{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_layout = \"SINGLE\", experiment.library_source = \"TRANSCRIPTOMIC\" and technology = \"10x\"", "rows": [[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", null, "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 \u00b5m strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 \u00b5m 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 \uf06dl 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/\u03bcl. 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\u2122 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\u2122 Controller to generate single cell GEMs. GEM RT was performed in a C1000 Touch Thermal cycler Bio Rad at the following conditions: 53\u00b0C for 45 min  85\u00b0C for 5 min  held at 4\u00b0C. 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\u00b0C for 3 min  12 cycles of 90\u00b0C for 15 s  67\u00b0C for 20 s and 72\u00b0C for 1 min  72\u00b0C for 1 min  held 4\u00b0C. Amplified cDNA was cleaned with the SPRIselect Reagent Kit Beckman Coulter and quality was assessed using 2100 Bioanalyser Agilent. Libraries were constructed using Chromium\u2122 Controller and Chromium\u2122 Single Cell three prime Library & Gel Bead Kit v2 10x Genomics according to the manufacturer's protocol. Briefly  for fragmentation  end repair and A tailing cDNA was incubated with Fragmentation Mix in pre cooled thermocycler at the following conditions: 32\u00b0C for 5 min  65\u00b0C for 30 min  held at 4\u00b0C. The libraries were then purified using beads. Next adaptor ligation was performed  samples were incubated with Adaptor Ligation Mix at 20\u00b0C for 15 min followed by post ligation clean up with beads and Sample Index PCR. Again libraries were purified using beads. Following a final Bioanalyzer quality check  the libraries were diluted to the concentration required for sequencing.", "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", null, null, null, null, null, null, null, null, "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 \u00b5m strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 \u00b5m 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 \uf06dl 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/\u03bcl. 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\u2122 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\u2122 Controller to generate single cell GEMs. GEM RT was performed in a C1000 Touch Thermal cycler Bio Rad at the following conditions: 53\u00b0C for 45 min  85\u00b0C for 5 min  held at 4\u00b0C. 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\u00b0C for 3 min  12 cycles of 90\u00b0C for 15 s  67\u00b0C for 20 s and 72\u00b0C for 1 min  72\u00b0C for 1 min  held 4\u00b0C. Amplified cDNA was cleaned with the SPRIselect Reagent Kit Beckman Coulter and quality was assessed using 2100 Bioanalyser Agilent. Libraries were constructed using Chromium\u2122 Controller and Chromium\u2122 Single Cell three prime Library & Gel Bead Kit v2 10x Genomics according to the manufacturer's protocol. Briefly  for fragmentation  end repair and A tailing cDNA was incubated with Fragmentation Mix in pre cooled thermocycler at the following conditions: 32\u00b0C for 5 min  65\u00b0C for 30 min  held at 4\u00b0C. The libraries were then purified using beads. Next adaptor ligation was performed  samples were incubated with Adaptor Ligation Mix at 20\u00b0C for 15 min followed by post ligation clean up with beads and Sample Index PCR. Again libraries were purified using beads. Following a final Bioanalyzer quality check  the libraries were diluted to the concentration required for sequencing.", "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, null, null, null, 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 \u00e2\u20ac\u201c 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 \u00e2\u20ac\u201c Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK|European Nucleotide Archive", 1, 0.87568, null, 0.2122, null, 0.82582, null, 0.5259, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United Kingdom", "2018-09-11", "Adult", "Adult", "Gut", "Digestive System"], [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", null, "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 \u00b5m strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 \u00b5m 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 \uf06dl 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/\u03bcl. 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\u2122 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\u2122 Controller to generate single cell GEMs. GEM RT was performed in a C1000 Touch Thermal cycler Bio Rad at the following conditions: 53\u00b0C for 45 min  85\u00b0C for 5 min  held at 4\u00b0C. 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\u00b0C for 3 min  12 cycles of 90\u00b0C for 15 s  67\u00b0C for 20 s and 72\u00b0C for 1 min  72\u00b0C for 1 min  held 4\u00b0C. Amplified cDNA was cleaned with the SPRIselect Reagent Kit Beckman Coulter and quality was assessed using 2100 Bioanalyser Agilent. Libraries were constructed using Chromium\u2122 Controller and Chromium\u2122 Single Cell three prime Library & Gel Bead Kit v2 10x Genomics according to the manufacturer's protocol. Briefly  for fragmentation  end repair and A tailing cDNA was incubated with Fragmentation Mix in pre cooled thermocycler at the following conditions: 32\u00b0C for 5 min  65\u00b0C for 30 min  held at 4\u00b0C. The libraries were then purified using beads. Next adaptor ligation was performed  samples were incubated with Adaptor Ligation Mix at 20\u00b0C for 15 min followed by post ligation clean up with beads and Sample Index PCR. Again libraries were purified using beads. Following a final Bioanalyzer quality check  the libraries were diluted to the concentration required for sequencing.", "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", null, null, null, null, null, null, null, null, "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 \u00b5m strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 \u00b5m 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 \uf06dl 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/\u03bcl. 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\u2122 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\u2122 Controller to generate single cell GEMs. GEM RT was performed in a C1000 Touch Thermal cycler Bio Rad at the following conditions: 53\u00b0C for 45 min  85\u00b0C for 5 min  held at 4\u00b0C. 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\u00b0C for 3 min  12 cycles of 90\u00b0C for 15 s  67\u00b0C for 20 s and 72\u00b0C for 1 min  72\u00b0C for 1 min  held 4\u00b0C. Amplified cDNA was cleaned with the SPRIselect Reagent Kit Beckman Coulter and quality was assessed using 2100 Bioanalyser Agilent. Libraries were constructed using Chromium\u2122 Controller and Chromium\u2122 Single Cell three prime Library & Gel Bead Kit v2 10x Genomics according to the manufacturer's protocol. Briefly  for fragmentation  end repair and A tailing cDNA was incubated with Fragmentation Mix in pre cooled thermocycler at the following conditions: 32\u00b0C for 5 min  65\u00b0C for 30 min  held at 4\u00b0C. The libraries were then purified using beads. Next adaptor ligation was performed  samples were incubated with Adaptor Ligation Mix at 20\u00b0C for 15 min followed by post ligation clean up with beads and Sample Index PCR. Again libraries were purified using beads. Following a final Bioanalyzer quality check  the libraries were diluted to the concentration required for sequencing.", "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, null, null, null, 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 \u00e2\u20ac\u201c 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 \u00e2\u20ac\u201c Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK|European Nucleotide Archive", 1, 0.86206, null, 0.18065, null, 0.83514, null, 0.53609, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United Kingdom", "2018-09-11", "Adult", "Adult", "Gut", "Digestive System"], [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", null, "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 \u00b5m strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 \u00b5m 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 \uf06dl 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/\u03bcl. 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\u2122 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\u2122 Controller to generate single cell GEMs. GEM RT was performed in a C1000 Touch Thermal cycler Bio Rad at the following conditions: 53\u00b0C for 45 min  85\u00b0C for 5 min  held at 4\u00b0C. 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\u00b0C for 3 min  12 cycles of 90\u00b0C for 15 s  67\u00b0C for 20 s and 72\u00b0C for 1 min  72\u00b0C for 1 min  held 4\u00b0C. Amplified cDNA was cleaned with the SPRIselect Reagent Kit Beckman Coulter and quality was assessed using 2100 Bioanalyser Agilent. Libraries were constructed using Chromium\u2122 Controller and Chromium\u2122 Single Cell three prime Library & Gel Bead Kit v2 10x Genomics according to the manufacturer's protocol. Briefly  for fragmentation  end repair and A tailing cDNA was incubated with Fragmentation Mix in pre cooled thermocycler at the following conditions: 32\u00b0C for 5 min  65\u00b0C for 30 min  held at 4\u00b0C. The libraries were then purified using beads. Next adaptor ligation was performed  samples were incubated with Adaptor Ligation Mix at 20\u00b0C for 15 min followed by post ligation clean up with beads and Sample Index PCR. Again libraries were purified using beads. Following a final Bioanalyzer quality check  the libraries were diluted to the concentration required for sequencing.", "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", null, null, null, null, null, null, null, null, "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 \u00b5m strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 \u00b5m 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 \uf06dl 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/\u03bcl. 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\u2122 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\u2122 Controller to generate single cell GEMs. GEM RT was performed in a C1000 Touch Thermal cycler Bio Rad at the following conditions: 53\u00b0C for 45 min  85\u00b0C for 5 min  held at 4\u00b0C. 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\u00b0C for 3 min  12 cycles of 90\u00b0C for 15 s  67\u00b0C for 20 s and 72\u00b0C for 1 min  72\u00b0C for 1 min  held 4\u00b0C. Amplified cDNA was cleaned with the SPRIselect Reagent Kit Beckman Coulter and quality was assessed using 2100 Bioanalyser Agilent. Libraries were constructed using Chromium\u2122 Controller and Chromium\u2122 Single Cell three prime Library & Gel Bead Kit v2 10x Genomics according to the manufacturer's protocol. Briefly  for fragmentation  end repair and A tailing cDNA was incubated with Fragmentation Mix in pre cooled thermocycler at the following conditions: 32\u00b0C for 5 min  65\u00b0C for 30 min  held at 4\u00b0C. The libraries were then purified using beads. Next adaptor ligation was performed  samples were incubated with Adaptor Ligation Mix at 20\u00b0C for 15 min followed by post ligation clean up with beads and Sample Index PCR. Again libraries were purified using beads. Following a final Bioanalyzer quality check  the libraries were diluted to the concentration required for sequencing.", "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, null, null, null, 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 \u00e2\u20ac\u201c 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 \u00e2\u20ac\u201c Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK|European Nucleotide Archive", 1, 0.88751, null, 0.21835, null, 0.83771, null, 0.53927, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United Kingdom", "2018-09-11", "Adult", "Adult", "Gut", "Digestive System"], [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", null, "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 \u00b5m strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 \u00b5m 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 \uf06dl 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/\u03bcl. 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\u2122 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\u2122 Controller to generate single cell GEMs. GEM RT was performed in a C1000 Touch Thermal cycler Bio Rad at the following conditions: 53\u00b0C for 45 min  85\u00b0C for 5 min  held at 4\u00b0C. 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\u00b0C for 3 min  12 cycles of 90\u00b0C for 15 s  67\u00b0C for 20 s and 72\u00b0C for 1 min  72\u00b0C for 1 min  held 4\u00b0C. Amplified cDNA was cleaned with the SPRIselect Reagent Kit Beckman Coulter and quality was assessed using 2100 Bioanalyser Agilent. Libraries were constructed using Chromium\u2122 Controller and Chromium\u2122 Single Cell three prime Library & Gel Bead Kit v2 10x Genomics according to the manufacturer's protocol. Briefly  for fragmentation  end repair and A tailing cDNA was incubated with Fragmentation Mix in pre cooled thermocycler at the following conditions: 32\u00b0C for 5 min  65\u00b0C for 30 min  held at 4\u00b0C. The libraries were then purified using beads. Next adaptor ligation was performed  samples were incubated with Adaptor Ligation Mix at 20\u00b0C for 15 min followed by post ligation clean up with beads and Sample Index PCR. Again libraries were purified using beads. Following a final Bioanalyzer quality check  the libraries were diluted to the concentration required for sequencing.", "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", null, null, null, null, null, null, null, null, "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 \u00b5m strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 \u00b5m 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 \uf06dl 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/\u03bcl. 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\u2122 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\u2122 Controller to generate single cell GEMs. GEM RT was performed in a C1000 Touch Thermal cycler Bio Rad at the following conditions: 53\u00b0C for 45 min  85\u00b0C for 5 min  held at 4\u00b0C. 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\u00b0C for 3 min  12 cycles of 90\u00b0C for 15 s  67\u00b0C for 20 s and 72\u00b0C for 1 min  72\u00b0C for 1 min  held 4\u00b0C. Amplified cDNA was cleaned with the SPRIselect Reagent Kit Beckman Coulter and quality was assessed using 2100 Bioanalyser Agilent. Libraries were constructed using Chromium\u2122 Controller and Chromium\u2122 Single Cell three prime Library & Gel Bead Kit v2 10x Genomics according to the manufacturer's protocol. Briefly  for fragmentation  end repair and A tailing cDNA was incubated with Fragmentation Mix in pre cooled thermocycler at the following conditions: 32\u00b0C for 5 min  65\u00b0C for 30 min  held at 4\u00b0C. The libraries were then purified using beads. Next adaptor ligation was performed  samples were incubated with Adaptor Ligation Mix at 20\u00b0C for 15 min followed by post ligation clean up with beads and Sample Index PCR. Again libraries were purified using beads. Following a final Bioanalyzer quality check  the libraries were diluted to the concentration required for sequencing.", "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, null, null, null, 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 \u00e2\u20ac\u201c 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 \u00e2\u20ac\u201c Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK|European Nucleotide Archive", 1, 0.88916, null, 0.21537, null, 0.83802, null, 0.5336, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United Kingdom", "2018-09-11", "Adult", "Adult", "Gut", "Digestive System"], [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.", null, null, null, null, "5b", null, "strain:Tgolig2:GFPvu12|age:5 dpf|sex:unknown|tissue:whole embryo|Replicate name:5b|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "scRNA seq of whole zebrafish embryos", "5b", "5b", "10X v2 chromium cDNA library", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP221273", null, "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, null, null, 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", null, "United States", "2019-12-10", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [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.", null, null, null, null, "5a", null, "strain:Tgolig2:GFPvu12|age:5 dpf|sex:unknown|tissue:whole embryo|Replicate name:5a|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "scRNA seq of whole zebrafish embryos", "5a", "5a", "10X v2 chromium cDNA library", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP221273", null, "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, null, null, 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", null, "United States", "2019-12-10", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [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.", null, null, null, null, "2b", null, "strain:Tgolig2:GFPvu12|age:2 dpf|sex:unknown|tissue:whole embryo|Replicate name:2b|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "scRNA seq of whole zebrafish embryos", "2b", "2b", "10X v2 chromium cDNA library", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP221273", null, "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, null, null, 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", null, "United States", "2019-12-10", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [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.", null, null, null, null, "2a", null, "strain:Tgelavl3:GCaMP6s|age:2 dpf|sex:unknown|tissue:whole embryo|Replicate name:2a|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "scRNA seq of whole zebrafish embryos", "2a", "2a", "10X v2 chromium cDNA library", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP221273", null, "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, null, null, 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", null, "United States", "2019-12-10", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [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.", null, null, null, null, "1b", null, "strain:Tgolig2:GFPvu12|age:1 dpf|sex:unknown|tissue:whole embryo|Replicate name:1b|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "scRNA seq of whole zebrafish embryos", "1b", "1b", "10X v2 chromium cDNA library", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP221273", null, "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, null, null, 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", null, "United States", "2019-12-10", "Pharyngula", "Embryo", "Whole Organism", "All anatomical structures"], [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.", null, null, null, null, "1a", null, "strain:Tgolig2:GFPvu12|age:1 dpf|sex:unknown|tissue:whole embryo|Replicate name:1a|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "scRNA seq of whole zebrafish embryos", "1a", "1a", "10X v2 chromium cDNA library", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP221273", null, "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, null, null, 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", null, "United States", "2019-12-10", "Pharyngula", "Embryo", "Whole Organism", "All anatomical structures"], [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.", null, "pubmed:35615540;pubmed:35799832", null, "dissociated bulk seq control testes   rep 3 compared to intact control testes", "GSM5820567", null, "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. \u00a0 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\u00b0C\u2013 30\u00b0C. 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP355202", null, null, "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, null, null, 535632392, 366862698, 429979337, 514873991, 23205, "SRX13799350", "SRS11681639", "SRA1357269", "University of Florida", "University of Florida", 1, 0.87212, null, 0.1857, null, 0.69372, null, 0.56886, null, 51, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2022-01-15", "Juvenile", "Juvenile", "Gonad", "Reproductive System"], [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.", null, "pubmed:35615540;pubmed:35799832", null, "dissociated bulk seq control testes   rep 3 compared to intact control testes", "GSM5820567", null, "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. \u00a0 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\u00b0C\u2013 30\u00b0C. 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP355202", null, null, "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, null, null, 529009592, 361883074, 424030274, 508289743, 18141, "SRX13799350", "SRS11681639", "SRA1357269", "University of Florida", "University of Florida", 1, 0.8708, null, 0.18714, null, 0.6955, null, 0.5716, null, 51, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2022-01-15", "Juvenile", "Juvenile", "Gonad", "Reproductive System"], [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.", null, "pubmed:35615540;pubmed:35799832", null, "dissociated bulk seq control testes   rep 2 compared to intact control testes", "GSM5820566", null, "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. \u00a0 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\u00b0C\u2013 30\u00b0C. 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP355202", null, null, "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, null, null, 163430759, 106016694, 122059136, 145048023, 6596, "SRX13799349", "SRS11681638", "SRA1357269", "University of Florida", "University of Florida", 1, 0.83573, null, 0.2005, null, 0.71056, null, 0.52825, null, 51, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2022-01-15", "Juvenile", "Juvenile", "Gonad", "Reproductive System"], [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.", null, "pubmed:35615540;pubmed:35799832", null, "dissociated bulk seq control testes   rep 2 compared to intact control testes", "GSM5820566", null, "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. \u00a0 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\u00b0C\u2013 30\u00b0C. 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP355202", null, null, "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, null, null, 161875304, 104815309, 120705456, 143576873, 5296, "SRX13799349", "SRS11681638", "SRA1357269", "University of Florida", "University of Florida", 1, 0.83663, null, 0.19964, null, 0.71104, null, 0.54143, null, 51, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2022-01-15", "Juvenile", "Juvenile", "Gonad", "Reproductive System"], [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.", null, "pubmed:35615540;pubmed:35799832", null, "dissociated bulk seq control testes   rep 1 compared to intact control testes", "GSM5820565", null, "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. \u00a0 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\u00b0C\u2013 30\u00b0C. 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP355202", null, null, "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, null, null, 155891194, 103400919, 120028554, 144451616, 6999, "SRX13799348", "SRS11681637", "SRA1357269", "University of Florida", "University of Florida", 1, 0.85957, null, 0.19557, null, 0.69501, null, 0.56637, null, 51, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2022-01-15", "Juvenile", "Juvenile", "Gonad", "Reproductive System"], [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.", null, "pubmed:35615540;pubmed:35799832", null, "dissociated bulk seq control testes   rep 1 compared to intact control testes", "GSM5820565", null, "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. \u00a0 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\u00b0C\u2013 30\u00b0C. 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP355202", null, null, "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, null, null, 153923180, 101966413, 118359254, 142647450, 5686, "SRX13799348", "SRS11681637", "SRA1357269", "University of Florida", "University of Florida", 1, 0.85795, null, 0.19403, null, 0.69627, null, 0.57159, null, 51, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2022-01-15", "Juvenile", "Juvenile", "Gonad", "Reproductive System"], [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.", null, "pubmed:35615540;pubmed:35799832", null, "bulk seq intact control testes   rep 3", "GSM5820564", null, "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. \u00a0 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\u00b0C\u2013 30\u00b0C. 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP355202", null, null, "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, null, null, 496655744, 334242155, 387205466, 455330132, 23383, "SRX13799347", "SRS11681636", "SRA1357269", "University of Florida", "University of Florida", 1, 0.8707, null, 0.22045, null, 0.71078, null, 0.60605, null, 51, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2022-01-15", "Juvenile", "Juvenile", "Gonad", "Reproductive System"], [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.", null, "pubmed:35615540;pubmed:35799832", null, "bulk seq intact control testes   rep 3", "GSM5820564", null, "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. \u00a0 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\u00b0C\u2013 30\u00b0C. 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP355202", null, null, "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, null, null, 489182217, 328774657, 380849646, 448358863, 19204, "SRX13799347", "SRS11681636", "SRA1357269", "University of Florida", "University of Florida", 1, 0.87032, null, 0.22081, null, 0.71261, null, 0.60917, null, 51, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2022-01-15", "Juvenile", "Juvenile", "Gonad", "Reproductive System"], [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.", null, "pubmed:35615540;pubmed:35799832", null, "bulk seq TCDD testes rep 2to be compared to scRNA seq TCDD testes", "GSM5820561", null, "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. \u00a0 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\u00b0C\u2013 30\u00b0C. 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP355202", null, null, "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, null, null, 447529477, 312467507, 374130013, 449667219, 21392, "SRX13799346", "SRS11681635", "SRA1357269", "University of Florida", "University of Florida", 1, 0.86982, null, 0.25275, null, 0.70774, null, 0.5721, null, 51, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2022-01-15", "Juvenile", "Juvenile", "Gonad", "Reproductive System"], [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.", null, "pubmed:35615540;pubmed:35799832", null, "bulk seq TCDD testes rep 2to be compared to scRNA seq TCDD testes", "GSM5820561", null, "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. \u00a0 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\u00b0C\u2013 30\u00b0C. 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP355202", null, null, "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, null, null, 442209708, 308400147, 369229792, 444230646, 17648, "SRX13799346", "SRS11681635", "SRA1357269", "University of Florida", "University of Florida", 1, 0.87035, null, 0.2527, null, 0.70682, null, 0.57673, null, 51, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2022-01-15", "Juvenile", "Juvenile", "Gonad", "Reproductive System"], [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.", null, "pubmed:35615540;pubmed:35799832", null, "bulk seq intact control testes   rep 2", "GSM5820563", null, "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. \u00a0 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\u00b0C\u2013 30\u00b0C. 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP355202", null, null, "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, null, null, 445588125, 289131502, 340459665, 418525850, 19527, "SRX13799345", "SRS11681634", "SRA1357269", "University of Florida", "University of Florida", 1, 0.85779, null, 0.20343, null, 0.69887, null, 0.56808, null, 51, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2022-01-15", "Juvenile", "Juvenile", "Gonad", "Reproductive System"], [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.", null, "pubmed:35615540;pubmed:35799832", null, "bulk seq intact control testes   rep 2", "GSM5820563", null, "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. \u00a0 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\u00b0C\u2013 30\u00b0C. 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP355202", null, null, "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, null, null, 440339743, 285301590, 335922618, 413432380, 16234, "SRX13799345", "SRS11681634", "SRA1357269", "University of Florida", "University of Florida", 1, 0.85783, null, 0.20221, null, 0.70102, null, 0.57116, null, 51, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2022-01-15", "Juvenile", "Juvenile", "Gonad", "Reproductive System"], [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.", null, "pubmed:35615540;pubmed:35799832", null, "bulk seq intact control testes   rep 1", "GSM5820562", null, "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. \u00a0 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\u00b0C\u2013 30\u00b0C. 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP355202", null, null, "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, null, null, 503613569, 361648917, 420357217, 497872153, 23840, "SRX13799344", "SRS11681633", "SRA1357269", "University of Florida", "University of Florida", 1, 0.88797, null, 0.22692, null, 0.69522, null, 0.57676, null, 51, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2022-01-15", "Juvenile", "Juvenile", "Gonad", "Reproductive System"], [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.", null, "pubmed:35615540;pubmed:35799832", null, "bulk seq intact control testes   rep 1", "GSM5820562", null, "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. \u00a0 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\u00b0C\u2013 30\u00b0C. 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP355202", null, null, "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, null, null, 496669418, 356271536, 414028881, 491077933, 19795, "SRX13799344", "SRS11681633", "SRA1357269", "University of Florida", "University of Florida", 1, 0.88843, null, 0.22792, null, 0.69619, null, 0.57488, null, 51, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2022-01-15", "Juvenile", "Juvenile", "Gonad", "Reproductive System"], [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.", null, "pubmed:35615540;pubmed:35799832", null, "bulk seq TCDD testes rep 1 to be compared to scRNA seq TCDD testes", "GSM5820560", null, "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. \u00a0 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\u00b0C\u2013 30\u00b0C. 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP355202", null, null, "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, null, null, 1025376436, 691776192, 829134506, 979443851, 49057, "SRX13799343", "SRS11681632", "SRA1357269", "University of Florida", "University of Florida", 1, 0.86505, null, 0.30929, null, 0.72074, null, 0.6373, null, 51, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2022-01-15", "Juvenile", "Juvenile", "Gonad", "Reproductive System"], [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.", null, "pubmed:35615540;pubmed:35799832", null, "bulk seq TCDD testes rep 1 to be compared to scRNA seq TCDD testes", "GSM5820560", null, "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. \u00a0 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\u00b0C\u2013 30\u00b0C. 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP355202", null, null, "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, null, null, 1012622841, 682305804, 817948602, 966881210, 40699, "SRX13799343", "SRS11681632", "SRA1357269", "University of Florida", "University of Florida", 1, 0.86392, null, 0.30933, null, 0.71863, null, 0.63706, null, 51, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2022-01-15", "Juvenile", "Juvenile", "Gonad", "Reproductive System"], [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.", null, "pubmed:35615540;pubmed:35799832", null, "bulk seq control testes rep 2  to be compared to scRNA seq control testes", "GSM5820558", null, "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. \u00a0 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\u00b0C\u2013 30\u00b0C. 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP355202", null, null, "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, null, null, 361072135, 254984535, 302043978, 346569617, 16872, "SRX13799342", "SRS11681631", "SRA1357269", "University of Florida", "University of Florida", 1, 0.86972, null, 0.31888, null, 0.71561, null, 0.6242, null, 51, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2022-01-15", "Juvenile", "Juvenile", "Gonad", "Reproductive System"], [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.", null, "pubmed:35615540;pubmed:35799832", null, "bulk seq control testes rep 2  to be compared to scRNA seq control testes", "GSM5820558", null, "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. \u00a0 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\u00b0C\u2013 30\u00b0C. 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP355202", null, null, "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, null, null, 356333809, 251264657, 297639103, 341883185, 13866, "SRX13799342", "SRS11681631", "SRA1357269", "University of Florida", "University of Florida", 1, 0.8683, null, 0.31544, null, 0.71332, null, 0.62605, null, 51, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2022-01-15", "Juvenile", "Juvenile", "Gonad", "Reproductive System"], [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.", null, "pubmed:35615540;pubmed:35799832", null, "bulk seq control testes rep 3  to be compared to scRNA seq control testes", "GSM5820559", null, "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. \u00a0 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\u00b0C\u2013 30\u00b0C. 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP355202", null, null, "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, null, null, 370125548, 258465981, 307735443, 362125609, 17976, "SRX13799341", "SRS11681630", "SRA1357269", "University of Florida", "University of Florida", 1, 0.87017, null, 0.23168, null, 0.7049, null, 0.43404, null, 51, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2022-01-15", "Juvenile", "Juvenile", "Gonad", "Reproductive System"], [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.", null, "pubmed:35615540;pubmed:35799832", null, "bulk seq control testes rep 3  to be compared to scRNA seq control testes", "GSM5820559", null, "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. \u00a0 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\u00b0C\u2013 30\u00b0C. 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP355202", null, null, "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, null, null, 365706822, 255117242, 303741803, 357696714, 14864, "SRX13799341", "SRS11681630", "SRA1357269", "University of Florida", "University of Florida", 1, 0.86967, null, 0.23412, null, 0.70447, null, 0.60084, null, 51, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2022-01-15", "Juvenile", "Juvenile", "Gonad", "Reproductive System"], [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.", null, "pubmed:35615540;pubmed:35799832", null, "bulk seq control testes rep 1 to be compared to scRNA seq control testes", "GSM5820557", null, "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. \u00a0 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\u00b0C\u2013 30\u00b0C. 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. 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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.", null, "pubmed:35615540;pubmed:35799832", null, "bulk seq control testes rep 1 to be compared to scRNA seq control testes", "GSM5820557", null, "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. \u00a0 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\u00b0C\u2013 30\u00b0C. 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP355202", null, null, "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, null, null, 100176173, 76199709, 88532838, 93436578, 4162, "SRX13799340", "SRS11681629", "SRA1357269", "University of Florida", "University of Florida", 1, 0.86034, null, 0.29588, null, 0.72346, null, 0.54277, null, 51, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2022-01-15", "Juvenile", "Juvenile", "Gonad", "Reproductive System"]], "truncated": false, "filtered_table_rows_count": 32, "expanded_columns": [], 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