq fastq fastq	30654488793.0	192795527.0	2a.gz	0:26 1:133	A:8922702024;C:6370087682;G:7321183700;T:8019014142;N:21501245	26	133	8922702024	6370087682	7321183700	8019014142	21501245	SRX6828142	SRS5370317	SRA960102	University of Oregon\|Institute of Neuroscience	University of Oregon	2	0.00427	0.91705	0.00106	0.08701	0.98999	0.8198	0.35255	0.50555	26	133	T	B	sc-like readlen	illumina	nextseq	unknown	unknown	unknown	sc	single_cell_droplet	10x	United States	2019-12-10	Hatching	Embryo	Whole Organism	All anatomical structures
54192	54192	SRR10095968	SRX6828141	SRS5370316	SRP221273	PRJNA564810	A Single Cell Transcriptome Atlas for Zebrafish Development	PRJNA564810	Other	The ability to define cell types and how they change during organogenesis is central to our understanding of animal development and human disease. Despite the crucial nature of this knowledge we have yet to fully characterize all distinct cell types and the gene expression differences that generate cell types during development. To address this knowledge gap we produced an Atlas using single cell RNA sequencing methods to investigate gene expression from the pharyngula to early larval stages in developing zebrafish. Our single cell transcriptome Atlas encompasses transcriptional profiles from 44 102 cells across four days of development using duplicate experiments that confirmed high reproducibility. We annotated 220 identified clusters and highlighted several strategies for interrogating changes in gene expression associated with the development of zebrafish embryos at single cell resolution. Furthermore we highlight the power of this analysis to assign new cell type or developmental stage specific expression information to many genes including those that are currently known only by sequence and/or that lack expression information altogether. The resulting Atlas is a resource of biologists to generate hypotheses for genetic mutant or functional analysis to launch an effort to define the diversity of cell types during zebrafish organogenesis and to examine the transcriptional profiles that produce each cell type over developmental time.					1b		strain:Tgolig2:GFPvu12\|age:1 dpf\|sex:unknown\|tissue:whole embryo\|Replicate name:1b\|BioSampleModel:Model organism or animal									scRNA seq of whole zebrafish embryos	1b	1b	10X v2 chromium cDNA library			RNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 4000		SRP221273		loader:latf load	olig2gfp24hb_S2_L001_R1_001.fastq olig2gfp24hb_S2_L001_R2_001.fastq olig2gfp24hb_S2_L002_R1_001.fastq olig2gfp24hb_S2_L002_R2_001.fastq olig2gfp24hb_S2_L003_R1_001.fastq olig2gfp24hb_S2_L003_R2_001.fastq olig2gfp24hb_S2_L004_R1_001.fastq olig2gfp24hb_S2_L004_R2_001.fastq olig2gfp24hb_S2_L005_R1_001.fastq olig2gfp24hb_S2_L005_R2_001.fastq olig2gfp24hb_S2_L006_R1_001.fastq olig2gfp24hb_S2_L006_R2_001.fastq olig2gfp24hb_S2_L007_R1_001.fastq olig2gfp24hb_S2_L007_R2_001.fastq olig2gfp24hb_S2_L008_R1_001.fastq olig2gfp24hb_S2_L008_R2_001.fastq	fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq	98193351273.0	617568247.0	1b.gz	0:26 1:133	A:27237053473;C:21828277485;G:22951157364;T:26162156154;N:14706797	26	133	27237053473	21828277485	22951157364	26162156154	14706797	SRX6828141	SRS5370316	SRA960102	University of Oregon\|Institute of Neuroscience	University of Oregon	2	0.01479	0.95138	0.00273	0.12104	0.97327	0.78293	0.39405	0.4998	26	133	T	B	sc-like readlen	illumina	hiseq_era	unknown	unknown	unknown	sc	single_cell_droplet	10x	United States	2019-12-10	Pharyngula	Embryo	Whole Organism	All anatomical structures
54193	54193	SRR10095969	SRX6828140	SRS5370315	SRP221273	PRJNA564810	A Single Cell Transcriptome Atlas for Zebrafish Development	PRJNA564810	Other	The ability to define cell types and how they change during organogenesis is central to our understanding of animal development and human disease. Despite the crucial nature of this knowledge we have yet to fully characterize all distinct cell types and the gene expression differences that generate cell types during development. To address this knowledge gap we produced an Atlas using single cell RNA sequencing methods to investigate gene expression from the pharyngula to early larval stages in developing zebrafish. Our single cell transcriptome Atlas encompasses transcriptional profiles from 44 102 cells across four days of development using duplicate experiments that confirmed high reproducibility. We annotated 220 identified clusters and highlighted several strategies for interrogating changes in gene expression associated with the development of zebrafish embryos at single cell resolution. Furthermore we highlight the power of this analysis to assign new cell type or developmental stage specific expression information to many genes including those that are currently known only by sequence and/or that lack expression information altogether. The resulting Atlas is a resource of biologists to generate hypotheses for genetic mutant or functional analysis to launch an effort to define the diversity of cell types during zebrafish organogenesis and to examine the transcriptional profiles that produce each cell type over developmental time.					1a		strain:Tgolig2:GFPvu12\|age:1 dpf\|sex:unknown\|tissue:whole embryo\|Replicate name:1a\|BioSampleModel:Model organism or animal									scRNA seq of whole zebrafish embryos	1a	1a	10X v2 chromium cDNA library			RNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 4000		SRP221273		loader:latf load	olig2gfp24ha_S1_L001_R1_001.fastq olig2gfp24ha_S1_L001_R2_001.fastq olig2gfp24ha_S1_L002_R1_001.fastq olig2gfp24ha_S1_L002_R2_001.fastq olig2gfp24ha_S1_L003_R1_001.fastq olig2gfp24ha_S1_L003_R2_001.fastq olig2gfp24ha_S1_L004_R1_001.fastq olig2gfp24ha_S1_L004_R2_001.fastq olig2gfp24ha_S1_L005_R1_001.fastq olig2gfp24ha_S1_L005_R2_001.fastq olig2gfp24ha_S1_L006_R1_001.fastq olig2gfp24ha_S1_L006_R2_001.fastq olig2gfp24ha_S1_L007_R1_001.fastq olig2gfp24ha_S1_L007_R2_001.fastq olig2gfp24ha_S1_L008_R1_001.fastq olig2gfp24ha_S1_L008_R2_001.fastq	fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq	99552249225.0	626114775.0	1a.gz	0:26 1:133	A:27540748865;C:22111148705;G:23108024457;T:26777444676;N:14882522	26	133	27540748865	22111148705	23108024457	26777444676	14882522	SRX6828140	SRS5370315	SRA960102	University of Oregon\|Institute of Neuroscience	University of Oregon	2	0.01166	0.95413	0.002	0.08635	0.9779	0.80034	0.44044	0.48046	26	133	T	B	sc-like readlen	illumina	hiseq_era	unknown	unknown	unknown	sc	single_cell_droplet	10x	United States	2019-12-10	Pharyngula	Embryo	Whole Organism	All anatomical structures
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

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